diff --git a/.gitea/workflows/build_and_test.yml b/.gitea/workflows/build_and_test.yml
index 48e6706ff..738fc2278 100644
--- a/.gitea/workflows/build_and_test.yml
+++ b/.gitea/workflows/build_and_test.yml
@@ -949,6 +949,27 @@ jobs:
       - name: Build documentation
         shell: bash
         run: bash make_doc.sh
+      # The Rugnux pages site is the gitea-pages branch of rugnux/gitea-pages, updated with a release.
+      # The HTML is pushed from a copy, so the checkout the release upload below works on is left as it was.
+      - name: Upload documentation to rugnux/gitea-pages
+        if: github.event_name == 'workflow_dispatch' && (github.event.inputs.create_release == 'true' || github.event.inputs.create_release == true)
+        shell: bash
+        env:
+          PAGES_TOKEN: ${{ secrets.RUGNUX_PAGES_TOKEN || secrets.PIP_REPOSITORY_API_TOKEN }}
+          PAGES_TOKEN_NAME: ${{ secrets.RUGNUX_PAGES_TOKEN && 'RUGNUX_PAGES_TOKEN' || 'PIP_REPOSITORY_API_TOKEN' }}
+        run: |
+          echo "Pushing with secret ${PAGES_TOKEN_NAME}"
+          rm -rf /tmp/rugnux-pages
+          mkdir /tmp/rugnux-pages
+          cp -a public/. /tmp/rugnux-pages/
+          cd /tmp/rugnux-pages
+          git init -q
+          git checkout -q -b gitea-pages
+          git config user.email "filip.leonarski@psi.ch"
+          git config user.name "Filip Leonarski (Gitea)"
+          git add .
+          git commit -q -m "Deploy site from ${GITHUB_REF_NAME} ${GITHUB_SHA::9}"
+          git push -f "https://${PAGES_TOKEN}@gitea.psi.ch/rugnux/gitea-pages.git" gitea-pages
       - name: Upload documentation
         if: github.event_name == 'workflow_dispatch' && (github.event.inputs.create_release == 'true' || github.event.inputs.create_release == true)
         shell: bash
diff --git a/.gitignore b/.gitignore
index 69b687423..3ce9253bb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -48,3 +48,5 @@ __pycache__/
 
 # tools/battery: the local site config (paths of this machine, private manifest); site.example.json is the template
 tools/battery/site.json
+# the restraint dictionary rugnux embeds (image_analysis/structure_refinement/monomers/update_monomers.py)
+!image_analysis/structure_refinement/monomers/*.cif
diff --git a/CLAUDE.md b/CLAUDE.md
index 0bb1218a2..f717306ec 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -15,9 +15,10 @@ usage message is the source of truth, not the docs.
 ## Build
 
 Out-of-source CMake build, C++20, heavy use of `FetchContent` (spdlog, zstd, HDF5,
-slsDetectorPackage, Catch2, cpp-httplib, libzmq, libtiff, FFTW, Ceres, fast-feedback-indexer, zlib-ng
-and Eigen are downloaded and statically linked — the **first configure needs network access** and is
-slow). **No library has to come from the host**: `zlib-devel`/`eigen3-devel` are no longer needed.
+slsDetectorPackage, Catch2, cpp-httplib, libzmq, libtiff, FFTW, Ceres, zlib-ng and Eigen are
+downloaded and statically linked — the **first configure needs network access** and is slow; the
+fast-feedback indexer behind FFBIDX is vendored in `image_analysis/indexing/fast-feedback-indexer/`).
+**No library has to come from the host**: `zlib-devel`/`eigen3-devel` are no longer needed.
 zlib (as zlib-ng in zlib-compat mode) is *built during the configure* into a prefix in the build tree
 and found there via `ZLIB_ROOT`; Eigen's headers are fetched and a generated `Eigen3Config.cmake` in
 the build tree is what every `find_package(Eigen3)` resolves — ours, Ceres' and ffbidx'. A copy
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 54e09879b..aaff6cbdc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -40,8 +40,9 @@ ENDIF()
 # CUDA's CCCL headers (cub, thrust, libcu++) stop with an #error under MSVC's traditional
 # preprocessor, which miscompiles their macros. nvcc preprocesses and compiles host code with cl.exe,
 # so the standard-conforming preprocessor is switched on for .cu sources here, reaching every CUDA
-# target, fetched ones included (VS 2019 16.5 or newer). ffbidx already sets the same for its own
-# CUB-using kernel, which is why the other CUDA targets never needed it. C++ sources keep the
+# target, fetched ones included (VS 2019 16.5 or newer). The vendored fast-feedback indexer
+# (image_analysis/indexing/fast-feedback-indexer) sets the same on its own target for its CUB-using kernel,
+# as upstream does, which is why the other CUDA targets never needed it. C++ sources keep the
 # default: none includes a CCCL header, and the switch would change the preprocessing of Qt, the
 # Windows SDK and every fetched dependency with nothing to gain.
 IF (MSVC)
@@ -493,10 +494,10 @@ IF (CMAKE_SYSTEM_PROCESSOR MATCHES "aarch64|arm64|ARM64")
 ENDIF()
 ADD_COMPILE_DEFINITIONS(JFJOCH_USE_FFTW)
 
-# Eigen (header-only), consumed by the analysis libraries directly and by Ceres and ffbidx through
-# their own find_package(Eigen3). The headers are fetched here and a two-file config package for
+# Eigen (header-only), consumed by the analysis libraries (the vendored fast-feedback indexer among them)
+# directly and by Ceres through its own find_package(Eigen3). The headers are fetched here and a two-file config package for
 # them is written into the build tree; Eigen3_DIR then points at it, so every find_package(Eigen3)
-# in the build -- ours, Ceres', ffbidx' -- resolves through the ordinary config path and gets this
+# in the build -- ours and Ceres' -- resolves through the ordinary config path and gets this
 # one copy. Nothing needs Eigen's own CMake, so the source is populated but never added.
 #
 # The obvious route, FetchContent_Declare(Eigen3 ... OVERRIDE_FIND_PACKAGE), IS BANNED and must not
diff --git a/THIRD_PARTY_NOTICES.md b/THIRD_PARTY_NOTICES.md
index 3093e081e..6b3a66af2 100644
--- a/THIRD_PARTY_NOTICES.md
+++ b/THIRD_PARTY_NOTICES.md
@@ -28,7 +28,6 @@ linked into the Jungfraujoch executables.
 | [FFTW](https://www.fftw.org/) | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | [fftw.txt](licenses/fftw.txt) |
 | [Ceres Solver](https://github.com/ceres-solver/ceres-solver) | (pinned) | Google Inc. and contributors | BSD-3-Clause | [ceres-solver.txt](licenses/ceres-solver.txt) |
 | [Abseil](https://github.com/abseil/abseil-cpp) | 20250127 (required by Ceres) | Google Inc. | Apache-2.0 | [abseil.txt](licenses/abseil.txt) |
-| [fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) | (pinned) | PSI | BSD-3-Clause | [fast-feedback-indexer.txt](licenses/fast-feedback-indexer.txt) |
 | [libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo) | 3.2.0 | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | [libjpeg-turbo.txt](licenses/libjpeg-turbo.txt) |
 | [Mbed TLS](https://github.com/Mbed-TLS/mbedtls) (with TF-PSA-Crypto) | 4.2.0 | The Mbed TLS Contributors | Apache-2.0 OR GPL-2.0-or-later (used under Apache-2.0) | [mbedtls.txt](licenses/mbedtls.txt), [tf-psa-crypto.txt](licenses/tf-psa-crypto.txt) |
 | [Catch2](https://github.com/catchorg/Catch2) | 3.16.0 | Catch2 Authors | BSL-1.0 | [catch2.txt](licenses/catch2.txt) |
@@ -60,7 +59,9 @@ These live in the source tree (see the path) rather than being fetched; traccc a
 | [Bitshuffle (h-perf)](https://github.com/kalcutter/bitshuffle) | `compression/bitshuffle_hperf/` | Kal Conley | Apache-2.0 | [bitshuffle-hperf.txt](licenses/bitshuffle-hperf.txt) |
 | [LZ4](https://github.com/lz4/lz4) | `compression/lz4/` | Yann Collet | BSD-2-Clause | [lz4.txt](licenses/lz4.txt) |
 | [HLS arbitrary-precision types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types) | `fpga/include/` | Xilinx, Inc. | Apache-2.0 | [xilinx-hls-headers.txt](licenses/xilinx-hls-headers.txt) |
+| [fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) (commit a94fd4f) | `image_analysis/indexing/fast-feedback-indexer/` | PSI | BSD-3-Clause | [fast-feedback-indexer.txt](licenses/fast-feedback-indexer.txt) |
 | [GEMMI](https://github.com/project-gemmi/gemmi) | `gemmi_gph/` | Global Phasing Ltd. | MPL-2.0 | [gemmi.txt](licenses/gemmi.txt) |
+| [CCP4 Monomer Library](https://github.com/MonomerLibrary/monomers) (subset: restraint dictionary data) | `image_analysis/structure_refinement/monomers/` | CCP4 / the Monomer Library authors (Vagin et al.) | LGPL-3.0-only | [ccp4-monomer-library.txt](licenses/ccp4-monomer-library.txt) |
 | [PEGTL](https://github.com/taocpp/PEGTL) | `gemmi_gph/gemmi/third_party/tao/` | Dr. Colin Hirsch and Daniel Frey | MIT | [pegtl.txt](licenses/pegtl.txt) |
 | [sajson](https://github.com/chadaustin/sajson) | `gemmi_gph/gemmi/third_party/sajson.h` | Chad Austin | MIT | [sajson.txt](licenses/sajson.txt) |
 | [fast_float](https://github.com/fastfloat/fast_float) | `gemmi_gph/gemmi/third_party/fast_float.h` | The fast_float authors (Daniel Lemire et al.) | Apache-2.0 OR MIT OR BSL-1.0 | [fast-float.txt](licenses/fast-float.txt) |
@@ -125,12 +126,19 @@ served frontend, so the shipped web UI carries its own attribution.
   its trust-region Levenberg-Marquardt minimiser, projected line search, polynomial step choice and
   sphere manifold for the crystal refinement, following its source. Both files name the origin at the
   top and are covered by `licenses/ceres-solver.txt`.
-* **fast-feedback-indexer** is also fetched and linked in CUDA builds (table above); separately,
+* **fast-feedback-indexer** is also vendored and linked in CUDA builds (table above); separately,
   `FFBIDXIndexerCPU.cpp` ports its CUDA kernels to the CPU. The file names the origin at the top and
   is covered by `licenses/fast-feedback-indexer.txt`.
 * **FFTW** is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
 * **Apache-2.0** components: where upstream ships a `NOTICE` file, it is reproduced in the
   corresponding `licenses/` text.
+* **CCP4 Monomer Library (LGPL-3.0)** is data, not code: the restraint dictionaries of the compounds
+  rugnux's refinement restrains, copied unmodified per compound into
+  `image_analysis/structure_refinement/monomers/` (`links_and_mods.cif` and `ener_lib.cif` cut down to
+  the entries those compounds use, and the library's metal-site distances of `metals.json` for its ions as
+  `metals.cif`), with the library's own `COPYING`. The build embeds them in the binary
+  as text, and `monomers/update_monomers.py` regenerates the subset from the upstream library, so the
+  copy can be replaced by a user with a version of their own.
 * **Qt (LGPL-3.0)** and **NVIDIA CUDA (EULA)** carry redistribution conditions beyond a copyright
   notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
   (`licenses/Qt6-LGPL-3.0.txt`, `licenses/NVIDIA-CUDA-EULA.txt`); the CUDA EULA is the one shipped
diff --git a/VERSION b/VERSION
index bfa826350..59f83b8bb 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.0.0-rc.179
+1.0.0-rc.180
diff --git a/broker/JFJochBrokerHttp.cpp b/broker/JFJochBrokerHttp.cpp
index a6e7255a6..b417085ab 100644
--- a/broker/JFJochBrokerHttp.cpp
+++ b/broker/JFJochBrokerHttp.cpp
@@ -262,10 +262,16 @@ void JFJochBrokerHttp::register_routes(httplib::Server &server) {
     server.Put("/config/rugnux/model", bind_req(&JFJochBrokerHttp::config_rugnux_model_put));
     server.Delete("/config/rugnux/model", bind_noarg(&JFJochBrokerHttp::config_rugnux_model_delete));
     server.Get("/rugnux/status", bind_noarg(&JFJochBrokerHttp::rugnux_status_get));
-    server.Get("/rugnux/model.cif", bind_noarg(&JFJochBrokerHttp::rugnux_model_cif_get));
+    server.Get("/rugnux/model.cif", [this](const httplib::Request &req, httplib::Response &res) {
+        try {
+            rugnux_model_cif_get(parse_query_string(req, "stage"), res);
+        } catch (const std::exception &e) {
+            send_error(res, handleOperationException(e));
+        }
+    });
     server.Get("/rugnux/map.ccp4", [this](const httplib::Request &req, httplib::Response &res) {
         try {
-            rugnux_map_ccp4_get(parse_query_string(req, "type"), res);
+            rugnux_map_ccp4_get(parse_query_string(req, "type"), parse_query_string(req, "stage"), res);
         } catch (const std::exception &e) {
             send_error(res, handleOperationException(e));
         }
@@ -1036,8 +1042,26 @@ void JFJochBrokerHttp::rugnux_status_get(httplib::Response &response) {
     ProcessOutput(Convert(state_machine.GetRugnuxStatus()), response);
 }
 
-void JFJochBrokerHttp::rugnux_model_cif_get(httplib::Response &response) {
-    const auto structure = state_machine.GetRugnuxStatus().structure;
+// The structure a viewer route serves: `stage` placed or refined; by default the refined one where there is one.
+// Null where there is none, or for an unknown stage (with the 400 already set).
+static std::shared_ptr<const RugnuxStructure> RugnuxStage(const RugnuxLiveSnapshot &s,
+                                                         const std::optional<std::string> &stage,
+                                                         httplib::Response &response) {
+    if (!stage)
+        return s.refined_structure ? s.refined_structure : s.structure;
+    if (stage == "placed")
+        return s.structure;
+    if (stage == "refined")
+        return s.refined_structure;
+    response.status = 400;
+    response.set_content("Unknown stage " + stage.value(), "text/plain");
+    return nullptr;
+}
+
+void JFJochBrokerHttp::rugnux_model_cif_get(const std::optional<std::string> &stage, httplib::Response &response) {
+    const auto structure = RugnuxStage(state_machine.GetRugnuxStatus(), stage, response);
+    if (response.status == 400)
+        return;
     if (!structure) {
         response.status = 404;
         return;
@@ -1045,16 +1069,23 @@ void JFJochBrokerHttp::rugnux_model_cif_get(httplib::Response &response) {
     response.set_content(structure->ModelCif(), "chemical/x-mmcif");
 }
 
-void JFJochBrokerHttp::rugnux_map_ccp4_get(const std::optional<std::string> &type, httplib::Response &response) {
+void JFJochBrokerHttp::rugnux_map_ccp4_get(const std::optional<std::string> &type,
+                                           const std::optional<std::string> &stage, httplib::Response &response) {
     const std::string t = type.value_or("2fofc");
     if (t != "2fofc" && t != "fofc" && t != "anom") {
         response.status = 400;
         response.set_content("Unknown map type " + t, "text/plain");
         return;
     }
-    const auto structure = state_machine.GetRugnuxStatus().structure;
+    const RugnuxLiveSnapshot status = state_machine.GetRugnuxStatus();
+    auto structure = RugnuxStage(status, stage, response);
+    if (response.status == 400)
+        return;
     const RugnuxMapType map_type = t == "2fofc" ? RugnuxMapType::TwoFoFc
                                    : t == "fofc" ? RugnuxMapType::FoFc : RugnuxMapType::Anomalous;
+    // The refined model's coefficients carry no anomalous map: it stays on the placed model's phases.
+    if (map_type == RugnuxMapType::Anomalous && structure)
+        structure = status.structure;
     const std::string map = structure ? structure->Map(map_type) : std::string();
     if (map.empty()) {
         response.status = 404;
diff --git a/broker/JFJochBrokerHttp.h b/broker/JFJochBrokerHttp.h
index a5ff26c41..f5085c6cf 100644
--- a/broker/JFJochBrokerHttp.h
+++ b/broker/JFJochBrokerHttp.h
@@ -206,8 +206,9 @@ class JFJochBrokerHttp {
     void config_rugnux_model_put(const httplib::Request &request, httplib::Response &response);
     void config_rugnux_model_delete(httplib::Response &response);
     void rugnux_status_get(httplib::Response &response);
-    void rugnux_model_cif_get(httplib::Response &response);
-    void rugnux_map_ccp4_get(const std::optional<std::string> &type, httplib::Response &response);
+    void rugnux_model_cif_get(const std::optional<std::string> &stage, httplib::Response &response);
+    void rugnux_map_ccp4_get(const std::optional<std::string> &type, const std::optional<std::string> &stage,
+                             httplib::Response &response);
     void config_bragg_integration_get(httplib::Response &response);
     void config_bragg_integration_put(const org::openapitools::server::model::Bragg_integration_settings &braggIntegrationSettings,
                                        httplib::Response &response);
diff --git a/broker/OpenAPIConvert.cpp b/broker/OpenAPIConvert.cpp
index 53168776a..c67f159a5 100644
--- a/broker/OpenAPIConvert.cpp
+++ b/broker/OpenAPIConvert.cpp
@@ -1278,7 +1278,70 @@ org::openapitools::server::model::Rugnux_live_status Convert(const RugnuxLiveSna
     ret.setSummary(summary);
     ret.setWarnings(input.warnings);
     ret.setPlacedModel(input.structure != nullptr);
+    ret.setRefinedModel(input.refined_structure != nullptr);
     ret.setAnomalousMap(input.structure != nullptr && input.structure->HasAnomalousMap());
+    ret.setAnomalousSignal(input.anomalous_signal);
+    if (!input.space_group.empty())
+        ret.setSpaceGroup(input.space_group);
+    if (input.d_min)
+        ret.setDMin(input.d_min.value());
+    if (input.isa)
+        ret.setIsa(input.isa.value());
+    if (input.model) {
+        const RugnuxLiveModel &m = input.model.value();
+        org::openapitools::server::model::Rugnux_live_model model;
+        model.setPlacement(m.placement);
+        model.setModelName(m.model_name);
+        model.setPredicted(m.predicted);
+        model.setReason(m.reason);
+        if (m.r_work) model.setRWork(m.r_work.value());
+        if (m.r_free) model.setRFree(m.r_free.value());
+        if (m.cc_model) model.setCcModel(m.cc_model.value());
+        if (m.fit_sigma) model.setFitSigma(m.fit_sigma.value());
+        if (m.map_atom_sigma) model.setMapAtomSigma(m.map_atom_sigma.value());
+        if (m.rigid_body_angle_deg) model.setRigidBodyAngleDeg(m.rigid_body_angle_deg.value());
+        if (m.rigid_body_shift_A) model.setRigidBodyShiftA(m.rigid_body_shift_A.value());
+        model.setMrDecision(m.mr_decision);
+        model.setMrSpaceGroup(m.mr_space_group);
+        if (m.copies) model.setCopies(m.copies.value());
+        if (m.tf_z) model.setTfZ(m.tf_z.value());
+        if (m.rf_z) model.setRfZ(m.rf_z.value());
+        if (m.llg_z) model.setLlgZ(m.llg_z.value());
+        if (m.mr_d_min) model.setMrDMin(m.mr_d_min.value());
+        model.setAnomalousSite(m.anomalous_site);
+        if (m.anomalous_site_sigma) model.setAnomalousSiteSigma(m.anomalous_site_sigma.value());
+        if (m.refinement) {
+            const RugnuxLiveRefinement &r = m.refinement.value();
+            org::openapitools::server::model::Rugnux_live_refinement refinement;
+            refinement.setPerformed(r.performed);
+            refinement.setCancelled(r.cancelled);
+            refinement.setReason(r.reason);
+            refinement.setOnGpu(r.on_gpu);
+            refinement.setSeconds(r.seconds);
+            if (r.r_work) refinement.setRWork(r.r_work.value());
+            if (r.r_free) refinement.setRFree(r.r_free.value());
+            if (r.rmsd_bonds_A) refinement.setRmsdBondsA(r.rmsd_bonds_A.value());
+            if (r.rmsd_angles_deg) refinement.setRmsdAnglesDeg(r.rmsd_angles_deg.value());
+            refinement.setBlobCount(r.blob_count);
+            std::vector<org::openapitools::server::model::Rugnux_live_blob> blobs;
+            for (const auto &b: r.blobs) {
+                org::openapitools::server::model::Rugnux_live_blob blob;
+                blob.setKind(b.kind);
+                blob.setX(b.x);
+                blob.setY(b.y);
+                blob.setZ(b.z);
+                blob.setPeakSigma(b.peak_sigma);
+                blob.setVolumeA3(b.volume_A3);
+                blob.setNearestAtom(b.nearest_atom);
+                if (b.nearest_atom_distance_A)
+                    blob.setNearestAtomDistanceA(*b.nearest_atom_distance_A);
+                blobs.push_back(blob);
+            }
+            refinement.setBlobs(blobs);
+            model.setRefinement(refinement);
+        }
+        ret.setModel(model);
+    }
     return ret;
 }
 
diff --git a/broker/gen/model/Azim_int_settings.cpp b/broker/gen/model/Azim_int_settings.cpp
index 5eb181267..833512e64 100644
--- a/broker/gen/model/Azim_int_settings.cpp
+++ b/broker/gen/model/Azim_int_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Azim_int_settings.h b/broker/gen/model/Azim_int_settings.h
index 632c8449f..5cfdbff2c 100644
--- a/broker/gen/model/Azim_int_settings.h
+++ b/broker/gen/model/Azim_int_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Bragg_integration_settings.cpp b/broker/gen/model/Bragg_integration_settings.cpp
index ec0aa6078..6f0820d8c 100644
--- a/broker/gen/model/Bragg_integration_settings.cpp
+++ b/broker/gen/model/Bragg_integration_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Bragg_integration_settings.h b/broker/gen/model/Bragg_integration_settings.h
index d0513f887..9b132c285 100644
--- a/broker/gen/model/Bragg_integration_settings.h
+++ b/broker/gen/model/Bragg_integration_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Broker_status.cpp b/broker/gen/model/Broker_status.cpp
index 80436ccb5..a593da3ba 100644
--- a/broker/gen/model/Broker_status.cpp
+++ b/broker/gen/model/Broker_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Broker_status.h b/broker/gen/model/Broker_status.h
index d9c2b18f3..a5bc2ac71 100644
--- a/broker/gen/model/Broker_status.h
+++ b/broker/gen/model/Broker_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Calibration_statistics_inner.cpp b/broker/gen/model/Calibration_statistics_inner.cpp
index 985c2b623..7c3f96f85 100644
--- a/broker/gen/model/Calibration_statistics_inner.cpp
+++ b/broker/gen/model/Calibration_statistics_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Calibration_statistics_inner.h b/broker/gen/model/Calibration_statistics_inner.h
index 80c17cc83..b84285fb2 100644
--- a/broker/gen/model/Calibration_statistics_inner.h
+++ b/broker/gen/model/Calibration_statistics_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dark_mask_settings.cpp b/broker/gen/model/Dark_mask_settings.cpp
index 3dac6d0e2..a5d35150d 100644
--- a/broker/gen/model/Dark_mask_settings.cpp
+++ b/broker/gen/model/Dark_mask_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dark_mask_settings.h b/broker/gen/model/Dark_mask_settings.h
index 84141189d..f7cc35de7 100644
--- a/broker/gen/model/Dark_mask_settings.h
+++ b/broker/gen/model/Dark_mask_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings.cpp b/broker/gen/model/Dataset_settings.cpp
index e174f99c4..5da814adc 100644
--- a/broker/gen/model/Dataset_settings.cpp
+++ b/broker/gen/model/Dataset_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings.h b/broker/gen/model/Dataset_settings.h
index 0afa4dc0c..723ea0b63 100644
--- a/broker/gen/model/Dataset_settings.h
+++ b/broker/gen/model/Dataset_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings_smargon.cpp b/broker/gen/model/Dataset_settings_smargon.cpp
index 770d2487e..0c06c01ea 100644
--- a/broker/gen/model/Dataset_settings_smargon.cpp
+++ b/broker/gen/model/Dataset_settings_smargon.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings_smargon.h b/broker/gen/model/Dataset_settings_smargon.h
index e511a1caf..1da2e7c57 100644
--- a/broker/gen/model/Dataset_settings_smargon.h
+++ b/broker/gen/model/Dataset_settings_smargon.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp
index 429df57f4..1a0a6671c 100644
--- a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp
+++ b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h
index 2c1417eb7..3f8df35f6 100644
--- a/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h
+++ b/broker/gen/model/Dataset_settings_xray_fluorescence_spectrum.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector.cpp b/broker/gen/model/Detector.cpp
index 5eb85f5a5..4ca016935 100644
--- a/broker/gen/model/Detector.cpp
+++ b/broker/gen/model/Detector.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector.h b/broker/gen/model/Detector.h
index 728d690b4..23352e313 100644
--- a/broker/gen/model/Detector.h
+++ b/broker/gen/model/Detector.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list.cpp b/broker/gen/model/Detector_list.cpp
index 5237182e8..c2332e842 100644
--- a/broker/gen/model/Detector_list.cpp
+++ b/broker/gen/model/Detector_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list.h b/broker/gen/model/Detector_list.h
index 695bff2b8..32255b629 100644
--- a/broker/gen/model/Detector_list.h
+++ b/broker/gen/model/Detector_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list_element.cpp b/broker/gen/model/Detector_list_element.cpp
index 8c592213b..873771c2d 100644
--- a/broker/gen/model/Detector_list_element.cpp
+++ b/broker/gen/model/Detector_list_element.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_list_element.h b/broker/gen/model/Detector_list_element.h
index 036fb8067..a2259f6fa 100644
--- a/broker/gen/model/Detector_list_element.h
+++ b/broker/gen/model/Detector_list_element.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module.cpp b/broker/gen/model/Detector_module.cpp
index c89209164..369fccac4 100644
--- a/broker/gen/model/Detector_module.cpp
+++ b/broker/gen/model/Detector_module.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module.h b/broker/gen/model/Detector_module.h
index 75ceca17f..1f24c1c11 100644
--- a/broker/gen/model/Detector_module.h
+++ b/broker/gen/model/Detector_module.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module_direction.cpp b/broker/gen/model/Detector_module_direction.cpp
index c8a982e96..55b0a505e 100644
--- a/broker/gen/model/Detector_module_direction.cpp
+++ b/broker/gen/model/Detector_module_direction.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_module_direction.h b/broker/gen/model/Detector_module_direction.h
index ca0d0bbb1..8bf48a5d2 100644
--- a/broker/gen/model/Detector_module_direction.h
+++ b/broker/gen/model/Detector_module_direction.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_power_state.cpp b/broker/gen/model/Detector_power_state.cpp
index fd07aa072..7c8bd783b 100644
--- a/broker/gen/model/Detector_power_state.cpp
+++ b/broker/gen/model/Detector_power_state.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_power_state.h b/broker/gen/model/Detector_power_state.h
index 389f2d87e..4d5fce3d3 100644
--- a/broker/gen/model/Detector_power_state.h
+++ b/broker/gen/model/Detector_power_state.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_selection.cpp b/broker/gen/model/Detector_selection.cpp
index 62efbcfaf..74e0d2c0e 100644
--- a/broker/gen/model/Detector_selection.cpp
+++ b/broker/gen/model/Detector_selection.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_selection.h b/broker/gen/model/Detector_selection.h
index 36e6bd025..0a5dd6490 100644
--- a/broker/gen/model/Detector_selection.h
+++ b/broker/gen/model/Detector_selection.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_settings.cpp b/broker/gen/model/Detector_settings.cpp
index a8703479e..2aa4a7c48 100644
--- a/broker/gen/model/Detector_settings.cpp
+++ b/broker/gen/model/Detector_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_settings.h b/broker/gen/model/Detector_settings.h
index cd3ccee68..ff8618dfa 100644
--- a/broker/gen/model/Detector_settings.h
+++ b/broker/gen/model/Detector_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_state.cpp b/broker/gen/model/Detector_state.cpp
index 35011d667..763d6c19e 100644
--- a/broker/gen/model/Detector_state.cpp
+++ b/broker/gen/model/Detector_state.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_state.h b/broker/gen/model/Detector_state.h
index 31aeb57aa..11dc3d41f 100644
--- a/broker/gen/model/Detector_state.h
+++ b/broker/gen/model/Detector_state.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_status.cpp b/broker/gen/model/Detector_status.cpp
index b6743070d..04f2f12a2 100644
--- a/broker/gen/model/Detector_status.cpp
+++ b/broker/gen/model/Detector_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_status.h b/broker/gen/model/Detector_status.h
index c058d0766..1de1b46d9 100644
--- a/broker/gen/model/Detector_status.h
+++ b/broker/gen/model/Detector_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_timing.cpp b/broker/gen/model/Detector_timing.cpp
index 3962b9671..db8a7d1d1 100644
--- a/broker/gen/model/Detector_timing.cpp
+++ b/broker/gen/model/Detector_timing.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_timing.h b/broker/gen/model/Detector_timing.h
index a3fa4c3d8..81b54bd6f 100644
--- a/broker/gen/model/Detector_timing.h
+++ b/broker/gen/model/Detector_timing.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_type.cpp b/broker/gen/model/Detector_type.cpp
index cccab64dc..3630540e2 100644
--- a/broker/gen/model/Detector_type.cpp
+++ b/broker/gen/model/Detector_type.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Detector_type.h b/broker/gen/model/Detector_type.h
index 6387098a7..39b3b049d 100644
--- a/broker/gen/model/Detector_type.h
+++ b/broker/gen/model/Detector_type.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Error_message.cpp b/broker/gen/model/Error_message.cpp
index a88e821c8..491a0b018 100644
--- a/broker/gen/model/Error_message.cpp
+++ b/broker/gen/model/Error_message.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Error_message.h b/broker/gen/model/Error_message.h
index bf408c53d..d0a72c33f 100644
--- a/broker/gen/model/Error_message.h
+++ b/broker/gen/model/Error_message.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_format.cpp b/broker/gen/model/File_writer_format.cpp
index 573810eaa..bd9b04866 100644
--- a/broker/gen/model/File_writer_format.cpp
+++ b/broker/gen/model/File_writer_format.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_format.h b/broker/gen/model/File_writer_format.h
index 554a025ef..5259ca938 100644
--- a/broker/gen/model/File_writer_format.h
+++ b/broker/gen/model/File_writer_format.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_settings.cpp b/broker/gen/model/File_writer_settings.cpp
index 0032c7724..c71993006 100644
--- a/broker/gen/model/File_writer_settings.cpp
+++ b/broker/gen/model/File_writer_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/File_writer_settings.h b/broker/gen/model/File_writer_settings.h
index d14cff05a..63e72ad39 100644
--- a/broker/gen/model/File_writer_settings.h
+++ b/broker/gen/model/File_writer_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Fpga_status_inner.cpp b/broker/gen/model/Fpga_status_inner.cpp
index 3c6286c01..c07654f3c 100644
--- a/broker/gen/model/Fpga_status_inner.cpp
+++ b/broker/gen/model/Fpga_status_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Fpga_status_inner.h b/broker/gen/model/Fpga_status_inner.h
index 61bbbbb40..b143f2215 100644
--- a/broker/gen/model/Fpga_status_inner.h
+++ b/broker/gen/model/Fpga_status_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Geom_refinement_algorithm.cpp b/broker/gen/model/Geom_refinement_algorithm.cpp
index 3332c5e65..6dd36ca50 100644
--- a/broker/gen/model/Geom_refinement_algorithm.cpp
+++ b/broker/gen/model/Geom_refinement_algorithm.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Geom_refinement_algorithm.h b/broker/gen/model/Geom_refinement_algorithm.h
index 6cb37b28b..5e2c31473 100644
--- a/broker/gen/model/Geom_refinement_algorithm.h
+++ b/broker/gen/model/Geom_refinement_algorithm.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Grid_scan.cpp b/broker/gen/model/Grid_scan.cpp
index 1fd8e01bf..30f82608d 100644
--- a/broker/gen/model/Grid_scan.cpp
+++ b/broker/gen/model/Grid_scan.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Grid_scan.h b/broker/gen/model/Grid_scan.h
index cee76dea7..44aba0284 100644
--- a/broker/gen/model/Grid_scan.h
+++ b/broker/gen/model/Grid_scan.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Helpers.cpp b/broker/gen/model/Helpers.cpp
index 7ddfe3cde..1e173d751 100644
--- a/broker/gen/model/Helpers.cpp
+++ b/broker/gen/model/Helpers.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Helpers.h b/broker/gen/model/Helpers.h
index d0c3e01b9..d168f38df 100644
--- a/broker/gen/model/Helpers.h
+++ b/broker/gen/model/Helpers.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_buffer_status.cpp b/broker/gen/model/Image_buffer_status.cpp
index 3470aa238..2ea9ab1fe 100644
--- a/broker/gen/model/Image_buffer_status.cpp
+++ b/broker/gen/model/Image_buffer_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_buffer_status.h b/broker/gen/model/Image_buffer_status.h
index 975a44332..e505e17e4 100644
--- a/broker/gen/model/Image_buffer_status.h
+++ b/broker/gen/model/Image_buffer_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_format_settings.cpp b/broker/gen/model/Image_format_settings.cpp
index c0e8418f4..103a31df2 100644
--- a/broker/gen/model/Image_format_settings.cpp
+++ b/broker/gen/model/Image_format_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_format_settings.h b/broker/gen/model/Image_format_settings.h
index a177753f6..52ba959c8 100644
--- a/broker/gen/model/Image_format_settings.h
+++ b/broker/gen/model/Image_format_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_status.cpp b/broker/gen/model/Image_pusher_status.cpp
index 4371e6ac8..5c1f947c2 100644
--- a/broker/gen/model/Image_pusher_status.cpp
+++ b/broker/gen/model/Image_pusher_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_status.h b/broker/gen/model/Image_pusher_status.h
index 4b16c62cf..fb9df6a6d 100644
--- a/broker/gen/model/Image_pusher_status.h
+++ b/broker/gen/model/Image_pusher_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_type.cpp b/broker/gen/model/Image_pusher_type.cpp
index e425dc6c3..f444201b1 100644
--- a/broker/gen/model/Image_pusher_type.cpp
+++ b/broker/gen/model/Image_pusher_type.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Image_pusher_type.h b/broker/gen/model/Image_pusher_type.h
index 1fa5d7130..a2c79900a 100644
--- a/broker/gen/model/Image_pusher_type.h
+++ b/broker/gen/model/Image_pusher_type.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_algorithm.cpp b/broker/gen/model/Indexing_algorithm.cpp
index 1230d8a4b..486aaf2f6 100644
--- a/broker/gen/model/Indexing_algorithm.cpp
+++ b/broker/gen/model/Indexing_algorithm.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_algorithm.h b/broker/gen/model/Indexing_algorithm.h
index bae3bbf8d..6d8ea4b93 100644
--- a/broker/gen/model/Indexing_algorithm.h
+++ b/broker/gen/model/Indexing_algorithm.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_settings.cpp b/broker/gen/model/Indexing_settings.cpp
index dbee64636..38d02d692 100644
--- a/broker/gen/model/Indexing_settings.cpp
+++ b/broker/gen/model/Indexing_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Indexing_settings.h b/broker/gen/model/Indexing_settings.h
index 61e0cba3e..e610d0830 100644
--- a/broker/gen/model/Indexing_settings.h
+++ b/broker/gen/model/Indexing_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Instrument_metadata.cpp b/broker/gen/model/Instrument_metadata.cpp
index 5211c4cf2..243fb960f 100644
--- a/broker/gen/model/Instrument_metadata.cpp
+++ b/broker/gen/model/Instrument_metadata.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Instrument_metadata.h b/broker/gen/model/Instrument_metadata.h
index 89748a30a..1f9f43f67 100644
--- a/broker/gen/model/Instrument_metadata.h
+++ b/broker/gen/model/Instrument_metadata.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Integration_model.cpp b/broker/gen/model/Integration_model.cpp
index d8c3ffd3c..f427b9119 100644
--- a/broker/gen/model/Integration_model.cpp
+++ b/broker/gen/model/Integration_model.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Integration_model.h b/broker/gen/model/Integration_model.h
index 4445967f5..946e1d5ce 100644
--- a/broker/gen/model/Integration_model.h
+++ b/broker/gen/model/Integration_model.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_settings.cpp b/broker/gen/model/Jfjoch_settings.cpp
index a9075174e..cc348b97f 100644
--- a/broker/gen/model/Jfjoch_settings.cpp
+++ b/broker/gen/model/Jfjoch_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_settings.h b/broker/gen/model/Jfjoch_settings.h
index f41050629..7e100951d 100644
--- a/broker/gen/model/Jfjoch_settings.h
+++ b/broker/gen/model/Jfjoch_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_statistics.cpp b/broker/gen/model/Jfjoch_statistics.cpp
index 411fa0655..a112d02a7 100644
--- a/broker/gen/model/Jfjoch_statistics.cpp
+++ b/broker/gen/model/Jfjoch_statistics.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Jfjoch_statistics.h b/broker/gen/model/Jfjoch_statistics.h
index dcd06d807..494a90a06 100644
--- a/broker/gen/model/Jfjoch_statistics.h
+++ b/broker/gen/model/Jfjoch_statistics.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Measurement_statistics.cpp b/broker/gen/model/Measurement_statistics.cpp
index 40c6aa250..50360ea57 100644
--- a/broker/gen/model/Measurement_statistics.cpp
+++ b/broker/gen/model/Measurement_statistics.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Measurement_statistics.h b/broker/gen/model/Measurement_statistics.h
index b94d10cfd..2b5d850e6 100644
--- a/broker/gen/model/Measurement_statistics.h
+++ b/broker/gen/model/Measurement_statistics.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pcie_devices_inner.cpp b/broker/gen/model/Pcie_devices_inner.cpp
index 45f112b23..8b5fd7696 100644
--- a/broker/gen/model/Pcie_devices_inner.cpp
+++ b/broker/gen/model/Pcie_devices_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pcie_devices_inner.h b/broker/gen/model/Pcie_devices_inner.h
index ccb6ea27c..7d727e0f4 100644
--- a/broker/gen/model/Pcie_devices_inner.h
+++ b/broker/gen/model/Pcie_devices_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pixel_mask_statistics.cpp b/broker/gen/model/Pixel_mask_statistics.cpp
index 4282a8564..49be9f5fc 100644
--- a/broker/gen/model/Pixel_mask_statistics.cpp
+++ b/broker/gen/model/Pixel_mask_statistics.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Pixel_mask_statistics.h b/broker/gen/model/Pixel_mask_statistics.h
index 3e4c0e063..02b40444c 100644
--- a/broker/gen/model/Pixel_mask_statistics.h
+++ b/broker/gen/model/Pixel_mask_statistics.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot.cpp b/broker/gen/model/Plot.cpp
index bdd1940c3..285961f49 100644
--- a/broker/gen/model/Plot.cpp
+++ b/broker/gen/model/Plot.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot.h b/broker/gen/model/Plot.h
index 74910c46f..66e3348c0 100644
--- a/broker/gen/model/Plot.h
+++ b/broker/gen/model/Plot.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot_unit_x.cpp b/broker/gen/model/Plot_unit_x.cpp
index bae5f1316..26b3ca835 100644
--- a/broker/gen/model/Plot_unit_x.cpp
+++ b/broker/gen/model/Plot_unit_x.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plot_unit_x.h b/broker/gen/model/Plot_unit_x.h
index 115ec5e4a..dc16fa29f 100644
--- a/broker/gen/model/Plot_unit_x.h
+++ b/broker/gen/model/Plot_unit_x.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plots.cpp b/broker/gen/model/Plots.cpp
index e51893833..58281b393 100644
--- a/broker/gen/model/Plots.cpp
+++ b/broker/gen/model/Plots.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Plots.h b/broker/gen/model/Plots.h
index 34147efb3..a58144f0c 100644
--- a/broker/gen/model/Plots.h
+++ b/broker/gen/model/Plots.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_fit_sigma.cpp b/broker/gen/model/Powder_calibration_fit_sigma.cpp
index c1b72c27a..8c91ea91d 100644
--- a/broker/gen/model/Powder_calibration_fit_sigma.cpp
+++ b/broker/gen/model/Powder_calibration_fit_sigma.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_fit_sigma.h b/broker/gen/model/Powder_calibration_fit_sigma.h
index fa7551dd3..38d42eaae 100644
--- a/broker/gen/model/Powder_calibration_fit_sigma.h
+++ b/broker/gen/model/Powder_calibration_fit_sigma.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_output.cpp b/broker/gen/model/Powder_calibration_output.cpp
index 4180f05b2..ded107086 100644
--- a/broker/gen/model/Powder_calibration_output.cpp
+++ b/broker/gen/model/Powder_calibration_output.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_output.h b/broker/gen/model/Powder_calibration_output.h
index 0ad009726..af0231874 100644
--- a/broker/gen/model/Powder_calibration_output.h
+++ b/broker/gen/model/Powder_calibration_output.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_quality.cpp b/broker/gen/model/Powder_calibration_quality.cpp
index c0460f452..423b8e8ec 100644
--- a/broker/gen/model/Powder_calibration_quality.cpp
+++ b/broker/gen/model/Powder_calibration_quality.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_quality.h b/broker/gen/model/Powder_calibration_quality.h
index 73dd89c28..a47f0e76f 100644
--- a/broker/gen/model/Powder_calibration_quality.h
+++ b/broker/gen/model/Powder_calibration_quality.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_spot_check.cpp b/broker/gen/model/Powder_calibration_spot_check.cpp
index 25a144799..877de4041 100644
--- a/broker/gen/model/Powder_calibration_spot_check.cpp
+++ b/broker/gen/model/Powder_calibration_spot_check.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Powder_calibration_spot_check.h b/broker/gen/model/Powder_calibration_spot_check.h
index f05677c37..1ef1b75ba 100644
--- a/broker/gen/model/Powder_calibration_spot_check.h
+++ b/broker/gen/model/Powder_calibration_spot_check.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azim_list.cpp b/broker/gen/model/Roi_azim_list.cpp
index f2e91b20f..b13ffb7c5 100644
--- a/broker/gen/model/Roi_azim_list.cpp
+++ b/broker/gen/model/Roi_azim_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azim_list.h b/broker/gen/model/Roi_azim_list.h
index ba6d57169..8b7f915aa 100644
--- a/broker/gen/model/Roi_azim_list.h
+++ b/broker/gen/model/Roi_azim_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azimuthal.cpp b/broker/gen/model/Roi_azimuthal.cpp
index 29bf6b680..c8f319f3b 100644
--- a/broker/gen/model/Roi_azimuthal.cpp
+++ b/broker/gen/model/Roi_azimuthal.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_azimuthal.h b/broker/gen/model/Roi_azimuthal.h
index 1fb9d96b3..b15885155 100644
--- a/broker/gen/model/Roi_azimuthal.h
+++ b/broker/gen/model/Roi_azimuthal.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box.cpp b/broker/gen/model/Roi_box.cpp
index 4d8c3d79b..ed20bbee3 100644
--- a/broker/gen/model/Roi_box.cpp
+++ b/broker/gen/model/Roi_box.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box.h b/broker/gen/model/Roi_box.h
index ba8617d43..aa92fb4f3 100644
--- a/broker/gen/model/Roi_box.h
+++ b/broker/gen/model/Roi_box.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box_list.cpp b/broker/gen/model/Roi_box_list.cpp
index 8b790af50..46401cc12 100644
--- a/broker/gen/model/Roi_box_list.cpp
+++ b/broker/gen/model/Roi_box_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_box_list.h b/broker/gen/model/Roi_box_list.h
index 45750e5d1..90dfbcd42 100644
--- a/broker/gen/model/Roi_box_list.h
+++ b/broker/gen/model/Roi_box_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle.cpp b/broker/gen/model/Roi_circle.cpp
index 81f517d53..f55912211 100644
--- a/broker/gen/model/Roi_circle.cpp
+++ b/broker/gen/model/Roi_circle.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle.h b/broker/gen/model/Roi_circle.h
index 87ddb8905..e96562b6d 100644
--- a/broker/gen/model/Roi_circle.h
+++ b/broker/gen/model/Roi_circle.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle_list.cpp b/broker/gen/model/Roi_circle_list.cpp
index 861c1179b..d6a2feb55 100644
--- a/broker/gen/model/Roi_circle_list.cpp
+++ b/broker/gen/model/Roi_circle_list.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_circle_list.h b/broker/gen/model/Roi_circle_list.h
index ea219340e..f7276fcb7 100644
--- a/broker/gen/model/Roi_circle_list.h
+++ b/broker/gen/model/Roi_circle_list.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_definitions.cpp b/broker/gen/model/Roi_definitions.cpp
index 82cde7be1..b6344bd10 100644
--- a/broker/gen/model/Roi_definitions.cpp
+++ b/broker/gen/model/Roi_definitions.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Roi_definitions.h b/broker/gen/model/Roi_definitions.h
index 3650b76db..6e6a9c266 100644
--- a/broker/gen/model/Roi_definitions.h
+++ b/broker/gen/model/Roi_definitions.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rotation_axis.cpp b/broker/gen/model/Rotation_axis.cpp
index 99cc9739f..f3faf4e4e 100644
--- a/broker/gen/model/Rotation_axis.cpp
+++ b/broker/gen/model/Rotation_axis.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rotation_axis.h b/broker/gen/model/Rotation_axis.h
index 83e78112c..124f40300 100644
--- a/broker/gen/model/Rotation_axis.h
+++ b/broker/gen/model/Rotation_axis.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_live_blob.cpp b/broker/gen/model/Rugnux_live_blob.cpp
new file mode 100644
index 000000000..a3feb18f2
--- /dev/null
+++ b/broker/gen/model/Rugnux_live_blob.cpp
@@ -0,0 +1,204 @@
+/**
+* Jungfraujoch
+* API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
+*
+* The version of the OpenAPI document: 1.0.0-rc.180
+* Contact: filip.leonarski@psi.ch
+*
+* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+* https://openapi-generator.tech
+* Do not edit the class manually.
+*/
+
+
+#include "Rugnux_live_blob.h"
+#include "Helpers.h"
+
+#include <sstream>
+
+namespace org::openapitools::server::model
+{
+
+Rugnux_live_blob::Rugnux_live_blob()
+{
+    m_Kind = "";
+    m_x = 0.0;
+    m_y = 0.0;
+    m_z = 0.0;
+    m_Peak_sigma = 0.0;
+    m_Volume_A3 = 0.0;
+    m_Nearest_atom = "";
+    m_Nearest_atom_distance_A = 0.0;
+    m_Nearest_atom_distance_AIsSet = false;
+    
+}
+
+void Rugnux_live_blob::validate() const
+{
+    std::stringstream msg;
+    if (!validate(msg))
+    {
+        throw org::openapitools::server::helpers::ValidationException(msg.str());
+    }
+}
+
+bool Rugnux_live_blob::validate(std::stringstream& msg) const
+{
+    return validate(msg, "");
+}
+
+bool Rugnux_live_blob::validate(std::stringstream& msg, const std::string& pathPrefix) const
+{
+    bool success = true;
+    const std::string _pathPrefix = pathPrefix.empty() ? "Rugnux_live_blob" : pathPrefix;
+
+                                    
+    return success;
+}
+
+bool Rugnux_live_blob::operator==(const Rugnux_live_blob& rhs) const
+{
+    return
+    
+    
+    (getKind() == rhs.getKind())
+     &&
+    
+    (getX() == rhs.getX())
+     &&
+    
+    (getY() == rhs.getY())
+     &&
+    
+    (getZ() == rhs.getZ())
+     &&
+    
+    (getPeakSigma() == rhs.getPeakSigma())
+     &&
+    
+    (getVolumeA3() == rhs.getVolumeA3())
+     &&
+    
+    (getNearestAtom() == rhs.getNearestAtom())
+     &&
+    
+    
+    ((!nearestAtomDistanceAIsSet() && !rhs.nearestAtomDistanceAIsSet()) || (nearestAtomDistanceAIsSet() && rhs.nearestAtomDistanceAIsSet() && getNearestAtomDistanceA() == rhs.getNearestAtomDistanceA()))
+    
+    ;
+}
+
+bool Rugnux_live_blob::operator!=(const Rugnux_live_blob& rhs) const
+{
+    return !(*this == rhs);
+}
+
+void to_json(nlohmann::json& j, const Rugnux_live_blob& o)
+{
+    j = nlohmann::json::object();
+    j["kind"] = o.m_Kind;
+    j["x"] = o.m_x;
+    j["y"] = o.m_y;
+    j["z"] = o.m_z;
+    j["peak_sigma"] = o.m_Peak_sigma;
+    j["volume_A3"] = o.m_Volume_A3;
+    j["nearest_atom"] = o.m_Nearest_atom;
+    if(o.nearestAtomDistanceAIsSet())
+        j["nearest_atom_distance_A"] = o.m_Nearest_atom_distance_A;
+    
+}
+
+void from_json(const nlohmann::json& j, Rugnux_live_blob& o)
+{
+    j.at("kind").get_to(o.m_Kind);
+    j.at("x").get_to(o.m_x);
+    j.at("y").get_to(o.m_y);
+    j.at("z").get_to(o.m_z);
+    j.at("peak_sigma").get_to(o.m_Peak_sigma);
+    j.at("volume_A3").get_to(o.m_Volume_A3);
+    j.at("nearest_atom").get_to(o.m_Nearest_atom);
+    if(j.find("nearest_atom_distance_A") != j.end())
+    {
+        j.at("nearest_atom_distance_A").get_to(o.m_Nearest_atom_distance_A);
+        o.m_Nearest_atom_distance_AIsSet = true;
+    } 
+    
+}
+
+std::string Rugnux_live_blob::getKind() const
+{
+    return m_Kind;
+}
+void Rugnux_live_blob::setKind(std::string const& value)
+{
+    m_Kind = value;
+}
+double Rugnux_live_blob::getX() const
+{
+    return m_x;
+}
+void Rugnux_live_blob::setX(double const value)
+{
+    m_x = value;
+}
+double Rugnux_live_blob::getY() const
+{
+    return m_y;
+}
+void Rugnux_live_blob::setY(double const value)
+{
+    m_y = value;
+}
+double Rugnux_live_blob::getZ() const
+{
+    return m_z;
+}
+void Rugnux_live_blob::setZ(double const value)
+{
+    m_z = value;
+}
+double Rugnux_live_blob::getPeakSigma() const
+{
+    return m_Peak_sigma;
+}
+void Rugnux_live_blob::setPeakSigma(double const value)
+{
+    m_Peak_sigma = value;
+}
+double Rugnux_live_blob::getVolumeA3() const
+{
+    return m_Volume_A3;
+}
+void Rugnux_live_blob::setVolumeA3(double const value)
+{
+    m_Volume_A3 = value;
+}
+std::string Rugnux_live_blob::getNearestAtom() const
+{
+    return m_Nearest_atom;
+}
+void Rugnux_live_blob::setNearestAtom(std::string const& value)
+{
+    m_Nearest_atom = value;
+}
+double Rugnux_live_blob::getNearestAtomDistanceA() const
+{
+    return m_Nearest_atom_distance_A;
+}
+void Rugnux_live_blob::setNearestAtomDistanceA(double const value)
+{
+    m_Nearest_atom_distance_A = value;
+    m_Nearest_atom_distance_AIsSet = true;
+}
+bool Rugnux_live_blob::nearestAtomDistanceAIsSet() const
+{
+    return m_Nearest_atom_distance_AIsSet;
+}
+void Rugnux_live_blob::unsetNearest_atom_distance_A()
+{
+    m_Nearest_atom_distance_AIsSet = false;
+}
+
+
+} // namespace org::openapitools::server::model
+
diff --git a/broker/gen/model/Rugnux_live_blob.h b/broker/gen/model/Rugnux_live_blob.h
new file mode 100644
index 000000000..20372f595
--- /dev/null
+++ b/broker/gen/model/Rugnux_live_blob.h
@@ -0,0 +1,128 @@
+/**
+* Jungfraujoch
+* API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
+*
+* The version of the OpenAPI document: 1.0.0-rc.180
+* Contact: filip.leonarski@psi.ch
+*
+* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+* https://openapi-generator.tech
+* Do not edit the class manually.
+*/
+/*
+ * Rugnux_live_blob.h
+ *
+ * A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on what is measured, to point a person at the density - not an identification. 
+ */
+
+#ifndef Rugnux_live_blob_H_
+#define Rugnux_live_blob_H_
+
+
+#include <string>
+#include <nlohmann/json.hpp>
+
+namespace org::openapitools::server::model
+{
+
+/// <summary>
+/// A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on what is measured, to point a person at the density - not an identification. 
+/// </summary>
+class  Rugnux_live_blob
+{
+public:
+    Rugnux_live_blob();
+    virtual ~Rugnux_live_blob() = default;
+
+
+    /// <summary>
+    /// Validate the current data in the model. Throws a ValidationException on failure.
+    /// </summary>
+    void validate() const;
+
+    /// <summary>
+    /// Validate the current data in the model. Returns false on error and writes an error
+    /// message into the given stringstream.
+    /// </summary>
+    bool validate(std::stringstream& msg) const;
+
+    /// <summary>
+    /// Helper overload for validate. Used when one model stores another model and calls it's validate.
+    /// Not meant to be called outside that case.
+    /// </summary>
+    bool validate(std::stringstream& msg, const std::string& pathPrefix) const;
+
+    bool operator==(const Rugnux_live_blob& rhs) const;
+    bool operator!=(const Rugnux_live_blob& rhs) const;
+
+    /////////////////////////////////////////////
+    /// Rugnux_live_blob members
+
+    /// <summary>
+    /// 
+    /// </summary>
+    std::string getKind() const;
+    void setKind(std::string const& value);
+    /// <summary>
+    /// Centroid, Cartesian Angstrom, in the frame of the refined model (&#x60;/rugnux/model.cif&#x60;)
+    /// </summary>
+    double getX() const;
+    void setX(double const value);
+    /// <summary>
+    /// 
+    /// </summary>
+    double getY() const;
+    void setY(double const value);
+    /// <summary>
+    /// 
+    /// </summary>
+    double getZ() const;
+    void setZ(double const value);
+    /// <summary>
+    /// The highest point, in map sigma
+    /// </summary>
+    double getPeakSigma() const;
+    void setPeakSigma(double const value);
+    /// <summary>
+    /// Volume above 3 sigma, in cubic Angstrom
+    /// </summary>
+    double getVolumeA3() const;
+    void setVolumeA3(double const value);
+    /// <summary>
+    /// e.g. \&quot;OG1 THR A42\&quot;
+    /// </summary>
+    std::string getNearestAtom() const;
+    void setNearestAtom(std::string const& value);
+    /// <summary>
+    /// Absent where no atom is within 12 Angstrom
+    /// </summary>
+    double getNearestAtomDistanceA() const;
+    void setNearestAtomDistanceA(double const value);
+    bool nearestAtomDistanceAIsSet() const;
+    void unsetNearest_atom_distance_A();
+
+    friend  void to_json(nlohmann::json& j, const Rugnux_live_blob& o);
+    friend  void from_json(const nlohmann::json& j, Rugnux_live_blob& o);
+protected:
+    std::string m_Kind;
+
+    double m_x;
+
+    double m_y;
+
+    double m_z;
+
+    double m_Peak_sigma;
+
+    double m_Volume_A3;
+
+    std::string m_Nearest_atom;
+
+    double m_Nearest_atom_distance_A;
+    bool m_Nearest_atom_distance_AIsSet;
+    
+};
+
+} // namespace org::openapitools::server::model
+
+#endif /* Rugnux_live_blob_H_ */
diff --git a/broker/gen/model/Rugnux_live_model.cpp b/broker/gen/model/Rugnux_live_model.cpp
new file mode 100644
index 000000000..da7ba982d
--- /dev/null
+++ b/broker/gen/model/Rugnux_live_model.cpp
@@ -0,0 +1,580 @@
+/**
+* Jungfraujoch
+* API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
+*
+* The version of the OpenAPI document: 1.0.0-rc.180
+* Contact: filip.leonarski@psi.ch
+*
+* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+* https://openapi-generator.tech
+* Do not edit the class manually.
+*/
+
+
+#include "Rugnux_live_model.h"
+#include "Helpers.h"
+
+#include <sstream>
+
+namespace org::openapitools::server::model
+{
+
+Rugnux_live_model::Rugnux_live_model()
+{
+    m_Placement = "";
+    m_Model_name = "";
+    m_Predicted = false;
+    m_Reason = "";
+    m_R_work = 0.0;
+    m_R_workIsSet = false;
+    m_R_free = 0.0;
+    m_R_freeIsSet = false;
+    m_Cc_model = 0.0;
+    m_Cc_modelIsSet = false;
+    m_Fit_sigma = 0.0;
+    m_Fit_sigmaIsSet = false;
+    m_Map_atom_sigma = 0.0;
+    m_Map_atom_sigmaIsSet = false;
+    m_Rigid_body_angle_deg = 0.0;
+    m_Rigid_body_angle_degIsSet = false;
+    m_Rigid_body_shift_A = 0.0;
+    m_Rigid_body_shift_AIsSet = false;
+    m_Mr_decision = "";
+    m_Mr_space_group = "";
+    m_Copies = 0L;
+    m_CopiesIsSet = false;
+    m_Tf_z = 0.0;
+    m_Tf_zIsSet = false;
+    m_Rf_z = 0.0;
+    m_Rf_zIsSet = false;
+    m_Llg_z = 0.0;
+    m_Llg_zIsSet = false;
+    m_Mr_d_min = 0.0;
+    m_Mr_d_minIsSet = false;
+    m_Anomalous_site = "";
+    m_Anomalous_site_sigma = 0.0;
+    m_Anomalous_site_sigmaIsSet = false;
+    m_RefinementIsSet = false;
+    
+}
+
+void Rugnux_live_model::validate() const
+{
+    std::stringstream msg;
+    if (!validate(msg))
+    {
+        throw org::openapitools::server::helpers::ValidationException(msg.str());
+    }
+}
+
+bool Rugnux_live_model::validate(std::stringstream& msg) const
+{
+    return validate(msg, "");
+}
+
+bool Rugnux_live_model::validate(std::stringstream& msg, const std::string& pathPrefix) const
+{
+    bool success = true;
+    const std::string _pathPrefix = pathPrefix.empty() ? "Rugnux_live_model" : pathPrefix;
+
+                                                                                        
+    return success;
+}
+
+bool Rugnux_live_model::operator==(const Rugnux_live_model& rhs) const
+{
+    return
+    
+    
+    (getPlacement() == rhs.getPlacement())
+     &&
+    
+    (getModelName() == rhs.getModelName())
+     &&
+    
+    (isPredicted() == rhs.isPredicted())
+     &&
+    
+    (getReason() == rhs.getReason())
+     &&
+    
+    
+    ((!rWorkIsSet() && !rhs.rWorkIsSet()) || (rWorkIsSet() && rhs.rWorkIsSet() && getRWork() == rhs.getRWork())) &&
+    
+    
+    ((!rFreeIsSet() && !rhs.rFreeIsSet()) || (rFreeIsSet() && rhs.rFreeIsSet() && getRFree() == rhs.getRFree())) &&
+    
+    
+    ((!ccModelIsSet() && !rhs.ccModelIsSet()) || (ccModelIsSet() && rhs.ccModelIsSet() && getCcModel() == rhs.getCcModel())) &&
+    
+    
+    ((!fitSigmaIsSet() && !rhs.fitSigmaIsSet()) || (fitSigmaIsSet() && rhs.fitSigmaIsSet() && getFitSigma() == rhs.getFitSigma())) &&
+    
+    
+    ((!mapAtomSigmaIsSet() && !rhs.mapAtomSigmaIsSet()) || (mapAtomSigmaIsSet() && rhs.mapAtomSigmaIsSet() && getMapAtomSigma() == rhs.getMapAtomSigma())) &&
+    
+    
+    ((!rigidBodyAngleDegIsSet() && !rhs.rigidBodyAngleDegIsSet()) || (rigidBodyAngleDegIsSet() && rhs.rigidBodyAngleDegIsSet() && getRigidBodyAngleDeg() == rhs.getRigidBodyAngleDeg())) &&
+    
+    
+    ((!rigidBodyShiftAIsSet() && !rhs.rigidBodyShiftAIsSet()) || (rigidBodyShiftAIsSet() && rhs.rigidBodyShiftAIsSet() && getRigidBodyShiftA() == rhs.getRigidBodyShiftA())) &&
+    
+    (getMrDecision() == rhs.getMrDecision())
+     &&
+    
+    (getMrSpaceGroup() == rhs.getMrSpaceGroup())
+     &&
+    
+    
+    ((!copiesIsSet() && !rhs.copiesIsSet()) || (copiesIsSet() && rhs.copiesIsSet() && getCopies() == rhs.getCopies())) &&
+    
+    
+    ((!tfZIsSet() && !rhs.tfZIsSet()) || (tfZIsSet() && rhs.tfZIsSet() && getTfZ() == rhs.getTfZ())) &&
+    
+    
+    ((!rfZIsSet() && !rhs.rfZIsSet()) || (rfZIsSet() && rhs.rfZIsSet() && getRfZ() == rhs.getRfZ())) &&
+    
+    
+    ((!llgZIsSet() && !rhs.llgZIsSet()) || (llgZIsSet() && rhs.llgZIsSet() && getLlgZ() == rhs.getLlgZ())) &&
+    
+    
+    ((!mrDMinIsSet() && !rhs.mrDMinIsSet()) || (mrDMinIsSet() && rhs.mrDMinIsSet() && getMrDMin() == rhs.getMrDMin())) &&
+    
+    (getAnomalousSite() == rhs.getAnomalousSite())
+     &&
+    
+    
+    ((!anomalousSiteSigmaIsSet() && !rhs.anomalousSiteSigmaIsSet()) || (anomalousSiteSigmaIsSet() && rhs.anomalousSiteSigmaIsSet() && getAnomalousSiteSigma() == rhs.getAnomalousSiteSigma())) &&
+    
+    
+    ((!refinementIsSet() && !rhs.refinementIsSet()) || (refinementIsSet() && rhs.refinementIsSet() && getRefinement() == rhs.getRefinement()))
+    
+    ;
+}
+
+bool Rugnux_live_model::operator!=(const Rugnux_live_model& rhs) const
+{
+    return !(*this == rhs);
+}
+
+void to_json(nlohmann::json& j, const Rugnux_live_model& o)
+{
+    j = nlohmann::json::object();
+    j["placement"] = o.m_Placement;
+    j["model_name"] = o.m_Model_name;
+    j["predicted"] = o.m_Predicted;
+    j["reason"] = o.m_Reason;
+    if(o.rWorkIsSet())
+        j["r_work"] = o.m_R_work;
+    if(o.rFreeIsSet())
+        j["r_free"] = o.m_R_free;
+    if(o.ccModelIsSet())
+        j["cc_model"] = o.m_Cc_model;
+    if(o.fitSigmaIsSet())
+        j["fit_sigma"] = o.m_Fit_sigma;
+    if(o.mapAtomSigmaIsSet())
+        j["map_atom_sigma"] = o.m_Map_atom_sigma;
+    if(o.rigidBodyAngleDegIsSet())
+        j["rigid_body_angle_deg"] = o.m_Rigid_body_angle_deg;
+    if(o.rigidBodyShiftAIsSet())
+        j["rigid_body_shift_A"] = o.m_Rigid_body_shift_A;
+    j["mr_decision"] = o.m_Mr_decision;
+    j["mr_space_group"] = o.m_Mr_space_group;
+    if(o.copiesIsSet())
+        j["copies"] = o.m_Copies;
+    if(o.tfZIsSet())
+        j["tf_z"] = o.m_Tf_z;
+    if(o.rfZIsSet())
+        j["rf_z"] = o.m_Rf_z;
+    if(o.llgZIsSet())
+        j["llg_z"] = o.m_Llg_z;
+    if(o.mrDMinIsSet())
+        j["mr_d_min"] = o.m_Mr_d_min;
+    j["anomalous_site"] = o.m_Anomalous_site;
+    if(o.anomalousSiteSigmaIsSet())
+        j["anomalous_site_sigma"] = o.m_Anomalous_site_sigma;
+    if(o.refinementIsSet())
+        j["refinement"] = o.m_Refinement;
+    
+}
+
+void from_json(const nlohmann::json& j, Rugnux_live_model& o)
+{
+    j.at("placement").get_to(o.m_Placement);
+    j.at("model_name").get_to(o.m_Model_name);
+    j.at("predicted").get_to(o.m_Predicted);
+    j.at("reason").get_to(o.m_Reason);
+    if(j.find("r_work") != j.end())
+    {
+        j.at("r_work").get_to(o.m_R_work);
+        o.m_R_workIsSet = true;
+    } 
+    if(j.find("r_free") != j.end())
+    {
+        j.at("r_free").get_to(o.m_R_free);
+        o.m_R_freeIsSet = true;
+    } 
+    if(j.find("cc_model") != j.end())
+    {
+        j.at("cc_model").get_to(o.m_Cc_model);
+        o.m_Cc_modelIsSet = true;
+    } 
+    if(j.find("fit_sigma") != j.end())
+    {
+        j.at("fit_sigma").get_to(o.m_Fit_sigma);
+        o.m_Fit_sigmaIsSet = true;
+    } 
+    if(j.find("map_atom_sigma") != j.end())
+    {
+        j.at("map_atom_sigma").get_to(o.m_Map_atom_sigma);
+        o.m_Map_atom_sigmaIsSet = true;
+    } 
+    if(j.find("rigid_body_angle_deg") != j.end())
+    {
+        j.at("rigid_body_angle_deg").get_to(o.m_Rigid_body_angle_deg);
+        o.m_Rigid_body_angle_degIsSet = true;
+    } 
+    if(j.find("rigid_body_shift_A") != j.end())
+    {
+        j.at("rigid_body_shift_A").get_to(o.m_Rigid_body_shift_A);
+        o.m_Rigid_body_shift_AIsSet = true;
+    } 
+    j.at("mr_decision").get_to(o.m_Mr_decision);
+    j.at("mr_space_group").get_to(o.m_Mr_space_group);
+    if(j.find("copies") != j.end())
+    {
+        j.at("copies").get_to(o.m_Copies);
+        o.m_CopiesIsSet = true;
+    } 
+    if(j.find("tf_z") != j.end())
+    {
+        j.at("tf_z").get_to(o.m_Tf_z);
+        o.m_Tf_zIsSet = true;
+    } 
+    if(j.find("rf_z") != j.end())
+    {
+        j.at("rf_z").get_to(o.m_Rf_z);
+        o.m_Rf_zIsSet = true;
+    } 
+    if(j.find("llg_z") != j.end())
+    {
+        j.at("llg_z").get_to(o.m_Llg_z);
+        o.m_Llg_zIsSet = true;
+    } 
+    if(j.find("mr_d_min") != j.end())
+    {
+        j.at("mr_d_min").get_to(o.m_Mr_d_min);
+        o.m_Mr_d_minIsSet = true;
+    } 
+    j.at("anomalous_site").get_to(o.m_Anomalous_site);
+    if(j.find("anomalous_site_sigma") != j.end())
+    {
+        j.at("anomalous_site_sigma").get_to(o.m_Anomalous_site_sigma);
+        o.m_Anomalous_site_sigmaIsSet = true;
+    } 
+    if(j.find("refinement") != j.end())
+    {
+        j.at("refinement").get_to(o.m_Refinement);
+        o.m_RefinementIsSet = true;
+    } 
+    
+}
+
+std::string Rugnux_live_model::getPlacement() const
+{
+    return m_Placement;
+}
+void Rugnux_live_model::setPlacement(std::string const& value)
+{
+    m_Placement = value;
+}
+std::string Rugnux_live_model::getModelName() const
+{
+    return m_Model_name;
+}
+void Rugnux_live_model::setModelName(std::string const& value)
+{
+    m_Model_name = value;
+}
+bool Rugnux_live_model::isPredicted() const
+{
+    return m_Predicted;
+}
+void Rugnux_live_model::setPredicted(bool const value)
+{
+    m_Predicted = value;
+}
+std::string Rugnux_live_model::getReason() const
+{
+    return m_Reason;
+}
+void Rugnux_live_model::setReason(std::string const& value)
+{
+    m_Reason = value;
+}
+double Rugnux_live_model::getRWork() const
+{
+    return m_R_work;
+}
+void Rugnux_live_model::setRWork(double const value)
+{
+    m_R_work = value;
+    m_R_workIsSet = true;
+}
+bool Rugnux_live_model::rWorkIsSet() const
+{
+    return m_R_workIsSet;
+}
+void Rugnux_live_model::unsetR_work()
+{
+    m_R_workIsSet = false;
+}
+double Rugnux_live_model::getRFree() const
+{
+    return m_R_free;
+}
+void Rugnux_live_model::setRFree(double const value)
+{
+    m_R_free = value;
+    m_R_freeIsSet = true;
+}
+bool Rugnux_live_model::rFreeIsSet() const
+{
+    return m_R_freeIsSet;
+}
+void Rugnux_live_model::unsetR_free()
+{
+    m_R_freeIsSet = false;
+}
+double Rugnux_live_model::getCcModel() const
+{
+    return m_Cc_model;
+}
+void Rugnux_live_model::setCcModel(double const value)
+{
+    m_Cc_model = value;
+    m_Cc_modelIsSet = true;
+}
+bool Rugnux_live_model::ccModelIsSet() const
+{
+    return m_Cc_modelIsSet;
+}
+void Rugnux_live_model::unsetCc_model()
+{
+    m_Cc_modelIsSet = false;
+}
+double Rugnux_live_model::getFitSigma() const
+{
+    return m_Fit_sigma;
+}
+void Rugnux_live_model::setFitSigma(double const value)
+{
+    m_Fit_sigma = value;
+    m_Fit_sigmaIsSet = true;
+}
+bool Rugnux_live_model::fitSigmaIsSet() const
+{
+    return m_Fit_sigmaIsSet;
+}
+void Rugnux_live_model::unsetFit_sigma()
+{
+    m_Fit_sigmaIsSet = false;
+}
+double Rugnux_live_model::getMapAtomSigma() const
+{
+    return m_Map_atom_sigma;
+}
+void Rugnux_live_model::setMapAtomSigma(double const value)
+{
+    m_Map_atom_sigma = value;
+    m_Map_atom_sigmaIsSet = true;
+}
+bool Rugnux_live_model::mapAtomSigmaIsSet() const
+{
+    return m_Map_atom_sigmaIsSet;
+}
+void Rugnux_live_model::unsetMap_atom_sigma()
+{
+    m_Map_atom_sigmaIsSet = false;
+}
+double Rugnux_live_model::getRigidBodyAngleDeg() const
+{
+    return m_Rigid_body_angle_deg;
+}
+void Rugnux_live_model::setRigidBodyAngleDeg(double const value)
+{
+    m_Rigid_body_angle_deg = value;
+    m_Rigid_body_angle_degIsSet = true;
+}
+bool Rugnux_live_model::rigidBodyAngleDegIsSet() const
+{
+    return m_Rigid_body_angle_degIsSet;
+}
+void Rugnux_live_model::unsetRigid_body_angle_deg()
+{
+    m_Rigid_body_angle_degIsSet = false;
+}
+double Rugnux_live_model::getRigidBodyShiftA() const
+{
+    return m_Rigid_body_shift_A;
+}
+void Rugnux_live_model::setRigidBodyShiftA(double const value)
+{
+    m_Rigid_body_shift_A = value;
+    m_Rigid_body_shift_AIsSet = true;
+}
+bool Rugnux_live_model::rigidBodyShiftAIsSet() const
+{
+    return m_Rigid_body_shift_AIsSet;
+}
+void Rugnux_live_model::unsetRigid_body_shift_A()
+{
+    m_Rigid_body_shift_AIsSet = false;
+}
+std::string Rugnux_live_model::getMrDecision() const
+{
+    return m_Mr_decision;
+}
+void Rugnux_live_model::setMrDecision(std::string const& value)
+{
+    m_Mr_decision = value;
+}
+std::string Rugnux_live_model::getMrSpaceGroup() const
+{
+    return m_Mr_space_group;
+}
+void Rugnux_live_model::setMrSpaceGroup(std::string const& value)
+{
+    m_Mr_space_group = value;
+}
+int64_t Rugnux_live_model::getCopies() const
+{
+    return m_Copies;
+}
+void Rugnux_live_model::setCopies(int64_t const value)
+{
+    m_Copies = value;
+    m_CopiesIsSet = true;
+}
+bool Rugnux_live_model::copiesIsSet() const
+{
+    return m_CopiesIsSet;
+}
+void Rugnux_live_model::unsetCopies()
+{
+    m_CopiesIsSet = false;
+}
+double Rugnux_live_model::getTfZ() const
+{
+    return m_Tf_z;
+}
+void Rugnux_live_model::setTfZ(double const value)
+{
+    m_Tf_z = value;
+    m_Tf_zIsSet = true;
+}
+bool Rugnux_live_model::tfZIsSet() const
+{
+    return m_Tf_zIsSet;
+}
+void Rugnux_live_model::unsetTf_z()
+{
+    m_Tf_zIsSet = false;
+}
+double Rugnux_live_model::getRfZ() const
+{
+    return m_Rf_z;
+}
+void Rugnux_live_model::setRfZ(double const value)
+{
+    m_Rf_z = value;
+    m_Rf_zIsSet = true;
+}
+bool Rugnux_live_model::rfZIsSet() const
+{
+    return m_Rf_zIsSet;
+}
+void Rugnux_live_model::unsetRf_z()
+{
+    m_Rf_zIsSet = false;
+}
+double Rugnux_live_model::getLlgZ() const
+{
+    return m_Llg_z;
+}
+void Rugnux_live_model::setLlgZ(double const value)
+{
+    m_Llg_z = value;
+    m_Llg_zIsSet = true;
+}
+bool Rugnux_live_model::llgZIsSet() const
+{
+    return m_Llg_zIsSet;
+}
+void Rugnux_live_model::unsetLlg_z()
+{
+    m_Llg_zIsSet = false;
+}
+double Rugnux_live_model::getMrDMin() const
+{
+    return m_Mr_d_min;
+}
+void Rugnux_live_model::setMrDMin(double const value)
+{
+    m_Mr_d_min = value;
+    m_Mr_d_minIsSet = true;
+}
+bool Rugnux_live_model::mrDMinIsSet() const
+{
+    return m_Mr_d_minIsSet;
+}
+void Rugnux_live_model::unsetMr_d_min()
+{
+    m_Mr_d_minIsSet = false;
+}
+std::string Rugnux_live_model::getAnomalousSite() const
+{
+    return m_Anomalous_site;
+}
+void Rugnux_live_model::setAnomalousSite(std::string const& value)
+{
+    m_Anomalous_site = value;
+}
+double Rugnux_live_model::getAnomalousSiteSigma() const
+{
+    return m_Anomalous_site_sigma;
+}
+void Rugnux_live_model::setAnomalousSiteSigma(double const value)
+{
+    m_Anomalous_site_sigma = value;
+    m_Anomalous_site_sigmaIsSet = true;
+}
+bool Rugnux_live_model::anomalousSiteSigmaIsSet() const
+{
+    return m_Anomalous_site_sigmaIsSet;
+}
+void Rugnux_live_model::unsetAnomalous_site_sigma()
+{
+    m_Anomalous_site_sigmaIsSet = false;
+}
+org::openapitools::server::model::Rugnux_live_refinement Rugnux_live_model::getRefinement() const
+{
+    return m_Refinement;
+}
+void Rugnux_live_model::setRefinement(org::openapitools::server::model::Rugnux_live_refinement const& value)
+{
+    m_Refinement = value;
+    m_RefinementIsSet = true;
+}
+bool Rugnux_live_model::refinementIsSet() const
+{
+    return m_RefinementIsSet;
+}
+void Rugnux_live_model::unsetRefinement()
+{
+    m_RefinementIsSet = false;
+}
+
+
+} // namespace org::openapitools::server::model
+
diff --git a/broker/gen/model/Rugnux_live_model.h b/broker/gen/model/Rugnux_live_model.h
new file mode 100644
index 000000000..d8ce3ced3
--- /dev/null
+++ b/broker/gen/model/Rugnux_live_model.h
@@ -0,0 +1,246 @@
+/**
+* Jungfraujoch
+* API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
+*
+* The version of the OpenAPI document: 1.0.0-rc.180
+* Contact: filip.leonarski@psi.ch
+*
+* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+* https://openapi-generator.tech
+* Do not edit the class manually.
+*/
+/*
+ * Rugnux_live_model.h
+ *
+ * What the run made of the model it was given, as the report&#39;s MODEL VALIDATION section states it. The R-factors here are those of the placed model with its own coordinates and B factors; what refinement made of it is in &#x60;refinement&#x60;. A value that is absent was not computed - the model was not placed, or not by molecular replacement. 
+ */
+
+#ifndef Rugnux_live_model_H_
+#define Rugnux_live_model_H_
+
+
+#include <string>
+#include "Rugnux_live_refinement.h"
+#include <nlohmann/json.hpp>
+
+namespace org::openapitools::server::model
+{
+
+/// <summary>
+/// What the run made of the model it was given, as the report&#39;s MODEL VALIDATION section states it. The R-factors here are those of the placed model with its own coordinates and B factors; what refinement made of it is in &#x60;refinement&#x60;. A value that is absent was not computed - the model was not placed, or not by molecular replacement. 
+/// </summary>
+class  Rugnux_live_model
+{
+public:
+    Rugnux_live_model();
+    virtual ~Rugnux_live_model() = default;
+
+
+    /// <summary>
+    /// Validate the current data in the model. Throws a ValidationException on failure.
+    /// </summary>
+    void validate() const;
+
+    /// <summary>
+    /// Validate the current data in the model. Returns false on error and writes an error
+    /// message into the given stringstream.
+    /// </summary>
+    bool validate(std::stringstream& msg) const;
+
+    /// <summary>
+    /// Helper overload for validate. Used when one model stores another model and calls it's validate.
+    /// Not meant to be called outside that case.
+    /// </summary>
+    bool validate(std::stringstream& msg, const std::string& pathPrefix) const;
+
+    bool operator==(const Rugnux_live_model& rhs) const;
+    bool operator!=(const Rugnux_live_model& rhs) const;
+
+    /////////////////////////////////////////////
+    /// Rugnux_live_model members
+
+    /// <summary>
+    /// RIGID_BODY (the model fits where it is), MR (molecular replacement placed it) or NOT_PLACED
+    /// </summary>
+    std::string getPlacement() const;
+    void setPlacement(std::string const& value);
+    /// <summary>
+    /// 
+    /// </summary>
+    std::string getModelName() const;
+    void setModelName(std::string const& value);
+    /// <summary>
+    /// Searched for as a predicted model
+    /// </summary>
+    bool isPredicted() const;
+    void setPredicted(bool const value);
+    /// <summary>
+    /// Why the model could not be searched for or validated; empty otherwise
+    /// </summary>
+    std::string getReason() const;
+    void setReason(std::string const& value);
+    /// <summary>
+    /// 
+    /// </summary>
+    double getRWork() const;
+    void setRWork(double const value);
+    bool rWorkIsSet() const;
+    void unsetR_work();
+    /// <summary>
+    /// 
+    /// </summary>
+    double getRFree() const;
+    void setRFree(double const value);
+    bool rFreeIsSet() const;
+    void unsetR_free();
+    /// <summary>
+    /// Correlation of the merged intensities with the placed model&#39;s, over all reflections
+    /// </summary>
+    double getCcModel() const;
+    void setCcModel(double const value);
+    bool ccModelIsSet() const;
+    void unsetCc_model();
+    /// <summary>
+    /// How far R-work stands below that of the same model in random orientations, in standard deviations
+    /// </summary>
+    double getFitSigma() const;
+    void setFitSigma(double const value);
+    bool fitSigmaIsSet() const;
+    void unsetFit_sigma();
+    /// <summary>
+    /// Mean 2mFo-DFc value at the atom centres, in map sigma
+    /// </summary>
+    double getMapAtomSigma() const;
+    void setMapAtomSigma(double const value);
+    bool mapAtomSigmaIsSet() const;
+    void unsetMap_atom_sigma();
+    /// <summary>
+    /// 
+    /// </summary>
+    double getRigidBodyAngleDeg() const;
+    void setRigidBodyAngleDeg(double const value);
+    bool rigidBodyAngleDegIsSet() const;
+    void unsetRigid_body_angle_deg();
+    /// <summary>
+    /// 
+    /// </summary>
+    double getRigidBodyShiftA() const;
+    void setRigidBodyShiftA(double const value);
+    bool rigidBodyShiftAIsSet() const;
+    void unsetRigid_body_shift_A();
+    /// <summary>
+    /// Molecular replacement&#39;s decision (AGREES, ENANTIOMORPH, SPACE_GROUP, TWIN_SUBGROUP, or why it placed nothing); empty where it did not run
+    /// </summary>
+    std::string getMrDecision() const;
+    void setMrDecision(std::string const& value);
+    /// <summary>
+    /// The group molecular replacement placed the model in; empty where it placed none
+    /// </summary>
+    std::string getMrSpaceGroup() const;
+    void setMrSpaceGroup(std::string const& value);
+    /// <summary>
+    /// Copies placed by molecular replacement
+    /// </summary>
+    int64_t getCopies() const;
+    void setCopies(int64_t const value);
+    bool copiesIsSet() const;
+    void unsetCopies();
+    /// <summary>
+    /// Translation-function Z-score, the highest of the copies&#39;
+    /// </summary>
+    double getTfZ() const;
+    void setTfZ(double const value);
+    bool tfZIsSet() const;
+    void unsetTf_z();
+    /// <summary>
+    /// Rotation-function Z-score of the first copy&#39;s orientation
+    /// </summary>
+    double getRfZ() const;
+    void setRfZ(double const value);
+    bool rfZIsSet() const;
+    void unsetRf_z();
+    /// <summary>
+    /// Likelihood Z-score after the rigid body, where a copy&#39;s translation function did not stand out
+    /// </summary>
+    double getLlgZ() const;
+    void setLlgZ(double const value);
+    bool llgZIsSet() const;
+    void unsetLlg_z();
+    /// <summary>
+    /// High-resolution limit of the molecular-replacement search, in Angstrom
+    /// </summary>
+    double getMrDMin() const;
+    void setMrDMin(double const value);
+    bool mrDMinIsSet() const;
+    void unsetMr_d_min();
+    /// <summary>
+    /// Atom with the strongest anomalous difference density, e.g. \&quot;SG CYS A7\&quot;; empty where there is no anomalous map
+    /// </summary>
+    std::string getAnomalousSite() const;
+    void setAnomalousSite(std::string const& value);
+    /// <summary>
+    /// Anomalous difference density at that atom, in map sigma
+    /// </summary>
+    double getAnomalousSiteSigma() const;
+    void setAnomalousSiteSigma(double const value);
+    bool anomalousSiteSigmaIsSet() const;
+    void unsetAnomalous_site_sigma();
+    /// <summary>
+    /// 
+    /// </summary>
+    org::openapitools::server::model::Rugnux_live_refinement getRefinement() const;
+    void setRefinement(org::openapitools::server::model::Rugnux_live_refinement const& value);
+    bool refinementIsSet() const;
+    void unsetRefinement();
+
+    friend  void to_json(nlohmann::json& j, const Rugnux_live_model& o);
+    friend  void from_json(const nlohmann::json& j, Rugnux_live_model& o);
+protected:
+    std::string m_Placement;
+
+    std::string m_Model_name;
+
+    bool m_Predicted;
+
+    std::string m_Reason;
+
+    double m_R_work;
+    bool m_R_workIsSet;
+    double m_R_free;
+    bool m_R_freeIsSet;
+    double m_Cc_model;
+    bool m_Cc_modelIsSet;
+    double m_Fit_sigma;
+    bool m_Fit_sigmaIsSet;
+    double m_Map_atom_sigma;
+    bool m_Map_atom_sigmaIsSet;
+    double m_Rigid_body_angle_deg;
+    bool m_Rigid_body_angle_degIsSet;
+    double m_Rigid_body_shift_A;
+    bool m_Rigid_body_shift_AIsSet;
+    std::string m_Mr_decision;
+
+    std::string m_Mr_space_group;
+
+    int64_t m_Copies;
+    bool m_CopiesIsSet;
+    double m_Tf_z;
+    bool m_Tf_zIsSet;
+    double m_Rf_z;
+    bool m_Rf_zIsSet;
+    double m_Llg_z;
+    bool m_Llg_zIsSet;
+    double m_Mr_d_min;
+    bool m_Mr_d_minIsSet;
+    std::string m_Anomalous_site;
+
+    double m_Anomalous_site_sigma;
+    bool m_Anomalous_site_sigmaIsSet;
+    org::openapitools::server::model::Rugnux_live_refinement m_Refinement;
+    bool m_RefinementIsSet;
+    
+};
+
+} // namespace org::openapitools::server::model
+
+#endif /* Rugnux_live_model_H_ */
diff --git a/broker/gen/model/Rugnux_live_refinement.cpp b/broker/gen/model/Rugnux_live_refinement.cpp
new file mode 100644
index 000000000..952cc5821
--- /dev/null
+++ b/broker/gen/model/Rugnux_live_refinement.cpp
@@ -0,0 +1,311 @@
+/**
+* Jungfraujoch
+* API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
+*
+* The version of the OpenAPI document: 1.0.0-rc.180
+* Contact: filip.leonarski@psi.ch
+*
+* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+* https://openapi-generator.tech
+* Do not edit the class manually.
+*/
+
+
+#include "Rugnux_live_refinement.h"
+#include "Helpers.h"
+
+#include <sstream>
+
+namespace org::openapitools::server::model
+{
+
+Rugnux_live_refinement::Rugnux_live_refinement()
+{
+    m_Performed = false;
+    m_Cancelled = false;
+    m_Reason = "";
+    m_On_gpu = false;
+    m_Seconds = 0.0;
+    m_R_work = 0.0;
+    m_R_workIsSet = false;
+    m_R_free = 0.0;
+    m_R_freeIsSet = false;
+    m_Rmsd_bonds_A = 0.0;
+    m_Rmsd_bonds_AIsSet = false;
+    m_Rmsd_angles_deg = 0.0;
+    m_Rmsd_angles_degIsSet = false;
+    m_Blob_count = 0L;
+    
+}
+
+void Rugnux_live_refinement::validate() const
+{
+    std::stringstream msg;
+    if (!validate(msg))
+    {
+        throw org::openapitools::server::helpers::ValidationException(msg.str());
+    }
+}
+
+bool Rugnux_live_refinement::validate(std::stringstream& msg) const
+{
+    return validate(msg, "");
+}
+
+bool Rugnux_live_refinement::validate(std::stringstream& msg, const std::string& pathPrefix) const
+{
+    bool success = true;
+    const std::string _pathPrefix = pathPrefix.empty() ? "Rugnux_live_refinement" : pathPrefix;
+
+                                                 
+    
+    /* Blobs */ {
+        const std::vector<org::openapitools::server::model::Rugnux_live_blob>& value = m_Blobs;
+        const std::string currentValuePath = _pathPrefix + ".blobs";
+                
+        
+        { // Recursive validation of array elements
+            const std::string oldValuePath = currentValuePath;
+            int i = 0;
+            for (const org::openapitools::server::model::Rugnux_live_blob& value : value)
+            { 
+                const std::string currentValuePath = oldValuePath + "[" + std::to_string(i) + "]";
+                        
+        success = value.validate(msg, currentValuePath + ".blobs") && success;
+ 
+                i++;
+            }
+        }
+
+    }
+    
+    return success;
+}
+
+bool Rugnux_live_refinement::operator==(const Rugnux_live_refinement& rhs) const
+{
+    return
+    
+    
+    (isPerformed() == rhs.isPerformed())
+     &&
+    
+    (isCancelled() == rhs.isCancelled())
+     &&
+    
+    (getReason() == rhs.getReason())
+     &&
+    
+    (isOnGpu() == rhs.isOnGpu())
+     &&
+    
+    (getSeconds() == rhs.getSeconds())
+     &&
+    
+    
+    ((!rWorkIsSet() && !rhs.rWorkIsSet()) || (rWorkIsSet() && rhs.rWorkIsSet() && getRWork() == rhs.getRWork())) &&
+    
+    
+    ((!rFreeIsSet() && !rhs.rFreeIsSet()) || (rFreeIsSet() && rhs.rFreeIsSet() && getRFree() == rhs.getRFree())) &&
+    
+    
+    ((!rmsdBondsAIsSet() && !rhs.rmsdBondsAIsSet()) || (rmsdBondsAIsSet() && rhs.rmsdBondsAIsSet() && getRmsdBondsA() == rhs.getRmsdBondsA())) &&
+    
+    
+    ((!rmsdAnglesDegIsSet() && !rhs.rmsdAnglesDegIsSet()) || (rmsdAnglesDegIsSet() && rhs.rmsdAnglesDegIsSet() && getRmsdAnglesDeg() == rhs.getRmsdAnglesDeg())) &&
+    
+    (getBlobCount() == rhs.getBlobCount())
+     &&
+    
+    (getBlobs() == rhs.getBlobs())
+    
+    
+    ;
+}
+
+bool Rugnux_live_refinement::operator!=(const Rugnux_live_refinement& rhs) const
+{
+    return !(*this == rhs);
+}
+
+void to_json(nlohmann::json& j, const Rugnux_live_refinement& o)
+{
+    j = nlohmann::json::object();
+    j["performed"] = o.m_Performed;
+    j["cancelled"] = o.m_Cancelled;
+    j["reason"] = o.m_Reason;
+    j["on_gpu"] = o.m_On_gpu;
+    j["seconds"] = o.m_Seconds;
+    if(o.rWorkIsSet())
+        j["r_work"] = o.m_R_work;
+    if(o.rFreeIsSet())
+        j["r_free"] = o.m_R_free;
+    if(o.rmsdBondsAIsSet())
+        j["rmsd_bonds_A"] = o.m_Rmsd_bonds_A;
+    if(o.rmsdAnglesDegIsSet())
+        j["rmsd_angles_deg"] = o.m_Rmsd_angles_deg;
+    j["blob_count"] = o.m_Blob_count;
+    j["blobs"] = o.m_Blobs;
+    
+}
+
+void from_json(const nlohmann::json& j, Rugnux_live_refinement& o)
+{
+    j.at("performed").get_to(o.m_Performed);
+    j.at("cancelled").get_to(o.m_Cancelled);
+    j.at("reason").get_to(o.m_Reason);
+    j.at("on_gpu").get_to(o.m_On_gpu);
+    j.at("seconds").get_to(o.m_Seconds);
+    if(j.find("r_work") != j.end())
+    {
+        j.at("r_work").get_to(o.m_R_work);
+        o.m_R_workIsSet = true;
+    } 
+    if(j.find("r_free") != j.end())
+    {
+        j.at("r_free").get_to(o.m_R_free);
+        o.m_R_freeIsSet = true;
+    } 
+    if(j.find("rmsd_bonds_A") != j.end())
+    {
+        j.at("rmsd_bonds_A").get_to(o.m_Rmsd_bonds_A);
+        o.m_Rmsd_bonds_AIsSet = true;
+    } 
+    if(j.find("rmsd_angles_deg") != j.end())
+    {
+        j.at("rmsd_angles_deg").get_to(o.m_Rmsd_angles_deg);
+        o.m_Rmsd_angles_degIsSet = true;
+    } 
+    j.at("blob_count").get_to(o.m_Blob_count);
+    j.at("blobs").get_to(o.m_Blobs);
+    
+}
+
+bool Rugnux_live_refinement::isPerformed() const
+{
+    return m_Performed;
+}
+void Rugnux_live_refinement::setPerformed(bool const value)
+{
+    m_Performed = value;
+}
+bool Rugnux_live_refinement::isCancelled() const
+{
+    return m_Cancelled;
+}
+void Rugnux_live_refinement::setCancelled(bool const value)
+{
+    m_Cancelled = value;
+}
+std::string Rugnux_live_refinement::getReason() const
+{
+    return m_Reason;
+}
+void Rugnux_live_refinement::setReason(std::string const& value)
+{
+    m_Reason = value;
+}
+bool Rugnux_live_refinement::isOnGpu() const
+{
+    return m_On_gpu;
+}
+void Rugnux_live_refinement::setOnGpu(bool const value)
+{
+    m_On_gpu = value;
+}
+double Rugnux_live_refinement::getSeconds() const
+{
+    return m_Seconds;
+}
+void Rugnux_live_refinement::setSeconds(double const value)
+{
+    m_Seconds = value;
+}
+double Rugnux_live_refinement::getRWork() const
+{
+    return m_R_work;
+}
+void Rugnux_live_refinement::setRWork(double const value)
+{
+    m_R_work = value;
+    m_R_workIsSet = true;
+}
+bool Rugnux_live_refinement::rWorkIsSet() const
+{
+    return m_R_workIsSet;
+}
+void Rugnux_live_refinement::unsetR_work()
+{
+    m_R_workIsSet = false;
+}
+double Rugnux_live_refinement::getRFree() const
+{
+    return m_R_free;
+}
+void Rugnux_live_refinement::setRFree(double const value)
+{
+    m_R_free = value;
+    m_R_freeIsSet = true;
+}
+bool Rugnux_live_refinement::rFreeIsSet() const
+{
+    return m_R_freeIsSet;
+}
+void Rugnux_live_refinement::unsetR_free()
+{
+    m_R_freeIsSet = false;
+}
+double Rugnux_live_refinement::getRmsdBondsA() const
+{
+    return m_Rmsd_bonds_A;
+}
+void Rugnux_live_refinement::setRmsdBondsA(double const value)
+{
+    m_Rmsd_bonds_A = value;
+    m_Rmsd_bonds_AIsSet = true;
+}
+bool Rugnux_live_refinement::rmsdBondsAIsSet() const
+{
+    return m_Rmsd_bonds_AIsSet;
+}
+void Rugnux_live_refinement::unsetRmsd_bonds_A()
+{
+    m_Rmsd_bonds_AIsSet = false;
+}
+double Rugnux_live_refinement::getRmsdAnglesDeg() const
+{
+    return m_Rmsd_angles_deg;
+}
+void Rugnux_live_refinement::setRmsdAnglesDeg(double const value)
+{
+    m_Rmsd_angles_deg = value;
+    m_Rmsd_angles_degIsSet = true;
+}
+bool Rugnux_live_refinement::rmsdAnglesDegIsSet() const
+{
+    return m_Rmsd_angles_degIsSet;
+}
+void Rugnux_live_refinement::unsetRmsd_angles_deg()
+{
+    m_Rmsd_angles_degIsSet = false;
+}
+int64_t Rugnux_live_refinement::getBlobCount() const
+{
+    return m_Blob_count;
+}
+void Rugnux_live_refinement::setBlobCount(int64_t const value)
+{
+    m_Blob_count = value;
+}
+std::vector<org::openapitools::server::model::Rugnux_live_blob> Rugnux_live_refinement::getBlobs() const
+{
+    return m_Blobs;
+}
+void Rugnux_live_refinement::setBlobs(std::vector<org::openapitools::server::model::Rugnux_live_blob> const& value)
+{
+    m_Blobs = value;
+}
+
+
+} // namespace org::openapitools::server::model
+
diff --git a/broker/gen/model/Rugnux_live_refinement.h b/broker/gen/model/Rugnux_live_refinement.h
new file mode 100644
index 000000000..2f4f91802
--- /dev/null
+++ b/broker/gen/model/Rugnux_live_refinement.h
@@ -0,0 +1,157 @@
+/**
+* Jungfraujoch
+* API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
+*
+* The version of the OpenAPI document: 1.0.0-rc.180
+* Contact: filip.leonarski@psi.ch
+*
+* NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+* https://openapi-generator.tech
+* Do not edit the class manually.
+*/
+/*
+ * Rugnux_live_refinement.h
+ *
+ * The placed model refined against the merge it was placed on, as the report&#39;s REFINE_ keys state it. Set where a placed model was refined or its refinement failed; absent where the model was not placed or refinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run&#39;s deadline or cancel can cut it. 
+ */
+
+#ifndef Rugnux_live_refinement_H_
+#define Rugnux_live_refinement_H_
+
+
+#include "Rugnux_live_blob.h"
+#include <string>
+#include <vector>
+#include <nlohmann/json.hpp>
+
+namespace org::openapitools::server::model
+{
+
+/// <summary>
+/// The placed model refined against the merge it was placed on, as the report&#39;s REFINE_ keys state it. Set where a placed model was refined or its refinement failed; absent where the model was not placed or refinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run&#39;s deadline or cancel can cut it. 
+/// </summary>
+class  Rugnux_live_refinement
+{
+public:
+    Rugnux_live_refinement();
+    virtual ~Rugnux_live_refinement() = default;
+
+
+    /// <summary>
+    /// Validate the current data in the model. Throws a ValidationException on failure.
+    /// </summary>
+    void validate() const;
+
+    /// <summary>
+    /// Validate the current data in the model. Returns false on error and writes an error
+    /// message into the given stringstream.
+    /// </summary>
+    bool validate(std::stringstream& msg) const;
+
+    /// <summary>
+    /// Helper overload for validate. Used when one model stores another model and calls it's validate.
+    /// Not meant to be called outside that case.
+    /// </summary>
+    bool validate(std::stringstream& msg, const std::string& pathPrefix) const;
+
+    bool operator==(const Rugnux_live_refinement& rhs) const;
+    bool operator!=(const Rugnux_live_refinement& rhs) const;
+
+    /////////////////////////////////////////////
+    /// Rugnux_live_refinement members
+
+    /// <summary>
+    /// Refinement ran; false with &#x60;reason&#x60; where it failed
+    /// </summary>
+    bool isPerformed() const;
+    void setPerformed(bool const value);
+    /// <summary>
+    /// The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the rest left out (cut before the first, the model is the placement&#39;s) 
+    /// </summary>
+    bool isCancelled() const;
+    void setCancelled(bool const value);
+    /// <summary>
+    /// Why refinement did not run to the end; empty otherwise
+    /// </summary>
+    std::string getReason() const;
+    void setReason(std::string const& value);
+    /// <summary>
+    /// 
+    /// </summary>
+    bool isOnGpu() const;
+    void setOnGpu(bool const value);
+    /// <summary>
+    /// Wall time of the refinement
+    /// </summary>
+    double getSeconds() const;
+    void setSeconds(double const value);
+    /// <summary>
+    /// R-work of the refined model (after the restrained stage, else after the rigid body and grouped B)
+    /// </summary>
+    double getRWork() const;
+    void setRWork(double const value);
+    bool rWorkIsSet() const;
+    void unsetR_work();
+    /// <summary>
+    /// R-free of the refined model, on the same reflections as &#x60;r_work&#x60;
+    /// </summary>
+    double getRFree() const;
+    void setRFree(double const value);
+    bool rFreeIsSet() const;
+    void unsetR_free();
+    /// <summary>
+    /// RMS deviation of the bond lengths from the dictionary, where the restrained stage ran
+    /// </summary>
+    double getRmsdBondsA() const;
+    void setRmsdBondsA(double const value);
+    bool rmsdBondsAIsSet() const;
+    void unsetRmsd_bonds_A();
+    /// <summary>
+    /// RMS deviation of the bond angles from the dictionary, where the restrained stage ran
+    /// </summary>
+    double getRmsdAnglesDeg() const;
+    void setRmsdAnglesDeg(double const value);
+    bool rmsdAnglesDegIsSet() const;
+    void unsetRmsd_angles_deg();
+    /// <summary>
+    /// Unexplained blobs of the refined model&#39;s mFo-DFc map (above 3 sigma, peaking above 4)
+    /// </summary>
+    int64_t getBlobCount() const;
+    void setBlobCount(int64_t const value);
+    /// <summary>
+    /// The strongest blobs, at most 50, strongest first
+    /// </summary>
+    std::vector<org::openapitools::server::model::Rugnux_live_blob> getBlobs() const;
+    void setBlobs(std::vector<org::openapitools::server::model::Rugnux_live_blob> const& value);
+
+    friend  void to_json(nlohmann::json& j, const Rugnux_live_refinement& o);
+    friend  void from_json(const nlohmann::json& j, Rugnux_live_refinement& o);
+protected:
+    bool m_Performed;
+
+    bool m_Cancelled;
+
+    std::string m_Reason;
+
+    bool m_On_gpu;
+
+    double m_Seconds;
+
+    double m_R_work;
+    bool m_R_workIsSet;
+    double m_R_free;
+    bool m_R_freeIsSet;
+    double m_Rmsd_bonds_A;
+    bool m_Rmsd_bonds_AIsSet;
+    double m_Rmsd_angles_deg;
+    bool m_Rmsd_angles_degIsSet;
+    int64_t m_Blob_count;
+
+    std::vector<org::openapitools::server::model::Rugnux_live_blob> m_Blobs;
+
+    
+};
+
+} // namespace org::openapitools::server::model
+
+#endif /* Rugnux_live_refinement_H_ */
diff --git a/broker/gen/model/Rugnux_live_status.cpp b/broker/gen/model/Rugnux_live_status.cpp
index d0382a3a2..8b5032085 100644
--- a/broker/gen/model/Rugnux_live_status.cpp
+++ b/broker/gen/model/Rugnux_live_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
@@ -23,7 +23,16 @@ Rugnux_live_status::Rugnux_live_status()
 {
     m_State = "";
     m_Placed_model = false;
+    m_Refined_model = false;
     m_Anomalous_map = false;
+    m_Anomalous_signal = false;
+    m_ModelIsSet = false;
+    m_Space_group = "";
+    m_Space_groupIsSet = false;
+    m_D_min = 0.0;
+    m_D_minIsSet = false;
+    m_Isa = 0.0;
+    m_IsaIsSet = false;
     m_Probe = "";
     m_Probe_s = 0.0;
     m_Probe_sIsSet = false;
@@ -69,7 +78,7 @@ bool Rugnux_live_status::validate(std::stringstream& msg, const std::string& pat
     bool success = true;
     const std::string _pathPrefix = pathPrefix.empty() ? "Rugnux_live_status" : pathPrefix;
 
-                                                     
+                                                                             
     if (stepProgressIsSet())
     {
         const float& value = m_Step_progress;
@@ -166,9 +175,27 @@ bool Rugnux_live_status::operator==(const Rugnux_live_status& rhs) const
     (isPlacedModel() == rhs.isPlacedModel())
      &&
     
+    (isRefinedModel() == rhs.isRefinedModel())
+     &&
+    
     (isAnomalousMap() == rhs.isAnomalousMap())
      &&
     
+    (isAnomalousSignal() == rhs.isAnomalousSignal())
+     &&
+    
+    
+    ((!modelIsSet() && !rhs.modelIsSet()) || (modelIsSet() && rhs.modelIsSet() && getModel() == rhs.getModel())) &&
+    
+    
+    ((!spaceGroupIsSet() && !rhs.spaceGroupIsSet()) || (spaceGroupIsSet() && rhs.spaceGroupIsSet() && getSpaceGroup() == rhs.getSpaceGroup())) &&
+    
+    
+    ((!dMinIsSet() && !rhs.dMinIsSet()) || (dMinIsSet() && rhs.dMinIsSet() && getDMin() == rhs.getDMin())) &&
+    
+    
+    ((!isaIsSet() && !rhs.isaIsSet()) || (isaIsSet() && rhs.isaIsSet() && getIsa() == rhs.getIsa())) &&
+    
     (getProbe() == rhs.getProbe())
      &&
     
@@ -236,7 +263,17 @@ void to_json(nlohmann::json& j, const Rugnux_live_status& o)
     j = nlohmann::json::object();
     j["state"] = o.m_State;
     j["placed_model"] = o.m_Placed_model;
+    j["refined_model"] = o.m_Refined_model;
     j["anomalous_map"] = o.m_Anomalous_map;
+    j["anomalous_signal"] = o.m_Anomalous_signal;
+    if(o.modelIsSet())
+        j["model"] = o.m_Model;
+    if(o.spaceGroupIsSet())
+        j["space_group"] = o.m_Space_group;
+    if(o.dMinIsSet())
+        j["d_min"] = o.m_D_min;
+    if(o.isaIsSet())
+        j["isa"] = o.m_Isa;
     j["probe"] = o.m_Probe;
     if(o.probeSIsSet())
         j["probe_s"] = o.m_Probe_s;
@@ -270,7 +307,29 @@ void from_json(const nlohmann::json& j, Rugnux_live_status& o)
 {
     j.at("state").get_to(o.m_State);
     j.at("placed_model").get_to(o.m_Placed_model);
+    j.at("refined_model").get_to(o.m_Refined_model);
     j.at("anomalous_map").get_to(o.m_Anomalous_map);
+    j.at("anomalous_signal").get_to(o.m_Anomalous_signal);
+    if(j.find("model") != j.end())
+    {
+        j.at("model").get_to(o.m_Model);
+        o.m_ModelIsSet = true;
+    } 
+    if(j.find("space_group") != j.end())
+    {
+        j.at("space_group").get_to(o.m_Space_group);
+        o.m_Space_groupIsSet = true;
+    } 
+    if(j.find("d_min") != j.end())
+    {
+        j.at("d_min").get_to(o.m_D_min);
+        o.m_D_minIsSet = true;
+    } 
+    if(j.find("isa") != j.end())
+    {
+        j.at("isa").get_to(o.m_Isa);
+        o.m_IsaIsSet = true;
+    } 
     j.at("probe").get_to(o.m_Probe);
     if(j.find("probe_s") != j.end())
     {
@@ -340,6 +399,14 @@ void Rugnux_live_status::setPlacedModel(bool const value)
 {
     m_Placed_model = value;
 }
+bool Rugnux_live_status::isRefinedModel() const
+{
+    return m_Refined_model;
+}
+void Rugnux_live_status::setRefinedModel(bool const value)
+{
+    m_Refined_model = value;
+}
 bool Rugnux_live_status::isAnomalousMap() const
 {
     return m_Anomalous_map;
@@ -348,6 +415,82 @@ void Rugnux_live_status::setAnomalousMap(bool const value)
 {
     m_Anomalous_map = value;
 }
+bool Rugnux_live_status::isAnomalousSignal() const
+{
+    return m_Anomalous_signal;
+}
+void Rugnux_live_status::setAnomalousSignal(bool const value)
+{
+    m_Anomalous_signal = value;
+}
+org::openapitools::server::model::Rugnux_live_model Rugnux_live_status::getModel() const
+{
+    return m_Model;
+}
+void Rugnux_live_status::setModel(org::openapitools::server::model::Rugnux_live_model const& value)
+{
+    m_Model = value;
+    m_ModelIsSet = true;
+}
+bool Rugnux_live_status::modelIsSet() const
+{
+    return m_ModelIsSet;
+}
+void Rugnux_live_status::unsetModel()
+{
+    m_ModelIsSet = false;
+}
+std::string Rugnux_live_status::getSpaceGroup() const
+{
+    return m_Space_group;
+}
+void Rugnux_live_status::setSpaceGroup(std::string const& value)
+{
+    m_Space_group = value;
+    m_Space_groupIsSet = true;
+}
+bool Rugnux_live_status::spaceGroupIsSet() const
+{
+    return m_Space_groupIsSet;
+}
+void Rugnux_live_status::unsetSpace_group()
+{
+    m_Space_groupIsSet = false;
+}
+double Rugnux_live_status::getDMin() const
+{
+    return m_D_min;
+}
+void Rugnux_live_status::setDMin(double const value)
+{
+    m_D_min = value;
+    m_D_minIsSet = true;
+}
+bool Rugnux_live_status::dMinIsSet() const
+{
+    return m_D_minIsSet;
+}
+void Rugnux_live_status::unsetD_min()
+{
+    m_D_minIsSet = false;
+}
+double Rugnux_live_status::getIsa() const
+{
+    return m_Isa;
+}
+void Rugnux_live_status::setIsa(double const value)
+{
+    m_Isa = value;
+    m_IsaIsSet = true;
+}
+bool Rugnux_live_status::isaIsSet() const
+{
+    return m_IsaIsSet;
+}
+void Rugnux_live_status::unsetIsa()
+{
+    m_IsaIsSet = false;
+}
 std::string Rugnux_live_status::getProbe() const
 {
     return m_Probe;
diff --git a/broker/gen/model/Rugnux_live_status.h b/broker/gen/model/Rugnux_live_status.h
index 2dd4d359c..5bc63f942 100644
--- a/broker/gen/model/Rugnux_live_status.h
+++ b/broker/gen/model/Rugnux_live_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
@@ -21,6 +21,7 @@
 
 #include "Rugnux_summary_row.h"
 #include <string>
+#include "Rugnux_live_model.h"
 #include "Rugnux_live_step.h"
 #include <vector>
 #include <nlohmann/json.hpp>
@@ -72,11 +73,49 @@ public:
     bool isPlacedModel() const;
     void setPlacedModel(bool const value);
     /// <summary>
+    /// The run refined the placed model: &#x60;/rugnux/model.cif&#x60; and &#x60;/rugnux/map.ccp4&#x60; serve the refined model and its maps unless asked for &#x60;stage&#x3D;placed&#x60;. 
+    /// </summary>
+    bool isRefinedModel() const;
+    void setRefinedModel(bool const value);
+    /// <summary>
     /// The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map (&#x60;/rugnux/map.ccp4?type&#x3D;anom&#x60;). 
     /// </summary>
     bool isAnomalousMap() const;
     void setAnomalousMap(bool const value);
     /// <summary>
+    /// The merged data carry usable anomalous signal (the summary&#39;s \&quot;Anomalous\&quot; row says so)
+    /// </summary>
+    bool isAnomalousSignal() const;
+    void setAnomalousSignal(bool const value);
+    /// <summary>
+    /// 
+    /// </summary>
+    org::openapitools::server::model::Rugnux_live_model getModel() const;
+    void setModel(org::openapitools::server::model::Rugnux_live_model const& value);
+    bool modelIsSet() const;
+    void unsetModel();
+    /// <summary>
+    /// Space group of the result (the summary&#39;s \&quot;Space group\&quot; row); absent until the run is over
+    /// </summary>
+    std::string getSpaceGroup() const;
+    void setSpaceGroup(std::string const& value);
+    bool spaceGroupIsSet() const;
+    void unsetSpace_group();
+    /// <summary>
+    /// High-resolution limit of the merge, in Angstrom; absent until the run is over, or without a merge
+    /// </summary>
+    double getDMin() const;
+    void setDMin(double const value);
+    bool dMinIsSet() const;
+    void unsetD_min();
+    /// <summary>
+    /// ISa of the error model; absent until the run is over, or where it was not determined
+    /// </summary>
+    double getIsa() const;
+    void setIsa(double const value);
+    bool isaIsSet() const;
+    void unsetIsa();
+    /// <summary>
     /// Answer of the early lattice probe on the first 60 degrees; empty until it answers
     /// </summary>
     std::string getProbe() const;
@@ -190,8 +229,20 @@ protected:
 
     bool m_Placed_model;
 
+    bool m_Refined_model;
+
     bool m_Anomalous_map;
 
+    bool m_Anomalous_signal;
+
+    org::openapitools::server::model::Rugnux_live_model m_Model;
+    bool m_ModelIsSet;
+    std::string m_Space_group;
+    bool m_Space_groupIsSet;
+    double m_D_min;
+    bool m_D_minIsSet;
+    double m_Isa;
+    bool m_IsaIsSet;
     std::string m_Probe;
 
     double m_Probe_s;
diff --git a/broker/gen/model/Rugnux_live_step.cpp b/broker/gen/model/Rugnux_live_step.cpp
index c1dd2b171..3db9278a6 100644
--- a/broker/gen/model/Rugnux_live_step.cpp
+++ b/broker/gen/model/Rugnux_live_step.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_live_step.h b/broker/gen/model/Rugnux_live_step.h
index 7f4d1fe91..f60d957c7 100644
--- a/broker/gen/model/Rugnux_live_step.h
+++ b/broker/gen/model/Rugnux_live_step.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_settings.cpp b/broker/gen/model/Rugnux_settings.cpp
index f70739811..65483eb9c 100644
--- a/broker/gen/model/Rugnux_settings.cpp
+++ b/broker/gen/model/Rugnux_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_settings.h b/broker/gen/model/Rugnux_settings.h
index 252dabe36..8a035fbfa 100644
--- a/broker/gen/model/Rugnux_settings.h
+++ b/broker/gen/model/Rugnux_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_status.cpp b/broker/gen/model/Rugnux_status.cpp
index f7624b0bc..31e566564 100644
--- a/broker/gen/model/Rugnux_status.cpp
+++ b/broker/gen/model/Rugnux_status.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_status.h b/broker/gen/model/Rugnux_status.h
index cc187fbec..662f0c0fb 100644
--- a/broker/gen/model/Rugnux_status.h
+++ b/broker/gen/model/Rugnux_status.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_summary_row.cpp b/broker/gen/model/Rugnux_summary_row.cpp
index 076d5e5cf..8db2fdf5f 100644
--- a/broker/gen/model/Rugnux_summary_row.cpp
+++ b/broker/gen/model/Rugnux_summary_row.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Rugnux_summary_row.h b/broker/gen/model/Rugnux_summary_row.h
index 0f933b8ec..cc9c31334 100644
--- a/broker/gen/model/Rugnux_summary_row.h
+++ b/broker/gen/model/Rugnux_summary_row.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result.cpp b/broker/gen/model/Scan_result.cpp
index b8f5b103e..bbfb6bc51 100644
--- a/broker/gen/model/Scan_result.cpp
+++ b/broker/gen/model/Scan_result.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result.h b/broker/gen/model/Scan_result.h
index a0bcc97e8..b57362156 100644
--- a/broker/gen/model/Scan_result.h
+++ b/broker/gen/model/Scan_result.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result_images_inner.cpp b/broker/gen/model/Scan_result_images_inner.cpp
index f4415e936..5d3683bd3 100644
--- a/broker/gen/model/Scan_result_images_inner.cpp
+++ b/broker/gen/model/Scan_result_images_inner.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Scan_result_images_inner.h b/broker/gen/model/Scan_result_images_inner.h
index e5a2748df..d0e019b56 100644
--- a/broker/gen/model/Scan_result_images_inner.h
+++ b/broker/gen/model/Scan_result_images_inner.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Spot_finding_settings.cpp b/broker/gen/model/Spot_finding_settings.cpp
index 72fb87a78..77f48415f 100644
--- a/broker/gen/model/Spot_finding_settings.cpp
+++ b/broker/gen/model/Spot_finding_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Spot_finding_settings.h b/broker/gen/model/Spot_finding_settings.h
index 28f4e111a..9a0d4bbcd 100644
--- a/broker/gen/model/Spot_finding_settings.h
+++ b/broker/gen/model/Spot_finding_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Standard_detector_geometry.cpp b/broker/gen/model/Standard_detector_geometry.cpp
index 36a08aab6..bd19b4e97 100644
--- a/broker/gen/model/Standard_detector_geometry.cpp
+++ b/broker/gen/model/Standard_detector_geometry.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Standard_detector_geometry.h b/broker/gen/model/Standard_detector_geometry.h
index ba628f8f0..1870ed6d3 100644
--- a/broker/gen/model/Standard_detector_geometry.h
+++ b/broker/gen/model/Standard_detector_geometry.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Tcp_settings.cpp b/broker/gen/model/Tcp_settings.cpp
index 907ffd0ec..1332d13e9 100644
--- a/broker/gen/model/Tcp_settings.cpp
+++ b/broker/gen/model/Tcp_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Tcp_settings.h b/broker/gen/model/Tcp_settings.h
index 6f231af30..993ee4c7a 100644
--- a/broker/gen/model/Tcp_settings.h
+++ b/broker/gen/model/Tcp_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Unit_cell.cpp b/broker/gen/model/Unit_cell.cpp
index 4bb1cf7cb..1406dcee7 100644
--- a/broker/gen/model/Unit_cell.cpp
+++ b/broker/gen/model/Unit_cell.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Unit_cell.h b/broker/gen/model/Unit_cell.h
index 08ae72199..66da75868 100644
--- a/broker/gen/model/Unit_cell.h
+++ b/broker/gen/model/Unit_cell.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_metadata_settings.cpp b/broker/gen/model/Zeromq_metadata_settings.cpp
index cee6e9997..f122f102a 100644
--- a/broker/gen/model/Zeromq_metadata_settings.cpp
+++ b/broker/gen/model/Zeromq_metadata_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_metadata_settings.h b/broker/gen/model/Zeromq_metadata_settings.h
index 67c223389..1ab0704cc 100644
--- a/broker/gen/model/Zeromq_metadata_settings.h
+++ b/broker/gen/model/Zeromq_metadata_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_preview_settings.cpp b/broker/gen/model/Zeromq_preview_settings.cpp
index af833b377..b8d423fbd 100644
--- a/broker/gen/model/Zeromq_preview_settings.cpp
+++ b/broker/gen/model/Zeromq_preview_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_preview_settings.h b/broker/gen/model/Zeromq_preview_settings.h
index 60c759fff..c6bde3c38 100644
--- a/broker/gen/model/Zeromq_preview_settings.h
+++ b/broker/gen/model/Zeromq_preview_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_settings.cpp b/broker/gen/model/Zeromq_settings.cpp
index 5cf921e73..9f03f3680 100644
--- a/broker/gen/model/Zeromq_settings.cpp
+++ b/broker/gen/model/Zeromq_settings.cpp
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/gen/model/Zeromq_settings.h b/broker/gen/model/Zeromq_settings.h
index 0a7e25fc9..c2015aba8 100644
--- a/broker/gen/model/Zeromq_settings.h
+++ b/broker/gen/model/Zeromq_settings.h
@@ -2,7 +2,7 @@
 * Jungfraujoch
 * API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland). Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU. Jungfraujoch uses FPGA boards to acquire data at high data rates.  # License Clarification  While this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply** when this file is used solely to generate OpenAPI clients or when implementing applications that interact with the API. Generated client code and applications using this API definition are not subject to the GPL license requirements and may be distributed under terms of your choosing.  This exception is similar in spirit to the Linux Kernel's approach to userspace API headers and the GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that user programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not derivative works of the kernel and are not subject to the terms of the GPL.  This exception is intended to allow wider use of this API specification without imposing GPL requirements on applications that merely interact with the API, regardless of whether they communicate through network calls or other mechanisms. 
 *
-* The version of the OpenAPI document: 1.0.0-rc.179
+* The version of the OpenAPI document: 1.0.0-rc.180
 * Contact: filip.leonarski@psi.ch
 *
 * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
diff --git a/broker/jfjoch_api.yaml b/broker/jfjoch_api.yaml
index ea8c7b01d..05174810f 100644
--- a/broker/jfjoch_api.yaml
+++ b/broker/jfjoch_api.yaml
@@ -22,7 +22,7 @@ info:
     requirements on applications that merely interact with the API, regardless of whether they
     communicate through network calls or other mechanisms.
 
-  version: 1.0.0-rc.179
+  version: 1.0.0-rc.180
   contact:
     name: Filip Leonarski (Paul Scherrer Institute)
     email: filip.leonarski@psi.ch
@@ -2767,6 +2767,192 @@ components:
           type: string
         value:
           type: string
+    rugnux_live_model:
+      type: object
+      description: |
+        What the run made of the model it was given, as the report's MODEL VALIDATION section states it. The
+        R-factors here are those of the placed model with its own coordinates and B factors; what refinement made
+        of it is in `refinement`. A value that is absent was not computed - the model was not placed, or not by
+        molecular replacement.
+      required:
+        - placement
+        - model_name
+        - predicted
+        - reason
+        - mr_decision
+        - mr_space_group
+        - anomalous_site
+      properties:
+        placement:
+          type: string
+          description: RIGID_BODY (the model fits where it is), MR (molecular replacement placed it) or NOT_PLACED
+        model_name:
+          type: string
+        predicted:
+          type: boolean
+          description: Searched for as a predicted model
+        reason:
+          type: string
+          description: Why the model could not be searched for or validated; empty otherwise
+        r_work:
+          type: number
+          format: double
+        r_free:
+          type: number
+          format: double
+        cc_model:
+          type: number
+          format: double
+          description: Correlation of the merged intensities with the placed model's, over all reflections
+        fit_sigma:
+          type: number
+          format: double
+          description: How far R-work stands below that of the same model in random orientations, in standard deviations
+        map_atom_sigma:
+          type: number
+          format: double
+          description: Mean 2mFo-DFc value at the atom centres, in map sigma
+        rigid_body_angle_deg:
+          type: number
+          format: double
+        rigid_body_shift_A:
+          type: number
+          format: double
+        mr_decision:
+          type: string
+          description: Molecular replacement's decision (AGREES, ENANTIOMORPH, SPACE_GROUP, TWIN_SUBGROUP, or why it placed nothing); empty where it did not run
+        mr_space_group:
+          type: string
+          description: The group molecular replacement placed the model in; empty where it placed none
+        copies:
+          type: integer
+          format: int64
+          description: Copies placed by molecular replacement
+        tf_z:
+          type: number
+          format: double
+          description: Translation-function Z-score, the highest of the copies'
+        rf_z:
+          type: number
+          format: double
+          description: Rotation-function Z-score of the first copy's orientation
+        llg_z:
+          type: number
+          format: double
+          description: Likelihood Z-score after the rigid body, where a copy's translation function did not stand out
+        mr_d_min:
+          type: number
+          format: double
+          description: High-resolution limit of the molecular-replacement search, in Angstrom
+        anomalous_site:
+          type: string
+          description: Atom with the strongest anomalous difference density, e.g. "SG CYS A7"; empty where there is no anomalous map
+        anomalous_site_sigma:
+          type: number
+          format: double
+          description: Anomalous difference density at that atom, in map sigma
+        refinement:
+          $ref: '#/components/schemas/rugnux_live_refinement'
+    rugnux_live_refinement:
+      type: object
+      description: |
+        The placed model refined against the merge it was placed on, as the report's REFINE_ keys state it. Set
+        where a placed model was refined or its refinement failed; absent where the model was not placed or
+        refinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run's deadline
+        or cancel can cut it.
+      required:
+        - performed
+        - cancelled
+        - reason
+        - on_gpu
+        - seconds
+        - blob_count
+        - blobs
+      properties:
+        performed:
+          type: boolean
+          description: Refinement ran; false with `reason` where it failed
+        cancelled:
+          type: boolean
+          description: |
+            The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the
+            rest left out (cut before the first, the model is the placement's)
+        reason:
+          type: string
+          description: Why refinement did not run to the end; empty otherwise
+        on_gpu:
+          type: boolean
+        seconds:
+          type: number
+          format: double
+          description: Wall time of the refinement
+        r_work:
+          type: number
+          format: double
+          description: R-work of the refined model (after the restrained stage, else after the rigid body and grouped B)
+        r_free:
+          type: number
+          format: double
+          description: R-free of the refined model, on the same reflections as `r_work`
+        rmsd_bonds_A:
+          type: number
+          format: double
+          description: RMS deviation of the bond lengths from the dictionary, where the restrained stage ran
+        rmsd_angles_deg:
+          type: number
+          format: double
+          description: RMS deviation of the bond angles from the dictionary, where the restrained stage ran
+        blob_count:
+          type: integer
+          format: int64
+          description: Unexplained blobs of the refined model's mFo-DFc map (above 3 sigma, peaking above 4)
+        blobs:
+          type: array
+          description: The strongest blobs, at most 50, strongest first
+          items:
+            $ref: '#/components/schemas/rugnux_live_blob'
+    rugnux_live_blob:
+      type: object
+      description: |
+        A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on
+        what is measured, to point a person at the density - not an identification.
+      required:
+        - kind
+        - x
+        - y
+        - z
+        - peak_sigma
+        - volume_A3
+        - nearest_atom
+      properties:
+        kind:
+          type: string
+          enum: [WATER, ION, LIGAND, MODEL_ERROR, UNASSIGNED]
+        x:
+          type: number
+          format: double
+          description: Centroid, Cartesian Angstrom, in the frame of the refined model (`/rugnux/model.cif`)
+        y:
+          type: number
+          format: double
+        z:
+          type: number
+          format: double
+        peak_sigma:
+          type: number
+          format: double
+          description: The highest point, in map sigma
+        volume_A3:
+          type: number
+          format: double
+          description: Volume above 3 sigma, in cubic Angstrom
+        nearest_atom:
+          type: string
+          description: e.g. "OG1 THR A42"
+        nearest_atom_distance_A:
+          type: number
+          format: double
+          description: Absent where no atom is within 12 Angstrom
     rugnux_live_status:
       type: object
       description: |
@@ -2786,7 +2972,9 @@ components:
         - warnings
         - probe
         - placed_model
+        - refined_model
         - anomalous_map
+        - anomalous_signal
       properties:
         state:
           type: string
@@ -2796,11 +2984,32 @@ components:
           description: |
             The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from
             `/rugnux/map.ccp4`.
+        refined_model:
+          type: boolean
+          description: |
+            The run refined the placed model: `/rugnux/model.cif` and `/rugnux/map.ccp4` serve the refined model and
+            its maps unless asked for `stage=placed`.
         anomalous_map:
           type: boolean
           description: |
             The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map
             (`/rugnux/map.ccp4?type=anom`).
+        anomalous_signal:
+          type: boolean
+          description: The merged data carry usable anomalous signal (the summary's "Anomalous" row says so)
+        model:
+          $ref: '#/components/schemas/rugnux_live_model'
+        space_group:
+          type: string
+          description: Space group of the result (the summary's "Space group" row); absent until the run is over
+        d_min:
+          type: number
+          format: double
+          description: High-resolution limit of the merge, in Angstrom; absent until the run is over, or without a merge
+        isa:
+          type: number
+          format: double
+          description: ISa of the error model; absent until the run is over, or where it was not determined
         probe:
           type: string
           description: Answer of the early lattice probe on the first 60 degrees; empty until it answers
@@ -3624,6 +3833,17 @@ paths:
         The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
         `_model.cif` file written beside the data: the data's cell and space group, with the input model's own
         metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
+        Where the run refined the model, the refined model unless asked for `stage=placed`.
+      parameters:
+        - in: query
+          name: stage
+          required: false
+          schema:
+            type: string
+            enum: [placed, refined]
+          description: |
+            `placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).
+            Default: the refined model where there is one, otherwise the placed one.
       security:
         - bearerAuth: []
       responses:
@@ -3634,6 +3854,12 @@ paths:
               schema:
                 type: string
                 format: binary
+        "400":
+          description: Unknown stage
+          content:
+            text/plain:
+              schema:
+                type: string
         "401":
           description: The current dataset is protected and no valid bearer token was presented.
           content:
@@ -3641,7 +3867,7 @@ paths:
               schema:
                 type: string
         "404":
-          description: The last rugnux live run placed no model
+          description: The last rugnux live run placed no model, or (`stage=refined`) refined none
   /rugnux/map.ccp4:
     get:
       summary: Get an electron-density map of the last rugnux live run
@@ -3649,7 +3875,9 @@ paths:
         The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map
         coefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where
         the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and
-        RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.
+        RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run
+        refined the model, the 2mFo-DFc and mFo-DFc maps are the refined model's unless asked for `stage=placed`;
+        the anomalous map stays on the placed model's phases.
       parameters:
         - in: query
           name: type
@@ -3662,6 +3890,15 @@ paths:
             `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map,
             (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map`
             in `/rugnux/status`)
+        - in: query
+          name: stage
+          required: false
+          schema:
+            type: string
+            enum: [placed, refined]
+          description: |
+            `placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).
+            Default: the refined model where there is one, otherwise the placed one.
       security:
         - bearerAuth: []
       responses:
@@ -3673,7 +3910,7 @@ paths:
                 type: string
                 format: binary
         "400":
-          description: Unknown map type
+          description: Unknown map type or stage
           content:
             text/plain:
               schema:
@@ -3685,7 +3922,7 @@ paths:
               schema:
                 type: string
         "404":
-          description: The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs
+          description: The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs, or (`stage=refined`) refined none
   /config/zeromq_preview:
     put:
       summary: Set ZeroMQ preview settings
diff --git a/broker/redoc-static.html b/broker/redoc-static.html
index 04e0ab299..e315e3020 100644
--- a/broker/redoc-static.html
+++ b/broker/redoc-static.html
@@ -426,7 +426,7 @@ This format doesn&#x27;t transmit information about X-axis, only values, so it i
           55.627 l 55.6165,55.627 -231.245496,231.24803 c -127.185,127.1864
           -231.5279,231.248 -231.873,231.248 -0.3451,0 -104.688,
           -104.0616 -231.873,-231.248 z
-        " fill="currentColor"></path></g></svg></div></div><div class="sc-eulNck iEaKWZ api-content"><div class="sc-dcJsrY bBkGhy"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx api-info"><h1 class="sc-imWYAI sc-ktJbId cILgPb UQJzT">Jungfraujoch<!-- --> <span>(<!-- -->1.0.0-rc.179<!-- -->)</span></h1><p>Download OpenAPI specification<!-- -->:</p><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><div class="sc-fiCwlc iQovLz"><div class="sc-jIGnZt cKLRU"><span class="sc-kMkxaj csEIgT">Filip Leonarski (Paul Scherrer Institute)<!-- -->:<!-- --> <a href="mailto:filip.leonarski@psi.ch">filip.leonarski@psi.ch</a></span> <!-- --> <span class="sc-kMkxaj csEIgT">License:<!-- --> <a href="https://www.gnu.org/licenses/gpl-3.0.html">GPL-3.0</a></span> </div></div></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-summary"></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-description"><p>API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).
+        " fill="currentColor"></path></g></svg></div></div><div class="sc-eulNck iEaKWZ api-content"><div class="sc-dcJsrY bBkGhy"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx api-info"><h1 class="sc-imWYAI sc-ktJbId cILgPb UQJzT">Jungfraujoch<!-- --> <span>(<!-- -->1.0.0-rc.180<!-- -->)</span></h1><p>Download OpenAPI specification<!-- -->:</p><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><div class="sc-fiCwlc iQovLz"><div class="sc-jIGnZt cKLRU"><span class="sc-kMkxaj csEIgT">Filip Leonarski (Paul Scherrer Institute)<!-- -->:<!-- --> <a href="mailto:filip.leonarski@psi.ch">filip.leonarski@psi.ch</a></span> <!-- --> <span class="sc-kMkxaj csEIgT">License:<!-- --> <a href="https://www.gnu.org/licenses/gpl-3.0.html">GPL-3.0</a></span> </div></div></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-summary"></div><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru" data-role="redoc-description"><p>API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).
 Jungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.
 Jungfraujoch uses FPGA boards to acquire data at high data rates.</p>
 </div></div></div></div><div id="section/License-Clarification" data-section-id="section/License-Clarification" class="sc-dcJsrY bBkGhy"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#section/License-Clarification" aria-label="section/License-Clarification"></a>License Clarification</h2></div></div><div class="sc-fqkvVR diIqQJ"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru redoc-markdown "><p>While this API definition is licensed under GPL-3.0, <strong>the GPL copyleft provisions do not apply</strong>
@@ -864,24 +864,32 @@ and validation of every following rugnux live collection, until it is removed wi
 </div></div><div class="sc-jaXxmE eqYzvz"><div class="sc-iMTnTL fkPTul"><h5 class="sc-dAlyuH sc-hwdzOV jbQuod JjoyL">Authorizations:</h5><svg class="sc-cwHptR iZRiKW" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></div><div class="sc-krNlru gkwgxc"><span class="sc-jMakVo bPNrjo"><span class="sc-ihgnxF jlNGfN"><i>bearerAuth</i></span></span></div></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Everything OK</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">401<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The current dataset is protected and no valid bearer token was presented.</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/rugnux/status</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
-</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/rugnux/status</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_jiia_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_jiia_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_jiia_0" aria-labelledby="tab_R_jiia_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"state"</span>: <span class="token string">&quot;Idle&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"placed_model"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"anomalous_map"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"start_to_first_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"message"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_expected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"expected_collection_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_received"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"elapsed_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"step_progress"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"steps"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"title"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"started_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"duration_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"notes"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_to_written_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict_text"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"summary"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"label"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"value"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"warnings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1rugnux~1model.cif/get" data-section-id="/paths/~1rugnux~1model.cif/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1rugnux~1model.cif/get" aria-label="/paths/~1rugnux~1model.cif/get"></a>Get the model as placed by the last rugnux live run<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
+</div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/rugnux/status</div></div></div></div></div><div><h3 class="sc-kpDqfm eBBgSB"> <!-- -->Response samples<!-- --> </h3><div class="sc-bXCLTC dHowgL" data-rttabs="true"><ul class="react-tabs__tab-list" role="tablist"><li class="tab-success react-tabs__tab--selected" role="tab" id="tab_R_jiia_0" aria-selected="true" aria-disabled="false" aria-controls="panel_R_jiia_0" tabindex="0" data-rttab="true">200</li></ul><div class="react-tabs__tab-panel react-tabs__tab-panel--selected" role="tabpanel" id="panel_R_jiia_0" aria-labelledby="tab_R_jiia_0"><div><div class="sc-bbSZdi gCVTxk"><span class="sc-fjvvzt jWReSk">Content type</span><div class="sc-JrDLc iTKzPJ">application/json</div></div><div class="sc-uVWWZ gQROPU"><div class="sc-esYiGF dWQNJI"><div class="sc-koXPp efufqz"><button><div class="sc-fhzFiK kwZDms">Copy</div></button><button> Expand all </button><button> Collapse all </button></div><div tabindex="0" class="sc-eeDRCY gTGgei sc-fXSgeo bnrBiz"><div class="redoc-json"><code><button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable "><span class="property token string">"state"</span>: <span class="token string">&quot;Idle&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"placed_model"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"refined_model"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"anomalous_map"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"anomalous_signal"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"model"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"placement"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"model_name"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"predicted"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"reason"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"r_work"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"r_free"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"cc_model"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"fit_sigma"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"map_atom_sigma"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rigid_body_angle_deg"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rigid_body_shift_A"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"mr_decision"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"mr_space_group"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"copies"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"tf_z"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rf_z"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"llg_z"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"mr_d_min"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"anomalous_site"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"anomalous_site_sigma"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"refinement"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"performed"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"cancelled"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"reason"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"on_gpu"</span>: <span class="token boolean">true</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"seconds"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"r_work"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"r_free"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rmsd_bonds_A"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"rmsd_angles_deg"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"blob_count"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"blobs"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"kind"</span>: <span class="token string">&quot;WATER&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"x"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"y"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"z"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"peak_sigma"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"volume_A3"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"nearest_atom"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"nearest_atom_distance_A"</span>: <span class="token number">0.1</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">}</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"space_group"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"d_min"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"isa"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"probe_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"start_to_first_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"message"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_expected"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"expected_collection_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"images_received"</span>: <span class="token number">0</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"elapsed_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"step_progress"</span>: <span class="token number">1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"steps"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"title"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"started_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"duration_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"notes"</span>: <button class="collapser" aria-label="expand"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"cut_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"last_image_to_written_s"</span>: <span class="token number">0.1</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"verdict_text"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"summary"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><button class="collapser" aria-label="expand"></button><span class="token punctuation">{</span><span class="ellipsis"></span><ul class="obj collapsible"><li><div class="hoverable collapsed"><span class="property token string">"label"</span>: <span class="token string">&quot;string&quot;</span><span class="token punctuation">,</span></div></li><li><div class="hoverable collapsed"><span class="property token string">"value"</span>: <span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">}</span></div></li></ul><span class="token punctuation">]</span><span class="token punctuation">,</span></div></li><li><div class="hoverable "><span class="property token string">"warnings"</span>: <button class="collapser" aria-label="collapse"></button><span class="token punctuation">[</span><span class="ellipsis"></span><ul class="array collapsible"><li><div class="hoverable collapsed"><span class="token string">&quot;string&quot;</span></div></li></ul><span class="token punctuation">]</span></div></li></ul><span class="token punctuation">}</span></code></div></div></div></div></div></div></div></div></div></div></div><div id="/paths/~1rugnux~1model.cif/get" data-section-id="/paths/~1rugnux~1model.cif/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1rugnux~1model.cif/get" aria-label="/paths/~1rugnux~1model.cif/get"></a>Get the model as placed by the last rugnux live run<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
 <code>_model.cif</code> file written beside the data: the data&#39;s cell and space group, with the input model&#39;s own
-metadata (entities, sequences, references, authors, software) kept. Kept as long as <code>/rugnux/status</code>.</p>
-</div></div><div class="sc-jaXxmE eqYzvz"><div class="sc-iMTnTL fkPTul"><h5 class="sc-dAlyuH sc-hwdzOV jbQuod JjoyL">Authorizations:</h5><svg class="sc-cwHptR iZRiKW" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></div><div class="sc-krNlru gkwgxc"><span class="sc-jMakVo bPNrjo"><span class="sc-ihgnxF jlNGfN"><i>bearerAuth</i></span></span></div></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Placed model</p>
+metadata (entities, sequences, references, authors, software) kept. Kept as long as <code>/rugnux/status</code>.
+Where the run refined the model, the refined model unless asked for <code>stage=placed</code>.</p>
+</div></div><div class="sc-jaXxmE eqYzvz"><div class="sc-iMTnTL fkPTul"><h5 class="sc-dAlyuH sc-hwdzOV jbQuod JjoyL">Authorizations:</h5><svg class="sc-cwHptR iZRiKW" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></div><div class="sc-krNlru gkwgxc"><span class="sc-jMakVo bPNrjo"><span class="sc-ihgnxF jlNGfN"><i>bearerAuth</i></span></span></div></div><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class="last "><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="stage"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">stage</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;placed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;refined&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p><code>placed</code>: the model as placed; <code>refined</code>: the model refined (<code>refined_model</code> in <code>/rugnux/status</code>).
+Default: the refined model where there is one, otherwise the placed one.</p>
+</div></div></div></td></tr></tbody></table></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Placed model</p>
+</div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">400<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Unknown stage</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">401<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The current dataset is protected and no valid bearer token was presented.</p>
-</div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The last rugnux live run placed no model</p>
+</div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The last rugnux live run placed no model, or (<code>stage=refined</code>) refined none</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/rugnux/model.cif</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/rugnux/model.cif</div></div></div></div></div></div></div></div><div id="/paths/~1rugnux~1map.ccp4/get" data-section-id="/paths/~1rugnux~1map.ccp4/get" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1rugnux~1map.ccp4/get" aria-label="/paths/~1rugnux~1map.ccp4/get"></a>Get an electron-density map of the last rugnux live run<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>The map of the placed model (<code>/rugnux/model.cif</code>) in CCP4 format (mode 2, float), made from the map
 coefficients written to <code>_maps.mtz</code> (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where
 the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and
-RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.</p>
-</div></div><div class="sc-jaXxmE eqYzvz"><div class="sc-iMTnTL fkPTul"><h5 class="sc-dAlyuH sc-hwdzOV jbQuod JjoyL">Authorizations:</h5><svg class="sc-cwHptR iZRiKW" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></div><div class="sc-krNlru gkwgxc"><span class="sc-jMakVo bPNrjo"><span class="sc-ihgnxF jlNGfN"><i>bearerAuth</i></span></span></div></div><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class="last "><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;2fofc&quot;</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;2fofc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;fofc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;anom&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p><code>2fofc</code>: the 2mFo-DFc map; <code>fofc</code>: the mFo-DFc difference map; <code>anom</code>: the anomalous difference map,
+RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run
+refined the model, the 2mFo-DFc and mFo-DFc maps are the refined model&#39;s unless asked for <code>stage=placed</code>;
+the anomalous map stays on the placed model&#39;s phases.</p>
+</div></div><div class="sc-jaXxmE eqYzvz"><div class="sc-iMTnTL fkPTul"><h5 class="sc-dAlyuH sc-hwdzOV jbQuod JjoyL">Authorizations:</h5><svg class="sc-cwHptR iZRiKW" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></div><div class="sc-krNlru gkwgxc"><span class="sc-jMakVo bPNrjo"><span class="sc-ihgnxF jlNGfN"><i>bearerAuth</i></span></span></div></div><div><h5 class="sc-dAlyuH jbQuod">query<!-- --> Parameters</h5><table class="sc-dAbbOL ccPhmY"><tbody><tr class=""><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="type"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">type</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Default:<!-- --> </span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;2fofc&quot;</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;2fofc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;fofc&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;anom&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p><code>2fofc</code>: the 2mFo-DFc map; <code>fofc</code>: the mFo-DFc difference map; <code>anom</code>: the anomalous difference map,
 (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (<code>anomalous_map</code>
 in <code>/rugnux/status</code>)</p>
+</div></div></div></td></tr><tr class="last "><td class="sc-dLMFU sc-eldPxv hZbWKe jXkfaY" kind="field" title="stage"><span class="sc-gFqAkR eRqgPI"></span><span class="property-name">stage</span></td><td class="sc-fPXMVe bAXEAa"><div><div><span class="sc-Nxspf sc-cfxfcM cXxAXt jrGEaR"></span><span class="sc-Nxspf sc-gFAWRd cXxAXt dYzdDr">string</span></div><div><span class="sc-Nxspf cXxAXt"> <!-- -->Enum<!-- -->:</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;placed&quot;</span> <span class="sc-Nxspf sc-ddjGPC cXxAXt jZOCAW">&quot;refined&quot;</span> </div> <div><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p><code>placed</code>: the model as placed; <code>refined</code>: the model refined (<code>refined_model</code> in <code>/rugnux/status</code>).
+Default: the refined model where there is one, otherwise the placed one.</p>
 </div></div></div></td></tr></tbody></table></div><div><h3 class="sc-fMMURN egoxtT">Responses</h3><div><button class="sc-kzqdkY jgSwKD"><svg class="sc-cwHptR hWEnWx" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">200<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Map</p>
-</div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">400<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Unknown map type</p>
+</div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">400<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>Unknown map type or stage</p>
 </div></button></div><div><button class="sc-kzqdkY bXzzUN"><svg class="sc-cwHptR cSkZlF" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg><strong class="sc-dSIIpw bpEYcE">401<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The current dataset is protected and no valid bearer token was presented.</p>
-</div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The last rugnux live run placed no model or made no maps, or (<code>anom</code>) has no Bijvoet pairs</p>
+</div></button></div><div><button class="sc-kzqdkY gnmLmb" disabled=""><strong class="sc-dSIIpw bpEYcE">404<!-- --> </strong><div class="sc-eeDRCY sc-eBMEME sc-dCFHLb gTGgei kekOtA kCaLQd"><p>The last rugnux live run placed no model or made no maps, or (<code>anom</code>) has no Bijvoet pairs, or (<code>stage=refined</code>) refined none</p>
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/rugnux/map.ccp4</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/rugnux/map.ccp4</div></div></div></div></div></div></div></div><div id="/paths/~1config~1zeromq_preview/put" data-section-id="/paths/~1config~1zeromq_preview/put" class="sc-dcJsrY cqVkUp"><div class="sc-kAyceB hBQWIZ"><div class="sc-fqkvVR oJKYx"><h2 class="sc-jXbUNg fWnwAh"><a class="sc-jlZhew kbdRLs" href="#/paths/~1config~1zeromq_preview/put" aria-label="/paths/~1config~1zeromq_preview/put"></a>Set ZeroMQ preview settings<!-- --> </h2><div class="sc-bVVIoq icSMtY"><div class="sc-eeDRCY sc-eBMEME gTGgei fMmru"><p>Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.
 Here settings of the socket can be adjusted.
@@ -1115,7 +1123,7 @@ then image might be replaced in the buffer between calling /images and /image.cb
 </div></button></div></div></div><div class="sc-iGgWBj sc-gsFSXq ibAZSi eDeKjd"><div class="sc-ejfMa-d bNUPQg"><button class="sc-EgOXT cFEcOl"><span type="get" class="sc-eZYNyq qGfV http-verb get">get</span><span class="sc-iEXKAA gUNSDu">/version</span><svg class="sc-cwHptR iVFMLx" style="margin-right:-25px" version="1.1" viewBox="0 0 24 24" x="0" xmlns="http://www.w3.org/2000/svg" y="0" aria-hidden="true"><polygon points="17.3 8.3 12 13.6 6.7 8.3 5.3 9.7 12 16.4 18.7 9.7 "></polygon></svg></button><div aria-hidden="true" class="sc-dlWCHZ kWacYr"><div class="sc-hHOBiw cndTNO"><div class="sc-eeDRCY sc-eBMEME gTGgei fbXBig"><p>Test Jungfraujoch system</p>
 </div><div tabindex="0" role="button"><div class="sc-kWtpeL gEncxT"><span>http://localhost:5232</span>/version</div></div></div></div></div></div></div></div></div><div class="sc-dExYaf gZbfaQ"></div></div></div>
       <script>
-      const __redoc_state = {"menu":{"activeItemIdx":-1},"spec":{"data":{"openapi":"3.0.3","info":{"title":"Jungfraujoch","description":"API to control Jungfraujoch developed by the Paul Scherrer Institute (Switzerland).\nJungfraujoch is a data acquisition and analysis system for pixel array detectors, primarly PSI JUNGFRAU.\nJungfraujoch uses FPGA boards to acquire data at high data rates.\n\n# License Clarification\n\nWhile this API definition is licensed under GPL-3.0, **the GPL copyleft provisions do not apply**\nwhen this file is used solely to generate OpenAPI clients or when implementing applications that\ninteract with the API. Generated client code and applications using this API definition are not\nsubject to the GPL license requirements and may be distributed under terms of your choosing.\n\nThis exception is similar in spirit to the Linux Kernel's approach to userspace API headers and\nthe GCC Runtime Library Exception. The Linux Kernel developers have explicitly stated that\nuser programs that merely use the kernel interfaces (syscalls, ioctl definitions, etc.) are not\nderivative works of the kernel and are not subject to the terms of the GPL.\n\nThis exception is intended to allow wider use of this API specification without imposing GPL\nrequirements on applications that merely interact with the API, regardless of whether they\ncommunicate through network calls or other mechanisms.\n","version":"1.0.0-rc.179","contact":{"name":"Filip Leonarski (Paul Scherrer Institute)","email":"filip.leonarski@psi.ch"},"license":{"name":"GPL-3.0","url":"https://www.gnu.org/licenses/gpl-3.0.html"}},"servers":[{"url":"http://localhost:5232","description":"Test Jungfraujoch system"}],"components":{"securitySchemes":{"bearerAuth":{"type":"http","scheme":"bearer","description":"Per-dataset secret. `/start` may carry one or more equivalent `tokens`; while the current\ndataset has any, the operations marked with this scheme require `Authorization: Bearer <token>`\nand answer 401 otherwise. A dataset started without `tokens` is not protected and the header is ignored.\n"}},"parameters":{"binning":{"in":"query","name":"binning","required":false,"schema":{"default":1,"type":"integer"},"description":"Binning of frames for the plot (0 = default binning)"},"experimental_coord":{"in":"query","name":"experimental_coord","required":false,"schema":{"type":"boolean","default":false},"description":"If measurement has goniometer axis defined, plot X-axis will represent rotation angle\nIf measurement has grid scan defined, plot X-axis and Y-axis will represent grid position, Z will be used as the final value\nFor still measurement the number is ignored\n"},"azint_unit":{"in":"query","name":"azint_unit","required":false,"schema":{"type":"string","enum":["Q_recipA","d_A","two_theta_deg"],"default":"Q_recipA"},"description":"Unit used for azim int.\n"},"fill_value":{"in":"query","name":"fill","required":false,"schema":{"type":"number","format":"float"},"description":"Fill value for elements that were missed during data collection\n"},"plot_type":{"in":"query","name":"type","required":true,"description":"Type of requested plot","schema":{"type":"string","enum":["bkg_estimate","spindle_blind_fraction","azint","azint_1d","spot_count","spot_count_low_res","spot_count_indexed","spot_count_ice","indexing_rate","indexing_lattice_count","indexing_unit_cell_length","indexing_unit_cell_angle","profile_radius","mosaicity","b_factor","error_pixels","saturated_pixels","image_collection_efficiency","receiver_delay","receiver_free_send_buf","strong_pixels","roi_sum","roi_mean","roi_max_count","roi_pixels","roi_weighted_x","roi_weighted_y","packets_received","max_pixel_value","resolution_estimate","pixel_sum","processing_time","beam_center_x","beam_center_y","integrated_reflections","image_scale_factor","image_scale_cc","compression_ratio","ice_ring_score"]}},"roi":{"in":"query","name":"roi","required":false,"schema":{"type":"string","minLength":1},"description":"Name of ROI for which plot is requested"},"image_id":{"in":"query","name":"id","required":false,"schema":{"type":"integer","format":"int64","default":-1,"minimum":-2},"description":"Image ID in the image buffer. 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[photons/s]\n"},"transmission":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"/entry/instrument/attenuator/attenuator_transmission\nTransmission of attenuator (filter) [no units]\n"},"beam_size_x_um":{"type":"number","format":"float","minimum":0,"description":"First element of /entry/instrument/beam/incident_beam_size in NXmx\nHorizontal size of the X-ray beam where it meets the sample - the FWHM of a focused beam,\nthe full width of a slit-defined one. [um]\n"},"beam_size_y_um":{"type":"number","format":"float","minimum":0,"description":"Second element of /entry/instrument/beam/incident_beam_size in NXmx\nVertical size of the X-ray beam where it meets the sample. [um]\n"},"goniometer":{"$ref":"#/components/schemas/rotation_axis"},"grid_scan":{"$ref":"#/components/schemas/grid_scan"},"header_appendix":{"description":"Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)\nIn general, it is not saved in HDF5 file.\n\nHowever, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file. \nThis applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.\nFor example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2.\n"},"image_appendix":{"description":"Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)\nNot saved in HDF5 file\n"},"data_reduction_factor_serialmx":{"type":"number","format":"float","default":1,"minimum":0,"maximum":1,"description":"Rate at which non-indexed images are accepted to be forwarded to writer. \nValue of 1.0 (default) means that all images are written.\nValues below zero mean that non-indexed images will be accepted with a given probability.\n"},"pixel_value_low_threshold":{"type":"integer","format":"int64","minimum":0,"description":"Set all counts lower than the value to zero. \nWhen the value is set, negative numbers other than error pixel value are always set to zero.\nSetting to zero is equivalent to turning the option off.\n"},"run_number":{"type":"integer","format":"int64","minimum":0,"description":"Number of run within an experimental session. \nTransferred over CBOR stream as \"series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this number unique for each data collection during experimental series.\nIf not provided, the number will be automatically incremented.\n"},"run_name":{"type":"string","description":"Unique ID of run.\nTransferred over CBOR stream as \"unique series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this name unique for each data collection during experimental series.\nIf not provided, the name will be automatically generated as number + colon + file_prefix.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number). \nTransferred over CBOR stream, though not saved in HDF5 file.\n"},"poisson_compression":{"type":"integer","format":"int64","minimum":0,"maximum":16,"description":"Enable lossy compression of pixel values that preserves Poisson statistics. \nRequires to provide a numerical factor SQ.\nPixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.\nCompression is turned off if the value is missing or it is set to zero.\n"},"write_nxmx_hdf5_master":{"type":"boolean","default":true,"description":"Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments\nand to turn off for other experiments.\n"},"save_calibration":{"type":"boolean","description":"Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer.\nIf parameter is not provided calibration will be saved only if more than 4 images are recorded.\n"},"polarization_factor":{"type":"number","description":"Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization","format":"float","minimum":-1,"maximum":1},"ring_current_mA":{"type":"number","format":"float","description":"Ring current at the beginning of the data collection","minimum":0},"sample_temperature_K":{"type":"number","format":"float","description":"Sample temperature in Kelvin","minimum":0},"poni_rot1_rad":{"type":"number","description":"PONI angle rot1 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot2_rad":{"type":"number","description":"PONI angle rot2 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot3_rad":{"type":"number","description":"PONI angle rot3 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"unit_cell":{"$ref":"#/components/schemas/unit_cell"},"spot_finding":{"type":"boolean","description":"Enable spot finding and save spots","default":true},"smargon":{"type":"object","description":"Geometry of Smargon goniometer at SLS 2.0 / MX beamlines. \nAssuming that Smargon is used as static positioner and not moving during the scan, allowing to reconstruct geometry.\n","required":["phi_deg","chi_deg"],"properties":{"phi_deg":{"type":"number","format":"float","description":"Phi angle in degrees"},"chi_deg":{"type":"number","format":"float","description":"Chi angle in degrees"},"phi_axis":{"type":"array","description":"Phi rotation axis","default":[1,0,0],"example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"chi_axis":{"type":"array","description":"Chi rotation axis","default":[0,0,1],"example":[0,0,1],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3}}},"max_spot_count":{"type":"integer","minimum":10,"maximum":2000,"default":250,"description":"Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected"},"detect_ice_rings":{"type":"boolean","description":"Flag spots as ice rings and reduce their effect on indexing"},"async_start":{"type":"boolean","default":false,"description":"When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement."},"tokens":{"type":"array","items":{"type":"string","minLength":1},"writeOnly":true,"description":"Bearer tokens that protect this dataset: any number, all equivalent (e.g. a beamline\nsecret and a dataset-specific user secret). While set, the endpoints marked with the\n`bearerAuth` security scheme require `Authorization: Bearer <token>` and answer 401 otherwise.\nEvery accepted `/start` replaces the previous dataset's tokens; omitted or empty means no\nprotection. Never returned by any endpoint.\n"},"xray_fluorescence_spectrum":{"type":"object","required":["energy_eV","data"],"properties":{"energy_eV":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan energy for each measurement point"},"data":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV"}}}}},"crystal_lattice":{"type":"array","items":{"type":"number","format":"float"},"minItems":9,"maxItems":9,"description":"Real-space crystal lattice 3D vectors in Angstrom.\nOrder is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)\n"},"unit_cell":{"type":"object","description":"Unit cell parameters. Necessary to run indexing. Units of angstrom and degree","required":["a","b","c","alpha","beta","gamma"],"properties":{"a":{"type":"number","format":"float","example":37,"minimum":0},"b":{"type":"number","format":"float","example":37,"minimum":0},"c":{"type":"number","format":"float","example":78,"minimum":0},"alpha":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"beta":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"gamma":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360}}},"file_writer_format":{"type":"string","enum":["NXmxOnlyData","NXmxLegacy","NXmxVDS","NXmxIntegrated","CBF","TIFF","NoFileWritten"],"default":"NXmxVDS","description":"NoFileWritten - no files are written at all\nNXmxOnlyData - only data files are written, no master file\nNXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia\nNXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling\nNXmxIntegrated - single HDF5 per dataset\nCBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\nTIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\n"},"file_writer_settings":{"type":"object","properties":{"overwrite":{"type":"boolean","default":false,"description":"Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.\n"},"format":{"$ref":"#/components/schemas/file_writer_format"}}},"pixel_mask_statistics":{"type":"object","properties":{"user_mask":{"description":"Number of pixels masked using the user mask","type":"integer","format":"int64","minimum":0},"too_high_pedestal_rms":{"description":"Number of pixels with G0 pedestal RMS higher than provided threshold","type":"integer","format":"int64","minimum":0},"wrong_gain":{"description":"Number of pixels that show wrong gain level during the pedestal procedure","type":"integer","format":"int64","minimum":0}}},"image_buffer_status":{"type":"object","required":["image_numbers","total_slots","in_preparation_slots","in_sending_slots","available_slots","max_image_number","min_image_number"],"properties":{"min_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Smallest image number available in the buffer"},"max_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Largest image number available in the buffer"},"image_numbers":{"type":"array","description":"Image numbers currently present in the buffer.","items":{"type":"integer","format":"int64"}},"total_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer. This number, compared to number of images in data collection and\nframe rate will determine \"retention\" rate of the image buffer.\n"},"available_slots":{"type":"integer","format":"int64","description":"Slots available for the data collection"},"in_preparation_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently in preparation for sending.\n"},"in_sending_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently sending/writing data.\n"},"current_counter":{"type":"integer","format":"int64","description":"Counter of changes in the image buffer - either new start message or new image added.\nFor optimization one can only load new images/datasets from the HTTP if this value changes.\nCounter is optional as it was not implemented in older versions to avoid breaking change\n"}}},"image_format_settings":{"type":"object","required":["summation","jungfrau_conversion","geometry_transform","mask_chip_edges","mask_module_edges","apply_mask"],"properties":{"summation":{"type":"boolean","description":"Enable summation of images to a given image_time\nIf disabled images are saved according to original detector speed, but image count is adjusted\n"},"geometry_transform":{"type":"boolean","description":"Place module read-out into their location on composed detector and extend multipixels\n"},"jungfrau_conversion":{"type":"boolean","description":"Convert pixel value in ADU to photon counts/energy\nOnly affects JUNGFRAU detector\n"},"jungfrau_conversion_factor_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to convert energy deposited into pixel to counts\nIf not provided incident_energy_keV is used\n"},"bit_depth_image":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of resulting image (it doesn't affect the detector read-out value)\nIf not provided value is adjusted automatically\n"},"signed_output":{"type":"boolean","description":"Controls if pixels have signed output\nIf not provided value is adjusted automatically\n"},"mask_module_edges":{"type":"boolean","default":true,"description":"Mask 1 pixel on the module boundary\n"},"mask_chip_edges":{"type":"boolean","default":true,"description":"Mask multipixels on chip boundary\n"},"jungfrau_mask_pixels_without_g0":{"type":"boolean","default":true,"description":"JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1.\nThis should be turned off for cases, where detector is operated at room temperature with long exposure time.\n"},"apply_mask":{"type":"boolean","default":false,"description":"Masked pixels are set to special value in the images produced by Jungfraujoch\n"},"jungfrau_pedestal_g0_rms_limit":{"type":"integer","format":"int64","default":100,"minimum":0,"description":"Pixels with pedestal G0 RMS above the threshold are marked as masked pixels"}}},"detector_power_state":{"type":"string","description":"Power on of ASICs","enum":["PowerOn","PowerOff","Partial"]},"detector_state":{"type":"string","description":"Current state of the detector","enum":["Idle","Waiting","Busy","Error","Not connected"]},"detector_status":{"type":"object","required":["state","powerchip","server_version","number_of_triggers_left","fpga_temp_degC","high_voltage_V"],"properties":{"state":{"$ref":"#/components/schemas/detector_state"},"powerchip":{"$ref":"#/components/schemas/detector_power_state"},"server_version":{"type":"string","description":"Detector server (on read-out boards) version"},"number_of_triggers_left":{"type":"integer","format":"int64","description":"Remaining triggers to the detector (max of all modules)"},"fpga_temp_degC":{"type":"array","description":"Temperature of detector FPGAs","items":{"type":"integer","format":"int64"}},"high_voltage_V":{"type":"array","description":"High voltage for detector modules","items":{"type":"integer","format":"int64"}}}},"detector_timing":{"type":"string","enum":["auto","trigger","burst","gated"],"default":"trigger"},"detector_settings":{"type":"object","required":["frame_time_us"],"properties":{"frame_time_us":{"type":"integer","description":"Interval between consecutive frames.\nThis is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.\nFor EIGER detector this is default frame time, not used otherwise\n","format":"int64","minimum":1},"count_time_us":{"type":"integer","description":"Integration time of the detector. \nIf not provided count time will be set to maximum value for a given frame time.\n","format":"int64"},"internal_frame_generator":{"type":"boolean","default":false,"description":"Use internal frame generator in FPGA instead of getting data from a real detector"},"internal_frame_generator_images":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":64,"description":"Number of images stored in the internal frame generator."},"detector_trigger_delay_ns":{"type":"integer","format":"int64","minimum":0,"default":0,"description":"Delay between TTL trigger and acquisition start [ns]"},"timing":{"$ref":"#/components/schemas/detector_timing"},"eiger_threshold_keV":{"type":"number","format":"float","minimum":1,"maximum":100,"description":"Threshold for the PSI EIGER detector and all DECTRIS detectors.\nIf value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy.\nIf value is not provided, threshold will be determined on start of acquisition as half of incident energy. \nThis might lead to increased start time.\n"},"eiger_bit_depth":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of PSI EIGER read-out. This is  \nIf value is not provided, depth will be determined based on the image time:\n* Exposure time < 500 microseconds depth of 8 bit will be used,\n* 500 <= exposure time < 2622 microseconds depth of 16 bit will be used\n* Exposure time >= 2622 microseconds depth of 32 bit will be used.\n"},"jungfrau_pedestal_g0_frames":{"type":"integer","format":"int64","default":2000,"minimum":0},"jungfrau_pedestal_g1_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_g2_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_min_image_count":{"type":"integer","format":"int64","default":128,"minimum":32,"description":"Minimum number of collected images for pedestal to consider it viable"},"jungfrau_storage_cell_count":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":16},"jungfrau_storage_cell_delay_ns":{"type":"integer","format":"int64","minimum":2100,"default":5000,"description":"Delay between two storage cells [ns]"},"jungfrau_fixed_gain_g1":{"type":"boolean","default":false,"description":"Fix gain to G1 (can be useful for storage cells)"},"jungfrau_use_gain_hg0":{"type":"boolean","default":false,"description":"Use high G0 (for low energy applications)"}}},"spot_finding_settings":{"type":"object","required":["enable","indexing","signal_to_noise_threshold","photon_count_threshold","max_pix_per_spot","min_pix_per_spot","quick_integration","high_resolution_limit_for_spot_count_low_res","ice_ring_width_q_recipA"],"properties":{"enable":{"type":"boolean","default":true,"description":"Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. \nEven if disabled spot finding information will still be send and written, though always with zero spots.\n"},"indexing":{"type":"boolean","default":true,"description":"Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.\n"},"signal_to_noise_threshold":{"type":"number","format":"float","minimum":0},"photon_count_threshold":{"type":"integer","format":"int64","minimum":0},"min_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"max_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"high_resolution_limit":{"type":"number","format":"float","description":"High resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding extends\nas far as the detector reaches, i.e. the detection is not clipped in resolution.\n"},"low_resolution_limit":{"type":"number","format":"float","description":"Low resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding is not\nclipped at the low-resolution end. A value of 0 is accepted and means the same thing.\n"},"high_resolution_limit_for_spot_count_low_res":{"type":"number","format":"float","description":"High resolution threshold to consider spot \"low resolution\" [Angstrom]","minimum":2,"maximum":8},"quick_integration":{"type":"boolean","default":false,"description":"Quick integration of Bragg spots in diffraction images.\nIf enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate.\n(experimental feature)\n"},"ice_ring_width_q_recipA":{"type":"number","format":"float","minimum":0,"maximum":1,"default":0.03,"description":"Half-width of the ice ring band in q (1/A). Matches the offline default in image_analysis/spot_finding/SpotFindingSettings.h, which was set from a measured ring FWHM of ~0.06; the two must agree or the same data gets a narrower ice band online."},"high_res_gap_Q_recipA":{"type":"number","format":"float","minimum":0.1,"maximum":5,"default":1.5,"description":"This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.\nIf there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter.\nThis option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.\n"},"adaptive_threshold":{"type":"boolean","default":false,"description":"Self-calibrating spot detection: replace the fixed photon_count_threshold by a per-resolution-ring\nthreshold derived from each image's own noise, so the same setting works across datasets without\nper-dataset tuning. photon_count_threshold is then ignored and false_pixels_per_frame sets the\noperating point instead.\nOnly available on detectors whose images are analysed in software (the DECTRIS/SIMPLON workflow).\nThe JUNGFRAU and EIGER workflows find spots on the FPGA, which applies its own fixed threshold,\nso enabling this there is rejected rather than silently ignored.\n"},"false_pixels_per_frame":{"type":"number","format":"float","minimum":1,"maximum":100000,"default":100,"description":"Operating point of the adaptive threshold: the number of noise pixels tolerated per frame.\nAbout 100 suits a multi-megapixel detector. Ignored unless adaptive_threshold is set.\n"}}},"azim_int_settings":{"type":"object","required":["solid_angle_corr","polarization_corr","low_q_recipA","q_spacing"],"properties":{"polarization_corr":{"type":"boolean","description":"Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)","default":true},"solid_angle_corr":{"type":"boolean","description":"Apply solid angle correction for azimuthal integration","default":true},"high_q_recipA":{"type":"number","minimum":0.00002,"maximum":10,"format":"float","description":"Upper q limit of the azimuthal integration [1/Angstrom]. Optional: if omitted, the integration\n(and the adaptive spot detection that shares these q bins) extends to the highest q the\ndetector reaches.\n"},"low_q_recipA":{"type":"number","format":"float","minimum":0.00001,"maximum":10},"q_spacing":{"type":"number","format":"float","minimum":0.00001},"azimuthal_bins":{"type":"integer","format":"int64","minimum":1,"maximum":512,"default":1,"description":"Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration"},"force_cpu":{"type":"boolean","default":false,"description":"Force CPU processing of azimuthal integration in the FPGA data acquisition workflow.\nThis allows to extend number of azimuthal integration bins, as well as to calculate standard deviation\nof the azimuthal integration results.\n"}}},"detector_list_element":{"type":"object","required":["id","nmodules","description","width","height","serial_number","base_ipv4_addr","udp_interface_count","readout_time_ns","min_frame_time_ns","min_count_time_ns"],"properties":{"id":{"type":"integer","format":"int64","minimum":0},"description":{"type":"string","example":"JUNGFRAU 4 Mpixel"},"serial_number":{"type":"string","example":"JF17T16V01"},"base_ipv4_addr":{"type":"string","example":"10.10.10.1"},"udp_interface_count":{"type":"integer","format":"int64","example":2,"description":"Number of UDP interfaces per detector module"},"nmodules":{"type":"integer","format":"int64","example":18},"width":{"type":"integer","format":"int64","example":2068},"height":{"type":"integer","format":"int64","example":2164},"pixel_size_mm":{"type":"number","format":"float","example":0.075},"readout_time_ns":{"type":"integer","format":"int64"},"min_frame_time_ns":{"type":"integer","format":"int64"},"min_count_time_ns":{"type":"integer","format":"int64"},"type":{"$ref":"#/components/schemas/detector_type"}}},"detector_list":{"type":"object","required":["detectors","current_id"],"properties":{"detectors":{"type":"array","items":{"$ref":"#/components/schemas/detector_list_element"}},"current_id":{"type":"integer","format":"int64","example":0}}},"detector_selection":{"type":"object","required":["id"],"properties":{"id":{"type":"integer","format":"int64","example":1}}},"measurement_statistics":{"type":"object","properties":{"file_prefix":{"type":"string"},"run_number":{"type":"integer","format":"int64","description":"Number of data collection run. This can be either automatically incremented or provided externally for each data collection.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number).\n"},"images_expected":{"type":"integer","format":"int64"},"images_collected":{"type":"integer","format":"int64","description":"Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.\n"},"images_sent":{"type":"integer","format":"int64","description":"Images sent to the writer. \nThe value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.\n"},"images_written":{"type":"integer","format":"int64","description":"Images successfully written to disk.\nThe value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.\n"},"images_discarded_lossy_compression":{"type":"integer","format":"int64","description":"Images discarded by the lossy compression filter"},"max_image_number_sent":{"type":"integer","format":"int64"},"collection_efficiency":{"type":"number","format":"float","example":1,"minimum":0,"maximum":1},"compression_ratio":{"type":"number","format":"float","example":5.3,"minimum":0},"cancelled":{"type":"boolean"},"max_receiver_delay":{"type":"integer","format":"int64"},"indexing_rate":{"type":"number","format":"float"},"detector_width":{"type":"integer","format":"int64"},"detector_height":{"type":"integer","format":"int64"},"detector_pixel_depth":{"type":"integer","format":"int64","enum":[2,4]},"bkg_estimate":{"type":"number","format":"float"},"unit_cell":{"type":"string"},"error_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of error pixels on the detector"},"saturated_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of saturated pixels on the detector"},"roi_beam_pixels":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor number of valid pixels within this ROI\n"},"roi_beam_sum":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor sum of valid pixels within this ROI\n"}}},"fpga_status":{"type":"array","items":{"type":"object","required":["pci_dev_id","serial_number","base_mac_addr","eth_link_status","eth_link_count","eth_link_speed","power_usage_W","fpga_temp_C","hbm_temp_C","packets_sls","packets_udp","idle","fw_version","pcie_link_speed","pcie_link_width"],"properties":{"pci_dev_id":{"type":"string"},"serial_number":{"type":"string"},"fw_version":{"type":"string"},"base_mac_addr":{"type":"string"},"eth_link_count":{"type":"integer","format":"int64"},"eth_link_status":{"type":"integer","format":"int64"},"power_usage_W":{"type":"number","format":"float"},"fpga_temp_C":{"type":"number","format":"float"},"hbm_temp_C":{"type":"number","format":"float"},"packets_udp":{"type":"integer","format":"int64"},"packets_sls":{"type":"integer","format":"int64"},"idle":{"type":"boolean"},"pcie_link_speed":{"type":"integer","format":"int64","description":"PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)"},"pcie_link_width":{"type":"integer","format":"int64","description":"PCIe link width (expected value is 8 == x8)"}}}},"broker_status":{"type":"object","required":["state"],"properties":{"state":{"type":"string","enum":["Inactive","Idle","Busy","Measuring","Pedestal","Error"]},"progress":{"type":"number","format":"float","description":"Progress of data collection (only available if receiving is running)","example":1,"minimum":0,"maximum":1},"message":{"type":"string","description":"Message to display besides state of the jfjoch_broker; mostly used for errors and warnings\nThis matters especially for async functions (start/initialize), where API won't return reason\nfor the error during async operation.\n"},"message_severity":{"type":"string","enum":["success","info","warning","error"],"default":"error","description":"Level of the message to display"},"gpu_count":{"type":"integer","format":"int32","description":"Number of installed GPUs"},"broker_version":{"type":"string","description":"Version of the jfjoch_broker","example":"1.0.0-rc.128"}}},"image_pusher_status":{"type":"object","required":["pusher_type","addr","connected_writers"],"description":"Informs about status of the image pusher.\n","properties":{"pusher_type":{"$ref":"#/components/schemas/image_pusher_type"},"addr":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"List of addresses of image pushers.\nFor HDF5 socket - no addresses will be returned.\nFor ZeroMQ - list of addresses for each socket will be provided.\nFor TCP/IP - single address to connect all writers will be provided.\n"},"connected_writers":{"type":"integer","format":"int64","minimum":0,"description":"Number of connected writers \nFor ZeroMQ image socket: number is constant\nFor TCP/IP image socket: number is updated live during operation\n"},"images_written":{"type":"integer","format":"int64","minimum":0,"description":"Number of images written to the image socket.\nThis number is updated live during operation for TCP/IP image socket and direct HDF5 writer.\nIt is updated at the end of experiment for ZeroMQ image socket.\n"},"images_write_error":{"type":"integer","format":"int64","minimum":0,"description":"Number of images that could not be written to the image socket.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"},"writer_fifo_utilization":{"type":"array","items":{"type":"integer","format":"int64","minimum":0},"description":"Utilization of internal writer FIFO.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"}}},"plot":{"type":"object","required":["x","y","title"],"description":"x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly","properties":{"title":{"type":"string","default":""},"x":{"type":"array","items":{"type":"number","format":"float"}},"y":{"type":"array","items":{"type":"number","format":"float","nullable":true}},"z":{"type":"array","items":{"type":"number","format":"float","nullable":true}}}},"plot_unit_x":{"type":"string","enum":["image_number","q_recipA","d_A","angle_deg","ADU","grid_um"],"default":"image_number"},"plots":{"type":"object","required":["plot","unit_x"],"properties":{"title":{"type":"string"},"unit_x":{"$ref":"#/components/schemas/plot_unit_x"},"size_x":{"type":"number","format":"float","description":"Max X range of the plot"},"size_y":{"type":"number","format":"float","description":"Max Y range of the plot"},"plot":{"type":"array","items":{"$ref":"#/components/schemas/plot"}}}},"scan_result":{"type":"object","description":"Results of a scan","required":["images"],"properties":{"file_prefix":{"type":"string"},"rotation_unit_cell":{"$ref":"#/components/schemas/unit_cell"},"rotation_crystal_lattice":{"$ref":"#/components/schemas/crystal_lattice"},"rotation_bravais":{"type":"string","description":"Bravais lattice type of the global rotation-indexing solution: crystal-system\nletter + centering, e.g. \"tP\", \"oC\", \"cF\", \"hR\", \"mP\". Empty if not determined.\n"},"images":{"type":"array","items":{"type":"object","required":["efficiency","number"],"properties":{"efficiency":{"type":"number","format":"float"},"number":{"type":"integer","format":"int64","description":"Detector image number for a given cell"},"nx":{"type":"integer","format":"int64","description":"Cell position in X for grid scan"},"ny":{"type":"integer","format":"int64","description":"Cell position in Y for grid scan"},"angle":{"type":"number","format":"float","description":"Rotation angle associated with the image"},"bkg":{"type":"number","format":"float","description":"Background estimate"},"spindle_blind":{"type":"number","format":"float","description":"Fraction (0-1) of a rotation sweep's blind double cone that this orientation makes unrecoverable, assuming the nearest plausible lattice row is a lone 2-fold (a worst-case bound, not an estimate). At 0.5 and above a recovery protocol (second sweep, reorientation) should engage. Absent means the frame could not be assessed, which automation must treat the same as above threshold - it is not a zero.\n"},"spots":{"type":"integer","format":"int64","description":"Spot count"},"spots_low_res":{"type":"integer","format":"int64","description":"Spot count in low resolution range"},"spots_indexed":{"type":"integer","format":"int64","description":"Spot count within indexing tolerance"},"spots_ice":{"type":"integer","format":"int64","description":"Spot count within common ice ring resolutions"},"ice":{"type":"number","format":"float","description":"Strongest hexagonal-ice ring intensity over the smooth radial background (1 = no ice)"},"index":{"type":"integer","format":"int64","description":"Indexing solution"},"latt_count":{"type":"integer","format":"int64","description":"Indexing lattice count"},"pr":{"type":"number","format":"float","description":"Profile radius, i.e. how far reflections are from the Ewald sphere"},"b":{"type":"number","format":"float","description":"B-Factor estimate"},"uc":{"$ref":"#/components/schemas/unit_cell"},"xfel_pulseid":{"type":"integer","format":"int64","description":"XFEL pulse ID"},"pixel_sum":{"type":"integer","format":"int64","description":"Total sum of all pixels"},"max":{"type":"integer","format":"int64","description":"Max viable pixel"},"sat":{"type":"integer","format":"int64","description":"Number of saturated pixels"},"err":{"type":"integer","format":"int64","description":"Number of error pixels"},"res":{"type":"number","format":"float","description":"Diffraction resolution estimate"}}}}}},"powder_calibration_fit_sigma":{"type":"object","description":"What the powder ring fit knows about its own answer, from the covariance of the converged\nproblem. Each sigma is in its parameter's own unit and is scaled by the residual scatter of\nthat fit, so it is the usual \"how far could this move before the fit got visibly worse\".\nThe two correlations are the ones that matter: a tilt and a beam-centre shift both displace a\nring's radius as cos(phi) and are told apart only by how that amplitude grows with the ring's\nradius, so as the rings run out the pair stops being separable and these approach 1.\nThe rotation sigmas and the correlations are absent when the tilt was not a free parameter.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI x [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI y [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Standard error of the fitted detector distance [mm]"},"poni_rot1_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot1 [rad]"},"poni_rot2_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot2 [rad]"},"correlation_beam_x_rot1":{"type":"number","format":"float","description":"Correlation between the fitted PONI x and rot1, -1 to 1"},"correlation_beam_y_rot2":{"type":"number","format":"float","description":"Correlation between the fitted PONI y and rot2, -1 to 1"}}},"powder_calibration_spot_check":{"type":"object","description":"Where the circle through the found spots puts the beam, and how far that is from the geometry\nactually fitted. An independent cross-check: it reads nothing from the file's own geometry, so\nit holds where the summed azimuthal profile does not - a profile binned about a badly wrong\ncentre shows each ring smeared across its sectors, and a fit on it converges on the wrong\nanswer without saying so. Two methods sharing no assumption, so the disagreement is the\nstatement. Absent when no spots were available.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Beam centre x the spots vote for [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Beam centre y the spots vote for [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Detector distance the spots imply [mm]"},"disagreement_pxl":{"type":"number","format":"float","description":"Distance between the spots' beam centre and the fitted one [pixels]"}}},"powder_calibration_quality":{"type":"object","description":"What a powder calibration knows about the geometry it produced. A calibration that has gone\nwrong - the wrong standard named, a header too far out for the rings to be found - looks\nexactly like one that has not until these are read.\n","properties":{"converged":{"type":"boolean","description":"Whether the geometry beside this is a measurement of the data at all. False means at least\none of its parameters was carried over from the input file rather than fitted - which looks\nexactly like a good fit in every other field here - and see not_converged_reason for which.\nrugnux --mode calibration writes no .poni file in that case, a PONI file having no field in\nwhich to say it, and exits non-zero.\n"},"not_converged_reason":{"type":"string","description":"What made converged false, in words. Absent when the calibration converged."},"calibrant":{"type":"string","description":"The powder standard the rings were fitted to, or the unit cell given in its place"},"method":{"type":"string","description":"How the rings were measured. rings fits the arcs of the run-summed (q x azimuth) azimuthal\nprofile; spots fits the pooled per-image spot lists.\n","enum":["rings","spots"]},"ring_points":{"type":"integer","format":"int64","description":"Ring measurements the fit used"},"rms_radial_pxl":{"type":"number","format":"float","description":"Scatter of those measurements about the fitted rings, as a radial distance [pixels]. The\nsingle number that separates a calibration that worked from one that did not.\n"},"beam_sigma_pxl":{"type":"number","format":"float","description":"Standard error the scatter implies on the beam centre [pixels], for a ring of that many\npoints. See powder_calibration_fit_sigma for what the fit itself says, which is not the same and\nis the larger of the two whenever the tilt is poorly separated.\n"},"direct_beam_x_pxl":{"type":"number","format":"float","description":"Where the direct beam lands [pixels]. NOT dataset_settings.beam_x_pxl, which is the PONI:\nthe two part company by distance*tan(tilt)/pixel as soon as the detector is tilted.\n"},"direct_beam_y_pxl":{"type":"number","format":"float","description":"Where the direct beam lands, y [pixels]"},"header_distance_mm":{"type":"number","format":"float","description":"The detector distance the input file declared, for comparison [mm]"},"ring_seed_distance_mm":{"type":"number","format":"float","description":"The distance measured from the ring radii before the fit ran [mm]. It is taken from the\nradii, the wavelength and the pixel size alone, so a large gap from header_distance_mm is\nthe answer to the question the calibration was run to ask. Absent when the profile showed\ntoo few rings to fix a scale.\n"},"tilt_refined":{"type":"boolean","description":"Whether the reported rot1/rot2 were measured by this fit. False means they were declined\nand pinned at the input file's values, because the rings could not separate a tilt from a\nshift of the beam centre.\n"},"tilt_significance":{"type":"number","format":"float","description":"How many of its own sigmas the fitted tilt stands from zero. Below about 3 it is not a\nmeasurement of a tilt but of a beam-centre shift, and the tilt is declined. Passing does\nnot certify a tilt: that estimator is limited by systematics rather than by this sigma.\n"},"fit_sigma":{"$ref":"#/components/schemas/powder_calibration_fit_sigma"},"spot_cross_check":{"$ref":"#/components/schemas/powder_calibration_spot_check"}}},"powder_calibration_output":{"type":"object","required":["dataset_settings"],"description":"The result of a powder-ring detector calibration - what rugnux --mode calibration writes as\n<prefix>.json, and what a calibration run over the image buffer would return.\n\ndataset_settings holds the geometry and nothing else, under the property names this API gives\nthem, so it can be POSTed or merged without translating a field. Its beam_x_pxl/beam_y_pxl is\nthe PONI, the foot of the perpendicular from the sample; where the beam actually lands is\ncalibration.direct_beam_x_pxl. The poni_rot*_rad are present whenever any of them is non-zero\nand absent when all are zero, since a body omitting them states a FLAT detector rather than an\nunstated one.\n","properties":{"dataset_settings":{"$ref":"#/components/schemas/dataset_settings"},"calibration":{"$ref":"#/components/schemas/powder_calibration_quality"},"jfjoch_version":{"type":"string","description":"Version of the program that produced this"}}},"calibration_statistics":{"type":"array","items":{"required":["module_number","storage_cell_number","pedestal_g0_mean","pedestal_g1_mean","pedestal_g2_mean","gain_g0_mean","gain_g1_mean","gain_g2_mean","masked_pixels"],"type":"object","properties":{"module_number":{"type":"integer","format":"int64"},"storage_cell_number":{"type":"integer","format":"int64"},"pedestal_g0_mean":{"type":"number","format":"float"},"pedestal_g1_mean":{"type":"number","format":"float"},"pedestal_g2_mean":{"type":"number","format":"float"},"gain_g0_mean":{"type":"number","format":"float"},"gain_g1_mean":{"type":"number","format":"float"},"gain_g2_mean":{"type":"number","format":"float"},"masked_pixels":{"type":"integer","format":"int64"}}}},"jfjoch_statistics":{"type":"object","description":"Pool statistics for Jungfraujoch to reduce transfers between frontend and jfjoch_broker","properties":{"detector":{"$ref":"#/components/schemas/detector_status"},"detector_list":{"$ref":"#/components/schemas/detector_list"},"detector_settings":{"$ref":"#/components/schemas/detector_settings"},"image_format_settings":{"$ref":"#/components/schemas/image_format_settings"},"instrument_metadata":{"$ref":"#/components/schemas/instrument_metadata"},"file_writer_settings":{"$ref":"#/components/schemas/file_writer_settings"},"data_processing_settings":{"$ref":"#/components/schemas/spot_finding_settings"},"measurement":{"$ref":"#/components/schemas/measurement_statistics"},"broker":{"$ref":"#/components/schemas/broker_status"},"fpga":{"$ref":"#/components/schemas/fpga_status"},"calibration":{"$ref":"#/components/schemas/calibration_statistics"},"zeromq_preview":{"$ref":"#/components/schemas/zeromq_preview_settings"},"zeromq_metadata":{"$ref":"#/components/schemas/zeromq_metadata_settings"},"dark_mask":{"$ref":"#/components/schemas/dark_mask_settings"},"pixel_mask":{"$ref":"#/components/schemas/pixel_mask_statistics"},"roi":{"$ref":"#/components/schemas/roi_definitions"},"az_int":{"$ref":"#/components/schemas/azim_int_settings"},"buffer":{"$ref":"#/components/schemas/image_buffer_status"},"indexing":{"$ref":"#/components/schemas/indexing_settings"},"bragg_integration":{"$ref":"#/components/schemas/bragg_integration_settings"},"image_pusher":{"$ref":"#/components/schemas/image_pusher_status"}}},"error_message":{"type":"object","required":["msg","reason"],"properties":{"msg":{"type":"string","description":"Human readable message","example":"Detector in wrong state"},"reason":{"type":"string","description":"Enumerate field for automated analysis","enum":["WrongDAQState","Other"]}}},"roi_azimuthal":{"type":"object","description":"ROI as Q-range (or resolution range), optionally restricted to an azimuthal-angle sector","required":["name","q_min_recipA","q_max_recipA"],"properties":{"name":{"type":"string","minLength":1,"description":"Name for the ROI; used in the plots"},"q_min_recipA":{"type":"number","format":"float","minimum":0.00001,"description":"Minimum Q-range for the ROI"},"q_max_recipA":{"type":"number","format":"float","minimum":0.00001,"description":"Maximum Q-range for the ROI"},"phi_min_deg":{"type":"number","format":"float","description":"Lower azimuthal-angle bound of the sector [degrees]. 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The frame rate is `(images_received - 1) / last_image_s`.\n","required":["state","message","images_expected","images_received","elapsed_s","steps","verdict","verdict_text","summary","warnings","probe","placed_model","anomalous_map"],"properties":{"state":{"type":"string","enum":["Idle","Running","Done","Failed","Cancelled","Skipped"]},"placed_model":{"type":"boolean","description":"The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from\n`/rugnux/map.ccp4`.\n"},"anomalous_map":{"type":"boolean","description":"The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map\n(`/rugnux/map.ccp4?type=anom`).\n"},"probe":{"type":"string","description":"Answer of the early lattice probe on the first 60 degrees; empty until it answers"},"probe_s":{"type":"number","format":"double","description":"When the probe answered, since the first image"},"start_to_first_image_s":{"type":"number","format":"double","description":"From the START message to the first image; set once the first image arrives"},"message":{"type":"string","description":"Why the run failed or was skipped"},"images_expected":{"type":"integer","format":"int64"},"expected_collection_s":{"type":"number","format":"double","description":"How long the collection is set up to take - images_expected times the image time; absent if not known"},"images_received":{"type":"integer","format":"int64"},"elapsed_s":{"type":"number","format":"double"},"step_progress":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"Fraction of the current pass's images"},"steps":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_live_step"}},"last_image_s":{"type":"number","format":"double","description":"When the last image arrived, since the first image; set once the collection is over"},"cut":{"type":"string","description":"Empty, or why the analysis was cut: `deadline` (`deadline_s` after the last image) or `cancel`\n(`POST /cancel`). The end message then carried what was established at the cut.\n"},"cut_s":{"type":"number","format":"double","description":"When the analysis was cut, since the first image"},"last_image_to_written_s":{"type":"number","format":"double","description":"From the last image received to all results written"},"verdict":{"type":"string","description":"OK, WARNINGS, UNUSABLE or FAILED; empty until the run is over"},"verdict_text":{"type":"string"},"summary":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_summary_row"}},"warnings":{"type":"array","items":{"type":"string"}}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\nIt also clears the image buffer, the previous collection's plots and live rugnux status, disables live rugnux analysis and removes the rugnux model.\nIt drops the previous dataset's bearer tokens and resets its settings, so nothing of that dataset stays readable.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\nOptional `tokens` protect the dataset: while set, its statistics, buffered images and plots\nrequire `Authorization: Bearer <token>`.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately.\nThe operation that finished either succeeded, was cancelled, or ended with a warning.\n"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code, or the operation that finished ended in an error -\nmissing packets, or a writer that could not write - see output message.\nA cancelled data collection is not an error.\n","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nWith rugnux live mode (`/config/rugnux`) the command also cuts the rugnux analysis, during the collection\nor after its last image alike: the collection ends with what the analysis has established\n(see `cut` in `/rugnux/status`). After the last image the collection itself is complete and is not\nmarked as cancelled.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/bragg_integration":{"put":{"summary":"Change Bragg integration settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get Bragg integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/rugnux":{"put":{"summary":"Change rugnux live mode settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get rugnux live mode settings and model status","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_status"}}}}}}},"/config/rugnux/model":{"put":{"summary":"Upload the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\nThe model (PDB or mmCIF, optionally gzipped; at most 64 MiB) is used for molecular replacement\nand validation of every following rugnux live collection, until it is removed with\n`DELETE /config/rugnux/model` or replaced by another upload.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Empty body, or not a model that can be read (PDB or mmCIF, optionally gzipped)"},"413":{"description":"Model larger than 64 MiB"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"delete":{"summary":"Remove the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"All good"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/rugnux/status":{"get":{"summary":"Get live rugnux processing status of the last collection","description":"Can be done anytime","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_live_status"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/rugnux/model.cif":{"get":{"summary":"Get the model as placed by the last rugnux live run","description":"The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the\n`_model.cif` file written beside the data: the data's cell and space group, with the input model's own\nmetadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.\n","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Placed model","content":{"chemical/x-mmcif":{"schema":{"type":"string","format":"binary"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model"}}}},"/rugnux/map.ccp4":{"get":{"summary":"Get an electron-density map of the last rugnux live run","description":"The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map\ncoefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where\nthe model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and\nRMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.\n","parameters":[{"in":"query","name":"type","required":false,"schema":{"type":"string","enum":["2fofc","fofc","anom"],"default":"2fofc"},"description":"`2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map,\n(F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map`\nin `/rugnux/status`)\n"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Map","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown map type","content":{"text/plain":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs"}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get settings for dark data collection to calculate mask","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}}}}},"/status":{"get":{"summary":"Get Jungfraujoch status","description":"Status of the data acquisition","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/broker_status"}}}}}}},"/fpga_status":{"get":{"summary":"Get status of FPGA devices","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/fpga_status"}}}}}}},"/xfel/pulse_id":{"get":{"summary":"Return XFEL pulse IDs for the current data acquisition","description":"Return array of XFEL pulse IDs - (-1) if image not recorded","responses":{"200":{"description":"Pulse ID collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/xfel/event_code":{"get":{"summary":"Return XFEL event codes for the current data acquisition","description":"Return array of XFEL event codes","responses":{"200":{"description":"Event codes collected","content":{"application/json":{"schema":{"type":"array","items":{"type":"integer","format":"int64"}}}}},"404":{"description":"Not in XFEL mode or no acquisition recorded"}}}},"/image_pusher/status":{"get":{"summary":"Get status of image pusher","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_pusher_status"}}}},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/detector/status":{"get":{"summary":"Get detector status","description":"Status of the JUNGFRAU detector","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_status"}}}},"404":{"description":"Running in \"simulator\" mode - no detector present"},"500":{"description":"Error encountered when trying to read status","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/roi":{"get":{"summary":"Get ROI definitions","responses":{"200":{"description":"OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}}}},"put":{"summary":"Upload ROI definitions","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/roi_definitions"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/statistics":{"get":{"summary":"Get general statistics","description":"`measurement` is omitted unless the request carries a valid bearer token for a protected\ndataset (see `tokens` in `/start`).\n","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/jfjoch_statistics"}}}}}}},"/statistics/data_collection":{"get":{"summary":"Get data collection statistics","description":"Results of the last data collection (dataset name, unit cell, ...)","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/measurement_statistics"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No data collection performed so far"}}}},"/statistics/calibration":{"get":{"summary":"Get calibration statistics","description":"Statistics are provided for each module/storage cell separately","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/calibration_statistics"}}}}}}},"/config/mask":{"get":{"summary":"Get mask of the detector (binary)","description":"Detector must be Initialized.\nGet full pixel mask of the detector.\nSee NXmx standard for meaning of pixel values.\n","responses":{"200":{"description":"Binary array (4 byte; unsigned)","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}}}}},"/config/user_mask":{"get":{"summary":"Detector must be Initialized.\nGet user mask of the detector (binary)\n","description":"Get user pixel mask of the detector in the actual detector coordinates: 0 - 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Special values: -1 - last image in the buffer, -2: last indexed image in the buffer"},"saturation":{"in":"query","name":"saturation","required":false,"schema":{"type":"number","format":"float","minimum":-32767,"maximum":32767},"description":"Saturation value to set contrast in the preview image; if not provided, then autocontrast procedure is used"},"background":{"in":"query","name":"background","required":false,"schema":{"type":"number","format":"float","default":0,"minimum":-32767,"maximum":32767},"description":"Background value to set contrast in the preview image"},"show_spots":{"in":"query","name":"show_spots","schema":{"type":"boolean","default":true},"description":"Show spot finding results on the image"},"show_predictions":{"in":"query","name":"show_predictions","schema":{"type":"boolean","default":false},"description":"Show Bragg spot predictions on the image (if available for the image)"},"show_beam_center":{"in":"query","name":"show_beam_center","schema":{"type":"boolean","default":true},"description":"Show beam center on the image"},"show_roi":{"in":"query","name":"show_roi","schema":{"type":"boolean","default":false},"description":"Show ROI areas on the image"},"jpeg_quality":{"in":"query","name":"jpeg_quality","description":"Quality of JPEG image (100 - highest; 0 - lowest)","schema":{"type":"integer","format":"int64","default":100,"minimum":0,"maximum":100}},"show_user_mask":{"in":"query","name":"show_user_mask","schema":{"type":"boolean","default":false},"description":"Show user mask"},"resolution_ring":{"in":"query","name":"show_res_ring","description":"Show resolution ring, provided in Angstrom","schema":{"type":"number","format":"float","default":0.1,"minimum":0.1,"maximum":100}},"resolution_estimate":{"in":"query","name":"show_res_est","description":"Show resolution estimation as a ring","schema":{"type":"boolean","default":false}},"color_scale":{"in":"query","name":"color","description":"Color scale for preview image","schema":{"type":"string","enum":["indigo","viridis","bw","wb","green","heat","magma","inferno"],"default":"indigo"}}},"schemas":{"grid_scan":{"description":"Definition of a grid scan. 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Can be negative. \nPositive number: top to bottom\nNegative number: bottom to top\n"},"vertical":{"type":"boolean","default":false,"description":"If disabled: fast direction = X, slow direction = Y\nIf enabled: fast direction = Y, slow direction = X\n"},"snake":{"type":"boolean","default":false,"description":"Flip fast direction for every second row\n"}}},"rotation_axis":{"description":"Definition of a crystal rotation axis","type":"object","required":["step","vector"],"properties":{"name":{"type":"string","default":"omega","minLength":1,"description":"Name of rotation axis (e.g., omega, phi)"},"step":{"type":"number","format":"float","example":0.1,"description":"Angle step (per image) in degrees. 0 for an axis that does not turn: the axis then\nrecords the angle the spindle stood at, which is how a grid scan or a set of stills\nstates its head position.\n"},"start":{"type":"number","format":"float","example":50,"description":"Start angle in degrees","default":0},"vector":{"type":"array","description":"Rotation axis","example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"helical_step_um":{"type":"array","description":"Translation (per image) for helical scan","example":[-5,-2,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"screening_wedge_deg":{"type":"number","format":"float","description":"Wedge angle value; used if rotation per image is smaller than increment between images (so particularly in screening)"}}},"indexing_algorithm":{"type":"string","description":"Selection of an indexing algorithm used by Jungfraujoch\n","enum":["FFBIDX","FFT","FFTW","Auto","None"],"default":"FFBIDX"},"geom_refinement_algorithm":{"type":"string","description":"Selection of an post-indexing least-square diffraction geometry refinement algorithm used by Jungfraujoch.\nBeamCenter - This option is refining both beam center and lattice (restricted to a chosen/detected Bravais lattice).\nOrientationOnly - This option is refining only orientation of the lattice.\nFlex - Tries all per-image refinements and keeps whichever indexes the most spots, letting the pipeline decide (the rugnux flex mode).\n","enum":["BeamCenter","OrientationOnly","Flex","None"]},"integration_model":{"type":"string","description":"Bragg spot integration model.\nProfileGaussian - profile fit with a measured-width Gaussian (Kabsch-style), the default; more\n  accurate intensities than box summation.\nProfileEmpirical - profile fit with a per-resolution-shell empirical profile learned from strong spots.\nBoxSum - classical uniform box summation minus a ring-mean background; the simpler, faster fallback.\n","enum":["ProfileGaussian","ProfileEmpirical","BoxSum"],"default":"ProfileGaussian"},"dataset_settings":{"type":"object","required":["beam_x_pxl","beam_y_pxl","detector_distance_mm","incident_energy_keV"],"properties":{"images_per_trigger":{"type":"integer","format":"int64","minimum":1,"default":1,"description":"For standard synchrotron data collection - this is number of images collected per one TTL trigger\nFor XFEL (pulsed source) - this number is ignored and set to 1\nFor storage cell mode - this number is ignored and set to number of storage cells\n"},"ntrigger":{"type":"integer","format":"int64","default":1,"minimum":1,"description":"Number of TTL trigger that the detector is expected to receive during data collection\n"},"image_time_us":{"type":"integer","format":"int64","minimum":0,"description":"Image time. \nIf not provided (or zero value) the frame time is assumed as default.\nFor JUNGFRAU image time must be multiple of frame time and max value is 256 * frame_time.            \nIn XFEL mode: summation happens for frames collected with multiple triggers.\nIgnored for storage cells and if raw data are saved.\n"},"beam_x_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_x in NXmx\nBeam center in X direction [pixels]\n"},"beam_y_pxl":{"type":"number","format":"float","description":"/entry/detector/beam_center_y in NXmx\nBeam center in X direction [pixels]\n"},"detector_distance_mm":{"type":"number","format":"float","minimum":0,"description":"/entry/detector/distance in NXmx Detector distance [mm]"},"incident_energy_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to calculate /entry/beam/incident_wavelength in NXmx\nIncident particle (photon, electron) energy in keV\n"},"file_prefix":{"type":"string","default":"","description":"Prefix for filenames. 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Currently used solely as metadata, not relevant for image processing done in Jungfraujoch."},"sample_name":{"type":"string","default":"","description":"/entry/sample/name in NXmx\nSample name\n"},"compression":{"type":"string","enum":["bslz4","bszstd","bszstd_rle","bszstd_rlehuf","none"],"default":"bslz4","description":"Compression type for the images transferred over ZeroMQ and saved to HDF5 file.\n"},"total_flux":{"type":"number","format":"float","description":"/entry/beam/total_flux in NXmx\nFlux incident on beam plane in photons per second. In other words this is the flux integrated over area. [photons/s]\n"},"transmission":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"/entry/instrument/attenuator/attenuator_transmission\nTransmission of attenuator (filter) [no units]\n"},"beam_size_x_um":{"type":"number","format":"float","minimum":0,"description":"First element of /entry/instrument/beam/incident_beam_size in NXmx\nHorizontal size of the X-ray beam where it meets the sample - the FWHM of a focused beam,\nthe full width of a slit-defined one. [um]\n"},"beam_size_y_um":{"type":"number","format":"float","minimum":0,"description":"Second element of /entry/instrument/beam/incident_beam_size in NXmx\nVertical size of the X-ray beam where it meets the sample. [um]\n"},"goniometer":{"$ref":"#/components/schemas/rotation_axis"},"grid_scan":{"$ref":"#/components/schemas/grid_scan"},"header_appendix":{"description":"Header appendix, added as user_data/user to start ZeroMQ message (can be any valid JSON)\nIn general, it is not saved in HDF5 file.\n\nHowever, if values are placed in \"hdf5\" object, `jfjoch_writer` will write them in /entry/user of the HDF5 file. \nThis applies solely to string and number (double floating-point). No arrays/sub-objects is allowed.\nFor example {\"hdf5\": {\"val1\":1, \"val2\":\"xyz\"}}, will write /entry/user/val1 and /entry/user/val2.\n"},"image_appendix":{"description":"Image appendix, added as user_data to image ZeroMQ message (can be any valid JSON)\nNot saved in HDF5 file\n"},"data_reduction_factor_serialmx":{"type":"number","format":"float","default":1,"minimum":0,"maximum":1,"description":"Rate at which non-indexed images are accepted to be forwarded to writer. \nValue of 1.0 (default) means that all images are written.\nValues below zero mean that non-indexed images will be accepted with a given probability.\n"},"pixel_value_low_threshold":{"type":"integer","format":"int64","minimum":0,"description":"Set all counts lower than the value to zero. \nWhen the value is set, negative numbers other than error pixel value are always set to zero.\nSetting to zero is equivalent to turning the option off.\n"},"run_number":{"type":"integer","format":"int64","minimum":0,"description":"Number of run within an experimental session. \nTransferred over CBOR stream as \"series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this number unique for each data collection during experimental series.\nIf not provided, the number will be automatically incremented.\n"},"run_name":{"type":"string","description":"Unique ID of run.\nTransferred over CBOR stream as \"unique series ID\", though not saved in HDF5 file.\nIt is highly recommended to keep this name unique for each data collection during experimental series.\nIf not provided, the name will be automatically generated as number + colon + file_prefix.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number). \nTransferred over CBOR stream, though not saved in HDF5 file.\n"},"poisson_compression":{"type":"integer","format":"int64","minimum":0,"maximum":16,"description":"Enable lossy compression of pixel values that preserves Poisson statistics. \nRequires to provide a numerical factor SQ.\nPixel value P will be transformed to round(sqrt(P) * SQ), with rounding to the closest integer.\nCompression is turned off if the value is missing or it is set to zero.\n"},"write_nxmx_hdf5_master":{"type":"boolean","default":true,"description":"Write NXmx formatted HDF5 master file. Recommended to use for macromolecular crystallography experiments\nand to turn off for other experiments.\n"},"save_calibration":{"type":"boolean","description":"Forward image calibration (at the moment pedestal and pedestal RMS for JUNGFRAU) using the ZeroMQ stream to writer.\nIf parameter is not provided calibration will be saved only if more than 4 images are recorded.\n"},"polarization_factor":{"type":"number","description":"Polarization factor for integration; 1.0 is horizontal polarization; -1.0 is vertical polarization","format":"float","minimum":-1,"maximum":1},"ring_current_mA":{"type":"number","format":"float","description":"Ring current at the beginning of the data collection","minimum":0},"sample_temperature_K":{"type":"number","format":"float","description":"Sample temperature in Kelvin","minimum":0},"poni_rot1_rad":{"type":"number","description":"PONI angle rot1 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot2_rad":{"type":"number","description":"PONI angle rot2 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"poni_rot3_rad":{"type":"number","description":"PONI angle rot3 (see PyFAI documentation for details) in radians","format":"float","minimum":-6.28318530718,"maximum":6.28318530718,"default":0},"unit_cell":{"$ref":"#/components/schemas/unit_cell"},"spot_finding":{"type":"boolean","description":"Enable spot finding and save spots","default":true},"smargon":{"type":"object","description":"Geometry of Smargon goniometer at SLS 2.0 / MX beamlines. \nAssuming that Smargon is used as static positioner and not moving during the scan, allowing to reconstruct geometry.\n","required":["phi_deg","chi_deg"],"properties":{"phi_deg":{"type":"number","format":"float","description":"Phi angle in degrees"},"chi_deg":{"type":"number","format":"float","description":"Chi angle in degrees"},"phi_axis":{"type":"array","description":"Phi rotation axis","default":[1,0,0],"example":[1,0,0],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3},"chi_axis":{"type":"array","description":"Chi rotation axis","default":[0,0,1],"example":[0,0,1],"items":{"type":"number","format":"float"},"minItems":3,"maxItems":3}}},"max_spot_count":{"type":"integer","minimum":10,"maximum":2000,"default":250,"description":"Maximum number of spots that are saved/used for indexing; spots with highest intensity are selected"},"detect_ice_rings":{"type":"boolean","description":"Flag spots as ice rings and reduce their effect on indexing"},"async_start":{"type":"boolean","default":false,"description":"When set to true, `/start` will not wait for detector and Jungfraujoch to be ready for the measurement."},"tokens":{"type":"array","items":{"type":"string","minLength":1},"writeOnly":true,"description":"Bearer tokens that protect this dataset: any number, all equivalent (e.g. a beamline\nsecret and a dataset-specific user secret). While set, the endpoints marked with the\n`bearerAuth` security scheme require `Authorization: Bearer <token>` and answer 401 otherwise.\nEvery accepted `/start` replaces the previous dataset's tokens; omitted or empty means no\nprotection. Never returned by any endpoint.\n"},"xray_fluorescence_spectrum":{"type":"object","required":["energy_eV","data"],"properties":{"energy_eV":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan energy for each measurement point"},"data":{"type":"array","items":{"type":"number","format":"float"},"description":"X-ray fluorescence scan result in arbitrary units; must be exactly the same length, as energy_eV"}}}}},"crystal_lattice":{"type":"array","items":{"type":"number","format":"float"},"minItems":9,"maxItems":9,"description":"Real-space crystal lattice 3D vectors in Angstrom.\nOrder is 1st vector (x,y,z), 2nd vector (x,y,z) and 3rd vector (x,y,z)\n"},"unit_cell":{"type":"object","description":"Unit cell parameters. Necessary to run indexing. Units of angstrom and degree","required":["a","b","c","alpha","beta","gamma"],"properties":{"a":{"type":"number","format":"float","example":37,"minimum":0},"b":{"type":"number","format":"float","example":37,"minimum":0},"c":{"type":"number","format":"float","example":78,"minimum":0},"alpha":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"beta":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360},"gamma":{"type":"number","format":"float","example":90,"minimum":0,"maximum":360}}},"file_writer_format":{"type":"string","enum":["NXmxOnlyData","NXmxLegacy","NXmxVDS","NXmxIntegrated","CBF","TIFF","NoFileWritten"],"default":"NXmxVDS","description":"NoFileWritten - no files are written at all\nNXmxOnlyData - only data files are written, no master file\nNXmxLegacy - legacy format with soft links to data files in the master file; necessary for DECTRIS Albula 4.0 and DECTRIS Neggia\nNXmxVDS - newer format with virtual dataset linking data files in the master file, also includes better metadata handling\nNXmxIntegrated - single HDF5 per dataset\nCBF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\nTIFF - DEPRECATED, no longer supported; kept for back compatibility only. Requests using this value are rejected. Only HDF5 formats are written.\n"},"file_writer_settings":{"type":"object","properties":{"overwrite":{"type":"boolean","default":false,"description":"Inform jfjoch_write to overwrite existing files. Otherwise files would be saved with .h5.{timestamp}.tmp suffix.\n"},"format":{"$ref":"#/components/schemas/file_writer_format"}}},"pixel_mask_statistics":{"type":"object","properties":{"user_mask":{"description":"Number of pixels masked using the user mask","type":"integer","format":"int64","minimum":0},"too_high_pedestal_rms":{"description":"Number of pixels with G0 pedestal RMS higher than provided threshold","type":"integer","format":"int64","minimum":0},"wrong_gain":{"description":"Number of pixels that show wrong gain level during the pedestal procedure","type":"integer","format":"int64","minimum":0}}},"image_buffer_status":{"type":"object","required":["image_numbers","total_slots","in_preparation_slots","in_sending_slots","available_slots","max_image_number","min_image_number"],"properties":{"min_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Smallest image number available in the buffer"},"max_image_number":{"type":"integer","format":"int64","minimum":0,"description":"Largest image number available in the buffer"},"image_numbers":{"type":"array","description":"Image numbers currently present in the buffer.","items":{"type":"integer","format":"int64"}},"total_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer. This number, compared to number of images in data collection and\nframe rate will determine \"retention\" rate of the image buffer.\n"},"available_slots":{"type":"integer","format":"int64","description":"Slots available for the data collection"},"in_preparation_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently in preparation for sending.\n"},"in_sending_slots":{"type":"integer","format":"int64","description":"Number of slots in the image buffer that are currently sending/writing data.\n"},"current_counter":{"type":"integer","format":"int64","description":"Counter of changes in the image buffer - either new start message or new image added.\nFor optimization one can only load new images/datasets from the HTTP if this value changes.\nCounter is optional as it was not implemented in older versions to avoid breaking change\n"}}},"image_format_settings":{"type":"object","required":["summation","jungfrau_conversion","geometry_transform","mask_chip_edges","mask_module_edges","apply_mask"],"properties":{"summation":{"type":"boolean","description":"Enable summation of images to a given image_time\nIf disabled images are saved according to original detector speed, but image count is adjusted\n"},"geometry_transform":{"type":"boolean","description":"Place module read-out into their location on composed detector and extend multipixels\n"},"jungfrau_conversion":{"type":"boolean","description":"Convert pixel value in ADU to photon counts/energy\nOnly affects JUNGFRAU detector\n"},"jungfrau_conversion_factor_keV":{"type":"number","format":"float","minimum":0.001,"maximum":500,"description":"Used to convert energy deposited into pixel to counts\nIf not provided incident_energy_keV is used\n"},"bit_depth_image":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of resulting image (it doesn't affect the detector read-out value)\nIf not provided value is adjusted automatically\n"},"signed_output":{"type":"boolean","description":"Controls if pixels have signed output\nIf not provided value is adjusted automatically\n"},"mask_module_edges":{"type":"boolean","default":true,"description":"Mask 1 pixel on the module boundary\n"},"mask_chip_edges":{"type":"boolean","default":true,"description":"Mask multipixels on chip boundary\n"},"jungfrau_mask_pixels_without_g0":{"type":"boolean","default":true,"description":"JUNGFRAU: mask pixels that don't operate in G0, but do operate in G1 and G1.\nThis should be turned off for cases, where detector is operated at room temperature with long exposure time.\n"},"apply_mask":{"type":"boolean","default":false,"description":"Masked pixels are set to special value in the images produced by Jungfraujoch\n"},"jungfrau_pedestal_g0_rms_limit":{"type":"integer","format":"int64","default":100,"minimum":0,"description":"Pixels with pedestal G0 RMS above the threshold are marked as masked pixels"}}},"detector_power_state":{"type":"string","description":"Power on of ASICs","enum":["PowerOn","PowerOff","Partial"]},"detector_state":{"type":"string","description":"Current state of the detector","enum":["Idle","Waiting","Busy","Error","Not connected"]},"detector_status":{"type":"object","required":["state","powerchip","server_version","number_of_triggers_left","fpga_temp_degC","high_voltage_V"],"properties":{"state":{"$ref":"#/components/schemas/detector_state"},"powerchip":{"$ref":"#/components/schemas/detector_power_state"},"server_version":{"type":"string","description":"Detector server (on read-out boards) version"},"number_of_triggers_left":{"type":"integer","format":"int64","description":"Remaining triggers to the detector (max of all modules)"},"fpga_temp_degC":{"type":"array","description":"Temperature of detector FPGAs","items":{"type":"integer","format":"int64"}},"high_voltage_V":{"type":"array","description":"High voltage for detector modules","items":{"type":"integer","format":"int64"}}}},"detector_timing":{"type":"string","enum":["auto","trigger","burst","gated"],"default":"trigger"},"detector_settings":{"type":"object","required":["frame_time_us"],"properties":{"frame_time_us":{"type":"integer","description":"Interval between consecutive frames.\nThis is internal frame time for the JUNGFRAU detector, image time has to be integer multiply of this number.\nFor EIGER detector this is default frame time, not used otherwise\n","format":"int64","minimum":1},"count_time_us":{"type":"integer","description":"Integration time of the detector. \nIf not provided count time will be set to maximum value for a given frame time.\n","format":"int64"},"internal_frame_generator":{"type":"boolean","default":false,"description":"Use internal frame generator in FPGA instead of getting data from a real detector"},"internal_frame_generator_images":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":64,"description":"Number of images stored in the internal frame generator."},"detector_trigger_delay_ns":{"type":"integer","format":"int64","minimum":0,"default":0,"description":"Delay between TTL trigger and acquisition start [ns]"},"timing":{"$ref":"#/components/schemas/detector_timing"},"eiger_threshold_keV":{"type":"number","format":"float","minimum":1,"maximum":100,"description":"Threshold for the PSI EIGER detector and all DECTRIS detectors.\nIf value is provided, it will be used for all subsequent acquisitions, irrespective of beam energy.\nIf value is not provided, threshold will be determined on start of acquisition as half of incident energy. \nThis might lead to increased start time.\n"},"eiger_bit_depth":{"type":"integer","format":"int64","enum":[8,16,32],"description":"Bit depth of PSI EIGER read-out. This is  \nIf value is not provided, depth will be determined based on the image time:\n* Exposure time < 500 microseconds depth of 8 bit will be used,\n* 500 <= exposure time < 2622 microseconds depth of 16 bit will be used\n* Exposure time >= 2622 microseconds depth of 32 bit will be used.\n"},"jungfrau_pedestal_g0_frames":{"type":"integer","format":"int64","default":2000,"minimum":0},"jungfrau_pedestal_g1_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_g2_frames":{"type":"integer","format":"int64","default":300,"minimum":0},"jungfrau_pedestal_min_image_count":{"type":"integer","format":"int64","default":128,"minimum":32,"description":"Minimum number of collected images for pedestal to consider it viable"},"jungfrau_storage_cell_count":{"type":"integer","format":"int64","default":1,"minimum":1,"maximum":16},"jungfrau_storage_cell_delay_ns":{"type":"integer","format":"int64","minimum":2100,"default":5000,"description":"Delay between two storage cells [ns]"},"jungfrau_fixed_gain_g1":{"type":"boolean","default":false,"description":"Fix gain to G1 (can be useful for storage cells)"},"jungfrau_use_gain_hg0":{"type":"boolean","default":false,"description":"Use high G0 (for low energy applications)"}}},"spot_finding_settings":{"type":"object","required":["enable","indexing","signal_to_noise_threshold","photon_count_threshold","max_pix_per_spot","min_pix_per_spot","quick_integration","high_resolution_limit_for_spot_count_low_res","ice_ring_width_q_recipA"],"properties":{"enable":{"type":"boolean","default":true,"description":"Enable spot finding. This is temporary setting, i.e. can be changed anytime during data collection. \nEven if disabled spot finding information will still be send and written, though always with zero spots.\n"},"indexing":{"type":"boolean","default":true,"description":"Enable indexing. This is temporary setting, i.e. can be changed anytime during data collection.\n"},"signal_to_noise_threshold":{"type":"number","format":"float","minimum":0},"photon_count_threshold":{"type":"integer","format":"int64","minimum":0},"min_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"max_pix_per_spot":{"type":"integer","format":"int64","minimum":1},"high_resolution_limit":{"type":"number","format":"float","description":"High resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding extends\nas far as the detector reaches, i.e. the detection is not clipped in resolution.\n"},"low_resolution_limit":{"type":"number","format":"float","description":"Low resolution limit for spot finding [Angstrom]. Optional: if omitted, spot finding is not\nclipped at the low-resolution end. A value of 0 is accepted and means the same thing.\n"},"high_resolution_limit_for_spot_count_low_res":{"type":"number","format":"float","description":"High resolution threshold to consider spot \"low resolution\" [Angstrom]","minimum":2,"maximum":8},"quick_integration":{"type":"boolean","default":false,"description":"Quick integration of Bragg spots in diffraction images.\nIf enabled it will likely reduce performance of Jungfraujoch for datasets with a very high indexing rate.\n(experimental feature)\n"},"ice_ring_width_q_recipA":{"type":"number","format":"float","minimum":0,"maximum":1,"default":0.03,"description":"Half-width of the ice ring band in q (1/A). Matches the offline default in image_analysis/spot_finding/SpotFindingSettings.h, which was set from a measured ring FWHM of ~0.06; the two must agree or the same data gets a narrower ice band online."},"high_res_gap_Q_recipA":{"type":"number","format":"float","minimum":0.1,"maximum":5,"default":1.5,"description":"This parameter is used to remove spurious spots at a very high resolution, that sometimes appear due to very low background close to the edge of the detector.\nIf there is a gap in (1/d)-space between spots of at least this size, spots on the side of the gap with high resolution will be discarded. This is optional parameter.\nThis option should be turned OFF for small molecule datasets or for crystals with very low mosaicity, when it is expected to see only few spots in any case.\n"},"adaptive_threshold":{"type":"boolean","default":false,"description":"Self-calibrating spot detection: replace the fixed photon_count_threshold by a per-resolution-ring\nthreshold derived from each image's own noise, so the same setting works across datasets without\nper-dataset tuning. photon_count_threshold is then ignored and false_pixels_per_frame sets the\noperating point instead.\nOnly available on detectors whose images are analysed in software (the DECTRIS/SIMPLON workflow).\nThe JUNGFRAU and EIGER workflows find spots on the FPGA, which applies its own fixed threshold,\nso enabling this there is rejected rather than silently ignored.\n"},"false_pixels_per_frame":{"type":"number","format":"float","minimum":1,"maximum":100000,"default":100,"description":"Operating point of the adaptive threshold: the number of noise pixels tolerated per frame.\nAbout 100 suits a multi-megapixel detector. Ignored unless adaptive_threshold is set.\n"}}},"azim_int_settings":{"type":"object","required":["solid_angle_corr","polarization_corr","low_q_recipA","q_spacing"],"properties":{"polarization_corr":{"type":"boolean","description":"Apply polarization correction for azimuthal integration (polarization factor must be configured in dataset settings)","default":true},"solid_angle_corr":{"type":"boolean","description":"Apply solid angle correction for azimuthal integration","default":true},"high_q_recipA":{"type":"number","minimum":0.00002,"maximum":10,"format":"float","description":"Upper q limit of the azimuthal integration [1/Angstrom]. Optional: if omitted, the integration\n(and the adaptive spot detection that shares these q bins) extends to the highest q the\ndetector reaches.\n"},"low_q_recipA":{"type":"number","format":"float","minimum":0.00001,"maximum":10},"q_spacing":{"type":"number","format":"float","minimum":0.00001},"azimuthal_bins":{"type":"integer","format":"int64","minimum":1,"maximum":512,"default":1,"description":"Numer of azimuthal (phi) bins; 1 = standard 1D azimuthal integration"},"force_cpu":{"type":"boolean","default":false,"description":"Force CPU processing of azimuthal integration in the FPGA data acquisition workflow.\nThis allows to extend number of azimuthal integration bins, as well as to calculate standard deviation\nof the azimuthal integration results.\n"}}},"detector_list_element":{"type":"object","required":["id","nmodules","description","width","height","serial_number","base_ipv4_addr","udp_interface_count","readout_time_ns","min_frame_time_ns","min_count_time_ns"],"properties":{"id":{"type":"integer","format":"int64","minimum":0},"description":{"type":"string","example":"JUNGFRAU 4 Mpixel"},"serial_number":{"type":"string","example":"JF17T16V01"},"base_ipv4_addr":{"type":"string","example":"10.10.10.1"},"udp_interface_count":{"type":"integer","format":"int64","example":2,"description":"Number of UDP interfaces per detector module"},"nmodules":{"type":"integer","format":"int64","example":18},"width":{"type":"integer","format":"int64","example":2068},"height":{"type":"integer","format":"int64","example":2164},"pixel_size_mm":{"type":"number","format":"float","example":0.075},"readout_time_ns":{"type":"integer","format":"int64"},"min_frame_time_ns":{"type":"integer","format":"int64"},"min_count_time_ns":{"type":"integer","format":"int64"},"type":{"$ref":"#/components/schemas/detector_type"}}},"detector_list":{"type":"object","required":["detectors","current_id"],"properties":{"detectors":{"type":"array","items":{"$ref":"#/components/schemas/detector_list_element"}},"current_id":{"type":"integer","format":"int64","example":0}}},"detector_selection":{"type":"object","required":["id"],"properties":{"id":{"type":"integer","format":"int64","example":1}}},"measurement_statistics":{"type":"object","properties":{"file_prefix":{"type":"string"},"run_number":{"type":"integer","format":"int64","description":"Number of data collection run. This can be either automatically incremented or provided externally for each data collection.\n"},"experiment_group":{"type":"string","description":"Name of group owning the data (e.g. p-group or proposal number).\n"},"images_expected":{"type":"integer","format":"int64"},"images_collected":{"type":"integer","format":"int64","description":"Images collected by the receiver. This number will be lower than images expected if there were issues with data collection performance.\n"},"images_sent":{"type":"integer","format":"int64","description":"Images sent to the writer. \nThe value does not include images discarded by lossy compression filter and images not forwarded due to full ZeroMQ queue.\n"},"images_written":{"type":"integer","format":"int64","description":"Images successfully written to disk.\nThe value is live updated for TCP/IP socket and direct HDF5 writer, while for ZeroMQ it is only updated at the end of experiment.\n"},"images_discarded_lossy_compression":{"type":"integer","format":"int64","description":"Images discarded by the lossy compression filter"},"max_image_number_sent":{"type":"integer","format":"int64"},"collection_efficiency":{"type":"number","format":"float","example":1,"minimum":0,"maximum":1},"compression_ratio":{"type":"number","format":"float","example":5.3,"minimum":0},"cancelled":{"type":"boolean"},"max_receiver_delay":{"type":"integer","format":"int64"},"indexing_rate":{"type":"number","format":"float"},"detector_width":{"type":"integer","format":"int64"},"detector_height":{"type":"integer","format":"int64"},"detector_pixel_depth":{"type":"integer","format":"int64","enum":[2,4]},"bkg_estimate":{"type":"number","format":"float"},"unit_cell":{"type":"string"},"error_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of error pixels on the detector"},"saturated_pixels":{"type":"number","format":"float","description":"Moving average of 1000 images counting number of saturated pixels on the detector"},"roi_beam_pixels":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor number of valid pixels within this ROI\n"},"roi_beam_sum":{"type":"number","format":"float","description":"If there is an ROI defined with name \"beam\", this number will hold moving average of 1000 images\nfor sum of valid pixels within this ROI\n"}}},"fpga_status":{"type":"array","items":{"type":"object","required":["pci_dev_id","serial_number","base_mac_addr","eth_link_status","eth_link_count","eth_link_speed","power_usage_W","fpga_temp_C","hbm_temp_C","packets_sls","packets_udp","idle","fw_version","pcie_link_speed","pcie_link_width"],"properties":{"pci_dev_id":{"type":"string"},"serial_number":{"type":"string"},"fw_version":{"type":"string"},"base_mac_addr":{"type":"string"},"eth_link_count":{"type":"integer","format":"int64"},"eth_link_status":{"type":"integer","format":"int64"},"power_usage_W":{"type":"number","format":"float"},"fpga_temp_C":{"type":"number","format":"float"},"hbm_temp_C":{"type":"number","format":"float"},"packets_udp":{"type":"integer","format":"int64"},"packets_sls":{"type":"integer","format":"int64"},"idle":{"type":"boolean"},"pcie_link_speed":{"type":"integer","format":"int64","description":"PCIe link speed measured by generation (expected value is 4 == PCIe Gen4)"},"pcie_link_width":{"type":"integer","format":"int64","description":"PCIe link width (expected value is 8 == x8)"}}}},"broker_status":{"type":"object","required":["state"],"properties":{"state":{"type":"string","enum":["Inactive","Idle","Busy","Measuring","Pedestal","Error"]},"progress":{"type":"number","format":"float","description":"Progress of data collection (only available if receiving is running)","example":1,"minimum":0,"maximum":1},"message":{"type":"string","description":"Message to display besides state of the jfjoch_broker; mostly used for errors and warnings\nThis matters especially for async functions (start/initialize), where API won't return reason\nfor the error during async operation.\n"},"message_severity":{"type":"string","enum":["success","info","warning","error"],"default":"error","description":"Level of the message to display"},"gpu_count":{"type":"integer","format":"int32","description":"Number of installed GPUs"},"broker_version":{"type":"string","description":"Version of the jfjoch_broker","example":"1.0.0-rc.128"}}},"image_pusher_status":{"type":"object","required":["pusher_type","addr","connected_writers"],"description":"Informs about status of the image pusher.\n","properties":{"pusher_type":{"$ref":"#/components/schemas/image_pusher_type"},"addr":{"type":"array","items":{"type":"string"},"example":["tcp://1.2.3.4:5000","tcp://1.2.3.4:5001"],"description":"List of addresses of image pushers.\nFor HDF5 socket - no addresses will be returned.\nFor ZeroMQ - list of addresses for each socket will be provided.\nFor TCP/IP - single address to connect all writers will be provided.\n"},"connected_writers":{"type":"integer","format":"int64","minimum":0,"description":"Number of connected writers \nFor ZeroMQ image socket: number is constant\nFor TCP/IP image socket: number is updated live during operation\n"},"images_written":{"type":"integer","format":"int64","minimum":0,"description":"Number of images written to the image socket.\nThis number is updated live during operation for TCP/IP image socket and direct HDF5 writer.\nIt is updated at the end of experiment for ZeroMQ image socket.\n"},"images_write_error":{"type":"integer","format":"int64","minimum":0,"description":"Number of images that could not be written to the image socket.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"},"writer_fifo_utilization":{"type":"array","items":{"type":"integer","format":"int64","minimum":0},"description":"Utilization of internal writer FIFO.\nThis number is updated live during operation for TCP/IP image socket.\nNo other socket use it.\n"}}},"plot":{"type":"object","required":["x","y","title"],"description":"x and y coordinates for plotting, it is OK to assume that both arrays have the same size; layout is optimized for Plotly","properties":{"title":{"type":"string","default":""},"x":{"type":"array","items":{"type":"number","format":"float"}},"y":{"type":"array","items":{"type":"number","format":"float","nullable":true}},"z":{"type":"array","items":{"type":"number","format":"float","nullable":true}}}},"plot_unit_x":{"type":"string","enum":["image_number","q_recipA","d_A","angle_deg","ADU","grid_um"],"default":"image_number"},"plots":{"type":"object","required":["plot","unit_x"],"properties":{"title":{"type":"string"},"unit_x":{"$ref":"#/components/schemas/plot_unit_x"},"size_x":{"type":"number","format":"float","description":"Max X range of the plot"},"size_y":{"type":"number","format":"float","description":"Max Y range of the plot"},"plot":{"type":"array","items":{"$ref":"#/components/schemas/plot"}}}},"scan_result":{"type":"object","description":"Results of a scan","required":["images"],"properties":{"file_prefix":{"type":"string"},"rotation_unit_cell":{"$ref":"#/components/schemas/unit_cell"},"rotation_crystal_lattice":{"$ref":"#/components/schemas/crystal_lattice"},"rotation_bravais":{"type":"string","description":"Bravais lattice type of the global rotation-indexing solution: crystal-system\nletter + centering, e.g. \"tP\", \"oC\", \"cF\", \"hR\", \"mP\". Empty if not determined.\n"},"images":{"type":"array","items":{"type":"object","required":["efficiency","number"],"properties":{"efficiency":{"type":"number","format":"float"},"number":{"type":"integer","format":"int64","description":"Detector image number for a given cell"},"nx":{"type":"integer","format":"int64","description":"Cell position in X for grid scan"},"ny":{"type":"integer","format":"int64","description":"Cell position in Y for grid scan"},"angle":{"type":"number","format":"float","description":"Rotation angle associated with the image"},"bkg":{"type":"number","format":"float","description":"Background estimate"},"spindle_blind":{"type":"number","format":"float","description":"Fraction (0-1) of a rotation sweep's blind double cone that this orientation makes unrecoverable, assuming the nearest plausible lattice row is a lone 2-fold (a worst-case bound, not an estimate). At 0.5 and above a recovery protocol (second sweep, reorientation) should engage. Absent means the frame could not be assessed, which automation must treat the same as above threshold - it is not a zero.\n"},"spots":{"type":"integer","format":"int64","description":"Spot count"},"spots_low_res":{"type":"integer","format":"int64","description":"Spot count in low resolution range"},"spots_indexed":{"type":"integer","format":"int64","description":"Spot count within indexing tolerance"},"spots_ice":{"type":"integer","format":"int64","description":"Spot count within common ice ring resolutions"},"ice":{"type":"number","format":"float","description":"Strongest hexagonal-ice ring intensity over the smooth radial background (1 = no ice)"},"index":{"type":"integer","format":"int64","description":"Indexing solution"},"latt_count":{"type":"integer","format":"int64","description":"Indexing lattice count"},"pr":{"type":"number","format":"float","description":"Profile radius, i.e. how far reflections are from the Ewald sphere"},"b":{"type":"number","format":"float","description":"B-Factor estimate"},"uc":{"$ref":"#/components/schemas/unit_cell"},"xfel_pulseid":{"type":"integer","format":"int64","description":"XFEL pulse ID"},"pixel_sum":{"type":"integer","format":"int64","description":"Total sum of all pixels"},"max":{"type":"integer","format":"int64","description":"Max viable pixel"},"sat":{"type":"integer","format":"int64","description":"Number of saturated pixels"},"err":{"type":"integer","format":"int64","description":"Number of error pixels"},"res":{"type":"number","format":"float","description":"Diffraction resolution estimate"}}}}}},"powder_calibration_fit_sigma":{"type":"object","description":"What the powder ring fit knows about its own answer, from the covariance of the converged\nproblem. Each sigma is in its parameter's own unit and is scaled by the residual scatter of\nthat fit, so it is the usual \"how far could this move before the fit got visibly worse\".\nThe two correlations are the ones that matter: a tilt and a beam-centre shift both displace a\nring's radius as cos(phi) and are told apart only by how that amplitude grows with the ring's\nradius, so as the rings run out the pair stops being separable and these approach 1.\nThe rotation sigmas and the correlations are absent when the tilt was not a free parameter.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI x [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Standard error of the fitted PONI y [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Standard error of the fitted detector distance [mm]"},"poni_rot1_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot1 [rad]"},"poni_rot2_rad":{"type":"number","format":"float","description":"Standard error of the fitted rot2 [rad]"},"correlation_beam_x_rot1":{"type":"number","format":"float","description":"Correlation between the fitted PONI x and rot1, -1 to 1"},"correlation_beam_y_rot2":{"type":"number","format":"float","description":"Correlation between the fitted PONI y and rot2, -1 to 1"}}},"powder_calibration_spot_check":{"type":"object","description":"Where the circle through the found spots puts the beam, and how far that is from the geometry\nactually fitted. An independent cross-check: it reads nothing from the file's own geometry, so\nit holds where the summed azimuthal profile does not - a profile binned about a badly wrong\ncentre shows each ring smeared across its sectors, and a fit on it converges on the wrong\nanswer without saying so. Two methods sharing no assumption, so the disagreement is the\nstatement. Absent when no spots were available.\n","properties":{"beam_x_pxl":{"type":"number","format":"float","description":"Beam centre x the spots vote for [pixels]"},"beam_y_pxl":{"type":"number","format":"float","description":"Beam centre y the spots vote for [pixels]"},"detector_distance_mm":{"type":"number","format":"float","description":"Detector distance the spots imply [mm]"},"disagreement_pxl":{"type":"number","format":"float","description":"Distance between the spots' beam centre and the fitted one [pixels]"}}},"powder_calibration_quality":{"type":"object","description":"What a powder calibration knows about the geometry it produced. A calibration that has gone\nwrong - the wrong standard named, a header too far out for the rings to be found - looks\nexactly like one that has not until these are read.\n","properties":{"converged":{"type":"boolean","description":"Whether the geometry beside this is a measurement of the data at all. False means at least\none of its parameters was carried over from the input file rather than fitted - which looks\nexactly like a good fit in every other field here - and see not_converged_reason for which.\nrugnux --mode calibration writes no .poni file in that case, a PONI file having no field in\nwhich to say it, and exits non-zero.\n"},"not_converged_reason":{"type":"string","description":"What made converged false, in words. Absent when the calibration converged."},"calibrant":{"type":"string","description":"The powder standard the rings were fitted to, or the unit cell given in its place"},"method":{"type":"string","description":"How the rings were measured. rings fits the arcs of the run-summed (q x azimuth) azimuthal\nprofile; spots fits the pooled per-image spot lists.\n","enum":["rings","spots"]},"ring_points":{"type":"integer","format":"int64","description":"Ring measurements the fit used"},"rms_radial_pxl":{"type":"number","format":"float","description":"Scatter of those measurements about the fitted rings, as a radial distance [pixels]. The\nsingle number that separates a calibration that worked from one that did not.\n"},"beam_sigma_pxl":{"type":"number","format":"float","description":"Standard error the scatter implies on the beam centre [pixels], for a ring of that many\npoints. See powder_calibration_fit_sigma for what the fit itself says, which is not the same and\nis the larger of the two whenever the tilt is poorly separated.\n"},"direct_beam_x_pxl":{"type":"number","format":"float","description":"Where the direct beam lands [pixels]. NOT dataset_settings.beam_x_pxl, which is the PONI:\nthe two part company by distance*tan(tilt)/pixel as soon as the detector is tilted.\n"},"direct_beam_y_pxl":{"type":"number","format":"float","description":"Where the direct beam lands, y [pixels]"},"header_distance_mm":{"type":"number","format":"float","description":"The detector distance the input file declared, for comparison [mm]"},"ring_seed_distance_mm":{"type":"number","format":"float","description":"The distance measured from the ring radii before the fit ran [mm]. It is taken from the\nradii, the wavelength and the pixel size alone, so a large gap from header_distance_mm is\nthe answer to the question the calibration was run to ask. Absent when the profile showed\ntoo few rings to fix a scale.\n"},"tilt_refined":{"type":"boolean","description":"Whether the reported rot1/rot2 were measured by this fit. False means they were declined\nand pinned at the input file's values, because the rings could not separate a tilt from a\nshift of the beam centre.\n"},"tilt_significance":{"type":"number","format":"float","description":"How many of its own sigmas the fitted tilt stands from zero. Below about 3 it is not a\nmeasurement of a tilt but of a beam-centre shift, and the tilt is declined. Passing does\nnot certify a tilt: that estimator is limited by systematics rather than by this sigma.\n"},"fit_sigma":{"$ref":"#/components/schemas/powder_calibration_fit_sigma"},"spot_cross_check":{"$ref":"#/components/schemas/powder_calibration_spot_check"}}},"powder_calibration_output":{"type":"object","required":["dataset_settings"],"description":"The result of a powder-ring detector calibration - what rugnux --mode calibration writes as\n<prefix>.json, and what a calibration run over the image buffer would return.\n\ndataset_settings holds the geometry and nothing else, under the property names this API gives\nthem, so it can be POSTed or merged without translating a field. Its beam_x_pxl/beam_y_pxl is\nthe PONI, the foot of the perpendicular from the sample; where the beam actually lands is\ncalibration.direct_beam_x_pxl. 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Set\nwhere a placed model was refined or its refinement failed; absent where the model was not placed or\nrefinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run's deadline\nor cancel can cut it.\n","required":["performed","cancelled","reason","on_gpu","seconds","blob_count","blobs"],"properties":{"performed":{"type":"boolean","description":"Refinement ran; false with `reason` where it failed"},"cancelled":{"type":"boolean","description":"The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the\nrest left out (cut before the first, the model is the placement's)\n"},"reason":{"type":"string","description":"Why refinement did not run to the end; empty otherwise"},"on_gpu":{"type":"boolean"},"seconds":{"type":"number","format":"double","description":"Wall time of the refinement"},"r_work":{"type":"number","format":"double","description":"R-work of the refined model (after the restrained stage, else after the rigid body and grouped B)"},"r_free":{"type":"number","format":"double","description":"R-free of the refined model, on the same reflections as `r_work`"},"rmsd_bonds_A":{"type":"number","format":"double","description":"RMS deviation of the bond lengths from the dictionary, where the restrained stage ran"},"rmsd_angles_deg":{"type":"number","format":"double","description":"RMS deviation of the bond angles from the dictionary, where the restrained stage ran"},"blob_count":{"type":"integer","format":"int64","description":"Unexplained blobs of the refined model's mFo-DFc map (above 3 sigma, peaking above 4)"},"blobs":{"type":"array","description":"The strongest blobs, at most 50, strongest first","items":{"$ref":"#/components/schemas/rugnux_live_blob"}}}},"rugnux_live_blob":{"type":"object","description":"A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on\nwhat is measured, to point a person at the density - not an identification.\n","required":["kind","x","y","z","peak_sigma","volume_A3","nearest_atom"],"properties":{"kind":{"type":"string","enum":["WATER","ION","LIGAND","MODEL_ERROR","UNASSIGNED"]},"x":{"type":"number","format":"double","description":"Centroid, Cartesian Angstrom, in the frame of the refined model (`/rugnux/model.cif`)"},"y":{"type":"number","format":"double"},"z":{"type":"number","format":"double"},"peak_sigma":{"type":"number","format":"double","description":"The highest point, in map sigma"},"volume_A3":{"type":"number","format":"double","description":"Volume above 3 sigma, in cubic Angstrom"},"nearest_atom":{"type":"string","description":"e.g. \"OG1 THR A42\""},"nearest_atom_distance_A":{"type":"number","format":"double","description":"Absent where no atom is within 12 Angstrom"}}},"rugnux_live_status":{"type":"object","description":"Live rugnux processing of the last collection; kept until the next collection starts or `POST /initialize`.\nTimes are taken when the image puller received a message, and are in seconds since the first image\n(before it arrives, since now). The frame rate is `(images_received - 1) / last_image_s`.\n","required":["state","message","images_expected","images_received","elapsed_s","steps","verdict","verdict_text","summary","warnings","probe","placed_model","refined_model","anomalous_map","anomalous_signal"],"properties":{"state":{"type":"string","enum":["Idle","Running","Done","Failed","Cancelled","Skipped"]},"placed_model":{"type":"boolean","description":"The run placed the model: it can be fetched from `/rugnux/model.cif` and its maps from\n`/rugnux/map.ccp4`.\n"},"refined_model":{"type":"boolean","description":"The run refined the placed model: `/rugnux/model.cif` and `/rugnux/map.ccp4` serve the refined model and\nits maps unless asked for `stage=placed`.\n"},"anomalous_map":{"type":"boolean","description":"The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map\n(`/rugnux/map.ccp4?type=anom`).\n"},"anomalous_signal":{"type":"boolean","description":"The merged data carry usable anomalous signal (the summary's \"Anomalous\" row says so)"},"model":{"$ref":"#/components/schemas/rugnux_live_model"},"space_group":{"type":"string","description":"Space group of the result (the summary's \"Space group\" row); absent until the run is over"},"d_min":{"type":"number","format":"double","description":"High-resolution limit of the merge, in Angstrom; absent until the run is over, or without a merge"},"isa":{"type":"number","format":"double","description":"ISa of the error model; absent until the run is over, or where it was not determined"},"probe":{"type":"string","description":"Answer of the early lattice probe on the first 60 degrees; empty until it answers"},"probe_s":{"type":"number","format":"double","description":"When the probe answered, since the first image"},"start_to_first_image_s":{"type":"number","format":"double","description":"From the START message to the first image; set once the first image arrives"},"message":{"type":"string","description":"Why the run failed or was skipped"},"images_expected":{"type":"integer","format":"int64"},"expected_collection_s":{"type":"number","format":"double","description":"How long the collection is set up to take - images_expected times the image time; absent if not known"},"images_received":{"type":"integer","format":"int64"},"elapsed_s":{"type":"number","format":"double"},"step_progress":{"type":"number","format":"float","minimum":0,"maximum":1,"description":"Fraction of the current pass's images"},"steps":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_live_step"}},"last_image_s":{"type":"number","format":"double","description":"When the last image arrived, since the first image; set once the collection is over"},"cut":{"type":"string","description":"Empty, or why the analysis was cut: `deadline` (`deadline_s` after the last image) or `cancel`\n(`POST /cancel`). The end message then carried what was established at the cut.\n"},"cut_s":{"type":"number","format":"double","description":"When the analysis was cut, since the first image"},"last_image_to_written_s":{"type":"number","format":"double","description":"From the last image received to all results written"},"verdict":{"type":"string","description":"OK, WARNINGS, UNUSABLE or FAILED; empty until the run is over"},"verdict_text":{"type":"string"},"summary":{"type":"array","items":{"$ref":"#/components/schemas/rugnux_summary_row"}},"warnings":{"type":"array","items":{"type":"string"}}}},"zeromq_metadata_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ metadata socket is enabled."},"period_ms":{"type":"integer","format":"int64","minimum":1,"default":1000,"description":"Period for generating metadata package sent to the ZeroMQ interface in milliseconds.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for image metadata information.\nImage metadata are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}},"zeromq_preview_settings":{"type":"object","required":["enabled","period_ms"],"properties":{"enabled":{"type":"boolean","default":true,"description":"ZeroMQ preview socket is enabled."},"period_ms":{"type":"integer","format":"int64","default":1000,"description":"Period for generating preview image sent to the ZeroMQ interface in milliseconds. Default is 1 second. \nIf set to zero, all images will be sent ZeroMQ (should be used only in case of relatively slow data collection).\nThis has no effect on HTTP based preview, which updates always at rate of 1 second.\n"},"socket_address":{"type":"string","description":"PUB ZeroMQ socket for preview images. This socket operates at a reduced frame rate.\nImages are serialized using CBOR.\nAddress follows ZeroMQ convention for sockets - in practice ipc://<socket file> and tcp://<IP address>:<port> sockets are OK.\n0.0.0.0 instead of IP address is accepted and means listening on all network interfaces.\n"}}}}},"paths":{"/initialize":{"post":{"summary":"Initialize detector and data acquisition","description":"Should be used in two cases:\n  - Detector is in `Inactive` state\n  - Detector is in `Error` state\nX-ray shutter must be closed. \nThis operation will reconfigure network interface of the detector. \nDuring operation of the detector it is recommended to use the `POST /pedestal` operation instead.\nIf storage cells are used, the execution time might be few minutes.\nIt also clears the image buffer, the previous collection's plots and live rugnux status, disables live rugnux analysis and removes the rugnux model.\nIt drops the previous dataset's bearer tokens and resets its settings, so nothing of that dataset stays readable.\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Initialization started"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/pedestal":{"post":{"summary":"Collect dark current for the detector","description":"Updates calibration of the JUNGFRAU detector. Must be in `Idle` state.\n\nX-ray shutter must be closed. Recommended to run once per hour for long integration times (> 100 us).\n\nThis is async function - one needs to use `POST /wait_till_done` to ensure operation is done.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/start":{"post":{"summary":"Start detector","description":"Start data acquisition.\nDetector must be in `Idle` state.\nDefault behavior is for the call to block until detector is ready to accept soft/TTL triggers.\nHowever, this behavior can be changed by settings `async_start` to true in the request body, \nin which case the call will return immediately and one needs to use `/wait_until_running` to ensure detector is ready to run.\nOptional `tokens` protect the dataset: while set, its statistics, buffered images and plots\nrequire `Authorization: Bearer <token>`.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dataset_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/wait_until_running":{"post":{"summary":"Wait for acquisition running","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till detector and Jungfraujoch are ready to collect data.\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Measuring` state"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/wait_till_done":{"post":{"summary":"Wait for acquisition done","parameters":[{"in":"query","name":"timeout","required":false,"schema":{"type":"integer","default":60,"minimum":0,"maximum":3600},"description":"Timeout in seconds (0 == immediate response)"}],"description":"Block execution of external script till initialization, data collection or pedestal is finished.\nRunning this command does not affect (cancel) running data collection, it is only to ensure synchronous execution of other software.\n\nTo not block web server for a indefinite period of time, the procedure is provided with a timeout.\nExtending timeout is possible, but requires to ensure safety that client will not close the connection and retry the connection.\n","responses":{"200":{"description":"Detector in `Idle` state, another data collection can start immediately.\nThe operation that finished either succeeded, was cancelled, or ended with a warning.\n"},"400":{"description":"Timeout parameter out of bounds"},"500":{"description":"Error within Jungfraujoch code, or the operation that finished ended in an error -\nmissing packets, or a writer that could not write - see output message.\nA cancelled data collection is not an error.\n","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}},"502":{"description":"Detector is inactive mode"},"504":{"description":"Timeout reached, need to restart operation"}}}},"/trigger":{"post":{"summary":"Send soft trigger to the detector","description":"Generate soft trigger","responses":{"200":{"description":"Trigger sent"}}}},"/cancel":{"post":{"summary":"Cancel running data collection","description":"Command will inform FPGA network card to stop pedestal or data collection at the current stage.\nAny frame that is currently being processed by CPU will be finished and sent to writer.\nGiven the command is making sure to gracefully stop data acquisition and detector, it might take some time to switch back after command finished to `Idle` state.\n\nWith rugnux live mode (`/config/rugnux`) the command also cuts the rugnux analysis, during the collection\nor after its last image alike: the collection ends with what the analysis has established\n(see `cut` in `/rugnux/status`). After the last image the collection itself is complete and is not\nmarked as cancelled.\n\nIf data collection is not running, the command has no effect.\n","responses":{"200":{"description":"Cancel request sent to FPGAs (or ignored, as data collection is not running)"}}}},"/deactivate":{"post":{"summary":"Prepare detector to turn off","description":"Should be in `Idle` or `Error` state.\nCommand deactivates data acquisition and turns off detector high voltage and ASIC.\nShould be used always before turning off power from the detector.\n","responses":{"200":{"description":"Detector ready to turn off"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/detector":{"put":{"summary":"Change detector configuration","description":"Detector settings are ones that have effect on calibration, i.e., pedestal has to be collected again after changing these settings.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\nIf detector is in `Idle` state , pedestal procedure will be executed automatically - there must be no X-rays on the detector during the operation.\nIf detector is in `Inactive` or `Error` states, new settings will be saved, but no calibration will be executed.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get detector configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_settings"}}}}}}},"/config/indexing":{"put":{"summary":"Change indexing algorithm settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get indexing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/indexing_settings"}}}}}}},"/config/bragg_integration":{"put":{"summary":"Change Bragg integration settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get Bragg integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/bragg_integration_settings"}}}}}}},"/config/file_writer":{"put":{"summary":"Change file writer settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get file writer settings","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/file_writer_settings"}}}}}}},"/config/instrument":{"put":{"summary":"Change instrument metadata","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get instrument metadata","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/instrument_metadata"}}}}}}},"/config/image_format":{"put":{"summary":"Change image output format","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get image output format","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/image_format_settings"}}}}}}},"/config/image_format/raw":{"post":{"summary":"Configure format for raw data collection","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/image_format/conversion":{"post":{"summary":"Configure format for data collection with full conversion","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"Everything OK"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/config/spot_finding":{"put":{"summary":"Configure spot finding","description":"Can be done anytime, also while data collection is running","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}},"get":{"summary":"Get data processing configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/spot_finding_settings"}}}}}}},"/config/azim_int":{"put":{"summary":"Configure azimuthal integration","description":"Can be done when detector is Inactive or Idle","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get azimuthal integration configuration","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/azim_int_settings"}}}}}}},"/config/internal_generator_image":{"put":{"summary":"Load binary image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires binary blob with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"name":"id","in":"query","description":"Image id to upload","required":false,"schema":{"type":"integer","format":"int64","minimum":0,"maximum":127}}],"requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/internal_generator_image.tiff":{"put":{"summary":"Load TIFF image for internal FPGA generator","description":"Load image for internal FPGA generator. This can only happen in Idle state of the detector.\nRequires TIFF with 16-bit integer numbers of size of detector in raw/converted coordinates \n(depending on detector settings).\n","parameters":[{"in":"query","name":"id","description":"Image ID to upload","required":false,"schema":{"type":"integer","minimum":0,"maximum":127}}],"requestBody":{"content":{"image/tiff":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}}}}},"/config/select_detector":{"put":{"summary":"Select detector","description":"Jungfraujoch allows to control multiple detectors and/or region-of-interests.\nThe command allows to choose one detector from the list (ID has to be consistent with one provided by GET response).\nChanging detector will set detector to `Inactive` state and will require reinitialization.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_selection"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"List available detectors","description":"Configured detectors that can be selected by used","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/detector_list"}}}}}}},"/config/rugnux":{"put":{"summary":"Change rugnux live mode settings","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get rugnux live mode settings and model status","description":"Can be done anytime","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_status"}}}}}}},"/config/rugnux/model":{"put":{"summary":"Upload the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\nThe model (PDB or mmCIF, optionally gzipped; at most 64 MiB) is used for molecular replacement\nand validation of every following rugnux live collection, until it is removed with\n`DELETE /config/rugnux/model` or replaced by another upload.\n","requestBody":{"content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"responses":{"200":{"description":"All good"},"400":{"description":"Empty body, or not a model that can be read (PDB or mmCIF, optionally gzipped)"},"413":{"description":"Model larger than 64 MiB"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"delete":{"summary":"Remove the model used by rugnux live mode","description":"This can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","responses":{"200":{"description":"All good"},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}}},"/rugnux/status":{"get":{"summary":"Get live rugnux processing status of the last collection","description":"Can be done anytime","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/rugnux_live_status"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}}}}},"/rugnux/model.cif":{"get":{"summary":"Get the model as placed by the last rugnux live run","description":"The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the\n`_model.cif` file written beside the data: the data's cell and space group, with the input model's own\nmetadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.\nWhere the run refined the model, the refined model unless asked for `stage=placed`.\n","parameters":[{"in":"query","name":"stage","required":false,"schema":{"type":"string","enum":["placed","refined"]},"description":"`placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).\nDefault: the refined model where there is one, otherwise the placed one.\n"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Placed model","content":{"chemical/x-mmcif":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown stage","content":{"text/plain":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model, or (`stage=refined`) refined none"}}}},"/rugnux/map.ccp4":{"get":{"summary":"Get an electron-density map of the last rugnux live run","description":"The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map\ncoefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where\nthe model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and\nRMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run\nrefined the model, the 2mFo-DFc and mFo-DFc maps are the refined model's unless asked for `stage=placed`;\nthe anomalous map stays on the placed model's phases.\n","parameters":[{"in":"query","name":"type","required":false,"schema":{"type":"string","enum":["2fofc","fofc","anom"],"default":"2fofc"},"description":"`2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map,\n(F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map`\nin `/rugnux/status`)\n"},{"in":"query","name":"stage","required":false,"schema":{"type":"string","enum":["placed","refined"]},"description":"`placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).\nDefault: the refined model where there is one, otherwise the placed one.\n"}],"security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Map","content":{"application/octet-stream":{"schema":{"type":"string","format":"binary"}}}},"400":{"description":"Unknown map type or stage","content":{"text/plain":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs, or (`stage=refined`) refined none"}}}},"/config/zeromq_preview":{"put":{"summary":"Set ZeroMQ preview settings","description":"Jungfraujoch can generate preview message stream on ZeroMQ SUB socket.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\nOptions set with this PUT request have no effect on HTTP based preview.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ preview settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_preview_settings"}}}}}}},"/config/zeromq_metadata":{"put":{"summary":"Set ZeroMQ metadata settings","description":"Jungfraujoch can generate metadata message stream on ZeroMQ PUB socket. This stream covers all images.\nHere settings of the socket can be adjusted.\nWhile the data structure contains also socket_address, this cannot be changed via HTTP and is ignore in PUT request.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - see output message.","content":{"application/json":{"schema":{"$ref":"#/components/schemas/error_message"}}}}}},"get":{"summary":"Get ZeroMQ metadata socket settings","responses":{"200":{"description":"Everything OK","content":{"application/json":{"schema":{"$ref":"#/components/schemas/zeromq_metadata_settings"}}}}}}},"/config/dark_mask":{"put":{"summary":"Set configuration for dark data collection to calculate mask","description":"This is only possible when operating DECTRIS detectors at the moment; it will be also available for PSI EIGER at some point.\nThis can only be done when detector is `Idle`, `Error` or `Inactive` states.\n","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/dark_mask_settings"}}}},"responses":{"200":{"description":"Everything OK"},"400":{"description":"Input parsing or validation error","content":{"text/plain":{"schema":{"type":"string","description":"Exception error"}}}},"500":{"description":"Error within Jungfraujoch code - 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Only one reader at a time. Events, each with a JSON `data` line:\n- `start` {run_number, run_name, file_prefix, number_of_images, images_per_file, cbor} - first,\n  once the start message is known: at once for a JUNGFRAU, when the detector sends its own for\n  a DECTRIS. `cbor` is the start message the writer of the master file received, CBOR in base64;\n  a reader builds the dataset from it;\n- `file` {file_number, file, first_image, image_count} - a data file closed and renamed into\n  place; `file` is relative to the collection's root, as the writer named it;\n- `end` {images, error?} - every writer acknowledged the end: the data files and the master\n  file are in place; `images` is the number of images collected. Also sent, with `error`, when\n  the measurement ends any other way - before the start message, for one. The stream then closes;\n- `superseded` {run_number} - a new collection began. The stream then closes.\nA comment line (`: keepalive`) every 10 s when nothing happens.\n","security":[{"bearerAuth":[]}],"responses":{"200":{"description":"Event stream","content":{"text/event-stream":{"schema":{"type":"string"}}}},"401":{"description":"The current dataset is protected and no valid bearer token was presented.","content":{"text/plain":{"schema":{"type":"string"}}}},"404":{"description":"No collection has started"},"409":{"description":"Another reader is following the collection, or the image pusher does not report closed data files"}}}},"/image_buffer/image.cbor":{"get":{"summary":"Get image message in CBOR format","description":"Contains full image data and metadata. 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
       var container = document.getElementById('redoc');
       Redoc.hydrate(__redoc_state, container);
diff --git a/common/JFJochMessages.h b/common/JFJochMessages.h
index e0da5f334..390707bd1 100644
--- a/common/JFJochMessages.h
+++ b/common/JFJochMessages.h
@@ -14,6 +14,7 @@
 #include <nlohmann/json.hpp>
 
 #include "CompressedImage.h"
+#include "StillsRunWidth.h"
 #include "SpotToSave.h"
 #include "UnitCell.h"
 #include "MtzTable.h"
@@ -405,6 +406,19 @@ struct PlacedModelMessage {
     std::string metadata_mmcif;
 };
 
+// The unexplained blobs of the refined model's mFo-DFc map (DensityBlob, image_analysis/structure_refinement/
+// DensityBlobs.h), strongest first, one vector per field, for the writer to write <prefix>_blobs.json. kind is
+// DensityBlobKindName's; centroid x, y, z in A (orthogonal), volume in A^3, score in sigma A^3.
+struct DensityBlobsMessage {
+    std::vector<std::string> kind;
+    std::vector<double> x, y, z;
+    std::vector<double> peak_sigma, volume, score;
+    std::vector<std::string> nearest_atom;
+    std::vector<double> nearest_atom_distance;
+    std::vector<int32_t> polar_contacts, metal_contacts;
+    std::vector<double> anomalous_sigma;
+};
+
 struct EndMessage {
     // The sample transformation chain, base first (see DetectorTransformation). Optional: when it is
     // empty the writer builds the same chain itself from the start message, so a producer that does
@@ -441,6 +455,10 @@ struct EndMessage {
     std::optional<CrystalLattice> rotation_lattice;
     std::vector<CrystalLattice> rotation_extra_lattices;
     std::optional<UnitCell> unit_cell;
+    // The e.s.d.s of unit_cell's six parameters, in its order (A and degrees; an angle the group fixes has
+    // zero), as the offline analysis measured them (CellEsd.h). Rotation only; absent where not measured.
+    // Written to /entry/sample/unit_cell_esd.
+    std::optional<UnitCell> unit_cell_esd;
     // Space group determined by the offline analysis (overrides the start message when writing the
     // master, since it is only known after merging). Both spellings are carried and a reader prefers
     // the name: only the name keeps the setting - "P 1 1 2" and "R 3:R" both come back from a number
@@ -455,6 +473,8 @@ struct EndMessage {
     // setting the merge works in - is only chosen afterwards, so the two settings are not always the
     // same one. Absent means they are, i.e. the identity.
     std::optional<std::array<int32_t, 9>> reindex_matrix;
+    // Stills: the rocking curve the partialities were computed from (and the frames predicted through).
+    std::optional<StillsRunWidth> stills_run_width;
 
     // Geometry refined by the offline analysis. When present these overwrite the master-file geometry
     // at finalization (rugnux writes the refined values; the broker leaves them empty and keeps the
@@ -524,6 +544,10 @@ struct EndMessage {
     std::optional<MtzTable> merged;             // MergedMtzTable (image_analysis/WriteReflections.h)
     std::optional<MtzTable> map_coefficients;   // ModelMaps::coefficients (ModelValidation.h)
     std::optional<PlacedModelMessage> placed_model;
+    // And of its refinement, where one ran: <file_prefix>_refined_model.cif, _refined_maps.mtz and _blobs.json.
+    std::optional<PlacedModelMessage> refined_model;
+    std::optional<MtzTable> refined_map_coefficients;
+    std::optional<DensityBlobsMessage> blobs;
 };
 
 struct MetadataMessage {
diff --git a/common/ScalingSettings.cpp b/common/ScalingSettings.cpp
index 2016afba5..8b70c6ac9 100644
--- a/common/ScalingSettings.cpp
+++ b/common/ScalingSettings.cpp
@@ -90,7 +90,7 @@ std::optional<double> ScalingSettings::GetRotationWedgeForScaling() const {
 }
 
 ScalingSettings &ScalingSettings::MinPartiality(double input) {
-    if (min_partiality < 0.0 || min_partiality > 1.0)
+    if (!(input >= 0.0 && input <= 1.0))
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Min partiality must be between 0 and 1");
     min_partiality = input;
     return *this;
diff --git a/common/ScalingSettings.h b/common/ScalingSettings.h
index 198c6366c..6e3d0b8e7 100644
--- a/common/ScalingSettings.h
+++ b/common/ScalingSettings.h
@@ -22,13 +22,12 @@ class ScalingSettings {
 
     bool merge_friedel = true;
     std::optional<double> high_resolution_limit_A;
-    // Low-resolution limit for scaling and merging. The beam-stop mask does not replace this: the stop
-    // suppresses air scatter well beyond the shadow it masks, so in the pixels the mask leaves open the
-    // background is measurably depressed - 30-44% of the field value on a real geometry, recovering to
-    // 95% of it only around d ~ 52 A. A background ring inside that zone over-estimates the background
-    // and the intensity comes out negative (74% negative past 50 A there, 2% just inside). The zone is
-    // set by the stop's angular size, so it tracks wavelength rather than detector distance, which is
-    // what makes a fixed d limit reasonable. 50 A is also XDS's own default when the input leaves it out.
+    // Low-resolution limit of the scale FIT. Reflections coarser than it are still merged and written -
+    // they are what maps and refinement want of the lowest resolutions - but are kept out of every fit
+    // of the scale model: on a large cell a few dozen of them, measured against a background the beam
+    // stop depresses, bent the model enough to move the merged 10-50 A intensities by tens of percent.
+    // Which coarse reflections are measured at all is the beam-stop mask's decision (a reflection whose
+    // signal disk reaches the shadow is not integrated, MXAnalysisWithoutFPGA). 50 A is XDS's default.
     std::optional<double> low_resolution_limit_A = 50.0;
     std::optional<double> wedge_for_scaling;
     std::optional<double> forced_mosaicity;   // diagnostic: fix the scaling mosaicity (deg) instead of the per-image seed
diff --git a/common/StillsRunWidth.h b/common/StillsRunWidth.h
new file mode 100644
index 000000000..41a27570c
--- /dev/null
+++ b/common/StillsRunWidth.h
@@ -0,0 +1,18 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <vector>
+
+// A stills run's rocking curve as measured by StillsPartialityRefine::MeasureRunWidth (see there): the
+// three-term width formula sigma^2 = gamma0^2 + (gamma_e d*)^2 + (bandwidth_sigma |q_z|)^2 (1/A, rad,
+// relative), the width measured in shells of d* (table_s at the shells' mean d*, 1/A; empty when too few
+// shells could be measured), and the radial scale of the reciprocal lattice the curve is centred on.
+// Carried in the EndMessage so the _process.h5 holds the curve its frames were predicted through and
+// --mode scale merges with it rather than measuring another.
+struct StillsRunWidth {
+    double gamma0 = 0.0, gamma_e = 0.0, bandwidth_sigma = 0.0;
+    double radial_scale = 1.0;
+    std::vector<double> table_dstar, table_s;
+};
diff --git a/docs/ACKNOWLEDGEMENT.md b/docs/ACKNOWLEDGEMENT.md
index 7238bb34f..064924338 100644
--- a/docs/ACKNOWLEDGEMENT.md
+++ b/docs/ACKNOWLEDGEMENT.md
@@ -367,6 +367,22 @@ S. C. Abrahams, H. D. Flack, E. Prince and A. J. C. Wilson, "Statistical descrip
 crystallography. II. Report of a Working Group on Expression of Uncertainty in Measurement" (1995),
 Acta Cryst. A51, 565-569 [doi:10.1107/S0108767395002340](https://doi.org/10.1107/S0108767395002340).
 
+**Unit-cell e.s.d.s** — that the e.s.d.s of a least-squares cell fit are too small, seeing only the
+scatter of the centroids, is Herbstein's survey; rugnux therefore also fits the cell on blocks of
+consecutive frames and writes the larger of the two estimates: F. H. Herbstein, "How precise are
+measurements of unit-cell dimensions from single crystals?" (2000), Acta Cryst. B56, 547-557
+[doi:10.1107/S010876810000269X](https://doi.org/10.1107/S010876810000269X).
+
+**Indexing ambiguity of serial data without a reference** — where a serial run's lattice is more
+symmetric than its crystals and no reference or model is given, each crystal is put into the indexing in
+which its intensities agree best with those of all the other crystals, crystal by crystal until none
+changes. The objective - the summed agreement between every pair of crystals - and the iteration that
+maximises it are taken from Brehm and Diederichs, whose method CrystFEL's `ambigator` also implements;
+rugnux measures the agreement as a product of standardised intensities rather than a correlation, which
+lets the sum over all partners be taken against one running sum instead of pair by pair.
+W. Brehm and K. Diederichs, "Breaking the indexing ambiguity in serial crystallography" (2014),
+Acta Cryst. D70, 101-109 [doi:10.1107/S1399004713025431](https://doi.org/10.1107/S1399004713025431).
+
 ### Physical corrections and calibration
 
 **Sensor absorption at oblique incidence, and the flight path** — the angle-dependent quantum
@@ -408,7 +424,11 @@ observed scale with an overall factor, an anisotropic B and a flat bulk-solvent
 model of A. Fokine and A. Urzhumtsev, "Flat bulk-solvent model: obtaining optimal parameters"
 (2002), Acta Cryst. D58, 1387-1392
 [doi:10.1107/S0907444902010284](https://doi.org/10.1107/S0907444902010284), which is also the source
-of the starting values and of the range those two parameters are physically meaningful over. The
+of the starting values and of the range those two parameters are physically meaningful over. The mask itself -
+the region a probe cannot reach from the atoms, shrunk back - is J.-S. Jiang and A. T. Brünger's, "Protein
+hydration observed by X-ray diffraction: solvation properties of penicillopepsin and neuraminidase crystal
+structures" (1994), J. Mol. Biol. 243, 100-115
+[doi:10.1006/jmbi.1994.1633](https://doi.org/10.1006/jmbi.1994.1633), drawn with the radii REFMAC5 uses. The
 procedure that fits them — a grid search over that range for the solvent pair, with the overall
 scale and the anisotropic B refitted at every grid point — follows P. V. Afonine,
 R. W. Grosse-Kunstleve and P. D. Adams, "A robust bulk-solvent correction and anisotropic scaling
@@ -508,6 +528,79 @@ molecular replacement; the error itself is AlphaFold's: J. Jumper, R. Evans, A.
 accurate protein structure prediction with AlphaFold" (2021), Nature 596, 583-589
 [doi:10.1038/s41586-021-03819-2](https://doi.org/10.1038/s41586-021-03819-2).
 
+**Structure refinement** (of a placed model) — the placed model is refined against the maximum-likelihood
+amplitude target, the Rice distribution of an observed amplitude given the model's (its centric
+counterpart for a centric reflection): N. S. Pannu and R. J. Read, "Improved structure refinement
+through maximum likelihood" (1996), Acta Cryst. A52, 659-668
+[doi:10.1107/S0108767396004370](https://doi.org/10.1107/S0108767396004370); G. N. Murshudov,
+A. A. Vagin and E. J. Dodson, "Refinement of macromolecular structures by the maximum-likelihood method"
+(1997), Acta Cryst. D53, 240-255 [doi:10.1107/S0907444996012255](https://doi.org/10.1107/S0907444996012255).
+Its two parameters are fitted by maximum likelihood in resolution bins - the variance on the free
+reflections, D on the working reflections with the measurement error added to that variance, which is how
+REFMAC5 divides them (Murshudov et al. 2011, above); the refined model's maps are weighted by the same D
+and figure of merit. Estimating the likelihood's parameters on free reflections follows V. Y. Lunin and T. P. Skovoroda, "R-free likelihood-based estimates of errors for phases
+calculated from atomic models" (1995), Acta Cryst. A51, 880-887
+[doi:10.1107/S010876739500688X](https://doi.org/10.1107/S010876739500688X); V. Y. Lunin, P. V. Afonine and
+A. G. Urzhumtsev, "Likelihood-based refinement. I. Irremovable model errors" (2002), Acta Cryst. A58,
+270-282 [doi:10.1107/S0108767302001046](https://doi.org/10.1107/S0108767302001046). The gradient with
+respect to every atom is taken by the FFT method - the derivatives of the target with respect to the
+structure factors transformed into a map and summed against each atom's density derivatives:
+R. C. Agarwal, "A new least-squares refinement technique based on the fast Fourier transform algorithm"
+(1978), Acta Cryst. A34, 791-809 [doi:10.1107/S0567739478001618](https://doi.org/10.1107/S0567739478001618).
+The positions and B factors are minimised by L-BFGS (rugnux's own, its memory kept from one macro-cycle to
+the next, the B factors' steps scaled by their estimated curvature): D. C. Liu and J. Nocedal, "On the limited
+memory BFGS method for large scale optimization" (1989), Math. Program. 45, 503-528
+[doi:10.1007/BF01589116](https://doi.org/10.1007/BF01589116), whose two-loop recursion is J. Nocedal's, "Updating
+quasi-Newton matrices with limited storage" (1980), Math. Comp. 35, 773-782
+[doi:10.1090/S0025-5718-1980-0572855-7](https://doi.org/10.1090/S0025-5718-1980-0572855-7). The geometry restraints are those of the CCP4
+Monomer Library, a subset of which rugnux carries (see THIRD_PARTY_NOTICES.md): A. A. Vagin,
+R. A. Steiner, A. A. Lebedev, L. Potterton, S. McNicholas, F. Long and G. N. Murshudov, "REFMAC5
+dictionary: organization of prior chemical knowledge and guidelines for its use" (2004), Acta Cryst. D60,
+2184-2195 [doi:10.1107/S0907444904023510](https://doi.org/10.1107/S0907444904023510); applied to the model
+through GEMMI's topology (links, modifications, planes, chiral volumes, torsions): M. Wojdyr, "GEMMI: A
+library for structural biology" (2022), J. Open Source Softw. 7, 4200
+[doi:10.21105/joss.04200](https://doi.org/10.21105/joss.04200). The torsion derivatives follow
+A. Blondel and M. Karplus, "New formulation for derivatives of torsion angles and improper torsion angles
+in molecular mechanics: elimination of singularities" (1996), J. Comput. Chem. 17, 1132-1141
+[doi:10.1002/(SICI)1096-987X(19960715)17:9<1132::AID-JCC5>3.0.CO;2-T](https://doi.org/10.1002/(SICI)1096-987X(19960715)17:9%3C1132::AID-JCC5%3E3.0.CO;2-T).
+The B factors of bonded atoms, and of atoms in contact, are restrained to each other in the
+Kullback-Leibler form REFMAC5 uses, whose tolerance grows with B (Murshudov et al. 2011, above; the divergence itself
+is S. Kullback and R. A. Leibler's, "On information and sufficiency" (1951), Ann. Math. Statist. 22, 79-86
+[doi:10.1214/aoms/1177729694](https://doi.org/10.1214/aoms/1177729694)), and the
+overall isotropic B of the scale is moved into the atoms as phenix.refine moves it (Afonine et al. 2012,
+below). The weights of the X-ray term against the geometry and against the B restraints start from the
+ratios of the gradients, as X-PLOR's crystallographic weight was first set: A. T. Brünger, M. Karplus and
+G. A. Petsko, "Crystallographic refinement by simulated annealing: application to crambin" (1989), Acta Cryst.
+A45, 50-61 [doi:10.1107/S0108767388009195](https://doi.org/10.1107/S0108767388009195); and they are chosen
+among short refinements by R-free with the geometry held within bounds, as phenix.refine chooses them: P. V. Afonine, R. W. Grosse-Kunstleve, N. Echols, J. J. Headd,
+N. W. Moriarty, M. Mustyakimov, T. C. Terwilliger, A. Urzhumtsev, P. H. Zwart and P. D. Adams,
+"Towards automated crystallographic structure refinement with phenix.refine" (2012), Acta Cryst. D68,
+352-367 [doi:10.1107/S0907444912001308](https://doi.org/10.1107/S0907444912001308). R-free itself:
+A. T. Brünger, "Free R value: a novel statistical quantity for assessing the accuracy of crystal
+structures" (1992), Nature 355, 472-475 [doi:10.1038/355472a0](https://doi.org/10.1038/355472a0).
+The model the refinement scores is scaled to the data with the overall scale and anisotropic B fitted by
+robust least squares - iteratively reweighted, with the pseudo-Huber weight of each reflection's residual -
+so that a few reflections the model cannot explain do not set the scale of the rest: P. J. Huber, "Robust
+estimation of a location parameter" (1964), Ann. Math. Statist. 35, 73-101
+[doi:10.1214/aoms/1177703732](https://doi.org/10.1214/aoms/1177703732), in the smooth (pseudo-Huber) form of
+P. Charbonnier, L. Blanc-Féraud, G. Aubert and M. Barlaud, "Deterministic edge-preserving regularization in
+computed imaging" (1997), IEEE Trans. Image Process. 6, 298-311
+[doi:10.1109/83.551699](https://doi.org/10.1109/83.551699).
+The bonds of metal ions to their donor atoms that the model's LINK records name are restrained at the
+distances of the Monomer Library's own statistics of metal sites (its `metals.json`, embedded as
+`monomers/metals.cif`; per metal, donor element and coordination number), in line with the surveys of
+M. M. Harding, "Geometry of metal-ligand interactions in proteins" (2001), Acta Cryst. D57, 401-411
+[doi:10.1107/S0907444900019168](https://doi.org/10.1107/S0907444900019168) and "Small revisions to
+predicted distances around metal sites in proteins" (2006), Acta Cryst. D62, 678-682
+[doi:10.1107/S0907444906014594](https://doi.org/10.1107/S0907444906014594), and, for Mg²⁺, Na⁺ and K⁺ at
+nucleic acids, F. Leonarski, L. D'Ascenzo and P. Auffinger, "Mg2+ ions: do they bind to nucleobase
+nitrogens?" (2017), Nucleic Acids Res. 45, 987-1004 [doi:10.1093/nar/gkw1175](https://doi.org/10.1093/nar/gkw1175).
+
+**Unmodelled density** — the blobs the refinement lists are the connected regions of the difference map above
+a cutoff, found by flood fill as Coot's "unmodelled blobs" finds them, in GEMMI's implementation
+(`find_blobs_by_flood_fill`): P. Emsley, B. Lohkamp, W. G. Scott and K. Cowtan, "Features and development
+of Coot" (2010), Acta Cryst. D66, 486-501 [doi:10.1107/S0907444910007493](https://doi.org/10.1107/S0907444910007493).
+
 ## Software and computing methods
 
 Decoding bitshuffle+LZ4 images on the GPU, rather than decompressing them on the host and uploading
diff --git a/docs/BATTERY_REPORT.md b/docs/BATTERY_REPORT.md
deleted file mode 100644
index 8acf0356f..000000000
--- a/docs/BATTERY_REPORT.md
+++ /dev/null
@@ -1,915 +0,0 @@
-# Rugnux battery - 20261009-1447_0b2dde_rc175-0b2dde2-full
-
-- rugnux 1.0.0-rc.175, sha256 8899fb310c03234f, build flags: Release CXX_FLAGS='-march=x86-64-v3' CUDA=ON
-- runner 0b2dde214, host mpc2898.psi.ch, 2026-10-09T14:47:18 -> 2026-10-09T16:14:38
-- hardware: AMD Ryzen 9 5950X 16-Core Processor, 3.40 GHz nominal (acpi_cppc), 5.08 GHz max boost, 16C/32T, 1 socket(s), 125 GiB RAM, GPU: NVIDIA GeForce RTX 5080 (16303 MiB)
-- arms: open, inhouse; 250 sets (full arm)
-- timing: GPU was not shared during the run
-- command options: (none beyond output selection)
-- command, open arm: `rugnux --model <deposited coordinates> <input>` (without --model where there is no deposited model: small molecules, unpublished sets)
-- command, inhouse arm: `rugnux --report-resolution <XDS d_min>,<XDS d_max> [--model <reference model>] <input>`: the second statistics table at XDS's range is report-only; where XDS kept Friedel mates apart the scorer reads the run's own per-hand table, which needs no flag. --model where the set names a PDB entry of its crystal form (the standard proteins)
-
-## Commentary
-
-This is the validation battery of the rc.175 branch at `0b2dde214`, the pushed state of rc.175,
-built with the CI flags and run once per set, against the battery of 7 October at `9ced4c444`
-(20261007-2139_9ced4c_rc175-p1-baseline) as baseline. Between the two, rotation processing takes the
-decisions made before pass 2 from the first part of the sweep, with a geometry pre-pass of at least
-120 deg, so that a sweep can be processed while it is still being collected; the first pass gained
-several fixes (deciding whether there is a lattice at all on the no-crystal controls, the index-2
-sub-lattices of the standing cell offered as hypotheses, the axis-harmonic arbiter testing the larger
-cell against its own sub-lattice, the long-axis rescue tried at both beam centres, and a wedge from
-the end of the first part as a last resort); model validation runs on the GPU; and a GPU
-out-of-memory failure in scaling was fixed. Verdicts are scored by the current scorer, which now
-passes a space group that the data cannot tell apart from the reference. The REFMAC model check was
-not run again: the R-free figure is that of the rc.174 battery (20261005-2102_3770f4_rc174-final-refmac).
-The private arm ran too; as always, only its aggregate is stated here: 23 pass, 2 fail, 2 not
-scored, with one verdict changed in each direction.
-
-- **Verdicts.** Open arm 187 pass / 13 fail / 3 not scored over 203 sets, in-house 46 / 1 over 47.
-  Two sets that passed now fail; both are accepted losses of taking the decisions from the first
-  part of the sweep: 5ky6 calls P2 instead of P2_1 (the screw axis), and the in-house
-  insu_I_x06da_low_isa, a cubic insulin set of low ISa, is indexed on a rhombohedral cell of twice the
-  primitive volume. KDP, scored against I-42d while Rugnux reports I4_1md, now passes as an
-  indistinguishable alternative: the two groups have the same absences and the intensities cannot
-  tell them apart. Every other verdict is as before; 6p8j still fails, now on a screw axis
-  (P112) rather than on too high a point group.
-- **Quality.** Five sets are clearly worse: 9qw8 (ISa 9.6 to 5.2, R_meas 20 to 27 %), 9qw2 (d_min
-  1.74 to 1.82 A), lyso_x06da_half_image (ISa 6.9 to 4.4), insu_I_x06da_low_isa (the wrong lattice
-  above) and myob_x06da_powder_2, which keeps its 1.47 A cut but with CC1/2 0.92 to 0.78 and R_free
-  0.48 to 0.50. Five are clearly better: 8qq7 (R_free 0.431 to 0.408), 8r5r (d_min 2.89 to 2.79 A,
-  ISa 15 to 19), 9yzk (ISa 7.1 to 8.8), 7bgu (ISa 10 to 16, R_free 0.303 to 0.266) and
-  myob_x06da_split, whose runaway cut of the 10-07 report is gone (1.21 to 1.86 A, R_meas 289 to
-  78 %, R_free 0.484 to 0.402). 5jk4, the other set the 10-07 report flagged, is back to an overall
-  CC1/2 of 0.998 at 0.96 A. R_free here is Rugnux's own placement-only number, a trend within a run.
-- **Resolution.** Rugnux's own cut is finer than the deposited one on 173 of 183 structures. The
-  median change of d_min from 10-07 is zero; the largest moves are finer on 6yqf and 8r5r and
-  coarser on 3meb, 8qj5, 6oww and 6p8j, besides the in-house sets above.
-- **R-free.** From the rc.174 battery: the deposited model refined by REFMAC against Rugnux's data
-  comes within 0.05 of the same refinement against the depositor's data on 174 of 182 structures.
-- **Processing time.** The whole battery took 4898 s of processing against 5795 s on 10-07; the
-  open arm 4424 s against 5263 s (median 18.3 s against 21.0 s), the in-house arm 474 s against
-  532 s (median 8.9 s against 10.6 s); the median over all 250 sets is 16 s. Most of the gain is
-  model validation, which the battery runs only because of `--model` and which now runs on the
-  GPU: 278 s in total against 1024 s. Without model validation the HDF5 sets took 1598 s against
-  1618 s (median 12.2 s against 11.6 s), so the processing itself is at the same speed. The slowest
-  sets are 8qaw (109 s), 9gdj (99 s) and 8tyy (84 s); in house, lyso_x10sa_strong (29 s). No set
-  shared the GPU.
-- **Small molecules.** SHELXL R1 against the published structures: aspirin 0.036-0.037, citric acid
-  0.039, HEPES 0.031 and KDP 0.048; YAG (0.101) and L-cystine (0.11-0.13) remain the weak cases.
-
-![Processing time of every open and in-house set](images/battery_time.png)
-
-![The same, over the first 60 s](images/battery_time_zoom.png)
-
-![Processing time of the in-house sets, over the first 60 s](images/battery_time_inhouse.png)
-
-![R-free of the deposited model refined against the depositor's data and against Rugnux's data (rc.174 battery)](images/battery_rfree.png)
-
-![High-resolution limit: deposition against Rugnux](images/battery_dmin.png)
-
-## Summary
-
-| arm | sets | pass | of which alt | fail | unscored | not run | pass rate | median res. gain | median ISa | median R_meas | median time s | total time min |
-|:--|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|
-| open | 203 | 187 | 4 | 13 | 3 | 0 | 187/200 (94%) | +11.9% | 13.5 | 14.0% | 18 | 73.7 |
-| inhouse | 47 | 46 | 0 | 1 | 0 | 0 | 46/47 (98%) | +6.2% | 22.6 | 9.5% | 9 | 7.9 |
-
-_Plot in report.html: verdicts per arm_
-
-Pass rate is over the scored sets (pass + fail). `of which alt` counts the passes that are already in `pass`: rows where the answer matched an accepted alternative reference rather than the deposition, listed under Accepted alternatives below. In the bar chart they are drawn as their own segment. Every number in this table is rugnux's own run at its own resolution cut: what a user gets. Resolution gain is (reference d_min - our d_min) / reference d_min: positive = finer than the deposition, or than XDS. Medians leave out the no-crystal controls. R_meas and CC1/2 are pooled over each run's own resolution range, so they describe a run and do not rank two; the like-for-like comparison with XDS is the reference-range table below. Each set runs once, so every time includes reading its images from disk (unless they were still in the page cache from before the run).
-
-### By population
-
-| arm | population | sets | pass rate | median res. gain |
-|:--|:--|--:|:--|--:|
-| open | SMV | 2 | 2/2 (100%) | +11.3% |
-| open | cbf | 97 | 90/95 (95%) | +11.7% |
-| open | cdte | 3 | 3/3 (100%) | +5.0% |
-| open | cubic | 13 | 13/13 (100%) | +15.5% |
-| open | diffuse | 4 | 4/4 (100%) | +9.9% |
-| open | h5 | 57 | 56/57 (98%) | +12.4% |
-| open | hexagonal | 16 | 15/15 (100%) | +13.8% |
-| open | home-source | 11 | 8/11 (73%) | +12.7% |
-| open | long-axis | 2 | 2/2 (100%) | +16.0% |
-| open | long-wavelength | 1 | 1/1 (100%) | - |
-| open | low-resolution | 1 | 1/1 (100%) | -8.3% |
-| open | marCCD | 15 | 14/15 (93%) | +13.9% |
-| open | marccd | 8 | 7/8 (88%) | +11.7% |
-| open | monoclinic | 50 | 43/50 (86%) | +11.7% |
-| open | nxs | 2 | 1/1 (100%) | +7.1% |
-| open | orthorhombic | 48 | 45/47 (96%) | +11.8% |
-| open | pseudo-merohedral | 5 | 2/5 (40%) | +8.4% |
-| open | pseudo-symmetry | 7 | 5/7 (71%) | +7.1% |
-| open | small-molecule | 6 | 5/5 (100%) | -12.9% |
-| open | smv | 22 | 17/22 (77%) | +10.6% |
-| open | tetragonal | 24 | 23/24 (96%) | +10.2% |
-| open | tncs | 5 | 3/5 (60%) | +12.6% |
-| open | triclinic | 13 | 13/13 (100%) | +8.6% |
-| open | trigonal | 19 | 18/19 (95%) | +13.8% |
-| open | twin | 15 | 10/15 (67%) | +9.7% |
-| open | two-wavelength | 2 | 2/2 (100%) | +10.8% |
-| inhouse | control | 2 | 2/2 (100%) | - |
-| inhouse | cubic | 1 | 1/1 (100%) | +2.4% |
-| inhouse | cytochrome-c | 3 | 3/3 (100%) | +9.1% |
-| inhouse | h5 | 47 | 46/47 (98%) | +6.2% |
-| inhouse | hexagonal | 2 | 2/2 (100%) | - |
-| inhouse | insulin | 9 | 8/9 (89%) | +4.9% |
-| inhouse | iodine | 2 | 2/2 (100%) | +16.2% |
-| inhouse | long-wavelength | 7 | 7/7 (100%) | +0.9% |
-| inhouse | lysozyme | 12 | 12/12 (100%) | +7.2% |
-| inhouse | monoclinic | 3 | 3/3 (100%) | +2.6% |
-| inhouse | myoglobin | 6 | 6/6 (100%) | -2.7% |
-| inhouse | orthorhombic | 1 | 1/1 (100%) | +2.8% |
-| inhouse | pink-beam | 3 | 3/3 (100%) | +15.6% |
-| inhouse | small-molecule | 8 | 8/8 (100%) | +2.7% |
-| inhouse | tetragonal | 1 | 1/1 (100%) | +10.3% |
-| inhouse | thaumatin | 7 | 7/7 (100%) | +2.7% |
-| inhouse | twin | 4 | 4/4 (100%) | -19.6% |
-
-### Distributions (sets that merged, controls left out)
-
-| arm | metric | n | min | q1 | median | q3 | max |
-|:--|:--|--:|--:|--:|--:|--:|--:|
-| open | ISa | 203 | 3.8 | 9.9 | 13.5 | 19.3 | 52.1 |
-| open | R_meas | 203 | 2.4% | 8.9% | 14.0% | 22.2% | 417.1% |
-| open | CC1/2 | 203 | 0.927 | 0.995 | 0.998 | 0.999 | 1.000 |
-| open | res. gain % | 199 | -68.3 | +7.6 | +11.9 | +16.6 | +34.3 |
-| open | low-res shell R_meas | 203 | 1.7% | 4.1% | 5.4% | 8.2% | 36.0% |
-| open | R_model, shell-scaled | 196 | 0.096 | 0.180 | 0.208 | 0.247 | 0.580 |
-| open | R_free (placement, within-run only) | 196 | 0.121 | 0.189 | 0.218 | 0.256 | 0.574 |
-| open | radial misfit | 196 | 0.02 | 0.09 | 0.12 | 0.16 | 0.72 |
-| open | R_free ratio | 196 | 0.804 | 0.958 | 1.026 | 1.116 | 3.386 |
-| open | anomalous map at the scatterers, sigma | 196 | -3.32 | 0.72 | 1.46 | 3.53 | 29.15 |
-| open | dCC vs depositor, all | 194 | -0.367 | -0.021 | -0.004 | +0.003 | +0.196 |
-| open | dCC vs depositor, outer 2 shells | 194 | -0.738 | -0.034 | -0.004 | +0.031 | +0.323 |
-| open | CC(Fc^2) past the deposited limit | 181 | -0.042 | 0.225 | 0.299 | 0.375 | 0.926 |
-| open | time s | 203 | 2 | 11 | 18 | 28 | 109 |
-| inhouse | ISa | 44 | 2.3 | 7.5 | 22.6 | 32.8 | 50.9 |
-| inhouse | R_meas | 45 | 2.7% | 6.3% | 9.5% | 30.1% | 245.2% |
-| inhouse | CC1/2 | 45 | 0.578 | 0.998 | 0.999 | 1.000 | 1.000 |
-| inhouse | res. gain % | 43 | -48.8 | +1.8 | +6.2 | +10.9 | +21.5 |
-| inhouse | ref-range ISa / XDS | 43 | 0.219 | 0.888 | 1.080 | 1.295 | 6.068 |
-| inhouse | ref-range R_meas / XDS | 43 | 0.220 | 0.838 | 0.953 | 1.054 | 3.643 |
-| inhouse | low-res shell R_meas | 45 | 2.2% | 3.8% | 4.8% | 9.6% | 44.7% |
-| inhouse | ref-range low-res R_meas / XDS | 43 | 0.279 | 0.871 | 1.025 | 1.149 | 2.429 |
-| inhouse | ref-range CC1/2 noise / XDS | 43 | 0.04 | 0.36 | 0.57 | 0.88 | 25.56 |
-| inhouse | R_model, shell-scaled | 37 | 0.183 | 0.228 | 0.262 | 0.298 | 0.492 |
-| inhouse | R_free (placement, within-run only) | 37 | 0.175 | 0.237 | 0.292 | 0.346 | 0.524 |
-| inhouse | radial misfit | 37 | 0.03 | 0.07 | 0.11 | 0.18 | 0.31 |
-| inhouse | R_free ratio | 37 | 0.940 | 1.224 | 1.567 | 1.908 | 2.402 |
-| inhouse | anomalous map at the scatterers, sigma | 37 | -0.27 | 1.48 | 3.24 | 6.12 | 11.77 |
-| inhouse | time s | 45 | 4 | 7 | 9 | 13 | 29 |
-
-### Per set, against the reference
-
-_Plot in report.html: open: d_min(rugnux, own cut) / d_min(reference), one point per set, sorted; below 1 = finer than the reference_
-
-_Plot in report.html: inhouse: d_min(rugnux, own cut) / d_min(reference), one point per set, sorted; below 1 = finer than the reference_
-
-_Plot in report.html: inhouse: ISa of the reference-range table (the error model refitted on it) / XDS's ISa; above 1 = rugnux's error model is the better one. One point per set, sorted._
-
-_Plot in report.html: inhouse: R_meas over the reference range / XDS's R_meas; below 1 = rugnux's merge is the more consistent one. One point per set, sorted._
-
-_Plot in report.html: inhouse: R_meas of the lowest-resolution shell of the reference-range table / of XDS's table; below 1 = rugnux's strong reflections agree better. One point per set, sorted._
-
-_Plot in report.html: inhouse: half-set noise over the reference range read off CC1/2 (1 / CC1/2 - 1) / XDS's; 2 = as noisy as XDS's merge would be with half its observations (not scored). One point per set, sorted._
-
-_Plot in report.html: R_free of the deposited model against our merge, as rugnux reports it with --model (a rigid-body placement, scored on rugnux's own free set: a trend number, not a refinement) / the R_free the depositor published, one point per set, sorted; below 1 = lower than published_
-
-### Against the depositor's data
-
-Per resolution shell, the rank correlation of our merged intensities with |Fc|^2 minus that of the depositor's own data, on the reflections both carry (d < 4 A, eight shells of equal count), |Fc| from the deposited model as it is (no bulk solvent, no refinement; depdata_check.py). The model was refined against the depositor's data, so zero is already a good result: across a corpus the median sits near -0.01. 'Past the limit' is CC(I, |Fc|^2) of our reflections in the outermost of up to three shells beyond the deposited data's limit, which the model never saw: clearly above zero there is signal. Reported, never scored.
-
-| set | dep. data | our d_min | dep. d_min | common refl. | dCC all | dCC outer 2 | CC past limit | to d A | REFMAC ratio | ISa | tags |
-|:--|:--|--:|--:|--:|--:|--:|--:|--:|--:|--:|:--|
-| 9b22 | I | 1.14 | 1.30 | 94661 | -0.316 | -0.738 | 0.146 | 1.12 | - | 16.4 | h5, monoclinic |
-| 3r6o | F | 1.53 | 1.95 | 16766 | -0.322 | -0.670 | 0.153 | 1.54 | - | 4.4 | smv, tetragonal, home-source |
-| 2wnq | F | 1.65 | 1.80 | 101895 | -0.145 | -0.550 | 0.077 | 1.65 | - | 10.6 | smv, monoclinic, twin, pseudo-merohedral |
-| 4bwl | F | 1.68 | 2.00 | 72820 | -0.318 | -0.522 | 0.118 | 1.68 | - | 13.7 | smv, monoclinic, twin, pseudo-merohedral |
-| 2xfw | F | 1.54 | 1.65 | 147572 | -0.107 | -0.451 | 0.301 | 1.54 | - | 15.3 | smv, monoclinic, twin, pseudo-merohedral |
-| 9qw8 | I | 1.69 | 1.80 | 37911 | -0.367 | -0.422 | 0.151 | 1.69 | - | 5.2 | h5, triclinic |
-| 3p85 | F | 1.62 | 1.90 | 24300 | -0.157 | -0.396 | 0.280 | 1.61 | - | 8.5 | smv, hexagonal, home-source |
-| 2wnn | F | 1.43 | 1.65 | 123464 | -0.056 | -0.348 | 0.211 | 1.43 | - | 15.2 | smv, monoclinic, twin, pseudo-merohedral |
-| 2wnz | F | 1.85 | 1.85 | 96590 | -0.091 | -0.340 | 0.078 | 1.84 | - | 17.4 | smv, monoclinic, pseudo-symmetry |
-| 3mc4 | F | 1.79 | 1.95 | 24519 | -0.158 | -0.328 | 0.285 | 1.79 | - | 12.1 | smv, trigonal, home-source |
-| 9qw2 | F | 1.82 | 1.92 | 43869 | -0.180 | -0.325 | 0.386 | 1.82 | - | 6.4 | cbf, monoclinic, pseudo-symmetry |
-| 9lxl | I | 2.08 | 2.19 | 18039 | -0.277 | -0.275 | 0.074 | 2.07 | - | 6.2 | h5, tetragonal |
-| 6yqf | I | 3.23 | 3.33 | 932 | -0.147 | -0.268 | 0.003 | 3.23 | - | 5.0 | cbf, orthorhombic |
-| 9hnc | F | 1.64 | 1.88 | 404682 | -0.061 | -0.234 | 0.377 | 1.63 | - | 13.6 | cbf, monoclinic |
-| 6r72 | F | 4.39 | 3.95 | 18987 | -0.092 | -0.231 | - | - | - | 16.6 | h5, monoclinic |
-| 5ky6 | F | 1.50 | 1.94 | 86175 | -0.129 | -0.212 | 0.169 | 1.50 | - | 6.9 | marccd |
-| 9rcs | I | 3.28 | 3.01 | 2042 | -0.219 | -0.177 | - | - | - | 7.4 | h5, monoclinic, cdte |
-| 7bgu | I | 2.32 | 2.43 | 14742 | -0.059 | -0.172 | -0.042 | 2.32 | - | 16.2 | marCCD, triclinic |
-| 3meb | F | 1.70 | 1.90 | 35260 | -0.048 | -0.138 | 0.234 | 1.71 | - | 13.2 | smv, monoclinic, home-source |
-| 9rci | F | 1.69 | 1.66 | 39470 | -0.033 | -0.129 | - | - | - | 7.5 | h5, triclinic, tncs |
-| 5epe | F | 1.78 | 1.90 | 22792 | -0.026 | -0.118 | 0.324 | 1.78 | - | 11.1 | marCCD, cubic |
-| 8qq7 | I | 3.15 | 3.62 | 5507 | -0.108 | -0.110 | -0.026 | 3.15 | - | 6.0 | cbf, hexagonal |
-| 8k1g | F | 1.62 | 2.09 | 34025 | -0.079 | -0.109 | 0.275 | 1.62 | - | 11.6 | cbf, tetragonal |
-| 6ze4 | I | 1.29 | 1.60 | 136771 | -0.104 | -0.107 | 0.288 | 1.30 | - | 10.5 | cbf, orthorhombic |
-| 6u7g | I | 1.89 | 2.35 | 87246 | -0.055 | -0.102 | 0.234 | 1.89 | - | 13.5 | h5, monoclinic |
-| 6zqr | F | 1.77 | 1.93 | 37169 | -0.047 | -0.099 | 0.296 | 1.76 | - | 8.9 | smv |
-| 6zqy | F | 1.69 | 1.85 | 47653 | -0.018 | -0.087 | 0.301 | 1.69 | - | 13.0 | smv |
-| 9hs7 | F | 1.66 | 1.70 | 9595 | -0.143 | -0.084 | 0.050 | 1.66 | - | 11.5 | cbf, hexagonal |
-| 9pbb | I | 1.81 | 2.16 | 11549 | -0.043 | -0.081 | 0.172 | 1.81 | - | 16.7 | cbf, monoclinic |
-| 8c3e | I | 1.79 | 2.10 | 4079 | -0.037 | -0.076 | 0.161 | 1.79 | - | 5.9 | cbf, trigonal, home-source, twin |
-| 7arr | I | 0.92 | 1.10 | 47747 | -0.031 | -0.074 | 0.330 | 0.92 | - | 18.7 | cbf, triclinic |
-| 6jgh | I | 0.88 | 0.94 | 139811 | -0.012 | -0.067 | 0.352 | 0.88 | - | 6.7 | marccd |
-| 6qaj | I | 2.78 | 2.63 | 4121 | -0.132 | -0.064 | - | - | - | 12.8 | cbf |
-| 5f6m | I | 1.09 | 1.10 | 68757 | -0.006 | -0.059 | 0.365 | 1.09 | - | 23.0 | cbf, orthorhombic, diffuse |
-| 7tcd | I | 1.67 | 1.70 | 27126 | -0.043 | -0.057 | 0.183 | 1.66 | - | 18.0 | h5, monoclinic |
-| 6z8o | F | 2.16 | 2.20 | 22410 | -0.154 | -0.055 | 0.130 | 2.16 | - | 14.5 | h5, monoclinic |
-| 5t39 | I | 1.00 | 1.10 | 92595 | -0.009 | -0.054 | 0.410 | 1.00 | - | 16.1 | marccd |
-| 8dyz | I | 1.14 | 1.27 | 24752 | -0.007 | -0.050 | 0.625 | 1.14 | - | 37.8 | cbf, tetragonal, diffuse |
-| 9upt | F | 2.03 | 2.37 | 24477 | -0.036 | -0.046 | 0.322 | 2.03 | - | 6.5 | SMV, hexagonal |
-| 7brr | I | 1.24 | 1.40 | 102801 | -0.024 | -0.044 | 0.265 | 1.24 | - | 16.4 | h5, monoclinic |
-| 6oww | F | 2.83 | 3.84 | 3373 | +0.035 | -0.043 | 0.079 | 2.83 | - | 12.4 | cbf, monoclinic, pseudo-symmetry |
-| 7raa | I | 2.64 | 2.69 | 7522 | -0.068 | -0.038 | 0.160 | 2.64 | - | 10.4 | cbf |
-| 5lzl | F | 2.89 | 3.47 | 21840 | -0.019 | -0.037 | 0.224 | 2.90 | - | 14.6 | cbf, trigonal |
-| 5uth | F | 1.72 | 1.95 | 27659 | -0.021 | -0.037 | 0.425 | 1.73 | - | 10.4 | smv, trigonal, home-source |
-| 9p7q | I | 1.78 | 2.21 | 12159 | -0.028 | -0.034 | 0.283 | 1.77 | - | 10.8 | cbf, monoclinic |
-| 5vml | F | 1.91 | 1.70 | 14312 | -0.015 | -0.034 | - | - | - | 11.0 | smv, tetragonal, home-source |
-| 5reo | F | 1.64 | 1.88 | 18391 | -0.032 | -0.034 | 0.340 | 1.64 | - | 23.0 | cbf, monoclinic |
-| 6rlr | I | 1.94 | 2.00 | 19974 | +0.002 | -0.034 | 0.245 | 1.94 | - | 16.3 | h5, triclinic, twin |
-| 9qvv | I | 2.53 | 2.72 | 16358 | -0.013 | -0.034 | 0.148 | 2.53 | - | 38.1 | nxs, orthorhombic, pseudo-symmetry |
-| 5m17 | I | 0.98 | 1.03 | 185105 | -0.006 | -0.031 | 0.312 | 0.98 | - | 16.1 | cbf, tetragonal |
-| 6oel | I | 2.85 | 3.10 | 13233 | -0.013 | -0.031 | 0.277 | 2.85 | - | 10.3 | SMV, cubic |
-| 8y74 | F | 1.69 | 1.90 | 58040 | -0.010 | -0.028 | 0.288 | 1.69 | - | 8.8 | h5, monoclinic |
-| 9zm0 | I | 1.79 | 2.10 | 13858 | -0.016 | -0.028 | 0.113 | 1.80 | - | 8.9 | h5, monoclinic |
-| 6iu8 | I | 2.34 | 2.70 | 15286 | +0.003 | -0.028 | 0.188 | 2.34 | - | 8.0 | cbf, trigonal |
-| 9gdj | I | 1.40 | 1.47 | 157444 | -0.008 | -0.025 | 0.296 | 1.40 | - | 12.9 | h5, tetragonal, cdte |
-| 9gjx | I | 2.07 | 2.40 | 52052 | -0.002 | -0.024 | 0.260 | 2.07 | - | 39.2 | h5, monoclinic |
-| 9zlo | I | 1.56 | 2.00 | 22408 | -0.008 | -0.024 | 0.243 | 1.57 | - | 23.5 | h5, orthorhombic |
-| 9q66 | F | 2.07 | 2.01 | 87802 | -0.019 | -0.024 | - | - | - | 13.0 | h5, monoclinic |
-| 7n2s | I | 2.56 | 2.37 | 10820 | -0.012 | -0.024 | - | - | - | 14.5 | cbf, monoclinic |
-| 6iu9 | I | 2.76 | 3.00 | 9191 | +0.000 | -0.024 | 0.196 | 2.76 | - | 5.5 | cbf, trigonal, twin |
-| 8r5r | F | 2.79 | 3.08 | 12960 | -0.032 | -0.023 | 0.231 | 2.79 | - | 18.9 | h5, orthorhombic |
-| 9h0q | I | 2.11 | 2.55 | 45699 | -0.006 | -0.022 | 0.332 | 2.12 | - | 18.2 | h5 |
-| 9ih9 | F | 1.40 | 1.70 | 78425 | -0.005 | -0.021 | 0.383 | 1.40 | - | 12.7 | h5, monoclinic |
-| 9fhc | F | 1.89 | 2.20 | 76515 | -0.002 | -0.021 | 0.348 | 1.90 | - | 11.9 | marCCD, cubic |
-| 7mzt | I | 3.18 | 4.05 | 8490 | -0.072 | -0.020 | 0.076 | 3.17 | - | 3.8 | cbf, orthorhombic |
-| 9c18 | I | 1.74 | 1.90 | 25041 | -0.001 | -0.019 | 0.260 | 1.74 | - | 10.5 | h5, triclinic |
-| 9crw | I | 2.28 | 2.49 | 53875 | -0.023 | -0.019 | 0.120 | 2.29 | - | 15.4 | h5, monoclinic |
-| 9yl4 | I | 3.61 | 3.70 | 1130 | -0.009 | -0.019 | 0.175 | 3.61 | - | 9.8 | cbf, orthorhombic |
-| 6iu6 | I | 2.35 | 2.90 | 10758 | +0.002 | -0.018 | 0.250 | 2.35 | - | 7.1 | cbf, trigonal, twin |
-| 6iu5 | I | 2.12 | 2.25 | 30820 | -0.010 | -0.018 | 0.234 | 2.12 | - | 8.0 | cbf, trigonal, twin |
-| 6fid | F | 1.98 | 2.20 | 10528 | -0.005 | -0.018 | 0.820 | 1.97 | - | 13.5 | cbf, orthorhombic |
-| 6cdl | I | 1.13 | 1.24 | 56393 | -0.004 | -0.017 | 0.609 | 1.12 | - | 10.0 | marccd |
-| 6w75 | F | 1.69 | 1.95 | 99979 | -0.010 | -0.017 | 0.323 | 1.69 | - | 15.9 | marccd |
-| 8xtf | I | 1.84 | 2.13 | 27230 | -0.003 | -0.017 | 0.415 | 1.83 | - | 7.6 | h5, trigonal |
-| 9e2t | I | 2.35 | 2.28 | 31869 | -0.106 | -0.016 | - | - | - | 6.6 | cbf, triclinic |
-| 6h5t | F | 1.45 | 1.69 | 28184 | -0.006 | -0.014 | 0.348 | 1.46 | - | 9.3 | marCCD, tetragonal |
-| 6p8p | I | 1.45 | 1.64 | 64791 | -0.013 | -0.013 | 0.299 | 1.45 | - | 16.0 | cbf, tetragonal |
-| 5mln | F | 1.27 | 1.59 | 60800 | -0.012 | -0.012 | 0.393 | 1.27 | - | 21.0 | cbf |
-| 6w4h | F | 1.62 | 1.80 | 70331 | -0.003 | -0.012 | 0.411 | 1.62 | - | 18.5 | marCCD, trigonal |
-| 7kcn | I | 1.39 | 1.46 | 43289 | -0.009 | -0.012 | 0.569 | 1.39 | - | 11.8 | cbf, tetragonal |
-| 7q6j | I | 2.00 | 2.20 | 41719 | +0.006 | -0.010 | 0.234 | 2.00 | - | 10.0 | cbf, orthorhombic, pseudo-symmetry |
-| 6rym | I | 1.45 | 1.46 | 17018 | -0.005 | -0.009 | - | - | - | 22.8 | smv, tetragonal |
-| 8dz7 | I | 1.19 | 1.34 | 13603 | -0.002 | -0.008 | 0.809 | 1.19 | - | 35.1 | cbf, orthorhombic, diffuse |
-| 9chw | I | 1.60 | 2.16 | 20358 | -0.005 | -0.008 | 0.652 | 1.60 | - | 21.2 | marCCD, hexagonal |
-| 9jq9 | I | 1.65 | 1.90 | 13865 | +0.002 | -0.008 | 0.504 | 1.65 | - | 19.2 | cbf, orthorhombic, home-source |
-| 7l84 | I | 1.70 | 1.71 | 11375 | -0.001 | -0.007 | - | - | - | 11.3 | cbf, tetragonal |
-| 7bgt | I | 1.79 | 1.93 | 33463 | -0.003 | -0.007 | 0.319 | 1.80 | - | 16.9 | marCCD, triclinic |
-| 6wzo | I | 1.04 | 1.42 | 91591 | -0.012 | -0.007 | 0.341 | 1.04 | - | 16.9 | cbf, triclinic |
-| 7os3 | I | 1.96 | 2.18 | 32896 | +0.010 | -0.006 | 0.419 | 1.95 | - | 23.8 | cbf, orthorhombic |
-| 6gvk | I | 1.42 | 1.55 | 32916 | +0.001 | -0.006 | 0.208 | 1.42 | - | 19.5 | cbf, monoclinic |
-| 6i3j | I | 2.33 | 2.59 | 34974 | -0.011 | -0.005 | 0.348 | 2.33 | - | 7.8 | marCCD, orthorhombic |
-| 6s1u | I | 1.76 | 1.90 | 17747 | +0.000 | -0.005 | 0.346 | 1.76 | - | 13.4 | marccd |
-| 8agq | I | 0.97 | 1.09 | 98573 | -0.013 | -0.005 | 0.309 | 0.97 | - | 14.1 | cbf, monoclinic |
-| 6fvz | F | 1.48 | 1.80 | 105993 | -0.016 | -0.005 | 0.391 | 1.48 | - | 20.8 | cbf, orthorhombic |
-| 7atg | I | 0.60 | 0.60 | 54330 | -0.002 | -0.005 | - | - | - | 23.1 | cbf, orthorhombic |
-| 8a1a | F | 1.91 | 2.05 | 101603 | -0.006 | -0.005 | 0.357 | 1.91 | - | 19.2 | h5, hexagonal |
-| 6hv2 | F | 1.40 | 1.71 | 19192 | -0.031 | -0.004 | 0.098 | 1.40 | - | 14.6 | h5, hexagonal |
-| 6o2h | I | 1.10 | 1.21 | 11612 | -0.002 | -0.003 | 0.926 | 1.10 | - | 23.9 | cbf, triclinic, diffuse |
-| 5ojv | I | 1.85 | 2.06 | 63718 | -0.023 | -0.003 | 0.283 | 1.85 | - | 12.6 | cbf, orthorhombic, pseudo-symmetry |
-| 6pxb | I | 1.41 | 1.75 | 50825 | +0.010 | -0.001 | 0.108 | 1.41 | - | 12.0 | cbf, trigonal |
-| 7l6j | F | 1.50 | 1.78 | 37485 | -0.002 | -0.001 | 0.415 | 1.50 | - | 10.5 | marCCD, cubic |
-| 6cee | I | 1.38 | 1.55 | 14202 | -0.001 | +0.001 | 0.683 | 1.38 | - | 24.1 | smv, orthorhombic, home-source |
-| 9i80 | I | 1.59 | 1.95 | 68449 | -0.010 | +0.001 | 0.343 | 1.59 | - | 6.8 | h5, tetragonal, twin |
-| 3ky7 | F | 1.92 | 2.35 | 11401 | +0.002 | +0.002 | 0.184 | 1.92 | - | 12.2 | marCCD, cubic |
-| 9sl0 | I | 1.37 | 1.60 | 67358 | +0.002 | +0.003 | 0.246 | 1.37 | - | 20.0 | h5, orthorhombic |
-| 8tyy | I | 1.27 | 1.68 | 44789 | -0.000 | +0.003 | 0.471 | 1.27 | - | 16.2 | cbf, cubic |
-| 3inp | I | 1.70 | 2.05 | 26251 | -0.005 | +0.003 | 0.290 | 1.70 | - | 13.2 | marCCD, cubic |
-| 6nen | I | 1.77 | 2.15 | 10259 | +0.003 | +0.003 | 0.325 | 1.77 | - | 6.1 | smv |
-| 8iya | F | 1.90 | 2.43 | 16262 | -0.004 | +0.004 | 0.218 | 1.90 | - | 5.8 | h5, monoclinic |
-| 6vww | F | 1.99 | 2.20 | 58979 | -0.003 | +0.004 | 0.346 | 1.98 | - | 8.0 | cbf, hexagonal, twin |
-| 9mh4 | I | 2.78 | 3.05 | 9490 | +0.006 | +0.006 | 0.211 | 2.79 | - | 13.8 | h5, cubic |
-| 7ris | I | 1.51 | 1.72 | 22161 | +0.003 | +0.006 | 0.222 | 1.51 | - | 30.9 | h5, trigonal |
-| 8dqb | I | 2.04 | 2.50 | 19165 | -0.002 | +0.006 | 0.374 | 2.04 | - | 22.1 | h5, cubic |
-| 9vyb | I | 1.67 | 2.12 | 5191 | -0.010 | +0.008 | 0.355 | 1.68 | - | 22.2 | h5, orthorhombic |
-| 7pq7 | F | 1.39 | 1.55 | 51887 | -0.007 | +0.009 | 0.140 | 1.39 | - | 13.6 | cbf, monoclinic |
-| 6v2r | I | 1.38 | 1.57 | 9330 | +0.000 | +0.009 | 0.482 | 1.38 | - | 24.6 | smv, tetragonal, home-source |
-| 8v4j | I | 1.10 | 1.30 | 41379 | +0.001 | +0.009 | 0.579 | 1.10 | - | 21.8 | smv, tetragonal |
-| 6cs9 | I | 1.71 | 1.85 | 5090 | -0.000 | +0.010 | 0.277 | 1.71 | - | 12.9 | smv, monoclinic |
-| 6zr0 | F | 1.64 | 1.94 | 40650 | -0.006 | +0.011 | 0.356 | 1.64 | - | 25.2 | cbf |
-| 9zmu | I | 1.72 | 1.98 | 21684 | -0.001 | +0.011 | 0.218 | 1.72 | - | 11.3 | h5, hexagonal |
-| 6f3p | F | 1.15 | 1.35 | 235840 | -0.002 | +0.013 | 0.459 | 1.15 | - | 9.3 | marccd |
-| 6g1f | I | 1.98 | 2.25 | 131737 | -0.001 | +0.013 | 0.289 | 1.98 | - | 20.8 | cbf |
-| 8egn | F | 1.63 | 1.95 | 38629 | -0.010 | +0.013 | 0.277 | 1.62 | - | 21.7 | cbf, orthorhombic |
-| 36gk | F | 2.10 | 2.28 | 84276 | -0.013 | +0.015 | 0.302 | 2.10 | - | 11.6 | h5, orthorhombic |
-| 7dkp | F | 1.20 | 1.45 | 131353 | +0.003 | +0.016 | 0.613 | 1.20 | - | 26.5 | h5, monoclinic |
-| 8sqq | I | 1.90 | 2.25 | 8697 | +0.006 | +0.016 | 0.329 | 1.90 | - | 17.8 | h5, cubic |
-| 9ig7 | F | 2.02 | 2.60 | 26626 | -0.006 | +0.017 | 0.255 | 2.02 | - | 11.0 | cbf, orthorhombic |
-| 6fwc | F | 1.41 | 1.70 | 126460 | -0.001 | +0.018 | 0.394 | 1.41 | - | 27.3 | cbf, orthorhombic |
-| 8qaw | F | 1.30 | 1.55 | 256134 | +0.001 | +0.018 | 0.354 | 1.30 | - | 10.8 | cbf, trigonal, long-axis |
-| 9bn8 | I | 1.19 | 1.35 | 119114 | -0.001 | +0.019 | 0.462 | 1.19 | - | 19.8 | h5, tetragonal |
-| 11if | I | 1.36 | 1.51 | 27273 | -0.004 | +0.020 | 0.271 | 1.36 | - | 26.1 | h5, tetragonal |
-| 7yzx | F | 1.87 | 1.90 | 83105 | -0.029 | +0.021 | 0.288 | 1.87 | - | 10.5 | cbf, hexagonal |
-| 8qj5 | I | 1.43 | 1.63 | 101762 | +0.003 | +0.021 | 0.382 | 1.43 | - | 8.3 | cbf, monoclinic |
-| 5jk4 | I | 0.96 | 1.01 | 134620 | -0.002 | +0.022 | 0.366 | 0.96 | - | 14.5 | smv, monoclinic |
-| 9jzo | F | 1.15 | 1.40 | 47877 | +0.001 | +0.022 | 0.774 | 1.15 | - | 8.3 | cbf, triclinic |
-| 5ebi | F | 0.86 | 1.09 | 39168 | +0.009 | +0.023 | 0.212 | 0.86 | - | 10.9 | marCCD, monoclinic, twin |
-| 8u0i | I | 1.38 | 1.54 | 16737 | +0.007 | +0.023 | 0.337 | 1.38 | - | 16.4 | cbf, tetragonal |
-| 7t5t | I | 1.24 | 1.35 | 101432 | -0.002 | +0.024 | 0.249 | 1.24 | - | 16.5 | cbf, tetragonal |
-| 9fcf | F | 1.78 | 2.36 | 9897 | -0.018 | +0.025 | 0.179 | 1.77 | - | 7.1 | cbf |
-| 8v2t | I | 1.15 | 1.40 | 33174 | +0.005 | +0.025 | 0.416 | 1.15 | - | 12.3 | cbf, tetragonal |
-| 8s38 | F | 1.64 | 1.89 | 121216 | -0.004 | +0.025 | 0.364 | 1.64 | - | 22.5 | cbf, orthorhombic |
-| 8sqt | I | 1.83 | 2.20 | 9296 | -0.002 | +0.026 | 0.307 | 1.83 | - | 24.1 | h5, cubic |
-| 6moj | I | 2.43 | 2.43 | 13971 | -0.050 | +0.026 | - | - | - | 8.4 | cbf, tetragonal |
-| 6h2p_1p89A | F | 1.76 | 1.88 | 85463 | +0.003 | +0.026 | 0.516 | 1.76 | - | 22.6 | cbf, orthorhombic, long-wavelength, two-wavelength |
-| 6pxc | F | 1.43 | 1.60 | 15636 | +0.008 | +0.028 | 0.317 | 1.43 | - | 10.5 | cbf, orthorhombic |
-| 8sqo | I | 1.31 | 1.55 | 33951 | +0.001 | +0.031 | 0.374 | 1.32 | - | 13.9 | h5, cubic |
-| 5nw5 | I | 7.04 | 6.50 | 9932 | -0.041 | +0.031 | - | - | - | 8.4 | cbf, orthorhombic, low-resolution |
-| 6jgj | F | 0.65 | 0.77 | 250563 | -0.049 | +0.032 | 0.377 | 0.65 | - | 15.1 | cbf, orthorhombic, cdte |
-| 8t7r | I | 3.30 | 3.84 | 13697 | +0.026 | +0.032 | 0.290 | 3.30 | - | 10.2 | cbf, monoclinic |
-| 9z72 | I | 2.00 | 2.38 | 28228 | +0.008 | +0.032 | 0.273 | 2.00 | - | 14.9 | cbf, trigonal, long-axis |
-| 5src | I | 0.97 | 1.05 | 138681 | +0.013 | +0.033 | 0.241 | 0.97 | - | 19.4 | cbf, tetragonal |
-| 6ukf | I | 0.95 | 1.00 | 143255 | +0.004 | +0.036 | 0.318 | 0.95 | - | 9.9 | cbf, monoclinic |
-| 8xtg | I | 1.55 | 2.00 | 177630 | -0.004 | +0.037 | 0.291 | 1.55 | - | 7.6 | cbf, trigonal |
-| 9khr | I | 1.40 | 2.00 | 11649 | +0.005 | +0.037 | 0.311 | 1.40 | - | 9.1 | marCCD, orthorhombic |
-| 5cc8 | F | 1.53 | 2.00 | 28178 | +0.041 | +0.037 | 0.432 | 1.53 | - | 10.8 | smv, orthorhombic, home-source, tncs |
-| 8pqd | F | 1.31 | 1.50 | 102730 | +0.003 | +0.038 | 0.255 | 1.31 | - | 14.6 | h5, orthorhombic |
-| 9s02 | F | 1.43 | 1.65 | 187371 | -0.009 | +0.038 | 0.244 | 1.43 | - | 25.6 | h5, orthorhombic |
-| 8xte | I | 1.64 | 1.99 | 195244 | +0.004 | +0.039 | 0.306 | 1.64 | - | 12.4 | cbf, trigonal |
-| 9o0h | I | 2.01 | 2.24 | 15449 | +0.028 | +0.040 | 0.284 | 2.02 | - | 5.4 | cbf, orthorhombic |
-| 9ea5 | I | 1.66 | 2.00 | 51522 | +0.009 | +0.041 | 0.321 | 1.66 | - | 26.7 | cbf, monoclinic |
-| 9w3y | I | 1.22 | 1.50 | 61343 | +0.006 | +0.042 | 0.446 | 1.21 | - | 18.6 | h5, orthorhombic |
-| 7ph1 | F | 1.09 | 1.18 | 120936 | -0.008 | +0.042 | 0.370 | 1.09 | - | 16.1 | cbf, orthorhombic |
-| 6h2p_native | F | 1.32 | 1.48 | 188245 | -0.005 | +0.042 | 0.296 | 1.32 | - | 19.8 | cbf, orthorhombic, two-wavelength |
-| 8tha | I | 1.34 | 1.68 | 8018 | +0.001 | +0.042 | 0.343 | 1.34 | - | 26.4 | cbf, hexagonal |
-| 9yzk | I | 3.87 | 4.50 | 13486 | +0.003 | +0.043 | 0.017 | 3.87 | - | 8.8 | cbf, monoclinic |
-| 8sa8 | I | 1.11 | 1.30 | 409825 | +0.007 | +0.045 | 0.482 | 1.11 | - | 21.7 | h5, monoclinic |
-| 9gqg | I | 1.82 | 2.00 | 15522 | +0.008 | +0.045 | 0.254 | 1.82 | - | 11.9 | h5, trigonal |
-| 8owm | F | 1.50 | 1.70 | 293905 | +0.003 | +0.046 | 0.414 | 1.50 | - | 21.1 | cbf, triclinic |
-| 6pb3 | I | 1.84 | 2.05 | 15266 | -0.003 | +0.046 | 0.242 | 1.84 | - | 24.8 | cbf, hexagonal |
-| 8rud | I | 1.65 | 2.10 | 77721 | +0.002 | +0.048 | 0.360 | 1.66 | - | 12.4 | cbf, monoclinic |
-| 9rp9 | I | 1.96 | 2.10 | 19430 | +0.020 | +0.052 | 0.384 | 1.96 | - | 28.6 | h5, monoclinic |
-| 6hwj | I | 1.70 | 1.98 | 52133 | +0.003 | +0.052 | 0.360 | 1.70 | - | 39.0 | cbf, monoclinic |
-| 8v4o | I | 2.12 | 2.70 | 59576 | +0.011 | +0.053 | 0.268 | 2.12 | - | 15.4 | h5, hexagonal |
-| 9q41 | I | 1.68 | 1.95 | 42194 | -0.004 | +0.053 | 0.403 | 1.67 | - | 7.5 | h5, orthorhombic |
-| 7orr | I | 1.64 | 1.79 | 16877 | -0.002 | +0.053 | 0.391 | 1.64 | - | 25.4 | h5, cubic |
-| 8oic | I | 2.34 | 2.51 | 78746 | -0.021 | +0.054 | 0.245 | 2.34 | - | 19.3 | h5, triclinic |
-| 7qis | F | 1.76 | 1.83 | 93162 | +0.014 | +0.056 | 0.271 | 1.76 | - | 17.2 | cbf, hexagonal |
-| 7n0i | I | 1.64 | 1.80 | 117514 | +0.017 | +0.057 | 0.132 | 1.64 | - | 10.5 | cbf, orthorhombic, tncs |
-| 9z44 | I | 6.78 | 7.20 | 1894 | +0.008 | +0.059 | 0.068 | 6.87 | - | 9.5 | cbf, monoclinic |
-| 9fcg | F | 1.38 | 1.54 | 37967 | +0.001 | +0.062 | 0.461 | 1.38 | - | 9.5 | cbf, tetragonal |
-| 6p8j | I | 1.38 | 1.47 | 191619 | -0.012 | +0.063 | 0.415 | 1.38 | - | 5.0 | cbf, monoclinic, pseudo-symmetry |
-| 7qij | I | 3.62 | 4.10 | 135378 | +0.032 | +0.066 | 0.097 | 3.62 | - | 9.2 | cbf, orthorhombic |
-| 6jgi | I | 0.75 | 0.85 | 187106 | +0.003 | +0.068 | 0.416 | 0.75 | - | 8.4 | marCCD, orthorhombic |
-| 7rji | I | 1.47 | 1.71 | 16699 | +0.003 | +0.084 | 0.345 | 1.47 | - | 7.8 | cbf, trigonal |
-| 7ou1 | F | 1.39 | 1.65 | 176428 | +0.008 | +0.085 | 0.389 | 1.39 | - | 9.0 | marccd |
-| 5jvn | I | 2.23 | 2.90 | 21045 | +0.028 | +0.086 | 0.226 | 2.24 | - | 14.9 | cbf, hexagonal |
-| 9t6s | I | 1.75 | 2.00 | 25145 | +0.015 | +0.086 | 0.224 | 1.75 | - | 28.4 | h5, orthorhombic, tncs |
-| 6ttn | I | 1.05 | 1.12 | 126145 | +0.021 | +0.092 | 0.288 | 1.05 | - | 14.5 | cbf, orthorhombic |
-| 7k1l | F | 1.91 | 2.25 | 54383 | +0.012 | +0.094 | 0.337 | 1.91 | - | 9.9 | cbf, hexagonal |
-| 8ys9 | I | 1.31 | 1.46 | 75646 | +0.007 | +0.096 | 0.375 | 1.31 | - | 15.3 | h5, orthorhombic |
-| 6toc | I | 1.65 | 1.85 | 6080 | +0.013 | +0.136 | 0.357 | 1.65 | - | 25.1 | cbf, tetragonal, twin |
-| 9i0a | F | 1.81 | 2.22 | 60317 | +0.005 | +0.143 | 0.183 | 1.80 | - | 11.6 | h5, orthorhombic |
-| 8xbp | F | 1.68 | 2.00 | 24156 | +0.015 | +0.235 | 0.105 | 1.68 | - | 18.8 | h5, monoclinic |
-| 5j23 | F | 2.20 | 2.30 | 56769 | +0.196 | +0.323 | 0.419 | 2.20 | - | 11.5 | marCCD, trigonal, twin |
-
-No comparison: 9min (the merge does not match the model in any setting); 6z9g (the merge does not match the model in any setting)
-
-### Like for like with XDS: the reference-range table
-
-The same merge, binned a second time over XDS's range (--report-resolution; report-only, nothing was processed differently for it), against XDS's CORRECT.LP totals. Where rugnux's own cut is coarser than the reference ('coverage' in the last column), the shells past it are not merged at all: the completeness there is coverage of XDS's range, not a quality loss, and the other rugnux numbers are over the shells it reached. XDS's totals are over its own merged range, which is the reference range except where the reference d_min was derived (see below).
-
-| set | arm | range A | own d_min | compl % (rugnux / XDS) | mult | I/sigma | R_meas | low-res R_meas (to d A) | CC1/2 | CC1/2 noise ratio | ISa | reading |
-|:--|:--|:--|--:|:--|:--|--:|:--|:--|:--|--:|:--|:--|
-| aspirin_x10sa_20keV | inhouse | 50.000 0.680 | 0.66 | 85.2 / 84.0 | 6.0 / 3.1 | 43.1 | 3.0% / 3.3% | 2.3% / 3.3% (2.04 / 2.01) | 0.9996 / 0.999 | 0.27 | 35.5 / 27.4 | like for like |
-| aspirin_x10sa_25keV | inhouse | 50.000 0.550 | 0.53 | 87.6 / 86.6 | 6.0 / 3.1 | 34.9 | 3.1% / 3.4% | 2.2% / 3.2% (1.65 / 1.63) | 0.9996 / 0.999 | 0.27 | 34.2 / 29.2 | like for like |
-| citricacid_x10sa_20keV | inhouse | 50.000 0.680 | 0.67 | 82.7 / 82.0 | 5.1 / 3.1 | 43.0 | 4.1% / 4.1% | 5.0% / 5.0% (2.04 / 2.02) | 0.9973 / 0.997 | 0.77 | 23.1 / 20.4 | like for like |
-| cytc_x06da_1 | inhouse | 50.000 1.875 | 1.71 | 100.0 / 99.9 | 10.5 / 7.7 | 14.8 | 8.4% / 8.4% | 3.8% / 3.3% (5.59 / 5.58) | 0.9996 / 0.999 | 0.27 | 17.9 / 24.5 | like for like |
-| cytc_x06da_2 | inhouse | 50.000 1.690 | 1.57 | 100.0 / 99.9 | 10.2 / 7.8 | 13.4 | 8.9% / 9.7% | 3.4% / 3.2% (5.05 / 5.03) | 0.9996 / 0.999 | 0.27 | 23.3 / 27.0 | like for like |
-| cytc_x10sa | inhouse | 50.000 2.039 | 1.95 | 99.9 / 99.8 | 10.6 / 10.7 | 9.5 | 17.9% / 23.2% | 3.9% / 3.6% (6.08 / 6.05) | 0.9991 / 0.999 | 0.60 | 26.8 / 31.8 | like for like |
-| hepes_x10sa_20keV | inhouse | 50.000 0.680 | 0.66 | 93.0 / 91.8 | 10.4 / 5.7 | 78.1 | 2.7% / 3.1% | 3.7% / 3.7% (2.04 / 2.00) | 0.9994 / 0.999 | 0.40 | 37.0 / 28.5 | like for like |
-| insu_H_x06da_notwin | inhouse | 50.000 1.544 | 1.41 | 98.7 / 97.4 | 4.8 / 3.5 | 15.5 | 6.0% / 6.8% | 4.3% / 4.5% (4.61 / 4.61) | 0.9988 / 0.998 | 0.48 | 20.6 / 17.7 | like for like |
-| insu_H_x06da_twin | inhouse | 50.000 1.455 | 1.38 | 96.8 / 95.0 | 4.5 / 3.6 | 8.0 | 12.8% / 11.8% | 10.9% / 10.6% (4.35 / 4.34) | 0.9865 / 0.988 | 1.08 | 6.2 / 6.8 | like for like |
-| insu_I_x06da_13keV | inhouse | 50.000 1.635 | 1.46 | 100.0 / 100.0 | 20.2 / 17.2 | 9.6 | 27.2% / 27.9% | 8.1% / 9.3% (4.88 / 4.85) | 0.9983 / 0.998 | 0.68 | 30.1 / 18.8 | like for like |
-| insu_I_x06da_5keV | inhouse | 50.000 2.450 | 2.43 | 95.7 / 91.7 | 15.4 / 11.2 | 33.9 | 6.2% / 7.3% | 4.4% / 4.8% (7.28 / 7.21) | 0.9994 / 0.999 | 0.40 | 27.9 / 17.5 | like for like |
-| insu_I_x06da_5keV_2 | inhouse | 50.000 2.450 | 2.43 | 96.3 / 91.8 | 15.9 / 12.7 | 29.4 | 7.4% / 7.6% | 5.1% / 4.8% (7.28 / 7.21) | 0.9994 / 0.999 | 0.40 | 32.2 / 20.0 | like for like |
-| insu_I_x06da_6keV | inhouse | 50.000 2.040 | 2.02 | 94.9 / 92.4 | 15.5 / 12.4 | 34.5 | 5.9% / 6.5% | 4.8% / 4.7% (6.08 / 6.03) | 0.9995 / 0.999 | 0.33 | 20.6 / 17.9 | like for like |
-| insu_I_x06da_low_isa | inhouse | 50.000 1.300 | 1.59 | 54.4 / 90.8 | 4.2 / 13.3 | 2.2 | 27.4% / 22.0% | 12.7% / 16.7% (3.89 / 3.92) | 0.9843 / 0.998 | 6.36 | 6.4 / 4.2 | coverage: own cut 1.59 A is coarser than the reference, 2 shell(s) not merged |
-| insu_I_x06da_ref | inhouse | 50.000 1.621 | 1.41 | 100.0 / 100.0 | 16.4 / 13.8 | 17.3 | 29.2% / 34.9% | 6.6% / 14.3% (4.84 / 4.82) | 0.9993 / 0.998 | 0.28 | 33.7 / 25.1 | like for like |
-| insu_I_x06da_weak | inhouse | 999.000 1.080 | 1.64 | 29.2 / 92.4 | 40.1 / 29.0 | 15.4 | 17.1% / 40.1% | 6.3% / 5.4% (3.24 / 3.22) | 0.9997 / 0.999 | 0.20 | 14.7 / 18.9 | coverage: own cut 1.64 A is coarser than the reference, 5 shell(s) not merged |
-| kdp_x10sa_20keV | inhouse | 50.000 0.740 | 0.66 | 100.0 / 99.2 | 10.3 / 6.1 | 44.8 | 5.3% / 24.1% | 4.8% / 17.2% (2.22 / 2.06) | 0.9987 / 0.969 | 0.04 | 24.9 / 4.1 | like for like |
-| lysoI_micromax_mono | inhouse | 50.000 1.650 | 1.37 | 100.0 / 100.0 | 6.5 / 6.8 | 21.7 | 5.8% / 6.8% | 3.0% / 2.8% (4.93 / 4.99) | 0.9994 / 0.999 | 0.40 | 38.0 / 31.4 | like for like |
-| lysoI_micromax_pink | inhouse | 50.000 1.650 | 1.39 | 100.0 / 100.0 | 6.5 / 6.8 | 20.2 | 6.6% / 7.9% | 3.2% / 2.8% (4.93 / 4.99) | 0.9993 / 0.999 | 0.47 | 36.5 / 29.2 | like for like |
-| lyso_micromax_mono | inhouse | 50.000 1.500 | 1.18 | 100.0 / 100.0 | 6.0 / 6.2 | 24.8 | 4.7% / 4.7% | 2.5% / 2.3% (4.48 / 4.54) | 0.9996 / 1.000 | 0.80 | 41.5 / 39.9 | like for like |
-| lyso_micromax_pink | inhouse | 50.000 1.450 | 1.20 | 99.9 / 99.9 | 5.8 / 6.0 | 21.9 | 4.9% / 5.1% | 2.4% / 2.2% (4.34 / 4.39) | 0.9995 / 1.000 | 1.00 | 42.1 / 37.4 | like for like |
-| lyso_x06da_5keV | inhouse | 50.000 2.450 | 2.44 | 88.0 / 86.4 | 11.1 / 8.8 | 34.2 | 5.7% / 6.4% | 5.4% / 4.7% (7.28 / 7.22) | 0.9991 / 0.998 | 0.36 | 26.9 / 19.4 | like for like |
-| lyso_x06da_atten_wedge | inhouse | 50.000 1.264 | 1.20 | 100.0 / 99.9 | 12.6 / 11.0 | 8.6 | 35.6% / 23.9% | 6.7% / 6.9% (3.78 / 3.76) | 0.9978 / 0.998 | 0.88 | 13.4 / 16.6 | like for like |
-| lyso_x06da_half_image | inhouse | 50.000 1.650 | 1.57 | 100.0 / 99.6 | 6.6 / 5.3 | 3.3 | 216.8% / 59.5% | 34.3% / 25.8% (4.93 / 4.91) | 0.8520 / 0.958 | 3.91 | 4.5 / 6.6 | like for like |
-| lyso_x06da_ice | inhouse | 50.000 1.431 | 1.33 | 100.0 / 100.0 | 10.5 / 11.9 | 9.3 | 16.6% / 21.9% | 4.7% / 5.5% (4.28 / 4.26) | 0.9986 / 0.998 | 0.56 | 23.3 / 23.3 | like for like |
-| lyso_x06da_ref | inhouse | 50.000 1.200 | 0.99 | 100.0 / 100.0 | 13.8 / 13.8 | 36.3 | 4.3% / 4.5% | 2.6% / 2.9% (3.59 / 3.58) | 0.9998 / 1.000 | 0.40 | 30.6 / 28.3 | like for like |
-| lyso_x10sa_90deg_1 | inhouse | 50.000 1.966 | 1.82 | 100.0 / 99.3 | 3.5 / 3.5 | 6.9 | 15.2% / 18.2% | 4.5% / 4.9% (5.86 / 5.83) | 0.9956 / 0.995 | 0.80 | 20.7 / 20.8 | like for like |
-| lyso_x10sa_90deg_2 | inhouse | 50.000 1.973 | 1.85 | 100.0 / 99.3 | 3.5 / 3.5 | 6.8 | 15.1% / 18.0% | 4.6% / 5.1% (5.88 / 5.86) | 0.9956 / 0.994 | 0.68 | 19.5 / 18.1 | like for like |
-| lyso_x10sa_strong | inhouse | 999.000 1.180 | 1.36 | 66.2 / 65.8 | 21.4 / 11.5 | 9.6 | 23.7% / 11.2% | 11.8% / 7.7% (3.54 / 3.52) | 0.9951 / 0.998 | 1.97 | 5.5 / 8.6 | coverage: own cut 1.36 A is coarser than the reference, 2 shell(s) not merged |
-| myob_x06da | inhouse | 50.000 1.422 | 1.24 | 99.8 / 99.4 | 3.5 / 3.5 | 7.2 | 12.7% / 23.2% | 4.4% / 10.5% (4.25 / 4.23) | 0.9963 / 0.987 | 0.27 | 23.9 / 7.6 | like for like |
-| myob_x06da_powder_1 | inhouse | 50.000 1.495 | 1.73 | 64.0 / 74.2 | 4.5 / 2.9 | 2.2 | 74.4% / 49.3% | 20.1% / 12.5% (4.47 / 4.44) | 0.5783 / 0.966 | 20.41 | 3.8 / 5.5 | coverage: own cut 1.73 A is coarser than the reference, 2 shell(s) not merged |
-| myob_x06da_powder_2 | inhouse | 999.000 0.990 | 1.47 | 30.7 / 58.0 | 5.5 / 4.7 | 0.8 | 174.0% / 110.6% | 54.2% / 70.6% (2.97 / 2.98) | 0.7833 / 0.655 | 0.52 | 2.3 / 2.2 | coverage: own cut 1.47 A is coarser than the reference, 4 shell(s) not merged |
-| myob_x06da_sparse | inhouse | 50.000 2.000 | 1.78 | 100.0 / 73.7 | 5.4 / 5.2 | 3.8 | 34.1% / 32.6% | 12.9% / 14.6% (5.96 / 5.92) | 0.9501 / 0.972 | 1.79 | 4.8 / 5.5 | like for like |
-| myob_x06da_split | inhouse | 50.000 1.506 | 1.86 | 53.8 / 77.7 | 5.7 / 4.4 | 1.9 | 78.2% / 57.7% | 22.1% / 9.1% (4.50 / 4.48) | 0.6999 / 0.984 | 25.56 | 2.7 / 12.4 | coverage: own cut 1.86 A is coarser than the reference, 3 shell(s) not merged |
-| myob_x10sa | inhouse | 50.000 1.742 | 1.56 | 98.1 / 97.7 | 3.2 / 3.3 | 6.1 | 15.5% / 24.7% | 7.7% / 18.6% (5.20 / 5.16) | 0.9900 / 0.965 | 0.27 | 11.3 / 5.2 | like for like |
-| thau_bl1a_3p8keV | inhouse | 100.000 3.100 | 3.02 | 93.6 / 92.2 | 9.1 / 7.9 | 31.9 | 6.1% / 5.7% | 5.5% / 3.9% (9.26 / 9.23) | 0.9973 / 0.997 | 0.77 | 31.5 / 30.8 | like for like |
-| thau_bl1a_4p6keV | inhouse | 100.000 2.530 | 2.47 | 93.2 / 92.0 | 9.1 / 7.9 | 26.9 | 6.5% / 6.2% | 5.1% / 3.9% (7.57 / 7.56) | 0.9978 / 0.998 | 0.88 | 35.1 / 35.6 | like for like |
-| thau_bl1a_6p5keV | inhouse | 100.000 1.780 | 1.74 | 93.2 / 91.8 | 9.0 / 8.0 | 19.5 | 7.3% / 7.2% | 4.7% / 4.1% (5.33 / 5.33) | 0.9988 / 0.999 | 0.80 | 43.1 / 34.5 | like for like |
-| thau_micromax_pink | inhouse | 50.000 1.400 | 1.24 | 99.0 / 98.5 | 9.5 / 9.4 | 15.3 | 8.7% / 8.0% | 4.9% / 4.0% (4.19 / 4.17) | 0.9991 / 0.999 | 0.60 | 15.8 / 21.2 | like for like |
-| thau_x10sa_0p1deg | inhouse | 50.000 2.197 | 1.89 | 99.5 / 99.0 | 11.4 / 11.4 | 12.3 | 13.8% / 23.0% | 6.7% / 10.4% (6.54 / 6.51) | 0.9980 / 0.997 | 0.57 | 10.9 / 9.2 | like for like |
-| thau_x10sa_16keV | inhouse | 50.000 1.300 | 1.22 | 94.3 / 94.3 | 18.5 / 18.4 | 24.7 | 7.1% / 7.2% | 2.9% / 2.7% (3.89 / 3.89) | 0.9997 / 1.000 | 0.60 | 51.2 / 44.5 | like for like |
-| thau_x10sa_injection | inhouse | 50.000 1.280 | 1.26 | 86.3 / 86.2 | 10.1 / 10.0 | 37.2 | 3.9% / 3.7% | 2.6% / 2.2% (3.83 / 3.83) | 0.9998 / 1.000 | 0.40 | 32.9 / 36.2 | like for like |
-| yag_x10sa_20keV | inhouse | 50.000 0.680 | 0.66 | 99.6 / 99.0 | 36.3 / 28.4 | 21.6 | 40.2% / 43.2% | 44.7% / 43.6% (2.04 / 1.99) | 0.8981 / 0.947 | 2.01 | 2.9 / 3.2 | like for like |
-
-Data quality is not scored; this table is for a human to judge. CC1/2 = S / (S + E) (signal and half-set error variances), so 1 / CC1/2 - 1 = E / S is the half-set noise; the noise ratio is rugnux's over XDS's, with XDS's CC1/2 taken at the bottom of its printed rounding (-0.0005); 2 would mean noisier than XDS's merge with half its observations. The low-resolution R_meas is the lowest shell of each table (the shells are XDS's, so both cover the same reflections); reported like everything here.
-
-### Small molecules: SHELXL refinement of the published structure
-
-The set's structure from the Crystallography Open Database (COD id) refined against our p.hkl by SHELXL with one fixed recipe (shelx_check.py: data reindexed into the COD setting, non-H anisotropic, H fixed at the COD positions, EXTI refined, three rounds with the weights SHELXL suggests, MERG 2), the way a chemical crystallographer judges data. WGHT a near its 0.2 ceiling and a large EXTI mean the strong reflections or the sigmas are off; K top is <Fo2>/<Fc2> of SHELXL's strongest analysis-of-variance bin (below 1: strong reflections read low). Fixed-model R1(F) scores the data against |Fc| of the COD model as published, one scale, nothing refined. R(int) means something only for unmerged data. Reported, never scored.
-
-| set | arm | COD | own d_min | R1 >4sig (n) | wR2 | GooF | EXTI | WGHT a / b | peak / hole e/A3 | R(int) / R(sigma) | K top | fixed-model R1(F) | status |
-|:--|:--|:--|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|:--|
-| cytidine | open | 2001311 | 0.58 | 0.0644 (3507) | 0.1842 | 1.075 | 0.072 | 0.040 / 0.16 | 0.29 / -0.25 | 0.0854 / 0.0893 | 1.025 | 0.1168 | ok |
-| dnba | open | 4510615 | 0.81 | 0.0269 (1171) | 0.0710 | 1.070 | 0.003 | 0.031 / 1.86 | 0.21 / -0.21 | 0.0196 / 0.0215 | 1.009 | 0.0791 | ok |
-| lalanine | open | 2311261 | 0.65 | 0.0367 (1066) | 0.1095 | 1.137 | 0.000 | 0.058 / 0.13 | 0.24 / -0.26 | 0.0194 / 0.0250 | 1.017 | 0.0500 | ok |
-| metformin | open | 2108029 | 0.51 | 0.0326 (4457) | 0.1031 | 1.123 | 0.000 | 0.047 / 0.38 | 0.64 / -0.37 | 0.0285 / 0.0205 | 1.011 | 0.0379 | ok |
-| nidppe | open | 2012031 | 0.51 | 0.0420 (9285) | 0.1050 | 1.038 | 0.004 | 0.039 / 0.54 | 0.63 / -0.71 | 0.0738 / 0.0533 | 0.993 | 0.1541 | ok |
-| aspirin_x10sa_20keV | inhouse | 7050897 | 0.66 | 0.0370 (2288) | 0.1152 | 1.128 | 0.010 | 0.059 / 0.31 | 0.40 / -0.38 | 0.0273 / 0.0172 | 1.006 | 0.0820 | ok |
-| aspirin_x10sa_25keV | inhouse | 7050897 | 0.53 | 0.0361 (4375) | 0.1188 | 1.073 | 0.011 | 0.073 / 0.10 | 0.59 / -0.45 | 0.0286 / 0.0183 | 1.008 | 0.0942 | ok |
-| citricacid_x10sa_20keV | inhouse | 5000063 | 0.67 | 0.0393 (2086) | 0.1060 | 1.098 | 0.180 | 0.052 / 0.39 | 0.40 / -0.26 | 0.0368 / 0.0289 | 1.013 | 0.2734 | ok |
-| hepes_x10sa_20keV | inhouse | 2224210 | 0.66 | 0.0307 (3355) | 0.0862 | 1.060 | 0.048 | 0.051 / 0.70 | 0.42 / -0.53 | 0.0260 / 0.0127 | 1.013 | 0.0424 | ok |
-| kdp_x10sa_20keV | inhouse | 9009999 | 0.66 | 0.0475 (305) | 0.1206 | 1.380 | 0.027 | 0.000 / 6.36 | 0.80 / -0.74 | 0.0521 / 0.0250 | 0.990 | 0.2662 | ok |
-| lcystine_x10sa_20keV | inhouse | 1513328 | 0.67 | 0.1251 (1154) | 0.3491 | 1.077 | 0.000 | 0.189 / 5.81 | 0.93 / -0.76 | 0.4085 / 0.1561 | 1.199 | 0.1758 | ok |
-| lcystine_x10sa_25keV | inhouse | 1513328 | 0.53 | 0.1116 (2019) | 0.3236 | 1.129 | 0.000 | 0.163 / 1.08 | 1.58 / -1.98 | 0.3961 / 0.1547 | 1.119 | 0.2390 | ok |
-| yag_x10sa_20keV | inhouse | 2003066 | 0.66 | 0.1005 (245) | 0.2385 | 1.110 | 0.533 | 0.177 / 23.16 | 2.74 / -4.37 | 0.5137 / 0.1066 | 0.871 | 0.1684 | ok |
-
-XDS merged past its own signal (CC1/2 of its finest shell not significant), so the reference d_min is where XDS's CC1/2 falls through 0.30, and that is also the d_min of the reference-range table: cytc_x10sa (XDS range 2.04 A, reference 2.27 A); insu_I_x06da_weak (XDS range 1.08 A, reference 1.81 A); lyso_x10sa_strong (XDS range 1.18 A, reference 1.24 A). XDS's pooled R_meas, CC1/2 and completeness are over its whole range.
-
-### Failures
-
-| set | arm | cause | reason |
-|:--|:--|:--|:--|
-| 3r6o | open | sym_over | I 41 2 2 vs reference I 41 |
-| 5cc8 | open | sym_screw | P 21 21 21 vs reference P 21 21 2 |
-| 5ebi | open | sym_over | C 2 2 21 vs reference P 1 21 1 |
-| 9hnc | open | sym_screw | P 1 21 1 vs reference P 1 2 1 |
-| 9min | open | lattice_halved | primitive volume ratio 0.49 |
-| 5ky6 | open | sym_screw | P 1 2 1 vs reference P 1 21 1 |
-| 6z9g | open | lattice_halved | primitive volume ratio 0.51 |
-| 8c3e | open | sym_over | P 6 2 2 vs reference P 31 2 1 |
-| 4bwl | open | sym_over | C 2 2 21 vs reference P 1 21 1 |
-| 2wnq | open | sym_over | C 2 2 21 vs reference P 1 21 1 |
-| 2ygz | open | sym_over | C 2 2 21 vs reference P 1 21 1 |
-| 6oww | open | sym_over | P 41 21 2 vs reference P 1 21 1 |
-| 6p8j | open | sym_screw | P 1 1 2 vs reference P 1 21 1 |
-| insu_I_x06da_low_isa | inhouse | lattice_doubled | primitive volume ratio 2.00 |
-
-Not scored: 7k1l (P 6 vs reference P 63: the screw along c is undeterminable from these data (offered P 61 | P 65 | P 62 | P 64 | P 63)); 7mzt (P 21 21 21 vs reference P 21 21 2: the screw along c is undeterminable from these data (offered P 21 21 2)); cuhf2 (no reference to score against)
-
-### Accepted alternatives
-
-4 of the passes above are rows that accept more than one reference: the deposition and our reduction disagree, the disagreement is real, and no test available to us settles it, so either answer passes as long as the program picks one of them. These are open questions, not errors attributed to the deposition; the manifest's `ref` keeps the deposited values verbatim in every one of them.
-
-- 6pxb (open): we report P 31 1 2, the reference is P 32; accepted as P 32 1 2. The deposition merged in point group 3 (its 55502 unique reflections to 1.747 A are what Laue class -3 holds, twice what -3 1 m would) and refined six chains in P 32. The intensities read point group 312 instead: the three added two-folds correlate at 0.98-0.99, at or above the three-folds nobody disputes (0.98), against 0.37-0.40 for the 321 and 622 operators, POINTLESS on our P1 merge picks P -3 1 m (likelihood 1.000), and the reflections centric in 312 but not in 3 are distributed as centric (+435 nats), which a twin law cannot produce. Against that, the deposited chains pair under the added two-fold at 0.3-0.7 A, more than coordinate error at 1.75 A, and the model tells the two indexings apart (R 0.22 against 0.25), so the two-fold may be a near-exact non-crystallographic one; ZANUDA settles on P 32 2 1, whose operators these data do not support. Neither answer is established, so both are accepted; P 31 1 2, which the data cannot separate from P 32 1 2, is accepted as its hand
-- 6toc (open): we report P 42 2 2, the reference is P 42; accepted as P 42 2 2. Our reduction and an independent POINTLESS run on our own P1 merge both read point group 422, and the deposited asymmetric unit's two chains are related by the very two-fold the higher group adds, to 0.16 A CA RMSD over 43 residues - coordinate error at 1.85 A. Merging in P 42 2 2 costs 0.0006 in R_meas for 1.75x the multiplicity and correlates better with the deposited model (0.9802 vs 0.9764). The refinement test is NOT unanimous: ZANUDA 1.097 refines P 42 2 2 to R-free 0.2561 against P 42's 0.2636 at half the parameters and reports the deposited assignment incorrect, while an independent Refmac 5.8.0431 comparison on a symmetry-consistent free set puts P 42 ahead by 0.004-0.020 depending on cycle count - less than the spread between refinement protocols. Neither answer is established: a pseudo-symmetry too exact for any test we have remains a live explanation, and so does the deposited assignment. Either is accepted
-- 8xte (open): we report P 31 2 1, the reference is P 32; accepted as P 31 2 1. The evidence favours the higher group here. The twin-immune centric zone of the added two-folds - reflections the higher group makes centric, which are their own twin mates and so cannot be made to read centric by a merohedral twin law - gives <|E^2-1|> = 0.946 +/- 0.012 against a centric expectation of 0.968 and an acentric 0.736, at +707 nats. Re-refinement on a shared free set with the twin law removed from both sides favours P 3_2 2 1 (0.2177/0.2322) over P 3_2 (0.2460/0.2612), and the deposited entry's published R values reproduce only with an undeclared twin law h,-h-k,-l at alpha = 0.50, which is itself a 321-symmetric target. No refinement R can close the question in principle, because a merohedral twin at exactly alpha = 0.5 and true 321 predict identical intensities; the case rests on the centric zone. Both answers are accepted, ours being the better supported
-- 8xtg (open): we report P 31 2 1, the reference is P 32; accepted as P 31 2 1. The evidence favours the DEPOSITION here, and this row must not be read as the 8xte one. Every correlation-based instrument we have - our own operator correlations, POINTLESS (0.85 on our P1 merge) - reads point group 321, but our own twin-immune centric-zone test, the only one that separates real symmetry from pseudo-symmetry, read <|E^2-1|> = 0.869 at -44.9 nats against the promotion when it assumed an untwinned zone; read at the fraction of the crystal's other twin laws (rc174) it now favours the promotion, with an L-test twin fraction of 0.20-0.26. Whether this crystal is partially twinned or purely pseudo-symmetric is not established. Both answers are accepted, the deposition being the better supported
-
-### Per set
-
-Space group: on the open arm the data's own determination. Where --model put the model's enantiomorph on the label, the label is in the note and the group scored is the search's.
-
-R_free and R_work describe one run against its model and do not carry across runs: the model is scaled to the data by an overall factor and an anisotropic B, so whatever the amplitudes' radial profile does that this shape cannot follow is reported as R, and a change in the profile alone moves R_free further than a real change in the data does. R_model (shell-scaled) is the same R with one free scale per resolution shell removing exactly that, over every reflection rather than the free 5%, and it is the column to read in a delta table. Radial misfit is how big that per-shell rescale had to be (the RMS of its logarithm): when it moves between two runs, R_free between them means little. Both are reported for a human to judge; nothing is scored on them.
-
-Anom. sigma is the anomalous difference map (F+ - F- on the model's phases) read at the model's anomalous scatterers - every atom from phosphorus up: the S of Met and Cys, metals, Cl, I - and averaged, in units of the map's r.m.s.: how much anomalous signal the merge carries, on the model's yardstick. Reported, never scored.
-
-| set | arm | verdict | space group | ref | cell dev % | V ratio | d_min | ref d_min | gain | compl % | mult | R_meas | low-res R_meas | CC1/2 | ISa | ref ISa | idx | R_model (shell-scaled) | radial misfit | CC model | R_free (within-run) | R_work | dep R_free | R_free ratio | anom. sigma | dCC dep. outer | model fit | time s | note |
-|:--|:--|:--|:--|:--|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|--:|:--|
-| 11if | open | pass | P 41 | P 43 | 0.14 | 0.998 | 1.36 | 1.51 | +9.9% | 88.6 | 11.1 | 4.8% | 2.8% | 1.000 | 26.1 | - | - | 0.192 | 0.140 | 0.966 | 0.189 | 0.198 | 0.210 | 0.899 | 3.090 | 0.020 | ACCEPTED | 8 | P 41 vs reference P 43 (hand only (needs anomalous)); labelled P 43 from the model |
-| 2wnn | open | pass | P 1 21 1 | P 1 21 1 | 0.09 | 1.003 | 1.43 | 1.65 | +13.3% | 72.2 | 3.6 | 6.7% | 4.2% | 0.998 | 15.2 | - | - | 0.279 | 0.187 | 0.914 | 0.287 | 0.284 | 0.249 | 1.154 | 1.040 | -0.348 | NOT_TESTED | 22 |  |
-| 2wnq | open | fail | C 2 2 21 | P 1 21 1 | 68.38 | 0.996 | 1.65 | 1.80 | +8.4% | 96.8 | 7.1 | 10.9% | 5.8% | 0.997 | 10.6 | - | - | 0.536 | 0.183 | 0.335 | 0.537 | 0.545 | 0.253 | 2.122 | -0.060 | -0.550 | NOT_TESTED | 26 | C 2 2 21 vs reference P 1 21 1 |
-| 2wnz | open | pass | P 1 21 1 | P 1 21 1 | 0.20 | 1.002 | 1.85 | 1.85 | +0.1% | 99.7 | 3.7 | 11.1% | 3.5% | 0.997 | 17.4 | - | - | 0.202 | 0.213 | 0.936 | 0.229 | 0.232 | 0.225 | 1.017 | 0.990 | -0.340 | ACCEPTED | 21 |  |
-| 2xfw | open | pass | P 1 21 1 | P 1 21 1 | 0.07 | 1.000 | 1.54 | 1.65 | +6.8% | 99.7 | 3.7 | 14.1% | 4.1% | 0.996 | 15.3 | - | - | 0.198 | 0.159 | 0.953 | 0.219 | 0.217 | 0.182 | 1.204 | 1.180 | -0.451 | ACCEPTED | 48 |  |
-| 2ygz | open | fail | C 2 2 21 | P 1 21 1 | 39.55 | 0.999 | 1.71 | 1.80 | +5.1% | 99.7 | 14.5 | 25.4% | 10.7% | 0.993 | 4.3 | - | - | - | - | - | - | - | - | - | - | - | - | 32 | C 2 2 21 vs reference P 1 21 1 |
-| 36gk | open | pass | I 2 2 2 | I 2 2 2 | 0.08 | 0.999 | 2.10 | 2.28 | +7.8% | 99.7 | 13.8 | 15.8% | 7.4% | 0.998 | 11.6 | - | - | 0.202 | 0.110 | 0.950 | 0.203 | 0.212 | 0.223 | 0.913 | 2.820 | 0.015 | NOT_TESTED | 23 |  |
-| 3inp | open | pass | F 41 3 2 | F 41 3 2 | 0.04 | 1.001 | 1.70 | 2.05 | +17.0% | 99.7 | 18.7 | 10.5% | 5.5% | 0.999 | 13.2 | - | - | 0.237 | 0.084 | 0.945 | 0.239 | 0.240 | 0.177 | 1.352 | 3.150 | 0.003 | NOT_TESTED | 22 |  |
-| 3ky7 | open | pass | P 43 3 2 | P 43 3 2 | 0.03 | 1.001 | 1.92 | 2.35 | +18.3% | 99.7 | 25.7 | 10.6% | 5.8% | 0.999 | 12.2 | - | - | 0.339 | 0.051 | 0.899 | 0.334 | 0.341 | 0.255 | 1.310 | 0.380 | 0.002 | NOT_TESTED | 19 |  |
-| 3mc4 | open | pass | R 3:H | H 3 | 0.15 | 0.997 | 1.79 | 1.95 | +8.0% | 79.9 | 3.3 | 10.2% | 8.5% | 0.994 | 12.1 | - | - | 0.251 | 0.061 | 0.901 | 0.256 | 0.253 | 0.156 | 1.640 | 1.550 | -0.328 | ACCEPTED | 6 |  |
-| 3meb | open | pass | P 1 21 1 | P 1 21 1 | 0.91 | 0.982 | 1.70 | 1.90 | +10.3% | 43.3 | 2.1 | 14.5% | 9.9% | 0.987 | 13.2 | - | - | 0.202 | 0.085 | 0.951 | 0.205 | 0.206 | 0.214 | 0.959 | -0.160 | -0.138 | NOT_TESTED | 5 |  |
-| 3p85 | open | pass | P 63 2 2 | P 63 2 2 | 0.47 | 1.007 | 1.62 | 1.90 | +14.7% | 86.4 | 10.8 | 11.6% | 9.4% | 0.998 | 8.5 | - | - | 0.194 | 0.131 | 0.952 | 0.201 | 0.201 | 0.216 | 0.930 | 7.830 | -0.396 | NOT_TESTED | 9 |  |
-| 3r6o | open | fail | I 41 2 2 | I 41 | 0.54 | 0.987 | 1.53 | 1.95 | +21.5% | 42.9 | 7.2 | 19.3% | 17.4% | 0.985 | 4.4 | - | - | 0.302 | 0.718 | 0.807 | 0.308 | 0.305 | 0.185 | 1.667 | 1.310 | -0.670 | NOT_TESTED | 4 | I 41 2 2 vs reference I 41 |
-| 4bwl | open | fail | C 2 2 21 | P 1 21 1 | 72.05 | 1.004 | 1.68 | 2.00 | +15.9% | 99.4 | 7.0 | 14.6% | 6.0% | 0.998 | 13.7 | - | - | 0.522 | 0.128 | 0.387 | 0.532 | 0.525 | 0.235 | 2.265 | 0.120 | -0.522 | NOT_TESTED | 21 | C 2 2 21 vs reference P 1 21 1 |
-| 5cc8 | open | fail | P 21 21 21 | P 21 21 2 | 0.11 | 1.000 | 1.53 | 1.75 | +12.7% | 44.9 | 4.1 | 8.1% | 7.0% | 0.997 | 10.8 | - | - | 0.168 | 0.239 | 0.958 | 0.182 | 0.176 | 0.194 | 0.942 | 4.510 | 0.037 | ACCEPTED | 7 | P 21 21 21 vs reference P 21 21 2 |
-| 5ebi | open | fail | C 2 2 21 | P 1 21 1 | 40.36 | 1.001 | 0.86 | 1.09 | +20.8% | 99.4 | 6.8 | 12.2% | 7.2% | 0.998 | 10.9 | - | - | 0.580 | 0.132 | 0.338 | 0.572 | 0.585 | 0.169 | 3.386 | -0.100 | 0.023 | REJECTED | 14 | C 2 2 21 vs reference P 1 21 1 |
-| 5epe | open | pass | F 2 3 | F 2 3 | 0.03 | 0.999 | 1.78 | 1.90 | +6.5% | 99.7 | 14.1 | 23.9% | 6.6% | 0.997 | 11.1 | - | - | 0.177 | 0.155 | 0.968 | 0.183 | 0.187 | 0.167 | 1.093 | 9.630 | -0.118 | ACCEPTED | 20 |  |
-| 5f6m | open | pass | P 21 21 21 | P 21 21 21 | 0.08 | 1.002 | 1.09 | 1.10 | +1.0% | 78.8 | 4.0 | 5.1% | 3.7% | 0.999 | 23.0 | - | - | 0.152 | 0.131 | 0.972 | 0.165 | 0.160 | 0.154 | 1.065 | 6.060 | -0.059 | NOT_TESTED | 6 |  |
-| 5j23 | open | pass | R 3:H | H 3 | 0.15 | 0.997 | 2.20 | 2.30 | +4.3% | 99.7 | 5.2 | 14.8% | 6.0% | 0.996 | 11.5 | - | - | 0.226 | 0.125 | 0.936 | 0.233 | 0.235 | 0.169 | 1.376 | 0.830 | 0.323 | ACCEPTED | 22 |  |
-| 5jk4 | open | pass | P 1 21 1 | P 1 21 1 | 0.15 | 1.000 | 0.96 | 1.10 | +12.3% | 75.2 | 3.9 | 9.1% | 4.2% | 0.998 | 14.5 | - | - | 0.111 | 0.153 | 0.980 | 0.128 | 0.125 | 0.125 | 1.026 | 3.690 | 0.022 | NOT_TESTED | 9 |  |
-| 5jvn | open | pass | P 6 2 2 | P 6 2 2 | 0.03 | 0.999 | 2.23 | 2.90 | +22.9% | 98.6 | 16.8 | 16.5% | 5.4% | 0.998 | 14.9 | - | - | 0.228 | 0.124 | 0.886 | 0.246 | 0.246 | 0.235 | 1.046 | 1.400 | 0.086 | NOT_TESTED | 29 |  |
-| 5ky6 | open | fail | P 1 2 1 | P 1 21 1 | 1.03 | 0.981 | 1.50 | 1.94 | +22.7% | 83.0 | 2.5 | 18.7% | 10.0% | 0.987 | 6.9 | - | - | 0.245 | 0.175 | 0.933 | 0.263 | 0.259 | 0.223 | 1.179 | 0.680 | -0.212 | NOT_TESTED | 18 | P 1 2 1 vs reference P 1 21 1 |
-| 5lzl | open | pass | P 31 2 1 | P 31 2 1 | 0.37 | 0.990 | 2.89 | 3.47 | +16.8% | 95.6 | 9.0 | 18.5% | 5.0% | 0.997 | 14.6 | - | - | 0.222 | 0.140 | 0.877 | 0.229 | 0.234 | 0.250 | 0.917 | 1.280 | -0.037 | NOT_TESTED | 10 |  |
-| 5m17 | open | pass | I 4 | I 4 | 0.10 | 0.998 | 0.98 | 1.03 | +4.7% | 92.3 | 6.0 | 5.5% | 5.1% | 0.996 | 16.1 | - | - | 0.132 | 0.216 | 0.961 | 0.158 | 0.157 | 0.130 | 1.214 | 7.030 | -0.031 | ACCEPTED | 64 |  |
-| 5mln | open | pass | P 21 21 2 | P 21 2 21 | 0.25 | 0.998 | 1.27 | 1.60 | +20.7% | 99.7 | 8.1 | 10.4% | 3.6% | 0.999 | 21.0 | - | - | 0.182 | 0.151 | 0.949 | 0.189 | 0.198 | 0.180 | 1.053 | 2.070 | -0.012 | ACCEPTED | 14 |  |
-| 5nw5 | open | pass | P 21 21 21 | P 21 21 21 | 0.24 | 0.996 | 7.04 | 6.50 | -8.3% | 99.6 | 6.3 | 32.8% | 14.5% | 0.937 | 8.4 | - | - | 0.396 | 0.237 | 0.775 | 0.462 | 0.414 | 0.277 | 1.671 | 0.110 | 0.031 | NOT_TESTED | 16 |  |
-| 5ojv | open | pass | P 21 21 2 | P 21 21 2 | 0.50 | 0.993 | 1.85 | 2.06 | +10.2% | 98.6 | 6.5 | 14.5% | 4.8% | 0.982 | 12.6 | - | - | 0.174 | 0.151 | 0.959 | 0.186 | 0.191 | 0.194 | 0.962 | 1.490 | -0.003 | NOT_TESTED | 34 |  |
-| 5reo | open | pass | C 1 2 1 | C 1 2 1 | 0.36 | 1.010 | 1.64 | 1.88 | +12.8% | 99.4 | 3.0 | 23.6% | 8.0% | 0.989 | 23.0 | - | - | 0.205 | 0.056 | 0.960 | 0.201 | 0.208 | 0.227 | 0.888 | 0.720 | -0.034 | NOT_TESTED | 7 |  |
-| 5src | open | pass | P 41 | P 43 | 0.15 | 0.998 | 0.97 | 1.05 | +7.8% | 99.0 | 6.2 | 5.7% | 3.1% | 0.999 | 19.4 | - | - | 0.161 | 0.189 | 0.962 | 0.182 | 0.180 | 0.175 | 1.040 | 5.970 | 0.033 | ACCEPTED | 28 | P 41 vs reference P 43 (hand only (needs anomalous)); labelled P 43 from the model |
-| 5t39 | open | pass | P 1 21 1 | P 1 21 1 | 0.17 | 1.004 | 1.00 | 1.10 | +8.9% | 89.9 | 4.2 | 7.3% | 4.4% | 0.998 | 16.1 | - | - | 0.151 | 0.079 | 0.956 | 0.156 | 0.154 | 0.154 | 1.016 | 6.350 | -0.054 | NOT_TESTED | 21 |  |
-| 5uth | open | pass | P 31 2 1 | P 31 2 1 | 0.23 | 0.994 | 1.72 | 1.95 | +11.7% | 82.7 | 8.4 | 12.6% | 7.2% | 0.997 | 10.4 | - | - | 0.196 | 0.184 | 0.952 | 0.221 | 0.212 | 0.202 | 1.092 | 2.600 | -0.037 | ACCEPTED | 5 |  |
-| 5vml | open | pass | P 42 21 2 | P 42 21 2 | 0.05 | 0.999 | 1.91 | 1.70 | -12.1% | 80.2 | 7.4 | 10.2% | 9.8% | 0.996 | 11.0 | - | - | 0.156 | 0.061 | 0.964 | 0.163 | 0.158 | 0.171 | 0.954 | 3.520 | -0.034 | NOT_TESTED | 5 |  |
-| 6cdl | open | pass | P 21 21 2 | P 21 21 2 | 0.94 | 1.013 | 1.13 | 1.25 | +9.8% | 71.5 | 6.6 | 8.5% | 6.9% | 0.996 | 10.0 | - | - | 0.147 | 0.149 | 0.950 | 0.154 | 0.153 | 0.181 | 0.851 | 4.350 | -0.017 | NOT_TESTED | 20 |  |
-| 6cee | open | pass | P 21 21 21 | P 21 21 21 | 0.05 | 1.001 | 1.38 | 1.55 | +10.8% | 87.8 | 6.1 | 5.4% | 3.5% | 0.999 | 24.1 | - | - | 0.166 | 0.131 | 0.952 | 0.174 | 0.182 | 0.169 | 1.030 | 8.930 | 0.001 | NOT_TESTED | 6 |  |
-| 6cs9 | open | pass | P 1 21 1 | P 1 21 1 | 0.07 | 0.999 | 1.71 | 1.85 | +7.8% | 90.1 | 3.8 | 10.1% | 4.3% | 0.998 | 12.9 | - | - | 0.211 | 0.146 | 0.903 | 0.206 | 0.227 | 0.227 | 0.908 | 0.790 | 0.010 | NOT_TESTED | 8 |  |
-| 6f3p | open | pass | C 1 2 1 | C 1 2 1 | 0.21 | 0.994 | 1.15 | 1.35 | +14.9% | 99.7 | 3.7 | 10.0% | 5.4% | 0.997 | 9.3 | - | - | 0.143 | 0.196 | 0.967 | 0.166 | 0.166 | 0.127 | 1.305 | -3.320 | 0.013 | NOT_TESTED | 32 |  |
-| 6fid | open | pass | P 21 21 21 | P 21 21 21 | 0.40 | 1.007 | 1.98 | 2.20 | +10.1% | 72.9 | 12.5 | 9.6% | 10.3% | 0.998 | 13.5 | - | - | 0.193 | 0.057 | 0.944 | 0.197 | 0.199 | 0.220 | 0.899 | 11.290 | -0.018 | NOT_TESTED | 20 |  |
-| 6fvz | open | pass | C 2 2 2 | C 2 2 2 | 0.18 | 0.996 | 1.48 | 1.80 | +17.7% | 99.4 | 6.7 | 24.5% | 5.1% | 0.996 | 20.8 | - | - | 0.198 | 0.091 | 0.954 | 0.202 | 0.206 | 0.199 | 1.019 | 1.330 | -0.005 | NOT_TESTED | 24 |  |
-| 6fwc | open | pass | C 2 2 2 | C 2 2 2 | 0.04 | 0.999 | 1.41 | 1.70 | +16.9% | 94.7 | 4.0 | 16.4% | 4.3% | 0.995 | 27.3 | - | - | 0.188 | 0.098 | 0.959 | 0.196 | 0.198 | 0.189 | 1.037 | 1.450 | 0.018 | NOT_TESTED | 14 |  |
-| 6g1f | open | pass | C 1 2 1 | C 1 2 1 | 0.06 | 0.999 | 1.98 | 2.25 | +12.1% | 99.6 | 3.8 | 11.2% | 3.8% | 0.997 | 20.8 | - | - | 0.206 | 0.112 | 0.953 | 0.218 | 0.217 | 0.211 | 1.038 | 1.040 | 0.013 | NOT_TESTED | 24 |  |
-| 6gvk | open | pass | C 1 2 1 | C 1 2 1 | 0.13 | 0.997 | 1.42 | 1.55 | +8.5% | 99.7 | 6.7 | 5.3% | 3.3% | 0.999 | 19.5 | - | - | 0.201 | 0.183 | 0.951 | 0.215 | 0.213 | 0.210 | 1.024 | 2.020 | -0.006 | NOT_TESTED | 17 |  |
-| 6h2p_1p89A | open | pass | C 2 2 21 | C 2 2 21 | 0.08 | 0.998 | 1.76 | - | - | 87.8 | 10.2 | 8.7% | 5.3% | 0.999 | 22.6 | - | - | 0.144 | 0.073 | 0.971 | 0.149 | 0.148 | 0.170 | 0.876 | 9.050 | 0.026 | NOT_TESTED | 26 |  |
-| 6h2p_native | open | pass | C 2 2 21 | C 2 2 21 | 0.06 | 0.999 | 1.32 | 1.48 | +10.8% | 99.5 | 6.6 | 13.6% | 4.0% | 0.999 | 19.8 | - | - | 0.160 | 0.070 | 0.973 | 0.165 | 0.165 | 0.170 | 0.968 | 3.320 | 0.042 | NOT_TESTED | 29 |  |
-| 6h5t | open | pass | I 4 2 2 | I 4 2 2 | 0.40 | 0.991 | 1.45 | 1.69 | +13.9% | 99.1 | 7.3 | 14.7% | 8.3% | 0.996 | 9.3 | - | - | 0.197 | 0.209 | 0.941 | 0.225 | 0.221 | 0.191 | 1.179 | 9.050 | -0.014 | NOT_TESTED | 13 |  |
-| 6hv2 | open | pass | P 61 2 2 | P 61 2 2 | 0.06 | 0.999 | 1.40 | 1.71 | +18.0% | 99.7 | 28.9 | 19.8% | 5.4% | 1.000 | 14.6 | - | - | 0.219 | 0.260 | 0.948 | 0.239 | 0.241 | 0.263 | 0.907 | 7.840 | -0.004 | NOT_TESTED | 19 |  |
-| 6hwj | open | pass | P 1 21 1 | P 1 21 1 | 0.10 | 1.001 | 1.70 | 1.98 | +13.9% | 97.5 | 3.5 | 9.2% | 2.5% | 0.999 | 39.0 | - | - | 0.189 | 0.102 | 0.961 | 0.190 | 0.196 | 0.214 | 0.887 | 1.500 | 0.052 | NOT_TESTED | 10 |  |
-| 6i3j | open | pass | F 2 2 2 | F 2 2 2 | 0.17 | 1.000 | 2.33 | 2.59 | +10.1% | 98.9 | 7.2 | 21.5% | 12.7% | 0.985 | 7.8 | - | - | 0.192 | 0.179 | 0.934 | 0.229 | 0.228 | 0.226 | 1.016 | 2.070 | -0.005 | NOT_TESTED | 19 |  |
-| 6iu5 | open | pass | P 31 | P 31 | 0.02 | 1.000 | 2.12 | 2.25 | +5.9% | 99.2 | 4.8 | 18.2% | 11.2% | 0.993 | 8.0 | - | - | 0.212 | 0.079 | 0.932 | 0.215 | 0.221 | 0.250 | 0.862 | 7.660 | -0.018 | ACCEPTED | 17 |  |
-| 6iu6 | open | pass | P 31 | P 31 | 0.33 | 0.996 | 2.35 | 2.90 | +19.0% | 97.0 | 4.2 | 11.7% | 8.2% | 0.996 | 7.1 | - | - | 0.221 | 0.170 | 0.947 | 0.234 | 0.239 | 0.211 | 1.110 | 3.540 | -0.018 | ACCEPTED | 16 |  |
-| 6iu8 | open | pass | P 31 | P 31 | 0.09 | 0.998 | 2.34 | 2.70 | +13.4% | 99.7 | 10.2 | 14.2% | 7.5% | 0.997 | 8.0 | - | - | 0.270 | 0.149 | 0.911 | 0.281 | 0.280 | 0.215 | 1.311 | 1.210 | -0.028 | ACCEPTED | 11 |  |
-| 6iu9 | open | pass | P 31 | P 31 | 0.20 | 1.002 | 2.76 | 3.00 | +8.0% | 99.6 | 4.8 | 13.9% | 9.7% | 0.994 | 5.5 | - | - | 0.313 | 0.106 | 0.819 | 0.323 | 0.315 | 0.265 | 1.218 | 1.470 | -0.024 | ACCEPTED | 17 |  |
-| 6jgh | open | pass | P 21 21 21 | P 21 21 21 | 0.34 | 1.008 | 0.88 | 0.94 | +6.3% | 99.3 | 7.3 | 23.0% | 10.7% | 0.990 | 6.7 | - | - | 0.134 | 0.155 | 0.964 | 0.153 | 0.154 | 0.129 | 1.184 | 2.060 | -0.067 | NOT_TESTED | 28 |  |
-| 6jgi | open | pass | P 21 21 21 | P 21 21 21 | 0.20 | 0.997 | 0.75 | 0.85 | +11.9% | 98.5 | 7.0 | 14.3% | 8.5% | 0.995 | 8.4 | - | - | 0.112 | 0.147 | 0.974 | 0.128 | 0.127 | 0.112 | 1.148 | 6.310 | 0.068 | NOT_TESTED | 31 |  |
-| 6jgj | open | pass | P 21 21 21 | P 21 21 21 | 0.37 | 0.992 | 0.65 | 0.77 | +16.0% | 84.5 | 7.0 | 7.4% | 4.6% | 0.999 | 15.1 | - | - | 0.163 | 0.052 | 0.965 | 0.167 | 0.166 | 0.125 | 1.333 | 2.590 | 0.032 | NOT_TESTED | 30 |  |
-| 6moj | open | pass | I 41 2 2 | I 41 2 2 | 0.14 | 0.997 | 2.43 | 2.43 | +0.0% | 99.7 | 26.2 | 51.5% | 8.8% | 0.998 | 8.4 | - | - | 0.248 | 0.196 | 0.917 | 0.258 | 0.262 | 0.250 | 1.029 | 1.140 | 0.026 | NOT_TESTED | 37 |  |
-| 6nen | open | pass | P 3 1 2 | P 3 1 2 | 0.17 | 0.998 | 1.77 | 2.15 | +17.8% | 99.6 | 22.0 | 26.2% | 10.4% | 0.997 | 6.1 | - | - | 0.208 | 0.116 | 0.936 | 0.217 | 0.216 | 0.208 | 1.046 | 0.250 | 0.003 | NOT_TESTED | 13 |  |
-| 6o2h | open | pass | P 1 | P 1 | 0.74 | 0.982 | 1.10 | 1.21 | +9.5% | 30.3 | 1.1 | 7.0% | 8.3% | 0.977 | 23.9 | - | - | 0.096 | 0.132 | 0.934 | 0.129 | 0.127 | 0.117 | 1.103 | 0.110 | -0.003 | ACCEPTED | 9 |  |
-| 6oel | open | pass | F 41 3 2 | F 41 3 2 | 0.09 | 0.997 | 2.85 | 3.10 | +8.2% | 99.7 | 40.2 | 36.1% | 8.0% | 0.998 | 10.3 | - | - | 0.248 | 0.134 | 0.812 | 0.255 | 0.258 | 0.256 | 0.998 | 0.610 | -0.031 | NOT_TESTED | 25 |  |
-| 6oww | open | fail | P 41 21 2 | P 1 21 1 | 0.24 | 0.997 | 2.83 | 3.84 | +26.3% | 99.7 | 41.4 | 177.6% | 13.4% | 0.995 | 12.4 | - | - | 0.355 | 0.060 | 0.866 | 0.366 | 0.358 | 0.340 | 1.075 | 2.060 | -0.043 | ACCEPTED | 29 | P 41 21 2 vs reference P 1 21 1 |
-| 6p8j | open | fail | P 1 1 2 | P 1 21 1 | 0.38 | 0.993 | 1.38 | 1.47 | +6.1% | 98.4 | 3.1 | 19.7% | 7.9% | 0.980 | 5.0 | - | - | 0.235 | 0.096 | 0.920 | 0.245 | 0.244 | 0.229 | 1.071 | 0.890 | 0.063 | ACCEPTED | 53 | P 1 1 2 vs reference P 1 21 1 |
-| 6p8p | open | pass | P 4 | P 4 | 0.12 | 1.003 | 1.45 | 1.64 | +11.5% | 99.7 | 6.7 | 13.6% | 5.0% | 0.998 | 16.0 | - | - | 0.191 | 0.112 | 0.951 | 0.203 | 0.202 | 0.198 | 1.024 | 1.890 | -0.013 | NOT_TESTED | 15 |  |
-| 6pb3 | open | pass | P 6 | P 6 | 0.11 | 1.003 | 1.84 | 2.05 | +10.1% | 93.5 | 10.3 | 6.6% | 3.0% | 1.000 | 24.8 | - | - | 0.214 | 0.102 | 0.957 | 0.227 | 0.218 | 0.252 | 0.903 | 10.520 | 0.046 | ACCEPTED | 25 |  |
-| 6pxb | open | pass | P 31 1 2 | P 32 | 0.27 | 0.994 | 1.41 | 1.75 | +19.5% | 99.7 | 10.0 | 8.7% | 4.7% | 0.999 | 12.0 | - | - | 0.239 | 0.240 | 0.959 | 0.276 | 0.259 | 0.263 | 1.050 | 0.650 | -0.001 | NOT_TESTED | 11 | P 31 1 2 vs reference P 32: accepted alternative P 32 1 2 - a knife-edge this battery does not decide |
-| 6pxc | open | pass | I 2 2 2 | I 2 2 2 | 0.24 | 0.995 | 1.43 | 1.60 | +10.9% | 96.8 | 5.7 | 7.7% | 5.3% | 0.998 | 10.5 | - | - | 0.209 | 0.166 | 0.960 | 0.215 | 0.217 | 0.210 | 1.024 | 0.670 | 0.028 | NOT_TESTED | 10 |  |
-| 6qaj | open | pass | C 2 2 21 | C 2 2 21 | 0.47 | 0.991 | 2.78 | 2.90 | +4.2% | 99.7 | 9.2 | 24.5% | 4.8% | 0.999 | 12.8 | - | - | 0.320 | 0.191 | 0.861 | 0.331 | 0.328 | 0.291 | 1.138 | 4.320 | -0.064 | NOT_TESTED | 15 |  |
-| 6r72 | open | pass | P 1 21 1 | P 1 21 1 | 1.47 | 0.978 | 4.39 | 3.95 | -11.1% | 99.7 | 7.1 | 16.5% | 3.6% | 1.000 | 16.6 | - | - | 0.364 | 0.045 | 0.588 | 0.369 | 0.366 | 0.321 | 1.151 | 0.130 | -0.231 | NOT_TESTED | 19 |  |
-| 6rlr | open | pass | P 1 | P 1 | 0.08 | 0.999 | 1.94 | 2.00 | +3.0% | 97.7 | 3.5 | 12.1% | 4.0% | 0.998 | 16.3 | - | - | 0.249 | 0.077 | 0.897 | 0.255 | 0.254 | 0.279 | 0.911 | 0.690 | -0.034 | NOT_TESTED | 10 |  |
-| 6rym | open | pass | P 41 | P 43 | 0.06 | 0.998 | 1.45 | 1.46 | +0.5% | 79.7 | 3.9 | 4.2% | 4.1% | 0.998 | 22.8 | - | - | 0.170 | 0.246 | 0.940 | 0.190 | 0.183 | 0.184 | 1.033 | 14.380 | -0.009 | ACCEPTED | 10 | P 41 vs reference P 43 (hand only (needs anomalous)); labelled P 43 from the model |
-| 6s1u | open | pass | P 1 21 1 | P 1 21 1 | 0.13 | 1.002 | 1.76 | 1.90 | +7.4% | 95.3 | 3.8 | 22.2% | 5.7% | 0.991 | 13.4 | - | - | 0.201 | 0.108 | 0.950 | 0.199 | 0.210 | 0.235 | 0.847 | 0.580 | -0.005 | NOT_TESTED | 10 |  |
-| 6toc | open | pass | P 42 2 2 | P 42 | 0.34 | 0.990 | 1.65 | 1.85 | +11.2% | 99.7 | 24.3 | 9.8% | 2.3% | 1.000 | 25.1 | - | - | 0.277 | 0.168 | 0.973 | 0.273 | 0.283 | 0.265 | 1.030 | 0.540 | 0.136 | ACCEPTED | 8 | P 42 2 2 vs reference P 42: accepted alternative P 42 2 2 - a knife-edge this battery does not decide |
-| 6ttn | open | pass | P 21 21 21 | P 21 21 21 | 0.13 | 1.000 | 1.05 | 1.12 | +6.2% | 96.4 | 11.3 | 10.4% | 4.6% | 0.999 | 14.5 | - | - | 0.134 | 0.088 | 0.975 | 0.143 | 0.140 | 0.146 | 0.982 | 8.310 | 0.092 | NOT_TESTED | 42 |  |
-| 6u7g | open | pass | P 1 21 1 | P 1 21 1 | 0.09 | 1.002 | 1.89 | 2.35 | +19.7% | 79.3 | 3.3 | 7.7% | 4.1% | 0.998 | 13.5 | - | - | 0.197 | 0.105 | 0.919 | 0.200 | 0.203 | 0.218 | 0.916 | 1.590 | -0.102 | NOT_TESTED | 12 |  |
-| 6ukf | open | pass | P 1 21 1 | P 1 21 1 | 0.07 | 1.000 | 0.95 | 1.00 | +5.3% | 90.3 | 7.1 | 9.8% | 5.8% | 0.998 | 9.9 | - | - | 0.164 | 0.016 | 0.959 | 0.159 | 0.165 | 0.166 | 0.958 | 2.380 | 0.036 | NOT_TESTED | 35 |  |
-| 6v2r | open | pass | P 41 21 2 | P 41 21 2 | 0.03 | 1.000 | 1.38 | 1.60 | +13.6% | 92.5 | 11.3 | 5.2% | 2.9% | 1.000 | 24.6 | - | - | 0.205 | 0.221 | 0.945 | 0.209 | 0.230 | 0.235 | 0.889 | 12.720 | 0.009 | NOT_TESTED | 6 |  |
-| 6vww | open | pass | P 63 | P 63 | 0.20 | 1.005 | 1.99 | 2.20 | +9.7% | 99.7 | 5.6 | 16.4% | 8.9% | 0.993 | 8.0 | - | - | 0.240 | 0.119 | 0.925 | 0.243 | 0.249 | 0.178 | 1.370 | 0.660 | 0.004 | NOT_TESTED | 10 |  |
-| 6w4h | open | pass | P 31 2 1 | P 31 2 1 | 0.02 | 1.000 | 1.62 | 1.80 | +10.2% | 97.5 | 6.9 | 7.6% | 3.9% | 0.999 | 18.5 | - | - | 0.163 | 0.168 | 0.967 | 0.169 | 0.176 | 0.163 | 1.041 | 4.710 | -0.012 | ACCEPTED | 22 |  |
-| 6w75 | open | pass | P 31 2 1 | P 32 2 1 | 0.02 | 1.000 | 1.69 | 1.95 | +13.6% | 99.7 | 10.5 | 11.9% | 4.7% | 0.999 | 15.9 | - | - | 0.175 | 0.169 | 0.957 | 0.187 | 0.187 | 0.174 | 1.073 | 3.650 | -0.017 | ACCEPTED | 24 | P 31 2 1 vs reference P 32 2 1 (hand only (needs anomalous)); labelled P 32 2 1 from the model |
-| 6wzo | open | pass | P 1 | P 1 | 0.05 | 0.999 | 1.04 | 1.42 | +26.4% | 68.3 | 3.8 | 6.1% | 3.6% | 0.999 | 16.9 | - | - | 0.174 | 0.123 | 0.958 | 0.175 | 0.176 | 0.173 | 1.011 | 2.780 | -0.007 | NOT_TESTED | 38 |  |
-| 6yqf | open | pass | P 21 21 2 | P 21 21 2 | 0.80 | 1.019 | 3.23 | 3.33 | +2.9% | 99.5 | 5.1 | 65.4% | 10.4% | 0.995 | 5.0 | - | - | 0.435 | 0.212 | 0.923 | 0.459 | 0.445 | 0.367 | 1.249 | -0.160 | -0.268 | NOT_TESTED | 28 |  |
-| 6z8o | open | pass | P 1 21 1 | P 1 21 1 | 0.61 | 1.016 | 2.16 | 2.20 | +1.8% | 88.1 | 3.6 | 19.0% | 5.4% | 0.995 | 14.5 | - | - | 0.283 | 0.061 | 0.900 | 0.289 | 0.287 | 0.275 | 1.054 | 1.180 | -0.055 | NOT_TESTED | 12 |  |
-| 6z9g | open | fail | P 1 21 1 | P 1 21 1 | 21.74 | 0.512 | 1.67 | 1.76 | +4.9% | 87.8 | 4.3 | 12.5% | 4.8% | 0.996 | 14.5 | - | - | 0.536 | 0.155 | 0.155 | 0.547 | 0.542 | 0.240 | 2.281 | 0.060 | - | NOT_TESTED | 17 | primitive volume ratio 0.51 |
-| 6ze4 | open | pass | P 21 21 21 | P 21 21 21 | 0.48 | 0.990 | 1.29 | 1.60 | +19.1% | 96.1 | 8.0 | 20.5% | 5.8% | 0.988 | 10.5 | - | - | 0.222 | 0.064 | 0.956 | 0.226 | 0.224 | 0.202 | 1.116 | 1.730 | -0.107 | NOT_TESTED | 35 |  |
-| 6zqr | open | pass | P 4 | P 4 | 0.33 | 1.008 | 1.77 | 1.93 | +8.4% | 99.7 | 8.2 | 20.0% | 8.3% | 0.995 | 8.9 | - | - | 0.197 | 0.155 | 0.950 | 0.202 | 0.210 | 0.191 | 1.055 | 1.420 | -0.099 | ACCEPTED | 14 |  |
-| 6zqy | open | pass | P 4 | P 4 | 0.12 | 0.997 | 1.69 | 1.85 | +8.9% | 98.5 | 7.8 | 22.0% | 5.5% | 0.994 | 13.0 | - | - | 0.209 | 0.146 | 0.950 | 0.217 | 0.222 | 0.196 | 1.105 | 1.440 | -0.087 | NOT_TESTED | 26 |  |
-| 6zr0 | open | pass | P 4 | P 4 | 0.07 | 1.001 | 1.64 | 1.94 | +15.3% | 97.6 | 3.7 | 12.9% | 4.0% | 0.993 | 25.2 | - | - | 0.215 | 0.073 | 0.961 | 0.218 | 0.218 | 0.210 | 1.037 | 1.820 | 0.011 | ACCEPTED | 23 |  |
-| 7arr | open | pass | P 1 | P 1 | 0.14 | 1.003 | 0.92 | 1.10 | +16.6% | 69.9 | 3.5 | 3.8% | 3.0% | 0.999 | 18.7 | - | - | 0.155 | 0.167 | 0.965 | 0.162 | 0.160 | 0.161 | 1.007 | -0.410 | -0.074 | ACCEPTED | 23 |  |
-| 7atg | open | pass | P 21 21 21 | P 21 21 21 | 0.02 | 1.000 | 0.60 | 0.60 | +0.3% | 86.7 | 3.8 | 5.1% | 7.2% | 0.994 | 23.1 | - | - | 0.125 | 0.134 | 0.437 | 0.160 | 0.159 | 0.095 | 1.687 | 6.770 | -0.005 | NOT_TESTED | 31 |  |
-| 7bgt | open | pass | P 1 | P 1 | 0.36 | 0.990 | 1.79 | 1.93 | +7.0% | 98.0 | 2.2 | 13.6% | 5.7% | 0.993 | 16.9 | - | - | 0.195 | 0.121 | 0.955 | 0.207 | 0.206 | 0.212 | 0.979 | 0.220 | -0.007 | NOT_TESTED | 9 |  |
-| 7bgu | open | pass | P 1 | P 1 | 0.12 | 0.997 | 2.32 | 2.43 | +4.7% | 95.5 | 2.9 | 10.8% | 4.0% | 0.942 | 16.2 | - | - | 0.254 | 0.087 | 0.864 | 0.266 | 0.270 | 0.236 | 1.127 | -0.360 | -0.172 | NOT_TESTED | 7 |  |
-| 7brr | open | pass | P 1 21 1 | P 1 21 1 | 0.13 | 0.998 | 1.24 | 1.35 | +7.9% | 96.7 | 6.3 | 6.7% | 3.8% | 0.999 | 16.4 | - | - | 0.192 | 0.088 | 0.962 | 0.190 | 0.195 | 0.197 | 0.965 | 3.080 | -0.044 | NOT_TESTED | 12 |  |
-| 7dkp | open | pass | P 1 21 1 | P 1 21 1 | 0.14 | 1.004 | 1.20 | 1.45 | +17.0% | 69.6 | 7.4 | 12.2% | 4.6% | 0.998 | 26.5 | - | - | 0.159 | 0.119 | 0.969 | 0.163 | 0.165 | 0.160 | 1.014 | 2.710 | 0.016 | ACCEPTED | 20 |  |
-| 7k1l | open | unscored | P 6 | P 63 | 0.28 | 0.995 | 1.91 | 2.25 | +15.2% | 98.9 | 6.5 | 16.2% | 8.3% | 0.994 | 9.9 | - | - | 0.261 | 0.099 | 0.909 | 0.268 | 0.268 | 0.192 | 1.401 | 0.790 | 0.094 | NOT_TESTED | 12 | P 6 vs reference P 63: the screw along c is undeterminable from these data (offered P 61 / P 65 / P 62 / P 64 / P 63) |
-| 7kcn | open | pass | P 41 2 2 | P 41 2 2 | 0.04 | 1.001 | 1.39 | 1.46 | +4.7% | 92.8 | 20.7 | 7.9% | 7.6% | 0.999 | 11.8 | - | - | 0.172 | 0.159 | 0.961 | 0.190 | 0.190 | 0.182 | 1.044 | 8.350 | -0.012 | NOT_TESTED | 25 |  |
-| 7l6j | open | pass | I 41 3 2 | I 41 3 2 | 0.00 | 1.000 | 1.50 | 1.78 | +15.5% | 99.7 | 29.0 | 21.0% | 7.5% | 0.999 | 10.5 | - | - | 0.172 | 0.184 | 0.963 | 0.188 | 0.189 | 0.154 | 1.215 | 29.150 | -0.001 | NOT_TESTED | 31 |  |
-| 7l84 | open | pass | P 41 21 2 | P 43 21 2 | 0.04 | 1.000 | 1.70 | 1.70 | +0.0% | 91.6 | 33.5 | 9.1% | 13.0% | 0.999 | 11.3 | - | - | 0.150 | 0.091 | 0.911 | 0.169 | 0.164 | 0.162 | 1.042 | 17.540 | -0.007 | ACCEPTED | 13 | P 41 21 2 vs reference P 43 21 2 (hand only (needs anomalous)); labelled P 43 21 2 from the model |
-| 7mzt | open | unscored | P 21 21 21 | P 21 21 2 | 0.63 | 0.997 | 3.18 | 4.07 | +21.9% | 99.6 | 9.9 | 417.1% | 36.0% | 0.977 | 3.8 | - | - | 0.414 | 0.102 | 0.519 | 0.419 | 0.419 | 0.372 | 1.125 | -0.180 | -0.020 | ACCEPTED | 28 | P 21 21 21 vs reference P 21 21 2: the screw along c is undeterminable from these data (offered P 21 21 2) |
-| 7n0i | open | pass | P 21 21 21 | P 21 21 21 | 0.28 | 0.993 | 1.64 | 2.20 | +25.6% | 99.7 | 6.6 | 14.0% | 5.6% | 0.998 | 10.5 | - | - | 0.267 | 0.270 | 0.920 | 0.292 | 0.293 | 0.271 | 1.077 | 0.610 | 0.057 | NOT_TESTED | 18 |  |
-| 7n2s | open | pass | P 1 21 1 | P 1 21 1 | 0.04 | 0.999 | 2.56 | 2.37 | -8.1% | 97.6 | 3.4 | 58.6% | 7.1% | 0.927 | 14.5 | - | - | 0.301 | 0.122 | 0.820 | 0.316 | 0.312 | 0.311 | 1.015 | 0.110 | -0.024 | NOT_TESTED | 9 |  |
-| 7orr | open | pass | I 2 3 | I 21 3 | 0.06 | 0.998 | 1.64 | 1.79 | +8.7% | 99.7 | 15.9 | 7.1% | 4.1% | 1.000 | 25.4 | - | - | 0.183 | 0.153 | 0.966 | 0.198 | 0.195 | 0.184 | 1.073 | 5.080 | 0.053 | ACCEPTED | 15 | I 2 3 vs reference I 21 3 (UNDECIDABLE from intensities) |
-| 7os3 | open | pass | P 21 21 21 | P 21 21 21 | 0.17 | 1.004 | 1.96 | 2.18 | +10.2% | 83.6 | 11.4 | 8.9% | 3.8% | 0.999 | 23.8 | - | - | 0.183 | 0.134 | 0.954 | 0.192 | 0.193 | 0.224 | 0.860 | 5.740 | -0.006 | NOT_TESTED | 23 |  |
-| 7ou1 | open | pass | P 1 21 1 | P 1 21 1 | 0.05 | 1.000 | 1.39 | 1.65 | +15.6% | 86.7 | 3.3 | 15.7% | 7.7% | 0.991 | 9.0 | - | - | 0.202 | 0.105 | 0.956 | 0.209 | 0.210 | 0.222 | 0.945 | 1.480 | 0.085 | NOT_TESTED | 14 |  |
-| 7ph1 | open | pass | I 2 2 2 | I 2 2 2 | 0.12 | 0.998 | 1.09 | 1.18 | +7.6% | 99.7 | 7.1 | 11.2% | 5.4% | 0.998 | 16.1 | - | - | 0.155 | 0.163 | 0.968 | 0.175 | 0.173 | 0.166 | 1.056 | 3.230 | 0.042 | NOT_TESTED | 50 |  |
-| 7pq7 | open | pass | C 1 2 1 | C 1 2 1 | 0.30 | 0.992 | 1.39 | 1.55 | +10.6% | 98.6 | 3.7 | 6.6% | 4.4% | 0.998 | 13.6 | - | - | 0.188 | 0.194 | 0.946 | 0.215 | 0.210 | 0.200 | 1.073 | 2.280 | 0.009 | NOT_TESTED | 9 |  |
-| 7q6j | open | pass | P 21 21 21 | P 21 21 21 | 0.40 | 0.995 | 2.00 | 2.20 | +8.9% | 99.7 | 7.3 | 14.5% | 5.4% | 0.998 | 10.0 | - | - | 0.224 | 0.125 | 0.945 | 0.234 | 0.238 | 0.236 | 0.990 | 1.420 | -0.010 | NOT_TESTED | 21 |  |
-| 7qij | open | pass | P 21 21 21 | P 21 21 21 | 0.42 | 0.991 | 3.62 | 4.10 | +11.8% | 99.7 | 6.8 | 24.5% | 5.8% | 0.996 | 9.2 | - | - | 0.359 | 0.063 | 0.826 | 0.366 | 0.364 | 0.325 | 1.127 | 0.160 | 0.066 | NOT_TESTED | 77 |  |
-| 7qis | open | pass | P 61 | P 61 | 0.06 | 0.999 | 1.76 | 1.83 | +4.0% | 99.6 | 9.2 | 21.2% | 6.3% | 0.997 | 17.2 | - | - | 0.166 | 0.199 | 0.964 | 0.193 | 0.192 | 0.189 | 1.024 | 1.410 | 0.056 | NOT_TESTED | 20 |  |
-| 7raa | open | pass | P 41 21 2 | P 43 21 2 | 0.10 | 0.997 | 2.64 | 2.69 | +1.9% | 99.2 | 35.8 | 17.8% | 5.8% | 1.000 | 10.4 | - | - | 0.297 | 0.186 | 0.901 | 0.335 | 0.304 | 0.294 | 1.139 | 0.490 | -0.038 | ACCEPTED | 19 | P 41 21 2 vs reference P 43 21 2 (hand only (needs anomalous)); labelled P 43 21 2 from the model |
-| 7ris | open | pass | P 31 2 1 | P 32 2 1 | 0.07 | 1.000 | 1.51 | 1.72 | +12.2% | 96.1 | 17.9 | 10.1% | 3.3% | 1.000 | 30.9 | - | - | 0.189 | 0.040 | 0.961 | 0.189 | 0.190 | 0.201 | 0.941 | 2.190 | 0.006 | ACCEPTED | 17 | P 31 2 1 vs reference P 32 2 1 (hand only (needs anomalous)); labelled P 32 2 1 from the model |
-| 7rji | open | pass | R 3 2:H | H 3 2 | 0.12 | 1.003 | 1.47 | 1.71 | +14.2% | 99.3 | 28.3 | 15.6% | 8.9% | 0.999 | 7.8 | - | - | 0.208 | 0.083 | 0.945 | 0.196 | 0.211 | 0.224 | 0.877 | 6.800 | 0.084 | NOT_TESTED | 17 |  |
-| 7t5t | open | pass | P 42 21 2 | P 42 21 2 | 0.06 | 0.999 | 1.24 | 1.35 | +8.1% | 98.5 | 12.6 | 6.5% | 4.4% | 0.999 | 16.5 | - | - | 0.163 | 0.249 | 0.960 | 0.193 | 0.189 | 0.168 | 1.147 | 11.250 | 0.024 | NOT_TESTED | 17 |  |
-| 7tcd | open | pass | C 1 2 1 | C 1 2 1 | 0.26 | 1.004 | 1.67 | 1.70 | +1.9% | 70.8 | 7.2 | 8.8% | 4.3% | 0.999 | 18.0 | - | - | 0.191 | 0.213 | 0.957 | 0.212 | 0.208 | 0.252 | 0.840 | 1.110 | -0.057 | NOT_TESTED | 18 |  |
-| 7yzx | open | pass | P 63 2 2 | P 63 2 2 | 0.24 | 0.994 | 1.87 | 1.90 | +1.6% | 99.7 | 14.2 | 20.4% | 6.1% | 0.998 | 10.5 | - | - | 0.211 | 0.108 | 0.952 | 0.214 | 0.215 | 0.229 | 0.935 | 1.400 | 0.021 | NOT_TESTED | 35 |  |
-| 8a1a | open | pass | P 61 | P 65 | 0.26 | 0.992 | 1.91 | 2.05 | +7.0% | 99.7 | 42.5 | 52.5% | 8.2% | 0.998 | 19.2 | - | - | 0.177 | 0.030 | 0.962 | 0.179 | 0.178 | 0.185 | 0.967 | 1.790 | -0.005 | ACCEPTED | 54 | P 61 vs reference P 65 (hand only (needs anomalous)); labelled P 65 from the model |
-| 8agq | open | pass | C 1 2 1 | C 1 2 1 | 0.34 | 0.991 | 0.97 | 1.09 | +11.3% | 95.6 | 6.0 | 9.2% | 4.4% | 0.999 | 14.1 | - | - | 0.182 | 0.220 | 0.944 | 0.207 | 0.205 | 0.149 | 1.391 | 6.500 | -0.005 | NOT_TESTED | 18 |  |
-| 8c3e | open | fail | P 6 2 2 | P 31 2 1 | 0.24 | 0.994 | 1.79 | 2.10 | +14.7% | 97.9 | 7.0 | 29.4% | 11.9% | 0.980 | 5.9 | - | - | 0.359 | 0.282 | 0.759 | 0.399 | 0.387 | 0.249 | 1.602 | 0.910 | -0.076 | ACCEPTED | 2 | P 6 2 2 vs reference P 31 2 1 |
-| 8dqb | open | pass | I 2 3 | I 2 3 | 0.08 | 0.998 | 2.04 | 2.50 | +18.3% | 97.3 | 10.2 | 14.3% | 4.4% | 0.996 | 22.1 | - | - | 0.230 | 0.113 | 0.939 | 0.237 | 0.243 | 0.239 | 0.992 | 3.070 | 0.006 | NOT_TESTED | 8 |  |
-| 8dyz | open | pass | P 41 21 2 | P 43 21 2 | 0.08 | 0.999 | 1.14 | 1.27 | +10.4% | 64.2 | 3.8 | 3.1% | 2.4% | 0.999 | 37.8 | - | - | 0.120 | 0.046 | 0.973 | 0.121 | 0.122 | 0.133 | 0.907 | 4.220 | -0.050 | ACCEPTED | 9 | P 41 21 2 vs reference P 43 21 2 (hand only (needs anomalous)); labelled P 43 21 2 from the model |
-| 8dz7 | open | pass | P 21 21 21 | P 21 21 21 | 0.08 | 0.998 | 1.19 | 1.34 | +11.2% | 37.2 | 3.2 | 3.0% | 2.7% | 0.999 | 35.1 | - | - | 0.118 | 0.068 | 0.968 | 0.128 | 0.122 | 0.136 | 0.942 | 5.140 | -0.008 | NOT_TESTED | 8 |  |
-| 8egn | open | pass | P 21 21 21 | P 21 21 21 | 0.12 | 1.002 | 1.63 | 1.95 | +16.6% | 91.3 | 5.4 | 6.5% | 3.8% | 0.999 | 21.7 | - | - | 0.198 | 0.142 | 0.950 | 0.211 | 0.204 | 0.219 | 0.961 | 2.510 | 0.013 | NOT_TESTED | 10 |  |
-| 8iya | open | pass | C 1 2 1 | C 1 2 1 | 0.33 | 0.995 | 1.90 | 2.43 | +21.9% | 97.5 | 5.6 | 22.4% | 11.6% | 0.988 | 5.8 | - | - | 0.248 | 0.046 | 0.944 | 0.233 | 0.250 | 0.247 | 0.943 | 0.220 | 0.004 | NOT_TESTED | 6 |  |
-| 8k1g | open | pass | I 4 2 2 | I 4 2 2 | 0.76 | 1.018 | 1.62 | 2.09 | +22.3% | 99.7 | 19.2 | 25.6% | 6.9% | 0.998 | 11.6 | - | - | 0.206 | 0.188 | 0.957 | 0.225 | 0.225 | 0.207 | 1.085 | 2.240 | -0.109 | NOT_TESTED | 26 |  |
-| 8oic | open | pass | P 1 | P 1 | 0.03 | 1.000 | 2.34 | 2.80 | +16.4% | 98.2 | 3.6 | 24.7% | 4.7% | 0.988 | 19.3 | - | - | 0.238 | 0.112 | 0.933 | 0.247 | 0.246 | 0.251 | 0.986 | 0.410 | 0.054 | NOT_TESTED | 23 |  |
-| 8owm | open | pass | P 1 | P 1 | 0.06 | 0.999 | 1.50 | 1.70 | +12.0% | 96.4 | 3.6 | 10.8% | 3.5% | 0.998 | 21.1 | - | - | 0.164 | 0.104 | 0.971 | 0.174 | 0.172 | 0.172 | 1.011 | 1.320 | 0.046 | NOT_TESTED | 44 |  |
-| 8pqd | open | pass | P 21 21 21 | P 21 21 21 | 0.06 | 1.000 | 1.31 | 1.50 | +12.4% | 95.1 | 13.5 | 8.9% | 5.5% | 0.999 | 14.6 | - | - | 0.184 | 0.197 | 0.961 | 0.204 | 0.199 | 0.194 | 1.048 | 3.530 | 0.038 | NOT_TESTED | 49 |  |
-| 8qaw | open | pass | R 3:H | H 3 | 0.06 | 0.998 | 1.30 | 1.55 | +15.9% | 99.4 | 10.0 | 12.3% | 7.7% | 0.998 | 10.8 | - | - | 0.142 | 0.176 | 0.958 | 0.155 | 0.159 | 0.161 | 0.963 | 11.320 | 0.018 | ACCEPTED | 109 |  |
-| 8qj5 | open | pass | P 1 21 1 | P 1 21 1 | 0.51 | 0.986 | 1.43 | 1.63 | +12.5% | 99.5 | 6.5 | 16.5% | 7.6% | 0.996 | 8.3 | - | - | 0.181 | 0.126 | 0.953 | 0.197 | 0.195 | 0.190 | 1.036 | 1.410 | 0.021 | NOT_TESTED | 16 |  |
-| 8qq7 | open | pass | P 62 2 2 | P 64 2 2 | 0.61 | 1.018 | 3.15 | 3.62 | +12.8% | 99.5 | 24.9 | 20.0% | 11.6% | 0.998 | 6.0 | - | - | 0.402 | 0.371 | 0.353 | 0.408 | 0.408 | 0.320 | 1.275 | 0.700 | -0.110 | ACCEPTED | 9 | P 62 2 2 vs reference P 64 2 2 (hand only (needs anomalous)); labelled P 64 2 2 from the model |
-| 8r5r | open | pass | P 21 21 21 | P 21 21 21 | 0.16 | 1.002 | 2.79 | 3.08 | +9.4% | 99.7 | 10.1 | 27.4% | 4.7% | 0.997 | 18.9 | - | - | 0.264 | 0.157 | 0.880 | 0.287 | 0.277 | 0.252 | 1.141 | 0.310 | -0.023 | NOT_TESTED | 21 |  |
-| 8rud | open | pass | P 1 21 1 | P 1 21 1 | 0.42 | 0.988 | 1.65 | 2.10 | +21.4% | 99.7 | 6.6 | 32.2% | 6.3% | 0.992 | 12.4 | - | - | 0.247 | 0.091 | 0.903 | 0.256 | 0.253 | 0.262 | 0.977 | 0.770 | 0.048 | NOT_TESTED | 42 |  |
-| 8s38 | open | pass | I 2 2 2 | I 21 21 21 | 0.17 | 0.995 | 1.64 | 1.89 | +13.3% | 99.6 | 6.7 | 8.7% | 3.4% | 0.999 | 22.5 | - | - | 0.179 | 0.143 | 0.962 | 0.185 | 0.187 | 0.187 | 0.989 | 2.300 | 0.025 | NOT_TESTED | 33 | I 2 2 2 vs reference I 21 21 21 (UNDECIDABLE from intensities) |
-| 8sa8 | open | pass | I 1 2 1 | I 1 2 1 | 0.01 | 1.000 | 1.11 | 1.30 | +14.5% | 86.5 | 7.2 | 11.8% | 3.7% | 0.999 | 21.7 | - | - | 0.155 | 0.148 | 0.971 | 0.170 | 0.171 | 0.152 | 1.116 | 3.790 | 0.045 | ACCEPTED | 44 |  |
-| 8sqo | open | pass | P 4 3 2 | P 4 3 2 | 0.15 | 0.995 | 1.31 | 1.55 | +15.2% | 99.7 | 69.7 | 25.2% | 6.1% | 1.000 | 13.9 | - | - | 0.185 | 0.113 | 0.958 | 0.200 | 0.193 | 0.177 | 1.129 | 6.550 | 0.031 | NOT_TESTED | 18 |  |
-| 8sqq | open | pass | F 4 3 2 | F 4 3 2 | 0.18 | 0.995 | 1.90 | 2.25 | +15.6% | 99.6 | 39.2 | 25.2% | 5.3% | 0.999 | 17.8 | - | - | 0.211 | 0.108 | 0.963 | 0.206 | 0.218 | 0.245 | 0.841 | 3.170 | 0.016 | NOT_TESTED | 50 |  |
-| 8sqt | open | pass | F 4 3 2 | F 4 3 2 | 0.10 | 0.997 | 1.83 | 2.20 | +16.8% | 99.7 | 38.9 | 21.0% | 4.3% | 1.000 | 24.1 | - | - | 0.222 | 0.147 | 0.968 | 0.225 | 0.233 | 0.262 | 0.858 | 2.880 | 0.026 | NOT_TESTED | 23 |  |
-| 8t7r | open | pass | C 1 2 1 | C 1 2 1 | 0.39 | 0.989 | 3.30 | 3.84 | +14.0% | 99.1 | 4.0 | 32.7% | 7.0% | 0.985 | 10.2 | - | - | 0.284 | 0.103 | 0.753 | 0.288 | 0.293 | 0.263 | 1.099 | 0.370 | 0.032 | NOT_TESTED | 39 |  |
-| 8tha | open | pass | P 62 | P 64 | 0.20 | 0.994 | 1.34 | 1.68 | +20.2% | 99.3 | 19.3 | 15.8% | 3.3% | 0.999 | 26.4 | - | - | 0.209 | 0.094 | 0.961 | 0.218 | 0.215 | 0.215 | 1.016 | 4.300 | 0.042 | ACCEPTED | 13 | P 62 vs reference P 64 (hand only (needs anomalous)); labelled P 64 from the model |
-| 8tyy | open | pass | F 4 3 2 | F 4 3 2 | 0.02 | 1.001 | 1.27 | 1.68 | +24.2% | 97.6 | 38.2 | 16.6% | 5.2% | 0.999 | 16.2 | - | - | 0.161 | 0.145 | 0.970 | 0.179 | 0.175 | 0.163 | 1.099 | 13.490 | 0.003 | NOT_TESTED | 84 |  |
-| 8u0i | open | pass | P 41 21 2 | P 43 21 2 | 0.08 | 1.000 | 1.38 | 1.54 | +10.3% | 98.3 | 11.0 | 8.3% | 3.5% | 0.999 | 16.4 | - | - | 0.179 | 0.055 | 0.963 | 0.182 | 0.182 | 0.210 | 0.868 | 3.400 | 0.023 | ACCEPTED | 14 | P 41 21 2 vs reference P 43 21 2 (hand only (needs anomalous)); labelled P 43 21 2 from the model |
-| 8v2t | open | pass | P 42 21 2 | P 42 21 2 | 0.20 | 1.006 | 1.15 | 1.40 | +17.8% | 87.7 | 9.8 | 8.0% | 4.9% | 0.999 | 12.3 | - | - | 0.167 | 0.210 | 0.969 | 0.180 | 0.179 | 0.163 | 1.105 | 10.970 | 0.025 | NOT_TESTED | 13 |  |
-| 8v4j | open | pass | P 42 21 2 | P 42 21 2 | 0.09 | 0.998 | 1.10 | 1.31 | +16.0% | 89.8 | 11.4 | 5.5% | 3.1% | 1.000 | 21.8 | - | - | 0.170 | 0.109 | 0.965 | 0.176 | 0.175 | 0.172 | 1.023 | 12.360 | 0.009 | NOT_TESTED | 19 |  |
-| 8v4o | open | pass | P 61 2 2 | P 61 2 2 | 0.06 | 0.999 | 2.12 | 2.70 | +21.7% | 99.7 | 20.4 | 30.8% | 5.9% | 0.998 | 15.4 | - | - | 0.235 | 0.151 | 0.929 | 0.251 | 0.252 | 0.240 | 1.046 | 0.970 | 0.053 | NOT_TESTED | 36 |  |
-| 8xbp | open | pass | C 1 2 1 | C 1 2 1 | 0.19 | 0.999 | 1.68 | 1.99 | +15.4% | 83.5 | 6.7 | 11.0% | 4.0% | 0.999 | 18.8 | - | - | 0.312 | 0.194 | 0.891 | 0.330 | 0.322 | 0.288 | 1.146 | 1.160 | 0.235 | NOT_TESTED | 18 |  |
-| 8xte | open | pass | P 31 2 1 | P 32 | 0.07 | 1.002 | 1.64 | 1.99 | +17.6% | 99.5 | 9.4 | 25.1% | 7.8% | 0.996 | 12.4 | - | - | 0.275 | 0.128 | 0.913 | 0.287 | 0.284 | 0.219 | 1.309 | 0.950 | 0.039 | NOT_TESTED | 21 | P 31 2 1 vs reference P 32: accepted alternative P 31 2 1 - a knife-edge this battery does not decide |
-| 8xtf | open | pass | R 3 2:H | H 3 2 | 0.23 | 1.006 | 1.84 | 2.13 | +13.8% | 99.6 | 20.8 | 86.6% | 18.5% | 0.988 | 7.6 | - | - | 0.193 | 0.041 | 0.964 | 0.186 | 0.194 | 0.210 | 0.888 | 1.510 | -0.017 | NOT_TESTED | 26 |  |
-| 8xtg | open | pass | P 31 2 1 | P 32 | 0.05 | 1.001 | 1.55 | 2.00 | +22.5% | 99.7 | 10.0 | 26.7% | 10.1% | 0.994 | 7.6 | - | - | 0.273 | 0.152 | 0.901 | 0.287 | 0.286 | 0.211 | 1.357 | 0.880 | 0.037 | ACCEPTED | 20 | P 31 2 1 vs reference P 32: accepted alternative P 31 2 1 - a knife-edge this battery does not decide |
-| 8y74 | open | pass | C 1 2 1 | C 1 2 1 | 0.36 | 0.992 | 1.69 | 1.90 | +11.2% | 97.7 | 6.2 | 13.0% | 7.7% | 0.997 | 8.8 | - | - | 0.214 | 0.105 | 0.945 | 0.225 | 0.220 | 0.240 | 0.936 | 1.230 | -0.028 | NOT_TESTED | 7 |  |
-| 8ys9 | open | pass | P 21 21 21 | P 21 21 21 | 0.20 | 0.998 | 1.31 | 1.46 | +10.2% | 99.7 | 13.4 | 13.2% | 4.6% | 0.999 | 15.3 | - | - | 0.176 | 0.107 | 0.961 | 0.189 | 0.183 | 0.197 | 0.958 | 3.110 | 0.096 | NOT_TESTED | 20 |  |
-| 9b22 | open | pass | P 1 21 1 | P 1 21 1 | 0.07 | 1.002 | 1.14 | 1.30 | +12.1% | 77.1 | 6.1 | 6.2% | 3.5% | 0.999 | 16.4 | - | - | 0.160 | 0.102 | 0.968 | 0.165 | 0.163 | 0.164 | 1.009 | 0.060 | -0.738 | ACCEPTED | 13 |  |
-| 9bn8 | open | pass | P 41 | P 41 | 0.10 | 0.997 | 1.19 | 1.35 | +11.7% | 93.8 | 11.5 | 8.0% | 3.9% | 1.000 | 19.8 | - | - | 0.151 | 0.126 | 0.967 | 0.162 | 0.159 | 0.158 | 1.025 | 3.800 | 0.019 | ACCEPTED | 15 |  |
-| 9c18 | open | pass | P 1 | P 1 | 0.74 | 0.984 | 1.74 | 1.90 | +8.6% | 97.5 | 3.6 | 26.1% | 8.6% | 0.988 | 10.5 | - | - | 0.219 | 0.071 | 0.945 | 0.219 | 0.223 | 0.229 | 0.957 | 0.730 | -0.019 | ACCEPTED | 7 |  |
-| 9chw | open | pass | P 61 | P 61 | 0.04 | 1.001 | 1.60 | 2.16 | +25.9% | 72.5 | 3.1 | 5.7% | 3.3% | 0.998 | 21.2 | - | - | 0.180 | 0.139 | 0.962 | 0.184 | 0.186 | 0.210 | 0.878 | 1.750 | -0.008 | NOT_TESTED | 21 |  |
-| 9crw | open | pass | P 1 21 1 | P 1 21 1 | 0.24 | 0.994 | 2.28 | 2.49 | +8.3% | 97.3 | 7.0 | 8.7% | 3.7% | 0.999 | 15.4 | - | - | 0.247 | 0.122 | 0.954 | 0.265 | 0.261 | 0.278 | 0.954 | 0.680 | -0.019 | NOT_TESTED | 11 |  |
-| 9e2t | open | pass | P 1 | P 1 | 0.10 | 0.999 | 2.35 | 2.28 | -3.3% | 91.6 | 5.7 | 29.2% | 7.2% | 0.991 | 6.6 | - | - | 0.229 | 0.052 | 0.929 | 0.232 | 0.233 | 0.242 | 0.958 | 0.380 | -0.016 | NOT_TESTED | 48 |  |
-| 9ea5 | open | pass | P 1 21 1 | P 1 21 1 | 0.11 | 0.997 | 1.66 | 2.00 | +16.8% | 92.3 | 6.7 | 18.0% | 4.3% | 0.997 | 26.7 | - | - | 0.195 | 0.107 | 0.953 | 0.201 | 0.204 | 0.207 | 0.972 | 1.210 | 0.041 | ACCEPTED | 17 |  |
-| 9fcf | open | pass | P 4 | P 4 | 0.21 | 1.001 | 1.78 | 2.36 | +24.7% | 99.7 | 12.8 | 34.9% | 10.3% | 0.995 | 7.1 | - | - | 0.286 | 0.073 | 0.921 | 0.292 | 0.288 | 0.257 | 1.136 | 0.770 | 0.025 | NOT_TESTED | 39 |  |
-| 9fcg | open | pass | P 4 | P 4 | 0.08 | 1.000 | 1.38 | 1.54 | +10.1% | 89.9 | 11.4 | 14.6% | 8.4% | 0.997 | 9.5 | - | - | 0.180 | 0.112 | 0.956 | 0.189 | 0.191 | 0.198 | 0.954 | 2.350 | 0.062 | NOT_TESTED | 36 |  |
-| 9fhc | open | pass | I 2 3 | I 2 3 | 0.27 | 0.992 | 1.89 | 2.20 | +14.0% | 94.2 | 17.5 | 16.7% | 4.7% | 0.999 | 11.9 | - | - | 0.239 | 0.100 | 0.914 | 0.246 | 0.245 | 0.238 | 1.034 | 1.360 | -0.021 | ACCEPTED | 36 |  |
-| 9gdj | open | pass | P 41 21 2 | P 41 21 2 | 0.05 | 0.999 | 1.40 | 1.47 | +5.0% | 99.7 | 13.1 | 11.1% | 6.1% | 0.999 | 12.9 | - | - | 0.154 | 0.214 | 0.967 | 0.175 | 0.179 | 0.175 | 0.998 | 2.950 | -0.025 | NOT_TESTED | 99 |  |
-| 9gjx | open | pass | P 1 21 1 | P 1 21 1 | 0.16 | 0.996 | 2.07 | 2.40 | +13.8% | 96.6 | 6.7 | 16.2% | 3.1% | 0.997 | 39.2 | - | - | 0.192 | 0.151 | 0.952 | 0.225 | 0.216 | 0.219 | 1.026 | 0.800 | -0.024 | NOT_TESTED | 18 |  |
-| 9gqg | open | pass | P 31 2 1 | P 32 2 1 | 0.01 | 1.000 | 1.82 | 2.00 | +8.8% | 99.8 | 7.7 | 12.3% | 6.6% | 0.998 | 11.9 | - | - | 0.233 | 0.143 | 0.917 | 0.250 | 0.249 | 0.261 | 0.959 | 1.270 | 0.045 | ACCEPTED | 15 | P 31 2 1 vs reference P 32 2 1 (hand only (needs anomalous)); labelled P 32 2 1 from the model |
-| 9h0q | open | pass | R 3 2:H | H 3 2 | 0.42 | 0.990 | 2.11 | 2.55 | +17.2% | 99.7 | 10.7 | 17.0% | 4.5% | 0.998 | 18.2 | - | - | 0.206 | 0.122 | 0.933 | 0.218 | 0.223 | 0.222 | 0.981 | 1.160 | -0.022 | NOT_TESTED | 30 |  |
-| 9hnc | open | fail | P 1 21 1 | P 1 2 1 | 0.07 | 0.999 | 1.64 | 1.88 | +13.0% | 91.0 | 7.0 | 12.8% | 5.3% | 0.998 | 13.6 | - | - | 0.245 | 0.151 | 0.947 | 0.254 | 0.253 | 0.211 | 1.204 | 0.880 | -0.234 | NOT_TESTED | 30 | P 1 21 1 vs reference P 1 2 1 |
-| 9hs7 | open | pass | P 61 | P 65 | 0.12 | 0.998 | 1.66 | 1.70 | +2.4% | 99.7 | 10.2 | 11.8% | 5.1% | 0.999 | 11.5 | - | - | 0.210 | 0.361 | 0.966 | 0.242 | 0.232 | 0.239 | 1.014 | 1.220 | -0.084 | ACCEPTED | 19 | P 61 vs reference P 65 (hand only (needs anomalous)); labelled P 65 from the model |
-| 9i0a | open | pass | P 21 21 2 | P 21 21 2 | 0.36 | 1.008 | 1.81 | 2.22 | +18.6% | 99.0 | 12.7 | 20.1% | 5.7% | 0.999 | 11.6 | - | - | 0.227 | 0.076 | 0.957 | 0.231 | 0.234 | 0.237 | 0.976 | 0.910 | 0.143 | NOT_TESTED | 30 |  |
-| 9i80 | open | pass | P 41 | P 41 | 0.11 | 1.002 | 1.59 | 1.95 | +18.4% | 99.7 | 13.3 | 24.5% | 10.5% | 0.992 | 6.8 | - | - | 0.217 | 0.132 | 0.875 | 0.221 | 0.225 | 0.203 | 1.089 | 1.900 | 0.001 | NOT_TESTED | 42 |  |
-| 9ig7 | open | pass | P 21 21 2 | P 21 21 2 | 0.21 | 0.995 | 2.02 | 2.60 | +22.4% | 99.7 | 13.8 | 21.2% | 7.3% | 0.992 | 11.0 | - | - | 0.231 | 0.081 | 0.931 | 0.247 | 0.237 | 0.259 | 0.955 | 0.860 | 0.017 | NOT_TESTED | 63 |  |
-| 9ih9 | open | pass | C 1 2 1 | C 1 2 1 | 0.21 | 0.997 | 1.40 | 1.70 | +17.5% | 96.0 | 2.4 | 11.2% | 5.0% | 0.996 | 12.7 | - | - | 0.199 | 0.075 | 0.952 | 0.207 | 0.204 | 0.203 | 1.019 | 1.020 | -0.021 | NOT_TESTED | 15 |  |
-| 9jq9 | open | pass | P 21 21 21 | P 21 21 21 | 0.17 | 0.996 | 1.65 | 1.90 | +13.2% | 84.9 | 10.7 | 6.9% | 4.3% | 0.999 | 19.2 | - | - | 0.212 | 0.146 | 0.937 | 0.241 | 0.222 | 0.237 | 1.019 | 4.730 | -0.008 | NOT_TESTED | 5 |  |
-| 9jzo | open | pass | P 1 | P 1 | 0.14 | 0.996 | 1.15 | 1.40 | +18.0% | 61.2 | 3.3 | 5.5% | 4.2% | 0.997 | 8.3 | - | - | 0.181 | 0.037 | 0.958 | 0.178 | 0.181 | 0.195 | 0.917 | 4.430 | 0.022 | NOT_TESTED | 8 |  |
-| 9khr | open | pass | P 21 21 21 | P 21 21 21 | 0.14 | 0.998 | 1.40 | 2.00 | +29.8% | 97.8 | 6.6 | 18.7% | 11.8% | 0.994 | 9.1 | - | - | 0.241 | 0.126 | 0.941 | 0.258 | 0.253 | 0.235 | 1.101 | 2.020 | 0.037 | NOT_TESTED | 11 |  |
-| 9lxl | open | pass | P 41 21 2 | P 41 21 2 | 0.62 | 1.015 | 2.08 | 2.19 | +5.2% | 99.7 | 14.7 | 42.1% | 10.1% | 0.997 | 6.2 | - | - | 0.300 | 0.092 | 0.896 | 0.314 | 0.298 | 0.234 | 1.341 | 0.750 | -0.275 | NOT_TESTED | 19 |  |
-| 9mh4 | open | pass | P 21 3 | P 21 3 | 0.31 | 0.991 | 2.78 | 3.05 | +8.7% | 99.7 | 40.5 | 20.0% | 4.9% | 1.000 | 13.8 | - | - | 0.229 | 0.168 | 0.922 | 0.233 | 0.238 | 0.215 | 1.083 | 1.000 | 0.006 | NOT_TESTED | 14 |  |
-| 9min | open | fail | P 21 21 2 | P 21 21 21 | 37.01 | 0.493 | 1.86 | 2.05 | +9.2% | 99.6 | 22.7 | 27.8% | 6.8% | 0.998 | 9.9 | - | - | 0.564 | 0.208 | 0.228 | 0.574 | 0.575 | 0.267 | 2.146 | -0.030 | - | NOT_TESTED | 48 | primitive volume ratio 0.49 |
-| 9o0h | open | pass | P 21 21 21 | P 21 21 21 | 0.34 | 0.991 | 2.01 | 2.24 | +10.1% | 99.6 | 12.7 | 67.7% | 13.5% | 0.985 | 5.4 | - | - | 0.241 | 0.068 | 0.944 | 0.251 | 0.245 | 0.249 | 1.008 | 0.330 | 0.040 | NOT_TESTED | 41 |  |
-| 9p7q | open | pass | C 1 2 1 | C 1 2 1 | 0.13 | 1.003 | 1.78 | 2.21 | +19.5% | 90.1 | 2.7 | 29.5% | 9.1% | 0.986 | 10.8 | - | - | 0.268 | 0.052 | 0.948 | 0.281 | 0.270 | 0.259 | 1.088 | 0.720 | -0.034 | NOT_TESTED | 9 |  |
-| 9pbb | open | pass | C 1 2 1 | C 1 2 1 | 0.15 | 0.997 | 1.81 | 2.17 | +16.5% | 79.3 | 2.5 | 23.6% | 6.6% | 0.993 | 16.7 | - | - | 0.233 | 0.034 | 0.972 | 0.231 | 0.234 | 0.223 | 1.037 | 0.450 | -0.081 | NOT_TESTED | 11 |  |
-| 9q41 | open | pass | C 2 2 21 | C 2 2 21 | 0.21 | 1.003 | 1.68 | 1.95 | +14.1% | 99.7 | 6.8 | 31.7% | 13.3% | 0.982 | 7.5 | - | - | 0.192 | 0.043 | 0.961 | 0.192 | 0.194 | 0.213 | 0.903 | 0.350 | 0.053 | NOT_TESTED | 16 |  |
-| 9q66 | open | pass | P 1 21 1 | P 1 21 1 | 0.39 | 0.989 | 2.07 | 2.01 | -2.8% | 99.7 | 7.1 | 30.9% | 8.1% | 0.990 | 13.0 | - | - | 0.201 | 0.084 | 0.903 | 0.214 | 0.213 | 0.266 | 0.804 | 0.660 | -0.024 | NOT_TESTED | 18 |  |
-| 9qvv | open | pass | I 2 2 2 | I 2 2 2 | 0.08 | 1.001 | 2.53 | 2.72 | +7.1% | 89.4 | 13.8 | 10.8% | 2.2% | 1.000 | 38.1 | - | - | 0.251 | 0.227 | 0.805 | 0.248 | 0.266 | 0.279 | 0.886 | 1.690 | -0.034 | NOT_TESTED | 17 |  |
-| 9qw2 | open | pass | P 1 21 1 | P 1 21 1 | 0.62 | 0.996 | 1.82 | 1.92 | +5.2% | 99.7 | 3.6 | 22.3% | 7.5% | 0.960 | 6.4 | - | - | 0.243 | 0.046 | 0.907 | 0.253 | 0.247 | 0.212 | 1.192 | 0.120 | -0.325 | ACCEPTED | 22 |  |
-| 9qw8 | open | pass | P 1 | P 1 | 0.67 | 0.993 | 1.69 | 1.80 | +6.2% | 97.3 | 3.4 | 27.0% | 12.2% | 0.975 | 5.2 | - | - | 0.323 | 0.142 | 0.831 | 0.329 | 0.331 | 0.243 | 1.354 | 0.300 | -0.422 | ACCEPTED | 34 |  |
-| 9rci | open | pass | P 1 | P 1 | 0.33 | 0.995 | 1.69 | 1.66 | -1.9% | 96.9 | 3.5 | 21.3% | 8.3% | 0.988 | 7.5 | - | - | 0.264 | 0.087 | 0.875 | 0.270 | 0.271 | 0.283 | 0.952 | 0.320 | -0.129 | ACCEPTED | 13 |  |
-| 9rcs | open | pass | P 1 21 1 | P 1 21 1 | 0.85 | 1.020 | 3.28 | 3.01 | -8.9% | 99.8 | 7.0 | 23.1% | 9.7% | 0.995 | 7.4 | - | - | 0.317 | 0.117 | 0.501 | 0.341 | 0.324 | 0.317 | 1.075 | 0.470 | -0.177 | ACCEPTED | 12 |  |
-| 9rp9 | open | pass | C 1 2 1 | C 1 2 1 | 0.25 | 0.994 | 1.96 | 2.10 | +6.9% | 99.7 | 6.2 | 16.4% | 4.7% | 0.998 | 28.6 | - | - | 0.202 | 0.125 | 0.928 | 0.234 | 0.227 | 0.222 | 1.055 | 2.310 | 0.052 | NOT_TESTED | 13 |  |
-| 9s02 | open | pass | P 21 21 2 | P 21 21 2 | 0.09 | 0.998 | 1.43 | 1.65 | +13.3% | 98.9 | 12.5 | 10.5% | 3.3% | 0.999 | 25.6 | - | - | 0.180 | 0.089 | 0.961 | 0.186 | 0.187 | 0.193 | 0.966 | 2.260 | 0.038 | ACCEPTED | 26 |  |
-| 9sl0 | open | pass | P 21 21 21 | P 21 21 21 | 0.39 | 0.991 | 1.37 | 1.60 | +14.6% | 99.4 | 12.4 | 8.0% | 3.7% | 1.000 | 20.0 | - | - | 0.245 | 0.150 | 0.912 | 0.254 | 0.255 | 0.264 | 0.963 | 2.230 | 0.003 | NOT_TESTED | 48 |  |
-| 9t6s | open | pass | P 21 21 21 | P 21 21 21 | 0.41 | 0.989 | 1.75 | 2.00 | +12.6% | 96.0 | 5.2 | 10.9% | 3.6% | 0.999 | 28.4 | - | - | 0.215 | 0.029 | 0.969 | 0.230 | 0.216 | 0.241 | 0.954 | 2.440 | 0.086 | NOT_TESTED | 18 |  |
-| 9upt | open | pass | P 6 | P 6 | 0.20 | 0.994 | 2.03 | 2.37 | +14.4% | 99.7 | 5.7 | 24.4% | 10.8% | 0.989 | 6.5 | - | - | 0.218 | 0.088 | 0.942 | 0.218 | 0.225 | 0.215 | 1.015 | 1.320 | -0.046 | NOT_TESTED | 19 |  |
-| 9vyb | open | pass | P 21 21 21 | P 21 21 21 | 0.41 | 0.988 | 1.67 | 2.12 | +21.1% | 87.4 | 10.1 | 8.2% | 3.5% | 1.000 | 22.2 | - | - | 0.247 | 0.070 | 0.934 | 0.254 | 0.249 | 0.269 | 0.941 | 0.410 | 0.008 | NOT_TESTED | 29 |  |
-| 9w3y | open | pass | P 21 21 21 | P 21 21 21 | 0.33 | 1.004 | 1.22 | 1.50 | +18.9% | 99.7 | 6.7 | 24.3% | 5.2% | 0.997 | 18.6 | - | - | 0.185 | 0.087 | 0.973 | 0.196 | 0.195 | 0.198 | 0.990 | 4.900 | 0.042 | NOT_TESTED | 8 |  |
-| 9yl4 | open | pass | P 21 21 21 | P 21 21 21 | 0.07 | 1.000 | 3.61 | 3.70 | +2.4% | 99.6 | 13.4 | 30.9% | 9.2% | 0.997 | 9.8 | - | - | 0.293 | 0.061 | 0.882 | 0.303 | 0.297 | 0.283 | 1.067 | 5.790 | -0.019 | NOT_TESTED | 19 |  |
-| 9yzk | open | pass | I 1 2 1 | I 1 2 1 | 0.26 | 0.996 | 3.87 | 5.10 | +24.2% | 98.6 | 3.3 | 31.9% | 4.0% | 0.999 | 8.8 | - | - | 0.352 | 0.323 | 0.875 | 0.410 | 0.413 | 0.304 | 1.348 | 0.130 | 0.043 | ACCEPTED | 10 |  |
-| 9z44 | open | pass | I 1 2 1 | I 1 2 1 | 1.25 | 0.965 | 6.78 | 7.20 | +5.8% | 98.4 | 3.3 | 21.8% | 9.1% | 0.974 | 9.5 | - | - | 0.333 | 0.153 | 0.791 | 0.328 | 0.341 | 0.345 | 0.950 | 0.020 | 0.059 | ACCEPTED | 15 |  |
-| 9z72 | open | pass | P 31 2 1 | P 31 2 1 | 0.14 | 1.004 | 2.00 | 2.38 | +16.1% | 99.7 | 9.8 | 93.3% | 11.5% | 0.988 | 14.9 | - | - | 0.241 | 0.043 | 0.913 | 0.256 | 0.244 | 0.269 | 0.950 | 0.730 | 0.032 | NOT_TESTED | 33 |  |
-| 9zlo | open | pass | P 21 21 21 | P 21 21 21 | 0.26 | 0.996 | 1.56 | 2.00 | +21.8% | 99.6 | 12.7 | 12.0% | 3.9% | 0.999 | 23.5 | - | - | 0.221 | 0.065 | 0.942 | 0.230 | 0.226 | 0.219 | 1.051 | 1.730 | -0.024 | NOT_TESTED | 16 |  |
-| 9zm0 | open | pass | P 1 21 1 | P 1 21 1 | 0.70 | 0.983 | 1.79 | 2.10 | +14.7% | 99.7 | 6.5 | 24.1% | 10.0% | 0.996 | 8.9 | - | - | 0.256 | 0.081 | 0.956 | 0.275 | 0.258 | 0.298 | 0.925 | 4.660 | -0.028 | NOT_TESTED | 6 |  |
-| 9zmu | open | pass | P 61 2 2 | P 65 2 2 | 0.07 | 1.001 | 1.72 | 1.98 | +13.2% | 99.7 | 29.5 | 29.8% | 6.9% | 0.999 | 11.3 | - | - | 0.277 | 0.150 | 0.894 | 0.282 | 0.288 | 0.294 | 0.961 | 1.230 | 0.011 | ACCEPTED | 20 | P 61 2 2 vs reference P 65 2 2 (hand only (needs anomalous)); labelled P 65 2 2 from the model |
-| cuhf2 | open | unscored | P 4 2 2 | - | - | - | 0.51 | - | - | 82.1 | 13.9 | 2.8% | 2.1% | 1.000 | 44.3 | - | - | - | - | - | - | - | - | - | - | - | - | 9 | no reference to score against |
-| cytidine | open | pass | P 21 21 21 | P 21 21 21 | 0.33 | 0.994 | 0.58 | - | - | 90.9 | 3.6 | 10.2% | 9.3% | 0.997 | 8.5 | - | - | - | - | - | - | - | - | - | - | - | - | 6 |  |
-| dnba | open | pass | C 1 2/c 1 | C 1 2/c 1 | 0.09 | 1.000 | 0.81 | 0.48 | -68.3% | 76.0 | 2.7 | 2.4% | 1.7% | 1.000 | 39.5 | - | - | - | - | - | - | - | - | - | - | - | - | 5 |  |
-| lalanine | open | pass | P 21 21 21 | P 21 21 21 | 0.09 | 0.999 | 0.65 | - | - | 78.0 | 2.6 | 2.6% | 1.8% | 1.000 | 52.1 | - | - | - | - | - | - | - | - | - | - | - | - | 8 |  |
-| metformin | open | pass | P 1 21/c 1 | P 1 21/c 1 | 0.17 | 1.001 | 0.51 | 0.45 | -12.9% | 73.5 | 4.8 | 3.1% | 2.8% | 1.000 | 31.0 | - | - | - | - | - | - | - | - | - | - | - | - | 3 |  |
-| nidppe | open | pass | P 1 21/c 1 | P 1 21/c 1 | 0.28 | 0.998 | 0.51 | 0.77 | +34.3% | 66.6 | 5.3 | 8.0% | 4.1% | 0.999 | 29.7 | - | - | - | - | - | - | - | - | - | - | - | - | 3 |  |
-| aspirin_x10sa_20keV | inhouse | pass | P 1 21/c 1 | P 1 21/c 1 | 0.04 | 1.000 | 0.66 | 0.68 | +2.6% | 79.5 | 5.9 | 3.0% | 2.2% | 1.000 | 35.5 | 27.4 | - | - | - | - | - | - | - | - | - | - | - | 8 |  |
-| aspirin_x10sa_25keV | inhouse | pass | P 1 21/c 1 | P 1 21/c 1 | 0.05 | 1.001 | 0.53 | 0.55 | +3.6% | 79.2 | 6.0 | 3.1% | 2.2% | 1.000 | 34.4 | 29.2 | - | - | - | - | - | - | - | - | - | - | - | 7 |  |
-| citricacid_x10sa_20keV | inhouse | pass | P 1 21/c 1 | P 1 21/c 1 | 0.11 | 1.000 | 0.67 | 0.68 | +1.8% | 78.7 | 5.1 | 4.1% | 4.8% | 0.997 | 23.0 | 20.4 | - | - | - | - | - | - | - | - | - | - | - | 7 |  |
-| cytc_x06da_1 | inhouse | pass | P 31 2 1 | P 31 2 1 | 0.03 | 0.999 | 1.71 | 1.88 | +9.1% | 98.7 | 18.1 | 9.3% | 3.9% | 1.000 | 17.5 | 24.5 | - | 0.264 | 0.268 | 0.927 | 0.335 | 0.292 | 0.296 | 1.132 | 5.410 | - | ACCEPTED | 8 | labelled P 32 2 1 from the model |
-| cytc_x06da_2 | inhouse | pass | P 31 2 1 | P 31 2 1 | 0.09 | 1.002 | 1.57 | 1.69 | +6.8% | 99.6 | 17.6 | 9.5% | 3.4% | 1.000 | 23.0 | 27.0 | - | 0.253 | 0.215 | 0.925 | 0.306 | 0.278 | 0.286 | 1.069 | 6.240 | - | ACCEPTED | 9 | labelled P 32 2 1 from the model |
-| cytc_x10sa | inhouse | pass | P 31 2 1 | P 31 2 1 | 0.10 | 1.003 | 1.95 | 2.27 | +13.8% | 99.7 | 20.1 | 20.0% | 4.0% | 1.000 | 26.4 | 31.8 | - | 0.262 | 0.258 | 0.938 | 0.357 | 0.287 | 0.340 | 1.048 | 2.740 | - | ACCEPTED | 14 | labelled P 32 2 1 from the model |
-| hepes_x10sa_20keV | inhouse | pass | P b c a | P b c a | 0.14 | 0.998 | 0.66 | 0.68 | +2.8% | 86.6 | 10.3 | 2.7% | 3.7% | 0.999 | 37.0 | 28.5 | - | - | - | - | - | - | - | - | - | - | - | 9 |  |
-| insu_H_x06da_notwin | inhouse | pass | R 3:H | R 3 | 0.07 | 0.999 | 1.41 | 1.54 | +8.5% | 91.1 | 8.6 | 6.2% | 4.2% | 0.999 | 20.4 | 17.7 | - | 0.229 | 0.109 | 0.935 | 0.215 | 0.233 | 0.229 | 0.940 | 5.990 | - | ACCEPTED | 6 |  |
-| insu_H_x06da_twin | inhouse | pass | R 3:H | R 3 | 0.03 | 1.000 | 1.38 | 1.46 | +4.9% | 90.9 | 8.5 | 12.4% | 11.0% | 0.995 | 6.2 | 6.8 | - | 0.264 | 0.089 | 0.883 | 0.254 | 0.266 | 0.229 | 1.112 | 4.430 | - | ACCEPTED | 6 |  |
-| insu_I_x06da_13keV | inhouse | pass | I 2 3 | I 2 3 | 0.03 | 0.999 | 1.46 | 1.64 | +10.9% | 99.7 | 38.8 | 33.2% | 8.4% | 0.999 | - | 18.8 | - | 0.234 | 0.028 | 0.941 | 0.258 | 0.234 | 0.161 | 1.600 | 1.190 | - | ACCEPTED | 9 |  |
-| insu_I_x06da_5keV | inhouse | pass | I 2 3 | I 2 3 | 0.04 | 0.999 | 2.43 | 2.45 | +0.9% | 95.3 | 28.1 | 6.6% | 4.5% | 1.000 | 27.9 | 17.5 | - | 0.221 | 0.103 | 0.923 | 0.246 | 0.228 | 0.161 | 1.530 | 8.090 | - | NOT_TESTED | 4 |  |
-| insu_I_x06da_5keV_2 | inhouse | pass | I 2 3 | I 2 3 | 0.07 | 0.998 | 2.43 | 2.45 | +0.9% | 94.5 | 29.6 | 7.8% | 5.1% | 1.000 | 32.1 | 20.0 | - | 0.236 | 0.306 | 0.876 | 0.333 | 0.309 | 0.161 | 2.065 | 9.340 | - | NOT_TESTED | 4 |  |
-| insu_I_x06da_6keV | inhouse | pass | I 2 3 | I 2 3 | 0.08 | 0.998 | 2.02 | 2.04 | +0.7% | 95.5 | 28.4 | 6.1% | 4.8% | 1.000 | 20.6 | 17.9 | - | 0.214 | 0.038 | 0.933 | 0.236 | 0.214 | 0.161 | 1.466 | 11.770 | - | NOT_TESTED | 4 |  |
-| insu_I_x06da_low_isa | inhouse | fail | R 3:R | I 2 3 | 0.07 | 1.996 | 1.59 | 1.30 | -22.2% | 99.7 | 8.3 | 26.9% | 12.5% | 0.994 | 6.4 | 4.2 | - | 0.315 | 0.187 | 0.823 | 0.368 | 0.324 | 0.161 | 2.283 | 1.530 | - | NOT_TESTED | 8 | primitive volume ratio 2.00 |
-| insu_I_x06da_ref | inhouse | pass | I 2 3 | I 2 3 | 0.14 | 1.004 | 1.41 | 1.62 | +12.8% | 99.7 | 25.6 | 34.6% | 6.6% | 0.999 | 32.6 | 25.1 | - | 0.226 | 0.083 | 0.937 | 0.244 | 0.227 | 0.161 | 1.519 | 3.280 | - | ACCEPTED | 7 |  |
-| insu_I_x06da_weak | inhouse | pass | I 2 3 | I 2 3 | 0.85 | 1.026 | 1.64 | 1.81 | +9.4% | 99.8 | 40.1 | 17.1% | 4.9% | 1.000 | 14.7 | 18.9 | - | 0.286 | 0.146 | 0.918 | 0.320 | 0.288 | 0.161 | 1.985 | 2.030 | - | NOT_TESTED | 11 |  |
-| kdp_x10sa_20keV | inhouse | pass | I 41 m d | I -4 2 d | 0.04 | 1.001 | 0.66 | 0.74 | +10.3% | 90.9 | 16.7 | 5.5% | 4.8% | 0.998 | 24.0 | 4.1 | - | - | - | - | - | - | - | - | - | - | - | 13 | I 41 m d vs reference I -4 2 d: same Laue class and absences, undecidable from intensities (listed in SPACE_GROUP_ALTERNATIVES) |
-| lcystine_x10sa_20keV | inhouse | pass | P 61 2 2 | P 61 2 2 | 0.52 | 0.991 | 0.67 | - | - | 92.7 | 18.4 | 40.7% | 16.7% | 0.999 | 3.8 | - | - | - | - | - | - | - | - | - | - | - | - | 18 |  |
-| lcystine_x10sa_25keV | inhouse | pass | P 61 2 2 | P 61 2 2 | 0.54 | 0.989 | 0.53 | - | - | 92.0 | 17.9 | 39.9% | 17.1% | 0.998 | 4.4 | - | - | - | - | - | - | - | - | - | - | - | - | 17 |  |
-| lysoI_micromax_mono | inhouse | pass | P 41 21 2 | P 43 21 2 | 0.06 | 0.999 | 1.37 | 1.65 | +16.8% | 99.1 | 9.8 | 7.0% | 2.9% | 1.000 | 36.2 | 31.4 | - | 0.271 | 0.078 | 0.906 | 0.292 | 0.276 | 0.177 | 1.648 | 3.240 | - | ACCEPTED | 15 | P 41 21 2 vs reference P 43 21 2 (screws not judged against XDS); labelled P 43 21 2 from the model |
-| lysoI_micromax_pink | inhouse | pass | P 41 21 2 | P 43 21 2 | 0.04 | 1.000 | 1.39 | 1.65 | +15.6% | 99.3 | 10.0 | 8.1% | 3.2% | 1.000 | 35.5 | 29.2 | - | 0.274 | 0.073 | 0.900 | 0.295 | 0.278 | 0.177 | 1.664 | 2.420 | - | ACCEPTED | 14 | P 41 21 2 vs reference P 43 21 2 (screws not judged against XDS); labelled P 43 21 2 from the model |
-| lyso_micromax_mono | inhouse | pass | P 41 21 2 | P 43 21 2 | 0.17 | 1.003 | 1.18 | 1.50 | +21.5% | 79.1 | 8.3 | 5.0% | 2.5% | 1.000 | 40.8 | 39.9 | - | 0.233 | 0.158 | 0.932 | 0.249 | 0.243 | 0.177 | 1.406 | 4.510 | - | ACCEPTED | 15 | P 41 21 2 vs reference P 43 21 2 (screws not judged against XDS); labelled P 43 21 2 from the model |
-| lyso_micromax_pink | inhouse | pass | P 41 21 2 | P 43 21 2 | 0.14 | 1.003 | 1.20 | 1.45 | +17.0% | 83.6 | 8.3 | 5.1% | 2.5% | 1.000 | 41.6 | 37.4 | - | 0.235 | 0.181 | 0.931 | 0.257 | 0.250 | 0.177 | 1.451 | 4.370 | - | ACCEPTED | 14 | P 41 21 2 vs reference P 43 21 2 (screws not judged against XDS); labelled P 43 21 2 from the model |
-| lyso_x06da_5keV | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.06 | 0.999 | 2.44 | 2.45 | +0.6% | 86.7 | 19.7 | 6.5% | 5.4% | 0.999 | 26.9 | 19.4 | - | 0.279 | 0.171 | 0.826 | 0.295 | 0.295 | 0.177 | 1.667 | 5.860 | - | ACCEPTED | 4 | labelled P 43 21 2 from the model |
-| lyso_x06da_atten_wedge | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.32 | 1.007 | 1.20 | 1.26 | +4.8% | 99.7 | 23.0 | 41.3% | 6.9% | 0.998 | 13.3 | 16.6 | - | 0.296 | 0.061 | 0.895 | 0.307 | 0.296 | 0.177 | 1.732 | 1.940 | - | ACCEPTED | 8 | labelled P 43 21 2 from the model |
-| lyso_x06da_half_image | inhouse | pass | P 41 21 2 | P 43 21 2 | 1.02 | 1.027 | 1.57 | 1.65 | +4.6% | 99.8 | 12.0 | 245.2% | 35.0% | 0.959 | 4.4 | 6.6 | - | 0.300 | 0.181 | 0.803 | 0.332 | 0.328 | 0.177 | 1.873 | 0.920 | - | ACCEPTED | 10 | P 41 21 2 vs reference P 43 21 2 (screws not judged against XDS); labelled P 43 21 2 from the model |
-| lyso_x06da_ice | inhouse | pass | P 41 21 2 | P 4 2 2 | 0.11 | 1.002 | 1.33 | 1.43 | +7.2% | 99.7 | 19.4 | 19.3% | 4.7% | 0.999 | 22.4 | 23.3 | - | 0.289 | 0.118 | 0.902 | 0.315 | 0.295 | 0.177 | 1.777 | 2.560 | - | ACCEPTED | 7 | P 41 21 2 vs reference P 4 2 2 (screws not judged against XDS); labelled P 43 21 2 from the model |
-| lyso_x06da_ref | inhouse | pass | P 41 21 2 | P 4 2 2 | 0.03 | 1.001 | 0.99 | 1.20 | +17.2% | 85.7 | 22.2 | 4.8% | 2.7% | 1.000 | 30.1 | 28.3 | - | 0.271 | 0.100 | 0.902 | 0.287 | 0.275 | 0.177 | 1.622 | 9.770 | - | ACCEPTED | 9 | P 41 21 2 vs reference P 4 2 2 (screws not judged against XDS); labelled P 43 21 2 from the model |
-| lyso_x10sa_90deg_1 | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.12 | 0.998 | 1.82 | 1.97 | +7.2% | 99.8 | 6.4 | 17.6% | 4.6% | 0.998 | 20.5 | 20.8 | - | 0.380 | 0.095 | 0.817 | 0.369 | 0.386 | 0.177 | 2.084 | 0.340 | - | ACCEPTED | 6 | labelled P 43 21 2 from the model |
-| lyso_x10sa_90deg_2 | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.16 | 0.997 | 1.85 | 1.97 | +6.2% | 99.8 | 6.4 | 17.0% | 4.8% | 0.998 | 19.0 | 18.1 | - | 0.380 | 0.104 | 0.821 | 0.376 | 0.386 | 0.177 | 2.120 | 0.580 | - | ACCEPTED | 6 | labelled P 43 21 2 from the model |
-| lyso_x10sa_strong | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.65 | 0.981 | 1.36 | 1.24 | -9.4% | 99.3 | 21.4 | 23.7% | 10.8% | 0.995 | 5.5 | 8.6 | - | 0.378 | 0.190 | 0.847 | 0.365 | 0.381 | 0.177 | 2.059 | 1.600 | - | ACCEPTED | 29 | labelled P 43 21 2 from the model |
-| myob_x06da | inhouse | pass | P 1 21 1 | P 1 21 1 | 0.13 | 1.002 | 1.24 | 1.42 | +12.7% | 99.7 | 6.7 | 17.0% | 4.3% | 0.998 | 22.9 | 7.6 | - | 0.229 | 0.115 | 0.952 | 0.236 | 0.237 | 0.218 | 1.081 | 3.500 | - | NOT_TESTED | 8 |  |
-| myob_x06da_powder_1 | inhouse | pass | P 1 21 1 | P 1 21 1 | 0.43 | 0.994 | 1.73 | 1.50 | -15.9% | 98.9 | 4.5 | 74.4% | 18.0% | 0.578 | 3.8 | 5.5 | - | 0.492 | 0.311 | 0.170 | 0.524 | 0.507 | 0.218 | 2.402 | -0.270 | - | ACCEPTED | 9 |  |
-| myob_x06da_powder_2 | inhouse | pass | P 1 21 1 | P 1 21 1 | 0.45 | 0.996 | 1.47 | 0.99 | -48.8% | 99.5 | 5.5 | 174.0% | 33.5% | 0.783 | 2.3 | 2.2 | - | 0.489 | 0.117 | 0.048 | 0.500 | 0.499 | 0.218 | 2.294 | 1.420 | - | NOT_TESTED | 12 |  |
-| myob_x06da_sparse | inhouse | pass | P 1 21 1 | P 1 21 1 | 0.41 | 0.995 | 1.78 | 2.00 | +10.9% | 99.7 | 5.4 | 41.2% | 13.6% | 0.950 | 4.4 | 5.5 | - | 0.423 | 0.112 | 0.776 | 0.423 | 0.424 | 0.218 | 1.943 | 1.060 | - | NOT_TESTED | 13 |  |
-| myob_x06da_split | inhouse | pass | P 1 21 1 | P 1 21 1 | 0.20 | 0.997 | 1.86 | 1.51 | -23.3% | 99.7 | 5.7 | 78.2% | 19.8% | 0.700 | 2.7 | 12.4 | - | 0.397 | 0.165 | 0.312 | 0.402 | 0.408 | 0.218 | 1.844 | 0.390 | - | NOT_TESTED | 9 |  |
-| myob_x10sa | inhouse | pass | P 1 21 1 | P 1 21 1 | 0.30 | 1.005 | 1.56 | 1.74 | +10.5% | 97.4 | 5.7 | 17.0% | 7.7% | 0.996 | 11.1 | 5.2 | - | 0.242 | 0.041 | 0.935 | 0.246 | 0.244 | 0.218 | 1.128 | 2.040 | - | NOT_TESTED | 10 |  |
-| nothing_1 | inhouse | pass | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | 11 | no lattice reported, as expected |
-| nothing_2 | inhouse | pass | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | 10 | no lattice reported, as expected |
-| thau_bl1a_3p8keV | inhouse | pass | P 41 21 2 | P 4 2 2 | 0.06 | 0.998 | 3.02 | 3.10 | +2.7% | 88.8 | 15.5 | 7.0% | 5.8% | 0.998 | 31.4 | 30.8 | - | 0.185 | 0.030 | 0.935 | 0.188 | 0.186 | 0.151 | 1.240 | 8.940 | - | NOT_TESTED | 7 | P 41 21 2 vs reference P 4 2 2 (screws not judged against XDS) |
-| thau_bl1a_4p6keV | inhouse | pass | P 41 21 2 | P 4 2 2 | 0.06 | 0.998 | 2.47 | 2.53 | +2.5% | 88.4 | 15.8 | 6.9% | 5.3% | 0.999 | 35.1 | 35.6 | - | 0.183 | 0.028 | 0.943 | 0.175 | 0.185 | 0.151 | 1.157 | 8.580 | - | NOT_TESTED | 6 | P 41 21 2 vs reference P 4 2 2 (screws not judged against XDS) |
-| thau_bl1a_6p5keV | inhouse | pass | P 41 21 2 | P 4 2 2 | 0.03 | 0.999 | 1.74 | 1.78 | +2.5% | 88.6 | 16.1 | 7.5% | 4.7% | 0.999 | 42.7 | 34.5 | - | 0.191 | 0.050 | 0.951 | 0.183 | 0.194 | 0.151 | 1.208 | 6.730 | - | NOT_TESTED | 8 | P 41 21 2 vs reference P 4 2 2 (screws not judged against XDS) |
-| thau_micromax_pink | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.21 | 0.995 | 1.24 | 1.40 | +11.8% | 94.1 | 13.7 | 8.8% | 5.1% | 0.999 | 15.7 | 21.2 | - | 0.190 | 0.182 | 0.963 | 0.207 | 0.208 | 0.151 | 1.369 | 3.900 | - | NOT_TESTED | 10 |  |
-| thau_x10sa_0p1deg | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.22 | 0.993 | 1.89 | 2.20 | +13.9% | 85.4 | 17.1 | 14.6% | 7.2% | 0.998 | 10.8 | 9.2 | - | 0.238 | 0.034 | 0.927 | 0.237 | 0.241 | 0.151 | 1.567 | 1.330 | - | NOT_TESTED | 14 |  |
-| thau_x10sa_16keV | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.02 | 1.000 | 1.22 | 1.30 | +6.3% | 82.5 | 17.6 | 7.1% | 2.9% | 1.000 | 50.9 | 44.5 | - | 0.228 | 0.122 | 0.942 | 0.231 | 0.235 | 0.151 | 1.527 | 2.390 | - | NOT_TESTED | 12 |  |
-| thau_x10sa_injection | inhouse | pass | P 41 21 2 | P 41 21 2 | 0.02 | 1.000 | 1.26 | 1.28 | +1.6% | 82.5 | 19.0 | 3.9% | 2.6% | 1.000 | 32.9 | 36.2 | - | 0.228 | 0.039 | 0.939 | 0.224 | 0.229 | 0.151 | 1.477 | 9.630 | - | NOT_TESTED | 17 |  |
-| yag_x10sa_20keV | inhouse | pass | I a -3 d | I a -3 d | 0.03 | 0.999 | 0.66 | 0.68 | +2.4% | 96.2 | 34.9 | 40.3% | 44.7% | 0.640 | 2.9 | 3.2 | - | - | - | - | - | - | - | - | - | - | - | 11 |  |
-
-## Delta vs baseline 20261007-2139_9ced4c_rc175-p1-baseline
-
-Baseline rugnux 1.0.0-rc.175. Pass rates on the sets both runs have:
-
-| arm | common sets | baseline | this run |
-|:--|--:|:--|:--|
-| open | 203 | 188/200 (94%) | 187/200 (94%) |
-| inhouse | 47 | 47/47 (100%) | 46/47 (98%) |
-
-Rows whose result moved beyond noise (thresholds in report.py NOISE; confirm with `compare --rerun-changed` before believing a single-set change):
-
-| set | arm | verdict | space group | d_min | ISa | R_meas | CC1/2 | cell dev % | R_model (shell-scaled) | R_free | radial misfit | anom. sigma | ref-range R_meas | ref-range low-res R_meas | SHELXL R1 | SHELXL wR2 | SHELXL GooF | SHELXL EXTI | time s | beyond noise |
-|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|:--|
-| aspirin_x10sa_25keV | inhouse | pass | P 1 21/c 1 | 0.53 | 36.7 -> 34.4 | 3.1% | 1.000 | 0.05 | - | - | - | - | 3.1% | 2.2% | 0.0358 -> 0.0361 | 0.1167 -> 0.1188 | 1.079 -> 1.073 | 0.013 -> 0.011 | 8 -> 7 | isa, refres_isa |
-| citricacid_x10sa_20keV | inhouse | pass | P 1 21/c 1 | 0.67 | 24.1 -> 23.0 | 3.5% -> 4.1% | 0.999 -> 0.997 | 0.10 -> 0.11 | - | - | - | - | 3.5% -> 4.1% | 3.8% -> 5.0% | 0.0375 -> 0.0393 | 0.1029 -> 0.1060 | 1.087 -> 1.098 | 0.140 -> 0.180 | 8 -> 7 | r_meas, refres_r_meas, refres_lowres_r_meas, SHELXL exti |
-| cytc_x06da_2 | inhouse | pass | P 31 2 1 | 1.57 | 21.2 -> 23.0 | 9.8% -> 9.5% | 1.000 | 0.11 -> 0.09 | 0.253 | 0.307 -> 0.306 | 0.23 -> 0.21 | 6.33 -> 6.24 | 9.1% -> 8.9% | 3.5% -> 3.4% | - | - | - | - | 12 -> 9 | isa, refres_isa |
-| hepes_x10sa_20keV | inhouse | pass | P b c a | 0.66 | 38.7 -> 37.0 | 2.6% -> 2.7% | 0.999 | 0.07 -> 0.14 | - | - | - | - | 2.6% -> 2.7% | 3.5% -> 3.7% | 0.0315 -> 0.0307 | 0.0907 -> 0.0862 | 1.070 -> 1.060 | 0.049 -> 0.048 | 10 -> 9 | refres_lowres_r_meas |
-| insu_H_x06da_twin | inhouse | pass | R 3:H | 1.38 | 6.2 | 12.1% -> 12.4% | 0.995 | 0.04 -> 0.03 | 0.267 -> 0.264 | 0.256 -> 0.254 | 0.09 | 4.40 -> 4.43 | 12.5% -> 12.8% | 10.3% -> 10.9% | - | - | - | - | 6 | refres_lowres_r_meas |
-| insu_I_x06da_5keV_2 | inhouse | pass | I 2 3 | 2.42 -> 2.43 | 25.0 -> 32.1 | 8.4% -> 7.8% | 1.000 | 0.04 -> 0.07 | 0.219 -> 0.236 | 0.295 -> 0.333 | 0.26 -> 0.31 | 9.13 -> 9.34 | 7.9% -> 7.4% | 5.7% -> 5.1% | - | - | - | - | 4 | isa, r_meas, rmodel_shell_scaled, rfree, refres_r_meas, refres_isa, refres_lowres_r_meas |
-| insu_I_x06da_low_isa | inhouse | pass -> fail | I 2 3 -> R 3:R | 1.44 -> 1.59 | 5.6 -> 6.4 | 22.4% -> 26.9% | 0.998 -> 0.994 | 0.08 -> 0.07 | 0.226 -> 0.315 | 0.261 -> 0.368 | 0.10 -> 0.19 | 3.12 -> 1.53 | 22.6% -> 27.4% | 16.1% -> 12.7% | - | - | - | - | 8 | verdict pass->fail, space group, lattice, d_min, isa, r_meas, rmodel_shell_scaled, radial_misfit, rfree, anom_sigma, refres_r_meas, refres_isa, refres_lowres_r_meas |
-| insu_I_x06da_ref | inhouse | pass | I 2 3 | 1.40 -> 1.41 | 32.1 -> 32.6 | 30.4% -> 34.6% | 0.999 | 0.13 -> 0.14 | 0.226 | 0.245 -> 0.244 | 0.08 | 3.31 -> 3.28 | 25.6% -> 29.2% | 6.1% -> 6.6% | - | - | - | - | 8 -> 7 | r_meas, refres_r_meas, refres_lowres_r_meas |
-| insu_I_x06da_weak | inhouse | pass | I 2 3 | 1.64 | 14.9 -> 14.7 | 16.8% -> 17.1% | 1.000 | 0.79 -> 0.85 | 0.290 -> 0.286 | 0.329 -> 0.320 | 0.19 -> 0.15 | 2.09 -> 2.03 | 16.8% -> 17.1% | 6.2% -> 6.3% | - | - | - | - | 10 -> 11 | rfree |
-| kdp_x10sa_20keV | inhouse | pass | I 41 m d | 0.66 | 24.1 -> 24.0 | 5.2% -> 5.5% | 0.999 -> 0.998 | 0.07 -> 0.04 | - | - | - | - | 5.0% -> 5.3% | 4.6% -> 4.8% | 0.0475 | 0.1213 -> 0.1206 | 1.391 -> 1.380 | 0.028 -> 0.027 | 19 -> 13 | r_meas, refres_r_meas |
-| lcystine_x10sa_20keV | inhouse | pass | P 61 2 2 | 0.66 -> 0.67 | 5.1 -> 3.8 | 39.5% -> 40.7% | 1.000 -> 0.999 | 0.48 -> 0.52 | - | - | - | - | - | - | 0.1078 -> 0.1251 | 0.2854 -> 0.3491 | 1.112 -> 1.077 | 0.000 | 17 -> 18 | isa, SHELXL r1, SHELXL wr2, SHELXL goof |
-| lcystine_x10sa_25keV | inhouse | pass | P 61 2 2 | 0.53 | 5.3 -> 4.4 | 26.2% -> 39.9% | 1.000 -> 0.998 | 0.52 -> 0.54 | - | - | - | - | - | - | 0.1440 -> 0.1116 | 0.4009 -> 0.3236 | 1.513 -> 1.129 | 0.000 | 14 -> 17 | isa, r_meas, SHELXL r1, SHELXL wr2, SHELXL goof |
-| lyso_x06da_atten_wedge | inhouse | pass | P 41 21 2 | 1.19 -> 1.20 | 13.1 -> 13.3 | 56.9% -> 41.3% | 0.998 | 0.25 -> 0.32 | 0.295 -> 0.296 | 0.306 -> 0.307 | 0.07 -> 0.06 | 1.91 -> 1.94 | 47.6% -> 35.6% | 7.7% -> 6.7% | - | - | - | - | 15 -> 8 | r_meas, refres_r_meas, refres_lowres_r_meas |
-| lyso_x06da_half_image | inhouse | pass | P 41 21 2 | 1.57 | 6.9 -> 4.4 | 116.0% -> 245.2% | 0.967 -> 0.959 | 0.71 -> 1.02 | 0.278 -> 0.300 | 0.289 -> 0.332 | 0.06 -> 0.18 | 0.87 -> 0.92 | 109.0% -> 216.8% | 31.5% -> 34.3% | - | - | - | - | 10 | isa, r_meas, cc_half, cell_dev_pct, rmodel_shell_scaled, radial_misfit, rfree, anom_sigma, refres_r_meas, refres_isa, refres_lowres_r_meas |
-| lyso_x10sa_90deg_1 | inhouse | pass | P 41 21 2 | 1.82 | 20.8 -> 20.5 | 17.9% -> 17.6% | 0.998 | 0.12 | 0.381 -> 0.380 | 0.371 -> 0.369 | 0.11 -> 0.10 | 0.30 -> 0.34 | 15.4% -> 15.2% | 4.5% | - | - | - | - | 7 -> 6 | anom_sigma |
-| lyso_x10sa_strong | inhouse | pass | P 41 21 2 | 1.37 -> 1.36 | 5.4 -> 5.5 | 23.3% -> 23.7% | 0.997 -> 0.995 | 0.63 -> 0.65 | 0.373 -> 0.378 | 0.365 | 0.13 -> 0.19 | 1.37 -> 1.60 | 23.3% -> 23.7% | 11.4% -> 11.8% | - | - | - | - | 34 -> 29 | radial_misfit, anom_sigma |
-| myob_x06da | inhouse | pass | P 1 21 1 | 1.23 -> 1.24 | 24.7 -> 22.9 | 17.0% | 0.998 | 0.12 -> 0.13 | 0.229 | 0.233 -> 0.236 | 0.10 -> 0.12 | 3.42 -> 3.50 | 12.5% -> 12.7% | 4.2% -> 4.4% | - | - | - | - | 6 -> 8 | isa, refres_isa |
-| myob_x06da_powder_1 | inhouse | pass | P 1 21 1 | 1.50 -> 1.73 | 1.7 -> 3.8 | 92.4% -> 74.4% | 0.852 -> 0.578 | 0.02 -> 0.43 | 0.516 -> 0.492 | 0.542 -> 0.524 | 0.23 -> 0.31 | 0.62 -> -0.27 | 92.4% -> 74.4% | 24.9% -> 20.1% | - | - | - | - | 11 -> 9 | d_min, isa, r_meas, cc_half, cell_dev_pct, rmodel_shell_scaled, radial_misfit, rfree, anom_sigma, refres_r_meas, refres_isa, refres_lowres_r_meas |
-| myob_x06da_powder_2 | inhouse | pass | P 1 21 1 | 1.48 -> 1.47 | 2.7 -> 2.3 | 111.4% -> 174.0% | 0.916 -> 0.783 | 0.34 -> 0.45 | 0.439 -> 0.489 | 0.476 -> 0.500 | 0.14 -> 0.12 | 0.88 -> 1.42 | 111.4% -> 174.0% | 45.0% -> 54.2% | - | - | - | - | 10 -> 12 | isa, r_meas, cc_half, rmodel_shell_scaled, rfree, anom_sigma, refres_r_meas, refres_isa, refres_lowres_r_meas |
-| myob_x06da_sparse | inhouse | pass | P 1 21 1 | 1.76 -> 1.78 | 3.0 -> 4.4 | 46.3% -> 41.2% | 0.903 -> 0.950 | 0.44 -> 0.41 | 0.399 -> 0.423 | 0.366 -> 0.423 | 0.14 -> 0.11 | 0.84 -> 1.06 | 39.0% -> 34.1% | 17.3% -> 12.9% | - | - | - | - | 11 -> 13 | isa, r_meas, cc_half, rmodel_shell_scaled, rfree, anom_sigma, refres_r_meas, refres_isa, refres_lowres_r_meas |
-| myob_x06da_split | inhouse | pass | P 1 21 1 | 1.21 -> 1.86 | 1.6 -> 2.7 | 288.5% -> 78.2% | 0.788 -> 0.700 | 0.24 -> 0.20 | 0.473 -> 0.397 | 0.484 -> 0.402 | 0.13 -> 0.17 | -0.18 -> 0.39 | 169.7% -> 78.2% | 28.9% -> 22.1% | - | - | - | - | 11 -> 9 | d_min, isa, r_meas, cc_half, rmodel_shell_scaled, rfree, anom_sigma, refres_r_meas, refres_isa, refres_lowres_r_meas |
-| myob_x10sa | inhouse | pass | P 1 21 1 | 1.55 -> 1.56 | 10.4 -> 11.1 | 17.8% -> 17.0% | 0.995 -> 0.996 | 0.30 | 0.245 -> 0.242 | 0.246 | 0.05 -> 0.04 | 2.06 -> 2.04 | 16.2% -> 15.5% | 7.7% | - | - | - | - | 10 | isa, refres_isa |
-| thau_micromax_pink | inhouse | pass | P 41 21 2 | 1.24 | 15.9 -> 15.7 | 8.7% -> 8.8% | 0.999 | 0.16 -> 0.21 | 0.190 | 0.212 -> 0.207 | 0.20 -> 0.18 | 4.03 -> 3.90 | 8.6% -> 8.7% | 4.9% | - | - | - | - | 12 -> 10 | rfree |
-| thau_x10sa_0p1deg | inhouse | pass | P 41 21 2 | 1.91 -> 1.89 | 10.7 -> 10.8 | 14.4% -> 14.6% | 0.998 | 0.23 -> 0.22 | 0.236 -> 0.238 | 0.231 -> 0.237 | 0.02 -> 0.03 | 1.32 -> 1.33 | 13.6% -> 13.8% | 6.9% -> 6.7% | - | - | - | - | 16 -> 14 | completeness, rfree |
-| yag_x10sa_20keV | inhouse | pass | I a -3 d | 0.67 -> 0.66 | 2.8 -> 2.9 | 41.2% -> 40.3% | 0.697 -> 0.640 | 0.03 | - | - | - | - | 41.2% -> 40.2% | 46.1% -> 44.7% | 0.0970 -> 0.1005 | 0.2338 -> 0.2385 | 1.112 -> 1.110 | 0.548 -> 0.533 | 13 -> 11 | isa, cc_half, refres_isa, SHELXL r1 |
-| 2wnn | open | pass | P 1 21 1 | 1.44 -> 1.43 | 14.2 -> 15.2 | 7.1% -> 6.7% | 0.997 -> 0.998 | 0.11 -> 0.09 | 0.279 | 0.286 -> 0.287 | 0.18 -> 0.19 | 1.01 -> 1.04 | - | - | - | - | - | - | 22 | isa, r_meas, completeness |
-| 2wnq | open | fail | C 2 2 21 | 1.66 -> 1.65 | 10.3 -> 10.6 | 10.8% -> 10.9% | 0.997 | 68.58 -> 68.38 | 0.535 -> 0.536 | 0.541 -> 0.537 | 0.28 -> 0.18 | -0.04 -> -0.06 | - | - | - | - | - | - | 28 -> 26 | cell_dev_pct, radial_misfit, anom_sigma |
-| 2wnz | open | pass | P 1 21 1 | 1.84 -> 1.85 | 14.7 -> 17.4 | 12.3% -> 11.1% | 0.996 -> 0.997 | 0.13 -> 0.20 | 0.207 -> 0.202 | 0.233 -> 0.229 | 0.23 -> 0.21 | 0.91 -> 0.99 | - | - | - | - | - | - | 27 -> 21 | isa, r_meas, rmodel_shell_scaled, anom_sigma |
-| 2xfw | open | pass | P 1 21 1 | 1.56 -> 1.54 | 14.3 -> 15.3 | 14.3% -> 14.1% | 0.996 | 0.13 -> 0.07 | 0.200 -> 0.198 | 0.221 -> 0.219 | 0.17 -> 0.16 | 1.08 -> 1.18 | - | - | - | - | - | - | 58 -> 48 | isa, anom_sigma |
-| 3inp | open | pass | F 41 3 2 | 1.70 | 13.2 | 10.8% -> 10.5% | 0.999 | 0.04 | 0.239 -> 0.237 | 0.239 | 0.07 -> 0.08 | 2.94 -> 3.15 | - | - | - | - | - | - | 33 -> 22 | anom_sigma, time |
-| 3ky7 | open | pass | P 43 3 2 | 1.92 | 12.2 | 10.7% -> 10.6% | 0.999 | 0.03 | 0.339 | 0.335 -> 0.334 | 0.04 -> 0.05 | 0.43 -> 0.38 | - | - | - | - | - | - | 17 -> 19 | anom_sigma |
-| 3mc4 | open | pass | R 3:H | 1.79 | 12.4 -> 12.1 | 10.1% -> 10.2% | 0.994 | 0.06 -> 0.15 | 0.253 -> 0.251 | 0.257 -> 0.256 | 0.08 -> 0.06 | 1.42 -> 1.55 | - | - | - | - | - | - | 9 -> 6 | anom_sigma |
-| 3meb | open | pass | P 1 21 1 | 1.53 -> 1.70 | 14.6 -> 13.2 | 11.9% -> 14.5% | 0.993 -> 0.987 | 0.71 -> 0.91 | 0.198 -> 0.202 | 0.200 -> 0.205 | 0.54 -> 0.09 | 0.30 -> -0.16 | - | - | - | - | - | - | 9 -> 5 | d_min, isa, r_meas, cc_half, completeness, radial_misfit, anom_sigma |
-| 3r6o | open | fail | I 41 2 2 | 1.53 | 4.4 | 19.5% -> 19.3% | 0.984 -> 0.985 | 0.57 -> 0.54 | 0.302 | 0.308 | 0.62 -> 0.72 | 1.35 -> 1.31 | - | - | - | - | - | - | 5 -> 4 | radial_misfit |
-| 4bwl | open | fail | C 2 2 21 | 1.68 | 14.4 -> 13.7 | 14.0% -> 14.6% | 0.998 | 72.04 -> 72.05 | 0.522 | 0.521 -> 0.532 | 0.14 -> 0.13 | 0.11 -> 0.12 | - | - | - | - | - | - | 20 -> 21 | rfree, anom_sigma |
-| 5cc8 | open | fail | P 21 21 21 | 1.53 | 11.3 -> 10.8 | 8.0% -> 8.1% | 0.997 | 0.06 -> 0.11 | 0.171 -> 0.168 | 0.184 -> 0.182 | 0.17 -> 0.24 | 4.04 -> 4.51 | - | - | - | - | - | - | 10 -> 7 | completeness, radial_misfit, anom_sigma |
-| 5ebi | open | fail | C 2 2 21 | 0.85 -> 0.86 | 10.9 | 12.3% -> 12.2% | 0.998 | 40.33 -> 40.36 | 0.579 -> 0.580 | 0.574 -> 0.572 | 0.14 -> 0.13 | -0.09 -> -0.10 | - | - | - | - | - | - | 21 -> 14 | anom_sigma |
-| 5epe | open | pass | F 2 3 | 1.77 -> 1.78 | 9.9 -> 11.1 | 16.5% -> 23.9% | 0.998 -> 0.997 | 0.00 -> 0.03 | 0.173 -> 0.177 | 0.181 -> 0.183 | 0.11 -> 0.15 | 11.96 -> 9.63 | - | - | - | - | - | - | 30 -> 20 | isa, r_meas, anom_sigma, time |
-| 5j23 | open | pass | R 3:H | 2.18 -> 2.20 | 11.6 -> 11.5 | 14.8% | 0.996 | 0.15 | 0.225 -> 0.226 | 0.233 | 0.13 -> 0.12 | 0.79 -> 0.83 | - | - | - | - | - | - | 26 -> 22 | anom_sigma |
-| 5jk4 | open | pass | P 1 21 1 | 1.06 -> 0.96 | 14.9 -> 14.5 | 8.8% -> 9.1% | 0.786 -> 0.998 | 0.17 -> 0.15 | 0.106 -> 0.111 | 0.120 -> 0.128 | 0.08 -> 0.15 | 3.78 -> 3.69 | - | - | - | - | - | - | 11 -> 9 | d_min, cc_half, completeness, radial_misfit, rfree |
-| 5jvn | open | pass | P 6 2 2 | 2.23 | 15.7 -> 14.9 | 16.4% -> 16.5% | 0.998 | 0.03 | 0.228 | 0.249 -> 0.246 | 0.14 -> 0.12 | 1.36 -> 1.40 | - | - | - | - | - | - | 29 | isa |
-| 5ky6 | open | pass -> fail | P 1 21 1 -> P 1 2 1 | 1.54 -> 1.50 | 6.1 -> 6.9 | 25.6% -> 18.7% | 0.986 -> 0.987 | 0.64 -> 1.03 | 0.233 -> 0.245 | 0.243 -> 0.263 | 0.12 -> 0.17 | 0.54 -> 0.68 | - | - | - | - | - | - | 26 -> 18 | verdict pass->fail, space group, d_min, isa, r_meas, completeness, cell_dev_pct, rmodel_shell_scaled, radial_misfit, rfree, anom_sigma |
-| 5lzl | open | pass | P 31 2 1 | 2.86 -> 2.89 | 15.0 -> 14.6 | 17.1% -> 18.5% | 0.997 | 0.30 -> 0.37 | 0.222 | 0.229 | 0.14 | 1.27 -> 1.28 | - | - | - | - | - | - | 22 -> 10 | r_meas, time |
-| 5mln | open | pass | P 21 21 2 | 1.26 -> 1.27 | 21.5 -> 21.0 | 10.4% | 0.999 | 0.10 -> 0.25 | 0.181 -> 0.182 | 0.188 -> 0.189 | 0.14 -> 0.15 | 2.19 -> 2.07 | - | - | - | - | - | - | 17 -> 14 | anom_sigma |
-| 5nw5 | open | pass | P 21 21 21 | 7.06 -> 7.04 | 7.8 -> 8.4 | 33.2% -> 32.8% | 0.928 -> 0.937 | 0.19 -> 0.24 | 0.392 -> 0.396 | 0.464 -> 0.462 | 0.27 -> 0.24 | 0.16 -> 0.11 | - | - | - | - | - | - | 11 -> 16 | isa, cc_half, anom_sigma |
-| 5ojv | open | pass | P 21 21 2 | 1.81 -> 1.85 | 13.2 -> 12.6 | 14.7% -> 14.5% | 0.998 -> 0.982 | 0.41 -> 0.50 | 0.174 | 0.185 -> 0.186 | 0.14 -> 0.15 | 2.01 -> 1.49 | - | - | - | - | - | - | 33 -> 34 | d_min, cc_half, anom_sigma |
-| 5reo | open | pass | C 1 2 1 | 1.67 -> 1.64 | 26.9 -> 23.0 | 21.9% -> 23.6% | 0.990 -> 0.989 | 0.78 -> 0.36 | 0.202 -> 0.205 | 0.201 | 0.07 -> 0.06 | 0.72 | - | - | - | - | - | - | 8 -> 7 | d_min, isa, r_meas, cell_dev_pct |
-| 5t39 | open | pass | P 1 21 1 | 1.02 -> 1.00 | 16.1 | 7.3% | 0.998 | 0.17 | 0.152 -> 0.151 | 0.160 -> 0.156 | 0.10 -> 0.08 | 6.27 -> 6.35 | - | - | - | - | - | - | 24 -> 21 | completeness |
-| 5uth | open | pass | P 31 2 1 | 1.72 | 9.6 -> 10.4 | 12.4% -> 12.6% | 0.997 | 0.21 -> 0.23 | 0.194 -> 0.196 | 0.217 -> 0.221 | 0.17 -> 0.18 | 2.87 -> 2.60 | - | - | - | - | - | - | 8 -> 5 | isa, anom_sigma |
-| 6cs9 | open | pass | P 1 21 1 | 1.72 -> 1.71 | 13.1 -> 12.9 | 9.8% -> 10.1% | 0.998 | 0.06 -> 0.07 | 0.211 | 0.207 -> 0.206 | 0.14 -> 0.15 | 0.76 -> 0.79 | - | - | - | - | - | - | 9 -> 8 | completeness |
-| 6f3p | open | pass | C 1 2 1 | 1.14 -> 1.15 | 9.4 -> 9.3 | 10.0% | 0.997 | 0.19 -> 0.21 | 0.143 | 0.168 -> 0.166 | 0.21 -> 0.20 | -3.38 -> -3.32 | - | - | - | - | - | - | 43 -> 32 | time |
-| 6fwc | open | pass | C 2 2 2 | 1.41 | 27.3 | 16.4% | 0.995 | 0.04 | 0.188 | 0.196 | 0.10 | 1.45 | - | - | - | - | - | - | 41 -> 14 | time |
-| 6g1f | open | pass | C 1 2 1 | 1.93 -> 1.98 | 21.6 -> 20.8 | 11.6% -> 11.2% | 0.997 | 0.04 -> 0.06 | 0.207 -> 0.206 | 0.223 -> 0.218 | 0.14 -> 0.11 | 1.07 -> 1.04 | - | - | - | - | - | - | 29 -> 24 | d_min |
-| 6gvk | open | pass | C 1 2 1 | 1.42 | 19.9 -> 19.5 | 5.2% -> 5.3% | 0.999 | 0.08 -> 0.13 | 0.201 | 0.214 -> 0.215 | 0.18 | 1.88 -> 2.02 | - | - | - | - | - | - | 20 -> 17 | anom_sigma |
-| 6hv2 | open | pass | P 61 2 2 | 1.41 -> 1.40 | 13.7 -> 14.6 | 19.7% -> 19.8% | 1.000 | 0.04 -> 0.06 | 0.220 -> 0.219 | 0.241 -> 0.239 | 0.35 -> 0.26 | 7.82 -> 7.84 | - | - | - | - | - | - | 22 -> 19 | isa, radial_misfit |
-| 6hwj | open | pass | P 1 21 1 | 1.72 -> 1.70 | 38.6 -> 39.0 | 8.6% -> 9.2% | 0.999 | 0.12 -> 0.10 | 0.187 -> 0.189 | 0.192 -> 0.190 | 0.13 -> 0.10 | 1.60 -> 1.50 | - | - | - | - | - | - | 12 -> 10 | r_meas, anom_sigma |
-| 6i3j | open | pass | F 2 2 2 | 2.32 -> 2.33 | 6.8 -> 7.8 | 24.6% -> 21.5% | 0.977 -> 0.985 | 0.08 -> 0.17 | 0.203 -> 0.192 | 0.236 -> 0.229 | 0.17 -> 0.18 | 1.73 -> 2.07 | - | - | - | - | - | - | 34 -> 19 | isa, r_meas, cc_half, rmodel_shell_scaled, rfree, anom_sigma, time |
-| 6iu9 | open | pass | P 31 | 2.74 -> 2.76 | 5.5 | 14.4% -> 13.9% | 0.992 -> 0.994 | 0.30 -> 0.20 | 0.311 -> 0.313 | 0.321 -> 0.323 | 0.08 -> 0.11 | 1.36 -> 1.47 | - | - | - | - | - | - | 19 -> 17 | anom_sigma |
-| 6jgh | open | pass | P 21 21 21 | 0.87 -> 0.88 | 6.6 -> 6.7 | 23.3% -> 23.0% | 0.990 | 0.39 -> 0.34 | 0.136 -> 0.134 | 0.156 -> 0.153 | 0.17 -> 0.15 | 2.17 -> 2.06 | - | - | - | - | - | - | 30 -> 28 | anom_sigma |
-| 6jgj | open | pass | P 21 21 21 | 0.65 | 15.1 | 7.4% | 0.999 | 0.28 -> 0.37 | 0.164 -> 0.163 | 0.167 | 0.06 -> 0.05 | 2.73 -> 2.59 | - | - | - | - | - | - | 39 -> 30 | anom_sigma |
-| 6moj | open | pass | I 41 2 2 | 2.43 | 8.3 -> 8.4 | 52.4% -> 51.5% | 0.998 | 0.08 -> 0.14 | 0.248 | 0.257 -> 0.258 | 0.21 -> 0.20 | 1.06 -> 1.14 | - | - | - | - | - | - | 48 -> 37 | anom_sigma |
-| 6nen | open | pass | P 3 1 2 | 1.79 -> 1.77 | 6.2 -> 6.1 | 25.6% -> 26.2% | 0.997 | 0.07 -> 0.17 | 0.208 | 0.218 -> 0.217 | 0.11 -> 0.12 | 0.37 -> 0.25 | - | - | - | - | - | - | 18 -> 13 | anom_sigma |
-| 6oel | open | pass | F 41 3 2 | 2.83 -> 2.85 | 10.7 -> 10.3 | 47.3% -> 36.1% | 0.997 -> 0.998 | 0.00 -> 0.09 | 0.249 -> 0.248 | 0.266 -> 0.255 | 0.19 -> 0.13 | 0.63 -> 0.61 | - | - | - | - | - | - | 23 -> 25 | r_meas, radial_misfit, rfree |
-| 6oww | open | fail | P 41 21 2 | 2.72 -> 2.83 | 11.8 -> 12.4 | 201.5% -> 177.6% | 0.994 -> 0.995 | 0.19 -> 0.24 | 0.361 -> 0.355 | 0.373 -> 0.366 | 0.09 -> 0.06 | 2.04 -> 2.06 | - | - | - | - | - | - | 40 -> 29 | d_min, r_meas, rmodel_shell_scaled, rfree, time |
-| 6p8j | open | fail | P 21 21 2 -> P 1 1 2 | 1.28 -> 1.38 | 5.4 -> 5.0 | 23.7% -> 19.7% | 0.990 -> 0.980 | 0.33 -> 0.38 | 0.249 -> 0.235 | 0.254 -> 0.245 | 0.09 -> 0.10 | 1.29 -> 0.89 | - | - | - | - | - | - | 64 -> 53 | space group, d_min, isa, r_meas, cc_half, completeness, rmodel_shell_scaled, rfree, anom_sigma |
-| 6p8p | open | pass | P 4 | 1.47 -> 1.45 | 15.5 -> 16.0 | 12.5% -> 13.6% | 0.998 | 0.14 -> 0.12 | 0.187 -> 0.191 | 0.205 -> 0.203 | 0.17 -> 0.11 | 1.90 -> 1.89 | - | - | - | - | - | - | 16 -> 15 | r_meas, radial_misfit |
-| 6pb3 | open | pass | P 6 | 1.85 -> 1.84 | 22.8 -> 24.8 | 6.5% -> 6.6% | 1.000 | 0.19 -> 0.11 | 0.214 | 0.229 -> 0.227 | 0.11 -> 0.10 | 10.83 -> 10.52 | - | - | - | - | - | - | 36 -> 25 | isa, time |
-| 6pxc | open | pass | I 2 2 2 | 1.41 -> 1.43 | 10.2 -> 10.5 | 8.0% -> 7.7% | 0.998 | 0.24 | 0.210 -> 0.209 | 0.214 -> 0.215 | 0.16 -> 0.17 | 0.91 -> 0.67 | - | - | - | - | - | - | 11 -> 10 | anom_sigma |
-| 6qaj | open | pass | C 2 2 21 | 2.70 -> 2.78 | 13.2 -> 12.8 | 24.5% | 0.997 -> 0.999 | 0.41 -> 0.47 | 0.321 -> 0.320 | 0.331 | 0.22 -> 0.19 | 4.45 -> 4.32 | - | - | - | - | - | - | 22 -> 15 | d_min |
-| 6r72 | open | pass | P 1 21 1 | 4.39 | 18.0 -> 16.6 | 16.6% -> 16.5% | 1.000 | 1.32 -> 1.47 | 0.362 -> 0.364 | 0.367 -> 0.369 | 0.04 | 0.13 | - | - | - | - | - | - | 21 -> 19 | isa |
-| 6s1u | open | pass | P 1 21 1 | 1.75 -> 1.76 | 13.7 -> 13.4 | 22.4% -> 22.2% | 0.989 -> 0.991 | 0.13 | 0.202 -> 0.201 | 0.200 -> 0.199 | 0.09 -> 0.11 | 0.63 -> 0.58 | - | - | - | - | - | - | 11 -> 10 | anom_sigma |
-| 6ukf | open | pass | P 1 21 1 | 0.95 | 9.3 -> 9.9 | 10.0% -> 9.8% | 0.998 | 0.24 -> 0.07 | 0.165 -> 0.164 | 0.161 -> 0.159 | 0.06 -> 0.02 | 2.26 -> 2.38 | - | - | - | - | - | - | 41 -> 35 | isa, anom_sigma |
-| 6yqf | open | pass | P 21 21 2 | 3.39 -> 3.23 | 4.8 -> 5.0 | 41.7% -> 65.4% | 0.983 -> 0.995 | 0.71 -> 0.80 | 0.407 -> 0.435 | 0.436 -> 0.459 | 0.13 -> 0.21 | 0.18 -> -0.16 | - | - | - | - | - | - | 17 -> 28 | d_min, r_meas, cc_half, rmodel_shell_scaled, radial_misfit, rfree, anom_sigma, time |
-| 6z8o | open | pass | P 1 21 1 | 2.21 -> 2.16 | 14.0 -> 14.5 | 17.4% -> 19.0% | 0.996 -> 0.995 | 0.63 -> 0.61 | 0.275 -> 0.283 | 0.281 -> 0.289 | 0.07 -> 0.06 | 1.25 -> 1.18 | - | - | - | - | - | - | 12 | d_min, r_meas, completeness, rmodel_shell_scaled, rfree, anom_sigma |
-| 6z9g | open | fail | P 1 21 1 | 1.60 -> 1.67 | 14.8 -> 14.5 | 11.5% -> 12.5% | 0.997 -> 0.996 | 22.48 -> 21.74 | 0.531 -> 0.536 | 0.542 -> 0.547 | 0.18 -> 0.15 | 0.01 -> 0.06 | - | - | - | - | - | - | 22 -> 17 | d_min, r_meas, completeness, cell_dev_pct, rfree, anom_sigma |
-| 6ze4 | open | pass | P 21 21 21 | 1.30 -> 1.29 | 10.3 -> 10.5 | 19.8% -> 20.5% | 0.992 -> 0.988 | 0.62 -> 0.48 | 0.216 -> 0.222 | 0.223 -> 0.226 | 0.09 -> 0.06 | 1.73 | - | - | - | - | - | - | 43 -> 35 | rmodel_shell_scaled |
-| 6zqr | open | pass | P 4 | 1.76 -> 1.77 | 9.1 -> 8.9 | 19.4% -> 20.0% | 0.995 | 0.40 -> 0.33 | 0.197 | 0.204 -> 0.202 | 0.17 -> 0.15 | 1.34 -> 1.42 | - | - | - | - | - | - | 15 -> 14 | anom_sigma |
-| 6zqy | open | pass | P 4 | 1.71 -> 1.69 | 12.3 -> 13.0 | 22.7% -> 22.0% | 0.994 | 0.11 -> 0.12 | 0.219 -> 0.209 | 0.226 -> 0.217 | 0.15 | 1.20 -> 1.44 | - | - | - | - | - | - | 15 -> 26 | isa, rmodel_shell_scaled, rfree, anom_sigma, time |
-| 6zr0 | open | pass | P 4 | 1.67 -> 1.64 | 23.4 -> 25.2 | 13.3% -> 12.9% | 0.996 -> 0.993 | 0.08 -> 0.07 | 0.218 -> 0.215 | 0.218 | 0.05 -> 0.07 | 1.67 -> 1.82 | - | - | - | - | - | - | 24 -> 23 | isa, anom_sigma |
-| 7arr | open | pass | P 1 | 0.92 | 18.9 -> 18.7 | 3.7% -> 3.8% | 0.999 | 0.28 -> 0.14 | 0.154 -> 0.155 | 0.165 -> 0.162 | 0.20 -> 0.17 | 0.06 -> -0.41 | - | - | - | - | - | - | 28 -> 23 | anom_sigma |
-| 7atg | open | pass | P 21 21 21 | 0.60 | 22.9 -> 23.1 | 5.2% -> 5.1% | 0.994 | 0.10 -> 0.02 | 0.128 -> 0.125 | 0.178 -> 0.160 | 0.21 -> 0.13 | 6.63 -> 6.77 | - | - | - | - | - | - | 24 -> 31 | radial_misfit, rfree |
-| 7bgt | open | pass | P 1 | 1.78 -> 1.79 | 17.2 -> 16.9 | 13.7% -> 13.6% | 0.993 | 0.32 -> 0.36 | 0.195 | 0.207 | 0.12 | 0.24 -> 0.22 | - | - | - | - | - | - | 9 | anom_sigma |
-| 7bgu | open | pass | P 1 | 2.30 -> 2.32 | 10.0 -> 16.2 | 12.6% -> 10.8% | 0.938 -> 0.942 | 0.17 -> 0.12 | 0.285 -> 0.254 | 0.303 -> 0.266 | 0.13 -> 0.09 | 0.28 -> -0.36 | - | - | - | - | - | - | 7 | isa, r_meas, rmodel_shell_scaled, rfree, anom_sigma |
-| 7dkp | open | pass | P 1 21 1 | 1.18 -> 1.20 | 26.0 -> 26.5 | 11.9% -> 12.2% | 0.998 | 0.03 -> 0.14 | 0.158 -> 0.159 | 0.161 -> 0.163 | 0.08 -> 0.12 | 2.84 -> 2.71 | - | - | - | - | - | - | 23 -> 20 | completeness |
-| 7mzt | open | unscored | P 21 21 21 | 3.15 -> 3.18 | 3.1 -> 3.8 | 356.5% -> 417.1% | 0.966 -> 0.977 | 0.56 -> 0.63 | 0.414 | 0.419 | 0.10 | 0.06 -> -0.18 | - | - | - | - | - | - | 30 -> 28 | isa, r_meas, cc_half, anom_sigma |
-| 7n2s | open | pass | P 1 21 1 | 2.56 | 9.9 -> 14.5 | 56.5% -> 58.6% | 0.918 -> 0.927 | 0.07 -> 0.04 | 0.299 -> 0.301 | 0.309 -> 0.316 | 0.12 | 0.30 -> 0.11 | - | - | - | - | - | - | 10 -> 9 | isa, cc_half, rfree, anom_sigma |
-| 7os3 | open | pass | P 21 21 21 | 1.96 | 24.3 -> 23.8 | 8.4% -> 8.9% | 0.999 | 0.11 -> 0.17 | 0.181 -> 0.183 | 0.194 -> 0.192 | 0.16 -> 0.13 | 6.13 -> 5.74 | - | - | - | - | - | - | 24 -> 23 | anom_sigma |
-| 7ou1 | open | pass | P 1 21 1 | 1.40 -> 1.39 | 9.1 -> 9.0 | 15.9% -> 15.7% | 0.991 | 0.04 -> 0.05 | 0.202 | 0.209 | 0.10 | 1.51 -> 1.48 | - | - | - | - | - | - | 17 -> 14 | completeness |
-| 7q6j | open | pass | P 21 21 21 | 2.00 | 11.0 -> 10.0 | 14.4% -> 14.5% | 0.996 -> 0.998 | 0.25 -> 0.40 | 0.224 | 0.235 -> 0.234 | 0.14 -> 0.12 | 1.67 -> 1.42 | - | - | - | - | - | - | 22 -> 21 | isa, anom_sigma |
-| 7qij | open | pass | P 21 21 21 | 3.59 -> 3.62 | 9.4 -> 9.2 | 24.1% -> 24.5% | 0.996 | 0.36 -> 0.42 | 0.357 -> 0.359 | 0.364 -> 0.366 | 0.07 -> 0.06 | 0.20 -> 0.16 | - | - | - | - | - | - | 79 -> 77 | anom_sigma |
-| 7qis | open | pass | P 61 | 1.80 -> 1.76 | 16.6 -> 17.2 | 20.7% -> 21.2% | 0.997 | 0.44 -> 0.06 | 0.165 -> 0.166 | 0.190 -> 0.193 | 0.19 -> 0.20 | 1.32 -> 1.41 | - | - | - | - | - | - | 35 -> 20 | d_min, cell_dev_pct, anom_sigma, time |
-| 7raa | open | pass | P 41 21 2 | 2.58 -> 2.64 | 11.1 -> 10.4 | 17.0% -> 17.8% | 1.000 | 0.04 -> 0.10 | 0.296 -> 0.297 | 0.337 -> 0.335 | 0.26 -> 0.19 | 0.53 -> 0.49 | - | - | - | - | - | - | 22 -> 19 | d_min, isa, radial_misfit, anom_sigma |
-| 7rji | open | pass | R 3 2:H | 1.49 -> 1.47 | 8.4 -> 7.8 | 13.1% -> 15.6% | 0.999 | 0.29 -> 0.12 | 0.205 -> 0.208 | 0.198 -> 0.196 | 0.12 -> 0.08 | 6.89 -> 6.80 | - | - | - | - | - | - | 19 -> 17 | isa, r_meas |
-| 7tcd | open | pass | C 1 2 1 | 1.66 -> 1.67 | 18.4 -> 18.0 | 8.6% -> 8.8% | 0.999 | 0.23 -> 0.26 | 0.191 | 0.212 | 0.20 -> 0.21 | 1.19 -> 1.11 | - | - | - | - | - | - | 20 -> 18 | anom_sigma |
-| 8a1a | open | pass | P 61 | 1.89 -> 1.91 | 20.5 -> 19.2 | 51.6% -> 52.5% | 0.997 -> 0.998 | 0.16 -> 0.26 | 0.178 -> 0.177 | 0.180 -> 0.179 | 0.03 | 1.76 -> 1.79 | - | - | - | - | - | - | 67 -> 54 | isa |
-| 8c3e | open | fail | P 6 2 2 | 1.78 -> 1.79 | 5.6 -> 5.9 | 29.2% -> 29.4% | 0.979 -> 0.980 | 0.24 | 0.359 | 0.391 -> 0.399 | 0.22 -> 0.28 | 1.46 -> 0.91 | - | - | - | - | - | - | 3 -> 2 | isa, radial_misfit, rfree, anom_sigma |
-| 8iya | open | pass | C 1 2 1 | 1.91 -> 1.90 | 5.9 -> 5.8 | 21.4% -> 22.4% | 0.989 -> 0.988 | 0.16 -> 0.33 | 0.247 -> 0.248 | 0.235 -> 0.233 | 0.03 -> 0.05 | 0.38 -> 0.22 | - | - | - | - | - | - | 7 -> 6 | anom_sigma |
-| 8owm | open | pass | P 1 | 1.48 -> 1.50 | 22.2 -> 21.1 | 10.2% -> 10.8% | 0.998 | 0.02 -> 0.06 | 0.163 -> 0.164 | 0.178 -> 0.174 | 0.13 -> 0.10 | 1.37 -> 1.32 | - | - | - | - | - | - | 53 -> 44 | isa, r_meas |
-| 8qj5 | open | pass | P 1 21 1 | 1.32 -> 1.43 | 8.5 -> 8.3 | 17.4% -> 16.5% | 0.996 | 0.44 -> 0.51 | 0.189 -> 0.181 | 0.204 -> 0.197 | 0.13 | 1.59 -> 1.41 | - | - | - | - | - | - | 16 | d_min, r_meas, rmodel_shell_scaled, rfree, anom_sigma |
-| 8qq7 | open | pass | P 62 2 2 | 3.16 -> 3.15 | 6.3 -> 6.0 | 19.2% -> 20.0% | 0.998 | 0.61 | 0.431 -> 0.402 | 0.431 -> 0.408 | 0.37 | 0.64 -> 0.70 | - | - | - | - | - | - | 11 -> 9 | isa, rmodel_shell_scaled, rfree, anom_sigma |
-| 8r5r | open | pass | P 21 21 21 | 2.89 -> 2.79 | 15.1 -> 18.9 | 27.8% -> 27.4% | 0.997 | 0.11 -> 0.16 | 0.274 -> 0.264 | 0.289 -> 0.287 | 0.13 -> 0.16 | 0.14 -> 0.31 | - | - | - | - | - | - | 20 -> 21 | d_min, isa, rmodel_shell_scaled, anom_sigma |
-| 8rud | open | pass | P 1 21 1 | 1.64 -> 1.65 | 12.4 | 32.6% -> 32.2% | 0.992 | 0.40 -> 0.42 | 0.246 -> 0.247 | 0.255 -> 0.256 | 0.09 | 0.70 -> 0.77 | - | - | - | - | - | - | 45 -> 42 | anom_sigma |
-| 8sa8 | open | pass | I 1 2 1 | 1.10 -> 1.11 | 22.0 -> 21.7 | 11.7% -> 11.8% | 0.999 | 0.02 -> 0.01 | 0.155 | 0.169 -> 0.170 | 0.14 -> 0.15 | 3.79 | - | - | - | - | - | - | 77 -> 44 | time |
-| 8sqo | open | pass | P 4 3 2 | 1.32 -> 1.31 | 14.2 -> 13.9 | 23.5% -> 25.2% | 1.000 | 0.13 -> 0.15 | 0.183 -> 0.185 | 0.206 -> 0.200 | 0.18 -> 0.11 | 7.00 -> 6.55 | - | - | - | - | - | - | 22 -> 18 | r_meas, radial_misfit, rfree, anom_sigma |
-| 8sqt | open | pass | F 4 3 2 | 1.86 -> 1.83 | 17.9 -> 24.1 | 19.3% -> 21.0% | 1.000 | 0.10 | 0.217 -> 0.222 | 0.217 -> 0.225 | 0.14 -> 0.15 | 3.15 -> 2.88 | - | - | - | - | - | - | 50 -> 23 | isa, r_meas, rfree, anom_sigma, time |
-| 8t7r | open | pass | C 1 2 1 | 3.23 -> 3.30 | 7.8 -> 10.2 | 31.3% -> 32.7% | 0.984 -> 0.985 | 0.28 -> 0.39 | 0.284 | 0.285 -> 0.288 | 0.08 -> 0.10 | 0.43 -> 0.37 | - | - | - | - | - | - | 51 -> 39 | d_min, isa, anom_sigma |
-| 8tha | open | pass | P 62 | 1.32 -> 1.34 | 27.6 -> 26.4 | 16.6% -> 15.8% | 0.999 | 0.17 -> 0.20 | 0.212 -> 0.209 | 0.221 -> 0.218 | 0.09 | 4.46 -> 4.30 | - | - | - | - | - | - | 16 -> 13 | r_meas |
-| 8tyy | open | pass | F 4 3 2 | 1.28 -> 1.27 | 16.3 -> 16.2 | 16.5% -> 16.6% | 0.999 | 0.06 -> 0.02 | 0.160 -> 0.161 | 0.180 -> 0.179 | 0.15 -> 0.14 | 13.55 -> 13.49 | - | - | - | - | - | - | 126 -> 84 | time |
-| 8v2t | open | pass | P 42 21 2 | 1.19 -> 1.15 | 11.9 -> 12.3 | 9.1% -> 8.0% | 0.999 | 0.35 -> 0.20 | 0.166 -> 0.167 | 0.182 -> 0.180 | 0.20 -> 0.21 | 10.66 -> 10.97 | - | - | - | - | - | - | 13 | d_min, r_meas, completeness |
-| 8v4o | open | pass | P 61 2 2 | 2.11 -> 2.12 | 14.8 -> 15.4 | 31.7% -> 30.8% | 0.998 | 0.44 -> 0.06 | 0.235 | 0.254 -> 0.251 | 0.16 -> 0.15 | 0.84 -> 0.97 | - | - | - | - | - | - | 43 -> 36 | cell_dev_pct, anom_sigma |
-| 8xbp | open | pass | C 1 2 1 | 1.66 -> 1.68 | 18.6 -> 18.8 | 11.1% -> 11.0% | 0.999 | 0.15 -> 0.19 | 0.313 -> 0.312 | 0.329 -> 0.330 | 0.18 -> 0.19 | 1.22 -> 1.16 | - | - | - | - | - | - | 15 -> 18 | completeness |
-| 8xte | open | pass | P 31 2 1 | 1.64 | 13.0 -> 12.4 | 24.8% -> 25.1% | 0.996 | 0.02 -> 0.07 | 0.274 -> 0.275 | 0.287 | 0.13 | 0.92 -> 0.95 | - | - | - | - | - | - | 65 -> 21 | time |
-| 8xtf | open | pass | R 3 2:H | 1.84 | 7.7 -> 7.6 | 86.8% -> 86.6% | 0.988 | 0.23 | 0.192 -> 0.193 | 0.187 -> 0.186 | 0.05 -> 0.04 | 1.39 -> 1.51 | - | - | - | - | - | - | 23 -> 26 | anom_sigma |
-| 8xtg | open | pass | P 31 2 1 | 1.54 -> 1.55 | 7.3 -> 7.6 | 27.4% -> 26.7% | 0.994 | 0.05 | 0.274 -> 0.273 | 0.284 -> 0.287 | 0.14 -> 0.15 | 0.90 -> 0.88 | - | - | - | - | - | - | 43 -> 20 | time |
-| 9b22 | open | pass | P 1 21 1 | 1.14 | 16.4 | 6.2% | 0.999 | 0.07 | 0.159 -> 0.160 | 0.166 -> 0.165 | 0.12 -> 0.10 | 0.14 -> 0.06 | - | - | - | - | - | - | 13 | anom_sigma |
-| 9bn8 | open | pass | P 41 | 1.21 -> 1.19 | 19.8 | 8.1% -> 8.0% | 1.000 | 0.09 -> 0.10 | 0.151 | 0.159 -> 0.162 | 0.11 -> 0.13 | 3.78 -> 3.80 | - | - | - | - | - | - | 21 -> 15 | completeness |
-| 9c18 | open | pass | P 1 | 1.72 -> 1.74 | 10.9 -> 10.5 | 26.9% -> 26.1% | 0.987 -> 0.988 | 0.61 -> 0.74 | 0.220 -> 0.219 | 0.221 -> 0.219 | 0.07 | 0.67 -> 0.73 | - | - | - | - | - | - | 8 -> 7 | anom_sigma |
-| 9e2t | open | pass | P 1 | 2.29 -> 2.35 | 6.9 -> 6.6 | 28.5% -> 29.2% | 0.992 -> 0.991 | 0.06 -> 0.10 | 0.229 | 0.232 | 0.06 -> 0.05 | 0.42 -> 0.38 | - | - | - | - | - | - | 52 -> 48 | d_min, anom_sigma |
-| 9ea5 | open | pass | P 1 21 1 | 1.64 -> 1.66 | 26.8 -> 26.7 | 17.9% -> 18.0% | 0.997 | 0.85 -> 0.11 | 0.196 -> 0.195 | 0.202 -> 0.201 | 0.11 | 1.20 -> 1.21 | - | - | - | - | - | - | 27 -> 17 | completeness, cell_dev_pct |
-| 9fcf | open | pass | P 4 | 1.76 -> 1.78 | 7.2 -> 7.1 | 31.6% -> 34.9% | 0.995 | 0.04 -> 0.21 | 0.290 -> 0.286 | 0.294 -> 0.292 | 0.06 -> 0.07 | 0.90 -> 0.77 | - | - | - | - | - | - | 44 -> 39 | r_meas, anom_sigma |
-| 9fhc | open | pass | I 2 3 | 1.92 -> 1.89 | 12.3 -> 11.9 | 16.9% -> 16.7% | 0.998 -> 0.999 | 0.25 -> 0.27 | 0.239 | 0.244 -> 0.246 | 0.07 -> 0.10 | 1.22 -> 1.36 | - | - | - | - | - | - | 49 -> 36 | anom_sigma, time |
-| 9gqg | open | pass | P 31 2 1 | 1.83 -> 1.82 | 12.9 -> 11.9 | 11.9% -> 12.3% | 0.998 | 0.01 | 0.233 | 0.246 -> 0.250 | 0.15 -> 0.14 | 1.53 -> 1.27 | - | - | - | - | - | - | 15 | isa, anom_sigma |
-| 9h0q | open | pass | R 3 2:H | 2.10 -> 2.11 | 18.6 -> 18.2 | 17.4% -> 17.0% | 0.998 | 0.41 -> 0.42 | 0.205 -> 0.206 | 0.214 -> 0.218 | 0.11 -> 0.12 | 1.10 -> 1.16 | - | - | - | - | - | - | 31 -> 30 | anom_sigma |
-| 9hnc | open | fail | P 1 21 1 | 1.63 -> 1.64 | 13.6 | 12.8% | 0.998 | 0.09 -> 0.07 | 0.246 -> 0.245 | 0.255 -> 0.254 | 0.15 | 0.88 | - | - | - | - | - | - | 62 -> 30 | time |
-| 9hs7 | open | pass | P 61 | 1.68 -> 1.66 | 13.8 -> 11.5 | 10.9% -> 11.8% | 0.999 | 0.07 -> 0.12 | 0.212 -> 0.210 | 0.240 -> 0.242 | 0.36 | 1.36 -> 1.22 | - | - | - | - | - | - | 18 -> 19 | isa, r_meas, anom_sigma |
-| 9i0a | open | pass | P 21 21 2 | 1.80 -> 1.81 | 12.2 -> 11.6 | 19.5% -> 20.1% | 0.999 | 0.45 -> 0.36 | 0.225 -> 0.227 | 0.233 -> 0.231 | 0.10 -> 0.08 | 1.07 -> 0.91 | - | - | - | - | - | - | 45 -> 30 | anom_sigma, time |
-| 9lxl | open | pass | P 41 21 2 | 2.06 -> 2.08 | 6.2 | 41.9% -> 42.1% | 0.996 -> 0.997 | 0.49 -> 0.62 | 0.306 -> 0.300 | 0.321 -> 0.314 | 0.10 -> 0.09 | 0.69 -> 0.75 | - | - | - | - | - | - | 19 | rmodel_shell_scaled, rfree, anom_sigma |
-| 9min | open | fail | P 21 21 2 | 1.86 | 10.5 -> 9.9 | 26.5% -> 27.8% | 0.999 -> 0.998 | 36.97 -> 37.01 | 0.566 -> 0.564 | 0.577 -> 0.574 | 0.21 | 0.00 -> -0.03 | - | - | - | - | - | - | 52 -> 48 | isa, r_meas, anom_sigma |
-| 9o0h | open | pass | P 21 21 21 | 2.04 -> 2.01 | 5.8 -> 5.4 | 64.3% -> 67.7% | 0.983 -> 0.985 | 0.11 -> 0.34 | 0.241 | 0.253 -> 0.251 | 0.09 -> 0.07 | 0.12 -> 0.33 | - | - | - | - | - | - | 44 -> 41 | isa, r_meas, cell_dev_pct, anom_sigma |
-| 9p7q | open | pass | C 1 2 1 | 1.76 -> 1.78 | 11.0 -> 10.8 | 23.7% -> 29.5% | 0.986 | 0.14 -> 0.13 | 0.270 -> 0.268 | 0.283 -> 0.281 | 0.04 -> 0.05 | 0.86 -> 0.72 | - | - | - | - | - | - | 11 -> 9 | r_meas, completeness, anom_sigma |
-| 9pbb | open | pass | C 1 2 1 | 1.80 -> 1.81 | 16.2 -> 16.7 | 22.9% -> 23.6% | 0.994 -> 0.993 | 0.15 | 0.234 -> 0.233 | 0.234 -> 0.231 | 0.03 | 0.38 -> 0.45 | - | - | - | - | - | - | 15 -> 11 | anom_sigma |
-| 9q41 | open | pass | C 2 2 21 | 1.68 | 7.9 -> 7.5 | 29.0% -> 31.7% | 0.985 -> 0.982 | 0.20 -> 0.21 | 0.188 -> 0.192 | 0.194 -> 0.192 | 0.10 -> 0.04 | 0.47 -> 0.35 | - | - | - | - | - | - | 18 -> 16 | r_meas, radial_misfit, anom_sigma |
-| 9q66 | open | pass | P 1 21 1 | 2.02 -> 2.07 | 13.1 -> 13.0 | 32.2% -> 30.9% | 0.990 | 0.34 -> 0.39 | 0.204 -> 0.201 | 0.216 -> 0.214 | 0.08 | 0.66 | - | - | - | - | - | - | 22 -> 18 | d_min |
-| 9qvv | open | pass | I 2 2 2 | 2.49 -> 2.53 | 37.5 -> 38.1 | 11.1% -> 10.8% | 1.000 | 0.42 -> 0.08 | 0.236 -> 0.251 | 0.241 -> 0.248 | 0.18 -> 0.23 | 1.67 -> 1.69 | - | - | - | - | - | - | 17 | completeness, cell_dev_pct, rmodel_shell_scaled, rfree |
-| 9qw2 | open | pass | P 1 21 1 | 1.74 -> 1.82 | 7.8 -> 6.4 | 18.8% -> 22.3% | 0.959 -> 0.960 | 0.77 -> 0.62 | 0.242 -> 0.243 | 0.246 -> 0.253 | 0.04 -> 0.05 | 0.60 -> 0.12 | - | - | - | - | - | - | 21 -> 22 | d_min, isa, r_meas, rfree, anom_sigma |
-| 9qw8 | open | pass | P 1 | 1.70 -> 1.69 | 9.6 -> 5.2 | 19.8% -> 27.0% | 0.990 -> 0.975 | 0.46 -> 0.67 | 0.294 -> 0.323 | 0.312 -> 0.329 | 0.15 -> 0.14 | 0.28 -> 0.30 | - | - | - | - | - | - | 30 -> 34 | isa, r_meas, cc_half, cell_dev_pct, rmodel_shell_scaled, rfree, anom_sigma |
-| 9rci | open | pass | P 1 | 1.65 -> 1.69 | 8.3 -> 7.5 | 19.3% -> 21.3% | 0.990 -> 0.988 | 0.18 -> 0.33 | 0.247 -> 0.264 | 0.253 -> 0.270 | 0.13 -> 0.09 | 0.55 -> 0.32 | - | - | - | - | - | - | 21 -> 13 | d_min, isa, r_meas, rmodel_shell_scaled, rfree, anom_sigma |
-| 9rcs | open | pass | P 1 21 1 | 3.27 -> 3.28 | 7.3 -> 7.4 | 23.1% | 0.994 -> 0.995 | 0.93 -> 0.85 | 0.317 | 0.340 -> 0.341 | 0.12 | 0.35 -> 0.47 | - | - | - | - | - | - | 14 -> 12 | anom_sigma |
-| 9rp9 | open | pass | C 1 2 1 | 1.90 -> 1.96 | 31.8 -> 28.6 | 15.8% -> 16.4% | 0.998 | 0.16 -> 0.25 | 0.205 -> 0.202 | 0.236 -> 0.234 | 0.15 -> 0.12 | 2.41 -> 2.31 | - | - | - | - | - | - | 19 -> 13 | d_min, isa |
-| 9s02 | open | pass | P 21 21 2 | 1.42 -> 1.43 | 26.0 -> 25.6 | 10.3% -> 10.5% | 0.999 | 0.06 -> 0.09 | 0.180 | 0.188 -> 0.186 | 0.10 -> 0.09 | 2.25 -> 2.26 | - | - | - | - | - | - | 43 -> 26 | time |
-| 9sl0 | open | pass | P 21 21 21 | 1.36 -> 1.37 | 20.2 -> 20.0 | 8.0% | 1.000 | 0.35 -> 0.39 | 0.245 | 0.255 -> 0.254 | 0.16 -> 0.15 | 2.21 -> 2.23 | - | - | - | - | - | - | 31 -> 48 | time |
-| 9t6s | open | pass | P 21 21 21 | 1.75 | 29.3 -> 28.4 | 11.0% -> 10.9% | 0.999 | 0.06 -> 0.41 | 0.215 | 0.231 -> 0.230 | 0.03 | 2.49 -> 2.44 | - | - | - | - | - | - | 12 -> 18 | cell_dev_pct |
-| 9upt | open | pass | P 6 | 2.03 | 6.4 -> 6.5 | 25.0% -> 24.4% | 0.989 | 0.20 | 0.219 -> 0.218 | 0.218 | 0.08 -> 0.09 | 1.23 -> 1.32 | - | - | - | - | - | - | 19 | anom_sigma |
-| 9vyb | open | pass | P 21 21 21 | 1.67 | 22.0 -> 22.2 | 8.2% | 0.999 -> 1.000 | 0.39 -> 0.41 | 0.246 -> 0.247 | 0.253 -> 0.254 | 0.08 -> 0.07 | 0.44 -> 0.41 | - | - | - | - | - | - | 31 -> 29 | anom_sigma |
-| 9w3y | open | pass | P 21 21 21 | 1.21 -> 1.22 | 19.6 -> 18.6 | 24.2% -> 24.3% | 0.997 | 0.24 -> 0.33 | 0.187 -> 0.185 | 0.197 -> 0.196 | 0.09 | 4.89 -> 4.90 | - | - | - | - | - | - | 9 -> 8 | isa |
-| 9yzk | open | pass | I 1 2 1 | 3.86 -> 3.87 | 7.1 -> 8.8 | 30.9% -> 31.9% | 0.996 -> 0.999 | 0.20 -> 0.26 | 0.357 -> 0.352 | 0.420 -> 0.410 | 0.38 -> 0.32 | 0.21 -> 0.13 | - | - | - | - | - | - | 10 | isa, rmodel_shell_scaled, radial_misfit, rfree, anom_sigma |
-| 9z44 | open | pass | I 1 2 1 | 6.84 -> 6.78 | 9.8 -> 9.5 | 22.4% -> 21.8% | 0.975 -> 0.974 | 1.43 -> 1.25 | 0.335 -> 0.333 | 0.324 -> 0.328 | 0.17 -> 0.15 | -0.05 -> 0.02 | - | - | - | - | - | - | 28 -> 15 | lattice, anom_sigma, time |
-| 9z72 | open | pass | P 31 2 1 | 1.93 -> 2.00 | 14.7 -> 14.9 | 92.2% -> 93.3% | 0.990 -> 0.988 | 0.15 -> 0.14 | 0.244 -> 0.241 | 0.260 -> 0.256 | 0.07 -> 0.04 | 0.74 -> 0.73 | - | - | - | - | - | - | 46 -> 33 | d_min, time |
-| 9zlo | open | pass | P 21 21 21 | 1.56 | 24.0 -> 23.5 | 12.1% -> 12.0% | 0.999 | 0.39 -> 0.26 | 0.224 -> 0.221 | 0.231 -> 0.230 | 0.06 -> 0.07 | 1.84 -> 1.73 | - | - | - | - | - | - | 18 -> 16 | anom_sigma |
-| 9zmu | open | pass | P 61 2 2 | 1.71 -> 1.72 | 11.1 -> 11.3 | 31.4% -> 29.8% | 0.999 | 0.07 | 0.276 -> 0.277 | 0.283 -> 0.282 | 0.16 -> 0.15 | 1.28 -> 1.23 | - | - | - | - | - | - | 25 -> 20 | r_meas |
-| cytidine | open | pass | P 21 21 21 | 0.58 | 8.7 -> 8.5 | 10.3% -> 10.2% | 0.993 -> 0.997 | 0.31 -> 0.33 | - | - | - | - | - | - | 0.0613 -> 0.0644 | 0.1759 -> 0.1842 | 1.061 -> 1.075 | 0.039 -> 0.072 | 10 -> 6 | SHELXL r1, SHELXL wr2, SHELXL exti |
-| dnba | open | pass | C 1 2/c 1 | 0.81 | 35.9 -> 39.5 | 2.5% -> 2.4% | 1.000 | 0.06 -> 0.09 | - | - | - | - | - | - | 0.0267 -> 0.0269 | 0.0708 -> 0.0710 | 1.071 -> 1.070 | 0.002 -> 0.003 | 5 | isa |
-| lalanine | open | pass | P 21 21 21 | 0.65 | 40.7 -> 52.1 | 2.5% -> 2.6% | 1.000 | 0.07 -> 0.09 | - | - | - | - | - | - | 0.0309 -> 0.0367 | 0.0922 -> 0.1095 | 1.149 -> 1.137 | 0.000 | 8 | isa, r_meas, SHELXL r1, SHELXL wr2 |
-| metformin | open | pass | P 1 21/c 1 | 0.51 | 31.1 -> 31.0 | 3.1% | 1.000 | 0.17 | - | - | - | - | - | - | 0.0323 -> 0.0326 | 0.0959 -> 0.1031 | 1.103 -> 1.123 | 0.000 | 3 | SHELXL wr2 |
-| nidppe | open | pass | P 1 21/c 1 | 0.51 | 32.9 -> 29.7 | 7.9% -> 8.0% | 0.999 | 0.28 | - | - | - | - | - | - | 0.0414 -> 0.0420 | 0.1021 -> 0.1050 | 1.035 -> 1.038 | 0.004 | 4 -> 3 | isa |
diff --git a/docs/CBOR.md b/docs/CBOR.md
index d98a3c267..ccaaef192 100644
--- a/docs/CBOR.md
+++ b/docs/CBOR.md
@@ -312,6 +312,7 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
 | spindle_lost_unique_fraction     | float                    | Fraction (0-1) of unique reflections the mounting made unmeasurable, exact under the measured point group; offline (Rugnux) only  |                           |
 | indexing_rate                    | float                    | Mean indexing rate for the whole run                                                                                              |                           |
 | unit_cell                        | object (optional)        | Unit cell of the system, based on the actual experiment: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]                   |                           |
+| unit_cell_esd                    | object (optional)        | e.s.d.s of `unit_cell`, same layout: a, b, c \[angstrom\] and alpha, beta, gamma \[degree\]; rotation, offline (Rugnux) and in-broker analysis only |                           |
 | rotation_lattice_type            | object                   | Bravais lattice classification of the total rotation solution over the run, if available; same schema as `lattice_type`           |                           |
 | - centering                      | string                   | One-letter centering code: P, A, B, C, I, F, or R                                                                                 |                           |
 | - niggli_class                   | int64                    | Integer identifier for the Niggli-reduced Bravais class                                                                           |                           |
@@ -347,10 +348,13 @@ See [DECTRIS documentation](https://github.com/dectris/documentation/tree/main/s
 | merged                           | object (optional)        | Merged reflections of an in-broker analysis run, written by the writer as `<file_prefix>.mtz`. An MTZ table (layout below) | |
 | map_coefficients                 | object (optional)        | Map coefficients of an in-broker analysis run, written as `<file_prefix>_maps.mtz`. An MTZ table (layout below) | |
 | placed_model                     | object (optional)        | Atomic model placed against the data, written as `<file_prefix>_model.cif` and `<file_prefix>_model.pdb`. `name` (string), `unit_cell` (object, as above), `space_group_name` (the data's, gemmi extended H-M), `model_space_group_name` (the coordinates'), then one array per atom: `model_number`, `seq_num`, `charge` (int32), `chain`, `residue_name`, `atom_name`, `element` (Array(string)), `icode` (uint8, space where none), `het_flag` (uint8, `A`, `H` or 0 where unknown), `altloc` (uint8, 0 where none), `x`, `y`, `z` (double, Angstrom), `b_iso`, `occupancy` (float), `aniso` (float, 6 per atom: U11 U22 U33 U12 U13 U23; empty where no atom has one), `subchain`, `entity_id` (Array(string), mmCIF label_asym_id / label_entity_id), `label_seq` (int32, label_seq_id, INT32_MIN where none) - these three optional; `metadata_mmcif` (string, optional): the input model's metadata (entities, sequences, references, authors, software, secondary structure) as mmCIF categories without coordinates, parsed by the writer with gemmi | |
+| refined_model                    | object (optional)        | The placed model after refinement, written as `<file_prefix>_refined_model.cif` and `<file_prefix>_refined_model.pdb`; same layout as `placed_model` | |
+| refined_map_coefficients         | object (optional)        | Map coefficients of the refined model, written as `<file_prefix>_refined_maps.mtz`. An MTZ table (layout below) | |
+| blobs                            | object (optional)        | Unexplained blobs of the refined model's mFo-DFc map, strongest first, written as `<file_prefix>_blobs.json`. One array per field, one entry per blob: `kind` (Array(string): `WATER`, `ION`, `LIGAND`, `MODEL_ERROR`, `UNASSIGNED`), `x`, `y`, `z` (double, centroid, Angstrom), `peak_sigma` (double, map rms), `volume` (double, Angstrom^3), `score` (double, sigma Angstrom^3), `nearest_atom` (Array(string)), `nearest_atom_distance` (double, Angstrom), `polar_contacts`, `metal_contacts` (int32), `anomalous_sigma` (double, 0 where there is no anomalous map) | |
 
 End-message vector fields are optional. When present, they provide master-file summary data so readers can inspect scan-level and per-image analysis results without opening every linked data file. Missing optional per-image values are encoded by the producer as zero unless otherwise noted.
 
-An MTZ table (`merged`, `map_coefficients`) carries an MTZ file's content as the writer writes it, column by column:
+An MTZ table (`merged`, `map_coefficients`, `refined_map_coefficients`) carries an MTZ file's content as the writer writes it, column by column:
 
 | Field name       | Type          | Description                                                                                          |
 |------------------|---------------|------------------------------------------------------------------------------------------------------|
diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
index 2f1c95d7e..6807fa598 100644
--- a/docs/CHANGELOG.md
+++ b/docs/CHANGELOG.md
@@ -1,6 +1,20 @@
 # Changelog
 ## 1.0.0
 
+### 1.0.0-rc.180
+
+* Rugnux: A placed model is refined by default - restrained maximum-likelihood refinement on the GPU (CPU without one), writing `<prefix>_refined_model.cif`, `<prefix>_refined_maps.mtz` and the difference-map blobs in `<prefix>_blobs.json`; `--no-refine` skips it.
+* Rugnux: `--mode refine` refines a model against merged structure factors from an MTZ or mmCIF file.
+* Rugnux: The embedded restraint dictionary covers amino acids, nucleotides including common modified RNA nucleotides, common cofactors, crystallisation additives, waters and ions, with metal sites restrained from the model's LINK records.
+* Rugnux: A model or reference file can be given among the inputs in any order, recognised by its contents.
+* Rugnux: The geometry refinement algorithm option is now `-r, --geom-refine` (was `--refine`).
+* Rugnux: Serial stills resolve the indexing ambiguity from the data when no model or reference is given, reject merge outliers by default, follow the run's measured rocking curve in prediction and partiality (also in `--mode scale`), and index reproducibly on the GPU.
+* Rugnux: Reflections touching the beam-stop shadow are not integrated, reflections coarser than the low-resolution limit are merged and written (but kept out of the scale fit), and the polarisation plane is measured more reliably.
+* Rugnux: Small-molecule runs report unit-cell e.s.d.s, in a SHELX `.ins` beside the `.hkl` and in the mmCIF.
+* jfjoch_broker: Live Rugnux refines the uploaded model after placement; the web frontend's Rugnux live page has a hero panel with resolution, ISa, space group, placement and refined R-work/R-free, and its Mol* viewer shows the refined model and maps.
+* Documentation: A new front page with download pages for Rugnux and the viewer, and the technical reference reorganised below it.
+* Build: The fast-feedback indexer is part of the source tree instead of being downloaded at build time.
+
 ### 1.0.0-rc.179
 
 * Rugnux: Stills processing needs only the unit cell and space group beyond what the file records - detector distance, beam centre, tilt, panel placement, saturation level, gain and polarisation plane are found from the images - and is up to twice as fast.
diff --git a/docs/CPU_DATA_ANALYSIS.md b/docs/CPU_DATA_ANALYSIS.md
index 7189d903c..6ae90cf23 100644
--- a/docs/CPU_DATA_ANALYSIS.md
+++ b/docs/CPU_DATA_ANALYSIS.md
@@ -18,21 +18,27 @@ This document describes the crystallographic algorithms implemented in Jungfrauj
 12. auxiliary statistics (Wilson plot, ⟨I/σ(I)⟩, CC1/2, CCref),
 13. amplitude estimation (French–Wilson) and R-free test-set flagging,
 14. optional model-based validation: rigid-body placement of a supplied model (molecular replacement where the rigid body does not place it, or for a predicted model), R-free against it, sigma_A-weighted 2mFo−DFc / mFo−DFc electron-density maps, and an anomalous difference map with the strongest anomalous sites named.
+15. restrained refinement of the placed model (wherever a model is placed): rigid bodies and group B, then positions and B against a maximum-likelihood amplitude target with the dictionary's geometry, the X-ray weight chosen by R-free within geometry bounds, and the unexplained blobs of the refined difference map.
 
 
-The reference is split into four parts, in pipeline order; the section numbers run continuously
+The reference is split into five parts, in pipeline order; the section numbers run continuously
 across them and are the ones the rest of the documentation cites.
 
 - [From images to spots (§0–§3)](CPU_DATA_ANALYSIS_IMAGE.md) — device-side decoding, geometry and
   reciprocal-space mapping, azimuthal integration, spot finding.
 - [Indexing and geometry refinement (§4–§7)](CPU_DATA_ANALYSIS_INDEXING.md) — FFT and fast-feedback
-  indexing, the lattice search, geometry refinement, post-refinement and powder calibration.
+  indexing, the lattice search, geometry refinement, post-refinement, powder calibration, and the stills
+  geometry with a given cell and detector modules.
 - [Prediction, integration, scaling and merging (§8–§12)](CPU_DATA_ANALYSIS_INTEGRATION.md) —
   reflection prediction, profile-fitted integration, scaling, merging, mosaicity and the auxiliary
   statistics.
 - [Space group and validation (§13–§14)](CPU_DATA_ANALYSIS_DECISIONS.md) — the space-group search,
   twinning and translational pseudo-symmetry, the resolution cutoff, diffraction anisotropy,
   model-based validation and molecular replacement.
+- [Refinement of a placed model (§15)](CPU_DATA_ANALYSIS_REFINEMENT.md) — the maximum-likelihood target and
+  its FFT gradient, the scale, bulk solvent and likelihood parameters, the dictionary and its restraints
+  (metal sites and B included), the minimiser, the weights chosen by trial, the refined maps and their
+  unexplained blobs, and what is not implemented yet.
 
 ## References
 
@@ -59,7 +65,21 @@ The methods draw on, and in places reimplement, solutions from:
 - P. H. C. Eilers, "A perfect smoother", *Anal. Chem.* **75** (2003), 3631-3636, after E. T. Whittaker, "On a new method of graduation", *Proc. Edinburgh Math. Soc.* **41** (1923), 63-75 (the penalised smoother of the fulls' per-frame scale, §10.6).
 - H. F. Walker & P. Ni, "Anderson acceleration for fixed-point iterations", *SIAM J. Numer. Anal.* **49** (2011), 1715-1735, after D. G. Anderson, "Iterative procedures for nonlinear integral equations", *J. ACM* **12** (1965), 547-560 (the acceleration of the per-frame scaling loops, §10.6).
 - R. A. Fisher, "Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population", *Biometrika* **10** (1915), 507-521 (the z-transformation on which the correction surfaces' held-out half-set CC1/2 is compared).
-- M. Wojdyr, "GEMMI: A library for structural biology", *J. Open Source Softw.* **7** (2022), 4200 (model / structure-factor / map machinery used in §14).
+- R. C. Agarwal, "A new least-squares refinement technique based on the fast Fourier transform algorithm", *Acta Cryst.* **A34** (1978), 791-809 (the gradient of the refinement target, §15).
+- N. S. Pannu & R. J. Read, "Improved structure refinement through maximum likelihood", *Acta Cryst.* **A52** (1996), 659-668, and G. N. Murshudov, A. A. Vagin & E. J. Dodson, "Refinement of macromolecular structures by the maximum-likelihood method", *Acta Cryst.* **D53** (1997), 240-255 (the maximum-likelihood amplitude target and the B restraints, §15).
+- V. Y. Lunin & T. P. Skovoroda, "R-free likelihood-based estimates of errors for phases calculated from atomic models", *Acta Cryst.* **A51** (1995), 880-887 (the likelihood parameters from the free set, §15).
+- A. A. Vagin et al., "REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use", *Acta Cryst.* **D60** (2004), 2184-2195 (the restraint dictionary, §15).
+- P. V. Afonine et al., "Towards automated crystallographic structure refinement with phenix.refine", *Acta Cryst.* **D68** (2012), 352-367 (the weight chosen among refinements by R-free, §15).
+- D. C. Liu & J. Nocedal, "On the limited memory BFGS method for large scale optimization", *Math. Program.* **45** (1989), 503-528 (the minimiser, §15).
+- J. Nocedal, "Updating quasi-Newton matrices with limited storage", *Math. Comp.* **35** (1980), 773-782 (the two-loop recursion of the minimiser, §15.6).
+- G. N. Murshudov, P. Skubák, A. A. Lebedev et al., "REFMAC5 for the refinement of macromolecular crystal structures", *Acta Cryst.* **D67** (2011), 355-367 (the likelihood's D from the working set and its variance from the free, and the Kullback-Leibler B restraints, §15.3, §15.5).
+- A. T. Brünger, M. Karplus & G. A. Petsko, "Crystallographic refinement by simulated annealing: application to crambin", *Acta Cryst.* **A45** (1989), 50-61 (the starting weight from the ratio of the gradients, §15.7).
+- P. J. Huber, "Robust estimation of a location parameter", *Ann. Math. Statist.* **35** (1964), 73-101, and P. Charbonnier, L. Blanc-Féraud, G. Aubert & M. Barlaud, "Deterministic edge-preserving regularization in computed imaging", *IEEE Trans. Image Process.* **6** (1997), 298-311 (the robust, pseudo-Huber scale fit of the refinement's score, §15.3).
+- J.-S. Jiang & A. T. Brünger, "Protein hydration observed by X-ray diffraction", *J. Mol. Biol.* **243** (1994), 100-115 (the flat bulk-solvent mask, §14.2, §15.3).
+- A. Blondel & M. Karplus, "New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: elimination of singularities", *J. Comput. Chem.* **17** (1996), 1132-1141 (the torsion derivatives, §15.5).
+- M. M. Harding, "Geometry of metal-ligand interactions in proteins", *Acta Cryst.* **D57** (2001), 401-411, and "Small revisions to predicted distances around metal sites in proteins", *Acta Cryst.* **D62** (2006), 678-682, and F. Leonarski, L. D'Ascenzo & P. Auffinger, "Mg2+ ions: do they bind to nucleobase nitrogens?", *Nucleic Acids Res.* **45** (2017), 987-1004 (the metal-site distances, §15.5).
+- P. Emsley, B. Lohkamp, W. G. Scott & K. Cowtan, "Features and development of Coot", *Acta Cryst.* **D66** (2010), 486-501 (unmodelled blobs, §15.9).
+- M. Wojdyr, "GEMMI: A library for structural biology", *J. Open Source Softw.* **7** (2022), 4200 (model / structure-factor / map machinery used in §14; the topology, riding hydrogens and blob search of §15).
 - J. P. Wright, "Experiences with GPU decompression for bitshuffle + LZ4 data", HDF5 User Group meeting (2021), and [github.com/jonwright/bslz4decoders](https://github.com/jonwright/bslz4decoders) (device-side decoding of bitshuffle+LZ4 images, §0).
 - A. Thorn & G. M. Sheldrick, "ANODE: anomalous and heavy-atom density calculation", *J. Appl. Cryst.* **44** (2011), 1285-1287 (anomalous difference density read at the model's sites).
 - R. Kahn, R. Fourme, A. Gadet, J. Janin, C. Dumas & D. Andre, "Macromolecular crystallography with synchrotron radiation: photographic data collection and polarization correction", *J. Appl. Cryst.* **15** (1982), 330-337 (the azimuthal polarization factor of §2.2, applied to the azimuthal profile, the Bragg intensities and the ring background the beam-stop shadow test compares against).
@@ -80,6 +100,7 @@ The methods draw on, and in places reimplement, solutions from:
 - C. Vonrhein, C. Flensburg, P. Keller et al., "Data processing and analysis with the autoPROC toolbox", *Acta Cryst.* **D67** (2011), 293-302 (the inspiration for not trusting header geometry and for finding the beam centre from the images, §1.4).
 - P. R. Evans & G. N. Murshudov, "How good are my data and what is the resolution?", *Acta Cryst.* **D69** (2013), 1204-1214 (AIMLESS: the anisotropic deltaB as the range of the principal components, and diffraction limits from a cone about each principal direction).
 - G. Assmann, W. Brehm & K. Diederichs, "Identification of rogue datasets in serial crystallography", *J. Appl. Cryst.* **49** (2016), 1021-1028, and G. M. Assmann, M. Wang & K. Diederichs, *Acta Cryst.* **D76** (2020), 636-652 (XDSCC12: sigma-tau CC1/2, delta-CC1/2, the Fisher transformation and the rejection discipline the frame disposition follows).
+- W. Brehm & K. Diederichs, "Breaking the indexing ambiguity in serial crystallography", *Acta Cryst.* **D70** (2014), 101-109 (serial stills without a reference: each crystal put into the indexing in which it agrees best with all the others).
 - K. Diederichs & P. A. Karplus, *Nat. Struct. Biol.* **4** (1997), 269-275, and P. A. Karplus & K. Diederichs, *Science* **336** (2012), 1030-1033 (R_meas / R_pim, CC1/2 and CC\*).
 - M. S. Weiss, "Global indicators of X-ray data quality", *J. Appl. Cryst.* **34** (2001), 130-135 (R_pim).
 - IUCr Commission on Crystallographic Nomenclature, "Statistical descriptors in crystallography", *Acta Cryst.* **A45** (1989), 63-75, and *Acta Cryst.* **A51** (1995), 565-569 (uncertainty conventions).
diff --git a/docs/CPU_DATA_ANALYSIS_DECISIONS.md b/docs/CPU_DATA_ANALYSIS_DECISIONS.md
index 08a820e98..7943fe4b2 100644
--- a/docs/CPU_DATA_ANALYSIS_DECISIONS.md
+++ b/docs/CPU_DATA_ANALYSIS_DECISIONS.md
@@ -1,6 +1,6 @@
 # Data analysis: space group and validation (§13–§14)
 
-Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its four parts.
+Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its parts.
 
 ```{contents} On this page
 :local:
@@ -74,7 +74,7 @@ Beside them, on rotation data with `--finalist-ledger`, the run reports **twin-i
 
 ### 13.3 Outlier rejection
 
-Merging applies an optional per-observation median-based $N\sigma$ cut (`--reject-outliers`, default 6σ for `rot3d`, off otherwise). On the rotation path the median is weighted by each full's counting variance taken at the reflection's **expected** intensity, as the merge weights are (§10.4): an observation's own Poisson variance falls with its own intensity, so own-variance weights hand the median to whichever equivalents came out low — on a strongly absorbing crystal, where some frames read equivalents ten to a hundred times down, the median sat on the absorbed ones and the test removed correct measurements far above it. The band about the median keeps the counting part linear, $\pm N\sigma_\text{counting}$, but takes the systematic part as a **factor**, $e^{\pm N s}$ about the expected intensity: the error model's systematic term is multiplicative — absorption, illuminated volume, a scale that is off — and as likely to be a factor $1/f$ as $f$, while a band symmetric in $I$ reaches far below the median and only a little above it once that term is large. $s$ is the spread of $\ln(I/\text{median})$ measured on the merge's own fulls (their weighted median of $|\ln(I/\text{median})|$, weighted by $(\langle I\rangle/\sigma_\text{counting})^2$ so the fulls whose ratio counting noise does not blur carry it), with the error model's $b$ as the fallback where it cannot be measured; to first order in $Ns$ the band is the linear one. The same $N\sigma$ cut is fed back into the error model: after an initial $a,b$ fit the parameters are re-fit once on the reflections that survive rejection (dropping any whose squared deviation exceeds $N^2\,[a\,\sigma^2 + (b\,\langle I\rangle)^2]$), so the calibrated errors describe the reflections that actually enter the merge rather than the pre-rejection pool.
+Merging applies a per-observation median-based $N\sigma$ cut (`--reject-outliers`, default 6σ on rotation, 10σ on stills). On the rotation path the median is weighted by each full's counting variance taken at the reflection's **expected** intensity, as the merge weights are (§10.4): an observation's own Poisson variance falls with its own intensity, so own-variance weights hand the median to whichever equivalents came out low — on a strongly absorbing crystal, where some frames read equivalents ten to a hundred times down, the median sat on the absorbed ones and the test removed correct measurements far above it. The band about the median keeps the counting part linear, $\pm N\sigma_\text{counting}$, but takes the systematic part as a **factor**, $e^{\pm N s}$ about the expected intensity: the error model's systematic term is multiplicative — absorption, illuminated volume, a scale that is off — and as likely to be a factor $1/f$ as $f$, while a band symmetric in $I$ reaches far below the median and only a little above it once that term is large. $s$ is the spread of $\ln(I/\text{median})$ measured on the merge's own fulls (their weighted median of $|\ln(I/\text{median})|$, weighted by $(\langle I\rangle/\sigma_\text{counting})^2$ so the fulls whose ratio counting noise does not blur carry it), with the error model's $b$ as the fallback where it cannot be measured; to first order in $Ns$ the band is the linear one. The same $N\sigma$ cut is fed back into the error model: after an initial $a,b$ fit the parameters are re-fit once on the reflections that survive rejection (dropping any whose squared deviation exceeds $N^2\,[a\,\sigma^2 + (b\,\langle I\rangle)^2]$), so the calibrated errors describe the reflections that actually enter the merge rather than the pre-rejection pool. On **stills** the band is the plain linear one, $\pm N\sqrt{a\,\sigma^2 + (b\,\langle I\rangle)^2}$ about the median: a still's observations of one reflection are partials and per-crystal scales, many of them near zero, so the spread of $\ln(I/\text{median})$ is wide and a band drawn from it let through a powder grain or a neighbour's spot in the box at hundreds of $\sigma$ — on a high-multiplicity run a single such observation was a weak reflection's whole merged intensity, and they took the low-resolution shells' $\mathrm{CC}_{1/2}$ down to 0.6. The error model's $b$ is that spread as it is. $N$ is wider than on rotation because a still's partials scatter with heavier tails than the band's normal core; what has to go sits tens to hundreds of $\sigma$ out.
 
 The median needs three observations, so a reflection measured once or twice — typically one good observation and one artefact (a hot pixel, a zinger) after Friedel merging — is never tested by it, and an artefact that looks precise (thousands of counts, a small relative $\sigma$) can outweigh mates from weak frames and become the median itself. Every observation of the written merge is therefore also judged by **Wilson statistics**. Beyond 4 Å its $E^2 = I/(\varepsilon\,\langle I/\varepsilon\rangle_\mathrm{shell})$ is compared with a bound set by a budget of $\alpha = 0.01$ expected false rejections per dataset: with $N$ observations tested, $\ln(2N/\alpha)$ for acentrics and twice that for centrics, and the observation's lower confidence limit $I - z\sigma$ (with its own $\sigma$, and $z$ from the same budget) must exceed it, so noise in weak shells does not trigger it; a shell whose $\langle I\rangle$ is not itself established at that significance is not judged. The bound is widened by the tail scale of the dataset's own intensity distribution, measured on its well-measured observations (1 for a Wilson crystal; larger under a pseudo-translation or anisotropy). An improbable singleton is dropped; an improbable observation with company only when most of the reflection's other observations are probable and it disagrees with their mean beyond the errors — several large observations confirm each other. An observation whose signal disk lost pixels to the mask or to saturation is never counted as such a witness, since its profile estimate may be low: a strong reflection is not replaced by its clipped mate. The count is `OBSERVATIONS_REJECTED_WILSON=` in the report (included in `OBSERVATIONS_REJECTED=`), and the developer report lists each observation with its image and detector position.
 
@@ -117,14 +117,14 @@ Everything lands in `<prefix>_report.txt` section 4 (`ANISOTROPY_*` keys), in th
 - **Bragg integration is profile-fitted by default** (per-shell Gaussian profile, Kabsch extraction; §9.3), with plain box summation available as a fallback (`--integrator boxsum`). The profiles are built per frame from that frame's strong spots, which suits fast-feedback and serial/streaming use; a profile shared across many frames (as in full offline workflows) is not currently formed.
 - **Space-group symmetry** beyond centering absences is not enforced during prediction/integration unless the space group is supplied and used downstream.
 - **Resolution masking** is controllable, and so is every stage of ice-ring handling (§3.3, §10.10). None of it runs unless the crystal is measured to have ice, because the fixed bands are a fixed cost in unique reflections whether it does or not.
-- **Rotation vs still modes** differ substantially in prediction and scaling: partiality is angle-driven in rotation data, while stills are predicted within an excitation-error window and get their partiality from the default-on per-crystal tilt post-refinement (§10.2) — or unit partiality with `--simple-stills`.
+- **Rotation vs still modes** differ substantially in prediction and scaling: partiality is angle-driven in rotation data, while stills are predicted within an excitation-error window that follows the run's rocking curve (§8.2) and get their partiality from the default-on per-crystal tilt post-refinement (§10.2) — or unit partiality with `--simple-stills`.
 - **Amplitudes and intensities.** The merged output carries both intensities (mmCIF `intensity_meas`, MTZ `IMEAN`/`SIGIMEAN`) and French–Wilson amplitudes (mmCIF `F_meas_au`, MTZ `F`/`SIGF`; §10.8), so a downstream program can refine against either.
 
 ---
 
 ## 14. Model-based validation: R-free against a model and electron-density maps
 
-Offline (`rugnux --model model.pdb`) the merged data can be scored against a supplied atomic model and electron-density maps computed — enough to confirm that a model fits the data and to inspect the density, not a substitute for refinement. **The structure itself is not refined**; the model is re-fractionalized into the data unit cell and then **placed as one rigid body** (§14.8) - or, where the rigid body does not place it and for a predicted model, by molecular replacement (§14.10) - and the observed amplitudes are the French–Wilson $|F|$ from §10.8, so the R-free and the maps use exactly the same amplitudes as the written reflection file. The model, structure-factor, bulk-solvent and FFT machinery is provided by GEMMI.
+Offline (`rugnux --model model.pdb`) the merged data can be scored against a supplied atomic model and electron-density maps computed — enough to confirm that a model fits the data and to inspect the density. **The numbers of this section are those of the model as placed, not refined** - a placed model is refined afterwards by default (`--no-refine` skips it), on the side and deciding nothing (§15, [Refinement of a placed model](CPU_DATA_ANALYSIS_REFINEMENT.md)); the model is re-fractionalized into the data unit cell and then **placed as one rigid body** (§14.8) - or, where the rigid body does not place it and for a predicted model, by molecular replacement (§14.10) - and the observed amplitudes are the French–Wilson $|F|$ from §10.8, so the R-free and the maps use exactly the same amplitudes as the written reflection file. The model, structure-factor, bulk-solvent and FFT machinery is provided by GEMMI.
 
 ### 14.1 Model structure factors
 
diff --git a/docs/CPU_DATA_ANALYSIS_IMAGE.md b/docs/CPU_DATA_ANALYSIS_IMAGE.md
index d90ea2f17..a670a355c 100644
--- a/docs/CPU_DATA_ANALYSIS_IMAGE.md
+++ b/docs/CPU_DATA_ANALYSIS_IMAGE.md
@@ -1,6 +1,6 @@
 # Data analysis: from images to spots (§0–§3)
 
-Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its four parts.
+Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its parts.
 
 ```{contents} On this page
 :local:
@@ -405,6 +405,19 @@ reflection — a maximum over the frames well above background, in a cluster, so
 zinger does not count — is given back, because a beam stop cannot have blocked a reflection that was
 measured.
 
+Pixels the finder reports that hold the detector's no-data mark (a PILATUS module gap stored as $-1$)
+are the darkest pixels there are, but they are not shadow: they are masked as dead (bit 10) instead, so
+that the reported shadow share is the shadow's and the test below does not drop every reflection a module
+gap clips. A mean of zero is not taken as dead, since a deep shadow on a still counts nothing.
+
+**A reflection whose signal disk reaches into the shadow is not integrated.** The profile fit keeps a
+disk that lost pixels to the mask and fits the pixels that remain (§9.3), which is right for a gap or a
+dead pixel but not for the shadow: the mask is drawn where the background is dimmed, and the Bragg
+half-shadow does not end there, so the rest of such a disk is attenuated too - measured against the
+symmetry mates, such observations read low by 12-60 %. The test is made where each image is integrated,
+so rotation, stills, the `_process.h5` and `--mode scale` see the same reflections; with no shadow in the
+mask (the broker) it does nothing.
+
 ### 1.6 Defective pixels
 
 A pixel that reads high frame after frame, whatever the crystal does, is integrated into whichever
@@ -499,9 +512,13 @@ says nothing (ADSC SMV, marCCD, NXmx) the default $P = 0.99$, an undulator value
 plane horizontal. The **plane**, unlike the degree, is measured: the beam-stop pre-scan compares the
 background's $\cos 2\phi$ harmonic with the profile a polarized source gives it, and where the background
 clearly follows the other plane (correlation above 0.5 and at least 0.3 of a fully polarized source's
-modulation) the stated degree is applied in that plane - to the shadow test and, from then on, to the
+modulation, but under twice it, which no source can give) the stated degree is applied in that plane - to the shadow test and, from then on, to the
 integration and every other correction of the run. Elsewhere the plane stays as stated, so a run whose
-beam stop is not detected (`--detect-beam-stop=off`) keeps the stated one. Bending-magnet and wiggler
+beam stop is not detected (`--detect-beam-stop=off`) keeps the stated one. The background is pooled
+over 9 x 9 pixels before the comparison, so that a sparse background - a fraction of a count per pixel
+over the frames read, as on a large photon-counting detector - still gives the sectors a level. The same
+decision is made for rotation sweeps and stills, and the log reports the correlation and the scale
+(`Polarization plane:`) on every run that detects the beam stop. Bending-magnet and wiggler
 beamlines are typically lower (0.8–0.95), and a known value for one should be passed with
 `--polarization`.
 
diff --git a/docs/CPU_DATA_ANALYSIS_INDEXING.md b/docs/CPU_DATA_ANALYSIS_INDEXING.md
index a83665b43..614c49d2d 100644
--- a/docs/CPU_DATA_ANALYSIS_INDEXING.md
+++ b/docs/CPU_DATA_ANALYSIS_INDEXING.md
@@ -1,6 +1,6 @@
 # Data analysis: indexing and geometry (§4–§7)
 
-Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its four parts.
+Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its parts.
 
 ```{contents} On this page
 :local:
@@ -381,7 +381,7 @@ The space group is determined **after** pass 2, on the geometry the run refined,
 
 Only pass 2 is written, as the canonical `<prefix>_*` output. Pass 1's merge exists to give the guard something to judge pass 2 against, so it stops short of the parts of the merge that only fill in a file — the correction surfaces, the twinning and radiation-damage analyses, the R-free flags and the amplitudes — and writes no merged files of its own.
 
-**Goniometer rotation scale.** A stage that turns further than it was commanded to leaves no trace in the file, because the stored $\omega$ values *are* the commanded ones; the excess then presents as the crystal drifting, in this program and in others. The excitation residual already measures it without a new degree of freedom: it rotates by $-\phi\,\mathbf{u}$ with $\mathbf{u}$ an **unnormalised** 3-vector, so $|\mathbf{u}|$ is the factor $k$ by which the stage actually turned, and normalising the axis throws it away. Pass 1 fits $k$ as a single parameter on its rocking events, with the crystal and the axis direction held at their committed values and the angle measured from the centre of the sweep. That fit **under-reads** a real error: it only sees the frames the stored angles still track, and a rate error is exactly what stops them tracking the rest. So it is not acted on directly. Between the passes, at the detector geometry pass 2 runs at, the lattice is indexed under the stored angles and under the fitted $k$, and each is scored on the validation frames spread over the whole sweep, as the share of their spots it puts on the lattice beyond what it puts there at a wrong spindle angle. The fitted $k$ is adopted only where it scores higher by more than the binomial noise of the two scores (z = 3.29); the run then integrates and post-refines at it, fits $k$ again on top of it, and repeats until the next $k$ no longer scores better - the fixed point of the fit. Otherwise the stored angles stand. The adopted $k$ drives every later pass (prediction, integration, scaling and the reported oscillation) and is reported as `GONIOMETER_ROTATION_SCALE`, with `GONIOMETER_ROTATION_SCALE_SUSPECT= TRUE`. `--rotation-scale <k>` asserts a calibration and skips all of this.
+**Goniometer rotation scale.** A stage that turns further than it was commanded to leaves no trace in the file, because the stored $\omega$ values *are* the commanded ones; the excess then presents as the crystal drifting, in this program and in others. The excitation residual already measures it without a new degree of freedom: it rotates by $-\phi\,\mathbf{u}$ with $\mathbf{u}$ an **unnormalised** 3-vector, so $|\mathbf{u}|$ is the factor $k$ by which the stage actually turned, and normalising the axis throws it away. Pass 1 fits $k$ as a single parameter on its rocking events, with the crystal and the axis direction held at their committed values and the angle measured from the centre of the sweep. That fit **under-reads** a real error: it only sees the frames the stored angles still track, and a rate error is exactly what stops them tracking the rest. So it is not acted on directly. Between the passes, at the detector geometry pass 2 runs at, the lattice is indexed under the stored angles and under the fitted $k$, and each is scored on the validation frames spread over the whole sweep, as the share of their spots it puts on the lattice beyond what it puts there at a wrong spindle angle. The fitted $k$ is adopted only where it scores higher by more than the binomial noise of the two scores (z = 3.29); the run then integrates and post-refines at it, fits $k$ again on top of it, and walks to the fixed point of the fit: once off the stored angles, a further step is refused only where the validation frames score it significantly worse, since a first pass indexes through a degree of drift late in the sweep and the frames can score two rates alike while integration at one of them loses half the signal. Where the run integrates pass 1's own lattice at the adopted $k$, that lattice (cell and orientation, the detector and axis held) is first refit at the angles the pass runs at, on the validation frames of the whole sweep, and kept where it indexes no fewer of them - a cell fitted at the stored angles has absorbed part of the rate error and would undo it. Otherwise the stored angles stand. The adopted $k$ drives every later pass (prediction, integration, scaling and the reported oscillation) and is reported as `GONIOMETER_ROTATION_SCALE`, with `GONIOMETER_ROTATION_SCALE_SUSPECT= TRUE`. `--rotation-scale <k>` asserts a calibration and skips all of this.
 
 ### 7.6 Detector geometry from powder rings
 
@@ -417,7 +417,10 @@ merging both mixes two structures. The frames merged are the population the give
 peak of the histogram of $v/v_\mathrm{given}-1$ nearest to zero, out to the valley on either side that
 separates it from another population, with a bin that follows the spread of the data, so neither a
 population's width nor its distance to the next is a fixed number. A run with one population has no
-such valley and keeps every frame. The log says how many frames were left out on either side.
+such valley and keeps every frame. The log says how many frames were left out on either side. The stills
+geometry refinement fits on the same population: its sampled frames are filtered by it before the bundle
+and the module placement are formed, the population told from the strong frames (at least 20 indexed
+spots), whose cells show the valley between two forms where a weak frame's cell spreads across it.
 
 **Detector modules.** Where the detector is described module by module
 ([Module geometry](RUGNUX_FORMATS.md#module-geometry)), the same refinement places each module with
diff --git a/docs/CPU_DATA_ANALYSIS_INTEGRATION.md b/docs/CPU_DATA_ANALYSIS_INTEGRATION.md
index ae4bdfd32..1bde68271 100644
--- a/docs/CPU_DATA_ANALYSIS_INTEGRATION.md
+++ b/docs/CPU_DATA_ANALYSIS_INTEGRATION.md
@@ -1,6 +1,6 @@
 # Data analysis: integration, scaling and merging (§8–§12)
 
-Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its four parts.
+Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its parts.
 
 ```{contents} On this page
 :local:
@@ -29,6 +29,8 @@ Accepted reflections are projected to the detector by intersecting the diffracte
 
 When the beam has a finite energy bandwidth, this window is **broadened radially per reflection**: the cutoff is combined in quadrature with a bandwidth smear, $\sqrt{\Delta_\mathrm{cut}^2 + (3\,\sigma_\mathrm{bw})^2}$, where $\sigma_\mathrm{bw}\propto|p_z|$ (the reciprocal-space depth along the beam, growing as $\sim 1/d^2$). This keeps high-resolution reflections — smeared by the bandwidth into radial streaks — from being clipped. The same $\sigma_\mathrm{bw}$ is deconvolved from the measured profile radius (§11.1), so it is not double-counted.
 
+**The window follows the run's rocking curve.** A cutoff of twice a frame's own profile radius (§11.1) is one width at every resolution, while the rocking curve widens with $d^*$: it predicts many widths at low resolution, mostly empty, and cuts the curve at high resolution. So, with the stills partiality post-refinement on (the default, §10.2), a sample of the run - a tenth of its frames, at least 2000 - is first integrated with that cutoff, scaled against its own merge, and the run's rocking curve measured on it as the merge measures it (§10.2): its width $\sigma(d^*)$ and its centre, the radial scale. Every frame is then predicted through $|\Delta_\mathrm{Ewald}| \le 2\,\sigma(d^*)$, with $\Delta_\mathrm{Ewald}$ taken on the reciprocal lattice scaled by that radial scale, and the bandwidth term enters through $\sigma(d^*)$ instead of the quadrature above. With `--simple-stills` the frame's own cutoff stays.
+
 ### 8.3 Rotation prediction (Laue equation + partiality model)
 
 For rotation/oscillation datasets, Jungfraujoch solves for rotation angles $\phi$ where the rotated reciprocal lattice point satisfies the Ewald-sphere condition. In an XDS-like notation, define:
@@ -196,7 +198,7 @@ spot-width variance rather than as an intensity scale.
 
 ### 9.5 Choosing the signal radius from the crystal's own spots (rotation)
 
-The three radii are one triple for the whole run, but on rotation data they are no longer a fixed constant: $r_1$ is measured from how wide *this* crystal's spots actually are (`--adaptive-integration-radius`, on by default for rotation, off for stills, ignored when `--integration-radius` is given).
+The three radii are one triple for the whole run, but on rotation data they are no longer a fixed constant: $r_1$ is measured from how wide *this* crystal's spots actually are (`--adaptive-integration-radius`, on by default, ignored when `--integration-radius` is given). On stills the same option measures instead how far the background ring should reach (§9.2, *When it is applied*).
 
 **Why $r_1$ matters even though it does not set the intensity.** In the default `gaussian` mode the intensity is a profile-fit amplitude over the grid $\lceil r_2\rceil$ (§9.3), so $r_1$ is not the integration domain. It *is* the aperture the profile **width** is learned over, and a second moment taken over a disk of radius $a$ saturates at $a^2/4$. At $r_1 = 4$ the learned $\sigma$ can therefore never exceed 2 px, and a crystal whose spots are broader than that is fitted with a profile the model cannot represent.
 
@@ -337,9 +339,9 @@ The partiality applied is fixed by the data type and scaling stage, not chosen f
 
 2. **Unity** ($P_{ij}=1$): used for the scale-on-fulls refit (§10.6), where each observation is already a complete reflection.
 
-3. **Fixed**: use the per-reflection partiality carried from prediction. Still/serial images are predicted with $P=1$, so a single-pass stills scale is effectively unity/fixed — which is exactly what `--simple-stills` keeps. By default the stills path instead **post-refines a physical partiality**: a small per-crystal orientation tilt $(\delta\psi_x,\delta\psi_y)$ about the two axes perpendicular to the beam is refined against the running merge, and every reflection's partiality is then recomputed analytically from the refined lattice through its excitation error $\Delta_\mathrm{Ewald}=\big|\,|\mathbf{q}+\mathbf{S}_0|-1/\lambda\,\big|$ and a Gaussian width $\sigma^2=\gamma_0^2+(\gamma_e d^*)^2+(\mathrm{bw}\,|q_z|)^2$ — the reciprocal-lattice point's own radius (resolution-independent), the mosaic/divergence spread, and the bandwidth smear along the beam, in quadrature. The fit typically drives $\gamma_e\to0$, leaving the resolution-independent $\gamma_0$ as the effective width. A tilt moves reflections on opposite sides of the Ewald sphere in opposite directions, so it reshapes the *spatial* pattern of partialities — a degree of freedom the per-image scale $G$ does not have, and the reason the tilt is refined rather than a scalar partiality width, which would be degenerate with $G$. Nothing is re-integrated (the integrated intensities are fixed); the tilt is hard-bounded at about 1° and held by a soft prior, so it stays inert on sparse or weak crystals. The cycle is merge → per-crystal tilt refinement (with $G$ profiled out by the same robust Cauchy IRLS used for the per-frame scales, §10.3) → recompute $P$ → re-merge, repeated a few times.
+3. **Fixed**: use the per-reflection partiality carried from prediction. Still/serial images are predicted with $P=1$, so a single-pass stills scale is effectively unity/fixed — which is exactly what `--simple-stills` keeps. By default the stills path instead **post-refines a physical partiality**: a small per-crystal orientation tilt $(\delta\psi_x,\delta\psi_y)$ about the two axes perpendicular to the beam is refined against the running merge, and every reflection's partiality is then recomputed analytically from the refined lattice through its excitation error $\Delta_\mathrm{Ewald}=\big|\,|\mathbf{q}+\mathbf{S}_0|-1/\lambda\,\big|$ and a Gaussian width $\sigma(d^*)$ — the run's rocking width, measured once on the intensity-weighted excitation errors and shared by every crystal. It is measured per group of frames of similar prediction window (four per shell), each against its own window, the shell taking the median of the groups whose curve is narrower than their window, so the frames with the widest windows do not set it everywhere; and it is measured in eight shells of equal width in $d^*$, made non-decreasing (pool-adjacent-violators, weighted by each shell's summed signal) and interpolated linearly in $d^*$ as a table. The three-term form $\sigma^2=\gamma_0^2+(\gamma_e d^*)^2+(\mathrm{bw}\,|q_z|)^2$ — the reciprocal-lattice point's own radius, the mosaic/divergence spread, and the bandwidth smear along the beam, in quadrature — is still fitted, sets the prediction window (§8.2) and stands in for the table where fewer than three shells are measurable. The curve is centred on the run's **radial scale** of the reciprocal lattice — a wavelength or cell a little off, which the spot positions cannot see since they fix only $\lambda d^*$ — measured from where the curve's centre lies against $d^{*2}$ and applied to $\mathbf{q}$. Where the frames were predicted through the measured window (§8.2), the post-refinement uses that same curve rather than measuring it again; the curve is written to `_process.h5` (`/entry/MX/stillsRockingWidth*`, `stillsRadialScale`), so `--mode scale` merges with it too. A tilt moves reflections on opposite sides of the Ewald sphere in opposite directions, so it reshapes the *spatial* pattern of partialities — a degree of freedom the per-image scale $G$ does not have, and the reason the tilt is refined rather than a scalar partiality width, which would be degenerate with $G$. Nothing is re-integrated (the integrated intensities are fixed); the tilt is hard-bounded at about 1° and held by a soft prior, so it stays inert on sparse or weak crystals. The cycle is merge → per-crystal tilt refinement (with $G$ profiled out by the same robust Cauchy IRLS used for the per-frame scales, §10.3) → recompute $P$ → re-merge, repeated a few times; the refined partiality is adopted on every crystal it was refined on. The per-crystal fits of $G$ and of the tilt measure each residual against its expected variance at the model, background + counting + $(0.3\,I_\mathrm{model})^2$: a still's strong reflections scatter about the model by tens of per cent, and in counting sigmas alone every strong reflection would be an outlier and the scale would be set by the weak ones.
 
-Reflections below a minimum partiality can be rejected from merging to avoid unstable corrections.
+Reflections below a minimum partiality are left out of the merge (`--min-partiality`, default 0.02 on rotation and 0.5 on stills): the empirical rocking curve of a still has a floor far out on its tail, from mis-oriented crystals, and dividing such an observation by a small model $p$ makes it biased, not merely noisy.
 
 ### 10.3 Smoothing of per-frame scales
 
@@ -369,8 +371,9 @@ An internal-consistency term can inflate uncertainties when multiple observation
 
 ### 10.5 Merging statistics
 
-The shells are **nine bins of equal width in $1/d^2$**, laid between the **declared** low-resolution
-limit (`--scaling-low-resolution`, or the whole sphere where it is switched off) and the
+The shells are **nine bins of equal width in $1/d^2$**, laid between the whole sphere ($1/d^2 = 0$; the
+low-resolution limit `--scaling-low-resolution` bounds only the scale fit, so the coarsest reflections are
+merged too, and those the beam stop hides count as missing) or the declared range of `--report-resolution`, and the
 highest-resolution reflection the merge actually kept — XDS's rule and XDS's count, so at the same
 resolution limits the two programs' tables have the same shell boundaries and can be read row for
 row. `--resolution-shells` changes the count; the binning rule does not change with it.
@@ -470,7 +473,11 @@ A reference dataset (`--reference`, MTZ or SF-mmCIF) supplies known intensities
 
 **Fix the space group and cell.** Unless overridden on the command line (`-S` for the space group, `-C` for the cell), the reference's space group is adopted and its cell is used as the soft reference cell — indexing may still drift the cell within tolerance, so a small mismatch between reference and data is absorbed rather than rejected. This applies to both stills and rotation data.
 
-**Resolve the indexing (merohedral) ambiguity.** When the lattice symmetry is higher than the crystal's Laue symmetry (e.g. $P3$, $P4$, $P6$, $C2$), more than one indexing of the same lattice is geometrically valid, and the two solutions produce *different* merged intensities that a self-consistent scale cannot tell apart — only an external reference can. The candidate reindexings are the identity together with the twin-law cosets of the metric symmetry (from the unit-cell metric and the Laue group); each is scored by the intensity correlation $\mathrm{CC}_\mathrm{ref}$ of the reindexed merge against the reference, and the data are re-merged in the best-correlating indexing. The reindex is **metric-preserving** — only the $hkl$ labels change, the cell is unchanged — and it is a no-op for a holohedral crystal, which has no twin laws (the lattice and Laue symmetry coincide). For rotation data this is done once, after the space group is determined, and the whole merge is then repeated in the chosen indexing. For stills it has to be done **per image**, at integration time: each crystal is indexed independently, so a run resolves the ambiguity image by image (the image's partiality/Lorentz-corrected intensities are correlated with the reference under each candidate operator, which is scale-invariant, and the best-correlating one is adopted once and for good) — otherwise the merge would average reflections that are not symmetry mates. In neither workflow is the reference a **scale** target: both scale against their own data (§10.2), so $\mathrm{ISa}$ and the merging statistics come from the data alone and no cross-dataset systematic is imported. Because the stills choice is made at integration time, a later re-merge of stored reflections cannot repair a dataset integrated without a reference. Where there is no reference dataset but there is a **model** (`--model`), the reference intensities are computed from it instead - $|F_\mathrm{model}|^2$ from the atomic structure factors with a flat bulk-solvent contribution at the standard constants ($k_\mathrm{sol}=0.35$, $B_\mathrm{sol}=46$ Å$^2$), which are not fitted because there are no observations yet. Nothing is scaled against them; they serve only to rank the candidate indexings, and the correlation that does the ranking is scale-invariant. This needs the cell and space group up front (`-C` / `-S`, as serial indexing wants anyway); on rotation data the same job is done after the merge, in §14.5, where a merge exists to fit the model to properly.
+**Resolve the indexing (merohedral) ambiguity.** When the lattice symmetry is higher than the crystal's Laue symmetry (e.g. $P3$, $P4$, $P6$, $C2$), more than one indexing of the same lattice is geometrically valid, and the two solutions produce *different* merged intensities that a self-consistent scale cannot tell apart — which of them is the reference's own, only an external reference can say. The candidate reindexings are the identity together with the twin-law cosets of the metric symmetry (from the unit-cell metric and the Laue group); each is scored by the intensity correlation $\mathrm{CC}_\mathrm{ref}$ of the reindexed merge against the reference, and the data are re-merged in the best-correlating indexing. The reindex is **metric-preserving** — only the $hkl$ labels change, the cell is unchanged — and it is a no-op for a holohedral crystal, which has no twin laws (the lattice and Laue symmetry coincide). For rotation data this is done once, after the space group is determined, and the whole merge is then repeated in the chosen indexing. For stills, where each crystal is indexed independently and a merge of mixed indexings would average reflections that are not symmetry mates, it is done **per image**, at integration time: a run with a reference resolves the ambiguity image by image (the image's partiality/Lorentz-corrected intensities are correlated with the reference under each candidate operator, which is scale-invariant, and the best-correlating one is adopted; a crystal whose own cell decides the indexing keeps it, as described below). In neither workflow is the reference a **scale** target: both scale against their own data (§10.2), so $\mathrm{ISa}$ and the merging statistics come from the data alone and no cross-dataset systematic is imported. Because the stills choice is made at integration time, a later re-merge of stored reflections (`--mode scale`) cannot repair a dataset integrated without a reference; the data-only resolution below runs in the full pipeline only. Where there is no reference dataset but there is a **model** (`--model`), the reference intensities are computed from it instead - $|F_\mathrm{model}|^2$ from the atomic structure factors with a flat bulk-solvent contribution at the standard constants ($k_\mathrm{sol}=0.35$, $B_\mathrm{sol}=46$ Å$^2$), which are not fitted because there are no observations yet. Nothing is scaled against them; they serve only to rank the candidate indexings, and the correlation that does the ranking is scale-invariant. This needs the cell and space group up front (`-C` / `-S`, as serial indexing wants anyway); on rotation data the same job is done after the merge, in §14.5, where a merge exists to fit the model to properly.
+
+**Serial stills without a reference or model.** The data cannot say which indexing is the *true* one, but they can say which crystals are in the *same* one, and that is all a merge needs. Where the space group is fixed (`-S`) and its lattice admits alternative indexings, the crystals are made consistent with each other before anything is scaled, following Brehm & Diederichs (2014). Each crystal's partiality- and Lorentz-corrected intensities are divided by the run's mean intensity in their resolution shell (20 shells of equal reciprocal volume), standardised within the crystal so that its unknown scale and offset drop out, and weighted by $1/(1+(\sigma/s)^2)$, $s$ being the crystal's spread, so that a weak or barely recorded reflection counts for little. The agreement of two crystals is the sum of the products of these values over the reflections they share, and the objective is that agreement summed over every pair of crystals, each in the indexing assigned to it. That sum is $(|M|^2 - \mathrm{const})/2$ with $M$ the per-reflection sum over all crystals, so a crystal's agreement with all the others is one dot product with $M$ less its own contribution: each crystal in turn takes the indexing in which that dot product is largest, $M$ is updated, and the passes repeat until no more than one crystal in a thousand moves. A pass costs one read of the reflections, not one per pair of crystals, which is what keeps tens of thousands of crystals to seconds. The objective only grows, so it converges; it is started four times (once from the indexing as found, three times from a seeded random assignment) and the start that ends highest is kept, and of the equally consistent answers related by an overall relabelling the one that moves the fewest crystals is taken. The order of every floating-point sum is fixed (crystals in image order, sequential passes), so the result does not depend on the thread count. The run reports how clearly the crystals separated: for each crystal the correlation with the mean of all the others in its chosen indexing and in the best other one, compared by Fisher's $z$ in units of its standard error ($\sqrt{2/(n-3)}$ for $n$ shared reflections) — the median of that margin and the share of crystals above $3\sigma$.
+
+A twin law is only an ambiguity for crystals whose own lattice cannot tell the indexings apart. On a pseudo-merohedral cell whose axes differ by a few per cent, each crystal's refined cell already says which axis is which, and the indexer has used that; letting the intensities overrule it there moves crystals that were right. So for each law the share of crystals whose refined cell fits the run's cell better as indexed than after the law is measured (a tie counting half — on an exactly merohedral lattice the share is about one half). Where it is at least 0.9 the law is decided by the cells: a crystal whose cell prefers its indexing stays there, as an anchor, and only the crystals whose cell does not are decided by the intensities, against the anchors. With a reference or a model the per-image choice above stands except where the cells decide: once all images are integrated, a crystal its own cell anchors goes back to that indexing, and the reference chooses only among the indexings left open to the others; the same data-only resolution is then run only to measure it: the report gives the number of crystals on which the data alone would have chosen otherwise.
 
 ### 10.10 Ice rings at the scale and merge stages
 
@@ -488,7 +495,7 @@ The “profile radius” is the intrinsic angular width of a reflection — crys
 $
 R \approx \sqrt{\tfrac{1}{N}\sum_i \Delta_{\mathrm{Ewald},i}^2}.
 $
-When the beam has a finite energy bandwidth, that bandwidth smears each reflection radially by $\sigma_\mathrm{bw}\approx \mathrm{bandwidth}\cdot\lambda/2d^2$ (largest at high resolution), which also broadens the measured $\Delta_\mathrm{Ewald}$ spread. Since prediction re-applies the bandwidth term per reflection (§8.2), this contribution is deconvolved from the estimate — $R^2 = \langle\Delta_\mathrm{Ewald}^2\rangle - \langle\sigma_\mathrm{bw}^2\rangle$ — so that $R$ is the intrinsic width and bandwidth is not double-counted. Still predictions use an excitation-error cutoff proportional to $R$.
+When the beam has a finite energy bandwidth, that bandwidth smears each reflection radially by $\sigma_\mathrm{bw}\approx \mathrm{bandwidth}\cdot\lambda/2d^2$ (largest at high resolution), which also broadens the measured $\Delta_\mathrm{Ewald}$ spread. Since prediction re-applies the bandwidth term per reflection (§8.2), this contribution is deconvolved from the estimate — $R^2 = \langle\Delta_\mathrm{Ewald}^2\rangle - \langle\sigma_\mathrm{bw}^2\rangle$ — so that $R$ is the intrinsic width and bandwidth is not double-counted. Still predictions use an excitation-error cutoff proportional to $R$ where the run's rocking curve is not measured (`--simple-stills`, and the sample the curve is measured on; §8.2).
 
 ### 11.2 Mosaicity from rotation data
 
diff --git a/docs/CPU_DATA_ANALYSIS_REFINEMENT.md b/docs/CPU_DATA_ANALYSIS_REFINEMENT.md
new file mode 100644
index 000000000..e63f0e730
--- /dev/null
+++ b/docs/CPU_DATA_ANALYSIS_REFINEMENT.md
@@ -0,0 +1,337 @@
+# Data analysis: refinement of a placed model (§15)
+
+Part of the [CPU/GPU data-analysis reference](CPU_DATA_ANALYSIS.md); the section numbers are continuous across its parts.
+
+```{contents} On this page
+:local:
+:depth: 2
+```
+
+## 15. Restrained refinement of a placed model
+
+Wherever a model is placed - it fits where it is (§14.8), or molecular replacement placed it (§14.10) -
+rugnux refines it against the merge it was placed on (`--no-refine` skips this). `rugnux --mode refine`
+runs the same refinement on a model and merged structure factors that already exist. How to use it, and
+what it writes, is in [Models and reference data](RUGNUX_MODEL_AND_REFERENCE.md#refinement); its report
+keys are in [The results report](RUGNUX_REPORT.md#refinement-refine_).
+
+The refinement comes **after every processing decision and changes none of them**. Nothing it finds is
+read by the space-group search, the indexing choice, the resolution cut or the files `<prefix>.mtz`,
+`<prefix>_model.cif` and `<prefix>_maps.mtz`; `R_WORK` and `R_FREE` stay those of the model as placed
+(§14.3). What it produces is written beside them: the refined model, its map coefficients, the blobs of its
+difference map and the `REFINE_` keys.
+
+The library reads and writes no file. The model and the reflections come in, the refined model, its
+statistics and its map coefficients go out; the restraint dictionary is compiled into the binary (§15.4).
+
+### 15.1 What is refined, and in what order
+
+The model is taken as the refinement can use it: the first model of the file only, its hydrogens removed,
+every anisotropic B replaced by its isotropic equivalent, and every B clamped to the range the refinement
+allows (2 Ų up to twice the model's largest B, within 100-300 Ų). Occupancies are kept as they are, and
+so are alternative conformations, each refined with its own restraints.
+
+Two stages follow.
+
+1. **Placement.** Each chain of at least 50 non-water atoms is moved as a rigid body - an angle-axis
+   rotation about its centroid, scaled by its rms radius so that a unit of rotation moves a typical atom by
+   about an angstrom, and a translation - against the X-ray target (§15.2), by Ceres' L-BFGS for 30
+   iterations. Then one B shift per residue. Each of the two is **kept only where it lowers R-free by more
+   than 0.001**: a deposited model was refined atom by atom already, and moving its chains or shifting its
+   B factors residue by residue then only makes it worse. The placement stage needs no dictionary.
+2. **Restrained refinement.** Every atom's position and isotropic B, against the X-ray target and the
+   geometry of the dictionary (§15.4-§15.5), in weight trials chosen by R-free (§15.7). Residues the
+   dictionary does not describe, and residues with an atom it does not know, are **held fixed**: they stay
+   in the structure factors, in the bulk-solvent mask and in the repulsions the refined atoms see, but
+   they do not move. So do atoms of zero occupancy.
+
+### 15.2 The X-ray target
+
+The target is the maximum-likelihood amplitude target: for an acentric reflection the Rice distribution of
+the observed amplitude $F_o$ given the model's $|F_\mathrm{model}|$, for a centric one its centric
+counterpart,
+
+$$
+-\ln L_\mathrm{acentric} = \ln\Sigma + \frac{F_o^2 + D^2|F_\mathrm{model}|^2}{\Sigma} - \ln I_0\!\left(\frac{2F_o D|F_\mathrm{model}|}{\Sigma}\right),\qquad
+-\ln L_\mathrm{centric} = \tfrac12\ln\Sigma + \frac{F_o^2 + D^2|F_\mathrm{model}|^2}{2\Sigma} - \ln\cosh\frac{F_o D|F_\mathrm{model}|}{\Sigma},
+$$
+
+(the terms that depend on neither the model nor the parameters left out) with $D$ the fraction of the model that is right and $\Sigma$ the variance that the rest of the structure and
+the measurement leave (§15.3), summed over the working reflections. $\ln I_0$ and $I_1/I_0$ are evaluated
+with the polynomial approximations of Abramowitz and Stegun, through the exponentially scaled form for large
+arguments so that nothing overflows. The amplitudes are the French-Wilson $|F|$ of §10.8 - the ones the
+written reflection file carries - and the free reflections are those of §10.7.
+
+$F_\mathrm{model}$ is the model of §14.2,
+
+$$
+F_\mathrm{model} = k\,e^{-\mathbf{s}^\top\mathbf{B}\mathbf{s}/4}\left(F_\mathrm{calc} + k_\mathrm{sol}\,e^{-B_\mathrm{sol}s^2/4}\,F_\mathrm{mask}\right),
+$$
+
+with the atoms' $F_\mathrm{calc}$ computed with the dictionary's riding hydrogens included (§15.4). The
+scale, the anisotropic B, the bulk solvent and the likelihood's parameters are fitted at the start of each
+**macro-cycle** (§15.3) and held fixed while the minimiser runs; the mask is drawn for the model as it is
+at that point.
+
+**The gradient by the FFT method.** The atoms' density is placed on a grid with a Gaussian blur (the one
+REFMAC-compatible density calculation uses, chosen for the lowest B a macro-cycle can reach) and transformed
+once; the crystal's symmetry is composed in reciprocal space from the transform of one copy, as for the rigid
+body (§14.8). The derivative of the target with respect to every structure factor, taken back to real space
+by one inverse transform through the adjoint of that composition, is a map; each atom's derivatives with
+respect to $x, y, z$ and $B$ are that map summed against the derivatives of its own blurred density. One
+evaluation of the target and of the gradient of every atom thus costs a density gather, two FFTs and a
+gradient gather, whatever the number of atoms. The derivative of a riding hydrogen is passed to its parent.
+
+### 15.3 Scale, bulk solvent and the likelihood parameters
+
+**Scale and solvent.** The flat bulk-solvent mask is drawn with the REFMAC radii (probe 1.0 Å, shrink 0.8 Å)
+on a grid of its own, with a spacing of $d_\mathrm{min}/3$ or 0.4 Å, whichever is finer (coarser only where
+a cell would need more than $2^{26}$ points). On the atoms' density grid the shrink is lost at low
+resolution: at 3 Å its 1 Å step leaves no grid point within the shrink radius. $k_\mathrm{sol}$ and
+$B_\mathrm{sol}$ are searched over their physical range on the working reflections, and the overall scale
+and anisotropic B are fitted at each point of that search (§14.2) - at the points of its fine pass by
+**robust least squares**:
+iteratively reweighted (four reweightings), each reflection's residual $r = F_o - |F_\mathrm{model}|$
+weighted by $1/\sqrt{1 + (r/c)^2}$ with $c$ the median $|r|$ of the unweighted fit. The fit then minimises
+the pseudo-Huber loss $\sum 2c^2\left(\sqrt{1 + (r/c)^2} - 1\right)$, quadratic for the bulk of the
+reflections and linear for the few a model cannot explain - a beam-stop shadow, an ice ring, a missing part
+of the model - which ordinary least squares would let set the scale of all the rest. When the B factors
+are refined, the overall isotropic part of the scale's B is moved into the atoms (and into $B_\mathrm{sol}$,
+so that $F_\mathrm{model}$ stays as it is); left in the scale, it and the atoms' B drift against each other
+as the B factors are refined.
+
+With these three choices - riding hydrogens, the fine mask grid and the robust scale - the R-work and
+R-free of a model as given (`REFINE_R_WORK_START`, `REFINE_R_FREE_START`) agree with REFMAC 5.8's 0-cycle
+values on the same model and data within 0.002 on twelve of fourteen depositions from 1.1 to 3.6 Å, and
+within 0.006 on the other two (`tools/battery/refine_parity.py`).
+
+**$D$ and $\Sigma$.** The two parameters of the likelihood are fitted by maximum likelihood in resolution
+bins of the free set (100 free reflections to a bin, at most 30 bins; where the free set has fewer than
+100 reflections, the working ones join it so that the likelihood still has a scale), and interpolated
+linearly in $1/d^2$ between the bins' centres:
+
+- $\beta$ on the **free** reflections, as the whole spread of $F_o$ about $D F_\mathrm{model}$ with variance
+  $\varepsilon\beta$ - the measurement error included;
+- $D$ then on the **working** reflections of the bin, with the variance
+  $\Sigma = \varepsilon\beta + 2\sigma^2$ for an acentric reflection and $\varepsilon\beta + \sigma^2$ for a
+  centric one, $\sigma$ the amplitude's own error.
+
+$\Sigma$ is also the variance of each reflection in the target. Where the measurement error is a large part
+of the spread - the weak high-resolution shells - it is counted twice, and $D$ falls towards 0 there, with
+the figure of merit. This division of the two parameters between the working and the free set is the one
+REFMAC5 describes; measured on REFMAC 5.8's own output it reproduces its $D$ by bin and its overall figure of
+merit (the mean over the working reflections) to about 0.01 on most depositions.
+
+### 15.4 The dictionary and the topology
+
+The restraints are those of the **CCP4 Monomer Library**, a subset of which is compiled into rugnux
+(`image_analysis/structure_refinement/monomers/`, regenerated by `update_monomers.py`; nothing is read from
+disk, and `$CLIBD` is never consulted): the 20 standard amino acids and MSE; the DNA and RNA nucleotides
+(DA, DC, DG, DT, A, C, G, U); the modified nucleotides of tRNA and rRNA met most often - pseudouridine (PSU),
+5-methylcytidine (5MC), 1-methyladenosine (1MA), the 2'-O-methyl nucleotides OMG, OMC and OMU, dihydrouridine
+(H2U), N2-methyl- and N2,N2-dimethylguanosine (2MG, M2G), 7-methylguanosine (7MG) and ribothymidine (5MU), polymer
+residues joined by the same backbone link; ATP, ADP, AMP, GTP, GDP and GMP; the cofactors NAD⁺ (NAD), NADH (NAI),
+NADP⁺ (NAP), NADPH (NDP), FAD, FMN, heme (HEM), heme C (HEC), S-adenosylmethionine (SAM) and
+S-adenosylhomocysteine (SAH), and dioxygen (OXY); DMSO; the PEG fragments PEG, PGE, PG4 and 1PE; glycerol,
+ethylene glycol, MPD, acetate, sulfate and phosphate; water; and the ions Na, K, Mg, Ca, Mn, Fe²⁺, Fe³⁺, Co, Ni,
+Cu, Zn, Cd, Cl, Br and I - 84 compounds - with the library's links and modifications that apply to them (among
+them heme C's two thioethers to its cysteines, HEC-CYS1 and HEC-CYS2, and the covalent links of heme and FAD to
+the protein) and the energy types those compounds use.
+
+The model's topology is built from it by GEMMI (`prepare_topology`): the links between residues (the peptide
+and cis-peptide, the nucleic-acid backbone, disulfides, and the model's LINK records where the library
+describes them), the modifications those links imply, and per residue the bonds, angles, torsions, chiral
+volumes and planes. Torsions are restrained where the dictionary gives them an esd, except the main-chain
+φ/ψ and the sugar puckers it lists as alternatives. The dictionary's **hydrogens** are added to every
+residue it describes (waters excepted), placed by GEMMI from the dictionary's geometry and moved with their
+parents: they take part in the structure factors and in no restraint, and are placed again on their
+parents at every macro-cycle. The refined model is written with them.
+
+### 15.5 Geometry, metal and B restraints
+
+Every restraint is a squared normalised deviation, $E = ((x - x_\mathrm{ideal})/\sigma)^2$, with its
+analytic derivatives:
+
+- **bonds and angles**, ideal and esd from the dictionary;
+- **torsions**, modulo the dictionary's period, with derivatives in the form of Blondel and Karplus, free of
+  the singularities of the arccos form;
+- **chiral volumes** $(\mathbf{a}_1 - \mathbf{c})\cdot((\mathbf{a}_2 - \mathbf{c})\times(\mathbf{a}_3 - \mathbf{c}))$,
+  $\sigma = 0.2$ ų;
+- **planes**: the distances of the atoms from their least-squares plane (the plane's normal the smallest
+  eigenvector of the atoms' scatter, by Jacobi rotations); the plane is optimal, so the derivative of each
+  distance carries no term from the plane moving;
+- **repulsions** of every pair of atoms closer than its contact distance, symmetry mates included, that no
+  bond, angle or 1-4 relation joins and that are not alternative conformations of each other, with at least
+  one of the two refinable: $E = ((d_0 - d)/0.2\,\text{Å})^2$ below the contact distance $d_0$ and nothing
+  above it, $d_0$ the sum of the energy types' van der Waals radii, 2.6 Å where both atoms can hydrogen-bond
+  and 1.9 Å between a metal and N, O or S. The list is rebuilt at every macro-cycle.
+
+**Metal sites.** A metal - an ion, or a metal atom of a ligand such as a heme's iron - is restrained to the
+donor atoms (O, N or S) that the model's LINK / `_struct_conn` records bind it to. Where the library has a link for the pair - its ZN-CYS, ZN-HISND,
+ZN-HISNE, FE-CYS, FE-HISND and FE-HISNE - that link is used as it is, with the modification it makes to
+the donor's residue (the proton the bond replaces). Every other record becomes a link of one bond at the
+distance of the library's own statistics of metal sites (its `metals.json`, carried as `monomers/metals.cif`)
+for the metal, the donor element and the site's coordination number - the number of such records the metal
+has, plus the bonds its own residue's dictionary gives it (a heme iron's four pyrrole nitrogens) - interpolated linearly between two tabulated coordination numbers (rows resting on at least 20 sites
+count; σ is the row's standard deviation, at least 0.02 Å). Only the bond is restrained, not
+the angles at the metal. A contact without a record stays a repulsion, and a record to a symmetry mate is
+left out, as every bond to a symmetry mate is. The rmsd of these bonds - with the dictionary's own bonds of
+a metal within a ligand, a heme iron's to its porphyrin - is reported apart from the covalent bonds'
+(`REFINE_RMSD_METAL_BONDS`).
+
+**B restraints.** The B factors of two atoms are restrained to each other in proportion to their size, by
+the symmetric Kullback-Leibler divergence of two isotropic Gaussians of variances $B_i$ and $B_j$:
+
+$$
+E = \frac{(B_i - B_j)^2}{\kappa^2 B_i B_j},
+$$
+
+a difference restraint whose $\sigma$ is $\kappa\sqrt{B_iB_j}$, so that atoms of high B may differ more than
+atoms of low B. $\kappa$ is 0.1 for bonded main-chain atoms and 0.133 for main-chain atoms bonded to a
+common atom, 0.2 and 0.3 for the side chains and the rest, and 0.5 for atoms within 4 Å of each other (waters
+among them, symmetry mates included) that no bond or angle relates. No atom's B goes below 2 Ų or above
+the ceiling of §15.1.
+
+### 15.6 The minimiser
+
+Positions and B factors are minimised in turn, each by an L-BFGS of rugnux's own (`RefinementMinimiser`),
+with the two-loop recursion of Nocedal and of Liu and Nocedal, a memory of 20 pairs and a backtracking line
+search from the full step to sufficient decrease, its first trial moving no position by more than 0.3 Å and
+no B by more than 10 Ų. What sets it apart from a textbook L-BFGS:
+
+- **Its memory is kept from one macro-cycle to the next.** A macro-cycle is a few dozen iterations on a target
+  whose scale and likelihood parameters were refitted in between; starting each from what the earlier ones
+  learnt of the curvature, instead of from a steepest-descent step, is what lets two macro-cycles of a
+  weight trial get as far as many restarted ones. Each weight trial starts with an empty memory.
+- **The B steps are scaled by their curvature.** The initial inverse Hessian of the B factors is a
+  diagonal: the X-ray target's curvature in each atom's B - its shape from the likelihood's curvature in
+  $|F_\mathrm{model}|$ and the atom's own scattering, summed in resolution shells, calibrated once per trial
+  against central differences of the gradient along a random $\pm1$ direction - plus the B restraints'
+  curvature, each element at least a thousandth of the median. The positions take none: their restraints'
+  curvature is that of stiff bonds and angles, which move atoms together, and as a diagonal it slows the soft
+  (torsion and X-ray) directions rather than scaling them.
+
+The diagonal is rescaled at each iteration by the latest pair (Oren-Shanno scaling in that metric). A solve
+stops after its iteration budget (30 for the positions and 20 for the B factors per macro-cycle) or where an
+iteration lowers the target by less than $10^{-7}$ of it.
+
+### 15.7 The weights, decided by trial
+
+The refined target is $w\,T_\mathrm{X\text{-}ray} + E_\mathrm{geometry}$ for the positions and
+$w_B\,T_\mathrm{X\text{-}ray} + E_B$ for the B factors. Rather than fixing $w$ and $w_B$ in advance, rugnux
+runs **short refinements at several weights and keeps the one that does best on the free set** - a weight
+chosen late, on the evidence, instead of early at a rule.
+
+The starting weights balance the gradients: $w_0 = |\nabla E_\mathrm{geometry}| / |\nabla T_\mathrm{X\text{-}ray}|$,
+the geometry's gradient taken on the model shaken by 0.1 Å (a refined model's geometry would give none), and
+$w_{B,0}$ likewise from the B restraints on the B factors shaken by 20%. Each **trial** is two macro-cycles
+(the scale, solvent and likelihood refitted, then the positions, then the B factors) from where it starts.
+A trial is **within bounds** where its rmsd from the dictionary is at most 0.02 Å for bonds and 2° for
+angles; one trial **displaces** another where it is within bounds and its R-free is lower by more than 0.001
+(differences smaller than that do not decide, and the trial listed first - on a ladder, the tighter
+geometry - is kept). The trials
+are:
+
+1. **The ladder from the placed model**: $w = w_0 \times \{1/1024, 1/128, 1/16\}$, each with the B factors
+   held and refined at $w_{B,0}$ - six trials.
+2. **The trajectory**: up to eight steps, each a set of trials from where the last step ended - the weights
+   as they are, and in turn the positions' weight halved and doubled (halved because the geometry loosens at
+   one weight as the model improves, until it leaves the bounds) or the B factors' weight divided and
+   multiplied by four. A step is taken while it lowers R-free or R-work by more than 0.001 and its R-free
+   stays within 0.001 of the best so far, and the trajectory ends at its best step. On a deposited model,
+   whose free set the depositor's refinement has already fitted, R-work falls while R-free rises, and the
+   trajectory ends where it began.
+3. **The final ladder**: the trajectory's weights times $\{0.5, 1, 2\}$, kept where one displaces it.
+
+$w$ never exceeds $w_0/8$. The trials of one set run side by side - on one GPU, on several, or on the CPU's
+threads - each from the same start and taking nothing from the one before it, so the result does not depend
+on how many run at once.
+
+The refinement can be cut short from outside (the broker's deadline or cancel, Ctrl+C): the check is made
+between the minimiser's iterations and before every trial, the trials that finished are chosen among as
+usual, and the report says so. Cut before the first trial, the model is the placement's.
+
+### 15.8 Maps of the refined model
+
+The refined model's map coefficients, `<prefix>_refined_maps.mtz`, are $2mF_o - DF_c$ and $mF_o - DF_c$ as in
+§14.4, but with $m$ and $D$ those of the refinement's own likelihood (§15.3) rather than the shell
+$\sigma_A$ of §14.4, so the maps carry the weights the target was minimised with; $m$ is
+$I_1(X)/I_0(X)$, $X = 2F_oD|F_\mathrm{model}|/\Sigma$, for an acentric reflection and $\tanh(X/2)$ for a
+centric one. Where the merge kept the Bijvoet pairs, the anomalous difference map is made on the refined
+model's phases too, and read by the blob finder below.
+
+### 15.9 Unexplained density: blobs
+
+The $mF_o - DF_c$ map of the refined model is searched for what the model leaves unexplained: the connected
+regions above 3 σ that peak above 4 σ, found by flood fill (GEMMI's `find_blobs_by_flood_fill`, the method
+of Coot's "unmodelled blobs"), each moved to the copy nearest the model and measured - peak, volume, the
+density integrated above the cutoff, the nearest atom, the polar (N, O) atoms at 2.4-3.4 Å and the N, O or S
+at 1.8-2.6 Å, and the anomalous map at its peak. Each gets one reading, by rules on what is measured:
+
+| Reading | Rule |
+|---|---|
+| `MODEL_ERROR` | within 1.6 Å of a model atom: the model's own atom out of place, or a missing alternative conformation |
+| `ION` | at least 1.8 Å from the model, and an anomalous peak of at least 4 σ, or two metal-like contacts and a peak of at least 8 σ |
+| `LIGAND` | larger than 1.5 times a single atom's blob at this resolution (a sphere of radius $d_\mathrm{min}/2$) and than 8 ų, at least 2.2 Šfrom the model |
+| `WATER` | at least 2.2 Å from the model with at least one polar contact |
+| `UNASSIGNED` | anything else |
+
+They are listed strongest first (by the integrated density) in `<prefix>_blobs.json`, and the five strongest
+in the report. A blob read as `LIGAND` is density of ligand size where the model has nothing: a buffer
+molecule or an unmodelled side chain is that as well as the compound that was soaked. The readings point a
+person at the density; they do not identify a compound.
+
+### 15.10 GPU and CPU
+
+On a CUDA build the target, the gradient and the restraints are evaluated on the card - the density gather,
+cuFFT, the composition of the symmetry and the target per reflection, the adjoint through a CSR list, the inverse transform and one warp per atom for its gradient; the restraints in one kernel whose
+per-atom gradient slots are summed in a fixed order; the robust scale fit and the fine solvent mask on the
+card as well - with no floating-point atomics, so the result is the same from run to run. The weight trials
+of a set run on as many cards as there are, each trial on an engine of its own. Where the case does not fit
+the card's budget, or with `--no-gpu`, or on a build without CUDA (macOS included: the refinement has no
+Metal path), the CPU engine computes the same target, to rounding, several times more slowly (seconds on a
+GPU, typically 2-15 minutes on the CPU).
+
+### 15.11 Not yet
+
+What the refinement does not do yet - each a known gap, not a design choice:
+
+- **Custom ligands and other monomer libraries.** Only the 84 compounds of §15.4 are restrained. Any other
+  residue is held fixed (it stays in $F_\mathrm{calc}$, the mask and the repulsions); no restraints are
+  generated for a new ligand, and neither a user's restraint CIF nor an external monomer library can be given.
+- **TLS** refinement.
+- **Anisotropic ADPs**: an anisotropic B is replaced by its isotropic equivalent, and only isotropic B is
+  refined.
+- **NCS restraints**: copies are refined independently.
+- **Twin refinement**: the target is not a twinned one, also where the twin hypothesis' merge was written.
+- **Water building**: waters are neither picked nor removed; the blob finder only points at candidates.
+- **Alternative conformations and occupancies**: existing conformers are refined in place; no occupancy is
+  refined and no conformer is added.
+- **Rotamer and peptide-flip search**, and **Ramachandran restraints**.
+- **Real-space refinement**, and **jelly-body or reference-model restraints**.
+- **A Metal (Apple GPU) path**: on macOS the refinement runs on the CPU.
+- **Validation beyond geometry**: the report gives the bond and angle rmsd, the metal-bond rmsd and the
+  number of clashes, not a MolProbity-style analysis (Ramachandran, rotamer and clashscore statistics).
+
+## References
+
+- R. C. Agarwal, "A new least-squares refinement technique based on the fast Fourier transform algorithm", *Acta Cryst.* **A34** (1978), 791-809 (the gradient by the FFT method, §15.2).
+- N. S. Pannu & R. J. Read, "Improved structure refinement through maximum likelihood", *Acta Cryst.* **A52** (1996), 659-668, and G. N. Murshudov, A. A. Vagin & E. J. Dodson, "Refinement of macromolecular structures by the maximum-likelihood method", *Acta Cryst.* **D53** (1997), 240-255 (the maximum-likelihood amplitude target and its figure of merit, §15.2, §15.8).
+- G. N. Murshudov, P. Skubák, A. A. Lebedev, N. S. Pannu, R. A. Steiner, R. A. Nicholls, M. D. Winn, F. Long & A. A. Vagin, "REFMAC5 for the refinement of macromolecular crystal structures", *Acta Cryst.* **D67** (2011), 355-367 (D from the working set and the variance from the free, §15.3; the Kullback-Leibler form of the B restraints, §15.5).
+- R. J. Read, "Improved Fourier coefficients for maps using phases from partial structures with errors", *Acta Cryst.* **A42** (1986), 140-149 (the m, D weighting of the map coefficients, §15.8).
+- V. Y. Lunin & T. P. Skovoroda, "R-free likelihood-based estimates of errors for phases calculated from atomic models", *Acta Cryst.* **A51** (1995), 880-887, and V. Y. Lunin, P. V. Afonine & A. G. Urzhumtsev, "Likelihood-based refinement. I. Irremovable model errors", *Acta Cryst.* **A58** (2002), 270-282 (the likelihood's parameters from the free set, §15.3).
+- J.-S. Jiang & A. T. Brünger, "Protein hydration observed by X-ray diffraction: solvation properties of penicillopepsin and neuraminidase crystal structures", *J. Mol. Biol.* **243** (1994), 100-115, and A. Fokine & A. Urzhumtsev, "Flat bulk-solvent model: obtaining optimal parameters", *Acta Cryst.* **D58** (2002), 1387-1392 (the flat bulk-solvent mask and its parameters, §15.3).
+- P. V. Afonine, R. W. Grosse-Kunstleve & P. D. Adams, "A robust bulk-solvent correction and anisotropic scaling procedure", *Acta Cryst.* **D61** (2005), 850-855 (the grid search over the solvent parameters, §15.3).
+- P. J. Huber, "Robust estimation of a location parameter", *Ann. Math. Statist.* **35** (1964), 73-101, and P. Charbonnier, L. Blanc-Féraud, G. Aubert & M. Barlaud, "Deterministic edge-preserving regularization in computed imaging", *IEEE Trans. Image Process.* **6** (1997), 298-311 (the robust scale fit and its smooth, pseudo-Huber loss, §15.3).
+- A. A. Vagin, R. A. Steiner, A. A. Lebedev, L. Potterton, S. McNicholas, F. Long & G. N. Murshudov, "REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use", *Acta Cryst.* **D60** (2004), 2184-2195 (the restraint dictionary, §15.4).
+- M. Wojdyr, "GEMMI: A library for structural biology", *J. Open Source Softw.* **7** (2022), 4200 (the topology, the riding hydrogens and the blob search, §15.4, §15.9).
+- A. Blondel & M. Karplus, "New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: elimination of singularities", *J. Comput. Chem.* **17** (1996), 1132-1141 (the torsion derivatives, §15.5).
+- M. M. Harding, "Geometry of metal-ligand interactions in proteins", *Acta Cryst.* **D57** (2001), 401-411, and "Small revisions to predicted distances around metal sites in proteins", *Acta Cryst.* **D62** (2006), 678-682; F. Leonarski, L. D'Ascenzo & P. Auffinger, "Mg2+ ions: do they bind to nucleobase nitrogens?", *Nucleic Acids Res.* **45** (2017), 987-1004 (the metal-site distances, §15.5).
+- J. Nocedal, "Updating quasi-Newton matrices with limited storage", *Math. Comp.* **35** (1980), 773-782, and D. C. Liu & J. Nocedal, "On the limited memory BFGS method for large scale optimization", *Math. Program.* **45** (1989), 503-528 (the minimiser, §15.6).
+- A. T. Brünger, M. Karplus & G. A. Petsko, "Crystallographic refinement by simulated annealing: application to crambin", *Acta Cryst.* **A45** (1989), 50-61 (the starting weight from the ratio of the gradients, §15.7).
+- P. V. Afonine et al., "Towards automated crystallographic structure refinement with phenix.refine", *Acta Cryst.* **D68** (2012), 352-367 (weights chosen among refinements by R-free within geometry bounds, and the overall B moved into the atoms, §15.3, §15.7).
+- A. T. Brünger, "Free R value: a novel statistical quantity for assessing the accuracy of crystal structures", *Nature* **355** (1992), 472-475 (R-free).
+- P. Emsley, B. Lohkamp, W. G. Scott & K. Cowtan, "Features and development of Coot", *Acta Cryst.* **D66** (2010), 486-501 (unmodelled blobs, §15.9).
+- M. Abramowitz & I. A. Stegun, *Handbook of Mathematical Functions*, National Bureau of Standards (1964), 9.8.1-9.8.4 (the Bessel functions of the target, §15.2).
+
+The full citations, with DOIs, are in [ACKNOWLEDGEMENT.md](ACKNOWLEDGEMENT.md).
diff --git a/docs/DEPLOYMENT.md b/docs/DEPLOYMENT.md
index b9f1872be..fe09bfc26 100644
--- a/docs/DEPLOYMENT.md
+++ b/docs/DEPLOYMENT.md
@@ -167,8 +167,9 @@ cmake -DJFJOCH_VIEWER_BUILD=ON -DCMAKE_INSTALL_PREFIX=<directory to install> ..
 make jfjoch_viewer
 ```
 
-Pre-built viewers for Windows and macOS, and a portable Linux archive, are on the Gitea release
-page — see [Release contents](RELEASE_CONTENTS.md) and [jfjoch_viewer](JFJOCH_VIEWER.md).
+Pre-built viewers for Windows and macOS, and a portable Linux archive, are on the
+[download page](VIEWER_DOWNLOAD.md) — see [Release contents](RELEASE_CONTENTS.md) and
+[jfjoch_viewer](JFJOCH_VIEWER.md).
 
 
 ## Install Jungfraujoch Python client
diff --git a/docs/EXTERNAL_TEST_DATA_STILLS.md b/docs/EXTERNAL_TEST_DATA_STILLS.md
index 490d4d97c..b68d40972 100644
--- a/docs/EXTERNAL_TEST_DATA_STILLS.md
+++ b/docs/EXTERNAL_TEST_DATA_STILLS.md
@@ -37,6 +37,15 @@ Every set of the manifest is in the table and every set in the table is in the m
 same CXIDB entry, PDB entry, space group and d<sub>min</sub>; `tools/battery/doc_check.py` checks
 this. The beamline of `pal90` is the CXIDB entry's (NCI); the PDB entry 6IRK records CSI.
 
+## How the battery runs them
+
+Each set is one rugnux command, the way a serial user runs: the deposited cell and space group given
+(`-C`, `-S`), the wavelength where the files do not state it, `--crystfel-geometry` for the AGIPD and
+JUNGFRAU sets (the geometry file of the entry; the SACLA, PAL and LCLS files are placed without one),
+and the deposited model with `--model`, so that the report carries its R-free against the merge. The
+exact arguments are the `args` of each set in `tools/battery/still_manifest.json`; the
+[stills section of the tutorial](RUGNUX_TUTORIAL.md#still--serial-data) explains them.
+
 ## The files we use
 
 Paths are relative to the still data root of the site config (`tools/battery/README.md`). CXIDB
@@ -69,8 +78,9 @@ that line differs.
 **The `_int16` sets.** The SwissFEL files store converted JUNGFRAU data as uncompressed float32 keV,
 68 MB (JF16M) or 17 MB (JF4M) a frame, which caps reading at about 74 or 295 frames/s at 5 GB/s. The
 `_int16` sets are copies with the same layout in which `/data/data` holds whole photons (keV divided
-by the photon energy, rounded) as int16 with bitshuffle/LZ4, about 25 times smaller; rugnux reads them
-with `--gain 1` and merges them to the same numbers. Make them with
+by the photon energy, rounded) as int16 with bitshuffle/LZ4, about 25 times smaller; the battery runs
+them with the same arguments as the float32 originals (rugnux measures the gain from the frames), and
+they merge to the same numbers. Make them with
 `tools/battery/still/float32_to_int16.py <in.h5> <out.h5> <photon energy keV>` (h5py and hdf5plugin),
 into `swissfel_103/conv/` (4.57 keV) and `swissfel_213/conv/` (12.037 keV, keeping the tarball's
 directory tree), named `<input>_int16.h5`. One MbCO dark run (`run_000238`) holds no frames and has no copy.
diff --git a/docs/GPU_DATA_ANALYSIS.md b/docs/GPU_DATA_ANALYSIS.md
index 61c69f57c..24a57b695 100644
--- a/docs/GPU_DATA_ANALYSIS.md
+++ b/docs/GPU_DATA_ANALYSIS.md
@@ -2,7 +2,8 @@
 
 Jungfraujoch runs most of its crystallographic analysis on NVIDIA GPUs where one is present: the
 per-image loop of `jfjoch_broker`, `jfjoch_viewer` and `rugnux`, and most of `rugnux`'s
-dataset-level steps - the pre-scan, scaling and merging, model validation and molecular replacement.
+dataset-level steps - the pre-scan, scaling and merging, model validation, molecular replacement and
+refinement.
 This page lists the GPU engines (all of them in `.cu` files under `image_analysis/`), with what each
 computes. The methods themselves are described once, in the
 [CPU/GPU data analysis](CPU_DATA_ANALYSIS.md) reference and its siblings, which each entry links to.
@@ -95,7 +96,8 @@ nothing.
 ## Prediction and integration
 
 - **Still prediction** (`BraggPredictionGPU.cu`) - the reflections of a lattice within the
-  excitation-error cutoff, with their detector positions and per-reflection corrections.
+  excitation-error cutoff - or the window that follows the run's rocking curve, centred on its radial
+  scale - with their detector positions and per-reflection corrections.
   [§8.2](CPU_DATA_ANALYSIS_INTEGRATION.md#82-still-prediction-excitation-error-cutoff)
 - **Rotation prediction** (`BraggPredictionRotGPU.cu`) - the reflections crossing the Ewald sphere
   within an image's rotation range, with their rotation angle and partiality; they are ordered, and
@@ -206,6 +208,119 @@ structure factors above; the likelihood scoring runs on the host. The search is
 [§14.10](CPU_DATA_ANALYSIS_DECISIONS.md#1410-molecular-replacement-placing-a-model-the-rigid-body-cannot), its keys and decision rules in
 [Molecular replacement](RUGNUX_REPORT.md#molecular-replacement).
 
+## Refinement
+
+The restrained refinement of a placed model ([§15](CPU_DATA_ANALYSIS_REFINEMENT.md)) evaluates its target and
+its gradients on the card: one engine (`RefinementGPU.cu`, with the host half in `RefinementGPU.cpp`) keeps the
+reflections, the grids, the symmetry and the restraints resident, and per evaluation takes only the atoms'
+positions up and one value and one gradient per atom back. Everything that depends on the cell, the group and
+the reflections - the grids, the operators, the adjoint's lists - is worked out once on the host with gemmi when
+the engine is made. The GPU and CPU engines compute the same target to rounding (float distances and densities,
+cuFFT for FFTW, summation order); the GPU's result is the same from run to run, as no sum of a result is a
+floating-point atomic: every per-point, per-reflection and per-atom sum is a gather in a fixed order, and every
+total a `cub::DeviceReduce` tree, whose order for a given size is fixed.
+
+One evaluation - target and gradient of every atom - is a density gather, a forward and an inverse transform
+and a gradient gather, whatever the number of atoms
+([§15.2](CPU_DATA_ANALYSIS_REFINEMENT.md#152-the-x-ray-target)):
+
+- **Density** (`ModelDensityGPU.cu`, the gather of model validation) - the atoms' blurred density of one copy
+  of the model on the structure-factor grid. The grid is cut into bricks of 8^3 points; each atom's box is
+  counted against the bricks it touches, the counts scanned (`cub::DeviceScan`) into a list of (brick, atom)
+  pairs, and the list sorted stably by brick (`cub::DeviceRadixSort`), so each brick holds its atoms in model
+  order. One block per brick then stages its atoms in shared memory (128 at a time) and every point adds, in
+  model order, each atom whose radius reaches it - no atomics, the grid the CPU walk's to the bit for the same
+  atoms. The pair count is the one wait inside an evaluation (it sizes the sort). The atoms' density
+  coefficients are uploaded again only where some atom's B changed; the positions go up through a pinned buffer.
+- **Forward transform** - cuFFT r2c of the grid into its half-u spectrum, the plans made once per engine with an
+  explicit work area.
+- **Composition and target** (`compose_target_kernel`, one thread per reflection) - F_calc of the reflection
+  composed from the spectrum over the group's operators (each operator's phase exp(2 pi i h.t) computed exactly
+  for the translation's fraction, sums in double), times the centring count and the unblur; then, on the working
+  reflections, F_model = k (F_calc + F_mask) with the macro-cycle's scale, mask and D, Σ held on the card, the
+  likelihood term -ln L of the reflection, and the coefficient conj(dT/dF) the derivative map is made of.
+  The terms are summed by `cub::DeviceReduce`.
+- **Adjoint of the composition** (`scatter_kernel`, one thread per spectrum point) - the coefficients taken back
+  onto the half-u spectrum as a gather, not a scatter: a CSR list made on the host at setup gives, for every
+  spectrum point a (reflection, operator) term lands on, the terms in a fixed order, conjugated where they land
+  as a Friedel mate and doubled onto the planes k_u = 0 and k_u = nu/2, which hold their own mates. Each point
+  sums its terms in double and is written once.
+- **Inverse transform** - cuFFT c2r of that spectrum into the derivative map, on the density's grid.
+- **Atom gradient** (`atom_gradient_kernel`, one warp per atom) - each atom's dT/dx, dy, dz and dB: the derivative
+  map summed against the derivatives of the atom's five-Gaussian density over the same box and radius as the
+  gather, the warp's 32 lanes walking the box's points in steps of 32 without an integer division (the box index
+  stepped on, the wrap into the grid by one subtraction), and the lanes' sums added in a fixed shuffle tree.
+  The riding hydrogens' derivatives are passed to their parents on the host.
+
+Beside the X-ray target, and in the same submission:
+
+- **Restraints** (`restraint_kernel`, one thread per restraint) - bonds, angles, torsions, chirals, planes (up to
+  32 atoms), repulsions (with their symmetry image), metal links and B similarity
+  ([§15.5](CPU_DATA_ANALYSIS_REFINEMENT.md#155-geometry-metal-and-b-restraints)), each restraint writing its
+  energy and its gradient into one slot per atom it involves; the energies summed by `cub::DeviceReduce`.
+- **Slot gather** (`slot_gather_kernel`, one thread per atom) - each atom's restraint gradient, its slots summed
+  in the order a CSR list gives. Two restraint sets are held (positions and B), set again when the repulsions
+  and contacts are rebuilt.
+
+`EvaluateWithRestraints` queues the X-ray evaluation, writes the restraints' positions into a pinned buffer
+while the card works on it, queues the restraints behind it and waits once; the target, the restraint energy
+and both gradients come back into pinned buffers. The minimiser (L-BFGS) stays on the host.
+
+Once per macro-cycle ([§15.3](CPU_DATA_ANALYSIS_REFINEMENT.md#153-scale-bulk-solvent-and-the-likelihood-parameters)):
+
+- **F_calc and F_mask** - the forward path above without the target, and the bulk-solvent mask drawn on the card
+  (`ModelMaskGPU.cu`) on **its own fine grid** (d_min/3 or 0.4 A, whichever is finer, at most 2^26 points),
+  with a grid, spectrum and cuFFT plan of its own where that grid is not the density's: one block per
+  (atom, symmetry image) sets the points within the atom's REFMAC radius, the islands are removed by a
+  union-find labelling (integer `atomicCAS`, rooted at each component's lowest index, so the partition does not
+  depend on the order of the unions), and the shrink is two passes - the edge points marked, then each edge
+  point's stencil written as solvent. Every write is an idempotent store, so the mask is the same bit for bit
+  from run to run; F_mask is read off at the reflections (`fmask_kernel`).
+- **Robust scale fit** (`ModelScaleGPU.cu`) - the k_sol/B_sol grid of fits, each fit's overall scale and
+  anisotropic B by gemmi's Levenberg-Marquardt, many fits per launch: the sums over the reflections (the WSSR,
+  J^T J and J^T r, in double) by a fixed launch shape of 48 blocks of 128 threads, a fixed shuffle tree within
+  each warp and the blocks summed in order; the damping and the 7x7 solve stay on the host. The fine pass is
+  robust: four rounds of residuals, weights 1/sqrt(1 + (r/c)^2) and the fit again, with c the median residual
+  of the first round found **on the card** by a radix select (`residual_median`: the residuals are not negative,
+  so their order is that of their bits, found a byte at a time in four passes of integer counts - the element
+  `std::nth_element` puts at n/2). After a trial's first macro-cycle the fit starts from the fine pass around the
+  previous winner, skipping the coarse one. Its stream has the card's highest priority, so that the fit's short,
+  host-waited launches do not queue behind the long kernels of the other trials on the card.
+- **D and Σ**, the likelihood's parameters, are fitted on the host (bin by bin, on all of the run's threads).
+
+**Trials, cards and waits.** The weight trials of one set
+([§15.7](CPU_DATA_ANALYSIS_REFINEMENT.md#157-the-weights-decided-by-trial)) run side by side, each on a slot of
+its own - a copy of the model, its topology, a refinement engine and a scale-fit engine - as many slots as the
+largest set of trials has (six at the defaults), the ones beside the main one built on
+their own threads while the placement runs. The slots' engines go on the cards in
+turn from the main one's, each card taking engines while they fit its budget; on a machine with several cards
+the trials are spread over all of them. A slot whose engine cannot be made is left out rather than moved to the
+CPU, and the outcome does not depend on how many trials run at once or on which card. The engine waits on its
+stream through an event made with `cudaEventBlockingSync` (`StreamWaiter`), so a waiting trial sleeps instead of
+spinning a core - with six engines on one card the spinning took half of the refinement's CPU time.
+
+**Memory.** `RefinementGPUEngine::DeviceBytes` counts the engine's reserve before anything is allocated: per atom
+(positions, boxes, densities, mask atoms, gradients), the grid, its spectrum and cuFFT's work area, the mask's
+own grid and spectrum, per reflection (indices, scales, F_o, the row model, F_calc, F_mask, coefficients,
+terms), the adjoint's lists, the gather's pair reserve - sized for every atom at the largest B a refinement may
+reach with the widest blur - and the restraints at about 30 records and 60 slots per atom. The engine goes on the
+card when that total, plus what is already resident there (a merge still at work), is within 80% of the card's
+total memory; the trial slots are counted against the same budget, card by card.
+
+**Falling back.** Where the GPU cannot take the case (an atom's box wider than the cell, more than 192 mask
+operators), where the engine is over the budget, or where CUDA fails while the
+engine is made, the refinement runs on the CPU engine, with a line in the log (`Refinement: on the CPU - ...`).
+`--no-gpu` and a build without CUDA take the CPU engine as well. The refinement has no Metal engine: on macOS it
+runs on the CPU.
+
+**Indicative timings** (RTX 5080, `-N 8`, the refinement alone): a 5,000-atom model (half of it riding
+hydrogens) at 1.65 A with 31k reflections refines in about 1.3 s; a 4,500-atom model at 1.09 A with 92k
+reflections in about 2 s; a 50,000-atom model at 3.6 A with 51k reflections in about 7 s, of which the kernels
+take 5 s - there the density gather and the atom gradient (about 0.9 and 0.8 ms per evaluation, over a thousand
+evaluations) are half or more of the kernel time, the scale fit 10-25% (more at high resolution) and the fine
+mask 15-18% at low resolution. Inside a full `rugnux --model` run of a 5,000-atom model the refinement took
+1.5 s of 8 s. The CPU engine (`-N 8`) takes about a minute and a half for a set the card refines in about 2 s.
+
 ## Apple GPUs (Metal)
 
 A macOS build has no CUDA, and three engines run on the Apple GPU instead (none under
diff --git a/docs/HDF5.md b/docs/HDF5.md
index fa82e587b..e6908eab6 100644
--- a/docs/HDF5.md
+++ b/docs/HDF5.md
@@ -285,6 +285,7 @@ DIALS/dxtbx reads it (one panel per module).
 | `temperature` | NXmx | K |
 | `transformations/` (NXtransformations) | NXmx | the sample chain, written in mounting order; hard-linked as `/entry/sample/goniometer` |
 | `unit_cell` | base | `[a, b, c, α, β, γ]` |
+| `unit_cell_esd` | | e.s.d.s of `unit_cell`, in its order `[σa, σb, σc, σα, σβ, σγ]` (Angstrom, degrees; zero for an angle the space group fixes); rotation runs analysed by rugnux, offline or in the broker |
 | `space_group_number` | base | International Tables number |
 | `space_group` | base | extended Hermann-Mauguin name, e.g. `P 43 21 2`, `R 3:H` — this is the field that carries the **setting**, and the one the reader takes the group from; the number alone always reads back as the reference setting |
 | `ub_matrix` | base | `[1, 3, 3]`, Angstrom⁻¹ |
@@ -394,6 +395,9 @@ variants.
 | `iceRingScoreMean` | ratio | mean `iceRingScore` over the run — the single "how icy was this dataset" number (1 = no ice) |
 | `indexedLatticeCount` | | per-image lattice count summary (master). *Note: data files use `indexingLatticeCount`; readers accept either.* |
 | `reindexMatrix` | | change of basis from the setting the per-image data are in to the setting of `/entry/sample/unit_cell` (`[9]`, `int32`, flattened 3×3, row major) — see below |
+| `stillsRockingWidthFormula` | 1/Å, rad, relative | stills: the run's rocking width σ² = γ₀² + (γₑ d\*)² + (σ_bw λ d\*²/2)², as `[γ₀, γₑ, σ_bw]`; offline (Rugnux) only |
+| `stillsRadialScale` | | stills: the scale of the reciprocal lattice the rocking curve is centred on |
+| `stillsRockingWidthTableDstar`, `stillsRockingWidthTable` | 1/Å | stills: the rocking width σ measured against d\*, which the partialities use (held beyond the first and last entry; the formula above is what the prediction window uses); `--mode scale` merges with formula and table instead of measuring another |
 
 **Reindex matrix.** The per-image `h`, `k`, `l` and `latticeIndexed` are written as each image is
 processed, in the setting that image was *indexed* in. The space group is only settled afterwards, by
diff --git a/docs/JFJOCH_BROKER.md b/docs/JFJOCH_BROKER.md
index b4350bba0..9e48cedb8 100644
--- a/docs/JFJOCH_BROKER.md
+++ b/docs/JFJOCH_BROKER.md
@@ -182,9 +182,11 @@ collection - one slot per image. Where it holds fewer, the collection is only fo
 as with the mode off; the live status reports it as skipped and the collection's statistics carry a
 warning saying how many images the buffer holds against how many the collection has.
 
-The results - the merged data, the map coefficients and, with a model, the placed model - travel to
-the writer in the end message, which writes them beside the master file as `<file_prefix>.mtz`,
-`<file_prefix>_maps.mtz`, `<file_prefix>_model.cif` and `<file_prefix>_model.pdb`. An end message
+The results - the merged data, the map coefficients and, with a model, the placed model and its
+refinement - travel to the writer in the end message, which writes them beside the master file as
+`<file_prefix>.mtz`, `<file_prefix>_maps.mtz`, `<file_prefix>_model.cif` and `<file_prefix>_model.pdb`,
+and `<file_prefix>_refined_model.cif` (and `.pdb`), `<file_prefix>_refined_maps.mtz` and
+`<file_prefix>_blobs.json`, as rugnux names them. An end message
 that would be too large for the pushers' buffer (256 MiB) goes without them, with an error in the log
 and a warning in the live status; the collection itself is not affected.
 
@@ -207,6 +209,14 @@ cut among its images merges those it has read, only the placed model is left out
 any other pass cut short gives way to the last one that ran to its end. The end message goes out at
 once with that, and the live status records the cut (`deadline` or `cancel`) and when.
 
+Where the uploaded model is placed, it is refined as `rugnux` refines it, after every decision of the run
+and before the end message - seconds on a GPU, minutes on a broker without one. A cut before it starts leaves it out, as the model; a
+cut while it runs cuts it short with what its finished weight trials found (`model.refinement.cancelled`). The refined model and its maps stay with the broker: the
+writer writes the placed model, as without refinement. `GET /rugnux/status` gives the refined R-work and
+R-free, the bond and angle rmsd, the time it took and the unexplained blobs of the refined difference map
+(`model.refinement`), and `/rugnux/model.cif` and `/rugnux/map.ccp4` serve the refined model and its maps
+(`stage=placed` for the model as placed; the anomalous map is always on the placed model's phases).
+
 `GET /rugnux/status` reports the live run of the last collection, kept until the next one starts: its
 state, the images received, the step it is on and how far into it, the steps so far with what each
 found, and once it is over the verdict, the summary, warnings and the time from the last image to
diff --git a/docs/JFJOCH_VIEWER.md b/docs/JFJOCH_VIEWER.md
index 0b6f342cb..03824237b 100644
--- a/docs/JFJOCH_VIEWER.md
+++ b/docs/JFJOCH_VIEWER.md
@@ -6,7 +6,7 @@ integration, per-image statistics), and can follow a live data collection by syn
 running [`jfjoch_broker`](JFJOCH_BROKER.md) over its HTTP interface.
 
 It is a standalone Qt 6 application, distributed pre-built for **Linux, Windows and macOS** on the
-Gitea release page, and for Linux also in the Jungfraujoch RPM/APT repositories — see
+[download page](VIEWER_DOWNLOAD.md), and for Linux also in the Jungfraujoch RPM/APT repositories — see
 [Release contents](RELEASE_CONTENTS.md) for what each package contains and what it requires, and
 [Deployment](DEPLOYMENT.md) for how to install it. The macOS build needs **macOS 13 (Ventura) or
 newer on an Apple Silicon Mac** (M1 and newer; Intel Macs are not supported) and has no CUDA — see
@@ -18,7 +18,7 @@ newer on an Apple Silicon Mac** (M1 and newer; Intel Macs are not supported) and
 | --- | --- | --- | --- |
 | [`jfjoch_broker`](JFJOCH_BROKER.md) | Online, real-time streaming analysis on FPGA + GPU | HTTP/REST + ZeroMQ | Live results and statistics, images streamed to [`jfjoch_writer`](JFJOCH_WRITER.md) |
 | **`jfjoch_viewer`** | **Interactive, on-screen exploration** | **Qt desktop application** | **On screen; a processing job can write the same files as `rugnux`** |
-| [`rugnux`](RUGNUX.md) | Offline batch processing of a stored dataset | Command-line interface | `_process.h5`, and `.mtz`/`.cif`/`.hkl` when merging |
+| [`rugnux`](RUGNUX.md) | Offline batch processing of a stored dataset | Command-line interface | `.mtz`/`.cif`/`.hkl` and the results report when merging (the default); `_process.h5` with `--no-merge` or `--write-process-h5` |
 
 ## Functionality
 
diff --git a/docs/JUNGFRAUJOCH.md b/docs/JUNGFRAUJOCH.md
new file mode 100644
index 000000000..6b4a8bb6a
--- /dev/null
+++ b/docs/JUNGFRAUJOCH.md
@@ -0,0 +1,51 @@
+# Jungfraujoch: data acquisition
+
+Jungfraujoch is the data-acquisition and real-time analysis system for the PSI **JUNGFRAU** and
+**EIGER** detectors, and, through their detector control unit, for DECTRIS detectors. It takes
+the detector's frames at the full frame rate, builds and analyses the images on the fly, and
+streams them out for writing, with a web interface and a REST API for the beamline. It is the streaming half of the software; [Rugnux](RUGNUX.md) is the
+processing half (see [Naming](NAMING.md)).
+
+## What runs where
+
+| Program | Role |
+| --- | --- |
+| [`jfjoch_broker`](JFJOCH_BROKER.md) | The central service: configures the detector and the FPGA cards, builds images from their output, runs the real-time analysis (masking, summation, spot finding, azimuthal and ROI integration, indexing on the GPU, compression), streams the images over ZeroMQ or TCP, and serves the HTTP/REST interface and the [web frontend](WEB_FRONTEND.md). |
+| [`jfjoch_writer`](JFJOCH_WRITER.md) | Receives the image stream and writes NeXus/NXmx HDF5 files; usually on a separate machine with the file system. |
+| [FPGA smartNIC](FPGA.md) | AMD Alveo U55C cards with the Jungfraujoch firmware, one per few JUNGFRAU modules; they receive the detector's UDP stream and run the first stages of the analysis in hardware. The DECTRIS path has no FPGA: the stream from the detector control unit goes through the same analysis on the CPU and GPU. |
+| [Web frontend](WEB_FRONTEND.md) | The browser interface served by the broker: detector state, live preview, plots of the on-line quality metrics, and the controls, including [Rugnux live mode](JFJOCH_BROKER.md#rugnux-live-mode), which processes a rotation sweep while it is being collected. |
+| [Python client](PYTHON_CLIENT.md) | `pip install jfjoch-client`: the REST API as a generated Python package, for beamline control software. |
+| [Viewer](JFJOCH_VIEWER.md) | Optional: the desktop viewer follows a live collection from the broker over HTTP. |
+
+The detectors, firmware and `slsDetectorPackage` versions the system is built against are in
+[Supported detectors](DETECTORS.md); the server, FPGA, GPU and switch it needs are in
+[Hardware requirements](HARDWARE.md).
+
+## Installing
+
+Jungfraujoch runs on Linux servers: RHEL / Rocky 8 and 9 are the supported platforms, Ubuntu
+22.04 / 24.04 experimental ([Software requirements](SOFTWARE.md)).
+
+- **Packages.** The [package repositories](REPOSITORIES.md) carry `jfjoch` (broker, frontend,
+  FPGA and detector tools), `jfjoch-driver-dkms` (the PCIe kernel module), `jfjoch-writer` and
+  `jfjoch-viewer`, in CUDA and non-CUDA variants and per `slsDetectorPackage` version. The writer's
+  `.rpm` / `.deb` are also attached to every
+  [release](https://gitea.psi.ch/mx/jungfraujoch/releases), for a file-writing machine without
+  the rest.
+- **FPGA firmware.** The `.mcs` images are attached to every release; the card is flashed once
+  with `xbflash.qspi` and keeps its image across software upgrades.
+- **From source.** `cmake` and `make` from the repository, with every dependency fetched during
+  the first configure; the frontend is built separately with `make frontend`.
+
+[Deployment](DEPLOYMENT.md) is the step-by-step guide: packages or source, flashing the cards,
+the kernel driver, the network switch, the broker's configuration file and running the services.
+[Release contents](RELEASE_CONTENTS.md) says what each package contains and what it needs on the
+machine.
+
+## Reading the output
+
+The broker streams images as CBOR messages compatible with the DECTRIS Stream2 protocol
+([Data streams](IMAGE_STREAM.md), [CBOR messages](CBOR.md)); the writer turns them into NXmx HDF5
+([HDF5 / NeXus data format](HDF5.md)). Which downstream programs read which of the three HDF5
+layouts, and the XDS plugin, are in [Integration with MX software](SOFTWARE_INTEGRATION.md). The
+command-line tools shipped beside the services are listed in [Tools](TOOLS.md).
diff --git a/docs/NAMING.md b/docs/NAMING.md
index fa6a7a83a..ce6cce2ed 100644
--- a/docs/NAMING.md
+++ b/docs/NAMING.md
@@ -7,7 +7,7 @@ steep mountain as efficiently as possible — usually by train. Throughput, in o
 | Part | Name | What it does |
 | --- | --- | --- |
 | Streaming / acquisition | **Jungfraujoch** | Receives detector data at high data rates, runs the FPGA/GPU pipeline, and streams images out for writing. |
-| Data processing | **Rugnux** | Offline crystallographic analysis of a stored dataset — indexing, integration, scaling and merging (the [`rugnux`](RUGNUX.md) tool). |
+| Data processing | **Rugnux** | Crystallographic analysis of a stored dataset, or of a collection while it is written — indexing, integration, scaling and merging, and refinement of a given model (the [`rugnux`](RUGNUX.md) tool). |
 
 ## Jungfraujoch
 
diff --git a/docs/RUGNUX.md b/docs/RUGNUX.md
index 807579b96..07aea9754 100644
--- a/docs/RUGNUX.md
+++ b/docs/RUGNUX.md
@@ -1,13 +1,15 @@
 # Rugnux
 
 `rugnux` is the **offline** crystallographic data-analysis tool of Jungfraujoch — the
-data-processing half of the system (see [Naming](NAMING.md) for where the name comes from).
-It takes a stored dataset, runs the full analysis pipeline — spot finding, indexing, geometry
-refinement, Bragg integration, scaling and merging — and writes the merged reflections
-(`.mtz`/`.cif`/`.hkl`), the unmerged MTZ and the results report; the per-image `_process.h5` is
-written only on request (`--write-process-h5`), or as the only output with `--no-merge`. A rotation run
-that finds no lattice still spot-finds every image and writes their per-image analysis there, then exits
-as failed.
+data-processing half of the system (see [Naming](NAMING.md) for where the name comes from). It takes
+a stored dataset from the diffraction images to merged data — spot finding, indexing, geometry
+refinement, Bragg integration, scaling and merging, written as `.mtz`/`.cif`/`.hkl` with the
+unmerged MTZ and the results report — and, with an atomic model, on to a refined structure and maps:
+the model is placed against the merge, refined, and written with its map coefficients and the
+difference-density blobs it leaves unexplained. The per-image `_process.h5` is written only on
+request (`--write-process-h5`), or as the only output with `--no-merge`. A rotation run that finds
+no lattice still spot-finds every image and writes their per-image analysis there, then exits as
+failed.
 
 It runs the *same* analysis code as the online and interactive tools, driven from the command line
 over files.
@@ -47,39 +49,78 @@ is ignored.
 
 ## Quick start
 
-Four commands cover most of what people ask of `rugnux`. Each takes the **master** file of the
-dataset — one written by Jungfraujoch, a DECTRIS EIGER master, or an NXmx master written by another
-facility's toolchain; a PILATUS miniCBF, marCCD or SMV sweep works too (see [What Rugnux reads](RUGNUX_FORMATS.md))
-— and names its output files from `-o`:
+Give `rugnux` the images, and nothing else. A dataset carrying a **goniometer axis** that turns is
+processed as a rotation sweep, one without (or with an axis that stands still) as **serial stills**;
+indexing, the space group, the cell, the resolution limit and the error model are all decided from
+the data, and scaling and merging run by default. `-o` names the output files (default `output`).
+
+**We expect no need to tune anything else.** The defaults are meant to be the answer, and a run that
+needed a flag to do well is one we want to hear about. The other options exist for unusual cases and
+for diagnosis; they are listed under [Command-line options](RUGNUX_ADVANCED.md#command-line-options).
+
+### Rotation data
 
 ```
-# 1. everything from the data - index, integrate, scale and merge with the defaults
-rugnux -o myrun dataset_master.h5
-
-# 2. with a reference dataset of the same crystal form: it fixes the space group and the cell,
-#    resolves the indexing ambiguity, and hands over its R-free set
-rugnux -o myrun -z reference.mtz dataset_master.h5
-
-# 3. with a known structure: R-work / R-free and sigma_A-weighted 2mFo-DFc / mFo-DFc maps
-#    (a predicted model, or one the rigid body cannot place, goes to molecular replacement)
-rugnux -o myrun --model model.pdb dataset_master.h5
-
-# 4. with the space group and the cell pinned (-S takes either spelling: P43212 or 96)
-rugnux -o myrun -S P43212 -C 79,79,38,90,90,90 dataset_master.h5
+rugnux -o myrun dataset_master.h5          # NXmx / EIGER / Jungfraujoch master file
+rugnux -o myrun sweep_00001.cbf            # a CBF, marCCD or SMV sweep: name its first frame
 ```
 
-Parallelism needs no asking for: a run already uses the machine's threads. `-N` is there to *limit*
-that, or to lift the per-image loop's default ceiling of 16 workers per GPU.
+### Serial stills
 
-Nothing more is needed to pick the workflow: a dataset carrying a **goniometer axis** that turns is
-processed as a rotation sweep, one without (or with an axis that stands still) as **independent
-stills**, and scaling and merging run by default
-in both. A rotation run that merges — the default — leaves eight files next to each other:
+```
+rugnux -o serial *_master.h5               # several NXmx masters of one setup, read as one run
+rugnux -o serial run*.h5                   # all the files of one dataset (SACLA); *.cxi, *.xtc alike
+```
+
+Inputs are always files, never a directory; a shell glob hands them over sorted by name, and they are
+read in that order and merged together. Without a cell the stills are indexed de novo.
+
+### Serial stills with a known cell, space group and a CrystFEL geometry file
+
+```
+rugnux -o serial -C 79,79,38,90,90,90 -S P43212 --crystfel-geometry detector.geom run*.h5
+```
+
+`-C` is the cell (`a,b,c,alpha,beta,gamma`), `-S` the space group as a symbol (`P43212`) or a number
+(`96`). With `-S` the run puts every crystal on one indexing where the space group admits two, from
+the data alone. `--crystfel-geometry` places the panels (and takes the masks it names) for HDF5/CXI
+input that does not place them itself. The wavelength and the detector distance come from the data
+files or the geometry file; only where neither states them add `--wavelength <A>` and
+`--detector-distance <mm>` (the distance is then held, not refined — without it a run with `-C`
+searches and refines it).
+
+### With a model
+
+```
+rugnux -o myrun dataset_master.h5 model.cif     # model and images in any order;
+rugnux -o myrun --model model.pdb dataset_master.h5   # or with --model
+```
+
+A model is told from the images by its contents (PDB, or mmCIF with atoms), gzipped or not. After
+merging it is **placed** — as a rigid body, or by molecular replacement where that does not place it or
+the model is a prediction (AlphaFold, ModelCIF) — then **refined** against the merge (restrained,
+maximum likelihood; seconds on a GPU, typically minutes on the CPU; `--no-refine` skips it), and the
+run writes the maps (σ<sub>A</sub>-weighted 2mFo−DFc / mFo−DFc), the placed and refined model, and
+the blobs of difference density the model does not explain. R-work / R-free are in the report.
+
+The model **does not change processing decisions**: the merge, its space group and resolution are
+the ones the data give without it (it only names the hand of an enantiomorphic pair, see below).
+The one exception is serial stills with `-C` and `-S` in a space
+group that admits two indexings: there the model picks which of them the crystals are put on, so the
+merge comes out in the model's indexing. Without a model the data resolve the ambiguity themselves,
+consistently but in an arbitrary one of the two. A reference reflection file (`-z reference.mtz`,
+also accepted as a positional input) does the same, and steers the processing from the start (see
+[Models and reference data](RUGNUX_MODEL_AND_REFERENCE.md)).
+
+### What comes out
+
+A rotation run that merges — the default — leaves these files next to each other:
 
 ```
 myrun.mtz            merged intensities + French-Wilson amplitudes, for CCP4 / phenix
 myrun.cif            the same, as mmCIF - the self-describing format, and what to deposit
 myrun.hkl            the scaled observations unmerged, as SHELX HKLF 4 - for SHELXL, SHELXC / ANODE
+myrun.ins            the SHELX instructions to go with it: CELL, ZERR (the cell's e.s.d.s), LATT, SYMM
 myrun_unmerged.mtz   every observation before scaling, for pointless / aimless / careless -
                      the largest file of the run (--no-export-unmerged skips it)
 myrun_report.txt     what the run determined: cell, space group, statistics, warnings
@@ -88,8 +129,22 @@ myrun_detector.jpg   the detector with the pixel mask and the beam-stop shadow d
 myrun_log.txt        the full timestamped log of the run (debug level)
 ```
 
-The two MTZ extras are most of the bytes a run writes — worth knowing when sizing a scratch
-directory for a campaign, and both have off switches.
+With a model, beside them:
+
+```
+myrun_maps.mtz            map coefficients on the placed model (Coot and PyMOL open it as maps)
+myrun_model.cif / .pdb    the model as placed, in the cell and space group of myrun.mtz
+myrun_refined_model.cif   the refined model (and .pdb)
+myrun_refined_maps.mtz    map coefficients on the refined model
+myrun_blobs.json          the unexplained difference-density blobs
+```
+
+A stills run writes the same merged files (its `.hkl` holds the merged reflections) and, on a
+detector of several modules, `serial_modules.h5` with where each module was placed.
+[Output files](RUGNUX_TUTORIAL.md#output-files) lists every file a run can write.
+
+Parallelism needs no asking for: a run already uses the machine's threads. `-N` is there to *limit*
+that, or to lift the per-image loop's default ceiling of 16 workers per GPU.
 
 Read `myrun_report.txt` first: it says which space group was chosen and on what evidence, how far
 the data go, and anything that needs attention.
@@ -145,9 +200,9 @@ A few things worth knowing before reaching for more flags:
   `--resolution-cutoff off` keeps the full measured range, `--scaling-high-resolution` fixes the
   limit by hand. A Rugnux file reaching less far than another program's on the same data is usually
   this default at work, not lost data.
-- **Rotation data are best left de novo.** Pinning the cell and space group (recipe 4) is the
+- **Rotation data are best left de novo.** Pinning the cell and space group (`-C`, `-S`) is the
   normal thing to do for **serial stills**, where the `ffbidx` indexer needs a cell; on a rotation
-  sweep it tends to *degrade* low-symmetry cases, so prefer recipe 1 and let the run determine both
+  sweep it tends to *degrade* low-symmetry cases, so give the images alone and let the run determine both
   (see [Rotation data](RUGNUX_TUTORIAL.md#rotation-data)). `-S` takes a Hermann-Mauguin symbol (`P43212`) or a
   space-group number (`96`), whichever is to hand.
 - **Anomalous data are there without `-A`.** A rotation merge always keeps the Bijvoet split: a
@@ -169,8 +224,9 @@ A few things worth knowing before reaching for more flags:
 - **`-z` and `--model` overlap but are not the same.** A reference MTZ steers the processing from
   the start; a model scores the merge and settles the frame it is written in — where the data
   accept it; a model they reject changes nothing. Either resolves an
-  [indexing ambiguity](RUGNUX_ADVANCED.md#the-indexing-ambiguity), which on serial data decides whether the merged
-  intensities are usable at all.
+  [indexing ambiguity](RUGNUX_ADVANCED.md#the-indexing-ambiguity) in its own indexing. On serial data the
+  ambiguity decides whether the merged intensities are usable at all; there the space group (`-S`) alone
+  already lets the run make the crystals consistent from the data.
 - **Small molecules need no flag either.** Short axes, spots wider than the integration disk and
   glide-plane space groups are handled by the default run, and `myrun.hkl` goes straight to SHELXT /
   SHELXL ([Small-molecule data](RUGNUX_TUTORIAL.md#small-molecule-data)).
@@ -181,6 +237,14 @@ A few things worth knowing before reaching for more flags:
   merging. [Installing Rugnux ▸ Memory](RUGNUX_INSTALL.md#memory) has the table and the two
   flags that lower it. A very large cell needs far more, and a CPU-only build most of all — tens of
   GB of host RAM ([Very large unit cells](RUGNUX_INSTALL.md#very-large-unit-cells)).
+- **When a run fails** it exits non-zero and says why on the terminal; `VERDICT=` and the `WARNING:`
+  lines of the report say what needs attention on a run that finished
+  ([The results report](RUGNUX_REPORT.md#the-summary-and-what-the-run-decided)). A rotation run that indexes
+  nothing most often has a wrong header: the beam centre is measured on every run, but the distance
+  and the wavelength are indexed at the values stated — `--detector-distance` and `--wavelength` override them
+  (`--beam-x`/`--beam-y` the centre); serial stills that index poorly want the cell (`-C`). A run that ends
+  with `Killed` ran out of memory ([When host memory runs out](RUGNUX_INSTALL.md#when-host-memory-runs-out)).
+  With any question about a run, send `myrun_report.txt` and `myrun_log.txt`.
 - Everything else is in [Running Rugnux](RUGNUX_TUTORIAL.md#running-rugnux) and the full
   [Command-line options](RUGNUX_ADVANCED.md#command-line-options).
 
@@ -189,8 +253,10 @@ A few things worth knowing before reaching for more flags:
 
 One page per job, so the answer needed is near the top of a short page:
 
-- [What Rugnux does](RUGNUX_OVERVIEW.md) — the pipeline from images to merged reflections,
+- [What Rugnux does](RUGNUX_OVERVIEW.md) — the pipeline from images to merged data and, with a model, a refined structure,
   in order. Read this one first.
+- [Download Rugnux](RUGNUX_DOWNLOAD.md) — the archive for Linux, macOS and Windows, and the
+  three commands that run it.
 - [Installing Rugnux](RUGNUX_INSTALL.md) — packages, the release archive, GPU drivers, building
   from source, hardware.
 - [What Rugnux reads](RUGNUX_FORMATS.md) — will it open your data: NXmx / EIGER masters, PILATUS
@@ -219,7 +285,7 @@ One page per job, so the answer needed is near the top of a short page:
 | --- | --- | --- | --- |
 | [`jfjoch_broker`](JFJOCH_BROKER.md) | Online, real-time streaming analysis on FPGA + GPU | HTTP/REST + ZeroMQ | Live results and statistics, images streamed to [`jfjoch_writer`](JFJOCH_WRITER.md) |
 | [`jfjoch_viewer`](JFJOCH_VIEWER.md) | Interactive, on-screen exploration | Qt desktop application | On screen; a processing job can write the same files as `rugnux` |
-| **`rugnux`** | **Offline batch processing of a stored dataset** | **Command-line interface** | **`_process.h5`, and `.mtz`/`.cif`/`.hkl` when merging** |
+| **`rugnux`** | **Offline batch processing of a stored dataset** | **Command-line interface** | **`.mtz`/`.cif`/`.hkl` and the report; `_process.h5` with `--no-merge` or `--write-process-h5`** |
 
 Use `rugnux` to re-analyse data after acquisition, to experiment with processing
 parameters, or to produce merged intensities for downstream structure solution.
diff --git a/docs/RUGNUX_ADVANCED.md b/docs/RUGNUX_ADVANCED.md
index 70c0c85a3..0981c315b 100644
--- a/docs/RUGNUX_ADVANCED.md
+++ b/docs/RUGNUX_ADVANCED.md
@@ -18,7 +18,7 @@ structure-factor file (`-z 1abc-sf.cif`, SF-mmCIF), gzipped or not; the format i
 file's content. From an mmCIF the first merged reflection block with a usable column is read (the log
 names it), its columns under the MTZ labels `gemmi cif2mtz` gives them (`IMEAN`, `FP`, `FC`, …), and
 its R-free set from `_refln.status` (`f` free, `o` working), or from `_refln.pdbx_r_free_flag` where
-the status marks no test set. It is read once, before processing starts, and used for four things:
+the status marks no test set. It is read once, before processing starts, and used for five things:
 
 - **It fixes the space group and the unit cell** the run works in, unless `-S` / `-C` override them.
   The cell is a *soft* reference: indexing may still drift within tolerance, so a small mismatch
@@ -31,7 +31,7 @@ the status marks no test set. It is read once, before processing starts, and use
   already on the reference's axes), `REFERENCE_CC=` and `REFERENCE_MATCHED_FRACTION=` how well the
   result matches.
 - **It resolves the indexing ambiguity** (below) — the one thing the data cannot settle for
-  themselves.
+  themselves: which of the equivalent indexings is the reference's own.
 - **It hands over its R-free test set**, where the file carries one, so every dataset of a campaign
   is scored on the same free reflections - in the reference's frame, and only where the merge
   matches the reference (CC at least 0.5 over at least half of the merged reflections in its
@@ -46,8 +46,9 @@ against a foreign dataset injects that dataset's systematics — so `-z` never p
 errors into the intensities. `--reference-column` picks the column to read where the automatic
 choice (`F-model`, else `IMEAN`/`I`, else `FP`/`FOBS`/`F`) is not the right one.
 
-For the second of those four jobs — and only that one — an atomic model does as well: `--model`
-computes the intensities it needs from the structure. Where a reference dataset exists, prefer it;
+For the indexing ambiguity an atomic model does as well: `--model` computes the intensities it
+needs from the structure (a model that fits also sets the hand label and the setting, see
+[Validating against a model](#validating-against-a-model-rugnux---model)). Where a reference dataset exists, prefer it;
 where only a model does, it resolves the ambiguity just the same.
 
 ### The indexing ambiguity
@@ -59,8 +60,8 @@ cell is metrically more symmetric than the Laue class by accident (*pseudo-meroh
 obliquity). The alternatives are related by the crystal's **twin laws** — reindexing operators such
 as `k,h,-l`.
 
-Nothing in the data breaks the tie: the merge is equally self-consistent either way, so which
-solution comes out is arbitrary. What that costs depends on the workflow:
+Nothing in the data says which solution is the *true* one: the merge is equally self-consistent
+either way, so which comes out is arbitrary. What that costs depends on the workflow:
 
 - **Rotation.** The whole sweep is one lattice, so the whole dataset lands in one indexing, picked
   at random. The merge itself is sound; it may simply be the *other* solution from an earlier
@@ -68,36 +69,49 @@ solution comes out is arbitrary. What that costs depends on the workflow:
   same model.
 - **Serial stills.** Every crystal is indexed independently, so a run mixes both indexings into one
   merge. That is not a labelling matter — reflections that are not symmetry mates get averaged
-  together, and CC1/2, R<sub>meas</sub> and the anomalous signal all degrade.
+  together, and CC1/2, R<sub>meas</sub> and the anomalous signal all degrade. The data *can* say
+  which crystals are in the same indexing, though, and that is what a merge needs: with the space
+  group given (`-S`) and no reference, Rugnux puts each crystal into the indexing in which it agrees
+  best with all the others, before anything is scaled. This takes seconds for tens of thousands of
+  crystals, and the report says how clearly the crystals separated (`AMBIGUITY_SEPARATION_SIGMA=`,
+  `AMBIGUITY_DECIDED_FRACTION=`) and how many were moved (`AMBIGUITY_REINDEXED=`). The indexing the
+  whole merge ends up in is still arbitrary against other data sets, exactly as on rotation data.
+  On a pseudo-merohedral cell whose axes differ by a few per cent, each crystal's own refined cell
+  already says which axis is which; there only the crystals whose cell does not are decided by the
+  intensities, and the others keep their indexing.
 
-Every run that merges tests for the ambiguity, and where it exists and nothing resolves it, says so
-in the log and in the report's warnings:
+Every run that merges tests for the ambiguity, and where it exists and nothing resolves it (serial
+stills whose space group was determined by the run rather than given), says so in the log and in the
+report's warnings:
 
 ```
 Indexing ambiguity: this cell / space group admits alternative indexing (reindex operator(s):
--h,-k,l). Serial-stills crystals are indexed in one hand at random, and rugnux can only break this
-against an external reference. WITHOUT one the merge mixes the hands and CC1/2 is degraded - supply
-a reference MTZ (-z) or a model (--model, which needs -C and -S here) to resolve it.
+-h,-k,l). Serial-stills crystals are indexed in one hand at random, and rugnux makes them consistent
+from the data only where the space group is given: here it was determined by the run, so the merge
+mixes the hands and CC1/2 is degraded. Giving the space group (-S) resolves it from the data; a
+reference MTZ (-z) or a model (--model, which needs -C and -S here) resolves it against them.
 ```
 
 Where something does resolve it, the run says so instead — `Indexing ambiguity present (reindex
-operator(s): -h,-k,l); resolved against the supplied model`.
+operator(s): -h,-k,l); resolved against the supplied reference` or `...; resolved from the data`.
 
 How to resolve it:
 
 | Situation | What to do |
 | --- | --- |
 | **Rotation**, a reference dataset exists | `-z reference.mtz`. Once the space group is settled, each candidate reindexing of the merged intensities is correlated with the reference and the best-correlating one is re-merged. Only the *hkl* labels change; the cell does not |
-| **Serial stills**, a reference dataset exists | `-z reference.mtz`. Resolved **per image**, at integration time, by correlating each crystal's intensities with the reference — so the merge never mixes hands in the first place |
+| **Serial stills**, a reference dataset exists | `-z reference.mtz`. Resolved **per image**, at integration time, by correlating each crystal's intensities with the reference — so the merge never mixes hands in the first place. Where the crystals' own cells tell the indexings apart (pseudo-merohedry), a crystal its cell decides keeps that indexing and the reference decides the rest. The data-only resolution below runs as a check: `AMBIGUITY_DATA_DISAGREES=` |
 | **Rotation**, only a model | `--model model.pdb`. The merged data are fitted to the model in each candidate indexing and the lowest R-free wins — provided the model first beats its random-orientation null (`MODEL_FIT= ACCEPTED`) and its lead over the runner-up beats the lead a random placement of the same model takes; the written reflections are then reindexed into it, so the file, the R-factors and the maps agree. Where either bar is missed the data keep the indexing they were merged in, and the report says by how much (`MODEL_INDEXING_MARGIN_SIGMA`). It is the **data** that are relabelled, never the model: every dataset of one crystal form processed against the same model comes out in that model's indexing, so the reflection files and maps of a screening campaign compare directly. The relabelling is a proper rotation of the lattice, so the merging statistics are unchanged and I(+)/I(-) keep their hand |
-| **Serial stills**, only a model | `--model model.pdb`, with the cell and space group given (`-C` / `-S`). Structure factors are computed from the model up front and used as the reference for the per-image test, exactly as a reference MTZ would be — the ambiguity has to be broken at integration time, and a model can supply the intensities to break it with |
-| Neither | The run warns and merges in whichever indexing it found: for rotation data a usable dataset in an arbitrary frame, for stills a degraded one |
+| **Serial stills**, only a model | `--model model.pdb`, with the cell and space group given (`-C` / `-S`). Structure factors are computed from the model up front and used as the reference for the per-image test, exactly as a reference MTZ would be, the crystals their own cell decides again excepted. The data-only resolution below is then run only as a check: `AMBIGUITY_DATA_DISAGREES=` counts the crystals on which it would have chosen otherwise |
+| **Serial stills**, neither, space group given (`-S`) | Nothing to do: the crystals are made consistent with each other from the data alone (`INDEXING_AMBIGUITY_RESOLVED= data`), in an indexing that is arbitrary against other data sets. A model or reference still settles the weakest crystals more reliably than the other crystals can, and puts the merge in its own indexing |
+| Neither | The run warns and merges in whichever indexing it found: for rotation data a usable dataset in an arbitrary frame; for stills whose space group the run determined, a merge of mixed indexings, which looks like a perfect twin and can pass for higher symmetry than the crystal has. Run again with `-S` |
 
 Two things to know about where the choice lands:
 
 - **`--mode scale` cannot repair a stills run after the fact.** The per-image test happens at
   integration time, so a `_process.h5` whose images were integrated without a reference — an MTZ or a
-  model — has already lost the distinction, and no re-merge brings it back. On rotation data, where
+  model — has already lost the distinction, and no re-merge brings it back; the data-only resolution
+  runs in the full pipeline, not in `--mode scale`. On rotation data, where
   the ambiguity is one choice for the whole dataset, `--mode scale --model model.pdb` does resolve it.
 - **The choice reaches the written reflections**, not only the R-factors and the maps: the merged
   `.mtz` / `.cif` / `.hkl` (and `_unmerged.mtz`, where it is asked for) are written in the indexing
@@ -159,7 +173,8 @@ maps. Where the merge kept the Bijvoet split (a rotation merge always does), an
 difference map is made too and read, not written: the report names its strongest sites
 (`ANOMALOUS_SITE_01`…`10`) and the map's mean height at the model's anomalous scatterers - every
 atom from phosphorus up - as one number for the anomalous signal (`ANOMALOUS_SCATTERER_MEAN_SIGMA`).
-The structure itself is not refined; the model is re-fractionalized into
+The model is not refined for these numbers (a placed model is refined afterwards, on the side - see
+[Refinement](RUGNUX_MODEL_AND_REFERENCE.md#refinement)); it is re-fractionalized into
 the data cell and then placed as **one rigid body**, so a deposited model from a crystal that is not
 quite isomorphous still sits where the density is. The placement runs on the GPU where there is one
 and on the CPU otherwise, with nothing to set; the two agree to rounding, not bit for bit.
@@ -202,6 +217,8 @@ PDB: PanDDA's per-dataset input is `<name>.pdb` beside `<name>.mtz`, and dimple
 pair. (The PDB is skipped, with a log line, for a cell its fixed-width format cannot hold; the mmCIF
 is unconditional.) That is the file to open with the maps, and the one
 to hand to REFMAC5 or `phenix.refine`; its starting R-free is the `R_FREE=` the report quotes.
+Rugnux's own refinement of it is written beside it as `<prefix>_refined_model.cif` with
+`<prefix>_refined_maps.mtz` ([Refinement](RUGNUX_MODEL_AND_REFERENCE.md#refinement)).
 (`<prefix>.cif` is the merged **reflections** — hence the separate name.)
 
 Where the run also wrote a **twin hypothesis** — `<prefix>_twin_<SG>.mtz`/`.cif`, the same data merged
@@ -272,7 +289,7 @@ A reference MTZ (`-z`) is accepted here on **stills** data, where it fixes the s
 reports CC<sub>ref</sub> and hands over its R-free flags; on rotation data the rotation scaler
 declines it and the run stops with a message saying so. `--model` works here as in a full run, except
 that the model is placed by the rigid body only: a model it does not place, or a prediction, is not
-searched for by molecular replacement, and `--mr` is refused. On rotation data, where the
+searched for by molecular replacement, `--mr` is refused, and the placed model is not refined. On rotation data, where the
 [indexing ambiguity](#the-indexing-ambiguity) is one choice for the whole dataset, it can settle the
 enantiomorph label and the indexing — under the same fit test as always — and the re-merged reflections are written in what it settled. What no re-merge can
 repair is a **stills** `_process.h5` integrated without a reference: there the ambiguity was
@@ -295,7 +312,8 @@ describes them - the cell and space group; `_software` with Rugnux named twice,
 beamline and its general class, the detector's make and model in `_diffrn_detector.type` and its
 class in `_diffrn_detector.detector`, and the collection date from the NXmx start time); and the
 merging statistics overall (`_reflns`) and per shell (`_reflns_shell`): completeness, multiplicity,
-<I/σ(I)>, R_merge, R_meas, R_pim, CC1/2 and CC\*, and SigAno where an anomalous split was made. A
+<I/σ(I)>, R_merge, R_meas, R_pim, CC1/2 and CC\*, and SigAno where an anomalous split was made; on rotation data the cell carries
+its e.s.d.s (`_cell.length_a_esd`, …). A
 quantity the input does not state is left out rather than guessed. The unmerged observations are in
 the `_unmerged.mtz` (unscaled) and the `.hkl` (scaled), not in the `.cif`.
 
@@ -327,9 +345,11 @@ General:
 | `-o, --output-prefix <txt>` | Output file prefix (default: `output`) |
 | `-N, --threads <num>` | Number of worker threads (default, and for any value ≤ 0: every CPU the run may use - its affinity and cgroup quota). Some stages take fewer, because past a point more workers make them slower: the per-image loop of `--mode mx` uses at most 16 per GPU unless `-N` was given a positive value, and first-pass spot finding and the beam-stop pre-scan have ceilings of their own that `-N` does not lift. On a small card the two ceilings, and the per-image loop's 16 where `-N` was left at its default, come down to as many workers as keep their buffers (about 24 bytes per detector pixel each) within half of the card's total memory. Scaling, merging and the space-group search use the full count |
 | `-s, --start-image <num>` | First image to process (default: 0) |
-| `-e, --end-image <num>` | Last image to process (default: all) |
+| `-e, --end-image <num>` | End image number, exclusive: `-s 0 -e 100` processes images 0-99 (default: all) |
 | `-t, --stride <num>` | Process every *n*-th image (default: 1) |
 | `-v, --verbose` | Show the whole log on the terminal in place of the steps; `<prefix>_log.txt` is written either way |
+| `--simulate-live <ms>` | Read a stored input as the collection it was while being written: image *i* becomes readable (*i*+1)·`ms` ms after the start (0: all at once). The run takes the live path a broker URL takes, with the same result; for testing the live workflow without a broker. `--mode mx` only |
+| `--fast-live` | With `--simulate-live` or a broker URL: run as the broker's rugnux live mode does — every decision stands where it was first taken, nothing is re-checked or run again once the sweep is in, the integration radius is fixed, and SIGINT cuts the run to what it has established. A difficult crystal can come out worse |
 | `--no-gpu` | Run on the CPU only, as on a machine without a GPU, even where one is present: CUDA is not touched (nor, on macOS, the Apple GPU that Bragg integration, the model density and the molecular-replacement rotation function otherwise run on) and every GPU step takes its CPU path (`-X FFT` indexes with FFTW and `-X FFBIDX` with its CPU implementation; `-X cuFFT` is refused) |
 
 Mode — `--mode <name>` (default `mx`):
@@ -340,26 +360,38 @@ Mode — `--mode <name>` (default `mx`):
 | `azint` | Only azimuthal integration (no spot finding/indexing); writes `<prefix>_process.h5` |
 | `scale` | Only re-scale/merge the already-integrated reflections in the input `_process.h5` (no re-integration) |
 | `calibration` | Determine the detector geometry from powder rings; writes `<prefix>.poni` and `<prefix>.json` |
+| `refine` | Refine the `--model` against merged structure factors (an MTZ or a structure-factor mmCIF) and process nothing; see [Refining a model against structure factors](RUGNUX_MODEL_AND_REFERENCE.md#refining-a-model-against-structure-factors-rugnux---mode-refine) (`--refine-score-only`, `--refine-d-min`) |
+
+Refinement (`--mode refine`): the columns are found, not named - amplitudes with their sigmas (F/SIGF,
+FP/SIGFP, ...) where the file has them, else intensities (IMEAN/SIGIMEAN, I/SIGI, ...) made into amplitudes by
+French-Wilson, else the mean of the anomalous pairs; the free set from a FreeR_flag-like column (0 the test set,
+or the minority value where 0 is the majority, as phenix writes it), drawn by rugnux where the file has none.
+The model is taken as placed in the data's cell, and refined in the data's space group.
+
+| Option | Description |
+| --- | --- |
+| `--refine-score-only` | Score the model as given and refine nothing: R-work/R-free, the scale, the bulk solvent, the likelihood and the geometry, each term under `REFINE_SCORE_` (`--developer` prints them all) |
+| `--refine-d-min <num>` | Leave out reflections finer than this (Å) |
 
 Calibration (`--mode calibration`):
 
 | Option | Description |
 | --- | --- |
-| `--calibrant <name>` | Powder standard: `lab6` \| `agbh` \| `ceo2` \| `si` \| `ice` (default `lab6`, case-insensitive) |
+| `--calibrant <name>` | Powder standard: `lab6` \| `agbh` \| `ceo2` \| `si` \| `ice` (default `lab6`, case-insensitive). A cell given with `-C` overrides it: that cell is the standard, its rings enumerated from the cell, with the absences of `-S` where given |
 | `--calibration <txt>` | How the rings are measured: `rings` \| `spots` (default `rings`; see above). `rings` defaults `--azim-phi-bins` to 32 |
-| `--no-refine-tilt` | Do not refine the detector tilt: hold rot1/rot2 at the header value and fit only the beam centre and the distance, for a calibration handed to a program that cannot express a tilted detector (XDS) |
+| `--no-refine-tilt` | Do not refine the detector tilt: hold rot1/rot2 at the header value and fit only the beam centre and the distance, for a calibration handed to a program that cannot express a tilted detector (XDS). On stills it holds the tilt in the geometry refinement too |
 
 Detector mask:
 
 | Option | Description |
 | --- | --- |
-| `--detect-beam-stop[=N\|off]` | Find the beam stop and its holder in a projection of N images and add them to the pixel mask as bit 9, so nothing shadowed by them is integrated. **On by default** (60 images); `=off` disables. Reflections behind the stop are attenuated but not flagged, so they integrate low with a plausible sigma and no existing rejection catches them |
+| `--detect-beam-stop[=N\|off]` | Find the beam stop and its holder in a projection of N images and add them to the pixel mask as bit 9, so nothing shadowed by them is integrated. **On by default** (60 images); `=off` disables. A reflection whose signal disk reaches into the shadow is not integrated: the rest of such a disk lies in the stop's half-shadow and reads low. Pixels the finder reports that hold the detector's no-data mark (a PILATUS gap) are masked as dead instead |
 
 Geometry:
 
 | Option | Description |
 | --- | --- |
-| `--beam-center-check[=off]` | Measure the beam centre from the isotropy of the scattered background on **every** run, report how far the file's value is from it (against how right this geometry needs it to be), and on rotation data index a **second first pass** at the measured centre. The fit reads the projection `--detect-beam-stop` already builds, so it costs no extra frames. **On by default**; `=off` disables it, and with it the measured centre's part in the post-refinement bound. The measured centre is adopted where the file's centre indexes nothing and the measured one indexes a majority; where the two return cells related by an integer volume factor (2 to 4) and the measured centre's cell, larger or smaller, carries materially more of the pooled validation spots against its own chance level; and, on a two-pass run, where the first pass is run at both centres and the measured one merges better — done where the two give the same cell in different metric symmetries, where they agree only once less of each frame is read, and where they agree but lie further apart than the geometry absorbs and the file's centre merges inconsistently in the lowest-resolution shell. Otherwise the file's centre is kept. Still runs when `--beam-x`/`--beam-y` are given. See [§1.4](CPU_DATA_ANALYSIS_IMAGE.md) |
+| `--beam-center-check[=off]` | Measure the beam centre from the isotropy of the scattered background on **every** run, report how far the file's value is from it (against how right this geometry needs it to be), and on rotation data index a **second first pass** at the measured centre. The fit reads the projection `--detect-beam-stop` already builds, so it costs no extra frames. **On by default**; `=off` disables it, and with it the measured centre's part in the post-refinement bound. The measured centre is adopted where the file's centre indexes nothing and the measured one indexes a majority; where the two return cells related by an integer volume factor (2 to 4) and the measured centre's cell, larger or smaller, carries materially more of the pooled validation spots against its own chance level; and, on a two-pass run, where the first pass is run at both centres and the measured one merges better — done where the two give the same cell in different metric symmetries, where they agree only once less of each frame is read, and where they agree but lie further apart than the geometry absorbs and the file's centre merges inconsistently in the lowest-resolution shell. Otherwise the file's centre is kept. On stills, where there is no first pass, the file's centre, the measured one and the point-symmetry capture's are each indexed on a sample of frames and the one putting materially more spots on the lattice is taken; with `-C` the detector distance is searched too (30-3000 mm, the file's value one hypothesis). Still runs when `--beam-x`/`--beam-y` are given. See [§1.4](CPU_DATA_ANALYSIS_IMAGE.md) |
 
 Spot finding:
 
@@ -412,8 +444,8 @@ For very long axes the direction grid's angular resolution binds well below 500
 | `-C, --unit-cell <cell>` | Reference unit cell `"a,b,c,alpha,beta,gamma"` (required by `ffbidx`). On rotation data it also widens the FFT search to cover the cell given, at both ends: the longest axis looked for is raised to reach it, and `--fft-min-unit-cell` is lowered to admit it |
 | `--fft-min-unit-cell <num>` | Shortest cell axis the FFT search accepts, Å (default: 10). A candidate with a shorter axis is discarded — but a de-novo rotation run also runs a **second first-pass hypothesis with the floor lowered to 5 Å by default**, adopted when the standing cell turns out to be an integer supercell of what it finds, so a small-molecule cell is indexed without this flag. `-C` lowers the floor on its own to cover the cell given (and the second hypothesis then stays out of the way). On stills, where neither applies, a crystal below the floor cannot be indexed unless this is lowered |
 | `--min-indexed-spots <num>` | Spots a frame must have on the lattice before it counts as indexed (default: 6, minimum 4). It sets the reported indexing rate and the count the rotation first pass ranks candidate lattices by; whether the run has a lattice at all is decided on the pooled spots instead ([§4.1](CPU_DATA_ANALYSIS_INDEXING.md#41-indexed-spot-decision-inlier-test)), and integration is not gated by it |
-| `-S, --space-group <num\|symbol>` | Space group number (`96`) or Hermann-Mauguin symbol (`P43212`) — for indexing and scaling |
-| `-r, --refine <txt>` | Geometry refinement: `none` \| `orientation` \| `beam_and_lattice` (default) \| `flex` (try all three per image, keep whichever indexes the most spots; alias `multi`) |
+| `-S, --space-group <num\|symbol>` | Space group number (`96`) or Hermann-Mauguin symbol (`P43212`) — for indexing and scaling. On serial stills whose group admits two indexings, it also lets the crystals be put on one from the data ([the indexing ambiguity](#the-indexing-ambiguity)) |
+| `-r, --geom-refine <txt>` | Geometry refinement: `none` \| `orientation` \| `beam_and_lattice` (default) \| `flex` (try all three per image, keep whichever indexes the most spots; alias `multi`) |
 | `-R, --two-pass-rotation[=num]` | Two-pass offline rotation indexing (default for goniometer data; optional first-pass image count, default 100) |
 | `--single-pass-rotation[=num]` | Online-like single-pass rotation indexing (optional min angular range, deg) |
 | `--force-rotation-lattice <vec>` | Force rotation lattice (9 floats, Å), skipping the first pass |
@@ -438,26 +470,27 @@ Scaling and merging:
 | `--relative-b[=deg]` | rot3d: fit a per-batch relative-*B* beyond the single decay slope over deg-degree batches, cross-validated (default 10° when bare; off otherwise) |
 | `--simple-stills` | Stills: treat every reflection as a full (*p* = 1, single-pass scale/merge) — disables the default-on physical partiality post-refinement |
 | `--no-expected-variance-merge` | Stills: disable the default expected-variance merge weighting (which rebuilds each weak observation's signal variance at the reflection mean to de-bias the inverse-variance merge); restores observed-sigma weighting |
-| `--capture-uncertainty <num>` | rot3d: systematic sigma on under-captured fulls, ~num·(1−captured_fraction)·I (default: 1.0 for rotation, 0 otherwise) |
+| `--capture-uncertainty <num>` | Systematic sigma num·(1−captured fraction)·⟨I⟩: on rot3d fulls the share of the rocking curve not captured, on stills the share of each partial its partiality does not see (default: 1.0 for rotation, 0 otherwise) |
 | `--min-captured-fraction <num>` | rot3d: drop a combined full whose rocking curve was captured below this fraction — edge-of-sweep truncated fulls (default: 0.7 for rotation, 0 otherwise; 0 = off) |
 | `--scaling-high-resolution <num>` | High-resolution limit for scaling, Å — manual override (default: no limit; disables the automatic cutoff below) |
-| `--scaling-low-resolution <num>` | Low-resolution limit for scaling and merging, Å (default: 50, which is also XDS's own default; 0 removes the limit). The beam stop suppresses air scatter well beyond the shadow it casts, so the background stays depressed across pixels the beam-stop mask leaves open — measured at 30–44% of the field value, recovering only around 50 Å. A background ring in that zone over-estimates the background, so reflections coarser than the limit mostly integrate negative. Beam-stop masking therefore does not make this redundant. A large cell (a few hundred Å) does have real reflections coarser than 50 Å, but on the geometries measured here they fall in that zone and are not usable as integrated; raise the limit only if the low-resolution shell statistics justify it |
+| `--scaling-low-resolution <num>` | Low-resolution limit of the scale fit, Å (default: 50, which is also XDS's own default; 0 removes the limit). Reflections coarser than it are merged and written but kept out of every fit of the scale model: on a large cell a few dozen of them, measured on a background the beam stop depresses, bent the model enough to move the merged 10–50 Å intensities by tens of percent. Which of them are measured at all is the beam-stop mask's decision - a reflection whose signal disk reaches the shadow is not integrated (`--detect-beam-stop`) |
 | `--resolution-cutoff <txt>` | Automatic high-resolution cutoff for the written reflections and reported shells: `cc-logistic` \| `off` (default: `cc-logistic`; ignored when `--scaling-high-resolution` is set) |
 | `--resolution-cc-target <num>` | CC1/2 target defining the `cc-logistic` fall-off (default: 0.30) |
 | `--resolution-shells <num>` | Number of resolution shells in the reported statistics table (default: 9). The bins are equal steps in 1/d² between the lowest- and highest-resolution reflection merged, which is XDS's rule, and 9 is XDS's count — so at the same resolution limits the two tables have the same shells and can be read row for row |
 | `--report-resolution <dmin>[,<dmax>]` | Also report the merging statistics over this resolution range, Å (either order; `dmax` defaults to the run's own low-resolution limit), as a second table beside the run's own — the `REFRES_*` keys of the [results report](RUGNUX_REPORT.md#the-reference-range-table) — binned from the same merged reflections, so a run can be read against another program's table at that program's range. Report-only: the cut, the scaling, the error model and every decision stay the run's own, and shells finer than the run's own limit are reported as not merged rather than filled from data the run did not keep |
-| `--min-partiality <num>` | Minimum partiality to accept a reflection (default: 0.02) |
+| `--min-partiality <num>` | Minimum partiality to accept a reflection (default: 0.02 for rotation, 0.5 for stills) |
 | `--ice-min-score <num>` | Ice-presence gate: the measured per-run ice score (1 = no ice) a dataset must reach before **any** ice handling is applied — the flagging and the exclusion from scaling (default: 1.5; 0 = no gate). The fixed hexagonal bands cover 16–26 % of the unique reflections whether or not the crystal has ice, so handling ice on a clean crystal only costs completeness |
 | `--ice-min-spot-ratio <num>` | The second ice-presence channel: found **spots** on the hexagonal rings over the same q width of ice-free flanks beside them (1 = spots spread evenly). Ice in large crystallites diffracts as discrete spots and leaves the radial profile flat, so `--ice-min-score` alone is blind to it (default: 2.0; 0 disables this channel) |
-| `--reject-outliers <num>` | Per-observation outlier rejection, N σ from the per-reflection median (default: 6 for `rot3d`, off otherwise) |
+| `--reject-outliers <num>` | Per-observation outlier rejection, N σ from the per-reflection median (default: 6 for rotation, 10 for stills; 0 = off) |
 | `--min-image-cc <num>` | Per-image CC limit, percent (default: no limit) |
 | `--search-min-zeta <num>` | De-novo space-group search only: also search a merge of just the observations whose Lorentz geometry \|ζ\| reaches this, and report both answers (default: 0.85 for rotation, 0 = single search). Reflections crossing the Ewald sphere near-tangentially are measured worst and can make a real symmetry operator look like a twin law. Where the two searches disagree, the merge of all the observations decides — as it always has for the systematic absences |
 | `--mosaicity <num>` | Diagnostic: fix the scaling mosaicity (°) instead of using the per-image seed |
 | `--scaling-iterations <num>` | Cap on the per-frame scaling iterations; the loop stops earlier once the scales settle, and a merge that hits the cap is flagged `SCALING_NOT_CONVERGED` (default: 100) |
 | `-z, --reference <file>` | Reference data of the same crystal form — an MTZ or a PDB structure-factor mmCIF (`-sf.cif`), gzipped or not, recognised by content; `--reference-mtz` is the same option: fixes the space group, its setting and the cell, resolves the [indexing ambiguity](#the-indexing-ambiguity), hands over the R-free set and reports CC<sub>ref</sub>. Not a scale anchor |
 | `--reference-column <label>` | Reference column to use, by MTZ label — an mmCIF under the labels `gemmi cif2mtz` gives it (default: auto — F-model, else IMEAN/I/…, else FP/FOBS/F) |
-| `--model <file>` | Validate the merged intensities against this atomic model (PDB or mmCIF, gzipped or not; the format is taken from the file's content) — R-work / R-free and maps (see [Validating against a model](#validating-against-a-model-rugnux---model)). An experimental model is placed as a rigid body, and by molecular replacement where the rigid body does not place it; a prediction (AlphaFold or ModelCIF) goes to molecular replacement straight away (`MODEL_PLACEMENT=`). It also settles the frame the reflections are written in: the enantiomorph, and the [indexing ambiguity](#the-indexing-ambiguity) where no `-z` did; another space group or the twin hypothesis' subgroup it chooses is written beside the answer as `<prefix>_mr.mtz`/`.cif`. For serial stills given `-C` / `-S`, the model's structure factors become the per-image reference |
+| `--model <file>` | Validate the merged intensities against this atomic model (PDB or mmCIF, gzipped or not; the format is taken from the file's content) — R-work / R-free and maps (see [Validating against a model](#validating-against-a-model-rugnux---model)). An experimental model is placed as a rigid body, and by molecular replacement where the rigid body does not place it; a prediction (AlphaFold or ModelCIF) goes to molecular replacement straight away (`MODEL_PLACEMENT=`). It also settles the frame the reflections are written in: the enantiomorph, and the [indexing ambiguity](#the-indexing-ambiguity) where no `-z` did; another space group or the twin hypothesis' subgroup it chooses is written beside the answer as `<prefix>_mr.mtz`/`.cif`. For serial stills given `-C` / `-S`, the model's structure factors become the per-image reference. A placed model is then [refined](RUGNUX_MODEL_AND_REFERENCE.md#refinement) against the merge it was placed on (`<prefix>_refined_model.cif`, `<prefix>_refined_maps.mtz`, `<prefix>_blobs.json`, `REFINE_` keys) - seconds on a GPU, typically 2-15 minutes on the CPU - which decides nothing about the processing |
 | `--mr <file>` | As `--model`, but placed by molecular replacement straight away, without trying the rigid body first. `--mode mx` only; not with `--model` |
+| `--no-refine` | Do not refine the placed model (for debugging): by default a model that `--model` or `--mr` places is refined |
 | `--write-process-h5` | Also write the (large) `_process.h5` when merging (default: only `.mtz`/`.cif`) |
 | `--developer` | Write the full `<prefix>_report.txt`: the pipeline-internal keys and the long explanations the default report leaves out. Nothing is computed differently — the same report, rendered in full (see [The results report](RUGNUX_REPORT.md#the-developer-report)) |
 | `--finalist-ledger` | Report the full-resolution evidence for each space group the search considered, not only the one it adopted, and the twin-immune zone evidence of the adopted group's 2-folds (report-only; the decision is unchanged). Both are read on a merge of the observations in P1 that only this option makes, so it costs one extra merge; rotation only, and not with a fixed centred `-S` |
@@ -471,11 +504,11 @@ Integration:
 | --- | --- |
 | `--integrator <txt>` | Spot integrator: `gaussian` (profile-fit, default) \| `empirical` \| `boxsum` (classical fallback) |
 | `--integration-radius <r>` | Signal-box radius `r1`, or `r1,r2,r3` (px). One value ⇒ `r2=r1+2`, `r3=r1+4` |
-| `--adaptive-integration-radius[=on\|off]` | Set the signal radius `r1` from how wide this crystal's spots actually are (default: **on** for rotation, off for stills). `r1` is not the integration domain — that is the profile-fit grid — but it *is* the aperture the profile **width** is learned over, and a second moment over a disk of radius `a` saturates at `a²/4`, so at the shipped `r1 = 4` the learned σ can never exceed 2 px and a broader spot is fitted with a profile the model cannot represent. The pre-scan reads `r80`, the radius holding 80 % of a spot's flux, off isolated strong spots over a fixed 14 px aperture that owes nothing to `r1`, fits it against `1/d` and evaluates it at 5 Å; then `r1 = clamp(round(2·r80), 4, 6)`, `r2 = r1 + 2`, and `r3` is taken so the `r2..r3` background ring keeps the area it has at the default `4,6,13`. The ceiling of 6 is pattern density: `r2` also drives the neighbour-ownership radius and the ring's inner edge, and past it a dense pattern starts losing reflections whose ring falls below six clean pixels. Ignored when `--integration-radius` is given. The widened radius applies to the **final** integration pass only — the two-pass geometry pre-pass keeps the radius the run started with, because the post-refinement fits the detector distance and beam to the observed reflection positions and those move with the signal disk (33 µm and 0.02 px between `r1 = 4` and `r1 = 6` on one crystal, enough for the second pass's de-novo lattice search to settle on a different lattice and index a fifth fewer frames). And where the widened radius leaves more than 1.1 % of the predicted reflections without a background ring — a pattern too dense for it — the final pass is re-integrated at the fixed 4 px radius, and the log says so. Over the rotation regression battery it moves 12 of 38 crystals and leaves the merged intensities of the other 26 unchanged; where it moves them, per-shell ⟨I/σ⟩ improves by up to 31 % and R_meas by up to 24 % |
+| `--adaptive-integration-radius[=on\|off]` | Set the signal radius `r1` from how wide this crystal's spots actually are (default: **on**). On stills it measures instead how far the background ring should reach: on empty apertures of the pre-scan frames, the `r3` (up to 14) whose ring best predicts the background under the signal disk. `r1` is not the integration domain — that is the profile-fit grid — but it *is* the aperture the profile **width** is learned over, and a second moment over a disk of radius `a` saturates at `a²/4`, so at the shipped `r1 = 4` the learned σ can never exceed 2 px and a broader spot is fitted with a profile the model cannot represent. The pre-scan reads `r80`, the radius holding 80 % of a spot's flux, off isolated strong spots over a fixed 14 px aperture that owes nothing to `r1`, fits it against `1/d` and evaluates it at 5 Å; then `r1 = clamp(round(2·r80), 4, 6)`, `r2 = r1 + 2`, and `r3` is taken so the `r2..r3` background ring keeps the area it has at the default `4,6,13`. The ceiling of 6 is pattern density: `r2` also drives the neighbour-ownership radius and the ring's inner edge, and past it a dense pattern starts losing reflections whose ring falls below six clean pixels. Ignored when `--integration-radius` is given. The widened radius applies to the **final** integration pass only — the two-pass geometry pre-pass keeps the radius the run started with, because the post-refinement fits the detector distance and beam to the observed reflection positions and those move with the signal disk (33 µm and 0.02 px between `r1 = 4` and `r1 = 6` on one crystal, enough for the second pass's de-novo lattice search to settle on a different lattice and index a fifth fewer frames). And where the widened radius leaves more than 1.1 % of the predicted reflections without a background ring — a pattern too dense for it — the final pass is re-integrated at the fixed 4 px radius, and the log says so. Over the rotation regression battery it moves 12 of 38 crystals and leaves the merged intensities of the other 26 unchanged; where it moves them, per-shell ⟨I/σ⟩ improves by up to 31 % and R_meas by up to 24 % |
 | `--integration-stencil <k>` | Push the `r2..r3` background ring out by `k` times the beam's radial streak `bandwidth·R_px`, per reflection (default `0` = the fixed circular ring). A fixed ring otherwise ends up on a streaked reflection's own tails at high resolution and measures them as background. Only the ring moves, and only radially — the `r1` signal box stays a circle — and the growth is capped at `2·r3`. The neighbour exclusion grows with it, so on a crowded pattern a few reflections can be left with too little background and dropped. On a monochromatic beam the streak is zero and this does nothing |
 | `--background-clip <n>` | High-side clip of the background ring at `mean + n·√mean` (default 4, whatever the bandwidth; 0 = off). The default background estimator — it rejects neighbour cores and zingers without the symmetric trim's Poisson skew bias. Ignored by `--integrator boxsum` |
 | `--background-trim <f>` | Use the old symmetric trimmed mean for the background ring instead of the clip, 0≤f<0.5 (`0.10` was the former default). Switches `--background-clip` off. A symmetric trim is biased low on Poisson data and adds ~5 counts to every partial, so this is for back compatibility only; `0` = plain ring mean. Rings holding more than 512 pixels fall back to the plain mean (the GPU sorts the ring in shared memory and the CPU now matches it), which the default radii never reach but wide ones do |
-| `--background-radial[=on\|off\|auto]` | Correct the background ring for the **curvature** of the radial background (default **auto**). Disk and ring are concentric, so a background linear in position cancels between them and only curvature survives — which on a smooth ice ring reaches +26 counts on a single reflection. `auto` applies it per image where that image's ice score shows a *smooth* powder ring, since the model is a function of radius alone: on ice made of discrete crystallite spots there is no smooth ring and the correction makes the bias worse. Ignored by `--integrator boxsum` (no clip pass to take the curve from) |
+| `--background-radial[=on\|off\|auto]` | Correct the background ring for the **curvature** of the radial background (default **auto**). Disk and ring are concentric, so a background linear in position cancels between them and only curvature survives — which on a smooth ice ring reaches +26 counts on a single reflection. `auto` decides per run in the pre-scan, on empty apertures of the pre-scan frames: on stills it is applied to every image where it makes the ring predict the background of empty apertures better at all; on rotation data to every image where it takes at least 10 % of that error away, and otherwise only to images whose ice score shows a *smooth* powder ring (ice made of discrete crystallite spots leaves no such ring, and the correction makes the bias worse). Ignored by `--integrator boxsum` (no clip pass to take the curve from) |
 | `--integration-high-resolution <num>` | High-resolution limit for prediction and integration. Omitted (or 0) means integration extends as far as the detector reaches — which is what the predictor can place on the detector anyway, since it rejects reflections that miss it. Set a value to integrate less than the detector offers |
 | `--max-hkl <n>` | Predict reflections with \|h\|,\|k\|,\|l\| ≤ `n` (max 511). By default this is derived per crystal from the refined cell as `ceil(max(a,b,c)/d_min) + 1`, which is the exact bound: the predictor keeps only \|q\| ≤ 1/d_min and `h = a·q`, so no reflection can lie outside it and no candidate inside it is wasted on a shorter axis. Set it only to override that |
 | `--bandwidth <num>` | Relative X-ray bandwidth FWHM (e.g. `0.01` for a 1% DMM). Default: the file's value; where the file states none, the one the pre-scan measures from how much longer strong spots are along their radius than across it, used where it is significant; otherwise 0 (monochromatic). `--bandwidth 0` forces a monochromatic beam |
@@ -490,16 +523,16 @@ Geometry overrides (defaults are taken from the input file; override them to rep
 | --- | --- |
 | `--beam-x <num>` | Beam centre X (pixel). `--beam-center-check` still runs and can adopt its measured centre ([§1.4](CPU_DATA_ANALYSIS_IMAGE.md)) |
 | `--beam-y <num>` | Beam centre Y (pixel). `--beam-center-check` still runs and can adopt its measured centre ([§1.4](CPU_DATA_ANALYSIS_IMAGE.md)) |
-| `--detector-distance <num>` | Detector distance (mm) |
+| `--detector-distance <num>` | Detector distance (mm). On stills it is then held: neither searched nor refined. Without it, stills with a reference cell (`-C`) search the distance and refine it with the cell |
 | `--wavelength <num>` | Wavelength (Å) |
 | `--pixel-size <num>` | Pixel size (µm), for a file that does not state it (an XTC stream of an unknown camera) |
-| `--gain <num>` | Detector units per photon, for input in detector units (SACLA, CXI, XTC, SMV, marCCD and `--crystfel-geometry` input). The frames are analysed in their own units and the gain enters where a photon count is assumed; the integrated intensities come out in photons. Default: measured on the background of a few frames ([Serial XFEL inputs](RUGNUX_FORMATS.md#serial-xfel-inputs)) |
+| `--gain <num>` | Detector units per photon, for input in detector units (SACLA, CXI, XTC, SMV, marCCD and `--crystfel-geometry` input). Where the background resolves single photons (SACLA, CXI and `--crystfel-geometry` input) the frames are counted in whole photons as they are read; otherwise they are analysed in their own units and the gain enters where a photon count is assumed. The integrated intensities come out in photons either way. Default: measured on the background of a few frames ([Serial XFEL inputs](RUGNUX_FORMATS.md#serial-xfel-inputs)) |
 | `--saturation <num>` | Pixel value from which a pixel is overloaded, in the units the frames are read in. Replaces the file's limit and the one stills read off the frames |
 | `--crystfel-geometry <file>` | Place the panels of an HDF5/CXI input by a CrystFEL geometry file instead of the file's own metadata: module geometry, camera length, mask arrays and bad regions (optional; [Serial XFEL inputs](RUGNUX_FORMATS.md#serial-xfel-inputs)) |
 | `--module-geometry <file>` | Where the detector's modules are: an NXmx file with one NXdetector_module per module (what a run writes as `<prefix>_modules.h5`) or a CrystFEL geometry file whose panels are laid on the image. Overrides the input's own |
-| `--refine-modules[=off]` | Stills: place each module as a rigid block in the geometry bundle adjustment, where that predicts held-out spots better (default: on). Used for a foreign multi-panel detector, measured and reported only for a JUNGFRAU; the placement is written to `<prefix>_modules.h5` |
+| `--refine-modules[=on\|off\|diagnose]` | Stills: place each module as a rigid block in the geometry bundle adjustment, where that predicts held-out spots better (default: on). Used for a foreign multi-panel detector, measured and reported only for a JUNGFRAU; the placement is written to `<prefix>_modules.h5` |
 | `--mask-good [<file>:]<dataset>[@<bits>]` / `--mask-bad [<file>:]<dataset>[@<bits>]` | HDF5/CXI stills: a mask array in the frames' stored layout, in `<file>` or in each data file; usable only where non-zero (or with all `<bits>`) / unusable where non-zero (or with any `<bits>`). Repeatable ([Serial XFEL inputs](RUGNUX_FORMATS.md#serial-xfel-inputs)) |
-| `--rot1 <num>` | PONI detector rotation 1 (rad) |
+| `--rot1 <num>` | PONI detector rotation 1 (rad). On stills, `--rot1` or `--rot2` holds the tilt (not refined); without them stills refine the tilt where held-out frames agree |
 | `--rot2 <num>` | PONI detector rotation 2 (rad) |
 | `--rot3 <num>` | PONI detector rotation 3, about the beam (rad) — the one `rugnux --mode calibration` writes into its `.poni`, so a refined third rotation can be given straight back |
 | `--detector-mirror-y` | The stored image is mirrored in Y relative to the frame the PONI angles are stated in |
diff --git a/docs/RUGNUX_BENCHMARKING.md b/docs/RUGNUX_BENCHMARKING.md
index e6785bd7e..0175538d7 100644
--- a/docs/RUGNUX_BENCHMARKING.md
+++ b/docs/RUGNUX_BENCHMARKING.md
@@ -26,6 +26,13 @@ the old ones were retired.
   and also checks that the answers are right. It answers *how fast, on this machine*. It takes
   minutes, and needs nothing on the machine but four open datasets.
 
+Serial stills have a battery of their own, `tools/battery/still_battery.py`, on the public datasets
+of [External test data: serial crystallography](EXTERNAL_TEST_DATA_STILLS.md). It shares the site
+config, the verbs and the run-directory layout, but scores nothing about the lattice or the symmetry
+(a serial user gives the cell and the space group): each row says what the merge is worth (R_split,
+the deposited model's R-free against it beside the deposition's own) and what it cost. The README's
+*The still battery* describes it.
+
 The two are kept apart on purpose. A battery run reads hundreds of gigabytes once, so its wall clock
 mostly measures the disk and the page cache (see [the page-cache trap](#the-page-cache)). Use the
 battery to judge correctness and the timing benchmark, run under controlled conditions, to judge
@@ -189,9 +196,11 @@ noise, and one that reproduces is a real change.
 
 ## The REFMAC model check
 
-R-free from `rugnux --model` is a **trend number**. It is a rigid-body placement scored on rugnux's
+R-free from `rugnux --model` is a **trend number**. `R_FREE=` is the placed model scored on rugnux's
 own free set, with a deliberately simple scale model, so it shows how a set moves between runs, but
-it cannot be compared with the deposition's R-free. `--model-check` adds an independent number that
+it cannot be compared with the deposition's R-free. rugnux then refines the placed model as well
+(`REFINE_R_FREE=`, recorded as `rfree_refined` in `results.json`, reported and never scored), still
+on its own free set, so that number is not comparable with the deposition's either. `--model-check` adds an independent number that
 can be. It runs `tools/battery/model_check.py` on every open-arm set with a deposited X-ray model,
 after rugnux has finished, so it cannot influence the processing. It needs CCP4: the runner sources
 `$CCP4_SETUP`, by default `/opt/xtal/ccp4-9/bin/ccp4.setup-sh`, and calls the `refmac5` found there
@@ -288,7 +297,7 @@ $B timing --rugnux $R [--benchmark standard|inhouse] [--threads N] [--label L] [
 
 The benchmark runs a few sets. Each starts from a model that the run has to place by molecular
 replacement, so a single run times every stage: reading, pre-scan, indexing, integration, scaling,
-the space-group search, MR and model validation. It also checks that every answer is right.
+the space-group search, MR, model validation and the refinement of the placed model. It also checks that every answer is right.
 
 `--benchmark standard`, the default, is the one to run on a new machine. It uses open data only:
 three EIGER 16M rotation sets of ordinary size and quality, and a virus capsid as the large case.
@@ -574,6 +583,8 @@ section. For a rotation run the steps are, in order:
 | Analyses | twinning, anisotropy and the other report-only analyses |
 | Model validation | `--model` only: structure factors, scale fits, rigid-body placement, maps |
 | Molecular replacement | only where the rigid body did not place the model (always, in the timing benchmark) |
+| Refinement | the placed model refined against the merge (wherever a model is placed, unless `--no-refine`) |
+| Doubled-cell hypothesis | only where an index-2 superstructure qualifies: the doubled cell integrated and merged as well ([Results report](RUGNUX_REPORT.md#index-2-superstructure)) |
 | Writing files | MTZ, mmCIF, HKL, report |
 
 A step that is slower on one machine than on another points at the code, and a step that is slower
diff --git a/docs/RUGNUX_CALIBRATION.md b/docs/RUGNUX_CALIBRATION.md
index f6ec498bb..95fef8562 100644
--- a/docs/RUGNUX_CALIBRATION.md
+++ b/docs/RUGNUX_CALIBRATION.md
@@ -41,6 +41,10 @@ else, and has two members:
 **`ice`** calibrates a real experiment against its own ice rings — no calibrant exposure needed —
 and is the reason a calibrant is a list of ring positions rather than a unit cell: hexagonal ice
 is P6<sub>3</sub>/mmc, so rings enumerated from its cell would include systematically absent ones.
+A standard that is not on the list is given by its unit cell instead: with `-C` the cell **is** the
+calibrant, its rings enumerated from the cell, with the absences of `-S` where that is given (taken as
+primitive where it is not). `-S` supplies symmetry absences only, so a standard whose extinctions come
+from its atomic basis — silicon's 222 — is better named with `--calibrant`.
 
 `--calibration` picks how the rings are measured, and **both aggregate over every processed image** — `-s`/`-e`/`-t`
 select which images:
diff --git a/docs/RUGNUX_DOWNLOAD.md b/docs/RUGNUX_DOWNLOAD.md
new file mode 100644
index 000000000..6db7a4985
--- /dev/null
+++ b/docs/RUGNUX_DOWNLOAD.md
@@ -0,0 +1,69 @@
+# Download Rugnux
+
+`rugnux` is one self-contained executable: no CUDA toolkit, no Qt, no service to run. Take the
+archive for your machine, unpack it into a directory of its own, and run it. The links point at the
+current release; the full list of what each release ships is on its release page.
+
+```{eval-rst}
+.. jfjoch-downloads:: rugnux
+```
+
+On a machine with an NVIDIA GPU take the **GPU** archive: it is the only one that uses the card,
+and it also runs on a machine without one (it reports zero CUDA devices and takes the CPU path).
+The **CPU only** archive is smaller and for machines that will never have a GPU. A V100 needs the
+CUDA 12 build; the CUDA 13 builds start at Turing (T4). The driver versions and the GPU generations
+each build covers are in [Release contents](RELEASE_CONTENTS.md#gpu-generations-and-the-nvidia-driver).
+
+## After downloading
+
+The archive has **no top-level directory**: it unpacks straight into `bin/` and `share/`, so always
+give it a directory of its own.
+
+```
+mkdir -p ~/rugnux
+tar xzf rugnux-<version>-linux-x86_64-cuda12.tgz -C ~/rugnux      # Linux, macOS
+~/rugnux/bin/rugnux                                               # prints the usage
+```
+
+On Windows, extract the `.zip` into a folder and run `bin\rugnux.exe` from a terminal. On macOS the
+binary is signed and notarized; the first run of a freshly downloaded copy checks the notarization
+online.
+
+Nothing is written outside that directory, nothing needs root, and several versions can sit side by
+side; to remove one, delete its directory. Put `bin/` on your `PATH` to type `rugnux` rather than
+the full path, then:
+
+```
+rugnux dataset_master.h5
+```
+
+[Rugnux](RUGNUX.md) takes it from there: what the run writes, what the terminal shows and the few
+options worth knowing.
+
+## Linux packages
+
+On RHEL / Rocky 8 and 9 and Ubuntu 22.04 / 24.04, `rugnux` is also a package of its own in the
+[package repositories](REPOSITORIES.md), which keeps it current with the system's package manager:
+
+```
+sudo dnf install rugnux          # RHEL / Rocky
+sudo apt install rugnux          # Ubuntu
+```
+
+The package depends on nothing from the acquisition side and installs `/usr/bin/rugnux`. The
+repository's CUDA variant keeps cuFFT as a system dependency, where the archive above links it in;
+either works on the same machine.
+
+## From source
+
+`cmake -S . -B build -DJFJOCH_RUGNUX_ONLY=ON` builds `rugnux` alone, on Linux, macOS and Windows,
+with every dependency fetched during the first configure. The flags that match the released
+binaries, and what a build needs on a Mac, are in
+[Installing Rugnux ▸ Building from source](RUGNUX_INSTALL.md#building-from-source).
+
+## Memory and hardware
+
+A run wants host and GPU memory in proportion to the number of reflections it integrates, not to
+the detector: 16 GB of RAM and a 6 GB card for an ordinary sweep, 32 GB and 8 GB for the largest
+measured, and far more for a very large unit cell. The sizing table and the flags that lower it are
+in [Installing Rugnux ▸ Memory](RUGNUX_INSTALL.md#memory).
diff --git a/docs/RUGNUX_FORMATS.md b/docs/RUGNUX_FORMATS.md
index a93f06f8a..75048fb6d 100644
--- a/docs/RUGNUX_FORMATS.md
+++ b/docs/RUGNUX_FORMATS.md
@@ -1,8 +1,10 @@
 # What Rugnux reads
 
 Which data `rugnux` opens, before anything is typed. The short answer: an HDF5 master (NXmx or
-DECTRIS, from any facility), a PILATUS miniCBF sweep, a marCCD sweep or an SMV sweep (ADSC or Rigaku d\*TREK) — nothing else
-is read, so any other format has to be converted to one of these first.
+DECTRIS, from any facility), a PILATUS miniCBF sweep, a marCCD sweep or an SMV sweep (ADSC or Rigaku d\*TREK), and
+for serial stills the files of the XFEL pipelines ([below](#serial-xfel-inputs)) — nothing else is
+read, so any other format has to be converted to one of these first. An atomic model and a reference
+reflection file may be given among the inputs too, told from the images by their contents.
 
 **Input** is files, never a directory: an HDF5 master file, or one frame of a PILATUS miniCBF, marCCD
 or SMV sweep. For rotation data one input is **one sweep of one crystal** — Rugnux does not combine sweeps or crystals in a run; process each
diff --git a/docs/RUGNUX_INSTALL.md b/docs/RUGNUX_INSTALL.md
index bf01230f5..ef8d06326 100644
--- a/docs/RUGNUX_INSTALL.md
+++ b/docs/RUGNUX_INSTALL.md
@@ -31,7 +31,8 @@ detector libraries, no Qt — so it can go on a machine that only processes data
 ## From the release archive
 
 For a machine no package manager covers — or for Windows, macOS and Arm, which have no repository —
-take the archive for your architecture from the Gitea release page:
+take the archive for your architecture from the [download page](RUGNUX_DOWNLOAD.md) or the Gitea
+release page:
 
 | Archive | For |
 | --- | --- |
@@ -77,8 +78,9 @@ The released Linux and Windows archives are CUDA builds (the macOS one is CPU-on
 an NVIDIA **driver** on the host — 525.60.13
 or newer for the CUDA 12 archive, 580.65.06 or newer for the CUDA 13 ones — and no CUDA toolkit,
 because everything CUDA is linked statically. With no GPU or no driver, `rugnux` reports zero CUDA
-devices and falls back to the CPU path, which works but is far slower and offers only the `fftw`
-indexer. A **V100 needs the CUDA 12 archive**; which generations each build covers is in
+devices and falls back to the CPU path, which works but is far slower: the FFT search runs on FFTW
+and `ffbidx` on its CPU implementation, and the refinement of a placed model takes minutes rather than
+seconds. A **V100 needs the CUDA 12 archive**; which generations each build covers is in
 [Release contents ▸ GPU generations and the NVIDIA driver](RELEASE_CONTENTS.md#gpu-generations-and-the-nvidia-driver).
 
 ## Building from source
@@ -115,8 +117,8 @@ preprocessing, azimuthal integration, spot finding, prediction and Bragg integra
 pre-scan (beam-stop mask, background beam-centre fit, spot widths, defective pixels; one accumulator
 per card), rotation scaling and merging from the ingest of the reflections onwards (sorting and the
 resolution cut included) with its correction surfaces, and `--model`: the structure factors, scale
-fits and rigid-body placement of the validation and the rotation and translation functions of
-molecular replacement. The CPU implementations are the path where there is no GPU, and the two agree
+fits and rigid-body placement of the validation, the rotation and translation functions of
+molecular replacement, and the refinement of the placed model. The CPU implementations are the path where there is no GPU, and the two agree
 to rounding rather than bit for bit (parts of the scaling and the model fits round differently
 on the card), so a GPU and a CPU run can differ in the last digits of the merged data. The choice is automatic;
 a CUDA build runs on the CPU when told to (`rugnux --no-gpu ...`).
diff --git a/docs/RUGNUX_INTEGRATION.md b/docs/RUGNUX_INTEGRATION.md
index a295624e9..ebbf59e05 100644
--- a/docs/RUGNUX_INTEGRATION.md
+++ b/docs/RUGNUX_INTEGRATION.md
@@ -13,7 +13,10 @@ downstream suite running on Rugnux output.
 **mmCIF.** Standard items carry their standard meanings — `_refln.intensity_meas` / `_intensity_sigma`,
 the `pdbx_I_plus`/`pdbx_I_minus` and `pdbx_F_plus`/`pdbx_F_minus` anomalous pairs, `_reflns.*` and
 `_reflns_shell.*` for the merging statistics, `_reflns.B_iso_Wilson_estimate` for the Wilson B, and
-`_cell.*` / `_diffrn_radiation_wavelength.wavelength` for the geometry.
+`_cell.*` / `_diffrn_radiation_wavelength.wavelength` for the geometry. On rotation data `_cell.*_esd`
+carries the cell's standard uncertainties (`.` for a parameter the symmetry fixes) and
+`_cell_measurement.reflns_used` / `theta_min` / `theta_max` the reflections they were measured on (see
+[Cell e.s.d.s](RUGNUX_REPORT.md#cell-esds)).
 
 Anything Rugnux reports that has no standard item is written under a **`jfjoch_`** prefix, inside the
 standard category it belongs to. That is a deliberate choice: a reader that does not know these items
@@ -39,8 +42,11 @@ ignores them, and one that does can find them without guessing.
 > `.cif` is not comparable with one taken from a newer one.
 
 **SHELX HKLF 4** (`<prefix>.hkl`). Fixed-format `3I4,2F8.2` — `h k l I σ(I)`, terminated by a
-`0 0 0` record — which is what **SHELXL**, **SHELXC**, **SHELXD** and **ANODE** expect. Two
-properties worth knowing before using it:
+`0 0 0` record — which is what **SHELXL**, **SHELXC**, **SHELXD** and **ANODE** expect. It is
+written with a SHELX instruction file, `<prefix>.ins`, beside it: `CELL`, `ZERR` (the cell's e.s.d.s,
+measured on rotation runs), `LATT` and `SYMM`, and a placeholder `SFAC`/`UNIT` (see
+[Small-molecule structures](#small-molecule-structures-with-shelxt-and-shelxl)). Two properties of
+the `.hkl` worth knowing before using it:
 
 - **On rotation data it is unmerged**: one record per full reflection (its partials summed), with the
   per-frame scale and every correction applied and the σ(I) the merge weighted it with, but not
@@ -113,7 +119,7 @@ file is self-contained, so several of them can be handed to pointless and aimles
 
 **Columns.** `H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP QE FLIGHT FLAG` —
 POINTLESS's own set down to `FLAG`, plus `QE` and `FLIGHT` (the sensor-efficiency and flight-path
-divisors described above; `QE` is DIALS's column) — then four Rugnux extras, `DELPHI` (offset from
+divisors described below; `QE` is DIALS's column) — then four Rugnux extras, `DELPHI` (offset from
 the centre of the rocking curve), `ZETA` (the Lorentz geometry of that curve), `BGMEAN` and `BGVAR`
 (the background that was subtracted, and its variance).
 `BATCH` is the image ordinal plus one, and a batch header is written for every batch that carries an
@@ -372,35 +378,24 @@ arrived without its `.mtz`.
 ## Small-molecule structures with SHELXT and SHELXL
 
 A small-molecule sweep (see [Small-molecule data](RUGNUX_TUTORIAL.md#small-molecule-data)) goes to
-SHELX as **`xtal.hkl`**, the rotation run's scaled reflections unmerged, in HKLF 4. `shelxt` and
-`shelxl` come with CCP4 as well as with the SHELX distribution. HKLF 4 carries no metadata, so the
-instruction file is written by hand: the wavelength and the cell from the report, the lattice and
-symmetry of the space group the report names, and the cell contents, which only the user knows.
+SHELX as **`xtal.hkl`**, the rotation run's scaled reflections unmerged, in HKLF 4, with the instruction
+file **`xtal.ins`** beside it. `shelxt` and `shelxl` come with CCP4 as well as with the SHELX
+distribution. The `.ins` holds what the data determine: `CELL` at the wavelength, `ZERR` with the
+cell's standard uncertainties (see [Cell e.s.d.s](RUGNUX_REPORT.md#cell-esds); its Z assumes one
+formula unit per general position), and the `LATT` and `SYMM` of the space group the report names.
+`SFAC` and `UNIT` are a placeholder - an organic composition at 18 ų per non-hydrogen atom - since
+the cell contents are what only the user knows; edit them before solving:
 
 ```
 cp xtal.hkl struct.hkl
-w=$(grep '^WAVELENGTH= ' xtal_report.txt | cut -d' ' -f2)
-cell=$(grep '^UNIT_CELL_CONSTANTS= ' xtal_report.txt | cut -d' ' -f2-)
-cat > struct.ins <<eof
-TITL struct
-CELL $w $cell
-ZERR 4 0.001 0.001 0.001 0.01 0.01 0.01
-LATT 1
-SYMM -X, 0.5+Y, 0.5-Z
-SFAC C H N O
-UNIT 40 48 4 8
-END
-eof
+cp xtal.ins struct.ins      # then set SFAC / UNIT to the formula
 shelxt struct
 ```
 
-The `LATT` and `SYMM` lines here are those of P2₁/c (`SPACE_GROUP_NAME= P 1 21/c 1`); write the ones
-of the group in the report, from International Tables or from a program that writes them. SHELXT
-takes the Laue group and the lattice from them and determines the space group itself, so where the
-report's `SPACE_GROUP_CENTRE=` is `NOT_DETERMINED` its choice is a second opinion on the centre of
-symmetry. `ZERR` carries Z and the cell's standard uncertainties; the values above are placeholders,
-since the report gives the cell without them. SHELXT writes its best solution as `struct_a.res`, with
-`struct_a.hkl` beside it in the setting it chose, and refinement continues from those:
+SHELXT takes the Laue group and the lattice from `LATT`/`SYMM` and determines the space group itself,
+so where the report's `SPACE_GROUP_CENTRE=` is `NOT_DETERMINED` its choice is a second opinion on the
+centre of symmetry. SHELXT writes its best solution as `struct_a.res`, with `struct_a.hkl` beside it
+in the setting it chose (and the cell and `ZERR` carried across), and refinement continues from those:
 
 ```
 cp struct_a.res struct_a.ins
@@ -441,8 +436,8 @@ with. `myrun_unmerged.mtz` is not part of this chain (it is unscaled), so a run
 `--no-export-unmerged` is not missing a file SHELX needs.
 
 **HKLF 4 carries no metadata**, so the cell and the space group have to be repeated on the SHELXC
-command — take them from `UNIT_CELL_CONSTANTS` and `SPACE_GROUP_NAME` in section 2 of the
-report, with the spaces taken out of the group's name. (SHELXC also puts a wavelength in the `CELL`
+command — take them from the `CELL` line of `myrun.ins`, or from `UNIT_CELL_CONSTANTS` and
+`SPACE_GROUP_NAME` in section 2 of the report, with the spaces taken out of the group's name. (SHELXC also puts a wavelength in the `CELL`
 line of the `.ins` files it writes; that is its own 0.98 Å default, not anything read from the data,
 and neither SHELXD nor SHELXE uses it.) The whole chain, for a sulfur substructure — the cell and
 group here are tetragonal lysozyme's, so substitute your own report's:
@@ -525,7 +520,7 @@ the beam), so the numbers are directly comparable, and a tilt appears as the two
 vectors rather than as angles, which is how XDS reports it after refinement. Two things to keep in
 mind: **`ORGX`/`ORGY` are 1-based**, because XDS counts pixels from 1 and Jungfraujoch from 0; and
 they are the **PONI**, the same quantity Jungfraujoch's beam centre is — so no correction is needed —
-but not the direct beam once the detector is tilted (see above). **`ROTATION_AXIS` is rugnux's axis
+but not the direct beam once the detector is tilted. **`ROTATION_AXIS` is rugnux's axis
 negated**: rugnux turns the crystal by -phi about its axis, XDS by +phi, and with rugnux's own sign
 `IDXREF` indexes only the chance floor of a mis-signed spindle. The detector axes appear only where the
 detector is tilted.
diff --git a/docs/RUGNUX_MODEL_AND_REFERENCE.md b/docs/RUGNUX_MODEL_AND_REFERENCE.md
index 65b32d536..8c6ce9b20 100644
--- a/docs/RUGNUX_MODEL_AND_REFERENCE.md
+++ b/docs/RUGNUX_MODEL_AND_REFERENCE.md
@@ -29,20 +29,29 @@ the rest walks through a run step by step.
   another space group, or a twinned subgroup, that merge is written *beside* the answer as
   `<prefix>_mr.mtz`/`.cif`, with the model as placed there. `<prefix>.mtz` stays the data's own
   answer.
+- **A placed model is then refined**, after every decision has been taken, and written beside the
+  answer as `<prefix>_refined_model.cif`/`.pdb` with its maps ([Refinement](#refinement)); `--no-refine`
+  skips it. The refinement changes nothing else the run writes.
 - **A reference dataset (`-z`) and a space group or cell you give (`-S`, `-C`) are different:** they
   are taken as facts about the crystal. They fix the space group and the cell before processing,
   so with them the space group is yours, not the data's.
-- **One exception to "processed the same":** on **serial stills** given `--model` together with
-  `-C` and `-S`, the model is used during integration to choose, crystal by crystal, between the two
-  equally valid indexings — the same job a reference dataset does there (see
-  [Serial stills](#serial-stills-the-one-place-a-model-acts-before-the-merge)).
+- **One exception to "processed the same", and only one:** on **serial stills** given `--model`
+  together with `-C` and `-S`, the model is used during integration to break the **indexing
+  ambiguity** — to choose, crystal by crystal, between the two equally valid indexings — the same job
+  a reference dataset does there (see
+  [Serial stills](#serial-stills-the-one-place-a-model-acts-before-the-merge)). Nothing else is
+  taken from it before the merge. This is deliberate: a structure of the same protein (often a cryo
+  structure) usually exists, and it settles the choice reliably. Where the lattice has no ambiguity
+  the model changes nothing. Without a model the crystals are made consistent with each other from
+  the data alone (with `-S` given), which recovers most of what the model gives; the model still
+  decides the weakest crystals better than the other crystals can.
 
 ## Every option that brings in a model or reference data
 
 | Option | What you give | What Rugnux uses it for | Can it change `<prefix>.mtz`? |
 |---|---|---|---|
 | *(none)* | — | Everything from the data | — |
-| `--model <file>` | An atomic model, PDB or mmCIF, gzipped or not, recognised by content: an experimental structure or a prediction | Validation after the merge (R-work/R-free, CC(model, data), maps, the placed model); a rigid-body placement checked against a null, with molecular replacement where the rigid body does not place it, and straight away for a prediction | Labels only (hand, indexing, axes), and only where the model fits. Other space groups → `<prefix>_mr.*` |
+| `--model <file>` | An atomic model, PDB or mmCIF, gzipped or not, recognised by content: an experimental structure or a prediction | Validation after the merge (R-work/R-free, CC(model, data), maps, the placed model); a rigid-body placement checked against a null, with molecular replacement where the rigid body does not place it, and straight away for a prediction; then [refinement](#refinement) of the placed model (`REFINE_` keys, `<prefix>_refined_model.cif`/`.pdb`, `_refined_maps.mtz`, `_blobs.json`), which decides nothing | Labels only (hand, indexing, axes), and only where the model fits. Other space groups → `<prefix>_mr.*` |
 | `--mr <file>` | The same kinds of model | As `--model`, but molecular replacement straight away, without the rigid body. `--mode mx` only, not together with `--model` | Hand label only. Other space groups → `<prefix>_mr.*` |
 | PAE file beside a prediction | `AF-<id>-F1-predicted_aligned_error_v<n>.json` next to `AF-<id>-F1-model_v<n>.cif` (read automatically, no option) | Cuts the prediction into rigid domains for molecular replacement | No (a domain alone can only confirm the answer's group) |
 | `-z, --reference <file>` (`--reference-mtz`) | Merged data of the same crystal form: an MTZ, or a PDB structure-factor mmCIF (`-sf.cif`) | Fixes the space group (in its own setting) and the cell (softly), puts the merge on its axes, resolves the indexing ambiguity, hands over its R-free set, reports CC<sub>ref</sub> on stills. Never a scale anchor | **Yes**: the space group, the axes, the indexing and the free set are the reference's |
@@ -52,6 +61,15 @@ the rest walks through a run step by step.
 | `--force-rotation-lattice` | Nine numbers: a lattice | Skips the first-pass indexing and uses this lattice | **Yes**: the lattice |
 | `--report-resolution <dmin>[,<dmax>]` | Another program's resolution range | A second statistics table at that range (`REFRES_*`) | No — report only |
 
+**Without the options.** A model and a reference reflection file can also be given among the inputs, in any
+order: `rugnux data_master.h5 model.cif`, `rugnux model.pdb.gz data_master.h5 ref.mtz`. Each file is told by
+its contents, never its name: an MTZ (its `MTZ ` magic) or an mmCIF with a `_refln` or `_diffrn_refln` loop
+(a PDB `-sf.cif`) is reference data, taken as `-z` - in `--mode refine` it is the input itself; a PDB file (a
+PDB record first, with an `ATOM` or `HETATM` record) or an mmCIF with an `_atom_site` loop is a model, taken
+as `--model`; anything else is images, for the readers. An mmCIF holding both coordinates and reflections is
+refused as ambiguous and has to be given with `--model` or `-z`. At most one model and one reference, counting
+`--model`/`--mr` and `-z` as well; gzipped files are read through.
+
 `-S`, `-C`, `-z` and `--force-rotation-lattice` are *assertions*: Rugnux takes them as true and
 does not test them against a null. Use them when you know; leave them out to let the data decide
 (a de-novo run is the recommended default — see [Running Rugnux](RUGNUX_TUTORIAL.md#rotation-data)).
@@ -96,7 +114,7 @@ these letters.
 | Point group, Laue class, centring | data (space-group search) | `-S` fixes it | the reference's | — | (a) |
 | Screw axes (space group within the point group) | data | `-S` | the reference's | a different choice → `<prefix>_mr.*` only | (a) in `p.mtz`, (c) beside it |
 | Hand (enantiomorph) | not decidable: `SPACE_GROUP_ENANTIOMORPH= UNDETERMINED` | `GIVEN` | `GIVEN` | relabelled to the model's where it fits, past the anomalous veto: `ASSUMED_FROM_MODEL` | (b) |
-| Indexing ambiguity (merohedral reindex) | arbitrary on rotation (`INDEXING_AMBIGUITY_OPERATORS=`); mixed on stills (warning) | — | resolved against the reference | resolved by the rigid-body model where its lead beats its null, rotation; per image on stills with `-C`/`-S`. Never by molecular replacement | (b) |
+| Indexing ambiguity (merohedral reindex) | arbitrary on rotation (`INDEXING_AMBIGUITY_OPERATORS=`); on stills with `-S` the crystals made consistent from the data, otherwise mixed (warning) | — | resolved against the reference | resolved by the rigid-body model where its lead beats its null, rotation; per image on stills with `-C`/`-S`. Never by molecular replacement | (b) |
 | Setting (which axis is a, b, c) | standard setting | `-C`'s axis order; `-S`'s symbol | the reference's | the model's, where it fits and there is no `-z` (`SETTING_SOURCE= MODEL`) | (b) |
 | Twinning check (L-test, twin laws) | data | — | — | — | (a) |
 | Twin hypothesis `<prefix>_twin_<SG>.*` | data (when the group may have absorbed a twin law) | — | — | the model may also *ask* for this merge; written then only where the model chooses it | (a) / (c) |
@@ -106,6 +124,7 @@ these letters.
 | `p.mtz` space-group label | data | yours | the reference's | hand relabel only | (b) |
 | `<prefix>_mr.mtz`/`.cif`, `<prefix>_mr_model.*` | not written | — | — | another group or the twin subgroup the model chose | (c) |
 | Maps, `<prefix>_model.*`, section 5 of the report | not written | — | — | always, whatever the verdict | (d) |
+| Refinement, `<prefix>_refined_*`, `<prefix>_blobs.json`, `REFINE_` keys | not written | — | — | where the model was placed (not with `--no-refine`) | (d) |
 
 ## A run with `--model`, step by step
 
@@ -156,14 +175,15 @@ these letters.
    for the placement that was kept, against the merge it was chosen on, and written:
    `<prefix>_maps.mtz` (map coefficients), `_model.cif`/`.pdb` — or the
    `<prefix>_mr_*` equivalents where the choice was `<prefix>_mr`. A rejected model gets its maps
-   too: that is the case where looking at it in the density is most useful.
+   too: that is the case where looking at it in the density is most useful. A placed model is then
+   [refined](#refinement) (`<prefix>_refined_model.cif`/`.pdb`, `_refined_maps.mtz`, `_blobs.json`).
 9. **The reflection files** — `<prefix>.mtz`, `.cif`, `.hkl`, `_unmerged.mtz` — are written last,
    carrying only the class-(b) labels from step 5 and the hand from step 7.
 
 `MODEL_PLACEMENT=` summarises steps 3–7: `RIGID_BODY`, `MR` or `NOT_PLACED`.
 
 In `--mode scale`, `--model` is steps 3–5 only: the rigid body, its null, and the hand and indexing
-it may settle. There is no molecular replacement, no setting change and no twin hypothesis, and
+it may settle. There is no molecular replacement, no setting change, no twin hypothesis and no refinement, and
 `--mr` is refused.
 
 ### Serial stills: the one place a model acts before the merge
@@ -179,9 +199,20 @@ This is the only point at which a model affects which observations are merged to
 not gated by the null — there is no merge yet to test the model on. It chooses only between
 indexings that are equally valid for each crystal; a model that does not belong to the crystal
 carries no information to choose with, so the crystals stay mixed, as they would without a model.
+Where the lattice is only pseudo-merohedral and the crystals' own cells already say which indexing is
+which, the cells win: a crystal its cell anchors keeps that indexing, and the model decides
+only the crystals whose cell cannot tell.
 After the merge, the model is validated as in the steps above. Without `-C` and `-S`, or on rotation
 data, the model is not used before the merge at all.
 
+Without a model or reference, a stills run given `-S` settles the same question from the data: it
+cannot say which indexing is the true one, but it can say which crystals share one, and puts each
+crystal into the indexing in which it agrees best with all the others, a crystal its own cell decides
+again keeping that indexing (`INDEXING_AMBIGUITY_RESOLVED= data`). Without `-S` - the space group then
+determined by the run, after the merge - nothing resolves it, and the run warns. With a model, that resolution
+still runs, as a check only: `AMBIGUITY_DATA_DISAGREES=` in the report counts the crystals on which
+the data alone would have chosen differently from the model.
+
 ## Where a model can touch the space group
 
 Spelled out, because this is the question that matters most:
@@ -222,6 +253,99 @@ The safeguards behind 2 and 3:
   replacement not placing the model and no model decision taken
   ("The wrong-model null" in `tools/battery/README.md`; see also [Tests](TESTS.md)).
 
+## Refinement
+
+Giving a model is the opt-in: wherever the model is placed - it fits where it is, or molecular replacement
+placed it - rugnux refines it against the merge it was placed on; a model that is not placed is not refined.
+A run that should not spend the time is given no model; `--no-refine` skips the refinement of a placed model
+(for debugging). It takes seconds on a GPU and typically 2-15 minutes on the CPU (no GPU, or `--no-gpu`).
+Refinement comes after every processing decision and changes none of them: `R_WORK`, `R_FREE` and every
+other key outside `REFINE_` stay those of the model as placed, and `<prefix>.mtz`, `<prefix>_model.cif` and
+`<prefix>_maps.mtz` are the same as they would be without it. The broker's live mode refines an uploaded model
+in the same way (see [Rugnux live mode](JFJOCH_BROKER.md#rugnux-live-mode)).
+
+What the dictionary restrains is fixed at build time: the 20 standard amino acids and MSE, the DNA/RNA
+nucleotides and the common modified RNA nucleotides (PSU, 5MC, 1MA, OMG, OMC, OMU, H2U, 2MG, M2G, 7MG, 5MU),
+ATP/ADP/AMP/GTP/GDP/GMP, the cofactors NAD, NAI, NAP, NDP, FAD, FMN, HEM, HEC, SAM and SAH, dioxygen (OXY),
+DMSO, PEG fragments (PEG, PGE, PG4, 1PE), glycerol, ethylene glycol, sulfate, phosphate, acetate, MPD, water
+and common ions (a subset of the CCP4 Monomer Library compiled into
+rugnux; nothing is read from disk). Any other residue is held fixed: it stays in the structure factors and
+the bulk-solvent mask, and the refined atoms are kept from clashing with it; `REFINE_RESIDUES_FIXED_NAMES`
+lists them. The dictionary's hydrogens are added and ride on their parents. Metal ions, and the iron of a heme, are
+restrained to the donor atoms (O, N, S) the model's LINK / `_struct_conn` records bind them to: by the dictionary's own Zn and Fe
+links to Cys and His where they apply, otherwise at the library's typical distance for the metal, the donor
+element and the number of such records of the ion (Mg-O 2.07 A, Na-O 2.42 A, K-O 2.82 A at their
+usual coordination). A contact without a record, or one to a symmetry mate, is not restrained as a bond. The B factors of bonded atoms and of
+atoms in contact (waters included) are restrained to each other in proportion to their size. The weights of
+the X-ray term against the geometry and against that B restraint are chosen by R-free among short
+refinements whose bond and angle rmsd stay within 0.02 A and 2 degrees: three weights from the placed
+model, each with the B factors held and refined; then a trajectory of further short refinements from the
+best, each trying the weights as they are and changed, taken while R-free or R-work falls beyond 0.001 and
+R-free stays within 0.001 of its best; then a short final ladder, kept only where it lowers R-free beyond
+0.001. The free set is the merge's own, so the refined R-free judges the refinement against reflections it
+never fitted - but where the model was deposited, those reflections were most likely its depositor's working
+reflections, and a refinement against new data then moves R-free up from the unrefined value rather than
+down. `R_WORK`/`R_FREE` of the model as given are never replaced. On a GPU a refinement takes seconds; the CPU
+engine computes the same and is several times slower.
+
+**How a model is scored.** R-work, R-free and the likelihood target of every stage - the model as given
+(`REFINE_R_WORK_START`) as much as the refined one - come from one model of the structure factors,
+F<sub>model</sub> = k exp(-s<sup>T</sup>Bs/4) (F<sub>calc</sub> + k<sub>sol</sub> exp(-B<sub>sol</sub>s<sup>2</sup>/4) F<sub>mask</sub>):
+the atoms with the dictionary's riding hydrogens and their B made isotropic; a flat bulk solvent masked with the
+REFMAC radii (probe 1.0 A, shrink 0.8 A) on a grid of its own, at most 0.4 A apart, so that the shrink acts at any
+resolution; k<sub>sol</sub> and B<sub>sol</sub> searched over the physical range on the working reflections, and the
+overall scale and anisotropic B fitted to them by robust least squares, so that a few reflections the model cannot
+explain (a beam-stop shadow, an ice ring, a missing part of the model) do not set the scale of the rest. On a set of
+fourteen depositions from 1.1 to 3.6 A this gives REFMAC 5.8's 0-cycle R-work and R-free on the same model and data
+within 0.002 on twelve, and within 0.006 on the other two (`tools/battery/refine_parity.py` runs the comparison;
+`--refine-score-only` prints each term under `REFINE_SCORE_`, see [`--mode refine`](#refining-a-model-against-structure-factors-rugnux---mode-refine)).
+
+The algorithms - the target and its gradient, the likelihood's parameters, the restraints, the minimiser and
+the weight trials - are described in [§15](CPU_DATA_ANALYSIS_REFINEMENT.md), and the keys in
+[The results report](RUGNUX_REPORT.md#refinement-refine_).
+
+**What it does not do yet.** The refinement is a first, automatic pass on a placed model, not a replacement
+for a refinement program. Not implemented yet:
+
+- custom ligands or a monomer library beyond the embedded compounds above: other residues are held fixed (they stay in
+  F<sub>calc</sub>, the solvent mask and the clash terms), and no restraints are generated for a new ligand;
+- TLS;
+- anisotropic ADPs: an ANISOU record is turned into its isotropic B, and only isotropic B is refined;
+- NCS restraints;
+- twin refinement (a twinned target);
+- water building or removal (the blobs only point at candidates);
+- occupancy refinement and new alternative conformations (existing ones are refined in place);
+- rotamer and peptide-flip search, Ramachandran restraints;
+- real-space refinement, jelly-body and reference-model restraints;
+- a Metal (Apple GPU) path: on macOS the refinement runs on the CPU;
+- validation beyond the geometry's rmsd and clash count: no MolProbity-style report.
+
+## Refining a model against structure factors (`rugnux --mode refine`)
+
+`--mode refine` refines a model against merged structure factors that already exist - processed elsewhere, a
+deposition's, or a rugnux `.mtz` - and processes nothing:
+
+```
+rugnux --mode refine --model model.cif -o refined data.mtz
+```
+
+The input is an MTZ or a structure-factor mmCIF (as the PDB distributes them), gzipped or not, recognised by
+content; the model is PDB or mmCIF, taken as placed in the data's cell and refined in the data's space group. The
+columns are found, not named: amplitudes with their sigmas (F/SIGF, FP/SIGFP, FOBS, ...; calculated amplitudes and
+map coefficients such as FC, FWT, DELFWT are passed over) where the file has them, else intensities (IMEAN/SIGIMEAN,
+I/SIGI, ...) made into amplitudes by French-Wilson, else the mean of the anomalous pairs. The free set is read from
+a FreeR_flag-like column (flag 0 is the test set; where 0 marks the majority, as phenix and CNS write it, the
+minority value is); a file without one gets rugnux's own 5 % set. The refinement is the one run after a merge on a placed model, and
+writes the same files - `<prefix>_refined_model.cif`/`.pdb`, `<prefix>_refined_maps.mtz`, `<prefix>_blobs.json` - with
+the `REFINE_` keys in `<prefix>_report.txt`, beside `REFINE_FRENCH_WILSON=` and `REFINE_FREE_FLAGS= FILE|GENERATED`
+saying what had to be made of the input.
+
+| Option | Description |
+| --- | --- |
+| `--model <file>` | The model (required; it can also be given among the inputs, told by content) |
+| `--refine-score-only` | Score the model as given and refine nothing; every term of the score - R-work and R-free overall and in 20 resolution shells, the overall scale, B and anisotropic B, k<sub>sol</sub> and B<sub>sol</sub>, the likelihood over the working and the free reflections and its figure of merit over the working reflections, and the geometry's rmsd and rmsZ - under `REFINE_SCORE_` keys (`--developer` prints them all) |
+| `--refine-d-min <A>` | Leave out reflections finer than this |
+
 ## Free set and model bias
 
 **How the free set is made.** Rugnux draws its own test set (5 %, raised towards about 500 reflections on small data but never above 10 %):
@@ -239,8 +363,9 @@ mates share a flag. With `-z`, the reference's flags are inherited where the mer
 overall scale, the anisotropic *B*, the bulk solvent, the rigid body — is fitted on the working
 reflections only. The free set is then used for a few discrete *selections*: whether the rigid-body
 step is kept, which indexing wins, and in molecular replacement which placement and which group.
-Each of those leaves R-free very slightly optimistic where it fires. The coordinates, B-factors and
-occupancies of the model are never refined.
+Each of those leaves R-free very slightly optimistic where it fires. For `R_WORK`/`R_FREE` the
+coordinates, B-factors and occupancies of the model are never refined; the refinement above refines them on
+the side, under `REFINE_` keys of its own.
 
 **What `R_FREE` means here — and what it does not.** It is the model as placed, scored on Rugnux's
 free set: a check that the model fits these data, and a trend number between datasets of one
@@ -271,7 +396,7 @@ the data, a weak shell says nothing about them, and nothing acts on it.
 **When to give a model.**
 
 - **You have a structure of this crystal form** (a fragment campaign, a ligand soak, a reference
-  structure): give it with `--model`. You get maps and a placed model ready for refinement, the
+  structure): give it with `--model`. You get maps, a placed model and Rugnux's own first refinement of it, the
   indexing of every dataset brought into the model's, and the hand fixed — the things that make a
   campaign's files directly comparable. A wrong or rejected model costs a few seconds and changes
   nothing.
@@ -294,6 +419,7 @@ the data, a weak shell says nothing about them, and nothing acts on it.
 |---|---|---|
 | `<prefix>.mtz` / `.cif` / `.hkl` | The answer: the data's space group, with only the class-(b) labels from the model | Refinement, deposition, everything by default |
 | `<prefix>_model.cif` / `.pdb`, `<prefix>_maps.mtz` | The model as placed, in the frame of `<prefix>.mtz`, and its map coefficients (Coot/PyMOL open them as maps) | Starting refinement (REFMAC5, phenix.refine), PanDDA, Coot |
+| `<prefix>_refined_model.cif`/`.pdb`, `<prefix>_refined_maps.mtz`, `<prefix>_blobs.json` | The placed model refined by rugnux, its map coefficients, and the unexplained blobs of its difference map | A first look at the refined density and at what the model leaves unexplained; continuing refinement |
 | `<prefix>_twin_<SG>.mtz` / `.cif` | The same data merged in a subgroup with a twin law — written from the data, model or not | Twin refinement, where you suspect the higher group absorbed a twin law |
 | `<prefix>_mr.mtz` / `.cif`, `<prefix>_mr_model.pdb` / `.cif`, `<prefix>_mr_*` maps | The merge in the space group the model chose (`MODEL_CHOICE_SPACE_GROUP=`), and the model placed there | Refinement *if* you accept the model's choice; compare R-free against the answer's |
 
diff --git a/docs/RUGNUX_OVERVIEW.md b/docs/RUGNUX_OVERVIEW.md
index 7899448a6..4fbbf9793 100644
--- a/docs/RUGNUX_OVERVIEW.md
+++ b/docs/RUGNUX_OVERVIEW.md
@@ -4,7 +4,7 @@ The map of a run, in the order it happens — one paragraph per stage, each link
 [data-analysis reference](CPU_DATA_ANALYSIS.md) where the algorithm lives. The walk-through is a
 rotation run with the defaults; stills differences are at the end.
 
-![The rotation pipeline: pass 1 integrates half the sweep at the file's geometry, pass 2 the whole sweep at the refined one, and the better of the two goes on to the space group and the written merge](images/rugnux_pipeline.svg)
+![The rotation pipeline: pass 1 integrates half the sweep at the file's geometry, pass 2 the whole sweep at the refined one, and the better of the two goes on to the space group and the written merge; with a model, the placement and the refinement follow, deciding nothing](images/rugnux_pipeline.svg)
 
 **Open the dataset.** The geometry, wavelength and goniometer come from the file
 ([What Rugnux reads](RUGNUX_FORMATS.md)). A goniometer axis that turns makes it a rotation run; none, or one
@@ -74,17 +74,30 @@ then gives R-work/R-free and σA-weighted maps. The model never changes how the
 [§14](CPU_DATA_ANALYSIS_DECISIONS.md)). It runs on every GPU of the machine, and on a Mac its
 model density and rotation function on the Apple GPU ([GPU data analysis](GPU_DATA_ANALYSIS.md#molecular-replacement)).
 
+**Model: refinement.** A placed model is then refined against the merge it was placed on (`--no-refine`
+skips it): its chains as rigid bodies and B per residue where that lowers R-free, then every atom's position
+and B by a restrained maximum-likelihood refinement whose weights are chosen by R-free in short trials run
+side by side; the refined model gives its own maps and the blobs of unexplained density. Like the
+validation it decides nothing - the merge, `R_WORK`/`R_FREE` and the placed model's files stay as they
+were, and the refined results are written beside them under `REFINE_`
+([Model and reference](RUGNUX_MODEL_AND_REFERENCE.md#refinement), [§15](CPU_DATA_ANALYSIS_REFINEMENT.md)).
+On a GPU it takes seconds, with the weight trials spread over every card
+([GPU data analysis](GPU_DATA_ANALYSIS.md#refinement)).
+
 **Write.** The merged `.mtz` / `.cif` / `.hkl`, the unmerged MTZ and the
 results report land next to each other ([Output files](RUGNUX_TUTORIAL.md#output-files)); with a
-model, the maps and the placed model are written too, and where molecular replacement chooses another
-space group or the twin hypothesis' subgroup, that merge is written beside the answer as
+model, the maps and the placed model are written too, and beside them the refined model, its maps and
+its blobs; where molecular replacement chooses another space group or the twin hypothesis' subgroup, that merge is written beside the answer as
 `<prefix>_mr.mtz`/`.cif` with the model placed there, `<prefix>_mr_model.pdb`.
 
 **Stills instead.** Serial data skip the two-pass machinery: each image is indexed independently
 (with the known-cell `ffbidx` indexer where a cell is given), partiality comes from a per-crystal
-orientation-tilt post-refinement rather than a rocking curve, and a merohedral indexing ambiguity
-has to be broken per image, at integration time, against a reference or a model
-([Advanced ▸ the indexing ambiguity](RUGNUX_ADVANCED.md#the-indexing-ambiguity)). The input may be
+orientation-tilt post-refinement rather than a rocking curve, and where the lattice admits a
+merohedral indexing ambiguity the crystals are put into one indexing before the first merge: from the
+data alone, each crystal into the indexing in which it agrees best with all the others, where the space
+group is given (`-S`); or per image against a reference or a model, which then decides the indexing
+the merge is written in. Either way a crystal whose own refined cell already tells the indexings apart
+keeps its indexing ([Advanced ▸ the indexing ambiguity](RUGNUX_ADVANCED.md#the-indexing-ambiguity)). The input may be
 several files given together - Jungfraujoch masters, or the files an XFEL pipeline writes, read without
 a geometry file ([Serial XFEL inputs](RUGNUX_FORMATS.md#serial-xfel-inputs)). Before the images are
 processed the beam centre is decided on a sample of frames, the file's against the measured ones, and a
@@ -94,4 +107,4 @@ each detector module as well ([§1.4](CPU_DATA_ANALYSIS_IMAGE.md#14-the-beam-cen
 [§7.7](CPU_DATA_ANALYSIS_INDEXING.md#77-stills-a-given-cell-and-the-detector-modules)). The report adds
 R_split and a CC1/2 from frame half-sets, as CrystFEL computes them ([Report](RUGNUX_REPORT.md)).
 
-![The stills pipeline: the beam centre (and, with a cell, the distance and the module placement) decided on the frames first, every image indexed on its own, and the crystals scaled and merged together](images/rugnux_pipeline_stills.svg)
+![The stills pipeline: the beam centre (and, with a cell, the distance and the module placement) decided on the frames first, every image indexed on its own, the crystals put into one indexing where the lattice admits two, then scaled and merged together; with a model, the placement and the refinement follow, deciding nothing](images/rugnux_pipeline_stills.svg)
diff --git a/docs/RUGNUX_REPORT.md b/docs/RUGNUX_REPORT.md
index c68e939b3..d88d3e004 100644
--- a/docs/RUGNUX_REPORT.md
+++ b/docs/RUGNUX_REPORT.md
@@ -119,10 +119,12 @@ The header block above section 1 records **how the result was produced**: `RUGNU
 
 Rates, per-image costs and progress remain on stdout only.
 
-Sections, in order: the `SUMMARY`, then `1. DATA SET AND GEOMETRY`, `2. CRYSTAL`,
-`3. MERGED DATA`, `4. DIAGNOSTICS` and `5. MODEL VALIDATION` only with `--model` or `--mr` - which
-also holds molecular replacement's keys where it ran ([below](#molecular-replacement))
-(see [The summary](#the-summary-and-what-the-run-decided) below). The numbering is contiguous, and
+Sections, in order: the `SUMMARY` ([below](#the-summary-and-what-the-run-decided)), then
+`1. DATA SET AND GEOMETRY`, `2. CRYSTAL`, `3. MERGED DATA`, `4. DIAGNOSTICS` and, only where a model
+was given (`--model`, `--mr`, or a model file among the inputs), `5. MODEL VALIDATION` - which also
+holds the keys of [molecular replacement](#molecular-replacement) and of the
+[refinement](#refinement-refine_) where they ran. A `--mode refine` report has one section,
+`1. REFINEMENT`. The numbering is contiguous, and
 the fifth section appearing renumbers nothing; a stage that did not run states that inside its
 section — `MERGE= NOT_PERFORMED` — rather than the section disappearing.
 
@@ -207,6 +209,29 @@ is ambiguous about which geometry produced it.
 **Not in the report:** timing, frame rates, thread counts, per-image progress and library banners.
 Those are process, not result, and stay on stdout.
 
+## The headline keys
+
+The keys most scripts read, by section; the rest of this page explains the ones that need it.
+
+| key | meaning |
+|---|---|
+| `EXPERIMENT_TYPE` | `ROTATION` or `STILLS` (section 1) |
+| `IMAGES_PROCESSED`, `WAVELENGTH` | Images the run read, and the wavelength (Å) |
+| `OSCILLATION_RANGE`, `STARTING_ANGLE`, `ROTATION_AXIS` | Rotation only: the per-image rotation the run integrated at (deg: the file's, scaled where the run adopted a goniometer rotation scale), the first image's angle and the axis |
+| `DETECTOR_DISTANCE`, `BEAM_CENTRE`, `DETECTOR_TILT` | The geometry the run integrated at (mm; the point of normal incidence in pixels; the three PONI rotations in degrees) - on a rotation run the post-refined one, not the header's |
+| `DIRECT_BEAM` | Where the direct beam meets the detector under that tilt (pixels) |
+| `LATTICE_FOUND`, `UNIT_CELL_CONSTANTS`, `CELL_ESD` | Section 2: whether a lattice was found, the cell (a b c α β γ, Å and degrees) and its e.s.d.s ([below](#cell-esds)) |
+| `SPACE_GROUP_NAME`, `SPACE_GROUP_NUMBER` | The space group the files are written in ([below](#the-space-group-and-the-sohncke-answer-beside-it)) |
+| `MOSAICITY_DEG` | Rotation only ([below](#mosaicity)) |
+| `MERGE` | Section 3: `PERFORMED` or `NOT_PERFORMED` (`--no-merge`) |
+| `INCLUDE_RESOLUTION_RANGE` | `dmax dmin` of the written reflections (Å), as XDS's keyword |
+| `FITTED_RESOLUTION` | Where the CC1/2 fall-off crosses the `--resolution-cc-target`; absent where the curve is not a fall-off (a `RESOLUTION_FIT` warning says why) |
+| `UNIQUE_REFLECTIONS`, `TOTAL_OBSERVATIONS`, `COMPLETENESS`, `MULTIPLICITY` | Over the written range; completeness in percent |
+| `I_OVER_SIGMA`, `R_MEAS`, `CC_HALF`, `WILSON_B` | The overall merging statistics; the shell table beside them is in the comment lines |
+| `SIGANO`, `CC_ANOM`, `FRIEDELS_LAW` | The anomalous signal, and whether Friedel pairs were merged (`FALSE` with `-A`) |
+| `ERROR_MODEL_A`, `ERROR_MODEL_B`, `ISA` | The error model in XDS's convention and ISa = 1/sqrt(a·b); `ISA= undetermined` where b is zero within its error, so 1/b would be noise |
+| `R_WORK`, `R_FREE` | Section 5: the model as placed against these data ([below](#model-validation)); the refined model's are `REFINE_R_WORK`/`REFINE_R_FREE` |
+
 ## The summary, and what the run decided
 
 The file opens with a **`SUMMARY`** section, above everything it summarises. It exists because the
@@ -238,14 +263,27 @@ and a run that produced a textbook data set read identically for their first thr
   correct cells show, an arbitrary indexing choice (`Indexing choice`, a rotation sweep whose cell
   admits alternative indexing: one sweep is indexed consistently, so it matters only against other data;
   the operators are **`INDEXING_AMBIGUITY_OPERATORS=`** in section 2). On serial stills the same ambiguity
-  mixes the hands in the merge, and is an `INDEXING_AMBIGUITY` warning. `INDEXING_RATE=` - the share of
+  mixes the hands in the merge. Where the space group was given (`-S`), the crystals are made
+  consistent from the data alone - by their own cells where those decide the indexing, and by the
+  intensities otherwise - and section 2 says so: **`INDEXING_AMBIGUITY_RESOLVED= data`**,
+  **`AMBIGUITY_CRYSTALS=`** (the crystals that took part), **`AMBIGUITY_REINDEXED=`** (of them, the ones
+  moved), **`AMBIGUITY_SEPARATION_SIGMA=`** (per crystal, how far its chosen indexing beats the best other
+  one in correlation with all the other crystals, in sigma; the median) and
+  **`AMBIGUITY_DECIDED_FRACTION=`** (the share of crystals decided at over 3 sigma). With a reference or
+  a model the choice is theirs, except for the crystals whose own cell decides
+  (`INDEXING_AMBIGUITY_RESOLVED= reference`); the data-only resolution then runs as a check, its
+  `AMBIGUITY_CRYSTALS=`, `AMBIGUITY_SEPARATION_SIGMA=` and `AMBIGUITY_DECIDED_FRACTION=` are given as
+  above, and **`AMBIGUITY_DATA_DISAGREES=`** takes the place of `AMBIGUITY_REINDEXED=`: the crystals on
+  which the data alone would have chosen otherwise. `AMBIGUITY_TIME_S=` (with `--developer`) is the
+  time the data-only resolution took. None of these keys is written by `--mode scale`, which does not run it. Where the space group was determined by the run instead, the mixed merge is an
+  `INDEXING_AMBIGUITY` warning. `INDEXING_RATE=` - the share of
   frames the per-image indexer took - is a stills measure: a rotation run indexes the sweep as a whole, so
   there it is written only with `--developer`, and `NO_LATTICE` rests on whether the sweep was indexed.
 - **`WARNING_COUNT=`** and the **`WARNING:`** lines follow, in the same section. They are what they
   always were; they have moved from the bottom of the file to the top.
 
 Then the numbered sections: **1. DATA SET AND GEOMETRY**, **2. CRYSTAL**,
-**3. MERGED DATA**, **4. DIAGNOSTICS**, and **5. MODEL VALIDATION** only with `--model`.
+**3. MERGED DATA**, **4. DIAGNOSTICS**, and **5. MODEL VALIDATION** only where a model was given.
 
 ## The reference-range table
 
@@ -315,8 +353,8 @@ per-zone screw table.
 reindexing operator from the axes the space group was determined on (CCP4 style, `h,k,l` where
 nothing moved) and what chose the setting - `STANDARD`, `CELL` (`-C`), `SPACE_GROUP` (a non-standard
 `-S`), `MODEL` (a `--model` that fits) or `REFERENCE` (`-z`). `SPACE_GROUP_NAME`, the cell and every
-file the run writes are in that setting (see RUGNUX_ADVANCED.md, "The setting the files are written
-in").
+file the run writes are in that setting (see
+[The setting the files are written in](RUGNUX_ADVANCED.md#the-setting-the-files-are-written-in)).
 
 `SOHNCKE_SPACE_GROUP=` in section 2 is written on every run whose space group was determined by the
 search; a run given its group with `-S` has no Sohncke candidate to name and omits the key. Where the
@@ -710,6 +748,36 @@ as the main one can still give data as good as XDS's, since the domains' reflect
 where they overlap the main lattice's. Look at the crystal, and at the result. The summary at the top of
 the report has a `Multiple lattices` line, `none found` where nothing was listed.
 
+## Cell e.s.d.s
+
+**`CELL_ESD=`** (section 2, rotation only) is the standard uncertainty of each of the six numbers of
+`UNIT_CELL_CONSTANTS=`, in the units of that line (Å, degrees) - the number to set beside XDS's
+`E.S.D. OF CELL PARAMETERS` in `CORRECT.LP`, and the one written as `ZERR` in the `.ins` and as
+`_cell.*_esd` in the mmCIF. A parameter the space group fixes (a right angle, γ = 120°) reads 0, and
+one it ties to another (b = a) has that one's e.s.d.
+
+It comes from the integrated observations the files are written from: every strong one (I > 3σ,
+unclipped, unsaturated, off the ice rings) gives 1/d at its observed centroid, which depends on the
+detector geometry but not on the crystal orientation, and q² = hᵀG\*h is linear in the reciprocal
+metric G\*. The components of G\* the point group leaves free are fitted by least squares (one
+e.s.d. on q for every observation, those more than 4σ off rejected), the covariance is scaled by the
+goodness of fit and carried onto a, b, c, α, β, γ - **`CELL_ESD_LSQ=`**. Least-squares cell e.s.d.s
+are known to be too small (F. H. Herbstein, "How precise are measurements of unit-cell dimensions
+from single crystals?" (2000), Acta Cryst. B56, 547-557
+[doi:10.1107/S010876810000269X](https://doi.org/10.1107/S010876810000269X)), as they see the scatter of the centroids and nothing that
+changes over the sweep, so the same fit is made on eight blocks of consecutive frames and the
+scatter of their cells, over √blocks, is **`CELL_ESD_BLOCKS=`** (where at least four blocks could be
+fitted; **`CELL_ESD_BLOCK_COUNT=`** says how many). `CELL_ESD=` is, per parameter, the larger of the
+two. **`CELL_ESD_REFLECTIONS=`** is the number of distinct reflections used and
+**`CELL_ESD_THETA_RANGE_DEG=`** their θ range, written as `_cell_measurement.reflns_used`,
+`theta_min` and `theta_max` in the mmCIF. With `--developer`, **`CELL_ESD_OBSERVATIONS=`** is the
+number of observations behind them and **`CELL_DSPACING_FIT=`** the cell the d-spacing fit itself
+returned.
+
+Neither estimate includes what is common to every observation - the wavelength and the detector
+distance scale the whole cell - so the e.s.d. is a precision, not an accuracy. Stills runs have no
+cell e.s.d.: the crystals' cells differ from one another by more than any one of them is measured to.
+
 ## Mosaicity
 
 **`MOSAICITY_DEG=`** (section 2, and a `Mosaicity` line in the summary) is the mosaic spread the merge
@@ -868,7 +936,8 @@ says so, since refinement and map interpretation should allow for it.
 
 ## Model validation
 
-Section 5 appears only with `--model`. It reports the supplied model against the merged data —
+Section 5 appears only where a model was given (`--model`, `--mr`, or a model file among the
+inputs). It reports the supplied model against the merged data —
 R-factors, maps, anomalous sites — and, separately, whether the data accepted the model at all.
 
 The two are not the same question, and the report keeps them apart. **The R-factors, the maps and the
@@ -943,7 +1012,8 @@ between those two runs cannot be read; `R_MODEL_SHELL_SCALED` can.
 
 Both R values are over **all** the reflections, not the free 5%. Nothing here is refined — the
 coordinates, the B-factors and the occupancies are the model's own, and only the scale and the
-placement are fitted — so work and free estimate the same quantity (they differ by a median 0.001
+placement are fitted (the refinement that follows is reported apart, under
+[`REFINE_*`](#refinement-refine_)) — so work and free estimate the same quantity (they differ by a median 0.001
 over our corpus) and the split buys no cross-validation while costing a factor of √20 in precision.
 
 None of this touches the maps: the map coefficients and `R_WORK` / `R_FREE` are
@@ -1103,3 +1173,55 @@ GPU where there is one (`MR_SEARCH_DEVICE=`). `MR_DECISION=` is then:
 With `SPACE_GROUP` and `TWIN_SUBGROUP` the placed model is written as `<prefix>_mr_model.pdb`/`.cif`.
 Apart from the enantiomorph label, the answer's own files are never changed by the model.
 
+
+## Refinement (`REFINE_*`)
+
+Where a model was placed and refined ([Refinement](RUGNUX_MODEL_AND_REFERENCE.md#refinement); the algorithms in
+[§15](CPU_DATA_ANALYSIS_REFINEMENT.md)), section `5. MODEL VALIDATION` ends with the refinement's keys. In
+`--mode refine` they make up the report's only section, `1. REFINEMENT`, after `MODEL_FILE=`, `SPACE_GROUP=`,
+`WAVELENGTH=` and what had to be made of the input. **No key outside `REFINE_` reads the refinement**:
+`R_WORK=` and `R_FREE=` above stay the model as placed, and so does every decision of the run. Keys marked
+*dev* are written with `--developer` only.
+
+| key | meaning |
+|---|---|
+| `REFINE` | `PERFORMED` \| `NOT_PERFORMED` (with `REFINE_REASON`) |
+| `REFINE_DEVICE`, `REFINE_SECONDS` | *dev*. `GPU` or `CPU`, and the time the refinement took |
+| `REFINE_D_MIN` | The finest reflection refined against, Å |
+| `REFINE_R_WORK_START`, `REFINE_R_FREE_START` | The model as given, scored as the refinement scores (riding hydrogens, B isotropic, the fine solvent mask, the robust scale): REFMAC's 0-cycle R-factors to about 0.002 on the same model and data. Not `R_WORK`/`R_FREE`, which are the validation's own scoring of the placed model |
+| `REFINE_RIGID_BODIES` | The chains moved as rigid bodies, where that step was kept (0: not kept) |
+| `REFINE_R_WORK_PLACEMENT`, `REFINE_R_FREE_PLACEMENT` | After the placement stage (rigid bodies, then one B per residue, each kept only where it lowers R-free) |
+| `REFINE_R_WORK`, `REFINE_R_FREE` | After the restrained stage: the refined model, the one written as `<prefix>_refined_model.cif` |
+| `REFINE_RMSD_BONDS`, `REFINE_RMSD_ANGLES` | The refined model's rmsd from the dictionary's bonds (Å) and angles (°); the weight is chosen within 0.02 Å and 2° |
+| `REFINE_RMSD_METAL_BONDS` | The rmsd of the metal-donor bonds made from the model's LINK records, apart from the covalent bonds. Present where there are any |
+| `REFINE_RMSD_BONDS_START`, `REFINE_RMSD_ANGLES_START` | *dev*. The same for the model as given |
+| `REFINE_CLASHES` | Pairs of atoms in the refined model more than 0.4 Å closer than their contact distance (symmetry mates included) |
+| `REFINE_XRAY_WEIGHT` | *dev*. The X-ray weight of the positions that was kept |
+| `REFINE_ATOMS`, `REFINE_ATOMS_REFINED` | The model's atoms (hydrogens not counted) and those refined: the atoms of the residues the dictionary describes, with an occupancy above zero |
+| `REFINE_RESIDUES_FIXED`, `REFINE_RESIDUES_FIXED_NAMES` | The residues the embedded dictionary does not describe, held fixed but kept in the structure factors, the solvent mask and the clash terms, and their names |
+| `REFINE_BULK_SOLVENT_K_SOL`, `REFINE_BULK_SOLVENT_B_SOL` | *dev*. The flat bulk solvent of the refined model |
+| `REFINE_BLOBS` | The blobs of the refined mFo-DFc map (above 3 σ, peaking above 4 σ) |
+| `REFINE_BLOBS_LIGAND`, `REFINE_BLOBS_WATER`, `REFINE_BLOBS_ION`, `REFINE_BLOBS_MODEL_ERROR` | How many of them are read as each ([§15.9](CPU_DATA_ANALYSIS_REFINEMENT.md#159-unexplained-density-blobs)); the rest are unassigned |
+
+A prose paragraph after them lists the five strongest blobs with their reading, peak, volume, position and
+nearest atom; all of them are in `<prefix>_blobs.json`, strongest first, one object per blob: `kind`,
+`centroid` (Å, Cartesian, the copy nearest the model), `peak_sigma`, `volume_A3`, `score_sigma_A3` (the
+density above the cutoff integrated), `nearest_atom`, `nearest_atom_distance_A`, `polar_contacts`,
+`metal_contacts` and `anomalous_sigma`.
+
+**The score of the model as given** follows, every term under `REFINE_SCORE_`: `REFINE_SCORE_R_WORK`,
+`REFINE_SCORE_R_FREE`, `REFINE_SCORE_N_WORK` and `REFINE_SCORE_N_FREE` by default, and with `--developer` the
+overall scale (`REFINE_SCORE_K_OVERALL`), its isotropic and anisotropic B (`REFINE_SCORE_B_ISO`,
+`REFINE_SCORE_B_ANISO`: B11 B22 B33 B12 B13 B23 less the isotropic part, Cartesian), the bulk solvent
+(`REFINE_SCORE_K_SOL`, `REFINE_SCORE_B_SOL`) and the spacing of its mask grid (`REFINE_SCORE_MASK_SPACING`), the
+riding hydrogens (`REFINE_SCORE_HYDROGENS`), the likelihood over the working and the free reflections
+(`REFINE_SCORE_NLL_WORK`, `REFINE_SCORE_NLL_FREE`) and its mean figure of merit over the working reflections
+(`REFINE_SCORE_FOM`), the geometry's rmsd and rmsZ (`REFINE_SCORE_RMSD_BONDS`, `REFINE_SCORE_RMSZ_BONDS`,
+`REFINE_SCORE_RMSD_ANGLES`, `REFINE_SCORE_RMSZ_ANGLES`, `REFINE_SCORE_RMSD_METAL_BONDS`,
+`REFINE_SCORE_RMSD_BONDS_ALL` for covalent and metal bonds together) and a table of R-work and R-free in 20
+resolution shells. `rugnux --mode refine --refine-score-only` writes this score and nothing else.
+
+In `--mode refine` the input's keys come first: `REFINE_REFLECTIONS` and `REFINE_FREE_REFLECTIONS` (those read,
+after any `--refine-d-min`), `REFINE_FRENCH_WILSON` (`TRUE` where the file had intensities only and the amplitudes
+were made by French-Wilson), `REFINE_FREE_FLAGS` (`FILE`, or `GENERATED` where the file had no free set and
+rugnux drew its own) and `REFINE_D_MIN_LIMIT` (the `--refine-d-min` given).
diff --git a/docs/RUGNUX_TUTORIAL.md b/docs/RUGNUX_TUTORIAL.md
index 3b5c707c0..2ec7e3be5 100644
--- a/docs/RUGNUX_TUTORIAL.md
+++ b/docs/RUGNUX_TUTORIAL.md
@@ -20,7 +20,8 @@ machine. Nothing is assumed about the crystal
 — the goniometer axis in the file tells Rugnux this is a rotation sweep, the unit cell comes from
 indexing the data, the space group from its systematic absences, and the resolution limit from where
 CC1/2 falls off. Progress, statistics and timing go to the terminal, and the output files land
-next to each other.
+next to each other. Serial stills and a run with a model start the same way, with the stills' files
+or the model added to the inputs ([Quick start](RUGNUX.md#quick-start)).
 
 `myrun_report.txt` is written for a person, top to bottom: it says which space group was chosen and
 on what evidence, how far the data go, and anything that needs attention. To pull one number out of
@@ -63,7 +64,8 @@ rugnux -o myrun --write-process-h5 dataset_master.h5
 # skip the unmerged MTZ (written by default), when only the merged data is wanted
 rugnux -o myrun --no-export-unmerged dataset_master.h5
 
-# check the merged data against a known structure: R-work / R-free and maps
+# check the merged data against a known structure: R-work / R-free, maps and the
+# refined model (the model may also be given as a second input, without --model)
 rugnux -o myrun --model model.pdb dataset_master.h5
 ```
 
@@ -162,24 +164,39 @@ disturbance of the sweep, not dose, and the report says so and points at the swe
 ## Still / serial data
 
 A dataset with **no goniometer axis**, or one whose axis does not turn (e.g. a serial grid scan), is
-processed as **independent stills automatically** — no flag needed. Known-cell indexing with the fast-feedback indexer,
-then merge against a reference structure:
+processed as **independent stills automatically** — no flag needed. A run spread over several files
+is given as all of them at once — several NXmx masters of one setup, or the files an XFEL pipeline
+writes ([Serial XFEL inputs](RUGNUX_FORMATS.md#serial-xfel-inputs)):
 
 ```
-rugnux serial_master.h5 \
-    -o serial_run \
-    -X ffbidx -C 79,79,38,90,90,90 -S 96 \
-    -z reference.mtz \
-    --scaling-high-resolution 1.8
+rugnux -o serial *_master.h5     # several NXmx masters, read and merged as one run
+rugnux -o serial run*.h5         # all the files of one stills dataset; *.cxi, *.xtc alike
 ```
 
+Where the cell and space group are known, give them; where the detector's panels are described by a
+CrystFEL geometry file, give that too:
+
+```
+rugnux -o serial -C 79,79,38,90,90,90 -S P43212 --crystfel-geometry detector.geom run*.h5
+```
+
+The wavelength and distance are read from the data or the geometry file; `--wavelength` and
+`--detector-distance` are only for files that state neither (a distance given there is held, not
+refined). A reference reflection file of the same crystal form (`-z reference.mtz`) or a model
+(`model.pdb` as a further input, or `--model`) can be added to any of these.
+
 A crystal form with an [indexing ambiguity](RUGNUX_ADVANCED.md#the-indexing-ambiguity) — P3, P4, P6 and their
-relatives — **needs** either the `-z` above or `--model model.pdb`, and needs it on the run that
-integrates: every crystal is indexed in its own hand, and the two are averaged together in the merge
-unless each image is put into the same hand as it is integrated.
+relatives — needs the space group on the run that integrates: every crystal is indexed in one of the
+alternative indexings at random, and they are averaged together in the merge unless the crystals are put
+into one first. With `-S` given, the run does that from the data alone, making the crystals consistent
+with each other (`INDEXING_AMBIGUITY_RESOLVED= data`); a reference (`-z`), or `--model model.pdb`
+together with `-C` and `-S`, puts each image into the reference's indexing instead, so that the merge
+also comes out in it. Without `-S` and without either, the mixed merge can look more symmetric than the
+crystal is, and the run warns.
 
-`ffbidx` requires a known cell (`-C`) and is the indexer of choice for sparse serial stills. The
-self-calibrating spot finder is on by default for both workflows (`--no-adaptive-spots` turns it off), and for
+`ffbidx` requires a known cell (`-C`) and is the indexer of choice for sparse serial stills; the
+default `-X Auto` picks it for stills whenever a cell is given, so there is no `-X` to set; without a
+cell the stills are indexed de novo. The self-calibrating spot finder is on by default for both workflows (`--no-adaptive-spots` turns it off), and for
 serial stills leave `--min-pix-per-spot` **unset** so it is chosen per image — across the still-target battery this
 combination raises the indexing rate and typically extends resolution over a fixed threshold and
 fixed min-pix, at equal or better CC1/2. (You can still pin a fixed threshold with `--spot-sigma` /
@@ -266,6 +283,9 @@ Absorption is corrected only by the empirical surface a rotation run fits and ke
     stills runs write the merged reflections (Bijvoet mates at `+hkl` and `-hkl`). Intensities are put
     on a common scale so the largest value fits the fixed-width field, and the file ends with the
     `0 0 0` terminator record.
+  - `<prefix>.ins` — the SHELX instructions to go with the `.hkl`: `CELL` at the wavelength, `ZERR`
+    with the cell's e.s.d.s, `LATT` and `SYMM` for the space group, and a placeholder `SFAC`/`UNIT` for the
+    user to replace with the formula (see [Small-molecule structures with SHELXT and SHELXL](RUGNUX_INTEGRATION.md#small-molecule-structures-with-shelxt-and-shelxl)).
 
   All three carry the **refined unit cell** (from rotation indexing) and the **space group determined
   from systematic absences** (constrained to the indexed lattice symmetry).
@@ -285,6 +305,10 @@ Absorption is corrected only by the empirical surface a rotation run fits and ke
   per-dataset input layout, and the pair dimple produces — and it is skipped, with a log line, for
   a cell the PDB format cannot hold. See
   [Validating against a model](RUGNUX_ADVANCED.md#validating-against-a-model-rugnux---model).
+- `<prefix>_refined_model.cif` / `.pdb`, `<prefix>_refined_maps.mtz` and `<prefix>_blobs.json` —
+  where the model was placed, the model as rugnux refined it, its map coefficients and the blobs of
+  density its difference map leaves unexplained; `--no-refine` skips them. See
+  [Refinement](RUGNUX_MODEL_AND_REFERENCE.md#refinement).
 - `<prefix>_twin_<SG>.mtz` / `.cif` — only where the chosen space group may have absorbed a twin law:
   the same data merged in a subgroup `<SG>`, with the twin law and its fraction, same resolution and
   free set as `<prefix>.mtz`, for refinement with that law. With `--model`, the maps come from
@@ -296,8 +320,13 @@ Absorption is corrected only by the empirical surface a rotation run fits and ke
   the model chose, beside the run's own answer, which is left as it was. See
   [Validating against a model](RUGNUX_ADVANCED.md#validating-against-a-model-rugnux---model).
 - `<prefix>_report.txt` — the **results report**: what the run determined, in a form both a person and
-  a beamline script can read. Always written, next to the files above. See
+  a beamline script can read. Written by every `mx` and `scale` run, next to the files above (an empty prefix, `-o ""`, writes nothing). See
   [The results report](RUGNUX_REPORT.md#the-results-report).
+- `<prefix>_log.txt` — the full timestamped log of the run, at debug level, written by every run with
+  an output prefix; send it with the report when asking about a run.
+- `<prefix>_modules.h5` — serial stills on a detector of several modules: where the geometry
+  refinement placed each module, readable back with `--module-geometry` (see
+  [Module geometry](RUGNUX_FORMATS.md#module-geometry)).
 - `<prefix>_plot.txt` — **the per-image table**, one row per processed image, whitespace-separated,
   with a single `#` legend line over its own columns so gnuplot plots it as it stands
   (`plot '<prefix>_plot.txt' using 1:4`). The columns are:
diff --git a/docs/TECHNICAL.md b/docs/TECHNICAL.md
new file mode 100644
index 000000000..dc99d5236
--- /dev/null
+++ b/docs/TECHNICAL.md
@@ -0,0 +1,59 @@
+# Technical reference
+
+The pages that describe how things work rather than how to use them: the algorithms behind the
+analysis, the file formats and streams, the programming interfaces, the hardware and the FPGA
+design. Nothing here is needed to run Rugnux or the viewer; all of it is needed to build on them.
+
+```{toctree}
+:caption: Data analysis
+:maxdepth: 1
+
+CPU_DATA_ANALYSIS
+CPU_DATA_ANALYSIS_IMAGE
+CPU_DATA_ANALYSIS_INDEXING
+CPU_DATA_ANALYSIS_INTEGRATION
+CPU_DATA_ANALYSIS_DECISIONS
+CPU_DATA_ANALYSIS_REFINEMENT
+GPU_DATA_ANALYSIS
+DETECTOR_GEOMETRY
+RUGNUX_BENCHMARKING
+EXTERNAL_TEST_DATA
+EXTERNAL_TEST_DATA_STILLS
+```
+
+```{toctree}
+:caption: Formats and interfaces
+:maxdepth: 1
+
+HDF5
+PIXEL_MASK
+IMAGE_STREAM
+CBOR
+OPENAPI
+OPENAPI_SPECS
+```
+
+```{toctree}
+:caption: Hardware and FPGA
+:maxdepth: 1
+
+HARDWARE
+SOFTWARE
+DETECTORS
+FPGA
+FPGA_DESIGN
+FPGA_DATA_ANALYSIS
+FPGA_NETWORK
+FPGA_PCIE_DRIVER
+FPGA_SETTINGS
+FPGA_LICENSE
+```
+
+```{toctree}
+:caption: Development
+:maxdepth: 1
+
+TESTS
+VERSIONING
+SECURITY
+```
diff --git a/docs/THIRD_PARTY_NOTICES.md b/docs/THIRD_PARTY_NOTICES.md
index e3f9591a1..8c9959ba5 100644
--- a/docs/THIRD_PARTY_NOTICES.md
+++ b/docs/THIRD_PARTY_NOTICES.md
@@ -33,7 +33,6 @@ linked into the Jungfraujoch executables.
 | [FFTW](https://www.fftw.org/) | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | [fftw.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/fftw.txt) |
 | [Ceres Solver](https://github.com/ceres-solver/ceres-solver) | (pinned) | Google Inc. and contributors | BSD-3-Clause | [ceres-solver.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/ceres-solver.txt) |
 | [Abseil](https://github.com/abseil/abseil-cpp) | 20250127 (required by Ceres) | Google Inc. | Apache-2.0 | [abseil.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/abseil.txt) |
-| [fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) | (pinned) | PSI | BSD-3-Clause | [fast-feedback-indexer.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/fast-feedback-indexer.txt) |
 | [libjpeg-turbo](https://github.com/libjpeg-turbo/libjpeg-turbo) | 3.2.0 | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | [libjpeg-turbo.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/libjpeg-turbo.txt) |
 | [Mbed TLS](https://github.com/Mbed-TLS/mbedtls) (with TF-PSA-Crypto) | 4.2.0 | The Mbed TLS Contributors | Apache-2.0 OR GPL-2.0-or-later (used under Apache-2.0) | [mbedtls.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/mbedtls.txt), [tf-psa-crypto.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/tf-psa-crypto.txt) |
 | [Catch2](https://github.com/catchorg/Catch2) | 3.16.0 | Catch2 Authors | BSL-1.0 | [catch2.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/catch2.txt) |
@@ -65,7 +64,9 @@ These live in the source tree (see the path) rather than being fetched; traccc a
 | [Bitshuffle (h-perf)](https://github.com/kalcutter/bitshuffle) | `compression/bitshuffle_hperf/` | Kal Conley | Apache-2.0 | [bitshuffle-hperf.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/bitshuffle-hperf.txt) |
 | [LZ4](https://github.com/lz4/lz4) | `compression/lz4/` | Yann Collet | BSD-2-Clause | [lz4.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/lz4.txt) |
 | [HLS arbitrary-precision types](https://github.com/Xilinx/HLS_arbitrary_Precision_Types) | `fpga/include/` | Xilinx, Inc. | Apache-2.0 | [xilinx-hls-headers.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/xilinx-hls-headers.txt) |
+| [fast-feedback-indexer](https://github.com/paulscherrerinstitute/fast-feedback-indexer) (commit a94fd4f) | `image_analysis/indexing/fast-feedback-indexer/` | PSI | BSD-3-Clause | [fast-feedback-indexer.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/fast-feedback-indexer.txt) |
 | [GEMMI](https://github.com/project-gemmi/gemmi) | `gemmi_gph/` | Global Phasing Ltd. | MPL-2.0 | [gemmi.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/gemmi.txt) |
+| [CCP4 Monomer Library](https://github.com/MonomerLibrary/monomers) (subset: restraint dictionary data) | `image_analysis/structure_refinement/monomers/` | CCP4 / the Monomer Library authors (Vagin et al.) | LGPL-3.0-only | [ccp4-monomer-library.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/ccp4-monomer-library.txt) |
 | [PEGTL](https://github.com/taocpp/PEGTL) | `gemmi_gph/gemmi/third_party/tao/` | Dr. Colin Hirsch and Daniel Frey | MIT | [pegtl.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/pegtl.txt) |
 | [sajson](https://github.com/chadaustin/sajson) | `gemmi_gph/gemmi/third_party/sajson.h` | Chad Austin | MIT | [sajson.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/sajson.txt) |
 | [fast_float](https://github.com/fastfloat/fast_float) | `gemmi_gph/gemmi/third_party/fast_float.h` | The fast_float authors (Daniel Lemire et al.) | Apache-2.0 OR MIT OR BSL-1.0 | [fast-float.txt](https://gitea.psi.ch/mx/jungfraujoch/src/branch/main/licenses/fast-float.txt) |
@@ -130,12 +131,19 @@ served frontend, so the shipped web UI carries its own attribution.
   its trust-region Levenberg-Marquardt minimiser, projected line search, polynomial step choice and
   sphere manifold for the crystal refinement, following its source. Both files name the origin at the
   top and are covered by `licenses/ceres-solver.txt`.
-* **fast-feedback-indexer** is also fetched and linked in CUDA builds (table above); separately,
+* **fast-feedback-indexer** is also vendored and linked in CUDA builds (table above); separately,
   `FFBIDXIndexerCPU.cpp` ports its CUDA kernels to the CPU. The file names the origin at the top and
   is covered by `licenses/fast-feedback-indexer.txt`.
 * **FFTW** is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
 * **Apache-2.0** components: where upstream ships a `NOTICE` file, it is reproduced in the
   corresponding `licenses/` text.
+* **CCP4 Monomer Library (LGPL-3.0)** is data, not code: the restraint dictionaries of the compounds
+  rugnux's refinement restrains, copied unmodified per compound into
+  `image_analysis/structure_refinement/monomers/` (`links_and_mods.cif` and `ener_lib.cif` cut down to
+  the entries those compounds use, and the library's metal-site distances of `metals.json` for its ions as
+  `metals.cif`), with the library's own `COPYING`. The build embeds them in the binary
+  as text, and `monomers/update_monomers.py` regenerates the subset from the upstream library, so the
+  copy can be replaced by a user with a version of their own.
 * **Qt (LGPL-3.0)** and **NVIDIA CUDA (EULA)** carry redistribution conditions beyond a copyright
   notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
   (`licenses/Qt6-LGPL-3.0.txt`, `licenses/NVIDIA-CUDA-EULA.txt`); the CUDA EULA is the one shipped
diff --git a/docs/VIEWER_DOWNLOAD.md b/docs/VIEWER_DOWNLOAD.md
new file mode 100644
index 000000000..570d1e106
--- /dev/null
+++ b/docs/VIEWER_DOWNLOAD.md
@@ -0,0 +1,52 @@
+# Download the Jungfraujoch Viewer
+
+`jfjoch_viewer` is a standalone desktop application, pre-built for Linux, macOS and Windows with
+the Qt runtime included. The links point at the current release; the full list of what each release
+ships is on its release page.
+
+```{eval-rst}
+.. jfjoch-downloads:: viewer
+```
+
+On a machine with an NVIDIA GPU take the **GPU** build: its embedded spot finding, indexing and
+integration run on the card, and it also starts on a machine without one, on the CPU. The **CPU
+only** build runs the same pipeline at lower throughput and is the smaller download. A V100 needs
+the CUDA 12 build; the CUDA 13 builds start at Turing (T4) — see
+[Release contents](RELEASE_CONTENTS.md#gpu-generations-and-the-nvidia-driver).
+
+## After downloading
+
+**Linux.** The archive has no top-level directory, so unpack it into a directory of its own, then
+run the program from its `bin/`:
+
+```
+mkdir -p ~/jfjoch_viewer
+tar xzf jfjoch_viewer-<version>-linux-cuda12.tgz -C ~/jfjoch_viewer
+~/jfjoch_viewer/bin/jfjoch_viewer dataset_master.h5
+```
+
+The archive also carries the desktop entry, icon and D-Bus service file under `share/`, which the
+desktop picks up when the archive is unpacked into a prefix it searches, such as `/usr/local`. The
+Linux repositories carry the viewer as the `jfjoch-viewer` package as well
+([package repositories](REPOSITORIES.md)).
+
+**macOS.** Open the disk image and drag `jfjoch_viewer` onto the *Applications* shortcut next to
+it. The image is signed and notarized by Apple, so it opens like any other application. Apple
+Silicon only; Intel Macs are not supported.
+
+**Windows.** Run the installer. The CUDA and CPU variants share one install directory and replace
+each other, and are told apart in *Add/Remove Programs* as *Jungfraujoch (CUDA)* and *Jungfraujoch
+(CPU)*.
+
+Then **File ▸ Open** a Jungfraujoch or NXmx master file, a `_process.h5` written by Rugnux, or any
+frame of a miniCBF, marCCD or SMV sweep; **File ▸ Open HTTP** follows a live collection from a
+running broker. [jfjoch_viewer](JFJOCH_VIEWER.md) is the manual, with a
+[guided tour](JFJOCH_VIEWER.md#a-guided-tour) of the four views most people use.
+
+## From source
+
+The viewer builds on Linux, Windows (MSVC and CUDA) and macOS; Qt 6 is the one dependency that
+has to be installed first, everything else is fetched by the configure. See
+[Building from source on Windows](JFJOCH_VIEWER.md#building-from-source-on-windows) and
+[on macOS](JFJOCH_VIEWER.md#building-from-source-on-macos); on Linux configure the full tree with
+`-DJFJOCH_VIEWER_BUILD=ON` ([Deployment](DEPLOYMENT.md#install-jungfraujoch-image-viewer)).
diff --git a/docs/_ext/jfjoch_downloads.py b/docs/_ext/jfjoch_downloads.py
new file mode 100644
index 000000000..71437a893
--- /dev/null
+++ b/docs/_ext/jfjoch_downloads.py
@@ -0,0 +1,123 @@
+"""Download buttons for the release archives, versioned from Sphinx's own ``release``.
+
+``.. jfjoch-downloads:: rugnux`` (or ``viewer``) renders one card per platform with a button per
+archive. Every link is built from the version Sphinx was configured with (``release`` in
+docs/conf.py, which update_version.sh rewrites from VERSION), so no version string on the page is
+maintained by hand. The page's script (_static/jfjoch_downloads.js) then asks the Gitea API for the
+newest published release and repoints the buttons at its assets - so a docs build older or newer
+than the current release still offers the archives that exist, and says which ones do not.
+
+The asset names follow CPack's naming in CMakeLists.txt; the regular expressions are what the
+script matches against the release's asset list, written loosely enough to survive a CUDA major
+bump.
+"""
+
+import pathlib
+import shutil
+
+from docutils import nodes
+from docutils.parsers.rst import Directive
+
+RELEASES = "https://gitea.psi.ch/mx/jungfraujoch/releases"
+
+# docs/landing/: the front page, rendered from its template into the output root as index.html at
+# the end of the build (write_landing below), with the same download blocks as the Sphinx pages.
+LANDING_FILES = ("landing.css", "landing.js", "hero_live_light.webp", "hero_live_dark.webp", "psi.png")
+
+# program -> [(platform, requirements, [(label, asset name with {v}, regex for the live lookup)])]
+# The first button of a platform is the recommended one and is drawn filled.
+PROGRAMS = {
+    "rugnux": [
+        ("Linux",
+         "x86-64 with AVX2 (Intel Haswell / AMD Zen or newer), any distribution from RHEL 8 on. "
+         "For the GPU: an NVIDIA driver, 525.60 or newer; no CUDA toolkit. "
+         "Arm 64: NVIDIA GH200 and DGX Spark, glibc 2.39 or newer.",
+         [("GPU, CUDA 12", "rugnux-{v}-linux-x86_64-cuda12.tgz", r"^rugnux-.*-linux-x86_64-cuda\d+\.tgz$"),
+          ("CPU only", "rugnux-{v}-linux-x86_64-cpu.tgz", r"^rugnux-.*-linux-x86_64-cpu\.tgz$"),
+          ("Arm 64, GPU, CUDA 13", "rugnux-{v}-linux-aarch64-cuda13.tgz", r"^rugnux-.*-linux-aarch64-cuda\d+\.tgz$")]),
+        ("macOS",
+         "Apple Silicon (M1 or newer), macOS 13 Ventura or newer. CPU, with Bragg integration and "
+         "molecular replacement on the Apple GPU; there is no CUDA on macOS. Intel Macs are not "
+         "supported.",
+         [("Apple Silicon", "rugnux-{v}-macos-arm64-cpu.tgz", r"^rugnux-.*-macos-arm64-.*\.tgz$")]),
+        ("Windows",
+         "64-bit Windows with AVX (built and verified on Windows 11). For the GPU: an NVIDIA R580 "
+         "driver or newer; no CUDA toolkit. Unpack the archive and run bin\\rugnux.exe.",
+         [("GPU, CUDA 13", "rugnux-{v}-win64-cuda13.zip", r"^rugnux-.*-win64-cuda\d+\.zip$"),
+          ("CPU only", "rugnux-{v}-win64-cpu.zip", r"^rugnux-.*-win64-cpu\.zip$")]),
+    ],
+    "viewer": [
+        ("Linux",
+         "x86-64 with AVX2, any distribution from RHEL 8 on; a portable archive with the program, "
+         "its desktop entry and icon. For the GPU: an NVIDIA driver, 525.60 or newer.",
+         [("GPU, CUDA 12", "jfjoch_viewer-{v}-linux-cuda12.tgz", r"^jfjoch_viewer-.*-linux-cuda\d+\.tgz$"),
+          ("CPU only", "jfjoch_viewer-{v}-linux-cpu.tgz", r"^jfjoch_viewer-.*-linux-cpu\.tgz$")]),
+        ("macOS",
+         "Apple Silicon (M1 or newer), macOS 13 Ventura or newer. Signed and notarized disk image; "
+         "drag the app to Applications. Intel Macs are not supported.",
+         [("Apple Silicon", "jfjoch-viewer-{v}-macos-arm64.dmg", r"^jfjoch-viewer-.*-macos-arm64\.dmg$")]),
+        ("Windows",
+         "64-bit Windows with AVX (built and verified on Windows 11). An installer with the Qt "
+         "runtime included. For the GPU: an NVIDIA R580 driver or newer; no CUDA toolkit.",
+         [("GPU, CUDA 13", "jfjoch-viewer-{v}-win64-cuda13.exe", r"^jfjoch-viewer-.*-win64-cuda\d+\.exe$"),
+          ("CPU only", "jfjoch-viewer-{v}-win64-cpu.exe", r"^jfjoch-viewer-.*-win64-cpu\.exe$")]),
+    ],
+}
+
+
+def _escape(text):
+    return text.replace("&", "&amp;").replace("<", "&lt;").replace(">", "&gt;").replace('"', "&quot;")
+
+
+def render(program, version):
+    out = ['<div class="jfj-dl" data-program="%s">' % program,
+           '<p class="jfj-dl__release">Version <strong data-jfj="version">%s</strong>'
+           ' &middot; <a data-jfj="release-url" href="%s/tag/%s">release notes</a>'
+           ' &middot; <a href="%s">all releases</a></p>' % (version, RELEASES, version, RELEASES),
+           '<div class="jfj-dl__grid">']
+    for platform, requirements, archives in PROGRAMS[program]:
+        out.append('<div class="jfj-dl__card" data-platform="%s"><h3 class="jfj-dl__platform">%s</h3>'
+                   % (platform.lower(), platform))
+        for i, (label, pattern, regex) in enumerate(archives):
+            name = pattern.format(v=version)
+            cls = "jfj-dl__btn" if i == 0 else "jfj-dl__btn jfj-dl__btn--secondary"
+            out.append('<a class="%s" href="%s/download/%s/%s" data-match="%s">%s'
+                       '<span class="jfj-dl__file">%s</span></a>'
+                       % (cls, RELEASES, version, name, _escape(regex), label, name))
+        out.append('<p class="jfj-dl__req">%s</p></div>' % requirements)
+    out.append('</div><p class="jfj-dl__note" data-jfj="note"></p></div>')
+    return "\n".join(out)
+
+
+class JfjochDownloads(Directive):
+    required_arguments = 1
+
+    def run(self):
+        program = self.arguments[0]
+        if program not in PROGRAMS:
+            raise self.error("jfjoch-downloads: unknown program %r (one of %s)"
+                             % (program, ", ".join(sorted(PROGRAMS))))
+        version = self.state.document.settings.env.config.release
+        return [nodes.raw("", render(program, version), format="html")]
+
+
+def write_landing(app, exception):
+    """Render docs/landing/index.html into the HTML output root, next to the Sphinx pages."""
+    if exception is not None or app.builder.name != "html":
+        return
+    src = pathlib.Path(app.confdir) / "landing"
+    out = pathlib.Path(app.outdir)
+    version = app.config.release
+    html = (src / "index.html").read_text(encoding="utf-8")
+    html = (html.replace("{{release}}", version)
+                .replace("{{downloads:rugnux}}", render("rugnux", version))
+                .replace("{{downloads:viewer}}", render("viewer", version)))
+    (out / "index.html").write_text(html, encoding="utf-8")
+    for name in LANDING_FILES:
+        shutil.copy(src / name, out / name)
+
+
+def setup(app):
+    app.add_directive("jfjoch-downloads", JfjochDownloads)
+    app.connect("build-finished", write_landing)
+    return {"parallel_read_safe": True, "parallel_write_safe": True}
diff --git a/docs/_static/jfjoch.css b/docs/_static/jfjoch.css
new file mode 100644
index 000000000..53cadb2e9
--- /dev/null
+++ b/docs/_static/jfjoch.css
@@ -0,0 +1,213 @@
+/* Jungfraujoch documentation: the home page's program cards and the download pages' buttons.
+   Colours follow the theme's indigo primary; sphinx_material has no dark mode, so there is one
+   palette. */
+
+:root {
+    --jfj-primary: #3f51b5;
+    --jfj-primary-dark: #303f9f;
+    --jfj-line: rgba(0, 0, 0, 0.12);
+    --jfj-muted: rgba(0, 0, 0, 0.58);
+    --jfj-surface: #fafafa;
+}
+
+/* ---- home page ------------------------------------------------------------------------------ */
+
+.md-typeset .jfj-lead {
+    font-size: 1.1em;
+    line-height: 1.55;
+    max-width: 40em;
+}
+
+.jfj-cards {
+    display: grid;
+    grid-template-columns: repeat(auto-fit, minmax(16em, 1fr));
+    gap: 1em;
+    margin: 1.4em 0 1.6em;
+}
+
+.md-typeset .jfj-card {
+    display: flex;
+    flex-direction: column;
+    border: 1px solid var(--jfj-line);
+    border-top: 3px solid var(--jfj-primary);
+    border-radius: 6px;
+    padding: 0.9em 1.1em 1em;
+    background: var(--jfj-surface);
+}
+
+.md-typeset .jfj-card__kicker {
+    font-size: 0.68em;
+    font-weight: 700;
+    letter-spacing: 0.08em;
+    text-transform: uppercase;
+    color: var(--jfj-primary);
+    margin: 0 0 0.3em;
+}
+
+.md-typeset .jfj-card__title {
+    font-size: 1.25em;
+    font-weight: 500;
+    line-height: 1.25;
+    margin: 0 0 0.5em;
+    color: inherit;
+}
+
+.md-typeset .jfj-card__text {
+    margin: 0 0 0.7em;
+    line-height: 1.5;
+    flex: 1 1 auto;
+}
+
+.md-typeset .jfj-card__run {
+    margin: 0 0 0.7em;
+    padding: 0.45em 0.7em;
+    border-radius: 4px;
+    background: rgba(63, 81, 181, 0.08);
+    font-family: "Roboto Mono", "SFMono-Regular", Consolas, monospace;
+    font-size: 0.85em;
+    white-space: pre-wrap;
+    word-break: break-word;
+}
+
+/* the sitemap under the cards: the index toctrees, as compact columns */
+.jfj-sitemap {
+    display: grid;
+    grid-template-columns: repeat(auto-fit, minmax(13em, 1fr));
+    gap: 0 1.5em;
+}
+
+.md-typeset .jfj-sitemap .toctree-wrapper > p.caption {
+    font-size: 0.85em;
+    font-weight: 700;
+    margin: 0.9em 0 0.2em;
+}
+
+.md-typeset .jfj-sitemap .toctree-wrapper ul {
+    list-style: none;
+    margin: 0;
+    padding: 0;
+    font-size: 0.82em;
+    line-height: 1.55;
+}
+
+.md-typeset .jfj-sitemap .toctree-wrapper ul ul {
+    padding-left: 1em;
+    font-size: 1em;
+}
+
+.md-typeset .jfj-card__links {
+    margin: 0;
+    padding: 0.6em 0 0;
+    border-top: 1px solid var(--jfj-line);
+    font-size: 0.92em;
+}
+
+.md-typeset .jfj-card__links a {
+    margin-right: 1em;
+    white-space: nowrap;
+}
+
+.md-typeset .jfj-card__links a:first-child {
+    font-weight: 700;
+}
+
+.md-typeset .jfj-platforms {
+    font-size: 0.78em;
+    color: var(--jfj-muted);
+    margin: 0 0 0.6em;
+}
+
+/* ---- download pages -------------------------------------------------------------------------- */
+
+.md-typeset .jfj-dl__release {
+    margin: 0 0 0.8em;
+}
+
+.jfj-dl__grid {
+    display: grid;
+    grid-template-columns: repeat(auto-fit, minmax(15em, 1fr));
+    gap: 1em;
+    margin: 0 0 0.8em;
+}
+
+.md-typeset .jfj-dl__card {
+    border: 1px solid var(--jfj-line);
+    border-radius: 6px;
+    padding: 0.9em 1.1em 0.5em;
+    background: var(--jfj-surface);
+}
+
+.md-typeset .jfj-dl__platform {
+    font-size: 1.1em;
+    font-weight: 500;
+    margin: 0 0 0.6em;
+}
+
+.md-typeset a.jfj-dl__btn {
+    display: block;
+    margin: 0 0 0.5em;
+    padding: 0.5em 0.8em;
+    border: 1px solid var(--jfj-primary);
+    border-radius: 4px;
+    background: var(--jfj-primary);
+    color: #fff;
+    font-weight: 500;
+    line-height: 1.3;
+    text-decoration: none;
+    transition: background 0.15s, box-shadow 0.15s;
+}
+
+.md-typeset a.jfj-dl__btn:hover,
+.md-typeset a.jfj-dl__btn:focus {
+    background: var(--jfj-primary-dark);
+    box-shadow: 0 2px 6px rgba(0, 0, 0, 0.2);
+    color: #fff;
+}
+
+.md-typeset a.jfj-dl__btn--secondary {
+    background: transparent;
+    color: var(--jfj-primary);
+}
+
+.md-typeset a.jfj-dl__btn--secondary:hover,
+.md-typeset a.jfj-dl__btn--secondary:focus {
+    background: rgba(63, 81, 181, 0.08);
+    color: var(--jfj-primary-dark);
+}
+
+.md-typeset a.jfj-dl__btn--missing,
+.md-typeset a.jfj-dl__btn--missing:hover {
+    background: transparent;
+    border-style: dashed;
+    border-color: var(--jfj-line);
+    color: var(--jfj-muted);
+    box-shadow: none;
+    cursor: default;
+}
+
+.md-typeset .jfj-dl__file {
+    display: block;
+    font-family: "Roboto Mono", "SFMono-Regular", Consolas, monospace;
+    font-size: 0.72em;
+    font-weight: 400;
+    opacity: 0.85;
+    margin-top: 0.15em;
+    word-break: break-all;
+}
+
+.md-typeset .jfj-dl__req {
+    font-size: 0.8em;
+    line-height: 1.45;
+    color: var(--jfj-muted);
+    margin: 0.4em 0 0.4em;
+}
+
+.md-typeset .jfj-dl__note {
+    font-size: 0.8em;
+    color: var(--jfj-muted);
+    margin: 0 0 1em;
+}
+
+.md-typeset .jfj-dl__note:empty {
+    display: none;
+}
diff --git a/docs/_static/jfjoch_downloads.js b/docs/_static/jfjoch_downloads.js
new file mode 100644
index 000000000..5fd5f9d33
--- /dev/null
+++ b/docs/_static/jfjoch_downloads.js
@@ -0,0 +1,55 @@
+// Download pages: repoint the buttons at the newest published release.
+//
+// The page is rendered with links for the version the documentation was built for
+// (docs/_ext/jfjoch_downloads.py). That version may not be released yet, or may be behind the
+// current release, so once the page is up this asks the Gitea API (anonymous, CORS-enabled) for
+// the newest non-draft release and rewrites each button from that release's asset list: the
+// matching asset's URL and size, or "not part of this release" where the platform has none.
+// Without network access, or if the API answers anything but 200, the built-in links stand.
+(function main() {
+    // Sphinx puts html_js_files into <head>, before the page's body exists.
+    if (document.readyState === "loading") {
+        document.addEventListener("DOMContentLoaded", main);
+        return;
+    }
+    var API = "https://gitea.psi.ch/api/v1/repos/mx/jungfraujoch/releases?limit=10";
+    var blocks = document.querySelectorAll(".jfj-dl");
+    if (!blocks.length || !window.fetch) return;
+
+    function megabytes(bytes) {
+        return (bytes / 1048576).toFixed(bytes < 10485760 ? 1 : 0) + " MB";
+    }
+
+    function apply(release) {
+        var date = release.published_at ? release.published_at.slice(0, 10) : "";
+        blocks.forEach(function (block) {
+            block.querySelectorAll("[data-jfj=version]").forEach(function (e) { e.textContent = release.tag_name; });
+            block.querySelectorAll("[data-jfj=release-url]").forEach(function (e) { e.href = release.html_url; });
+            block.querySelectorAll("a[data-match]").forEach(function (a) {
+                var re = new RegExp(a.getAttribute("data-match"));
+                var asset = release.assets.filter(function (x) { return re.test(x.name); })[0];
+                var file = a.querySelector(".jfj-dl__file");
+                if (asset) {
+                    a.href = asset.browser_download_url;
+                    a.classList.remove("jfj-dl__btn--missing");
+                    if (file) file.textContent = asset.name + " · " + megabytes(asset.size);
+                } else {
+                    a.removeAttribute("href");
+                    a.classList.add("jfj-dl__btn--missing");
+                    if (file) file.textContent = "not part of release " + release.tag_name;
+                }
+            });
+            var note = block.querySelector("[data-jfj=note]");
+            if (note) note.textContent = "Links checked against the release page: release " +
+                release.tag_name + (date ? ", published " + date : "") + ".";
+        });
+    }
+
+    fetch(API)
+        .then(function (r) { return r.ok ? r.json() : Promise.reject(r.status); })
+        .then(function (releases) {
+            var release = releases.filter(function (r) { return !r.draft && r.assets; })[0];
+            if (release) apply(release);
+        })
+        .catch(function () { /* offline or API unavailable: the built-in links stand */ });
+})();
diff --git a/docs/conf.py b/docs/conf.py
index d94d84660..393d3a17b 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -9,16 +9,27 @@
 project = 'Jungfraujoch'
 copyright = '2024, Paul Scherrer Institute'
 author = 'Filip Leonarski'
-release = '1.0.0-rc.179'
+release = '1.0.0-rc.180'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
+import os
+import sys
+
+# docs/_ext/jfjoch_downloads.py: the download pages' buttons, versioned from `release` above.
+sys.path.insert(0, os.path.abspath('_ext'))
+
 extensions = [
     'myst_parser',
     'sphinx.ext.mathjax',
+    'jfjoch_downloads',
 ]
 
+# The site's front page is docs/landing/index.html, a standalone page the jfjoch_downloads
+# extension renders into the output root as index.html; the Sphinx tree starts one page below it.
+root_doc = 'documentation'
+
 templates_path = ['_templates']
 # docs/review/ is gitignored working material (review reports, work plans); Sphinx renders
 # whatever is on disk, so without this a local review file would become a published page.
@@ -55,7 +66,11 @@ mathjax3_config = {
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = 'sphinx_material'
-html_static_path = ['../broker/redoc-static.html']
+html_static_path = ['../broker/redoc-static.html', '_static']
+# The home page's program cards and the download pages' buttons (docs/_static); the script asks
+# the Gitea API for the newest release and repoints the download buttons at its assets.
+html_css_files = ['jfjoch.css']
+html_js_files = ['jfjoch_downloads.js']
 #html_theme_options = {
 #    'sidebar_width': '300px',
 #    'page_width': 'auto'
diff --git a/docs/documentation.rst b/docs/documentation.rst
new file mode 100644
index 000000000..f0dab2b51
--- /dev/null
+++ b/docs/documentation.rst
@@ -0,0 +1,138 @@
+Documentation
+=============
+
+.. raw:: html
+
+   <p class="jfj-lead">The manuals and reference of Jungfraujoch and Rugnux, open-source software
+   from the <a href="https://www.psi.ch">Paul Scherrer Institute</a> for X-ray diffraction data.
+   The <a href="index.html">front page</a> has the overview and the downloads; this page is the
+   map of the documentation.</p>
+
+   <div class="jfj-cards">
+
+   <div class="jfj-card">
+   <p class="jfj-card__kicker">Data processing</p>
+   <h2 class="jfj-card__title">Rugnux</h2>
+   <p class="jfj-card__text">Processes a stored macromolecular diffraction dataset, a rotation
+   sweep or serial stills, from the images to merged data: spot finding, indexing, integration,
+   scaling and merging, with the space group, cell and resolution decided from the data and a
+   report that says on what evidence. Given an atomic model it goes on to a refined structure and
+   maps: the model is placed (rigid body or molecular replacement) and refined against the merge.
+   One command, no parameters.</p>
+   <pre class="jfj-card__run"><code>rugnux &lt;diffraction image file&gt;
+   rugnux &lt;diffraction image file&gt; &lt;CIF/PDB model file&gt;</code></pre>
+   <p class="jfj-platforms">Linux &middot; macOS &middot; Windows &middot; fast on an NVIDIA GPU,
+   works without one</p>
+   <p class="jfj-card__links"><a href="RUGNUX.html">Get started</a>
+   <a href="RUGNUX_DOWNLOAD.html">Download</a>
+   <a href="RUGNUX_OVERVIEW.html">What it does</a>
+   <a href="RUGNUX_TUTORIAL.html">Manual</a></p>
+   </div>
+
+   <div class="jfj-card">
+   <p class="jfj-card__kicker">Desktop application</p>
+   <h2 class="jfj-card__title">Jungfraujoch Viewer</h2>
+   <p class="jfj-card__text">Shows what is in a diffraction dataset: every image with its spots,
+   predictions and resolution rings, per-image statistics over the sweep, grid-scan maps, and
+   the same processing pipeline as Rugnux, run from a settings panel on the open file. Follows a
+   live collection from a running Jungfraujoch broker.</p>
+   <p class="jfj-platforms">Linux &middot; macOS &middot; Windows &middot; Qt 6</p>
+   <p class="jfj-card__links"><a href="JFJOCH_VIEWER.html">Get started</a>
+   <a href="VIEWER_DOWNLOAD.html">Download</a>
+   <a href="JFJOCH_VIEWER.html#a-guided-tour">Guided tour</a></p>
+   </div>
+
+   <div class="jfj-card">
+   <p class="jfj-card__kicker">Data acquisition</p>
+   <h2 class="jfj-card__title">Jungfraujoch</h2>
+   <p class="jfj-card__text">The data-acquisition and real-time analysis system for the PSI
+   JUNGFRAU and EIGER detectors, and for DECTRIS detectors through their control unit: an FPGA
+   and GPU pipeline that takes the detector's frames at full rate, analyses them on the fly,
+   streams them to the NXmx HDF5 writer and serves a web interface and REST API to the
+   beamline.</p>
+   <p class="jfj-platforms">Linux servers &middot; AMD Alveo U55C FPGA &middot; NVIDIA GPUs</p>
+   <p class="jfj-card__links"><a href="JUNGFRAUJOCH.html">Get started</a>
+   <a href="DEPLOYMENT.html">Install</a>
+   <a href="JFJOCH_BROKER.html">Broker</a>
+   <a href="JFJOCH_WRITER.html">Writer</a></p>
+   </div>
+
+   </div>
+
+**Licence.** Rugnux, the viewer and the Jungfraujoch services are free software under the
+:doc:`GNU General Public License v3 <LICENSE>`; the FPGA design is released under the
+:doc:`CERN Open Hardware Licence v2, strongly reciprocal <FPGA_LICENSE>`. Both let anyone, in
+academia or industry, use, study and modify the software and the hardware design at no charge,
+commercial use included; what they ask is that a modified version which is passed on is shared
+under the same terms. The released binaries bundle third-party components under GPL-compatible
+licences, and the CUDA builds the NVIDIA CUDA runtime under NVIDIA's own EULA: see the
+:doc:`third-party notices <THIRD_PARTY_NOTICES>`.
+
+All pages
+---------
+
+Everything a user of Rugnux or the viewer needs comes first; the :doc:`technical reference <TECHNICAL>`
+holds the algorithms, the file formats and streams, the interfaces and the FPGA design. The names
+are explained in :doc:`Naming <NAMING>`, the releases in the :doc:`changelog <CHANGELOG>`.
+
+.. raw:: html
+
+   <div class="jfj-sitemap">
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Rugnux
+
+   Getting started <RUGNUX>
+   Download <RUGNUX_DOWNLOAD>
+   RUGNUX_OVERVIEW
+   RUGNUX_INSTALL
+   RUGNUX_FORMATS
+   RUGNUX_TUTORIAL
+   RUGNUX_REPORT
+   RUGNUX_INTEGRATION
+   RUGNUX_ADVANCED
+   RUGNUX_MODEL_AND_REFERENCE
+   Detector calibration <RUGNUX_CALIBRATION>
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Jungfraujoch Viewer
+
+   Using the viewer <JFJOCH_VIEWER>
+   Download <VIEWER_DOWNLOAD>
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Jungfraujoch
+
+   Overview <JUNGFRAUJOCH>
+   DEPLOYMENT
+   REPOSITORIES
+   RELEASE_CONTENTS
+   JFJOCH_BROKER
+   JFJOCH_WRITER
+   WEB_FRONTEND
+   MX software integration <SOFTWARE_INTEGRATION>
+   TOOLS
+   Python client <PYTHON_CLIENT>
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Reference
+
+   TECHNICAL
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Project
+
+   ACKNOWLEDGEMENT
+   LICENSE
+   THIRD_PARTY_NOTICES
+   NAMING
+   CHANGELOG
+
+.. raw:: html
+
+   </div>
diff --git a/docs/images/rugnux_pipeline.svg b/docs/images/rugnux_pipeline.svg
index 890325212..710f00e80 100644
--- a/docs/images/rugnux_pipeline.svg
+++ b/docs/images/rugnux_pipeline.svg
@@ -84,45 +84,55 @@
 <text x="1140.0" y="564" text-anchor="middle" font-size="13" fill="#6B6B6B" font-style="italic">pass 1</text>
 <path d="M1450,572 L1490,572 L1490,80 L322,80 L322,400" fill="none" stroke="#555" stroke-width="2.2" stroke-dasharray="8,6" marker-end="url(#arr)"/>
 <text x="900" y="72" text-anchor="middle" font-size="14" fill="#6B6B6B" font-style="italic">pass 2, repeated while it gains</text>
-<text x="542" y="740" font-size="21" font-weight="bold" fill="#1A8A7D">Whole dataset</text>
-<rect x="300" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
-<text x="415.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge (P1)</text>
-<text x="415.0" y="828" text-anchor="middle" font-size="15" fill="#222222">3D combine of partials</text>
-<rect x="468" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
-<text x="494.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
-<rect x="555" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
-<text x="670.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Symmetry</text>
-<text x="670.0" y="828" text-anchor="middle" font-size="14" fill="#222222">space group, twinning, tNCS</text>
-<rect x="713" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
-<text x="744.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
-<rect x="810" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
-<text x="925.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge</text>
-<text x="925.0" y="828" text-anchor="middle" font-size="14" fill="#222222">in space group, resolution cut</text>
-<text x="925.0" y="847" text-anchor="middle" font-size="14" fill="#222222">decay, absorption, modulation</text>
-<rect x="968" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
-<text x="999.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
-<rect x="908" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
-<text x="934.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
-<rect x="1065" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#8E44AD" stroke-width="3" stroke-dasharray="9,6"/>
-<text x="1180.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#8E44AD">Structure &amp; map</text>
-<text x="1180.0" y="828" text-anchor="middle" font-size="14" fill="#222222">placement or MR, σA maps</text>
-<rect x="1223" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
-<text x="1254.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
-<rect x="1163" y="869" width="52" height="20" rx="4" fill="#555555"/>
-<text x="1189.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">Metal</text>
-<rect x="1103" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
-<text x="1129.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
-<rect x="1320" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#E8740C" stroke-width="3"/>
-<text x="1435.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#E8740C">Report</text>
-<text x="1435.0" y="828" text-anchor="middle" font-size="15" fill="#222222">MTZ, mmCIF, maps</text>
-<path d="M530,822 L553,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M785,822 L808,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M1040,822 L1063,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M1295,822 L1318,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M1000,770 L1000,744 L1360,744 L1360,768" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<text x="1180.0" y="736" text-anchor="middle" font-size="13" fill="#6B6B6B" font-style="italic">without a model</text>
-<path d="M1020,625 L1020,710 L420,710 L420,768" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<text x="435" y="702" text-anchor="start" font-size="13" fill="#6B6B6B" font-style="italic">pass 2, or pass 1 if it merges better</text>
+<rect x="297" y="770" width="215" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
+<text x="404.5" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge (P1)</text>
+<text x="404.5" y="828" text-anchor="middle" font-size="15" fill="#222222">3D combine of partials</text>
+<rect x="450" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
+<text x="476.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
+<rect x="532" y="770" width="200" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
+<text x="632.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Symmetry</text>
+<text x="632.0" y="828" text-anchor="middle" font-size="14" fill="#222222">space group, twinning, tNCS</text>
+<rect x="660" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
+<text x="691.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
+<rect x="752" y="770" width="218" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
+<text x="861.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge</text>
+<text x="861.0" y="828" text-anchor="middle" font-size="14" fill="#222222">in space group, resolution cut</text>
+<text x="861.0" y="847" text-anchor="middle" font-size="14" fill="#222222">decay, absorption, modulation</text>
+<rect x="898" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
+<text x="929.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
+<rect x="838" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
+<text x="864.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
+<rect x="990" y="770" width="205" height="127" rx="12" ry="12" fill="white" stroke="#8E44AD" stroke-width="3" stroke-dasharray="9,6"/>
+<text x="1092.5" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#8E44AD">Structure &amp; map</text>
+<text x="1092.5" y="828" text-anchor="middle" font-size="14" fill="#222222">placement or MR, σA maps</text>
+<rect x="1123" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
+<text x="1154.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
+<rect x="1063" y="869" width="52" height="20" rx="4" fill="#555555"/>
+<text x="1089.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">Metal</text>
+<rect x="1003" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
+<text x="1029.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
+<rect x="1215" y="770" width="175" height="127" rx="12" ry="12" fill="white" stroke="#8E44AD" stroke-width="3" stroke-dasharray="9,6"/>
+<text x="1302.5" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#8E44AD">Refinement</text>
+<text x="1302.5" y="828" text-anchor="middle" font-size="14" fill="#222222">restrained ML,</text>
+<text x="1302.5" y="847" text-anchor="middle" font-size="14" fill="#222222">maps, blobs</text>
+<rect x="1318" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
+<text x="1349.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
+<rect x="1258" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
+<text x="1284.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
+<rect x="1410" y="770" width="150" height="127" rx="12" ry="12" fill="white" stroke="#E8740C" stroke-width="3"/>
+<text x="1485.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#E8740C">Report</text>
+<text x="1485.0" y="828" text-anchor="middle" font-size="15" fill="#222222">MTZ, mmCIF, maps</text>
+<path d="M512,822 L530,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M732,822 L750,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M970,822 L988,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M1195,822 L1213,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M1390,822 L1408,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M930,770 L930,744 L1450,744 L1450,768" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<text x="1190.0" y="736" text-anchor="middle" font-size="13" fill="#6B6B6B" font-style="italic">without a model</text>
+<text x="1190.0" y="919" text-anchor="middle" font-size="13" fill="#6B6B6B" font-style="italic">with a model only - decides nothing</text>
+<text x="524" y="740" font-size="21" font-weight="bold" fill="#1A8A7D">Whole dataset</text>
+<path d="M1020,625 L1020,710 L417,710 L417,768" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<text x="432" y="702" text-anchor="start" font-size="13" fill="#6B6B6B" font-style="italic">pass 2, or pass 1 if it merges better</text>
 <rect x="60" y="936" width="52" height="20" rx="4" fill="#2F6FDE"/>
 <text x="86.0" y="951" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
 <text x="124" y="951" font-size="15" fill="#222222">CUDA kernel when a GPU is present</text>
diff --git a/docs/images/rugnux_pipeline_fig.py b/docs/images/rugnux_pipeline_fig.py
index 3a94bb767..0191c5214 100644
--- a/docs/images/rugnux_pipeline_fig.py
+++ b/docs/images/rugnux_pipeline_fig.py
@@ -79,22 +79,39 @@ R1Y, R2Y = 350, 520                                 # rows inside panel
 LX = 322                                            # loop-return / pass-2 column
 IX, IY, IW, IH = 60, 150, 220, 80                   # input
 SY = 120                                            # pre-scan row
-QY, QBW, QBH = 770, 230, BH + 22                    # whole-dataset row
-QX = [300, 555, 810, 1065, 1320]
+QY, QBH = 770, BH + 22                              # whole-dataset row
+QGAP, QEND = 20, 1560                               # gap between its boxes, right end of the row
 OUTY = 710
 
-def dataset_row(merge_p1, symmetry, merge, gpu):
-    a(f'<text x="{QX[0]+QBW+12}" y="{QY-30}" font-size="21" font-weight="bold" fill="{TEAL}">Whole dataset</text>')
-    box(QX[0], QY, QBW, QBH, "Scale &amp; merge (P1)", merge_p1, TEAL, gpu=gpu)
-    box(QX[1], QY, QBW, QBH, "Symmetry", symmetry, TEAL, tested=True, bs=14)
-    box(QX[2], QY, QBW, QBH, "Scale &amp; merge", merge, TEAL, gpu=gpu, tested=gpu, bs=14)
-    box(QX[3], QY, QBW, QBH, "Structure &amp; map", "placement or MR, σA maps", PURPLE, gpu=True, metal=True, tested=True, dashed=True, bs=14)
-    box(QX[4], QY, QBW, QBH, "Report", "MTZ, mmCIF, maps", ORANGE)
-    for i in range(4):
-        path(f"M{QX[i]+QBW},{QY+52} L{QX[i+1]-2},{QY+52}")
+def dataset_row(merge_p1, symmetry, merge, gpu, ambiguity=False):
+    # (title, body, colour, width, keywords) left to right; the model branch is dashed: it decides nothing
+    boxes = []
+    if ambiguity:
+        boxes.append(("Ambiguity", ["crystals reindexed alike:", "from the data, or a", "reference / model"],
+                      TEAL, 190, dict(bs=14)))
+    boxes += [("Scale &amp; merge (P1)", merge_p1, TEAL, 215, dict(gpu=gpu)),
+              ("Symmetry", symmetry, TEAL, 200, dict(tested=True, bs=14)),
+              ("Scale &amp; merge", merge, TEAL, 218, dict(gpu=gpu, tested=gpu, bs=14)),
+              ("Structure &amp; map", "placement or MR, σA maps", PURPLE, 205,
+               dict(gpu=True, metal=True, tested=True, dashed=True, bs=14)),
+              ("Refinement", ["restrained ML,", "maps, blobs"], PURPLE, 175,
+               dict(gpu=True, tested=True, dashed=True, bs=14)),
+              ("Report", "MTZ, mmCIF, maps", ORANGE, 150, {})]
+    x = QEND - sum(b[3] for b in boxes) - QGAP * (len(boxes) - 1)
+    xs = []
+    for title, body, color, w, kw in boxes:
+        box(x, QY, w, QBH, title, body, color, **kw)
+        xs.append((x, w))
+        x += w + QGAP
+    for (x0, w0), (x1, _) in zip(xs, xs[1:]):
+        path(f"M{x0+w0},{QY+52} L{x1-2},{QY+52}")
     # without a model the merge goes straight to the report
-    path(f"M{QX[2]+QBW-40},{QY} L{QX[2]+QBW-40},{QY-26} L{QX[4]+40},{QY-26} L{QX[4]+40},{QY-2}")
-    label(QX[3]+QBW/2, QY-34, "without a model", size=13)
+    (mx, mw), (sx, sw), (rx, rw), (ox, ow) = xs[-4], xs[-3], xs[-2], xs[-1]
+    path(f"M{mx+mw-40},{QY} L{mx+mw-40},{QY-26} L{ox+40},{QY-26} L{ox+40},{QY-2}")
+    label((sx+rx+rw)/2, QY-34, "without a model", size=13)
+    label((sx+rx+rw)/2, QY+QBH+22, "with a model only - decides nothing", size=13)
+    a(f'<text x="{xs[0][0]+xs[0][1]+12}" y="{QY-30}" font-size="21" font-weight="bold" fill="{TEAL}">Whole dataset</text>')
+    return xs[0][0] + 120                           # where the per-image results come in
 
 
 def rotation():
@@ -156,10 +173,10 @@ def rotation():
     label(900, TOPY-8, "pass 2, repeated while it gains", size=14)
 
     # ---------- Whole-dataset chain
-    dataset_row("3D combine of partials", "space group, twinning, tNCS",
-                ["in space group, resolution cut", "decay, absorption, modulation"], gpu=True)
-    path(f"M{C[2]+160},{R2Y+BH} L{C[2]+160},{OUTY} L{QX[0]+120},{OUTY} L{QX[0]+120},{QY-2}")
-    label(QX[0]+135, OUTY-8, "pass 2, or pass 1 if it merges better", anchor="start", size=13)
+    inx = dataset_row("3D combine of partials", "space group, twinning, tNCS",
+                      ["in space group, resolution cut", "decay, absorption, modulation"], gpu=True)
+    path(f"M{C[2]+160},{R2Y+BH} L{C[2]+160},{OUTY} L{inx},{OUTY} L{inx},{QY-2}")
+    label(inx+15, OUTY-8, "pass 2, or pass 1 if it merges better", anchor="start", size=13)
 
     legend()
     finish("rugnux_pipeline.svg")
@@ -204,10 +221,10 @@ def stills():
     label(SX+132, SY+BH+22+28, "masks", anchor="start", size=13)
 
     # ---------- Whole-dataset chain
-    dataset_row(["consensus cell, crystal form,", "per-image scale"], "space group, twinning, tNCS",
-                ["in space group, resolution cut", "partiality, error model"], gpu=False)
-    path(f"M{C[1]+110},{R2Y+BH} L{C[1]+110},{OUTY} L{QX[0]+120},{OUTY} L{QX[0]+120},{QY-2}")
-    label(QX[0]+135, OUTY-8, "every crystal", anchor="start", size=13)
+    inx = dataset_row(["consensus cell, crystal form,", "per-image scale"], "space group, twinning, tNCS",
+                      ["in space group, resolution cut", "partiality, error model"], gpu=False, ambiguity=True)
+    path(f"M{C[1]+110},{R2Y+BH} L{C[1]+110},{OUTY} L{inx},{OUTY} L{inx},{QY-2}")
+    label(inx+15, OUTY-8, "every crystal", anchor="start", size=13)
 
     legend()
     finish("rugnux_pipeline_stills.svg")
diff --git a/docs/images/rugnux_pipeline_stills.svg b/docs/images/rugnux_pipeline_stills.svg
index 3ca41a8c9..c9d20e2a3 100644
--- a/docs/images/rugnux_pipeline_stills.svg
+++ b/docs/images/rugnux_pipeline_stills.svg
@@ -72,40 +72,56 @@
 <text x="692" y="275" text-anchor="start" font-size="13" fill="#6B6B6B" font-style="italic">geometry</text>
 <path d="M1020,247 L1020,298" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
 <text x="1032" y="275" text-anchor="start" font-size="13" fill="#6B6B6B" font-style="italic">masks</text>
-<text x="542" y="740" font-size="21" font-weight="bold" fill="#1A8A7D">Whole dataset</text>
-<rect x="300" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
-<text x="415.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge (P1)</text>
-<text x="415.0" y="828" text-anchor="middle" font-size="15" fill="#222222">consensus cell, crystal form,</text>
-<text x="415.0" y="847" text-anchor="middle" font-size="15" fill="#222222">per-image scale</text>
-<rect x="555" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
-<text x="670.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Symmetry</text>
-<text x="670.0" y="828" text-anchor="middle" font-size="14" fill="#222222">space group, twinning, tNCS</text>
-<rect x="713" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
-<text x="744.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
-<rect x="810" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
-<text x="925.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge</text>
-<text x="925.0" y="828" text-anchor="middle" font-size="14" fill="#222222">in space group, resolution cut</text>
-<text x="925.0" y="847" text-anchor="middle" font-size="14" fill="#222222">partiality, error model</text>
-<rect x="1065" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#8E44AD" stroke-width="3" stroke-dasharray="9,6"/>
-<text x="1180.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#8E44AD">Structure &amp; map</text>
-<text x="1180.0" y="828" text-anchor="middle" font-size="14" fill="#222222">placement or MR, σA maps</text>
-<rect x="1223" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
-<text x="1254.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
-<rect x="1163" y="869" width="52" height="20" rx="4" fill="#555555"/>
-<text x="1189.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">Metal</text>
-<rect x="1103" y="869" width="52" height="20" rx="4" fill="#2F6FDE"/>
-<text x="1129.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
-<rect x="1320" y="770" width="230" height="127" rx="12" ry="12" fill="white" stroke="#E8740C" stroke-width="3"/>
-<text x="1435.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#E8740C">Report</text>
-<text x="1435.0" y="828" text-anchor="middle" font-size="15" fill="#222222">MTZ, mmCIF, maps</text>
-<path d="M530,822 L553,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M785,822 L808,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M1040,822 L1063,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M1295,822 L1318,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<path d="M1000,770 L1000,744 L1360,744 L1360,768" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<text x="1180.0" y="736" text-anchor="middle" font-size="13" fill="#6B6B6B" font-style="italic">without a model</text>
-<path d="M720,625 L720,710 L420,710 L420,768" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
-<text x="435" y="702" text-anchor="start" font-size="13" fill="#6B6B6B" font-style="italic">every crystal</text>
+<rect x="87" y="770" width="190" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
+<text x="182.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Ambiguity</text>
+<text x="182.0" y="828" text-anchor="middle" font-size="14" fill="#222222">crystals reindexed alike:</text>
+<text x="182.0" y="847" text-anchor="middle" font-size="14" fill="#222222">from the data, or a</text>
+<text x="182.0" y="866" text-anchor="middle" font-size="14" fill="#222222">reference / model</text>
+<rect x="297" y="770" width="215" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
+<text x="404.5" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge (P1)</text>
+<text x="404.5" y="828" text-anchor="middle" font-size="15" fill="#222222">consensus cell, crystal form,</text>
+<text x="404.5" y="847" text-anchor="middle" font-size="15" fill="#222222">per-image scale</text>
+<rect x="532" y="770" width="200" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
+<text x="632.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Symmetry</text>
+<text x="632.0" y="828" text-anchor="middle" font-size="14" fill="#222222">space group, twinning, tNCS</text>
+<rect x="660" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
+<text x="691.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
+<rect x="752" y="770" width="218" height="127" rx="12" ry="12" fill="white" stroke="#1A8A7D" stroke-width="3"/>
+<text x="861.0" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#1A8A7D">Scale &amp; merge</text>
+<text x="861.0" y="828" text-anchor="middle" font-size="14" fill="#222222">in space group, resolution cut</text>
+<text x="861.0" y="847" text-anchor="middle" font-size="14" fill="#222222">partiality, error model</text>
+<rect x="990" y="770" width="205" height="127" rx="12" ry="12" fill="white" stroke="#8E44AD" stroke-width="3" stroke-dasharray="9,6"/>
+<text x="1092.5" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#8E44AD">Structure &amp; map</text>
+<text x="1092.5" y="828" text-anchor="middle" font-size="14" fill="#222222">placement or MR, σA maps</text>
+<rect x="1123" y="869" width="62" height="20" rx="4" fill="#1DB38B"/>
+<text x="1154.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">tested</text>
+<rect x="1063" y="869" width="52" height="20" rx="4" fill="#555555"/>
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+<text x="1029.0" y="884" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
+<rect x="1215" y="770" width="175" height="127" rx="12" ry="12" fill="white" stroke="#8E44AD" stroke-width="3" stroke-dasharray="9,6"/>
+<text x="1302.5" y="802" text-anchor="middle" font-size="20" font-weight="bold" fill="#8E44AD">Refinement</text>
+<text x="1302.5" y="828" text-anchor="middle" font-size="14" fill="#222222">restrained ML,</text>
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+<text x="1485.0" y="828" text-anchor="middle" font-size="15" fill="#222222">MTZ, mmCIF, maps</text>
+<path d="M277,822 L295,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
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+<path d="M732,822 L750,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M970,822 L988,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M1195,822 L1213,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<path d="M1390,822 L1408,822" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
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+<text x="1190.0" y="736" text-anchor="middle" font-size="13" fill="#6B6B6B" font-style="italic">without a model</text>
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+<text x="289" y="740" font-size="21" font-weight="bold" fill="#1A8A7D">Whole dataset</text>
+<path d="M720,625 L720,710 L207,710 L207,768" fill="none" stroke="#555" stroke-width="2.2" marker-end="url(#arr)"/>
+<text x="222" y="702" text-anchor="start" font-size="13" fill="#6B6B6B" font-style="italic">every crystal</text>
 <rect x="60" y="936" width="52" height="20" rx="4" fill="#2F6FDE"/>
 <text x="86.0" y="951" text-anchor="middle" font-size="13" font-weight="bold" fill="white">CUDA</text>
 <text x="124" y="951" font-size="15" fill="#222222">CUDA kernel when a GPU is present</text>
diff --git a/docs/index.rst b/docs/index.rst
deleted file mode 100644
index 9c2a3dc52..000000000
--- a/docs/index.rst
+++ /dev/null
@@ -1,94 +0,0 @@
-.. image:: jfjoch.png
-   :width: 256
-   :align: left
-
-PSI Jungfraujoch
-================
-
-Jungfraujoch is data acquisition and on-the-fly analysis system developed by the `Paul Scherrer Institut <https://www.psi.ch>`__.
-
-It can be currently used with PSI and DECTRIS detectors.
-
-Its data-processing half is **rugnux** — start at :doc:`rugnux <RUGNUX>` to process a stored
-dataset, and at :doc:`the broker <JFJOCH_BROKER>` to acquire one.
-
-Jungfraujoch is distributed under the GPLv3 license.
-
-.. toctree::
-   :maxdepth: 1
-   :caption: rugnux — data processing
-
-   RUGNUX
-   RUGNUX_OVERVIEW
-   RUGNUX_INSTALL
-   RUGNUX_FORMATS
-   RUGNUX_TUTORIAL
-   RUGNUX_INTEGRATION
-   RUGNUX_REPORT
-   RUGNUX_ADVANCED
-   RUGNUX_MODEL_AND_REFERENCE
-   RUGNUX_CALIBRATION
-   RUGNUX_BENCHMARKING
-   CPU_DATA_ANALYSIS
-   CPU_DATA_ANALYSIS_IMAGE
-   CPU_DATA_ANALYSIS_INDEXING
-   CPU_DATA_ANALYSIS_INTEGRATION
-   CPU_DATA_ANALYSIS_DECISIONS
-   GPU_DATA_ANALYSIS
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Jungfraujoch — acquisition
-
-   JFJOCH_BROKER
-   JFJOCH_WRITER
-   JFJOCH_VIEWER
-   SOFTWARE_INTEGRATION
-   TOOLS
-   DEPLOYMENT
-   DETECTORS
-   HARDWARE
-   SOFTWARE
-
-.. toctree::
-   :maxdepth: 1
-   :caption: FPGA
-
-   FPGA
-   FPGA_LICENSE
-   FPGA_DESIGN
-   FPGA_NETWORK
-   FPGA_PCIE_DRIVER
-   FPGA_SETTINGS
-   FPGA_DATA_ANALYSIS
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Reference
-
-   DETECTOR_GEOMETRY
-   OPENAPI
-   OPENAPI_SPECS
-   PYTHON_CLIENT
-   CBOR
-   HDF5
-   IMAGE_STREAM
-   PIXEL_MASK
-   WEB_FRONTEND
-   TESTS
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Project
-
-   ACKNOWLEDGEMENT
-   EXTERNAL_TEST_DATA
-   EXTERNAL_TEST_DATA_STILLS
-   LICENSE
-   THIRD_PARTY_NOTICES
-   VERSIONING
-   SECURITY
-   RELEASE_CONTENTS
-   REPOSITORIES
-   NAMING
-   CHANGELOG
diff --git a/docs/landing/hero_live_dark.webp b/docs/landing/hero_live_dark.webp
new file mode 100644
index 000000000..1049b993d
Binary files /dev/null and b/docs/landing/hero_live_dark.webp differ
diff --git a/docs/landing/hero_live_light.webp b/docs/landing/hero_live_light.webp
new file mode 100644
index 000000000..88eac6406
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diff --git a/docs/landing/index.html b/docs/landing/index.html
new file mode 100644
index 000000000..cd3a11ce3
--- /dev/null
+++ b/docs/landing/index.html
@@ -0,0 +1,164 @@
+<!doctype html>
+<!-- The front page of the documentation site. docs/_ext/jfjoch_downloads.py renders this template
+     at the end of a Sphinx build (the {{...}} placeholders) into the output root as index.html,
+     next to the Sphinx pages, so it is served wherever the documentation is: Read the Docs, the
+     gitea-pages branch and the broker's frontend bundle. The Sphinx home page is documentation.html. -->
+<html lang="en">
+<head>
+<meta charset="utf-8">
+<meta name="viewport" content="width=device-width, initial-scale=1">
+<title>Jungfraujoch and Rugnux: X-ray diffraction data, from the detector to merged data and structures</title>
+<meta name="description" content="Open-source software from the Paul Scherrer Institute: Rugnux processes macromolecular diffraction data with one command, to merged data and, with a model, a structure, the Jungfraujoch Viewer shows it, and Jungfraujoch acquires it from JUNGFRAU and EIGER detectors at full speed.">
+<link rel="icon" href="_static/jfjoch.png">
+<link rel="stylesheet" href="landing.css">
+<script>
+// Apply the saved theme before the first paint, so a dark page does not flash light.
+try { var t = localStorage.getItem("jfj-theme"); if (t) document.documentElement.setAttribute("data-theme", t); } catch (e) {}
+</script>
+</head>
+<body>
+
+<header class="top">
+  <a class="brand" href="index.html"><img src="_static/jfjoch.png" alt="" width="36" height="33"><span>Jungfraujoch</span></a>
+  <nav class="top__nav" aria-label="Sections">
+    <a href="#programs">Programs</a>
+    <a href="#download">Download</a>
+    <a href="documentation.html">Documentation</a>
+    <a href="https://gitea.psi.ch/mx/jungfraujoch">Source</a>
+  </nav>
+  <button class="theme-toggle" type="button" aria-label="Switch between light and dark theme" title="Light / dark">
+    <svg class="theme-toggle__sun" viewBox="0 0 24 24" width="20" height="20" aria-hidden="true"><circle cx="12" cy="12" r="4.5" fill="none" stroke="currentColor" stroke-width="2"/><path d="M12 2v3M12 19v3M2 12h3M19 12h3M4.9 4.9l2.1 2.1M17 17l2.1 2.1M4.9 19.1 7 17M17 7l2.1-2.1" stroke="currentColor" stroke-width="2" stroke-linecap="round"/></svg>
+    <svg class="theme-toggle__moon" viewBox="0 0 24 24" width="20" height="20" aria-hidden="true"><path d="M20 15.5A8.5 8.5 0 0 1 8.5 4a8.5 8.5 0 1 0 11.5 11.5z" fill="none" stroke="currentColor" stroke-width="2" stroke-linejoin="round"/></svg>
+  </button>
+  <a class="psi-logo" href="https://www.psi.ch" title="Paul Scherrer Institute - www.psi.ch"><img src="psi.png" alt="Paul Scherrer Institute" width="59" height="36"></a>
+</header>
+
+<main>
+
+<section class="hero">
+  <figure class="hero__art">
+    <img class="hero__art-light" src="hero_live_light.webp" width="1120" height="848"
+         alt="A diffraction image beside the placed model in its electron density, over the timeline of the live analysis: the detector lane of an 18 s collection and the Rugnux lane ending 4.9 s after the last image">
+    <img class="hero__art-dark" src="hero_live_dark.webp" width="1120" height="848" alt="">
+    <figcaption>Cytochrome C at SLS X10SA: 1800 images at 100&nbsp;Hz, merged and the AlphaFold model placed 4.9&nbsp;s after the last image</figcaption>
+  </figure>
+  <div class="hero__text">
+    <p class="eyebrow">Paul Scherrer Institute &middot; open source</p>
+    <h1>From the detector to merged data and structures.</h1>
+    <p class="lede">Software for X-ray diffraction data: <strong>Rugnux</strong> takes a stored
+    dataset from the images to merged data with one command, and with a model on to a
+    structure and maps; the <strong>Viewer</strong> shows what is in it, and
+    <strong>Jungfraujoch</strong> acquires it from the detector at full speed.</p>
+    <p class="hero__ops">All three are in user operation at the MX beamlines of the Swiss Light Source SLS&nbsp;2.0.</p>
+    <div class="hero__actions">
+      <a class="btn btn--primary" href="#download">Download</a>
+      <a class="btn btn--ghost" href="documentation.html">Read the documentation</a>
+    </div>
+    <p class="hero__run"><code>rugnux &lt;diffraction image file&gt;</code><code>rugnux &lt;diffraction image file&gt; &lt;CIF/PDB model file&gt;</code></p>
+  </div>
+</section>
+
+<section class="programs" id="programs">
+  <div class="programs__grid">
+
+    <article class="program">
+      <p class="program__kicker">Data processing</p>
+      <h2>Rugnux</h2>
+      <p>Takes a macromolecular diffraction dataset, a synchrotron rotation sweep or XFEL serial stills, from the
+      images to merged data: spot finding, indexing, integration, scaling and merging, with the
+      space group, cell and resolution decided from the data and a report that says on what
+      evidence. Writes <code>.mtz</code>, <code>.cif</code> and <code>.hkl</code> for the programs
+      that come next. Given an atomic model it goes on to a structure: the model is placed
+      (as a rigid body or by molecular replacement) and refined, and the maps and the unexplained
+      difference-density blobs are written beside it. Validated on public data:
+      <a href="EXTERNAL_TEST_DATA.html">over 200 rotation datasets</a> and
+      <a href="EXTERNAL_TEST_DATA_STILLS.html">eleven XFEL serial datasets</a>.</p>
+      <p class="program__meta">Linux &middot; macOS &middot; Windows &middot; command line &middot; fast on an NVIDIA GPU, works without one</p>
+      <p class="program__links"><a href="RUGNUX.html">Get started</a><a href="RUGNUX_OVERVIEW.html">What it does</a><a href="RUGNUX_TUTORIAL.html">Manual</a><a href="#dl-rugnux">Download</a></p>
+    </article>
+
+    <article class="program">
+      <p class="program__kicker">Desktop application</p>
+      <h2>Jungfraujoch Viewer</h2>
+      <p>Shows what is in a dataset: every image with its spots, predictions and resolution rings,
+      per-image statistics over the sweep, grid-scan maps, and the same processing pipeline as
+      Rugnux, run from a settings panel on the open file. Follows a live collection from a running
+      Jungfraujoch broker.</p>
+      <p class="program__meta">Linux &middot; macOS &middot; Windows &middot; Qt 6</p>
+      <p class="program__links"><a href="JFJOCH_VIEWER.html">Get started</a><a href="JFJOCH_VIEWER.html#a-guided-tour">Guided tour</a><a href="#dl-viewer">Download</a></p>
+    </article>
+
+    <article class="program">
+      <p class="program__kicker">Data acquisition</p>
+      <h2>Jungfraujoch</h2>
+      <p>The acquisition and real-time analysis system for the PSI JUNGFRAU and EIGER detectors,
+      and for DECTRIS detectors through their control unit: an FPGA and GPU pipeline that takes
+      the detector's frames at full rate, analyses them on the fly, streams them to the NXmx HDF5
+      writer and serves a web interface and REST API to the beamline.</p>
+      <p class="program__meta">Linux servers &middot; AMD Alveo U55C FPGA &middot; NVIDIA GPUs</p>
+      <p class="program__links"><a href="JUNGFRAUJOCH.html">Get started</a><a href="DEPLOYMENT.html">Install</a><a href="JFJOCH_BROKER.html">Broker</a><a href="JFJOCH_WRITER.html">Writer</a></p>
+    </article>
+
+  </div>
+</section>
+
+<section class="download" id="download">
+  <div class="download__head">
+    <h2>Download</h2>
+    <p>Pre-built, signed where the platform asks for it, nothing to install beside them.
+    <span data-os-note></span></p>
+  </div>
+
+  <div class="download__program" id="dl-rugnux">
+    <h3>Rugnux</h3>
+    <p>One self-contained executable. Unpack the archive into a directory of its own and run
+    <code>bin/rugnux</code>; no CUDA toolkit, no Qt, no service. On a machine with an NVIDIA GPU
+    take the GPU build, which also runs without one. <a href="RUGNUX_DOWNLOAD.html">Details, packages and building from source</a>.</p>
+    {{downloads:rugnux}}
+  </div>
+
+  <div class="download__program" id="dl-viewer">
+    <h3>Jungfraujoch Viewer</h3>
+    <p>A desktop application with the Qt runtime included: a portable archive on Linux, a
+    notarized disk image on macOS, an installer on Windows. <a href="VIEWER_DOWNLOAD.html">Details and building from source</a>.</p>
+    {{downloads:viewer}}
+  </div>
+
+  <div class="download__program download__program--text">
+    <h3>Jungfraujoch, the acquisition system</h3>
+    <p>Installed on the beamline's Linux servers from the <a href="REPOSITORIES.html">RPM and APT
+    repositories</a> (<code>jfjoch</code>, <code>jfjoch-writer</code>, <code>jfjoch-driver-dkms</code>,
+    <code>jfjoch-viewer</code>, <code>rugnux</code>), with the FPGA firmware and the writer's
+    packages attached to every <a href="https://gitea.psi.ch/mx/jungfraujoch/releases">release</a>.
+    <a href="DEPLOYMENT.html">Deployment</a> is the step-by-step guide; <a href="RELEASE_CONTENTS.html">Release contents</a> says what each package needs on the machine.</p>
+  </div>
+</section>
+
+<section class="licence">
+  <h2>Free to use, in academia and industry</h2>
+  <p>Rugnux, the viewer and the Jungfraujoch services are free software under the
+  <a href="LICENSE.html">GNU General Public License v3</a>; the FPGA design is released under the
+  <a href="FPGA_LICENSE.html">CERN Open Hardware Licence v2, strongly reciprocal</a>. Both let
+  anyone use, study and modify the software and the hardware design at no charge, commercial use
+  included; modified versions that are distributed must be released under the same licence. The released binaries bundle third-party components under GPL-compatible licences, and the
+  CUDA builds the NVIDIA CUDA runtime under NVIDIA's EULA: see the
+  <a href="THIRD_PARTY_NOTICES.html">third-party notices</a>.</p>
+  <p>The software builds on many existing algorithms, reimplemented (see the
+  <a href="ACKNOWLEDGEMENT.html">acknowledgements</a>), many of them moved to the GPU and made faster
+  across a range of computing configurations; it was developed with the help of generative AI
+  (Claude Opus, Anthropic).</p>
+</section>
+
+</main>
+
+<footer class="foot">
+  <p>Documentation for Jungfraujoch {{release}} &middot; <a href="CHANGELOG.html">changelog</a> &middot;
+  <a href="documentation.html">documentation</a> &middot; <a href="NAMING.html">why the names</a> &middot;
+  <a href="ACKNOWLEDGEMENT.html">acknowledgements</a> &middot; <a href="https://gitea.psi.ch/mx/jungfraujoch">source</a></p>
+  <p>&copy; Paul Scherrer Institute.</p>
+</footer>
+
+<script src="_static/jfjoch_downloads.js"></script>
+<script src="landing.js"></script>
+</body>
+</html>
diff --git a/docs/landing/landing.css b/docs/landing/landing.css
new file mode 100644
index 000000000..ce06d85b2
--- /dev/null
+++ b/docs/landing/landing.css
@@ -0,0 +1,388 @@
+/* The front page (docs/landing/index.html). Self-contained: system fonts, no framework, one
+   palette per theme. The download blocks use the same jfj-dl markup as the Sphinx download pages
+   (docs/_ext/jfjoch_downloads.py) and are styled here for this page. */
+
+:root {
+    --bg: #fbfbfd;
+    --bg-raised: #ffffff;
+    --bg-tint: #eef0fa;
+    --fg: #1b1d2a;
+    --fg-muted: #5b6072;
+    --line: rgba(27, 29, 42, 0.12);
+    --primary: #3949ab;
+    --primary-strong: #2c3a8f;
+    --primary-soft: rgba(57, 73, 171, 0.1);
+    --on-primary: #ffffff;
+    --accent: #e9a23b;
+    --accent-soft: rgba(233, 162, 59, 0.16);
+    --shadow: 0 1px 2px rgba(27, 29, 42, 0.06), 0 8px 24px rgba(27, 29, 42, 0.06);
+}
+
+@media (prefers-color-scheme: dark) {
+    :root:not([data-theme="light"]) {
+        --bg: #11131c;
+        --bg-raised: #181b27;
+        --bg-tint: #1d2130;
+        --fg: #e8e9f1;
+        --fg-muted: #9ea3b8;
+        --line: rgba(232, 233, 241, 0.12);
+        --primary: #8e9dff;
+        --primary-strong: #aab5ff;
+        --primary-soft: rgba(142, 157, 255, 0.14);
+        --on-primary: #0d1030;
+        --accent: #f0b65b;
+        --accent-soft: rgba(240, 182, 91, 0.16);
+        --shadow: 0 1px 2px rgba(0, 0, 0, 0.4), 0 8px 24px rgba(0, 0, 0, 0.35);
+    }
+}
+
+:root[data-theme="dark"] {
+    --bg: #11131c;
+    --bg-raised: #181b27;
+    --bg-tint: #1d2130;
+    --fg: #e8e9f1;
+    --fg-muted: #9ea3b8;
+    --line: rgba(232, 233, 241, 0.12);
+    --primary: #8e9dff;
+    --primary-strong: #aab5ff;
+    --primary-soft: rgba(142, 157, 255, 0.14);
+    --on-primary: #0d1030;
+    --accent: #f0b65b;
+    --accent-soft: rgba(240, 182, 91, 0.16);
+    --shadow: 0 1px 2px rgba(0, 0, 0, 0.4), 0 8px 24px rgba(0, 0, 0, 0.35);
+}
+
+* { box-sizing: border-box; }
+
+html { scroll-behavior: smooth; }
+
+body {
+    margin: 0;
+    background: var(--bg);
+    color: var(--fg);
+    font: 16px/1.55 -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, "Helvetica Neue", Arial, sans-serif;
+    -webkit-font-smoothing: antialiased;
+}
+
+a { color: var(--primary); text-decoration: none; }
+a:hover { color: var(--primary-strong); text-decoration: underline; }
+
+code {
+    font-family: "SFMono-Regular", Menlo, Consolas, "Roboto Mono", monospace;
+    font-size: 0.92em;
+    background: var(--primary-soft);
+    padding: 0.1em 0.35em;
+    border-radius: 4px;
+}
+
+h1, h2, h3 { line-height: 1.2; letter-spacing: -0.01em; margin: 0; }
+
+main > section, .top, .foot {
+    max-width: 1120px;
+    margin: 0 auto;
+    padding: 0 24px;
+}
+
+/* ---- header ---------------------------------------------------------------------------------- */
+
+.top {
+    display: flex;
+    align-items: center;
+    gap: 24px;
+    padding-top: 18px;
+    padding-bottom: 18px;
+}
+
+.brand {
+    display: inline-flex;
+    align-items: center;
+    gap: 10px;
+    color: var(--fg);
+    font-weight: 600;
+    font-size: 1.05em;
+}
+.brand:hover { text-decoration: none; }
+.brand img { display: block; }
+
+.top__nav { display: flex; gap: 22px; margin-left: auto; font-weight: 500; }
+.top__nav a { color: var(--fg-muted); }
+.top__nav a:hover { color: var(--primary); text-decoration: none; }
+
+.theme-toggle {
+    display: inline-flex;
+    align-items: center;
+    justify-content: center;
+    width: 38px; height: 38px;
+    border: 1px solid var(--line);
+    border-radius: 50%;
+    background: var(--bg-raised);
+    color: var(--fg-muted);
+    cursor: pointer;
+}
+.theme-toggle:hover { color: var(--primary); border-color: var(--primary); }
+
+/* The PSI logo is black only, so the dark theme shows it inverted (as the viewer does). */
+.psi-logo { display: inline-flex; }
+.psi-logo img { display: block; }
+:root[data-theme="dark"] .psi-logo img { filter: invert(1); }
+@media (prefers-color-scheme: dark) {
+    :root:not([data-theme="light"]) .psi-logo img { filter: invert(1); }
+}
+.theme-toggle__moon { display: none; }
+:root[data-theme="dark"] .theme-toggle__sun { display: none; }
+:root[data-theme="dark"] .theme-toggle__moon { display: block; }
+@media (prefers-color-scheme: dark) {
+    :root:not([data-theme="light"]) .theme-toggle__sun { display: none; }
+    :root:not([data-theme="light"]) .theme-toggle__moon { display: block; }
+}
+
+/* ---- hero ------------------------------------------------------------------------------------ */
+
+.hero {
+    position: relative;
+    display: grid;
+    grid-template-columns: minmax(0, 1fr) minmax(0, 560px);
+    align-items: center;
+    gap: 32px;
+    padding-top: 56px;
+    padding-bottom: 64px;
+}
+
+.hero__art {
+    grid-column: 2;
+    grid-row: 1;
+    width: 100%;
+    max-width: 560px;
+    justify-self: end;
+    margin: 0;
+}
+/* A detector frame beside the placed model in its density, over the live analysis' timeline, drawn
+   on the page's own colours: one file per theme, shown by the same rules that pick the theme's tokens. */
+.hero__art img {
+    display: block;
+    width: 100%;
+    height: auto;
+}
+.hero__art .hero__art-dark { display: none; }
+:root[data-theme="dark"] .hero__art .hero__art-light { display: none; }
+:root[data-theme="dark"] .hero__art .hero__art-dark { display: block; }
+@media (prefers-color-scheme: dark) {
+    :root:not([data-theme="light"]) .hero__art .hero__art-light { display: none; }
+    :root:not([data-theme="light"]) .hero__art .hero__art-dark { display: block; }
+}
+.hero__art figcaption {
+    margin-top: 10px;
+    font-size: 0.78em;
+    color: var(--fg-muted);
+    text-align: right;
+}
+
+.hero__text { grid-column: 1; grid-row: 1; max-width: 600px; }
+
+.eyebrow {
+    margin: 0 0 14px;
+    font-size: 0.78em;
+    font-weight: 700;
+    letter-spacing: 0.1em;
+    text-transform: uppercase;
+    color: var(--primary);
+}
+
+.hero h1 {
+    font-size: clamp(2.1rem, 4.6vw, 3.4rem);
+    font-weight: 700;
+    letter-spacing: -0.025em;
+    margin-bottom: 18px;
+}
+
+.lede { font-size: 1.2em; color: var(--fg-muted); margin: 0 0 14px; }
+.hero__ops { color: var(--fg-muted); margin: 0 0 26px; }
+.lede strong { color: var(--fg); font-weight: 600; }
+
+.hero__actions { display: flex; flex-wrap: wrap; gap: 12px; margin-bottom: 26px; }
+
+.btn {
+    display: inline-block;
+    padding: 11px 20px;
+    border-radius: 8px;
+    font-weight: 600;
+    border: 1px solid transparent;
+    transition: transform 0.12s, box-shadow 0.12s, background 0.12s;
+}
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+.btn--ghost { border-color: var(--line); color: var(--fg); background: var(--bg-raised); }
+.btn--ghost:hover { border-color: var(--primary); color: var(--primary); }
+
+.hero__run {
+    display: flex;
+    flex-direction: column;
+    align-items: flex-start;
+    gap: 8px;
+    margin: 0;
+    font-size: 0.95em;
+}
+.hero__run code { font-size: 1em; padding: 0.35em 0.7em; max-width: 100%; overflow-wrap: anywhere; }
+
+/* ---- programs -------------------------------------------------------------------------------- */
+
+.programs { padding-bottom: 56px; }
+
+.programs__grid {
+    display: grid;
+    grid-template-columns: repeat(auto-fit, minmax(280px, 1fr));
+    gap: 20px;
+}
+
+.program {
+    display: flex;
+    flex-direction: column;
+    padding: 24px 24px 20px;
+    border: 1px solid var(--line);
+    border-radius: 14px;
+    background: var(--bg-raised);
+    box-shadow: var(--shadow);
+}
+.program__kicker {
+    margin: 0 0 8px;
+    font-size: 0.74em;
+    font-weight: 700;
+    letter-spacing: 0.1em;
+    text-transform: uppercase;
+    color: var(--primary);
+}
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+.program__links {
+    margin: 0;
+    padding-top: 14px;
+    border-top: 1px solid var(--line);
+    display: flex;
+    flex-wrap: wrap;
+    gap: 6px 18px;
+    font-weight: 500;
+}
+.program__links a:first-child { font-weight: 700; }
+
+/* ---- download -------------------------------------------------------------------------------- */
+
+.download {
+    padding-top: 48px;
+    padding-bottom: 24px;
+    border-top: 1px solid var(--line);
+}
+.download__head { max-width: 640px; margin-bottom: 28px; }
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+
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+
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+}
+
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+    padding: 18px 18px 8px;
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+}
+.jfj-dl__card.is-yours {
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+    box-shadow: 0 0 0 3px var(--accent-soft), var(--shadow);
+}
+.jfj-dl__card.is-yours::after {
+    content: "Your system";
+    position: absolute;
+    top: -11px; right: 14px;
+    padding: 2px 10px;
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+.jfj-dl__note:empty { display: none; }
+
+/* ---- licence, footer ------------------------------------------------------------------------- */
+
+.licence {
+    padding-top: 40px;
+    padding-bottom: 48px;
+    border-top: 1px solid var(--line);
+}
+.licence h2 { font-size: 1.5em; font-weight: 650; margin-bottom: 12px; }
+.licence p { margin: 0 0 12px; max-width: 760px; color: var(--fg-muted); }
+
+.foot {
+    padding-top: 24px;
+    padding-bottom: 40px;
+    border-top: 1px solid var(--line);
+    font-size: 0.88em;
+    color: var(--fg-muted);
+}
+.foot p { margin: 0 0 6px; }
+
+/* ---- small screens --------------------------------------------------------------------------- */
+
+@media (max-width: 760px) {
+    body { font-size: 15px; }
+    .top { gap: 14px; flex-wrap: wrap; }
+    .top__nav { gap: 14px; margin-left: 0; order: 3; width: 100%; font-size: 0.95em; }
+    .theme-toggle { margin-left: auto; }
+    .hero { grid-template-columns: 1fr; padding-top: 28px; padding-bottom: 40px; }
+    .hero__art { grid-column: 1; grid-row: 1; max-width: 360px; justify-self: center; }
+    .hero__art figcaption { text-align: center; }
+    .hero__text { grid-row: 2; }
+    .programs__grid { grid-template-columns: 1fr; }
+}
diff --git a/docs/landing/landing.js b/docs/landing/landing.js
new file mode 100644
index 000000000..ba94b5979
--- /dev/null
+++ b/docs/landing/landing.js
@@ -0,0 +1,29 @@
+// The front page: theme toggle and the download section's
+// "your system" highlight. The download buttons themselves are repointed at the newest release by
+// _static/jfjoch_downloads.js, shared with the Sphinx download pages.
+(function () {
+    // ---- theme: follows the system until the toggle is used, then remembered -----------------
+    var root = document.documentElement;
+    var toggle = document.querySelector(".theme-toggle");
+    function isDark() {
+        var set = root.getAttribute("data-theme");
+        if (set) return set === "dark";
+        return window.matchMedia && window.matchMedia("(prefers-color-scheme: dark)").matches;
+    }
+    if (toggle) toggle.addEventListener("click", function () {
+        var next = isDark() ? "light" : "dark";
+        root.setAttribute("data-theme", next);
+        try { localStorage.setItem("jfj-theme", next); } catch (e) {}
+    });
+
+    // ---- "your system": highlight the platform the browser runs on ----------------------------
+    var ua = navigator.userAgent || "", platform = navigator.platform || "";
+    var os = /Windows/.test(ua) ? "windows" : /Mac/.test(platform) || /Macintosh/.test(ua) ? "macos" :
+             /Linux|X11/.test(platform + ua) && !/Android/.test(ua) ? "linux" : null;
+    if (os) {
+        document.querySelectorAll('.jfj-dl__card[data-platform="' + os + '"]').forEach(function (c) { c.classList.add("is-yours"); });
+        var note = document.querySelector("[data-os-note]");
+        var names = { windows: "Windows", macos: "macOS", linux: "Linux" };
+        if (note) note.textContent = "The " + names[os] + " builds are marked for you.";
+    }
+})();
diff --git a/docs/landing/psi.png b/docs/landing/psi.png
new file mode 100644
index 000000000..49bbde890
Binary files /dev/null and b/docs/landing/psi.png differ
diff --git a/docs/python_client/README.md b/docs/python_client/README.md
index e60e5ad0c..0d8aa2e67 100644
--- a/docs/python_client/README.md
+++ b/docs/python_client/README.md
@@ -22,8 +22,8 @@ communicate through network calls or other mechanisms.
 
 This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
-- API version: 1.0.0-rc.179
-- Package version: 1.0.0-rc.179
+- API version: 1.0.0-rc.180
+- Package version: 1.0.0-rc.180
 - Generator version: 7.20.0
 - Build package: org.openapitools.codegen.languages.PythonClientCodegen
 
@@ -231,6 +231,9 @@ Class | Method | HTTP request | Description
  - [RoiCircleList](docs/RoiCircleList.md)
  - [RoiDefinitions](docs/RoiDefinitions.md)
  - [RotationAxis](docs/RotationAxis.md)
+ - [RugnuxLiveBlob](docs/RugnuxLiveBlob.md)
+ - [RugnuxLiveModel](docs/RugnuxLiveModel.md)
+ - [RugnuxLiveRefinement](docs/RugnuxLiveRefinement.md)
  - [RugnuxLiveStatus](docs/RugnuxLiveStatus.md)
  - [RugnuxLiveStep](docs/RugnuxLiveStep.md)
  - [RugnuxSettings](docs/RugnuxSettings.md)
diff --git a/docs/python_client/docs/DefaultApi.md b/docs/python_client/docs/DefaultApi.md
index 4b3be85e3..b733809a2 100644
--- a/docs/python_client/docs/DefaultApi.md
+++ b/docs/python_client/docs/DefaultApi.md
@@ -4076,14 +4076,16 @@ This endpoint does not need any parameter.
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
 
 # **rugnux_map_ccp4_get**
-> bytearray rugnux_map_ccp4_get(type=type)
+> bytearray rugnux_map_ccp4_get(type=type, stage=stage)
 
 Get an electron-density map of the last rugnux live run
 
 The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map
 coefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where
 the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and
-RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.
+RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run
+refined the model, the 2mFo-DFc and mFo-DFc maps are the refined model's unless asked for `stage=placed`;
+the anomalous map stays on the placed model's phases.
 
 
 ### Example
@@ -4116,10 +4118,11 @@ with jfjoch_client.ApiClient(configuration) as api_client:
     # Create an instance of the API class
     api_instance = jfjoch_client.DefaultApi(api_client)
     type = 2fofc # str | `2fofc`: the 2mFo-DFc map; `fofc`: the mFo-DFc difference map; `anom`: the anomalous difference map, (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (`anomalous_map` in `/rugnux/status`)  (optional) (default to 2fofc)
+    stage = 'stage_example' # str | `placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`). Default: the refined model where there is one, otherwise the placed one.  (optional)
 
     try:
         # Get an electron-density map of the last rugnux live run
-        api_response = api_instance.rugnux_map_ccp4_get(type=type)
+        api_response = api_instance.rugnux_map_ccp4_get(type=type, stage=stage)
         print("The response of DefaultApi->rugnux_map_ccp4_get:\n")
         pprint(api_response)
     except Exception as e:
@@ -4134,6 +4137,7 @@ with jfjoch_client.ApiClient(configuration) as api_client:
 Name | Type | Description  | Notes
 ------------- | ------------- | ------------- | -------------
  **type** | **str**| &#x60;2fofc&#x60;: the 2mFo-DFc map; &#x60;fofc&#x60;: the mFo-DFc difference map; &#x60;anom&#x60;: the anomalous difference map, (F(+) - F(-)) on the model phases less 90 degrees, where the merge kept the Bijvoet pairs (&#x60;anomalous_map&#x60; in &#x60;/rugnux/status&#x60;)  | [optional] [default to 2fofc]
+ **stage** | **str**| &#x60;placed&#x60;: the model as placed; &#x60;refined&#x60;: the model refined (&#x60;refined_model&#x60; in &#x60;/rugnux/status&#x60;). Default: the refined model where there is one, otherwise the placed one.  | [optional] 
 
 ### Return type
 
@@ -4153,20 +4157,21 @@ Name | Type | Description  | Notes
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
 **200** | Map |  -  |
-**400** | Unknown map type |  -  |
+**400** | Unknown map type or stage |  -  |
 **401** | The current dataset is protected and no valid bearer token was presented. |  -  |
-**404** | The last rugnux live run placed no model or made no maps, or (&#x60;anom&#x60;) has no Bijvoet pairs |  -  |
+**404** | The last rugnux live run placed no model or made no maps, or (&#x60;anom&#x60;) has no Bijvoet pairs, or (&#x60;stage&#x3D;refined&#x60;) refined none |  -  |
 
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
 
 # **rugnux_model_cif_get**
-> bytearray rugnux_model_cif_get()
+> bytearray rugnux_model_cif_get(stage=stage)
 
 Get the model as placed by the last rugnux live run
 
 The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
 `_model.cif` file written beside the data: the data's cell and space group, with the input model's own
 metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
+Where the run refined the model, the refined model unless asked for `stage=placed`.
 
 
 ### Example
@@ -4198,10 +4203,11 @@ configuration = jfjoch_client.Configuration(
 with jfjoch_client.ApiClient(configuration) as api_client:
     # Create an instance of the API class
     api_instance = jfjoch_client.DefaultApi(api_client)
+    stage = 'stage_example' # str | `placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`). Default: the refined model where there is one, otherwise the placed one.  (optional)
 
     try:
         # Get the model as placed by the last rugnux live run
-        api_response = api_instance.rugnux_model_cif_get()
+        api_response = api_instance.rugnux_model_cif_get(stage=stage)
         print("The response of DefaultApi->rugnux_model_cif_get:\n")
         pprint(api_response)
     except Exception as e:
@@ -4212,7 +4218,10 @@ with jfjoch_client.ApiClient(configuration) as api_client:
 
 ### Parameters
 
-This endpoint does not need any parameter.
+
+Name | Type | Description  | Notes
+------------- | ------------- | ------------- | -------------
+ **stage** | **str**| &#x60;placed&#x60;: the model as placed; &#x60;refined&#x60;: the model refined (&#x60;refined_model&#x60; in &#x60;/rugnux/status&#x60;). Default: the refined model where there is one, otherwise the placed one.  | [optional] 
 
 ### Return type
 
@@ -4232,8 +4241,9 @@ This endpoint does not need any parameter.
 | Status code | Description | Response headers |
 |-------------|-------------|------------------|
 **200** | Placed model |  -  |
+**400** | Unknown stage |  -  |
 **401** | The current dataset is protected and no valid bearer token was presented. |  -  |
-**404** | The last rugnux live run placed no model |  -  |
+**404** | The last rugnux live run placed no model, or (&#x60;stage&#x3D;refined&#x60;) refined none |  -  |
 
 [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
 
diff --git a/docs/python_client/docs/RugnuxLiveBlob.md b/docs/python_client/docs/RugnuxLiveBlob.md
new file mode 100644
index 000000000..25f8cee89
--- /dev/null
+++ b/docs/python_client/docs/RugnuxLiveBlob.md
@@ -0,0 +1,37 @@
+# RugnuxLiveBlob
+
+A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on what is measured, to point a person at the density - not an identification. 
+
+## Properties
+
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**kind** | **str** |  | 
+**x** | **float** | Centroid, Cartesian Angstrom, in the frame of the refined model (&#x60;/rugnux/model.cif&#x60;) | 
+**y** | **float** |  | 
+**z** | **float** |  | 
+**peak_sigma** | **float** | The highest point, in map sigma | 
+**volume_a3** | **float** | Volume above 3 sigma, in cubic Angstrom | 
+**nearest_atom** | **str** | e.g. \&quot;OG1 THR A42\&quot; | 
+**nearest_atom_distance_a** | **float** |  | 
+
+## Example
+
+```python
+from jfjoch_client.models.rugnux_live_blob import RugnuxLiveBlob
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RugnuxLiveBlob from a JSON string
+rugnux_live_blob_instance = RugnuxLiveBlob.from_json(json)
+# print the JSON string representation of the object
+print(RugnuxLiveBlob.to_json())
+
+# convert the object into a dict
+rugnux_live_blob_dict = rugnux_live_blob_instance.to_dict()
+# create an instance of RugnuxLiveBlob from a dict
+rugnux_live_blob_from_dict = RugnuxLiveBlob.from_dict(rugnux_live_blob_dict)
+```
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+
diff --git a/docs/python_client/docs/RugnuxLiveModel.md b/docs/python_client/docs/RugnuxLiveModel.md
new file mode 100644
index 000000000..a2e7171de
--- /dev/null
+++ b/docs/python_client/docs/RugnuxLiveModel.md
@@ -0,0 +1,50 @@
+# RugnuxLiveModel
+
+What the run made of the model it was given, as the report's MODEL VALIDATION section states it. The R-factors here are those of the placed model with its own coordinates and B factors; what refinement made of it is in `refinement`. A value that is absent was not computed - the model was not placed, or not by molecular replacement. 
+
+## Properties
+
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**placement** | **str** | RIGID_BODY (the model fits where it is), MR (molecular replacement placed it) or NOT_PLACED | 
+**model_name** | **str** |  | 
+**predicted** | **bool** | Searched for as a predicted model | 
+**reason** | **str** | Why the model could not be searched for or validated; empty otherwise | 
+**r_work** | **float** |  | [optional] 
+**r_free** | **float** |  | [optional] 
+**cc_model** | **float** | Correlation of the merged intensities with the placed model&#39;s, over all reflections | [optional] 
+**fit_sigma** | **float** | How far R-work stands below that of the same model in random orientations, in standard deviations | [optional] 
+**map_atom_sigma** | **float** | Mean 2mFo-DFc value at the atom centres, in map sigma | [optional] 
+**rigid_body_angle_deg** | **float** |  | [optional] 
+**rigid_body_shift_a** | **float** |  | [optional] 
+**mr_decision** | **str** | Molecular replacement&#39;s decision (AGREES, ENANTIOMORPH, SPACE_GROUP, TWIN_SUBGROUP, or why it placed nothing); empty where it did not run | 
+**mr_space_group** | **str** | The group molecular replacement placed the model in; empty where it placed none | 
+**copies** | **int** | Copies placed by molecular replacement | [optional] 
+**tf_z** | **float** | Translation-function Z-score, the highest of the copies&#39; | [optional] 
+**rf_z** | **float** | Rotation-function Z-score of the first copy&#39;s orientation | [optional] 
+**llg_z** | **float** | Likelihood Z-score after the rigid body, where a copy&#39;s translation function did not stand out | [optional] 
+**mr_d_min** | **float** | High-resolution limit of the molecular-replacement search, in Angstrom | [optional] 
+**anomalous_site** | **str** | Atom with the strongest anomalous difference density, e.g. \&quot;SG CYS A7\&quot;; empty where there is no anomalous map | 
+**anomalous_site_sigma** | **float** | Anomalous difference density at that atom, in map sigma | [optional] 
+**refinement** | [**RugnuxLiveRefinement**](RugnuxLiveRefinement.md) |  | [optional] 
+
+## Example
+
+```python
+from jfjoch_client.models.rugnux_live_model import RugnuxLiveModel
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RugnuxLiveModel from a JSON string
+rugnux_live_model_instance = RugnuxLiveModel.from_json(json)
+# print the JSON string representation of the object
+print(RugnuxLiveModel.to_json())
+
+# convert the object into a dict
+rugnux_live_model_dict = rugnux_live_model_instance.to_dict()
+# create an instance of RugnuxLiveModel from a dict
+rugnux_live_model_from_dict = RugnuxLiveModel.from_dict(rugnux_live_model_dict)
+```
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+
diff --git a/docs/python_client/docs/RugnuxLiveRefinement.md b/docs/python_client/docs/RugnuxLiveRefinement.md
new file mode 100644
index 000000000..8c71018ba
--- /dev/null
+++ b/docs/python_client/docs/RugnuxLiveRefinement.md
@@ -0,0 +1,40 @@
+# RugnuxLiveRefinement
+
+The placed model refined against the merge it was placed on, as the report's REFINE_ keys state it. Set where a placed model was refined or its refinement failed; absent where the model was not placed or refinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run's deadline or cancel can cut it. 
+
+## Properties
+
+Name | Type | Description | Notes
+------------ | ------------- | ------------- | -------------
+**performed** | **bool** | Refinement ran; false with &#x60;reason&#x60; where it failed | 
+**cancelled** | **bool** | The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the rest left out (cut before the first, the model is the placement&#39;s)  | 
+**reason** | **str** | Why refinement did not run to the end; empty otherwise | 
+**on_gpu** | **bool** |  | 
+**seconds** | **float** | Wall time of the refinement | 
+**r_work** | **float** | R-work of the refined model (after the restrained stage, else after the rigid body and grouped B) | [optional] 
+**r_free** | **float** | R-free of the refined model, on the same reflections as &#x60;r_work&#x60; | [optional] 
+**rmsd_bonds_a** | **float** | RMS deviation of the bond lengths from the dictionary, where the restrained stage ran | [optional] 
+**rmsd_angles_deg** | **float** | RMS deviation of the bond angles from the dictionary, where the restrained stage ran | [optional] 
+**blob_count** | **int** | Unexplained blobs of the refined model&#39;s mFo-DFc map (above 3 sigma, peaking above 4) | 
+**blobs** | [**List[RugnuxLiveBlob]**](RugnuxLiveBlob.md) | The strongest blobs, at most 50, strongest first | 
+
+## Example
+
+```python
+from jfjoch_client.models.rugnux_live_refinement import RugnuxLiveRefinement
+
+# TODO update the JSON string below
+json = "{}"
+# create an instance of RugnuxLiveRefinement from a JSON string
+rugnux_live_refinement_instance = RugnuxLiveRefinement.from_json(json)
+# print the JSON string representation of the object
+print(RugnuxLiveRefinement.to_json())
+
+# convert the object into a dict
+rugnux_live_refinement_dict = rugnux_live_refinement_instance.to_dict()
+# create an instance of RugnuxLiveRefinement from a dict
+rugnux_live_refinement_from_dict = RugnuxLiveRefinement.from_dict(rugnux_live_refinement_dict)
+```
+[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
+
+
diff --git a/docs/python_client/docs/RugnuxLiveStatus.md b/docs/python_client/docs/RugnuxLiveStatus.md
index b3b127ddf..5b50a0d62 100644
--- a/docs/python_client/docs/RugnuxLiveStatus.md
+++ b/docs/python_client/docs/RugnuxLiveStatus.md
@@ -8,7 +8,13 @@ Name | Type | Description | Notes
 ------------ | ------------- | ------------- | -------------
 **state** | **str** |  | 
 **placed_model** | **bool** | The run placed the model: it can be fetched from &#x60;/rugnux/model.cif&#x60; and its maps from &#x60;/rugnux/map.ccp4&#x60;.  | 
+**refined_model** | **bool** | The run refined the placed model: &#x60;/rugnux/model.cif&#x60; and &#x60;/rugnux/map.ccp4&#x60; serve the refined model and its maps unless asked for &#x60;stage&#x3D;placed&#x60;.  | 
 **anomalous_map** | **bool** | The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map (&#x60;/rugnux/map.ccp4?type&#x3D;anom&#x60;).  | 
+**anomalous_signal** | **bool** | The merged data carry usable anomalous signal (the summary&#39;s \&quot;Anomalous\&quot; row says so) | 
+**model** | [**RugnuxLiveModel**](RugnuxLiveModel.md) |  | [optional] 
+**space_group** | **str** | Space group of the result (the summary&#39;s \&quot;Space group\&quot; row); absent until the run is over | [optional] 
+**d_min** | **float** | High-resolution limit of the merge, in Angstrom; absent until the run is over, or without a merge | [optional] 
+**isa** | **float** | ISa of the error model; absent until the run is over, or where it was not determined | [optional] 
 **probe** | **str** | Answer of the early lattice probe on the first 60 degrees; empty until it answers | 
 **probe_s** | **float** | When the probe answered, since the first image | [optional] 
 **start_to_first_image_s** | **float** | From the START message to the first image; set once the first image arrives | [optional] 
diff --git a/fpga/hdl/action_config.v b/fpga/hdl/action_config.v
index d3dca7b94..309610924 100644
--- a/fpga/hdl/action_config.v
+++ b/fpga/hdl/action_config.v
@@ -10,7 +10,7 @@ localparam signed [31:0] INT32_MIN = 32'sh80000000;
 `define JFJOCH_FPGA_MAJOR_VERSION 8'd1
 `define JFJOCH_FPGA_MINOR_VERSION 8'd0
 `define JFJOCH_FPGA_PATCH_VERSION 8'd0
-`define JFJOCH_FPGA_PRERELEASE 64'h3937312E6372
+`define JFJOCH_FPGA_PRERELEASE 64'h3038312E6372
 
 `define GIT_SHA1 32'h
 `define MAX_MODULES_FPGA 32'd16
diff --git a/fpga/pcie_driver/dkms.conf b/fpga/pcie_driver/dkms.conf
index 0970e1089..11383e44a 100644
--- a/fpga/pcie_driver/dkms.conf
+++ b/fpga/pcie_driver/dkms.conf
@@ -1,5 +1,5 @@
 PACKAGE_NAME=jfjoch
-PACKAGE_VERSION=1.0.0-rc.179
+PACKAGE_VERSION=1.0.0-rc.180
 
 DEST_MODULE_LOCATION=/extra
 BUILT_MODULE_NAME=jfjoch
diff --git a/fpga/pcie_driver/install_dkms.sh b/fpga/pcie_driver/install_dkms.sh
index 59fb39322..fdccdfbb5 100755
--- a/fpga/pcie_driver/install_dkms.sh
+++ b/fpga/pcie_driver/install_dkms.sh
@@ -2,7 +2,7 @@
 
 # Copyright (2019-2024) Paul Scherrer Institute
 
-VERSION=1.0.0-rc.179
+VERSION=1.0.0-rc.180
 
 mkdir -p /usr/src/jfjoch-${VERSION}/src
 cp dkms.conf /usr/src/jfjoch-${VERSION}
diff --git a/fpga/pcie_driver/jfjoch_drv.c b/fpga/pcie_driver/jfjoch_drv.c
index b4980cc31..b464ece6f 100644
--- a/fpga/pcie_driver/jfjoch_drv.c
+++ b/fpga/pcie_driver/jfjoch_drv.c
@@ -12,7 +12,7 @@
 MODULE_AUTHOR("Filip Leonarski; Paul Scherrer Institute");
 MODULE_DESCRIPTION("Jungfraujoch device module");
 MODULE_LICENSE("GPL");
-MODULE_VERSION("1.0.0-rc.179");
+MODULE_VERSION("1.0.0-rc.180");
 
 #define PCI_DEV_ID_JUNGFRAUJOCH        (0x3450)
 
diff --git a/fpga/pcie_driver/postinstall.sh b/fpga/pcie_driver/postinstall.sh
index dea2a44d1..f1a117f56 100755
--- a/fpga/pcie_driver/postinstall.sh
+++ b/fpga/pcie_driver/postinstall.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # Taken from https://schneide.blog/2015/08/10/packaging-kernel-modulesdrivers-using-dkms/
 
-VERSION=1.0.0-rc.179
+VERSION=1.0.0-rc.180
 
 occurrences=`/usr/sbin/dkms status | grep jfjoch | grep ${VERSION} | wc -l`
 
diff --git a/fpga/pcie_driver/preuninstall.sh b/fpga/pcie_driver/preuninstall.sh
index 275e83800..85f7e1eee 100755
--- a/fpga/pcie_driver/preuninstall.sh
+++ b/fpga/pcie_driver/preuninstall.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 # Taken from https://schneide.blog/2015/08/10/packaging-kernel-modulesdrivers-using-dkms/
 
-VERSION=1.0.0-rc.179
+VERSION=1.0.0-rc.180
 
 /usr/sbin/dkms remove -m jfjoch -v ${VERSION} --all
 
diff --git a/frame_serialize/CBORStream2Deserializer.cpp b/frame_serialize/CBORStream2Deserializer.cpp
index d6f4e647e..f5e56cc52 100644
--- a/frame_serialize/CBORStream2Deserializer.cpp
+++ b/frame_serialize/CBORStream2Deserializer.cpp
@@ -1679,6 +1679,30 @@ namespace {
         return m;
     }
 
+    DensityBlobsMessage ProcessDensityBlobsElement(CborValue &value) {
+        DensityBlobsMessage b;
+        CborValue map_value;
+        cborErr(cbor_value_enter_container(&value, &map_value));
+        while (!cbor_value_at_end(&map_value)) {
+            auto key = GetCBORString(map_value);
+            if (key == "kind") GetCBORStringArray(map_value, b.kind);
+            else if (key == "x") GetCBORDoubleArray(map_value, b.x);
+            else if (key == "y") GetCBORDoubleArray(map_value, b.y);
+            else if (key == "z") GetCBORDoubleArray(map_value, b.z);
+            else if (key == "peak_sigma") GetCBORDoubleArray(map_value, b.peak_sigma);
+            else if (key == "volume") GetCBORDoubleArray(map_value, b.volume);
+            else if (key == "score") GetCBORDoubleArray(map_value, b.score);
+            else if (key == "nearest_atom") GetCBORStringArray(map_value, b.nearest_atom);
+            else if (key == "nearest_atom_distance") GetCBORDoubleArray(map_value, b.nearest_atom_distance);
+            else if (key == "polar_contacts") GetCBORInt32Array(map_value, b.polar_contacts);
+            else if (key == "metal_contacts") GetCBORInt32Array(map_value, b.metal_contacts);
+            else if (key == "anomalous_sigma") GetCBORDoubleArray(map_value, b.anomalous_sigma);
+            else SkipCBORValue(map_value);
+        }
+        cborErr(cbor_value_leave_container(&value, &map_value));
+        return b;
+    }
+
     bool ProcessEndMessageElement(EndMessage &message, CborValue &value) {
         if (cbor_value_at_end(&value))
             return false;
@@ -1769,6 +1793,8 @@ namespace {
                 GetCBORUInt8Array(value, message.niggli_class);
             else if (key == "unit_cell")
                 message.unit_cell = ProcessUnitCellElement(value);
+            else if (key == "unit_cell_esd")
+                message.unit_cell_esd = ProcessUnitCellElement(value);
             else if (key == "space_group_name")
                 message.space_group_name = GetCBORString(value);
             else if (key == "space_group_number")
@@ -1781,6 +1807,12 @@ namespace {
                 message.map_coefficients = ProcessMtzTableElement(value);
             else if (key == "placed_model")
                 message.placed_model = ProcessPlacedModelElement(value);
+            else if (key == "refined_model")
+                message.refined_model = ProcessPlacedModelElement(value);
+            else if (key == "refined_map_coefficients")
+                message.refined_map_coefficients = ProcessMtzTableElement(value);
+            else if (key == "blobs")
+                message.blobs = ProcessDensityBlobsElement(value);
             else if (key == "rotation_lattice") {
                 std::vector<float> tmp;
                 GetCBORFloatArray(value, tmp);
diff --git a/frame_serialize/CBORStream2Serializer.cpp b/frame_serialize/CBORStream2Serializer.cpp
index 4e9615615..ec07c26f3 100644
--- a/frame_serialize/CBORStream2Serializer.cpp
+++ b/frame_serialize/CBORStream2Serializer.cpp
@@ -630,6 +630,25 @@ inline void CBOR_ENC(CborEncoder &encoder, const char* key, const PlacedModelMes
     cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
 }
 
+inline void CBOR_ENC(CborEncoder &encoder, const char* key, const DensityBlobsMessage &b) {
+    CborEncoder mapEncoder;
+    cborErr(cbor_encode_text_stringz(&encoder, key));
+    cborErr(cbor_encoder_create_map(&encoder, &mapEncoder, CborIndefiniteLength));
+    CBOR_ENC(mapEncoder, "kind", b.kind);
+    CBOR_ENC(mapEncoder, "x", b.x);
+    CBOR_ENC(mapEncoder, "y", b.y);
+    CBOR_ENC(mapEncoder, "z", b.z);
+    CBOR_ENC(mapEncoder, "peak_sigma", b.peak_sigma);
+    CBOR_ENC(mapEncoder, "volume", b.volume);
+    CBOR_ENC(mapEncoder, "score", b.score);
+    CBOR_ENC(mapEncoder, "nearest_atom", b.nearest_atom);
+    CBOR_ENC(mapEncoder, "nearest_atom_distance", b.nearest_atom_distance);
+    CBOR_ENC(mapEncoder, "polar_contacts", b.polar_contacts);
+    CBOR_ENC(mapEncoder, "metal_contacts", b.metal_contacts);
+    CBOR_ENC(mapEncoder, "anomalous_sigma", b.anomalous_sigma);
+    cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
+}
+
 // Add encoder for LatticeMessage
 inline void CBOR_ENC(CborEncoder &encoder, const char* key, const LatticeMessage &val) {
     CborEncoder mapEncoder;
@@ -969,6 +988,7 @@ void CBORStream2Serializer::SerializeSequenceEnd(const EndMessage& message) {
     CBOR_ENC(mapEncoder, "niggli_class", message.niggli_class);
     CBOR_ENC(mapEncoder, "pixel_sum", message.pixel_sum);
     CBOR_ENC(mapEncoder, "unit_cell", message.unit_cell);
+    CBOR_ENC(mapEncoder, "unit_cell_esd", message.unit_cell_esd);
     // Both spellings of the determined group. The name carries the setting and is what a reader
     // should take; the number is beside it for a reader written before the name existed.
     CBOR_ENC(mapEncoder, "space_group_name", message.space_group_name);
@@ -976,6 +996,9 @@ void CBORStream2Serializer::SerializeSequenceEnd(const EndMessage& message) {
     CBOR_ENC(mapEncoder, "merged", message.merged);
     CBOR_ENC(mapEncoder, "map_coefficients", message.map_coefficients);
     CBOR_ENC(mapEncoder, "placed_model", message.placed_model);
+    CBOR_ENC(mapEncoder, "refined_model", message.refined_model);
+    CBOR_ENC(mapEncoder, "refined_map_coefficients", message.refined_map_coefficients);
+    CBOR_ENC(mapEncoder, "blobs", message.blobs);
 
     cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
 
diff --git a/frontend/package-lock.json b/frontend/package-lock.json
index d7a461143..af16ca536 100644
--- a/frontend/package-lock.json
+++ b/frontend/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "jungfraujoch-frontend",
-  "version": "1.0.0-rc.179",
+  "version": "1.0.0-rc.180",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "jungfraujoch-frontend",
-      "version": "1.0.0-rc.179",
+      "version": "1.0.0-rc.180",
       "license": "GPL-3.0",
       "dependencies": {
         "@emotion/react": "^11.10.4",
diff --git a/frontend/package.json b/frontend/package.json
index dab3160ea..f0ac6d5e6 100644
--- a/frontend/package.json
+++ b/frontend/package.json
@@ -1,6 +1,6 @@
 {
   "name": "jungfraujoch-frontend",
-  "version": "1.0.0-rc.179",
+  "version": "1.0.0-rc.180",
   "license": "GPL-3.0",
   "private": true,
   "homepage": "/frontend",
diff --git a/frontend/src/App.tsx b/frontend/src/App.tsx
index d24cf6086..3b6287ac6 100644
--- a/frontend/src/App.tsx
+++ b/frontend/src/App.tsx
@@ -105,8 +105,9 @@ function PanelColumns({ columns = 2, children }: { columns?: number; children: R
 
 // An item either renders a panel inside the app (render) or links out to an
 // external page in a new tab (href), e.g. the source repository.
+// wide: the page uses the screen's width instead of the 1300 px reading column
 type NavItem = { id: string; label: string; icon: ReactNode; disabled?: boolean;
-                 href?: string; render?: () => ReactNode };
+                 href?: string; render?: () => ReactNode; wide?: boolean };
 type NavSection = { subheader?: string; items: NavItem[] };
 
 /** Documentation / API reference shown inside the app area, with a new-tab escape hatch. */
@@ -192,7 +193,7 @@ function App() {
             { id: 'data-collection', label: 'Data collection', icon: <VideocamIcon/>, render: () => (
                 <DataCollection frame_time_us={s.detector_settings?.frame_time_us ?? 500}/>
             )},
-            { id: 'rugnux', label: 'Rugnux live', icon: <AutoGraphIcon/>, render: () => (
+            { id: 'rugnux', label: 'Rugnux live', icon: <AutoGraphIcon/>, wide: true, render: () => (
                 <RugnuxPage measuring={isMeasuring || s.broker?.state === 'Busy'}/>
             )},
         ]},
@@ -253,7 +254,7 @@ function App() {
                 <DocFrame title="API reference" src="/frontend/openapi.html"/>
             )},
             { id: 'documentation', label: 'Documentation', icon: <MenuBookIcon/>, render: () => (
-                <DocFrame title="Documentation" src="/frontend/docs/index.html"/>
+                <DocFrame title="Documentation" src="/frontend/docs/documentation.html"/>
             )},
             { id: 'changelog', label: 'Changelog', icon: <HistoryIcon/>, render: () => (
                 <MarkdownDoc md={changelogMd}/>
@@ -308,7 +309,7 @@ function App() {
             <Box component="main" sx={{ flexGrow: 1, p: 3, pb: '84px', minWidth: 0 }}>
                 <Toolbar/>
                 <ErrorMessage s={s.broker}/>
-                <Box sx={{ maxWidth: 1300, mx: 'auto', mt: 2 }}>
+                <Box sx={{ maxWidth: activeItem.wide ? 2400 : 1300, mx: 'auto', mt: 2 }}>
                     {activeItem.render?.()}
                 </Box>
             </Box>
diff --git a/frontend/src/client/@tanstack/react-query.gen.ts b/frontend/src/client/@tanstack/react-query.gen.ts
index 291d2a39a..f6c61c8af 100644
--- a/frontend/src/client/@tanstack/react-query.gen.ts
+++ b/frontend/src/client/@tanstack/react-query.gen.ts
@@ -793,6 +793,7 @@ export const getRugnuxModelCifQueryKey = (options?: Options<getRugnuxModelCifDat
  * The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
  * `_model.cif` file written beside the data: the data's cell and space group, with the input model's own
  * metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
+ * Where the run refined the model, the refined model unless asked for `stage=placed`.
  *
  */
 export const getRugnuxModelCifOptions = (options?: Options<getRugnuxModelCifData>) => queryOptions<getRugnuxModelCifResponse, getRugnuxModelCifError, getRugnuxModelCifResponse, ReturnType<typeof getRugnuxModelCifQueryKey>>({
@@ -816,7 +817,9 @@ export const getRugnuxMapCcp4QueryKey = (options?: Options<getRugnuxMapCcp4Data>
  * The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map
  * coefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where
  * the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and
- * RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.
+ * RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run
+ * refined the model, the 2mFo-DFc and mFo-DFc maps are the refined model's unless asked for `stage=placed`;
+ * the anomalous map stays on the placed model's phases.
  *
  */
 export const getRugnuxMapCcp4Options = (options?: Options<getRugnuxMapCcp4Data>) => queryOptions<getRugnuxMapCcp4Response, getRugnuxMapCcp4Error, getRugnuxMapCcp4Response, ReturnType<typeof getRugnuxMapCcp4QueryKey>>({
diff --git a/frontend/src/client/index.ts b/frontend/src/client/index.ts
index ad6640672..5d347e0f2 100644
--- a/frontend/src/client/index.ts
+++ b/frontend/src/client/index.ts
@@ -1,4 +1,4 @@
 // This file is auto-generated by @hey-api/openapi-ts
 
 export { deleteConfigRugnuxModel, getConfigAzimInt, getConfigBraggIntegration, getConfigDarkMask, getConfigDetector, getConfigFileWriter, getConfigImageFormat, getConfigIndexing, getConfigInstrument, getConfigMask, getConfigMaskTiff, getConfigRoi, getConfigRugnux, getConfigSelectDetector, getConfigSpotFinding, getConfigUserMask, getConfigUserMaskTiff, getConfigZeromqMetadata, getConfigZeromqPreview, getDetectorStatus, getFpgaStatus, getImageBufferImageCbor, getImageBufferImageJpeg, getImageBufferImageTiff, getImageBufferStartCbor, getImageBufferStatus, getImagePusherStatus, getLiveEvents, getPreviewPedestalTiff, getPreviewPlot, getPreviewPlotBin, getResultScan, getRugnuxMapCcp4, getRugnuxModelCif, getRugnuxStatus, getStatistics, getStatisticsCalibration, getStatisticsDataCollection, getStatus, getVersion, getXfelEventCode, getXfelPulseId, type Options, postCancel, postConfigImageFormatConversion, postConfigImageFormatRaw, postDeactivate, postImageBufferClear, postInitialize, postPedestal, postStart, postTrigger, postWaitTillDone, postWaitUntilRunning, putConfigAzimInt, putConfigBraggIntegration, putConfigDarkMask, putConfigDetector, putConfigFileWriter, putConfigImageFormat, putConfigIndexing, putConfigInstrument, putConfigInternalGeneratorImage, putConfigInternalGeneratorImageTiff, putConfigRoi, putConfigRugnux, putConfigRugnuxModel, putConfigSelectDetector, putConfigSpotFinding, putConfigUserMask, putConfigUserMaskTiff, putConfigZeromqMetadata, putConfigZeromqPreview } from './sdk.gen';
-export { type azim_int_settings, azint_unit, type background, type binning, type bragg_integration_settings, type broker_status, type calibration_statistics, type ClientOptions, color_scale, type crystal_lattice, type dark_mask_settings, type dataset_settings, type dataset_settingsWritable, type deleteConfigRugnuxModelData, type deleteConfigRugnuxModelError, type deleteConfigRugnuxModelErrors, type deleteConfigRugnuxModelResponses, type detector, type detector_list, type detector_list_element, type detector_module, detector_module_direction, detector_power_state, type detector_selection, type detector_settings, detector_state, type detector_status, detector_timing, detector_type, type error_message, type experimental_coord, file_writer_format, type file_writer_settings, type fill_value, type fpga_status, geom_refinement_algorithm, type getConfigAzimIntData, type getConfigAzimIntResponse, type getConfigAzimIntResponses, type getConfigBraggIntegrationData, type getConfigBraggIntegrationResponse, type getConfigBraggIntegrationResponses, type getConfigDarkMaskData, type getConfigDarkMaskResponse, type getConfigDarkMaskResponses, type getConfigDetectorData, type getConfigDetectorResponse, type getConfigDetectorResponses, type getConfigFileWriterData, type getConfigFileWriterResponse, type getConfigFileWriterResponses, type getConfigImageFormatData, type getConfigImageFormatResponse, type getConfigImageFormatResponses, type getConfigIndexingData, type getConfigIndexingResponse, type getConfigIndexingResponses, type getConfigInstrumentData, type getConfigInstrumentResponse, type getConfigInstrumentResponses, type getConfigMaskData, type getConfigMaskResponse, type getConfigMaskResponses, type getConfigMaskTiffData, type getConfigMaskTiffResponse, type getConfigMaskTiffResponses, type getConfigRoiData, type getConfigRoiResponse, type getConfigRoiResponses, type getConfigRugnuxData, type getConfigRugnuxResponse, type getConfigRugnuxResponses, type getConfigSelectDetectorData, type getConfigSelectDetectorResponse, type getConfigSelectDetectorResponses, type getConfigSpotFindingData, type getConfigSpotFindingResponse, type getConfigSpotFindingResponses, type getConfigUserMaskData, type getConfigUserMaskResponse, type getConfigUserMaskResponses, type getConfigUserMaskTiffData, type getConfigUserMaskTiffResponse, type getConfigUserMaskTiffResponses, type getConfigZeromqMetadataData, type getConfigZeromqMetadataResponse, type getConfigZeromqMetadataResponses, type getConfigZeromqPreviewData, type getConfigZeromqPreviewResponse, type getConfigZeromqPreviewResponses, type getDetectorStatusData, type getDetectorStatusError, type getDetectorStatusErrors, type getDetectorStatusResponse, type getDetectorStatusResponses, type getFpgaStatusData, type getFpgaStatusResponse, type getFpgaStatusResponses, type getImageBufferImageCborData, type getImageBufferImageCborError, type getImageBufferImageCborErrors, type getImageBufferImageCborResponse, type getImageBufferImageCborResponses, type getImageBufferImageJpegData, type getImageBufferImageJpegError, type getImageBufferImageJpegErrors, type getImageBufferImageJpegResponse, type getImageBufferImageJpegResponses, type getImageBufferImageTiffData, type getImageBufferImageTiffError, type getImageBufferImageTiffErrors, type getImageBufferImageTiffResponse, type getImageBufferImageTiffResponses, type getImageBufferStartCborData, type getImageBufferStartCborError, type getImageBufferStartCborErrors, type getImageBufferStartCborResponse, type getImageBufferStartCborResponses, type getImageBufferStatusData, type getImageBufferStatusError, type getImageBufferStatusErrors, type getImageBufferStatusResponse, type getImageBufferStatusResponses, type getImagePusherStatusData, type getImagePusherStatusError, type getImagePusherStatusErrors, type getImagePusherStatusResponse, type getImagePusherStatusResponses, type getLiveEventsData, type getLiveEventsError, type getLiveEventsErrors, type getLiveEventsResponse, type getLiveEventsResponses, type getPreviewPedestalTiffData, type getPreviewPedestalTiffErrors, type getPreviewPedestalTiffResponse, type getPreviewPedestalTiffResponses, type getPreviewPlotBinData, type getPreviewPlotBinError, type getPreviewPlotBinErrors, type getPreviewPlotBinResponse, type getPreviewPlotBinResponses, type getPreviewPlotData, type getPreviewPlotError, type getPreviewPlotErrors, type getPreviewPlotResponse, type getPreviewPlotResponses, type getResultScanData, type getResultScanError, type getResultScanErrors, type getResultScanResponse, type getResultScanResponses, type getRugnuxMapCcp4Data, type getRugnuxMapCcp4Error, type getRugnuxMapCcp4Errors, type getRugnuxMapCcp4Response, type getRugnuxMapCcp4Responses, type getRugnuxModelCifData, type getRugnuxModelCifError, type getRugnuxModelCifErrors, type getRugnuxModelCifResponse, type getRugnuxModelCifResponses, type getRugnuxStatusData, type getRugnuxStatusError, type getRugnuxStatusErrors, type getRugnuxStatusResponse, type getRugnuxStatusResponses, type getStatisticsCalibrationData, type getStatisticsCalibrationResponse, type getStatisticsCalibrationResponses, type getStatisticsData, type getStatisticsDataCollectionData, type getStatisticsDataCollectionError, type getStatisticsDataCollectionErrors, type getStatisticsDataCollectionResponse, type getStatisticsDataCollectionResponses, type getStatisticsResponse, type getStatisticsResponses, type getStatusData, type getStatusResponse, type getStatusResponses, type getVersionData, type getVersionResponse, type getVersionResponses, type getXfelEventCodeData, type getXfelEventCodeErrors, type getXfelEventCodeResponse, type getXfelEventCodeResponses, type getXfelPulseIdData, type getXfelPulseIdErrors, type getXfelPulseIdResponse, type getXfelPulseIdResponses, type grid_scan, type image_buffer_status, type image_format_settings, type image_id, type image_pusher_status, image_pusher_type, indexing_algorithm, type indexing_settings, type instrument_metadata, integration_model, type jfjoch_settings, type jfjoch_statistics, type jpeg_quality, type measurement_statistics, type pcie_devices, type pixel_mask_statistics, type plot, plot_type, plot_unit_x, type plots, type postCancelData, type postCancelResponses, type postConfigImageFormatConversionData, type postConfigImageFormatConversionError, type postConfigImageFormatConversionErrors, type postConfigImageFormatConversionResponses, type postConfigImageFormatRawData, type postConfigImageFormatRawError, type postConfigImageFormatRawErrors, type postConfigImageFormatRawResponses, type postDeactivateData, type postDeactivateError, type postDeactivateErrors, type postDeactivateResponses, type postImageBufferClearData, type postImageBufferClearError, type postImageBufferClearErrors, type postImageBufferClearResponses, type postInitializeData, type postInitializeError, type postInitializeErrors, type postInitializeResponses, type postPedestalData, type postPedestalError, type postPedestalErrors, type postPedestalResponses, type postStartData, type postStartError, type postStartErrors, type postStartResponses, type postTriggerData, type postTriggerResponses, type postWaitTillDoneData, type postWaitTillDoneError, type postWaitTillDoneErrors, type postWaitTillDoneResponses, type postWaitUntilRunningData, type postWaitUntilRunningError, type postWaitUntilRunningErrors, type postWaitUntilRunningResponses, type powder_calibration_fit_sigma, type powder_calibration_output, type powder_calibration_outputWritable, type powder_calibration_quality, type powder_calibration_spot_check, type putConfigAzimIntData, type putConfigAzimIntError, type putConfigAzimIntErrors, type putConfigAzimIntResponses, type putConfigBraggIntegrationData, type putConfigBraggIntegrationError, type putConfigBraggIntegrationErrors, type putConfigBraggIntegrationResponses, type putConfigDarkMaskData, type putConfigDarkMaskError, type putConfigDarkMaskErrors, type putConfigDarkMaskResponses, type putConfigDetectorData, type putConfigDetectorError, type putConfigDetectorErrors, type putConfigDetectorResponses, type putConfigFileWriterData, type putConfigFileWriterError, type putConfigFileWriterErrors, type putConfigFileWriterResponses, type putConfigImageFormatData, type putConfigImageFormatError, type putConfigImageFormatErrors, type putConfigImageFormatResponses, type putConfigIndexingData, type putConfigIndexingError, type putConfigIndexingErrors, type putConfigIndexingResponses, type putConfigInstrumentData, type putConfigInstrumentError, type putConfigInstrumentErrors, type putConfigInstrumentResponses, type putConfigInternalGeneratorImageData, type putConfigInternalGeneratorImageError, type putConfigInternalGeneratorImageErrors, type putConfigInternalGeneratorImageResponses, type putConfigInternalGeneratorImageTiffData, type putConfigInternalGeneratorImageTiffError, type putConfigInternalGeneratorImageTiffErrors, type putConfigInternalGeneratorImageTiffResponses, type putConfigRoiData, type putConfigRoiError, type putConfigRoiErrors, type putConfigRoiResponses, type putConfigRugnuxData, type putConfigRugnuxError, type putConfigRugnuxErrors, type putConfigRugnuxModelData, type putConfigRugnuxModelError, type putConfigRugnuxModelErrors, type putConfigRugnuxModelResponses, type putConfigRugnuxResponses, type putConfigSelectDetectorData, type putConfigSelectDetectorError, type putConfigSelectDetectorErrors, type putConfigSelectDetectorResponses, type putConfigSpotFindingData, type putConfigSpotFindingError, type putConfigSpotFindingErrors, type putConfigSpotFindingResponses, type putConfigUserMaskData, type putConfigUserMaskError, type putConfigUserMaskErrors, type putConfigUserMaskResponses, type putConfigUserMaskTiffData, type putConfigUserMaskTiffError, type putConfigUserMaskTiffErrors, type putConfigUserMaskTiffResponses, type putConfigZeromqMetadataData, type putConfigZeromqMetadataError, type putConfigZeromqMetadataErrors, type putConfigZeromqMetadataResponses, type putConfigZeromqPreviewData, type putConfigZeromqPreviewError, type putConfigZeromqPreviewErrors, type putConfigZeromqPreviewResponses, type resolution_estimate, type resolution_ring, type roi, type roi_azim_list, type roi_azimuthal, type roi_box, type roi_box_list, type roi_circle, type roi_circle_list, type roi_definitions, type rotation_axis, type rugnux_live_status, type rugnux_live_step, type rugnux_settings, type rugnux_status, type rugnux_summary_row, type saturation, type scan_result, type show_beam_center, type show_predictions, type show_roi, type show_spots, type show_user_mask, type spot_finding_settings, type standard_detector_geometry, type tcp_settings, type unit_cell, type zeromq_metadata_settings, type zeromq_preview_settings, type zeromq_settings } from './types.gen';
+export { type azim_int_settings, azint_unit, type background, type binning, type bragg_integration_settings, type broker_status, type calibration_statistics, type ClientOptions, color_scale, type crystal_lattice, type dark_mask_settings, type dataset_settings, type dataset_settingsWritable, type deleteConfigRugnuxModelData, type deleteConfigRugnuxModelError, type deleteConfigRugnuxModelErrors, type deleteConfigRugnuxModelResponses, type detector, type detector_list, type detector_list_element, type detector_module, detector_module_direction, detector_power_state, type detector_selection, type detector_settings, detector_state, type detector_status, detector_timing, detector_type, type error_message, type experimental_coord, file_writer_format, type file_writer_settings, type fill_value, type fpga_status, geom_refinement_algorithm, type getConfigAzimIntData, type getConfigAzimIntResponse, type getConfigAzimIntResponses, type getConfigBraggIntegrationData, type getConfigBraggIntegrationResponse, type getConfigBraggIntegrationResponses, type getConfigDarkMaskData, type getConfigDarkMaskResponse, type getConfigDarkMaskResponses, type getConfigDetectorData, type getConfigDetectorResponse, type getConfigDetectorResponses, type getConfigFileWriterData, type getConfigFileWriterResponse, type getConfigFileWriterResponses, type getConfigImageFormatData, type getConfigImageFormatResponse, type getConfigImageFormatResponses, type getConfigIndexingData, type getConfigIndexingResponse, type getConfigIndexingResponses, type getConfigInstrumentData, type getConfigInstrumentResponse, type getConfigInstrumentResponses, type getConfigMaskData, type getConfigMaskResponse, type getConfigMaskResponses, type getConfigMaskTiffData, type getConfigMaskTiffResponse, type getConfigMaskTiffResponses, type getConfigRoiData, type getConfigRoiResponse, type getConfigRoiResponses, type getConfigRugnuxData, type getConfigRugnuxResponse, type getConfigRugnuxResponses, type getConfigSelectDetectorData, type getConfigSelectDetectorResponse, type getConfigSelectDetectorResponses, type getConfigSpotFindingData, type getConfigSpotFindingResponse, type getConfigSpotFindingResponses, type getConfigUserMaskData, type getConfigUserMaskResponse, type getConfigUserMaskResponses, type getConfigUserMaskTiffData, type getConfigUserMaskTiffResponse, type getConfigUserMaskTiffResponses, type getConfigZeromqMetadataData, type getConfigZeromqMetadataResponse, type getConfigZeromqMetadataResponses, type getConfigZeromqPreviewData, type getConfigZeromqPreviewResponse, type getConfigZeromqPreviewResponses, type getDetectorStatusData, type getDetectorStatusError, type getDetectorStatusErrors, type getDetectorStatusResponse, type getDetectorStatusResponses, type getFpgaStatusData, type getFpgaStatusResponse, type getFpgaStatusResponses, type getImageBufferImageCborData, type getImageBufferImageCborError, type getImageBufferImageCborErrors, type getImageBufferImageCborResponse, type getImageBufferImageCborResponses, type getImageBufferImageJpegData, type getImageBufferImageJpegError, type getImageBufferImageJpegErrors, type getImageBufferImageJpegResponse, type getImageBufferImageJpegResponses, type getImageBufferImageTiffData, type getImageBufferImageTiffError, type getImageBufferImageTiffErrors, type getImageBufferImageTiffResponse, type getImageBufferImageTiffResponses, type getImageBufferStartCborData, type getImageBufferStartCborError, type getImageBufferStartCborErrors, type getImageBufferStartCborResponse, type getImageBufferStartCborResponses, type getImageBufferStatusData, type getImageBufferStatusError, type getImageBufferStatusErrors, type getImageBufferStatusResponse, type getImageBufferStatusResponses, type getImagePusherStatusData, type getImagePusherStatusError, type getImagePusherStatusErrors, type getImagePusherStatusResponse, type getImagePusherStatusResponses, type getLiveEventsData, type getLiveEventsError, type getLiveEventsErrors, type getLiveEventsResponse, type getLiveEventsResponses, type getPreviewPedestalTiffData, type getPreviewPedestalTiffErrors, type getPreviewPedestalTiffResponse, type getPreviewPedestalTiffResponses, type getPreviewPlotBinData, type getPreviewPlotBinError, type getPreviewPlotBinErrors, type getPreviewPlotBinResponse, type getPreviewPlotBinResponses, type getPreviewPlotData, type getPreviewPlotError, type getPreviewPlotErrors, type getPreviewPlotResponse, type getPreviewPlotResponses, type getResultScanData, type getResultScanError, type getResultScanErrors, type getResultScanResponse, type getResultScanResponses, type getRugnuxMapCcp4Data, type getRugnuxMapCcp4Error, type getRugnuxMapCcp4Errors, type getRugnuxMapCcp4Response, type getRugnuxMapCcp4Responses, type getRugnuxModelCifData, type getRugnuxModelCifError, type getRugnuxModelCifErrors, type getRugnuxModelCifResponse, type getRugnuxModelCifResponses, type getRugnuxStatusData, type getRugnuxStatusError, type getRugnuxStatusErrors, type getRugnuxStatusResponse, type getRugnuxStatusResponses, type getStatisticsCalibrationData, type getStatisticsCalibrationResponse, type getStatisticsCalibrationResponses, type getStatisticsData, type getStatisticsDataCollectionData, type getStatisticsDataCollectionError, type getStatisticsDataCollectionErrors, type getStatisticsDataCollectionResponse, type getStatisticsDataCollectionResponses, type getStatisticsResponse, type getStatisticsResponses, type getStatusData, type getStatusResponse, type getStatusResponses, type getVersionData, type getVersionResponse, type getVersionResponses, type getXfelEventCodeData, type getXfelEventCodeErrors, type getXfelEventCodeResponse, type getXfelEventCodeResponses, type getXfelPulseIdData, type getXfelPulseIdErrors, type getXfelPulseIdResponse, type getXfelPulseIdResponses, type grid_scan, type image_buffer_status, type image_format_settings, type image_id, type image_pusher_status, image_pusher_type, indexing_algorithm, type indexing_settings, type instrument_metadata, integration_model, type jfjoch_settings, type jfjoch_statistics, type jpeg_quality, type measurement_statistics, type pcie_devices, type pixel_mask_statistics, type plot, plot_type, plot_unit_x, type plots, type postCancelData, type postCancelResponses, type postConfigImageFormatConversionData, type postConfigImageFormatConversionError, type postConfigImageFormatConversionErrors, type postConfigImageFormatConversionResponses, type postConfigImageFormatRawData, type postConfigImageFormatRawError, type postConfigImageFormatRawErrors, type postConfigImageFormatRawResponses, type postDeactivateData, type postDeactivateError, type postDeactivateErrors, type postDeactivateResponses, type postImageBufferClearData, type postImageBufferClearError, type postImageBufferClearErrors, type postImageBufferClearResponses, type postInitializeData, type postInitializeError, type postInitializeErrors, type postInitializeResponses, type postPedestalData, type postPedestalError, type postPedestalErrors, type postPedestalResponses, type postStartData, type postStartError, type postStartErrors, type postStartResponses, type postTriggerData, type postTriggerResponses, type postWaitTillDoneData, type postWaitTillDoneError, type postWaitTillDoneErrors, type postWaitTillDoneResponses, type postWaitUntilRunningData, type postWaitUntilRunningError, type postWaitUntilRunningErrors, type postWaitUntilRunningResponses, type powder_calibration_fit_sigma, type powder_calibration_output, type powder_calibration_outputWritable, type powder_calibration_quality, type powder_calibration_spot_check, type putConfigAzimIntData, type putConfigAzimIntError, type putConfigAzimIntErrors, type putConfigAzimIntResponses, type putConfigBraggIntegrationData, type putConfigBraggIntegrationError, type putConfigBraggIntegrationErrors, type putConfigBraggIntegrationResponses, type putConfigDarkMaskData, type putConfigDarkMaskError, type putConfigDarkMaskErrors, type putConfigDarkMaskResponses, type putConfigDetectorData, type putConfigDetectorError, type putConfigDetectorErrors, type putConfigDetectorResponses, type putConfigFileWriterData, type putConfigFileWriterError, type putConfigFileWriterErrors, type putConfigFileWriterResponses, type putConfigImageFormatData, type putConfigImageFormatError, type putConfigImageFormatErrors, type putConfigImageFormatResponses, type putConfigIndexingData, type putConfigIndexingError, type putConfigIndexingErrors, type putConfigIndexingResponses, type putConfigInstrumentData, type putConfigInstrumentError, type putConfigInstrumentErrors, type putConfigInstrumentResponses, type putConfigInternalGeneratorImageData, type putConfigInternalGeneratorImageError, type putConfigInternalGeneratorImageErrors, type putConfigInternalGeneratorImageResponses, type putConfigInternalGeneratorImageTiffData, type putConfigInternalGeneratorImageTiffError, type putConfigInternalGeneratorImageTiffErrors, type putConfigInternalGeneratorImageTiffResponses, type putConfigRoiData, type putConfigRoiError, type putConfigRoiErrors, type putConfigRoiResponses, type putConfigRugnuxData, type putConfigRugnuxError, type putConfigRugnuxErrors, type putConfigRugnuxModelData, type putConfigRugnuxModelError, type putConfigRugnuxModelErrors, type putConfigRugnuxModelResponses, type putConfigRugnuxResponses, type putConfigSelectDetectorData, type putConfigSelectDetectorError, type putConfigSelectDetectorErrors, type putConfigSelectDetectorResponses, type putConfigSpotFindingData, type putConfigSpotFindingError, type putConfigSpotFindingErrors, type putConfigSpotFindingResponses, type putConfigUserMaskData, type putConfigUserMaskError, type putConfigUserMaskErrors, type putConfigUserMaskResponses, type putConfigUserMaskTiffData, type putConfigUserMaskTiffError, type putConfigUserMaskTiffErrors, type putConfigUserMaskTiffResponses, type putConfigZeromqMetadataData, type putConfigZeromqMetadataError, type putConfigZeromqMetadataErrors, type putConfigZeromqMetadataResponses, type putConfigZeromqPreviewData, type putConfigZeromqPreviewError, type putConfigZeromqPreviewErrors, type putConfigZeromqPreviewResponses, type resolution_estimate, type resolution_ring, type roi, type roi_azim_list, type roi_azimuthal, type roi_box, type roi_box_list, type roi_circle, type roi_circle_list, type roi_definitions, type rotation_axis, type rugnux_live_blob, type rugnux_live_model, type rugnux_live_refinement, type rugnux_live_status, type rugnux_live_step, type rugnux_settings, type rugnux_status, type rugnux_summary_row, type saturation, type scan_result, type show_beam_center, type show_predictions, type show_roi, type show_spots, type show_user_mask, type spot_finding_settings, type standard_detector_geometry, type tcp_settings, type unit_cell, type zeromq_metadata_settings, type zeromq_preview_settings, type zeromq_settings } from './types.gen';
diff --git a/frontend/src/client/sdk.gen.ts b/frontend/src/client/sdk.gen.ts
index 1dcd6afcf..8cb530076 100644
--- a/frontend/src/client/sdk.gen.ts
+++ b/frontend/src/client/sdk.gen.ts
@@ -444,6 +444,7 @@ export const getRugnuxStatus = <ThrowOnError extends boolean = false>(options?:
  * The model placed against the data by molecular replacement or validation, as mmCIF - the same text as the
  * `_model.cif` file written beside the data: the data's cell and space group, with the input model's own
  * metadata (entities, sequences, references, authors, software) kept. Kept as long as `/rugnux/status`.
+ * Where the run refined the model, the refined model unless asked for `stage=placed`.
  *
  */
 export const getRugnuxModelCif = <ThrowOnError extends boolean = false>(options?: Options<getRugnuxModelCifData, ThrowOnError>): RequestResult<getRugnuxModelCifResponses, getRugnuxModelCifErrors, ThrowOnError> => (options?.client ?? client).get<getRugnuxModelCifResponses, getRugnuxModelCifErrors, ThrowOnError>({
@@ -458,7 +459,9 @@ export const getRugnuxModelCif = <ThrowOnError extends boolean = false>(options?
  * The map of the placed model (`/rugnux/model.cif`) in CCP4 format (mode 2, float), made from the map
  * coefficients written to `_maps.mtz` (FWT/PHWT, DELFWT/PHDELWT, ANOM/PHANOM). It covers one unit cell centred on the model - along an axis where
  * the model reaches further than the cell, the model plus 5 A instead - sampled every d_min/3; the mean and
- * RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones.
+ * RMS in its header are those of the unit cell, so contour levels in sigma are the usual ones. Where the run
+ * refined the model, the 2mFo-DFc and mFo-DFc maps are the refined model's unless asked for `stage=placed`;
+ * the anomalous map stays on the placed model's phases.
  *
  */
 export const getRugnuxMapCcp4 = <ThrowOnError extends boolean = false>(options?: Options<getRugnuxMapCcp4Data, ThrowOnError>): RequestResult<getRugnuxMapCcp4Responses, getRugnuxMapCcp4Errors, ThrowOnError> => (options?.client ?? client).get<getRugnuxMapCcp4Responses, getRugnuxMapCcp4Errors, ThrowOnError>({
diff --git a/frontend/src/client/types.gen.ts b/frontend/src/client/types.gen.ts
index 8bc26b92d..fa85ac4ed 100644
--- a/frontend/src/client/types.gen.ts
+++ b/frontend/src/client/types.gen.ts
@@ -1942,6 +1942,166 @@ export type rugnux_summary_row = {
     value: string;
 };
 
+/**
+ * What the run made of the model it was given, as the report's MODEL VALIDATION section states it. The
+ * R-factors here are those of the placed model with its own coordinates and B factors; what refinement made
+ * of it is in `refinement`. A value that is absent was not computed - the model was not placed, or not by
+ * molecular replacement.
+ *
+ */
+export type rugnux_live_model = {
+    /**
+     * RIGID_BODY (the model fits where it is), MR (molecular replacement placed it) or NOT_PLACED
+     */
+    placement: string;
+    model_name: string;
+    /**
+     * Searched for as a predicted model
+     */
+    predicted: boolean;
+    /**
+     * Why the model could not be searched for or validated; empty otherwise
+     */
+    reason: string;
+    r_work?: number;
+    r_free?: number;
+    /**
+     * Correlation of the merged intensities with the placed model's, over all reflections
+     */
+    cc_model?: number;
+    /**
+     * How far R-work stands below that of the same model in random orientations, in standard deviations
+     */
+    fit_sigma?: number;
+    /**
+     * Mean 2mFo-DFc value at the atom centres, in map sigma
+     */
+    map_atom_sigma?: number;
+    rigid_body_angle_deg?: number;
+    rigid_body_shift_A?: number;
+    /**
+     * Molecular replacement's decision (AGREES, ENANTIOMORPH, SPACE_GROUP, TWIN_SUBGROUP, or why it placed nothing); empty where it did not run
+     */
+    mr_decision: string;
+    /**
+     * The group molecular replacement placed the model in; empty where it placed none
+     */
+    mr_space_group: string;
+    /**
+     * Copies placed by molecular replacement
+     */
+    copies?: number;
+    /**
+     * Translation-function Z-score, the highest of the copies'
+     */
+    tf_z?: number;
+    /**
+     * Rotation-function Z-score of the first copy's orientation
+     */
+    rf_z?: number;
+    /**
+     * Likelihood Z-score after the rigid body, where a copy's translation function did not stand out
+     */
+    llg_z?: number;
+    /**
+     * High-resolution limit of the molecular-replacement search, in Angstrom
+     */
+    mr_d_min?: number;
+    /**
+     * Atom with the strongest anomalous difference density, e.g. "SG CYS A7"; empty where there is no anomalous map
+     */
+    anomalous_site: string;
+    /**
+     * Anomalous difference density at that atom, in map sigma
+     */
+    anomalous_site_sigma?: number;
+    refinement?: rugnux_live_refinement;
+};
+
+/**
+ * The placed model refined against the merge it was placed on, as the report's REFINE_ keys state it. Set
+ * where a placed model was refined or its refinement failed; absent where the model was not placed or
+ * refinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run's deadline
+ * or cancel can cut it.
+ *
+ */
+export type rugnux_live_refinement = {
+    /**
+     * Refinement ran; false with `reason` where it failed
+     */
+    performed: boolean;
+    /**
+     * The deadline or a cancel cut the refinement short: the weight trials that ran were chosen among, the
+     * rest left out (cut before the first, the model is the placement's)
+     *
+     */
+    cancelled: boolean;
+    /**
+     * Why refinement did not run to the end; empty otherwise
+     */
+    reason: string;
+    on_gpu: boolean;
+    /**
+     * Wall time of the refinement
+     */
+    seconds: number;
+    /**
+     * R-work of the refined model (after the restrained stage, else after the rigid body and grouped B)
+     */
+    r_work?: number;
+    /**
+     * R-free of the refined model, on the same reflections as `r_work`
+     */
+    r_free?: number;
+    /**
+     * RMS deviation of the bond lengths from the dictionary, where the restrained stage ran
+     */
+    rmsd_bonds_A?: number;
+    /**
+     * RMS deviation of the bond angles from the dictionary, where the restrained stage ran
+     */
+    rmsd_angles_deg?: number;
+    /**
+     * Unexplained blobs of the refined model's mFo-DFc map (above 3 sigma, peaking above 4)
+     */
+    blob_count: number;
+    /**
+     * The strongest blobs, at most 50, strongest first
+     */
+    blobs: Array<rugnux_live_blob>;
+};
+
+/**
+ * A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on
+ * what is measured, to point a person at the density - not an identification.
+ *
+ */
+export type rugnux_live_blob = {
+    kind: 'WATER' | 'ION' | 'LIGAND' | 'MODEL_ERROR' | 'UNASSIGNED';
+    /**
+     * Centroid, Cartesian Angstrom, in the frame of the refined model (`/rugnux/model.cif`)
+     */
+    x: number;
+    y: number;
+    z: number;
+    /**
+     * The highest point, in map sigma
+     */
+    peak_sigma: number;
+    /**
+     * Volume above 3 sigma, in cubic Angstrom
+     */
+    volume_A3: number;
+    /**
+     * e.g. "OG1 THR A42"
+     */
+    nearest_atom: string;
+    /**
+     * Absent where no atom is within 12 Angstrom
+     */
+    nearest_atom_distance_A?: number;
+};
+
 /**
  * Live rugnux processing of the last collection; kept until the next collection starts or `POST /initialize`.
  * Times are taken when the image puller received a message, and are in seconds since the first image
@@ -1956,12 +2116,35 @@ export type rugnux_live_status = {
      *
      */
     placed_model: boolean;
+    /**
+     * The run refined the placed model: `/rugnux/model.cif` and `/rugnux/map.ccp4` serve the refined model and
+     * its maps unless asked for `stage=placed`.
+     *
+     */
+    refined_model: boolean;
     /**
      * The merge kept the Bijvoet pairs, so with the placed model there is an anomalous difference map
      * (`/rugnux/map.ccp4?type=anom`).
      *
      */
     anomalous_map: boolean;
+    /**
+     * The merged data carry usable anomalous signal (the summary's "Anomalous" row says so)
+     */
+    anomalous_signal: boolean;
+    model?: rugnux_live_model;
+    /**
+     * Space group of the result (the summary's "Space group" row); absent until the run is over
+     */
+    space_group?: string;
+    /**
+     * High-resolution limit of the merge, in Angstrom; absent until the run is over, or without a merge
+     */
+    d_min?: number;
+    /**
+     * ISa of the error model; absent until the run is over, or where it was not determined
+     */
+    isa?: number;
     /**
      * Answer of the early lattice probe on the first 60 degrees; empty until it answers
      */
@@ -3327,17 +3510,28 @@ export type getRugnuxStatusResponse = getRugnuxStatusResponses[keyof getRugnuxSt
 export type getRugnuxModelCifData = {
     body?: never;
     path?: never;
-    query?: never;
+    query?: {
+        /**
+         * `placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).
+         * Default: the refined model where there is one, otherwise the placed one.
+         *
+         */
+        stage?: 'placed' | 'refined';
+    };
     url: '/rugnux/model.cif';
 };
 
 export type getRugnuxModelCifErrors = {
+    /**
+     * Unknown stage
+     */
+    400: string;
     /**
      * The current dataset is protected and no valid bearer token was presented.
      */
     401: string;
     /**
-     * The last rugnux live run placed no model
+     * The last rugnux live run placed no model, or (`stage=refined`) refined none
      */
     404: unknown;
 };
@@ -3364,13 +3558,19 @@ export type getRugnuxMapCcp4Data = {
          *
          */
         type?: '2fofc' | 'fofc' | 'anom';
+        /**
+         * `placed`: the model as placed; `refined`: the model refined (`refined_model` in `/rugnux/status`).
+         * Default: the refined model where there is one, otherwise the placed one.
+         *
+         */
+        stage?: 'placed' | 'refined';
     };
     url: '/rugnux/map.ccp4';
 };
 
 export type getRugnuxMapCcp4Errors = {
     /**
-     * Unknown map type
+     * Unknown map type or stage
      */
     400: string;
     /**
@@ -3378,7 +3578,7 @@ export type getRugnuxMapCcp4Errors = {
      */
     401: string;
     /**
-     * The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs
+     * The last rugnux live run placed no model or made no maps, or (`anom`) has no Bijvoet pairs, or (`stage=refined`) refined none
      */
     404: unknown;
 };
diff --git a/frontend/src/client/zod.gen.ts b/frontend/src/client/zod.gen.ts
index c4f96eac8..62dbf0631 100644
--- a/frontend/src/client/zod.gen.ts
+++ b/frontend/src/client/zod.gen.ts
@@ -823,6 +823,80 @@ export const zRugnuxSummaryRow = z.object({
     value: z.string()
 });
 
+/**
+ * A blob of positive mFo-DFc density the refined model leaves unexplained, with its likely reading: a rule on
+ * what is measured, to point a person at the density - not an identification.
+ *
+ */
+export const zRugnuxLiveBlob = z.object({
+    kind: z.enum([
+        'WATER',
+        'ION',
+        'LIGAND',
+        'MODEL_ERROR',
+        'UNASSIGNED'
+    ]),
+    x: z.number(),
+    y: z.number(),
+    z: z.number(),
+    peak_sigma: z.number(),
+    volume_A3: z.number(),
+    nearest_atom: z.string(),
+    nearest_atom_distance_A: z.number().optional()
+});
+
+/**
+ * The placed model refined against the merge it was placed on, as the report's REFINE_ keys state it. Set
+ * where a placed model was refined or its refinement failed; absent where the model was not placed or
+ * refinement was skipped. On a machine without a GPU it runs on the CPU, slower, and the run's deadline
+ * or cancel can cut it.
+ *
+ */
+export const zRugnuxLiveRefinement = z.object({
+    performed: z.boolean(),
+    cancelled: z.boolean(),
+    reason: z.string(),
+    on_gpu: z.boolean(),
+    seconds: z.number(),
+    r_work: z.number().optional(),
+    r_free: z.number().optional(),
+    rmsd_bonds_A: z.number().optional(),
+    rmsd_angles_deg: z.number().optional(),
+    blob_count: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }),
+    blobs: z.array(zRugnuxLiveBlob)
+});
+
+/**
+ * What the run made of the model it was given, as the report's MODEL VALIDATION section states it. The
+ * R-factors here are those of the placed model with its own coordinates and B factors; what refinement made
+ * of it is in `refinement`. A value that is absent was not computed - the model was not placed, or not by
+ * molecular replacement.
+ *
+ */
+export const zRugnuxLiveModel = z.object({
+    placement: z.string(),
+    model_name: z.string(),
+    predicted: z.boolean(),
+    reason: z.string(),
+    r_work: z.number().optional(),
+    r_free: z.number().optional(),
+    cc_model: z.number().optional(),
+    fit_sigma: z.number().optional(),
+    map_atom_sigma: z.number().optional(),
+    rigid_body_angle_deg: z.number().optional(),
+    rigid_body_shift_A: z.number().optional(),
+    mr_decision: z.string(),
+    mr_space_group: z.string(),
+    copies: z.coerce.bigint().min(BigInt('-9223372036854775808'), { error: 'Invalid value: Expected int64 to be >= -9223372036854775808' }).max(BigInt('9223372036854775807'), { error: 'Invalid value: Expected int64 to be <= 9223372036854775807' }).optional(),
+    tf_z: z.number().optional(),
+    rf_z: z.number().optional(),
+    llg_z: z.number().optional(),
+    mr_d_min: z.number().optional(),
+    anomalous_site: z.string(),
+    anomalous_site_sigma: z.number().optional(),
+    refinement: zRugnuxLiveRefinement.optional()
+});
+
 /**
  * Live rugnux processing of the last collection; kept until the next collection starts or `POST /initialize`.
  * Times are taken when the image puller received a message, and are in seconds since the first image
@@ -839,7 +913,13 @@ export const zRugnuxLiveStatus = z.object({
         'Skipped'
     ]),
     placed_model: z.boolean(),
+    refined_model: z.boolean(),
     anomalous_map: z.boolean(),
+    anomalous_signal: z.boolean(),
+    model: zRugnuxLiveModel.optional(),
+    space_group: z.string().optional(),
+    d_min: z.number().optional(),
+    isa: z.number().optional(),
     probe: z.string(),
     probe_s: z.number().optional(),
     start_to_first_image_s: z.number().optional(),
@@ -1269,6 +1349,10 @@ export const zPutConfigRugnuxModelBody = z.string();
  */
 export const zGetRugnuxStatusResponse = zRugnuxLiveStatus;
 
+export const zGetRugnuxModelCifQuery = z.object({
+    stage: z.enum(['placed', 'refined']).optional()
+});
+
 /**
  * Placed model
  */
@@ -1279,7 +1363,8 @@ export const zGetRugnuxMapCcp4Query = z.object({
         '2fofc',
         'fofc',
         'anom'
-    ]).optional().default('2fofc')
+    ]).optional().default('2fofc'),
+    stage: z.enum(['placed', 'refined']).optional()
 });
 
 /**
diff --git a/frontend/src/components/RugnuxHero.tsx b/frontend/src/components/RugnuxHero.tsx
new file mode 100644
index 000000000..759c24c22
--- /dev/null
+++ b/frontend/src/components/RugnuxHero.tsx
@@ -0,0 +1,139 @@
+import {Box, Paper, Tooltip, Typography} from "@mui/material";
+import {green, grey, indigo, red} from "@mui/material/colors";
+import {keyframes} from "@mui/system";
+import {rugnux_live_status} from "../client";
+
+// The headline of a rugnux live run as big numbers, as jfjoch_viewer's merge-statistics window opens:
+// resolution, ISa, space group, and whether the model was placed. "—" until the run is over.
+
+const fadeIn = keyframes`
+    from { opacity: 0; transform: scale(.94); }
+    to { opacity: 1; transform: none; }
+`;
+
+// The short Hermann-Mauguin symbol with screw axes subscripted and rotoinversions overlined, as the viewer
+// writes it: "P 1 21 1" -> P2₁, "P 41 21 2" -> P4₁2₁2, "R 3 :H" -> H3.
+function SpaceGroup({hm}: { hm: string }) {
+    const [symbol, setting] = hm.split(":").map(x => x.trim());
+    let s = symbol;
+    // the monoclinic shortening: "P 1 21 1" -> "P 21"
+    const t = s.split(" ");
+    if (t.length === 4 && t[1] === "1" && t[3] === "1")
+        s = `${t[0]} ${t[2]}`;
+    if (setting === "H")
+        s = "H" + s.slice(1);
+    return <>{s.split(" ").filter(x => x).map((token, i) => {
+        if (token.length >= 2 && token[0] === "-")
+            return <span key={i}><span style={{textDecoration: "overline"}}>{token[1]}</span>{token.slice(2)}</span>;
+        if (token.length >= 2 && /\d/.test(token[0]) && /\d/.test(token[1]))
+            return <span key={i}>{token[0]}<sub style={{fontSize: "0.6em", lineHeight: 0}}>{token[1]}</sub>{token.slice(2)}</span>;
+        return <span key={i}>{token}</span>;
+    })}</>;
+}
+
+type Tone = "plain" | "pending" | "good" | "bad" | "neutral";
+
+const TONE: Record<Tone, { bg: string, border: string, value: string }> = {
+    plain: {bg: "#fff", border: indigo[100], value: indigo[900]},
+    pending: {bg: grey[50], border: grey[200], value: indigo[200]},
+    good: {bg: green[50], border: green[400], value: green[800]},
+    bad: {bg: red[50], border: red[300], value: red[800]},
+    neutral: {bg: grey[100], border: grey[300], value: grey[600]},
+};
+
+function Card({value, caption, sub, tip, tone}:
+                  { value: React.ReactNode, caption: string, sub?: string, tip: React.ReactNode, tone: Tone }) {
+    const c = TONE[tone];
+    return (
+        <Tooltip title={tip} arrow placement="bottom">
+            <Paper variant="outlined" sx={{px: 2, py: 1.5, textAlign: "center", minWidth: 0, bgcolor: c.bg,
+                borderColor: c.border, borderWidth: tone === "good" || tone === "bad" ? 2 : 1}}>
+                <Typography key={String(value)} component="div"
+                            sx={{fontSize: "clamp(1.4rem, 2.4vw, 2.75rem)", lineHeight: 1.15, fontWeight: 800, color: c.value,
+                                fontVariantNumeric: "tabular-nums", whiteSpace: "nowrap", overflow: "hidden",
+                                textOverflow: "ellipsis", animation: `${fadeIn} 500ms ease-out`,
+                                "@media (prefers-reduced-motion: reduce)": {animation: "none"}}}>
+                    {value}
+                </Typography>
+                <Typography sx={{fontSize: "0.8rem", fontWeight: 700, letterSpacing: ".08em", textTransform: "uppercase",
+                    color: "text.secondary"}}>
+                    {caption}
+                </Typography>
+                <Typography sx={{fontSize: "0.85rem", color: "text.secondary", minHeight: "1.3em", whiteSpace: "nowrap",
+                    overflow: "hidden", textOverflow: "ellipsis"}}>
+                    {sub ?? ""}
+                </Typography>
+            </Paper>
+        </Tooltip>
+    );
+}
+
+const FIT_TIP = "Fit over random: how far the placed model's R-work stands below that of the same model refitted "
+    + "in random orientations, in standard deviations of those. It is the test rugnux places a model by, for "
+    + "molecular replacement and for a model that fits where it is alike. Green: rugnux placed the model; "
+    + "red: it did not.";
+
+const REFINED_TIP = "R-work and R-free of the placed model after rugnux refined it against these data (rigid bodies "
+    + "and grouped B, then every atom restrained by the dictionary), R-free on the merge's own free set.";
+
+// The model card: green where rugnux placed the model (by molecular replacement or where it was), red where it
+// did not, grey where there was no model to place; once refined, the refined R-free is its context line.
+// modelLoaded: a model is uploaded now.
+function ModelCard({s, modelLoaded}: { s: rugnux_live_status, modelLoaded: boolean }) {
+    const m = s.model;
+    const fit = m?.fit_sigma != null ? `${m.fit_sigma >= 0 ? "+" : ""}${m.fit_sigma.toFixed(1)} σ` : undefined;
+    if (m && m.placement !== "NOT_PLACED") {
+        const how = m.placement === "MR"
+            ? `MR · ${m.copies ?? 1} ${m.copies === 1 || m.copies === undefined ? "copy" : "copies"}`
+            : "fits where it is";
+        // Refined: its R-work / R-free are the headline, the card's green still says the model was placed
+        const rf = m.refinement?.performed ? m.refinement : undefined;
+        if (rf && rf.r_work != null && rf.r_free != null)
+            return <Card value={`${rf.r_work.toFixed(2)} / ${rf.r_free.toFixed(2)}`} caption="R-work / R-free, refined"
+                         sub={`placed: ${how}${fit ? ` · fit ${fit}` : ""}`} tone="good"
+                         tip={<>{REFINED_TIP}{rf.cancelled && " The deadline cut the refinement short."}<br/><br/>{FIT_TIP}</>}/>;
+        return <Card value={fit ?? "Placed"} caption="Model placed" sub={how} tone="good" tip={FIT_TIP}/>;
+    }
+    if (m) {
+        // "NOT_PLACED: no group of ..." -> "no group of ..."
+        const why = m.reason || m.mr_decision.replace(/^[A-Z_]+: /, "");
+        return <Card value={fit ?? "Not placed"} caption="Model not placed" sub={why} tone="bad"
+                     tip={<>{FIT_TIP}{why && <><br/><br/>{why}</>}</>}/>;
+    }
+    if (s.state === "Running" && modelLoaded) {
+        const step = s.steps.length > 0 ? s.steps[s.steps.length - 1].title : "";
+        const sub = step === "Molecular replacement" ? "searching…" : step === "Refinement" ? "refining…"
+            : "placed after merging";
+        return <Card value="—" caption="Model" sub={sub} tone="pending" tip={FIT_TIP}/>;
+    }
+    if (s.state === "Running" || !modelLoaded)
+        return <Card value="No model" caption="Model" sub="upload one below" tone="neutral"
+                     tip="No model was uploaded for this run, so none was placed. Molecular replacement runs on the next collection after a model is uploaded below."/>;
+    return <Card value="—" caption="Model" sub="not used in this run" tone="neutral"
+                 tip="The run ended without placing the model - the steps and warnings say why."/>;
+}
+
+function RugnuxHero({s, modelLoaded}: { s: rugnux_live_status, modelLoaded: boolean }) {
+    const pending = s.state === "Running";
+    const later = pending ? "when the run is over" : undefined;
+    const tone: Tone = pending ? "pending" : "plain";
+    const mrGroup = s.model?.mr_space_group;
+    return (
+        <Box sx={{display: "grid", gap: 2, gridTemplateColumns: {xs: "repeat(2, minmax(0, 1fr))", md: "repeat(4, minmax(0, 1fr))"}}}>
+            <Card value={s.d_min !== undefined ? `${s.d_min.toFixed(2)} Å` : "—"} caption="Resolution" sub={later}
+                  tone={s.d_min !== undefined ? "plain" : tone}
+                  tip="High-resolution limit of the merge (d_min); the Resolution row of the result says where the CC½ fall-off is fitted."/>
+            <Card value={s.isa !== undefined ? s.isa.toFixed(1) : "—"} caption="ISa"
+                  sub={later ?? (s.isa === undefined ? "not determined" : undefined)}
+                  tone={s.isa !== undefined ? "plain" : tone}
+                  tip="ISa: the I/σ the strongest reflections level off at, from the error model (XDS's meaning). It measures the crystal and the instrument, not the exposure."/>
+            <Card value={s.space_group ? <SpaceGroup hm={s.space_group}/> : "—"} caption="Space group"
+                  sub={later ?? (mrGroup && s.space_group && mrGroup !== s.space_group ? `model placed in ${mrGroup}` : s.space_group)}
+                  tone={s.space_group ? "plain" : tone}
+                  tip="Space group rugnux determined from the data. Where molecular replacement placed the model in another group, the card says which."/>
+            <ModelCard s={s} modelLoaded={modelLoaded}/>
+        </Box>
+    );
+}
+
+export default RugnuxHero;
diff --git a/frontend/src/components/RugnuxPage.tsx b/frontend/src/components/RugnuxPage.tsx
index 9e062c3d8..4230cfa2d 100644
--- a/frontend/src/components/RugnuxPage.tsx
+++ b/frontend/src/components/RugnuxPage.tsx
@@ -7,21 +7,27 @@ import {useTokenRequired} from "../auth";
 import EmptyState from "./EmptyState";
 import RugnuxTimeline from "./RugnuxTimeline";
 import RugnuxSettings from "./RugnuxSettings";
-import {CutAlert, lastImageTime, ProbeAlert, RunMessage, StateChip, StepTable, VerdictAlert} from "./RugnuxParts";
+import RugnuxHero from "./RugnuxHero";
+import {CutAlert, lastImageTime, ModelScores, ProbeAlert, RunMessage, StateChip, StepTable, VerdictAlert} from "./RugnuxParts";
 import BoltIcon from "@mui/icons-material/Bolt";
 import {lazy, Suspense} from "react";
+import {keyframes} from "@mui/system";
 
 // Mol* is large: loaded only when there is a model to show.
 const RugnuxStructureViewer = lazy(() => import("./RugnuxStructureViewer"));
 
-// The summary rows rugnux writes; the ones a crystallographer looks at first get a stronger tile, and
-// space group and cell share a row.
+// The summary rows rugnux writes; the ones a crystallographer looks at first get a stronger tile.
 const KEY_ROW = /unit cell|space group|resolution|signal|r-?free|model/i;
-const PAIRED_ROW = /space group|unit cell/i;
 
-function Section({title, children}: { title: string, children: React.ReactNode }) {
+// The model section's entrance under the timeline, once the run has placed a model
+const slideIn = keyframes`
+    from { opacity: 0; transform: translateY(24px); }
+    to { opacity: 1; transform: none; }
+`;
+
+function Section({title, children, sx}: { title: string, children: React.ReactNode, sx?: object }) {
     return (
-        <Paper sx={{p: 3, height: "100%"}}>
+        <Paper sx={{p: 3, height: "100%", ...sx}}>
             <Typography sx={{fontSize: "0.8rem", fontWeight: 700, letterSpacing: ".08em", textTransform: "uppercase",
                 color: "primary.dark", mb: 2}}>
                 {title}
@@ -86,12 +92,12 @@ function SummaryTiles({s}: { s: rugnux_live_status }) {
     if (s.summary.length === 0)
         return null;
     return (
-        <Box sx={{display: "grid", gridTemplateColumns: {xs: "1fr", sm: "1fr 1fr"}, gap: 1.5, mt: 2}}>
+        <Box sx={{display: "grid", gridTemplateColumns: "repeat(auto-fill, minmax(300px, 1fr))", gap: 1.5, mt: 2}}>
             {s.summary.map((row, i) => {
                 const key = KEY_ROW.test(row.label);
                 const short = row.value.length <= 24;
                 return (
-                    <Box key={i} sx={{p: 1.5, borderRadius: 2, gridColumn: PAIRED_ROW.test(row.label) ? "auto" : "1 / -1",
+                    <Box key={i} sx={{p: 1.5, borderRadius: 2,
                         bgcolor: key ? indigo[50] : grey[50],
                         border: "1px solid", borderColor: key ? indigo[100] : grey[200]}}>
                         <Typography sx={{fontSize: "0.75rem", fontWeight: 700, letterSpacing: ".06em",
@@ -109,6 +115,24 @@ function SummaryTiles({s}: { s: rugnux_live_status }) {
     );
 }
 
+function ModelSection({s}: { s: rugnux_live_status }) {
+    const m = s.model!;
+    const mrSeconds = s.steps.find(step => step.title === "Molecular replacement")?.duration_s;
+    return (
+        <Section title={(m.placement === "MR" ? "Molecular replacement" : "Model") + (m.predicted ? " · predicted model" : "")}
+                 sx={{animation: `${slideIn} 700ms ease-out`, "@media (prefers-reduced-motion: reduce)": {animation: "none"}}}>
+            <ModelScores m={m} mrSeconds={mrSeconds} anomalousSignal={s.anomalous_signal}/>
+            {s.placed_model && <Box sx={{mt: 2}}>
+                <Suspense fallback={<Typography color="text.secondary">Loading viewer...</Typography>}>
+                    <RugnuxStructureViewer resultKey={`${s.elapsed_s}`} anomalous={s.anomalous_map}
+                                           anomalousSignal={s.anomalous_signal} refined={s.refined_model}
+                                           blobs={s.refined_model ? m.refinement?.blobs ?? [] : []}/>
+                </Suspense>
+            </Box>}
+        </Section>
+    );
+}
+
 function RugnuxPage({measuring}: { measuring: boolean }) {
     const {data: settings} = useQuery({...getConfigRugnuxOptions(), refetchInterval: 2000});
     const enabled = settings?.enable === true;
@@ -133,12 +157,15 @@ function RugnuxPage({measuring}: { measuring: boolean }) {
         live = (
             <Stack spacing={2}>
                 <Header s={s}/>
+                <RugnuxHero s={s} modelLoaded={settings?.model_loaded === true}/>
                 <CutAlert s={s}/>
                 <ProbeAlert s={s} large/>
                 <Section title="Timeline">
                     <RugnuxTimeline s={s} deadline_s={settings?.deadline_s ?? 0}/>
                 </Section>
-                <Box sx={{display: "grid", gridTemplateColumns: {xs: "1fr", lg: "1fr 1fr"}, gap: 2}}>
+                {s.model && s.state !== 'Running' && <ModelSection s={s}/>}
+                <Box sx={{display: "grid", gridTemplateColumns: {xs: "1fr", lg: "minmax(400px, 1fr) 2fr"}, gap: 2,
+                    alignItems: "start"}}>
                     <Section title="Processing">
                         <CurrentStep s={s}/>
                         <StepTable steps={s.steps}/>
@@ -155,12 +182,6 @@ function RugnuxPage({measuring}: { measuring: boolean }) {
                         </Stack>
                     </Section>
                 </Box>
-                {s.placed_model && s.state !== 'Running' &&
-                    <Section title="Placed model and electron density">
-                        <Suspense fallback={<Typography color="text.secondary">Loading viewer...</Typography>}>
-                            <RugnuxStructureViewer resultKey={`${s.elapsed_s}`} anomalous={s.anomalous_map}/>
-                        </Suspense>
-                    </Section>}
             </Stack>
         );
 
diff --git a/frontend/src/components/RugnuxParts.tsx b/frontend/src/components/RugnuxParts.tsx
index cbd6502a0..6a8a9105e 100644
--- a/frontend/src/components/RugnuxParts.tsx
+++ b/frontend/src/components/RugnuxParts.tsx
@@ -1,7 +1,7 @@
 import {Alert, AlertTitle, Box, Chip, Paper, Table, TableBody, TableCell, TableContainer, TableRow, Typography} from "@mui/material";
 import {indigo, lime, deepOrange, grey} from "@mui/material/colors";
 import {SxProps, Theme} from "@mui/material/styles";
-import {rugnux_live_status, rugnux_live_step} from "../client";
+import {rugnux_live_model, rugnux_live_status, rugnux_live_step} from "../client";
 
 // Pieces of the rugnux live status shared by the dashboard card and the Rugnux page.
 
@@ -113,3 +113,73 @@ export function StepTable({steps}: { steps: rugnux_live_step[] }) {
         </TableContainer>
     );
 }
+
+function ScoreTile({label, value, sub, accent}: { label: string, value: string, sub?: string, accent?: boolean }) {
+    return (
+        <Box sx={{p: 1.5, borderRadius: 2, border: "1px solid", minWidth: 0,
+            bgcolor: accent ? indigo[50] : grey[50], borderColor: accent ? indigo[100] : grey[200]}}>
+            <Typography sx={{fontSize: "0.72rem", fontWeight: 700, letterSpacing: ".06em", textTransform: "uppercase",
+                color: accent ? "primary.main" : "text.secondary", whiteSpace: "nowrap"}}>{label}</Typography>
+            <Typography sx={{fontSize: "1.6rem", lineHeight: 1.2, fontWeight: 700, color: "primary.dark",
+                fontVariantNumeric: "tabular-nums", whiteSpace: "nowrap", overflow: "hidden", textOverflow: "ellipsis"}}>
+                {value}</Typography>
+            {sub && <Typography sx={{fontSize: "0.8rem", color: "text.secondary"}}>{sub}</Typography>}
+        </Box>
+    );
+}
+
+const PLACEMENT: Record<string, string> = {MR: "MR", RIGID_BODY: "Rigid body", NOT_PLACED: "Not placed"};
+
+// What the run made of the model, in the numbers of the report's MODEL VALIDATION section; mrSeconds is how long
+// the molecular-replacement step took. Nothing is refined, so the R-factors are those of the model as placed.
+// The strongest anomalous peak is shown only where the data carry anomalous signal: without it, it is noise.
+export function ModelScores({m, mrSeconds, anomalousSignal}:
+                                { m: rugnux_live_model, mrSeconds?: number, anomalousSignal: boolean }) {
+    const tiles: { label: string, value: string, sub?: string, accent?: boolean }[] = [];
+    let placedSub = m.reason || m.mr_decision;
+    if (m.placement === "MR" && m.copies != null)
+        placedSub = `${m.copies} ${m.copies === 1 ? "copy" : "copies"} in ${m.mr_space_group}`
+            + (mrSeconds !== undefined ? `, found in ${mrSeconds.toFixed(1)} s` : "");
+    else if (m.placement === "RIGID_BODY")
+        placedSub = m.rigid_body_shift_A != null
+            ? `moved ${m.rigid_body_angle_deg?.toFixed(1)}° and ${m.rigid_body_shift_A.toFixed(2)} Å`
+            : "fits where it is";
+    tiles.push({label: "Placement", value: PLACEMENT[m.placement] ?? m.placement, sub: placedSub,
+        accent: m.placement !== "NOT_PLACED"});
+    if (m.tf_z != null)
+        tiles.push({label: "TFZ", value: m.tf_z.toFixed(1),
+            sub: [m.rf_z != null && `RFZ ${m.rf_z.toFixed(1)}`, m.llg_z != null && `LLG-Z ${m.llg_z.toFixed(1)}`,
+                m.mr_d_min != null && `search to ${m.mr_d_min.toFixed(1)} Å`].filter(Boolean).join(" · ")});
+    if (m.r_free != null)
+        tiles.push({label: "R-free", value: m.r_free.toFixed(3), accent: true,
+            sub: `R-work ${m.r_work?.toFixed(3)} · model as placed, unrefined`});
+    if (m.cc_model != null)
+        tiles.push({label: "CC (model, data)", value: m.cc_model.toFixed(2), sub: "intensities, all reflections"});
+    if (m.fit_sigma != null)
+        tiles.push({label: "Fit over random", value: `${m.fit_sigma >= 0 ? "+" : ""}${m.fit_sigma.toFixed(1)} σ`,
+            sub: "R-work against the model in random orientations"});
+    if (m.map_atom_sigma != null)
+        tiles.push({label: "2Fo−Fc at atoms", value: `${m.map_atom_sigma.toFixed(1)} σ`, sub: "mean at the atom centres"});
+    if (anomalousSignal && m.anomalous_site && m.anomalous_site_sigma != null)
+        tiles.push({label: "Anomalous peak", value: `${m.anomalous_site_sigma.toFixed(1)} σ`, sub: m.anomalous_site});
+    const rf = m.refinement;
+    if (rf && rf.performed && rf.r_free != null)
+        tiles.push({label: "R-free, refined", value: rf.r_free.toFixed(3), accent: true,
+            sub: [`R-work ${rf.r_work?.toFixed(3)}`, rf.rmsd_bonds_A != null && `bonds ${rf.rmsd_bonds_A.toFixed(3)} Å`,
+                `${rf.seconds.toFixed(1)} s on ${rf.on_gpu ? "GPU" : "CPU"}`, rf.cancelled && "cut short"]
+                .filter(Boolean).join(" · ")});
+    else if (rf)
+        tiles.push({label: "Refinement", value: "failed", sub: rf.reason});
+    if (rf && rf.performed) {
+        const count = (kind: string) => rf.blobs.filter(b => b.kind === kind).length;
+        const kinds = ([["LIGAND", "ligand"], ["WATER", "water"], ["ION", "ion"], ["MODEL_ERROR", "model error"]] as const)
+            .map(([k, label]) => count(k) > 0 && `${count(k)} ${label}`).filter(Boolean).join(" · ");
+        tiles.push({label: "Unexplained blobs", value: String(rf.blob_count),
+            sub: (rf.blob_count > rf.blobs.length ? `strongest ${rf.blobs.length}: ` : "") + (kinds || "mFo−DFc above 4 σ")});
+    }
+    return (
+        <Box sx={{display: "grid", gap: 1.5, gridTemplateColumns: "repeat(auto-fit, minmax(190px, 1fr))"}}>
+            {tiles.map(t => <ScoreTile key={t.label} {...t}/>)}
+        </Box>
+    );
+}
diff --git a/frontend/src/components/RugnuxStructureViewer.tsx b/frontend/src/components/RugnuxStructureViewer.tsx
index cd92d0108..c69c23445 100644
--- a/frontend/src/components/RugnuxStructureViewer.tsx
+++ b/frontend/src/components/RugnuxStructureViewer.tsx
@@ -7,11 +7,16 @@ import {applyModelDisplay, clearScene, getStructureAtoms, getStructureBox, Loade
     from "./structure/loadModel";
 import {loadMapLayer, MAP_COLORS, MapLayer, setLayerVisible, updateLayerSigma} from "./structure/loadMaps";
 import {fullCellFromCcp4, prepareMap} from "./structure/densityCrop";
+import {revealCamera} from "./structure/reveal";
+import {Blob, BLOB_COLORS, loadBlobs, setBlobsVisible} from "./structure/loadBlobs";
 
-// The model rugnux live placed, with its 2mFo-DFc, mFo-DFc and (where the merge kept the Bijvoet pairs) anomalous
+// The model rugnux live placed - refined, where the run refined it, with the unexplained blobs of its difference map as
+// markers (off at first) - with its 2mFo-DFc, mFo-DFc and (where the merge kept the Bijvoet pairs) anomalous
 // difference maps, in Mol*. Set up as aaredb's structure viewer (gitea.psi.ch/mx/aaredb, pages/StructureView.tsx
 // and components/Structure/, the PSI MX group's own code): its plugin, Coot mouse controls, model presets, map
-// meshes, crop and carve, panel and defaults - on a black stage. Mol* is only loaded with this component
+// meshes, crop and carve, panel and defaults - on a black stage. Departures for the live page: every map is carved
+// within the same radius of the atoms (aaredb carves 2Fo-Fc only), Fo-Fc starts at +-3.5 sigma, the anomalous map
+// is shown at first only where the data carry anomalous signal, and the first model makes an entrance (reveal.ts). Mol* is only loaded with this component
 // (React.lazy in RugnuxPage), and every Mol* import lives in ./structure.
 
 type Kind = 'twofofc' | 'fofc' | 'anom';
@@ -60,8 +65,19 @@ async function fetchBytes(path: string, signal: AbortSignal): Promise<ArrayBuffe
     return res.arrayBuffer();
 }
 
-// resultKey: changes when a new result is there to load; anomalous: it has an anomalous difference map.
-function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anomalous: boolean }) {
+const REVEAL_MS = 1600;
+const reducedMotion = () => window.matchMedia?.('(prefers-reduced-motion: reduce)').matches ?? false;
+const nextFrames = () => new Promise(r => requestAnimationFrame(() => requestAnimationFrame(r)));
+
+const BLOB_LABELS: [string, string][] = [['LIGAND', 'ligand'], ['WATER', 'water'], ['ION', 'ion'],
+    ['MODEL_ERROR', 'model error'], ['UNASSIGNED', 'other']];
+
+// resultKey: changes when a new result is there to load; anomalous: it has an anomalous difference map;
+// anomalousSignal: the data carry usable anomalous signal, so that map is worth showing from the start;
+// refined: the broker serves the refined model and its maps; blobs: what the refined model leaves unexplained.
+function RugnuxStructureViewer({resultKey, anomalous, anomalousSignal, refined, blobs}:
+                                   { resultKey: string, anomalous: boolean, anomalousSignal: boolean,
+                                     refined: boolean, blobs: Blob[] }) {
     const pluginRef = useRef<PluginContext | null>(null);
     const [pluginReady, setPluginReady] = useState(0);
     const [error, setError] = useState<string>();
@@ -73,22 +89,29 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
     // First load frames the molecule; later results keep the user's camera and clip (aaredb StructureView.tsx:117-121)
     const sceneLoadedRef = useRef(false);
     const [hasMap, setHasMap] = useState<Record<Kind, boolean>>({twofofc: false, fofc: false, anom: false});
+    // The stage stays dark until the first model and its maps are in, then fades up as the camera eases in.
+    const [revealed, setRevealed] = useState(false);
 
-    // aaredb factory defaults (state/viewerDefaults.ts:16-23); anomalous as a difference map, +4 sigma
-    const [show, setShow] = useState<Record<Kind, boolean>>({twofofc: true, fofc: true, anom: true});
-    const [sigma, setSigma] = useState<Record<Kind, number>>({twofofc: 1.0, fofc: 3.0, anom: 4.0});
+    // aaredb factory defaults (state/viewerDefaults.ts:16-23), but Fo-Fc at +-3.5 sigma rather than 3: carved or not,
+    // a difference map at 3 sigma over a whole molecule shows dozens of noise peaks; anomalous as a difference map,
+    // +4 sigma
+    const [show, setShow] = useState<Record<Kind, boolean>>({twofofc: true, fofc: true, anom: anomalousSignal});
+    const [sigma, setSigma] = useState<Record<Kind, number>>({twofofc: 1.0, fofc: 3.5, anom: 4.0});
     const [reprMode, setReprMode] = useState<ReprMode>('cartoon');
     const [showWaters, setShowWaters] = useState(false);
-    const displayRef = useRef({show, sigma, reprMode, showWaters});
-    displayRef.current = {show, sigma, reprMode, showWaters};
+    // The blobs can be dozens of waters: off until asked for
+    const [showBlobs, setShowBlobs] = useState(false);
+    const blobRefsRef = useRef<string[]>([]);
+    const displayRef = useRef({show, sigma, reprMode, showWaters, showBlobs});
+    displayRef.current = {show, sigma, reprMode, showWaters, showBlobs};
 
     const onPluginReady = useCallback((plugin: PluginContext) => {
         pluginRef.current = plugin;
         setPluginReady(n => n + 1);
     }, []);
 
-    // The model, then its maps (aaredb StructureView.tsx maybeLoad / computeAndAttachMaps, 212-295): 2Fo-Fc cropped
-    // to the model's box + 6 A and carved 4.5 A around the atoms; the difference maps cropped only.
+    // The model, then its maps (aaredb StructureView.tsx maybeLoad / computeAndAttachMaps, 212-295): each map cropped
+    // to the model's box + 6 A and carved 4.5 A around the atoms.
     useEffect(() => {
         const plugin = pluginRef.current;
         if (!plugin)
@@ -101,6 +124,7 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
             try {
                 await clearScene(plugin);
                 layersRef.current = {};
+                blobRefsRef.current = [];
                 setHasMap({twofofc: false, fofc: false, anom: false});
                 const [cif, map2, map1, mapA] = await Promise.all([
                     fetchBytes("/rugnux/model.cif", abort.signal),
@@ -113,7 +137,8 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
                     setError("No placed model");
                     return;
                 }
-                const loaded = await loadModel(plugin, cif, 'model', {resetCamera: !sceneLoadedRef.current, format: 'mmcif'});
+                const firstScene = !sceneLoadedRef.current;
+                const loaded = await loadModel(plugin, cif, 'model', {resetCamera: firstScene, format: 'mmcif'});
                 sceneLoadedRef.current = true;
                 modelRefsRef.current = loaded.refs;
                 const d = displayRef.current;
@@ -121,6 +146,8 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
                 const box = getStructureBox(loaded.structure);
                 const crop = box ? {...box, marginA: 6} : null;
                 const atoms = getStructureAtoms(loaded.structure);
+                if (blobs.length > 0)
+                    blobRefsRef.current = await loadBlobs(plugin, blobs, d.showBlobs);
                 setModelLoading(false);
                 setMapsLoading(true);
                 const maps: [Kind, '2fofc' | 'fofc' | 'anom', ArrayBuffer | undefined][] =
@@ -128,14 +155,18 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
                 for (const [kind, name, bytes] of maps) {
                     if (!bytes || abort.signal.aborted)
                         continue;
-                    const computed = prepareMap(name, fullCellFromCcp4(bytes), crop,
-                        kind === 'twofofc' && atoms.length ? atoms : null);
+                    const computed = prepareMap(name, fullCellFromCcp4(bytes), crop, atoms.length ? atoms : null);
                     const layer = await loadMapLayer(plugin, computed, name, d.sigma[kind]);
                     layersRef.current[kind] = layer;
                     if (!displayRef.current.show[kind])
                         setLayerVisible(plugin, layer, false);
                     setHasMap(h => ({...h, [kind]: true}));
                 }
+                if (firstScene && !abort.signal.aborted) {
+                    await nextFrames();   // the camera reset loadModel asked for is applied on a draw
+                    if (!reducedMotion())
+                        revealCamera(plugin, REVEAL_MS);
+                }
             } catch (e) {
                 if (!abort.signal.aborted)
                     setError(e instanceof Error ? e.message : String(e));
@@ -143,6 +174,7 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
                 if (!abort.signal.aborted) {
                     setModelLoading(false);
                     setMapsLoading(false);
+                    setRevealed(true);
                 }
             }
         })();
@@ -178,20 +210,31 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
             applyModelDisplay(plugin, modelRefsRef.current, mode, waters);
     }, []);
 
+    const toggleBlobs = useCallback((visible: boolean) => {
+        setShowBlobs(visible);
+        const plugin = pluginRef.current;
+        if (plugin)
+            setBlobsVisible(plugin, blobRefsRef.current, visible);
+    }, []);
+
     const mapsDisabled = mapsLoading;
     return (
         <Box sx={{display: 'grid', gridTemplateColumns: {xs: '1fr', md: '1fr 300px'}, border: '1px solid',
             borderColor: 'divider', borderRadius: 1, overflow: 'hidden'}}>
-            <Box sx={{position: 'relative', bgcolor: '#000', height: {xs: '55vh', md: 560}}}>
-                <MolstarCanvas onReady={onPluginReady}/>
-                {modelLoading && !error && <Box sx={{position: 'absolute', inset: 0, display: 'flex', alignItems: 'center',
+            <Box sx={{position: 'relative', bgcolor: '#000', height: {xs: '55vh', md: 'clamp(520px, 64vh, 820px)'}}}>
+                <Box sx={{position: 'absolute', inset: 0, opacity: revealed ? 1 : 0,
+                    transition: 'opacity 900ms ease-out', '@media (prefers-reduced-motion: reduce)': {transition: 'none'}}}>
+                    <MolstarCanvas onReady={onPluginReady}/>
+                </Box>
+                {(modelLoading || (mapsLoading && !revealed)) && !error && <Box sx={{position: 'absolute', inset: 0, display: 'flex', alignItems: 'center',
                     justifyContent: 'center', pointerEvents: 'none'}}>
-                    <Typography sx={{fontSize: '0.875rem', color: '#8aa0b5'}}>loading model…</Typography>
+                    <Typography sx={{fontSize: '0.875rem', color: '#8aa0b5'}}>
+                        {modelLoading ? 'loading model…' : 'computing density maps…'}</Typography>
                 </Box>}
             </Box>
             <Box sx={{borderLeft: {md: '1px solid'}, borderColor: {md: 'divider'}, p: 1.75}}>
                 {error && <Alert severity="warning" sx={{mb: 1}}>{error}</Alert>}
-                <SectionTitle>Model</SectionTitle>
+                <SectionTitle>{refined ? 'Model · refined' : 'Model'}</SectionTitle>
                 <Box sx={{display: 'flex', gap: 0.75, flexWrap: 'wrap', alignItems: 'center', mb: 0.75}}>
                     {(['cartoon', 'sticks', 'both'] as const).map((m) => (
                         <Typography key={m} role="button" tabIndex={0}
@@ -227,6 +270,25 @@ function RugnuxStructureViewer({resultKey, anomalous}: { resultKey: string, anom
                 {!modelLoading && !mapsLoading && !hasMap.twofofc &&
                     <Typography sx={{fontSize: '0.8125rem', color: 'text.secondary'}}>No maps</Typography>}
 
+                {blobs.length > 0 && <>
+                    <SectionTitle>Unexplained blobs</SectionTitle>
+                    <Box sx={{display: 'flex', alignItems: 'center', justifyContent: 'space-between'}}>
+                        <Typography sx={{fontSize: '0.8125rem'}}>{blobs.length} in mFo−DFc</Typography>
+                        <Switch size="small" checked={showBlobs} disabled={modelLoading}
+                                onChange={(e) => toggleBlobs(e.target.checked)}/>
+                    </Box>
+                    <Box sx={{display: 'flex', flexWrap: 'wrap', columnGap: 1.5, rowGap: 0.5, mt: 0.5}}>
+                        {BLOB_LABELS.filter(([k]) => blobs.some(b => b.kind === k)).map(([k, label]) => (
+                            <Box key={k} sx={{display: 'flex', alignItems: 'center', gap: 0.5}}>
+                                <Box sx={{width: 9, height: 9, borderRadius: '50%', bgcolor: hex(BLOB_COLORS[k]),
+                                    border: '1px solid', borderColor: 'divider'}}/>
+                                <Typography sx={{fontSize: '0.75rem', color: 'text.secondary'}}>
+                                    {blobs.filter(b => b.kind === k).length} {label}</Typography>
+                            </Box>
+                        ))}
+                    </Box>
+                </>}
+
                 <SectionTitle>Controls</SectionTitle>
                 {([
                     ['left drag', 'rotate'],
diff --git a/frontend/src/components/structure/densityCrop.ts b/frontend/src/components/structure/densityCrop.ts
index 36fb3bbf9..3cf1597fe 100644
--- a/frontend/src/components/structure/densityCrop.ts
+++ b/frontend/src/components/structure/densityCrop.ts
@@ -1,6 +1,6 @@
 // The density preparation of aaredb's density worker (gitea.psi.ch/mx/aaredb, the PSI MX group's own code,
 // frontend/public/structure-worker/density-worker.js at 8ece2c2): crop the periodic map to the model's box plus a
-// margin, carve the 2Fo-Fc map around the atoms, encode as CCP4 with the full cell's mean and RMS. aaredb computes
+// margin, carve it around the atoms, encode as CCP4 with the full cell's mean and RMS. aaredb computes
 // the full-cell map from an MTZ with gemmi wasm; here the broker serves it (/rugnux/map.ccp4), so it is first read
 // back into aaredb's full-cell z-fastest grid (fullCellFromCcp4).
 
@@ -226,8 +226,9 @@ function carveBlock(block: Float32Array, start: number[], dims: number[], n: num
     }
 }
 
-/* One map as the worker's onmessage loop makes it: cropped to `crop`, carved around `carveAtoms` (2Fo-Fc only -
- * never a difference map: unmodelled blobs sit away from every atom), with the full cell's mean and RMS. */
+/* One map as the worker's onmessage loop makes it: cropped to `crop`, carved around `carveAtoms`, with the full
+ * cell's mean and RMS. aaredb carves the 2Fo-Fc map only; the live page carves the difference maps as well, within
+ * the same radius, so what it shows is the density about the model - unmodelled blobs further away are left out. */
 export function prepareMap(name: string, full: FullCellMap, crop: CropBox | null, carveAtoms: Float32Array | null,
                            carveRadiusA = 4.5): ComputedMap {
     const [nx, ny, nz] = full.n;
diff --git a/frontend/src/components/structure/loadBlobs.ts b/frontend/src/components/structure/loadBlobs.ts
new file mode 100644
index 000000000..8083dbae2
--- /dev/null
+++ b/frontend/src/components/structure/loadBlobs.ts
@@ -0,0 +1,56 @@
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { setSubtreeVisibility } from 'molstar/lib/mol-plugin/behavior/static/state';
+import { Color } from 'molstar/lib/mol-util/color';
+
+// The unexplained blobs of the refined model's difference map as small spheres, one structure per reading so each
+// gets its own colour. Colours stay clear of the maps (blue 2Fo-Fc, green/red Fo-Fc, magenta anomalous) and of the
+// chain palette (loadModel.ts).
+export const BLOB_COLORS: Record<string, number> = {
+    LIGAND: 0xffe000,       // yellow
+    WATER: 0x40e0ff,        // cyan
+    ION: 0xffffff,          // white
+    MODEL_ERROR: 0xff8c00,  // orange
+    UNASSIGNED: 0x9e9e9e,   // grey
+};
+
+// What the hover label shows as the residue name
+const RESIDUE: Record<string, string> = {LIGAND: 'LIG', WATER: 'WAT', ION: 'ION', MODEL_ERROR: 'ERR', UNASSIGNED: 'UNK'};
+
+export interface Blob { kind: string; x: number; y: number; z: number; peak_sigma: number; }
+
+// One PDB HETATM record (fixed columns): the peak height in sigma goes in the B column.
+function hetatm(serial: number, b: Blob): string {
+    const num = (v: number, w: number, d: number) => v.toFixed(d).padStart(w);
+    return 'HETATM' + String(serial).padStart(5) + '  O   ' + (RESIDUE[b.kind] ?? 'UNK') + ' X'
+        + String(serial).padStart(4) + '    ' + num(b.x, 8, 3) + num(b.y, 8, 3) + num(b.z, 8, 3)
+        + '  1.00' + num(Math.min(b.peak_sigma, 999), 6, 2) + '           O';
+}
+
+/** Load the blobs; returns the refs to show or hide them by (setBlobsVisible). */
+export async function loadBlobs(plugin: PluginContext, blobs: Blob[], visible: boolean): Promise<string[]> {
+    const refs: string[] = [];
+    for (const [kind, color] of Object.entries(BLOB_COLORS)) {
+        const mine = blobs.filter(b => b.kind === kind);
+        if (mine.length === 0)
+            continue;
+        const pdb = mine.map((b, i) => hetatm(i + 1, b)).join('\n') + '\nEND\n';
+        const data = await plugin.builders.data.rawData({ data: pdb, label: `blobs ${kind}` });
+        const trajectory = await plugin.builders.structure.parseTrajectory(data, 'pdb');
+        const model = await plugin.builders.structure.createModel(trajectory);
+        const structure = await plugin.builders.structure.createStructure(model);
+        await plugin.builders.structure.representation.addRepresentation(structure, {
+            type: 'spacefill',
+            typeParams: { sizeFactor: 0.45 },
+            color: 'uniform',
+            colorParams: { value: Color(color) },
+        });
+        refs.push(data.ref);
+        if (!visible) setSubtreeVisibility(plugin.state.data, data.ref, true);
+    }
+    return refs;
+}
+
+export function setBlobsVisible(plugin: PluginContext, refs: string[], visible: boolean): void {
+    // setSubtreeVisibility's boolean is "isHidden"
+    for (const ref of refs) setSubtreeVisibility(plugin.state.data, ref, !visible);
+}
diff --git a/frontend/src/components/structure/reveal.ts b/frontend/src/components/structure/reveal.ts
new file mode 100644
index 000000000..14a9e8103
--- /dev/null
+++ b/frontend/src/components/structure/reveal.ts
@@ -0,0 +1,16 @@
+import { PluginContext } from 'molstar/lib/mol-plugin/context';
+import { Quat, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
+
+// The entrance of a freshly placed model: the camera starts further out and turned a little about the vertical,
+// then eases in to the view a plain reset frames. Only the camera moves, and it ends exactly where the reset put
+// it, so nothing after the reveal differs from a viewer without one.
+export function revealCamera(plugin: PluginContext, durationMs: number): void {
+    const camera = plugin.canvas3d?.camera;
+    if (!camera) return;
+    const end = camera.getSnapshot();
+    const dir = Vec3.sub(Vec3(), end.position, end.target);
+    Vec3.transformQuat(dir, dir, Quat.setAxisAngle(Quat(), end.up, -0.6));   // about 35 degrees
+    Vec3.scale(dir, dir, 2.2);
+    camera.setState({ ...end, position: Vec3.add(Vec3(), end.target, dir) }, 0);
+    camera.setState(end, durationMs, { easing: 'cubic-out' });
+}
diff --git a/frontend/src/version.ts b/frontend/src/version.ts
index c4bf15db1..121287506 100644
--- a/frontend/src/version.ts
+++ b/frontend/src/version.ts
@@ -1 +1 @@
-export const JFJOCH_VERSION : string = "1.0.0-rc.179";
\ No newline at end of file
+export const JFJOCH_VERSION : string = "1.0.0-rc.180";
\ No newline at end of file
diff --git a/gemmi_gph/CMakeLists.txt b/gemmi_gph/CMakeLists.txt
index c9c129ecf..c2e2b01ed 100644
--- a/gemmi_gph/CMakeLists.txt
+++ b/gemmi_gph/CMakeLists.txt
@@ -11,11 +11,15 @@
 # against the data on disk. to_mmcif.cpp calls use_hetatm() out of to_pdb.cpp, so the two come together.
 #
 # assembly.cpp expands a deposited model's strict-NCS operators into the full asymmetric unit.
+#
+# monlib/topo/riding_h are the restraint side: a monomer library read from memory (MonLib) and the
+# topology of a model built from it (prepare_topology), for rugnux's restrained refinement.
 ADD_LIBRARY(gemmi STATIC
         symmetry.cpp gz.cpp mtz.cpp sprintf.cpp xds_ascii.cpp
         pdb.cpp resinfo.cpp polyheur.cpp calculate.cpp eig3.cpp ccp4.cpp
         read_cif.cpp mmcif.cpp json.cpp mmread_gz.cpp
         to_mmcif.cpp to_pdb.cpp assembly.cpp
+        monlib.cpp topo.cpp riding_h.cpp
         gemmi/cellred.hpp
         gemmi/symmetry.hpp
         gemmi/fail.hpp
diff --git a/gemmi_gph/monlib.cpp b/gemmi_gph/monlib.cpp
new file mode 100644
index 000000000..887529b7f
--- /dev/null
+++ b/gemmi_gph/monlib.cpp
@@ -0,0 +1,633 @@
+// Copyright 2018-2023 Global Phasing Ltd.
+
+#include <gemmi/monlib.hpp>
+#include <gemmi/calculate.hpp>  // for calculate_chiral_volume
+#include <gemmi/modify.hpp>     // for rename_atom_names
+#include <gemmi/read_cif.hpp>   // for read_cif_gz
+#include <gemmi/numb.hpp>       // for as_number
+
+namespace gemmi {
+
+int ChemLink::calculate_score(const Residue& res1, const Residue* res2,
+                              char alt, char alt2,
+                              const ChemComp::Aliasing* aliasing1,
+                              const ChemComp::Aliasing* aliasing2) const {
+  int link_score = side1.specificity() + side2.specificity();
+
+  auto get_from = [&](const Restraints::AtomId& atomid) {
+    const auto* aliasing = (atomid.comp != 2 || res2 == nullptr) ? aliasing1 : aliasing2;
+    if (aliasing)
+      if (const std::string* real_id = aliasing->name_from_alias(atomid.atom))
+        return Restraints::AtomId{atomid.comp, *real_id}.get_from(res1, res2, alt, alt2);
+    return atomid.get_from(res1, res2, alt, alt2);
+  };
+
+  // check chirality
+  for (const Restraints::Chirality& chirality : rt.chirs)
+    if (chirality.sign != ChiralityType::Both) {
+      const Atom* a1 = get_from(chirality.id_ctr);
+      const Atom* a2 = get_from(chirality.id1);
+      const Atom* a3 = get_from(chirality.id2);
+      const Atom* a4 = get_from(chirality.id3);
+      if (a1 && a2 && a3 && a4) {
+        double vol = calculate_chiral_volume(a1->pos, a2->pos,
+                                             a3->pos, a4->pos);
+        if (chirality.is_wrong(vol))
+          link_score -= 10;
+      }
+    }
+  // check fixed torsion angle (_chem_link_tor.period == 0)
+  for (const Restraints::Torsion& tor : rt.torsions)
+    if (tor.period == 0) {
+      const Atom* a1 = get_from(tor.id1);
+      const Atom* a2 = get_from(tor.id2);
+      const Atom* a3 = get_from(tor.id3);
+      const Atom* a4 = get_from(tor.id4);
+      double z = 10.;
+      if (a1 && a2 && a3 && a4)
+        z = angle_z(calculate_dihedral(a1->pos, a2->pos, a3->pos, a4->pos),
+                    tor);
+      link_score -= (int) z;
+    }
+  return link_score;
+}
+
+namespace {
+
+Restraints read_link_restraints(const cif::Block& block_) {
+  auto read_aid = [](cif::Table::Row& row, int n) {
+    return Restraints::AtomId{cif::as_int(row[n]), row.str(n+1)};
+  };
+  Restraints rt;
+  cif::Block& block = const_cast<cif::Block&>(block_);
+  for (auto row : block.find("_chem_link_bond.",
+                             {"atom_1_comp_id", "atom_id_1",
+                              "atom_2_comp_id", "atom_id_2",
+                              "type",
+                              "value_dist", "value_dist_esd"}))
+    rt.bonds.push_back({read_aid(row, 0), read_aid(row, 2),
+                        bond_type_from_string(row[4]), false,
+                        cif::as_number(row[5]), cif::as_number(row[6]),
+                        NAN, NAN});
+  for (auto row : block.find("_chem_link_angle.",
+                             {"atom_1_comp_id", "atom_id_1",
+                              "atom_2_comp_id", "atom_id_2",
+                              "atom_3_comp_id", "atom_id_3",
+                              "value_angle", "value_angle_esd"}))
+    rt.angles.push_back({read_aid(row, 0), read_aid(row, 2), read_aid(row, 4),
+                         cif::as_number(row[6]), cif::as_number(row[7])});
+  for (auto row : block.find("_chem_link_tor.",
+                             {"id",
+                              "atom_1_comp_id", "atom_id_1",
+                              "atom_2_comp_id", "atom_id_2",
+                              "atom_3_comp_id", "atom_id_3",
+                              "atom_4_comp_id", "atom_id_4",
+                              "value_angle", "value_angle_esd",
+                              "period"}))
+    rt.torsions.push_back({row.str(0),
+                           read_aid(row, 1), read_aid(row, 3),
+                           read_aid(row, 5), read_aid(row, 7),
+                           cif::as_number(row[9]), cif::as_number(row[10]),
+                           cif::as_int(row[11])});
+  for (auto row : block.find("_chem_link_chir.",
+                             {"atom_centre_comp_id", "atom_id_centre",
+                              "atom_1_comp_id", "atom_id_1",
+                              "atom_2_comp_id", "atom_id_2",
+                              "atom_3_comp_id", "atom_id_3",
+                              "volume_sign"}))
+    if (row[4][0] != 'c') // ignore crossN
+      rt.chirs.push_back({read_aid(row, 0), read_aid(row, 2),
+                          read_aid(row, 4), read_aid(row, 6),
+                          chirality_from_string(row[8])});
+  for (auto row : block.find("_chem_link_plane.",
+                             {"plane_id", "atom_comp_id", "atom_id",
+                              "dist_esd"})) {
+    Restraints::Plane& plane = rt.get_or_add_plane(row.str(0));
+    if (plane.esd == 0.0)
+      plane.esd = cif::as_number(row[3]);
+    plane.ids.push_back(read_aid(row, 1));
+  }
+  return rt;
+}
+
+void insert_chemlinks_into(const cif::Document& doc, std::map<std::string,ChemLink>& links) {
+  const cif::Block* list_block = doc.find_block("link_list");
+  auto use_chem_link = [](const cif::Block& block, ChemLink& link) {
+    for (auto row : const_cast<cif::Block&>(block).find("_chem_link.",
+                                   {"id", "?name",
+                                    "?comp_id_1", "?mod_id_1", "?group_comp_1",
+                                    "?comp_id_2", "?mod_id_2", "?group_comp_2"})) {
+      if (row.str(0) == link.id) {
+        if (row.has2(1))
+          link.name = row.str(1);
+        if (row.has2(2))
+          link.side1.comp = row.str(2);
+        if (row.has2(3))
+          link.side1.mod = row.str(3);
+        if (row.has2(4))
+          link.side1.group = ChemComp::read_group(row[4]);
+        if (row.has2(5))
+          link.side2.comp = row.str(5);
+        if (row.has2(6))
+          link.side2.mod = row.str(6);
+        link.side2.group = ChemComp::read_group(row[7]);
+        break;
+      }
+    }
+  };
+  for (const cif::Block& block : doc.blocks)
+    if (starts_with(block.name, "link_") && block.name != "link_list") {
+      ChemLink link;
+      link.id = block.name.substr(5);
+      if (list_block)
+        use_chem_link(*list_block, link);
+      use_chem_link(block, link);
+      link.rt = read_link_restraints(block);
+      link.block = block;
+      links.emplace(link.id, link);
+    }
+}
+
+// Helper function. str is one of "add", "delete", "change".
+int chem_mod_type(const std::string& str) {
+  char c = str[0] | 0x20;
+  if (c != 'a' && c != 'd' && c != 'c')
+    fail("Unexpected value of _chem_mod_*.function: " + str);
+  return c;
+}
+
+Restraints read_restraint_modifications(const cif::Block& block_) {
+  Restraints rt;
+  cif::Block& block = const_cast<cif::Block&>(block_);
+  for (auto row : block.find("_chem_mod_bond.",
+                             {"function", "atom_id_1", "atom_id_2",
+                              "new_type",
+                              "new_value_dist", "new_value_dist_esd",
+                              "?new_value_dist_nucleus", "?new_value_dist_nucleus_esd"}))
+    rt.bonds.push_back({Restraints::AtomId{chem_mod_type(row[0]), row.str(1)},
+                        Restraints::AtomId{1, row.str(2)},
+                        bond_type_from_string(row[3]), false,
+                        cif::as_number(row[4]), cif::as_number(row[5]),
+                        row.has(6) ? cif::as_number(row[6]) : NAN,
+                        row.has(7) ? cif::as_number(row[7]) : NAN});
+  for (auto row : block.find("_chem_mod_angle.",
+                             {"function", "atom_id_1",
+                              "atom_id_2", "atom_id_3",
+                              "new_value_angle", "new_value_angle_esd"}))
+    rt.angles.push_back({{chem_mod_type(row[0]), row.str(1)},
+                         {1, row.str(2)}, {1, row.str(3)},
+                         cif::as_number(row[4]), cif::as_number(row[5])});
+  for (auto row : block.find("_chem_mod_tor.",
+                              {"function", "?id", "atom_id_1",
+                               "atom_id_2", "atom_id_3", "atom_id_4",
+                               "new_value_angle", "new_value_angle_esd",
+                               "?new_period"}))
+    rt.torsions.push_back({row.has(1) ? row.str(1) : "",
+                           {chem_mod_type(row[0]), row.str(2)},
+                           {1, row.str(3)}, {1, row.str(4)}, {1, row.str(5)},
+                           cif::as_number(row[6]), cif::as_number(row[7]),
+                           row.has(8) ? cif::as_int(row[8], 0) : -1});
+  for (auto row : block.find("_chem_mod_chir.",
+                             {"function", "atom_id_centre", "atom_id_1",
+                              "atom_id_2", "atom_id_3",
+                              "new_volume_sign"}))
+    rt.chirs.push_back({{1, row.str(1)}, {chem_mod_type(row[0]), row.str(2)},
+                        {1, row.str(3)}, {1, row.str(4)},
+                        chirality_from_string(row[5])});
+  for (auto row : block.find("_chem_mod_plane_atom.",
+                             {"function", "plane_id", "atom_id" ,
+                              "new_dist_esd"})) {
+    Restraints::Plane& plane = rt.get_or_add_plane(row.str(1));
+    if (plane.esd == 0.0)
+      plane.esd = cif::as_number(row[3]);
+    plane.ids.push_back({chem_mod_type(row[0]), row.str(2)});
+  }
+  return rt;
+}
+
+void insert_chemmods_into(const cif::Document& doc, std::map<std::string, ChemMod>& mods) {
+  const cif::Block* list_block = doc.find_block("mod_list");
+  auto use_chem_mod = [](const cif::Block& block, ChemMod& mod) {
+    for (auto row : const_cast<cif::Block&>(block).find("_chem_mod.",
+                                    {"id", "?name", "?comp_id", "?group_id"}))
+      if (row.str(0) == mod.id) {
+        if (row.has2(1))
+          mod.name = row.str(1);
+        if (row.has2(2))
+          mod.comp_id = row.str(2);
+        if (row.has2(3))
+          mod.group_id = row.str(3);
+        break;
+      }
+  };
+  for (const cif::Block& block : doc.blocks)
+    if (starts_with(block.name, "mod_") && block.name != "mod_list") {
+      ChemMod mod;
+      mod.id = block.name.substr(4);
+      if (list_block)
+        use_chem_mod(*list_block, mod);
+      use_chem_mod(block, mod);
+      for (auto ra : const_cast<cif::Block&>(block).find("_chem_mod_atom.",
+                                {"function", "atom_id", "new_atom_id",
+                                 "new_type_symbol", "new_type_energy",
+                                 "?new_charge", "?new_partial_charge"}))
+        mod.atom_mods.push_back({chem_mod_type(ra[0]), ra.str(1), ra.str(2),
+                                 Element(ra.str(3)),
+                                 (float) cif::as_number(ra.one_of(5, 6)),
+                                 ra.str(4)});
+      mod.rt = read_restraint_modifications(block);
+      mod.block = block;
+      mods.emplace(mod.id, mod);
+    }
+}
+
+} // anonymous namespace
+
+void ChemMod::apply_to(ChemComp& chemcomp, ChemComp::Group alias_group) const {
+  auto real = [&chemcomp, alias_group](const std::string& atom_id) -> const std::string& {
+    if (alias_group != ChemComp::Group::Null) {
+      const ChemComp::Aliasing& aliasing = chemcomp.get_aliasing(alias_group);
+      if (const std::string* real_id = aliasing.name_from_alias(atom_id))
+        return *real_id;
+    }
+    return atom_id;  // NOLINT(bugprone-return-const-ref-from-parameter)
+  };
+  cat_to(chemcomp.name, '+', id);
+  // _chem_mod_atom
+  for (const AtomMod& mod : atom_mods) {
+    if (mod.func == 'a') {
+      if (mod.new_id.empty())
+        fail("New atom id is not given");
+      if (!chemcomp.has_atom(real(mod.new_id)))
+        chemcomp.atoms.push_back({mod.new_id, "", mod.el,
+                                  std::isnan(mod.charge) ? mod.charge : 0,
+                                  mod.chem_type, "", Position()});
+      continue;
+    }
+    const std::string& old = real(mod.old_id);
+    auto it = chemcomp.find_atom(old);
+    switch (mod.func) {
+      case 'd':
+        if (it != chemcomp.atoms.end()) {
+          chemcomp.atoms.erase(it);
+          // delete restraints containing mod.old_id
+          vector_remove_if(chemcomp.rt.bonds, [&](const Restraints::Bond& b) {
+              return b.id1 == old || b.id2 == old;
+          });
+          vector_remove_if(chemcomp.rt.angles, [&](const Restraints::Angle& a) {
+              return a.id1 == old || a.id2 == old || a.id3 == old;
+          });
+          vector_remove_if(chemcomp.rt.torsions,
+              [&](const Restraints::Torsion& t) {
+                return t.id1 == old || t.id2 == old || t.id3 == old ||
+                       t.id4 == old;
+          });
+          vector_remove_if(chemcomp.rt.chirs,
+              [&](const Restraints::Chirality& c) {
+                return c.id_ctr == old || c.id1 == old || c.id2 == old ||
+                       c.id3 == old;
+          });
+          for (Restraints::Plane& plane : chemcomp.rt.planes)
+            vector_remove_if(plane.ids, [&](const Restraints::AtomId& a) {
+                return a.atom == old;
+            });
+        }
+        break;
+      case 'c':
+        if (it != chemcomp.atoms.end()) {
+          // the modification shouldn't change the atom name, so we don't do:
+          // if (!mod.new_id.empty())
+          //   it->id = mod.new_id;
+          if (mod.el != El::X)
+            it->el = mod.el;
+          if (!std::isnan(mod.charge))
+            it->charge = mod.charge;
+          if (!mod.chem_type.empty())
+            it->chem_type = mod.chem_type;
+        }
+        break;
+    }
+  }
+
+  // _chem_mod_bond
+  for (const Restraints::Bond& mod : rt.bonds) {
+    auto it = chemcomp.rt.find_bond(real(mod.id1.atom), real(mod.id2.atom));
+    switch (mod.id1.comp) {
+      case 'a':
+        if (it == chemcomp.rt.bonds.end()) {
+          chemcomp.rt.bonds.push_back(mod);
+          // id1.comp was temporarily set to 'a', set it back to 1
+          chemcomp.rt.bonds.back().id1.comp = 1;
+        }
+        break;
+      case 'd':
+        if (it != chemcomp.rt.bonds.end())
+          chemcomp.rt.bonds.erase(it);
+        break;
+      case 'c':
+        if (it != chemcomp.rt.bonds.end()) {
+          if (mod.type != BondType::Unspec)
+            it->type = mod.type;
+          if (!std::isnan(mod.value))
+            it->value = mod.value;
+          if (!std::isnan(mod.esd))
+            it->esd = mod.esd;
+          if (!std::isnan(mod.value_nucleus))
+            it->value_nucleus = mod.value_nucleus;
+          if (!std::isnan(mod.esd_nucleus))
+            it->esd_nucleus = mod.esd_nucleus;
+        }
+        break;
+    }
+  }
+
+  // _chem_mod_angle
+  for (const Restraints::Angle& mod : rt.angles) {
+    auto it = chemcomp.rt.find_angle(real(mod.id1.atom),
+                                     real(mod.id2.atom),
+                                     real(mod.id3.atom));
+    switch (mod.id1.comp) {
+      case 'a':
+        if (it == chemcomp.rt.angles.end()) {
+          chemcomp.rt.angles.push_back(mod);
+          chemcomp.rt.angles.back().id1.comp = 1;
+        }
+        break;
+      case 'd':
+        if (it != chemcomp.rt.angles.end())
+          chemcomp.rt.angles.erase(it);
+        break;
+      case 'c':
+        if (it != chemcomp.rt.angles.end()) {
+          if (!std::isnan(mod.value))
+            it->value = mod.value;
+          if (!std::isnan(mod.esd))
+            it->esd = mod.esd;
+        }
+        break;
+    }
+  }
+
+  // _chem_mod_tor
+  for (const Restraints::Torsion& mod : rt.torsions) {
+    auto it = chemcomp.rt.find_torsion(real(mod.id1.atom), real(mod.id2.atom),
+                                       real(mod.id3.atom), real(mod.id4.atom));
+    switch (mod.id1.comp) {
+      case 'a':
+        if (it == chemcomp.rt.torsions.end()) {
+          chemcomp.rt.torsions.push_back(mod);
+          chemcomp.rt.torsions.back().id1.comp = 1;
+        }
+        break;
+      case 'd':
+        if (it != chemcomp.rt.torsions.end())
+          chemcomp.rt.torsions.erase(it);
+        break;
+      case 'c':
+        if (it != chemcomp.rt.torsions.end()) {
+          if (!mod.label.empty())
+            it->label = mod.label;
+          if (!std::isnan(mod.value))
+            it->value = mod.value;
+          if (!std::isnan(mod.esd))
+            it->esd = mod.esd;
+          if (mod.period != -1)
+            it->period = mod.period;
+        }
+        break;
+    }
+  }
+
+  // _chem_mod_chir
+  for (const Restraints::Chirality& mod : rt.chirs) {
+    auto it = chemcomp.rt.find_chir(real(mod.id_ctr.atom), real(mod.id1.atom),
+                                    real(mod.id2.atom), real(mod.id3.atom));
+    switch (mod.id1.comp) {
+      case 'a':
+        if (it == chemcomp.rt.chirs.end()) {
+          chemcomp.rt.chirs.push_back(mod);
+          chemcomp.rt.chirs.back().id1.comp = 1;
+        }
+        break;
+      case 'd':
+        if (it != chemcomp.rt.chirs.end())
+          chemcomp.rt.chirs.erase(it);
+        break;
+      case 'c':
+        if (it != chemcomp.rt.chirs.end())
+          it->sign = mod.sign;
+        break;
+    }
+  }
+
+  // _chem_mod_plane_atom
+  for (const Restraints::Plane& mod : rt.planes)
+    for (const Restraints::AtomId& atom_id : mod.ids) {
+      const std::string& real_id = real(atom_id.atom);
+      if (atom_id.comp == 'a') {
+        Restraints::Plane& plane = chemcomp.rt.get_or_add_plane(mod.label);
+        if (plane.esd == 0.0 && !std::isnan(mod.esd))
+          plane.esd = mod.esd;
+        auto it = std::find(plane.ids.begin(), plane.ids.end(), real_id);
+        if (it == plane.ids.end())
+          plane.ids.push_back({1, real_id});
+      } else if (atom_id.comp == 'd') {
+        auto it = chemcomp.rt.get_plane(mod.label);
+        if (it != chemcomp.rt.planes.end()) {
+          auto item = std::find(it->ids.begin(), it->ids.end(), real_id);
+          if (item != it->ids.end())
+            it->ids.erase(item);
+        }
+      }
+    }
+}
+
+void EnerLib::read(const cif::Document& doc) {
+  cif::Block& block = const_cast<cif::Block&>(doc.blocks[0]);
+  for (const auto& row : block.find("_lib_atom.",
+                  {"type", "hb_type", "vdw_radius", "vdwh_radius",
+                   "ion_radius", "element", "valency", "sp"}))
+    atoms.emplace(row[0], Atom{Element(row[5]), row[1][0], cif::as_number(row[2]),
+                               cif::as_number(row[3]), cif::as_number(row[4]),
+                               cif::as_int(row[6], -1), cif::as_int(row[7], -1)});
+  for (const auto& row : block.find("_lib_bond.",
+                  {"atom_type_1", "atom_type_2", "type", "length", "value_esd"}))
+    bonds.emplace(row.str(0), Bond{row.str(1), bond_type_from_string(row[2]),
+                               cif::as_number(row[3]), cif::as_number(row[4])});
+}
+
+std::string MonLib::relative_monomer_path(const std::string& code) {
+  std::string path;
+  if (!code.empty()) {
+    path += lower(code[0]);
+    path += '/';  // works also on Windows
+    path += code;
+    // On Windows several names are reserved (CON, PRN, AUX, ...), see
+    // https://docs.microsoft.com/en-us/windows/win32/fileio/naming-a-file
+    // The workaround in CCP4 monomer library is to use CON_CON.cif, etc.
+    if (code.size() == 3)
+      switch (ialpha3_id(code.c_str())) {
+        case ialpha3_id("AUX"):
+        case ialpha3_id("COM"):
+        case ialpha3_id("CON"):
+        case ialpha3_id("LPT"):
+        case ialpha3_id("PRN"):
+          path += '_';
+          path += code;
+      }
+    path += ".cif";
+  }
+  return path;
+}
+
+void MonLib::read_monomer_doc(const cif::Document& doc) {
+  // ChemComp
+  if (const cif::Block* block = doc.find_block("comp_list"))
+    for (auto row : const_cast<cif::Block*>(block)->find("_chem_comp.", {"id", "group"}))
+      cc_groups.emplace(row.str(0), ChemComp::read_group(row.str(1)));
+  for (const cif::Block& block : doc.blocks)
+    add_monomer_if_present(block);
+  // ChemLink
+  insert_chemlinks_into(doc, links);
+  // ChemMod
+  insert_chemmods_into(doc, modifications);
+}
+
+namespace {
+
+const std::string* find_chemtype(const std::map<std::string, ChemComp>& monomers,
+                                 const const_CRA& cra) {
+  auto cc = monomers.find(cra.residue->name);
+  if (cc != monomers.end()) {
+    auto cc_atom = cc->second.find_atom(cra.atom->name);
+    if (cc_atom != cc->second.atoms.end())
+      return &cc_atom->chem_type;
+  }
+  return nullptr;
+}
+
+// Searches data from _lib_atom in ener_lib.cif.
+double find_radius(const EnerLib& ener_lib, const std::string& chemtype,
+                   EnerLib::RadiusType type) {
+  double r = 0;
+  auto it = ener_lib.atoms.find(chemtype);
+  if (it != ener_lib.atoms.end()) {
+    if (type == EnerLib::RadiusType::Ion)
+      r = it->second.ion_radius;
+    else if (type == EnerLib::RadiusType::Vdw)
+      r = it->second.vdw_radius;
+    else if (type == EnerLib::RadiusType::Vdwh)
+      r = it->second.vdwh_radius;
+  }
+  return std::isnan(r) ? 0 : r;
+}
+
+} // anonymous namespace
+
+void MonLib::read_monomer_cif(const std::string& path_) {
+  read_monomer_doc(read_cif_gz(path_));
+}
+
+bool MonLib::read_monomer_lib(const std::string& monomer_dir_,
+                              const std::vector<std::string>& resnames,
+                              const Logger& logger) {
+  if (monomer_dir_.empty())
+    fail("read_monomer_lib: monomer_dir not specified.");
+  set_monomer_dir(monomer_dir_);
+
+  // Only recent versions of CCP4 Monomer Library have links_and_mods.cif
+  try {
+    read_monomer_cif(monomer_dir + "links_and_mods.cif");
+  } catch (std::system_error&) {
+    read_monomer_cif(monomer_dir + "list/mon_lib_list.cif");
+  }
+  ener_lib.read(read_cif_gz(monomer_dir + "ener_lib.cif"));
+
+  bool ok = true;
+  for (const std::string& name : resnames) {
+    if (monomers.find(name) != monomers.end())
+      continue;
+    try {
+      const cif::Document& doc = read_cif_gz(path(name));
+      read_monomer_doc(doc);
+    } catch (std::system_error& err) {
+      if (err.code().value() == ENOENT)
+        logger.mesg("Monomer not in the library: ", name, '.');
+      else
+        logger.mesg("Failed to read ", name, ": ", err.what(), '.');
+      ok = false;
+    } catch (std::runtime_error& err) {
+      logger.mesg("Failed to read ", name, ": ", err.what(), '.');
+      ok = false;
+    }
+  }
+  return ok;
+}
+
+
+double MonLib::find_ideal_distance(const const_CRA& cra1, const const_CRA& cra2) const {
+  std::string types[2] = {cra1.atom->element.uname(),
+                          cra2.atom->element.uname()};
+  if (const std::string* tmp = find_chemtype(monomers, cra1))
+    types[0] = *tmp;
+  if (const std::string* tmp = find_chemtype(monomers, cra2))
+    types[1] = *tmp;
+  // if either one is metal, use ion radius + ion radius
+  if (cra1.atom->element.is_metal() != cra2.atom->element.is_metal()) {
+    // return if ion radius is found for both of them
+    double r1 = find_radius(ener_lib, types[0], EnerLib::RadiusType::Ion);
+    double r2 = find_radius(ener_lib, types[1], EnerLib::RadiusType::Ion);
+    if (r1 > 0 && r2 > 0)
+      return r1 + r2;
+  }
+  // otherwise, look for defined distance or use average of distances
+  double r[2] = {0, 0};
+  for (int j = 0; j < 2; ++j) {
+    auto range = ener_lib.bonds.equal_range(types[j]);
+    for (auto i = range.first; i != range.second; ++i)
+      if (i->second.atom_type_2 == types[1-j] && !std::isnan(i->second.length))
+        return i->second.length;
+      else if (i->second.atom_type_2.empty() && i->second.type == BondType::Single)
+        r[j] = i->second.length / 2;
+    if ((r[j] == 0 || std::isnan(r[j])) && range.first != range.second)
+      r[j] = range.first->second.length / 2;
+    if (r[j] == 0 || std::isnan(r[j]))
+      r[j] = (j==0 ? cra1 : cra2).atom->element.covalent_r();
+  }
+  return r[0] + r[1];
+}
+
+void MonLib::update_old_atom_names(Structure& st, const Logger& logger) const {
+  for (const auto& it : monomers)
+    // monomers should have only monomers needed for this structure.
+    // Few of them (usually none or one) have old names defined.
+    if (it.second.has_old_names()) {
+      const std::string& resname = it.first;
+      const ChemComp& cc = it.second;
+      int old_vs_new = 0;
+      for (const Model& model : st.models)
+        for (const Chain& chain : model.chains)
+          for (const Residue& res : chain.residues)
+            if (res.name == resname) {
+              for (const Atom& atom : res.atoms) {
+                if (cc.find_atom(atom.name) == cc.atoms.end())
+                  ++old_vs_new;
+                if (cc.find_atom_by_old_name(atom.name) == cc.atoms.end())
+                  --old_vs_new;
+              }
+            }
+      if (old_vs_new > 0) {
+        std::string msg = cat("Updating atom names in ", resname, ':');
+        std::map<std::string, std::string> mapping;
+        for (const ChemComp::Atom& a : cc.atoms)
+          if (!a.old_id.empty() && a.old_id != a.id) {
+            mapping.emplace(a.old_id, a.id);
+            cat_to(msg, ' ', a.old_id, "->", a.id);
+          }
+        logger.mesg(msg);
+        rename_atom_names(st, resname, mapping);
+      }
+    }
+}
+
+} // namespace gemmi
diff --git a/gemmi_gph/riding_h.cpp b/gemmi_gph/riding_h.cpp
new file mode 100644
index 000000000..2b2dee439
--- /dev/null
+++ b/gemmi_gph/riding_h.cpp
@@ -0,0 +1,480 @@
+// Copyright 2018-2022 Global Phasing Ltd.
+
+#include <gemmi/riding_h.hpp>
+
+namespace gemmi {
+
+namespace {
+
+struct BondedAtom {
+  Atom* ptr;
+  Position& pos;  // == ptr->pos;
+  double dist;
+};
+
+// Calculate position using one angle (theta) and one dihedral angle (tau).
+// Returns position of x4 in x1-x2-x3-x4, where dist=|x3-x4| and
+// theta is angle(x2, x3, x4).
+// Based on section 3.3 of Paciorek et al, Acta Cryst. A52, 349 (1996).
+Position position_from_angle_and_torsion(const Position& x1,
+                                         const Position& x2,
+                                         const Position& x3,
+                                         double dist,  // |x3-x4|
+                                         double theta, // angle x2-x3-x4
+                                         double tau) { // dihedral angle
+  Vec3 u = x2 - x1;
+  Vec3 v = x3 - x2;
+  Vec3 e1 = v.normalized();
+  Vec3 e2 = -(u - u.dot(e1) * e1).normalized();
+  Vec3 e3 = e1.cross(e2);
+  Vec3 e23 = std::cos(tau) * e2 + std::sin(tau) * e3;
+  return x3 + Position(dist * (-std::cos(theta) * e1 + std::sin(theta) * e23));
+}
+
+// Similar to position_from_angle_and_torsion(), but x1 and tau are not given.
+Position arbitrary_position_from_angle(const Position& x2,
+                                       const Position& x3,
+                                       double dist,     // |x3-x4|
+                                       double theta) {  // angle x2-x3-x4
+  Vec3 u(1, 0, 0);
+  Vec3 v = x3 - x2;
+  Vec3 e1 = v.normalized();
+  Vec3 e2_ = -(u - u.dot(e1) * e1);
+  if (e2_.length_sq() < 1e-6) {
+    // u || v, let's take any non-parallel u
+    u = Vec3(0, 1, 0);
+    e2_ = -(u - u.dot(e1) * e1);
+  }
+  Vec3 e2 = e2_.normalized();
+  return x3 + Position(dist * (-std::cos(theta) * e1 + std::sin(theta) * e2));
+}
+
+
+Vec3 get_vector_to_line(const Position& point,
+                        const Position& point_on_the_line,
+                        const Vec3& unit_vector) {
+  // en.wikipedia.org/wiki/Distance_from_a_point_to_a_line#Vector_formulation
+  // the component of a - p perpendicular to the line is: (a-p) - ((a-p).n)n
+  Vec3 ap = point_on_the_line - point;
+  return ap - ap.dot(unit_vector) * unit_vector;
+}
+
+// If no points satisfy the distances returns a pair of NaNs
+std::pair<Position, Position> trilaterate(const Position& p1, double r1sq,
+                                          const Position& p2, double r2sq,
+                                          const Position& p3, double r3sq) {
+  // It was based on https://en.wikipedia.org/wiki/Trilateration
+  // but apparently that page has changed in the meantime.
+  Vec3 ex = (p2 - p1).normalized();
+  double i = ex.dot(p3-p1);
+  Vec3 ey = (Vec3(p3) - p1 - i*ex).normalized();
+  Vec3 ez = ex.cross(ey);
+  double d = (p2-p1).length();
+  double j = ey.dot(p3-p1);
+  double x = (r1sq - r2sq + d*d) / (2*d);
+  double y = (r1sq - r3sq + i*i + j*j) / (2*j) - x*i/j;
+  double z2 = r1sq - x*x - y*y;
+  double z = std::sqrt(z2);  // may result in NaN
+  return std::make_pair(p1 + Position(x*ex + y*ey + z*ez),
+                        p1 + Position(x*ex + y*ey - z*ez));
+}
+
+// Calculate position using two angles.
+// Returns p4. Topology: p1 is bonded to p2, p3 and p4.
+std::pair<Position, Position>
+position_from_two_angles(const Position& p1,
+                         const Position& p2,
+                         const Position& p3,
+                         double dist14,     // |p4-p1|
+                         double theta214,   // angle p2-p1-p4
+                         double theta314) { // angle p3-p1-p4
+  double d12sq = p1.dist_sq(p2);
+  double d13sq = p1.dist_sq(p3);
+  double d14sq = dist14 * dist14;
+  // the law of cosines
+  double d24sq = d14sq + d12sq - 2 * std::sqrt(d14sq * d12sq) * cos(theta214);
+  double d34sq = d14sq + d13sq - 2 * std::sqrt(d14sq * d13sq) * cos(theta314);
+  return trilaterate(p1, d14sq, p2, d24sq, p3, d34sq);
+}
+
+// Returns angle between hydrogen and the plane of heavy atoms
+// in 2H tetrahedral configuration. theta0 is the angle between heavy atoms.
+double calculate_tetrahedral_delta(double theta0, double theta1, double theta2) {
+  // simplified trilateration:
+  //   auto r = trilaterate(Position(0, 0, 0), 1,
+  //                        Position(1, 0, 0), 2 - 2 * std::cos(theta1),
+  //                        Position(std::cos(theta0), std::sin(theta0), 0),
+  //                        2 - 2 * std::cos(theta2));
+  //   return std::asin(std::fabs(r.first.z));
+  double x = std::cos(theta1);
+  double y = (std::cos(theta2) - x * std::cos(theta0)) / std::sin(theta0);
+  double z2 = 1 - x*x - y*y;
+  double z = std::sqrt(z2);  // may result in NaN
+  return std::asin(z);
+}
+
+double angle_in_triangle(double a, double b, double c) {
+  return std::acos((a * a + c * c - b * b) / (2 * a * c));
+}
+
+// Used in rare cases when one angle is missing in 2H-tetrahedral configuration.
+// Currently it can happen only with metal sites.
+//   b   c(metal)
+//    \ /
+//   atom -- h (possibly two H atoms, symmetric wrt plane abc)
+// Angle c-atom-h is missing, b-atom-h is equal alpha, b-atom-c is theta.
+// For two H atoms we also need angle h-atom-h.
+double missing_angle_2H_tetrahedral(const Topo& topo, const Atom& atom,
+                                    const std::vector<BondedAtom>& hs,
+                                    double alpha, double theta) {
+  if (hs.size() == 1)
+    return 2 * pi() - alpha - theta;  // make it coplanar
+  if (hs.size() == 2) {
+    if (const Restraints::Angle* hh = topo.take_angle(hs[0].ptr, &atom, hs[1].ptr)) {
+      double xh = std::cos(alpha);
+      double zh = std::sin(0.5 * hh->radians());
+      double yh = std::sqrt(1 - xh*xh - zh*zh);
+      double st = std::sin(theta);
+      double ct = std::cos(theta);
+      Vec3 ah = Vec3(xh, -yh * st, zh * st);
+      double angle = std::acos((ct * ah.x + st * ah.y) / ah.length());
+      //printf("missing_angle: %s %g\n", atom.name.c_str(), deg(angle));
+      return angle;
+    }
+  }
+  return 0;
+}
+
+[[noreturn]]
+void giveup(const std::string& message, const std::vector<BondedAtom>& hs) {
+  for (const BondedAtom& bonded_h : hs) {
+    bonded_h.ptr->occ = 0;
+    bonded_h.ptr->calc_flag = CalcFlag::Dummy;
+  }
+  fail(message);
+}
+
+// known and hs are lists of heavy atoms and hydrogens bonded to atom.
+// hs is const, but nevertheless atoms it points to are modified.
+void place_hydrogens(const Topo& topo, const Atom& atom,
+                     const std::vector<BondedAtom>& known,
+                     const std::vector<BondedAtom>& hs) {
+  using Angle = Restraints::Angle;
+  assert(!hs.empty());
+
+  for (const BondedAtom& bonded_h : hs)
+    bonded_h.ptr->calc_flag = CalcFlag::Calculated;
+
+  // ==== only hydrogens ====
+  if (known.size() == 0) {
+    // we can only arbitrarily pick directions of atoms
+    for (const BondedAtom& bonded_h : hs)
+      bonded_h.ptr->occ = 0;
+    hs[0].pos = atom.pos + Position(hs[0].dist, 0, 0);
+    if (hs.size() > 1) {
+      double theta = pi();
+      if (const Angle* ang = topo.take_angle(hs[1].ptr, &atom, hs[0].ptr))
+        theta = ang->radians();
+      hs[1].pos = atom.pos + Position(hs[1].dist * cos(theta),
+                                      hs[1].dist * sin(theta), 0);
+    }
+    if (hs.size() > 2) {
+      const Angle* ang0 = topo.take_angle(hs[2].ptr, &atom, hs[0].ptr);
+      const Angle* ang1 = topo.take_angle(hs[2].ptr, &atom, hs[1].ptr);
+      double theta0 = rad(ang0 ? ang0->value : 109.47122);
+      double theta1 = rad(ang1 ? ang1->value : 109.47122);
+      auto pos = position_from_two_angles(atom.pos, hs[0].pos, hs[1].pos,
+                                          hs[2].dist, theta0, theta1);
+      hs[2].pos = pos.first;
+      // 3 hydrogens: for now happens only NH3 (NH2.cif and NH3.cif)
+      // 4 hydrogens: CH4 (CH2.cif) and NH4 (NH4.cif)
+      if (hs.size() == 4)
+        hs[3].pos = pos.second;
+    }
+
+  // ==== one heavy atom and hydrogens ====
+  } else if (known.size() == 1) {
+    const BondedAtom& h = hs[0];
+    const BondedAtom& heavy = known[0];
+    const Restraints::Angle* angle = topo.take_angle(h.ptr, &atom, heavy.ptr);
+    if (!angle)
+      giveup("No angle restraint for " + h.ptr->name + ".\n", hs);
+    if (std::abs(angle->value - 180.0) < 0.5) {
+      Vec3 u = atom.pos - h.pos;
+      h.pos = atom.pos + Position(u * (h.dist / u.length()));
+      if (hs.size() > 1)
+        giveup("Unusual: one of two H atoms has angle restraint 180 deg.", hs);
+      return;
+    }
+    double theta = angle->radians();
+    double tau = 0.0;
+    int period = 0;
+    const Atom* tau_end = nullptr;
+    auto plane_range = topo.plane_index.equal_range(&atom);
+    for (auto i = plane_range.first; i != plane_range.second; ++i) {
+      const Topo::Plane& plane = *i->second;
+      // only Topo::Plane with atoms.size() >= 4 is put into planes
+      if (plane.has(h.ptr) && plane.has(heavy.ptr)) {
+        for (const Atom* a : plane.atoms) {
+          if (!a->is_hydrogen() && a != &atom && a != heavy.ptr) {
+            tau_end = a;
+            break;
+          }
+        }
+        break;
+      }
+    }
+    Atom* torsion_h = nullptr;
+    if (!tau_end) {
+      // Using one dihedral angle.
+      // We don't check here for which hydrogen the torsion angle is defined.
+      // If an atom has 2 or 3 hydrogens, the torsion angle may not be given
+      // for the first one, but only for the 2nd or 3rd (e.g. HD22 in ASN).
+      auto tor_range = topo.torsion_index.equal_range(&atom);
+      for (auto i = tor_range.first; i != tor_range.second; ++i) {
+        const Topo::Torsion& tor = *i->second;
+        if (tor.atoms[1] == &atom && tor.atoms[2] == heavy.ptr &&
+            tor.atoms[0]->is_hydrogen() && !tor.atoms[3]->is_hydrogen()) {
+          tau = rad(tor.restr->value);
+          torsion_h = tor.atoms[0];
+          tau_end = tor.atoms[3];
+          period = tor.restr->period;
+          break;
+        }
+        if (tor.atoms[2] == &atom && tor.atoms[1] == heavy.ptr &&
+            tor.atoms[3]->is_hydrogen() && !tor.atoms[0]->is_hydrogen()) {
+          tau = rad(tor.restr->value);
+          torsion_h = tor.atoms[3];
+          tau_end = tor.atoms[0];
+          period = tor.restr->period;
+          break;
+        }
+      }
+    }
+
+    if (tau_end)
+      h.pos = position_from_angle_and_torsion(tau_end->pos, heavy.pos, atom.pos,
+                                              h.dist, theta, tau);
+    else
+      h.pos = arbitrary_position_from_angle(heavy.pos, atom.pos, h.dist, theta);
+    if (std::isnan(h.pos.x)) {
+      h.pos = Position(0, 0, 0);
+      giveup("bonded atoms are exactly overlapping (case 1).", hs);
+    }
+    if (hs.size() == 2) {
+      // I think we can assume the two hydrogens are symmetric.
+      Vec3 axis = (heavy.pos - atom.pos).normalized();
+      Vec3 perpendicular = get_vector_to_line(hs[0].pos, atom.pos, axis);
+      hs[1].pos = hs[0].pos + Position(2 * perpendicular);
+    } else if (hs.size() == 3) {
+      // Here we assume the three hydrogens are in the same distance from
+      // the parent atom and that they make an equilateral triangle.
+      // First check for which hydrogen was the torsion restraint (if any).
+      int idx = 0;
+      for (int i : {1, 2})
+        if (torsion_h == hs[i].ptr) {
+          idx = i;
+          hs[i].pos = h.pos;
+        }
+      // Now get the other positions by rotation
+      Vec3 axis = (heavy.pos - atom.pos).normalized();
+      Vec3 v1 = h.pos - atom.pos;
+      Vec3 v2 = rotate_about_axis(v1, axis, rad(120));
+      Vec3 v3 = rotate_about_axis(v1, axis, rad(-120));
+      hs[(idx+1) % 3].pos = atom.pos + Position(v2);
+      hs[(idx+2) % 3].pos = atom.pos + Position(v3);
+    } else if (hs.size() >= 4) {
+      giveup("Unusual: atom bonded to one heavy atoms and 4+ hydrogens.", hs);
+    }
+    if (!tau_end || period > (int)hs.size())
+      for (const BondedAtom& bonded_h : hs)
+        bonded_h.ptr->occ = 0;
+  // ==== two heavy atoms and hydrogens ====
+  } else if (known.size() == 2) {
+    if (hs.size() >= 3)
+      giveup("Unusual: atom bonded to 2+ heavy atoms and 3+ hydrogens.", hs);
+    const Angle* ang1 = topo.take_angle(hs[0].ptr, &atom, known[0].ptr);
+    const Angle* ang2 = topo.take_angle(hs[0].ptr, &atom, known[1].ptr);
+    const Angle* ang3 = topo.take_angle(known[0].ptr, &atom, known[1].ptr);
+
+    double theta1 = ang1 ? ang1->radians() : 0;
+    double theta2 = ang2 ? ang2->radians() : 0;
+    double theta3 = ang3 ? ang3->radians() : 0;
+    if (!ang3) {
+      // If ang3 atoms form a bonded triangle (e.g. C11-C12-PT in DVW),
+      // we can calculate theta3 from the bond lengths.
+      const Restraints::Bond* aptr = topo.take_bond(&atom, known[1].ptr);
+      const Restraints::Bond* bptr = topo.take_bond(known[0].ptr, known[1].ptr);
+      const Restraints::Bond* cptr = topo.take_bond(known[0].ptr, &atom);
+      if (!aptr || !bptr || !cptr)
+        giveup(cat("Missing angle restraint ", known[0].ptr->name, '-', atom.name,
+                   '-', known[1].ptr->name, ".\n"), hs);
+      theta3 = angle_in_triangle(aptr->value, bptr->value, cptr->value);
+    }
+    // Some configurations with metals have only distance restraints.
+    // In such cases, we assume that hydrogens are as far as possible from the metal.
+    if (!ang1 && ang2 && known[0].ptr->element.is_metal())
+      theta1 = missing_angle_2H_tetrahedral(topo, atom, hs, theta2, theta3);
+    if (!ang2 && ang1 && known[1].ptr->element.is_metal())
+      theta2 = missing_angle_2H_tetrahedral(topo, atom, hs, theta1, theta3);
+    if (theta1 == 0 || theta2 == 0)
+      giveup(cat("Missing angle restraint ", hs[0].ptr->name, '-', atom.name,
+                 '-', known[theta1 == 0 ? 0 : 1].ptr->name, ".\n"), hs);
+
+    // Co-planar case. The sum of angles should be 360 degrees,
+    // but in some cif files it differs slightly.
+    if (theta1 + theta2 + theta3 > rad(360 - 3)) {
+      Vec3 v12 = known[0].pos - atom.pos;
+      Vec3 v13 = known[1].pos - atom.pos;
+      // theta3 is the ideal restraint value, cur_theta3 is the current value
+      double cur_theta3 = v12.angle(v13);
+      double ratio = (2 * pi() - cur_theta3) / (theta1 + theta2);
+      Vec3 axis = v13.cross(v12).normalized();
+      Vec3 v14 = rotate_about_axis(v12, axis, theta1 * ratio);
+      hs[0].pos = atom.pos + Position(hs[0].dist / v14.length() * v14);
+      if (hs.size() > 1) {
+        topo.logger.err("Unhandled topology of ", hs.size(), " hydrogens bonded to ", atom.name);
+        for (size_t i = 1; i < hs.size(); ++i) {
+          hs[i].ptr->occ = 0;
+          hs[i].ptr->calc_flag = CalcFlag::Dummy;
+        }
+      }
+      return;
+    }
+
+    // Tetrahedral or similar configuration.
+    double hh_half = 0;
+    if (hs.size() == 2)
+      if (const Angle* hh = topo.take_angle(hs[0].ptr, &atom, hs[1].ptr))
+        hh_half = 0.5 * hh->radians();
+    if (hh_half == 0)
+      hh_half = calculate_tetrahedral_delta(theta3, theta1, theta2);
+
+    // Based on Liebschner et al (2020) doi:10.1016/bs.mie.2020.01.007
+    // sec. 2.3. 2H-tetrahedral configuration
+    double c0 = std::cos(theta3);
+    double c1 = std::cos(theta1);
+    double c2 = std::cos(theta2);
+    double den = 1 / (1 - c0*c0);
+    double a = den * (c1 - c0 * c2);
+    double b = den * (c2 - c0 * c1);
+    // I think the paper defines u10 and u20 in the opposite direction,
+    // but I had to reverse it somewhere to make it work.
+    Vec3 u10 = (known[0].pos - atom.pos).normalized();
+    Vec3 u20 = (known[1].pos - atom.pos).normalized();
+    Vec3 v = u10.cross(u20);
+    if (std::isnan(v.x))
+      giveup("bonded atoms are exactly overlapping (case 2).", hs);
+    Vec3 d = a * u10 + b * u20;
+    double dist_sin = hs[0].dist * std::sin(hh_half);
+    double dist_cos = hs[0].dist * std::cos(hh_half);
+    Vec3 v0s = v.changed_magnitude(dist_sin);
+    Vec3 d0c = d.changed_magnitude(dist_cos);
+    hs[0].pos = atom.pos + Position(d0c + v0s);
+    Position other_pos = atom.pos + Position(d0c - v0s);
+
+    if (hs.size() == 1) {
+      const Topo::Chirality* chir = topo.get_chirality(&atom);
+      if (chir && chir->restr->sign != ChiralityType::Both) {
+        if (!chir->check())
+          hs[0].pos = other_pos;
+      } else {
+        hs[0].ptr->occ = 0;
+      }
+    } else {  // hs.size() == 2
+      hs[1].pos = other_pos;
+    }
+
+  } else {  // known.size() >= 3
+    if (hs.size() > 1)
+      giveup("Unusual: atom bonded to 3+ heavy atoms and 2+ hydrogens.", hs);
+    // Based on Liebschner et al (2020) doi:10.1016/bs.mie.2020.01.007
+    // sec. 2.4. 1H-tetrahedral configuration
+    Vec3 u10 = (known[0].pos - atom.pos).normalized();
+    Vec3 u20 = (known[1].pos - atom.pos).normalized();
+    Vec3 u30 = (known[2].pos - atom.pos).normalized();
+    auto cos_tetrahedral = [&](size_t n) {
+      const Angle* angle = topo.take_angle(known[n].ptr, &atom, hs[0].ptr);
+      return angle ? std::cos(angle->radians()) : -1./3.;
+    };
+    SMat33<double> m{1., 1., 1., u10.dot(u20), u10.dot(u30), u20.dot(u30)};
+    Vec3 rhs(cos_tetrahedral(0), cos_tetrahedral(1), cos_tetrahedral(2));
+    double det = m.determinant();
+    if (std::fabs(det) < 1e-12)
+      giveup("tetrahedral configuration with four co-planar atoms.", hs);
+    Vec3 abc = m.inverse_(det).multiply(rhs);
+    Vec3 h_dir = abc.x * u10 + abc.y * u20 + abc.z * u30;
+    hs[0].pos = atom.pos + Position(h_dir.changed_magnitude(hs[0].dist));
+  }
+}
+
+}  // anonymous namespace
+
+void place_hydrogens_on_all_atoms(Topo& topo) {
+  std::vector<BondedAtom> known;
+  std::vector<BondedAtom> hs;
+  auto filter = [](char alt, const std::vector<BondedAtom>& v) {
+    std::vector<BondedAtom> out;
+    out.reserve(v.size());
+    for (const BondedAtom& ba : v)
+      if (ba.ptr->altloc_matches(alt))
+        out.push_back(ba);
+    return out;
+  };
+  for (Topo::ChainInfo& chain_info : topo.chain_infos)
+    for (Topo::ResInfo& ri : chain_info.res_infos) {
+      // If we don't have monomer description from a cif file,
+      // only ad-hoc restraints, don't try to place hydrogens.
+      if (ri.orig_chemcomp == nullptr)
+        continue;
+      for (Atom& atom : ri.res->atoms) {
+        if (atom.is_hydrogen())
+          continue;
+        try {
+          // gather bonded atoms
+          known.clear();
+          hs.clear();
+          auto range = topo.bond_index.equal_range(&atom);
+          for (auto i = range.first; i != range.second; ++i) {
+            const Topo::Bond* t = i->second;
+            Atom* other = t->atoms[t->atoms[0] == &atom ? 1 : 0];
+            if (other->altloc && atom.altloc) {
+              // We support links between different altlocs in Topo (e.g. link A-B),
+              // although these are rare, special cases.
+              // But if we had bonds between atom 1 (A/B) and atom 2 (A/B/C),
+              // and we had bonds B-B and B-C, we'd want to use only one of them (B-B).
+              // Checking atom's name is not robust, but should suffice here.
+              if (atom.altloc != other->altloc &&
+                  in_vector_f([&](const BondedAtom& a) { return a.ptr->name == other->name; },
+                              known))
+                continue;
+            }
+            auto& atom_list = other->is_hydrogen() ? hs : known;
+            atom_list.push_back({other, other->pos, t->restr->value});
+          }
+          if (hs.size() == 0)
+            continue;
+          std::string altlocs;
+          // In a special case: Hs with altlocs on a parent without altloc,
+          // we need to process conformations one by one.
+          if (atom.altloc == '\0')
+            for (const auto& h : hs) {
+              char alt = h.ptr->altloc;
+              if (alt && altlocs.find(alt) == std::string::npos) {
+                altlocs += alt;
+                place_hydrogens(topo, atom, filter(alt, known), filter(alt, hs));
+              }
+            }
+          // In all other cases, all bonded atoms are from the same conformation.
+          if (altlocs.empty())
+            place_hydrogens(topo, atom, known, hs);
+        } catch (const std::runtime_error& e) {
+          topo.logger.err("Placing of hydrogen bonded to ",
+                          atom_str(chain_info.chain_ref, *ri.res, atom),
+                          " failed:\n  ", e.what());
+        }
+      }
+    }
+}
+
+}  // namespace gemmi
diff --git a/gemmi_gph/topo.cpp b/gemmi_gph/topo.cpp
new file mode 100644
index 000000000..673a487da
--- /dev/null
+++ b/gemmi_gph/topo.cpp
@@ -0,0 +1,1084 @@
+// Copyright 2018-2022 Global Phasing Ltd.
+
+#include <gemmi/topo.hpp>
+#include <cmath>               // for sqrt, round
+#include <map>                 // for multimap
+#include <unordered_map>       // for unordered_multimap
+#include <gemmi/polyheur.hpp>  // for get_or_check_polymer_type, ...
+#include <gemmi/riding_h.hpp>  // for place_hydrogens_on_all_atoms, ...
+#include <gemmi/modify.hpp>    // for remove_hydrogens
+
+namespace gemmi {
+
+std::unique_ptr<ChemComp> make_chemcomp_with_restraints(const Residue& res) {
+  std::unique_ptr<ChemComp> cc(new ChemComp());
+  cc->name = res.name;
+  cc->group = ChemComp::Group::Null;
+  cc->has_coordinates = true;
+  // add atoms
+  cc->atoms.reserve(res.atoms.size());
+  for (const Atom& a : res.atoms) {
+    if (a.altloc != '\0' && cc->has_atom(a.name))
+      continue;
+    Element el = a.element;
+    if (el == El::X)
+      el = El::N;
+    if (el == El::D)
+      el = El::H;
+    const std::string& chem_type = el.uname();
+    cc->atoms.push_back(ChemComp::Atom{a.name, "", el, float(a.charge), chem_type, "", a.pos});
+  }
+  // prepare pairs of atoms
+  struct Pair {
+    size_t n1, n2;
+    double dist;
+  };
+  std::vector<Pair> pairs;
+  // first heavy atoms only
+  for (size_t i = 0; i != res.atoms.size(); ++i) {
+    const Atom& at1 = res.atoms[i];
+    if (at1.is_hydrogen())
+      continue;
+    float r1 = at1.element.covalent_r();
+    for (size_t j = i+1; j != res.atoms.size(); ++j) {
+      const Atom& at2 = res.atoms[j];
+      if (at2.is_hydrogen() || !at2.same_conformer(at1))
+        continue;
+      double d2 = at1.pos.dist_sq(at2.pos);
+      float r2 = at2.element.covalent_r();
+      double dmax = std::max(2.0, 1.3 * std::max(r1, r2));
+      if (d2 < sq(dmax))
+        pairs.push_back(Pair{i, j, std::sqrt(d2)});
+    }
+  }
+  // now each hydrogen with the nearest heavy atom
+  for (size_t i = 0; i != res.atoms.size(); ++i) {
+    const Atom& at1 = res.atoms[i];
+    if (at1.is_hydrogen()) {
+      size_t nearest = (size_t)-1;
+      double min_d2 = sq(2.5);
+      for (size_t j = 0; j != res.atoms.size(); ++j) {
+        const Atom& at2 = res.atoms[j];
+        if (!at2.is_hydrogen() && at2.same_conformer(at1)) {
+          double d2 = at1.pos.dist_sq(at2.pos);
+          if (d2 < min_d2) {
+            min_d2 = d2;
+            nearest = j;
+          }
+        }
+      }
+      if (nearest != (size_t)-1) {
+        pairs.push_back(Pair{nearest, i, std::sqrt(min_d2)});
+      }
+    }
+  }
+
+  // add bonds
+  // note: duplicated bonds (from different conformations) are not a problem
+  for (const Pair& p : pairs) {
+    Restraints::Bond bond;
+    bond.id1 = Restraints::AtomId{1, res.atoms[p.n1].name};
+    bond.id2 = Restraints::AtomId{1, res.atoms[p.n2].name};
+    bond.type = BondType::Unspec;
+    bond.aromatic = false;
+    double rounded_dist = 0.001 * std::round(1000 * p.dist);
+    bond.value = bond.value_nucleus = rounded_dist;
+    bond.esd = bond.esd_nucleus = 0.02;
+    cc->rt.bonds.push_back(bond);
+  }
+  // add angles
+  struct Triple {
+    size_t n1, n2, n3;
+  };
+  std::vector<Triple> triples;
+  for (size_t i = 0; i != pairs.size(); ++i)
+    for (size_t j = i+1; j != pairs.size(); ++j) {
+      if (pairs[i].n1 == pairs[j].n1)
+        triples.push_back(Triple{pairs[i].n2, pairs[i].n1, pairs[j].n2});
+      else if (pairs[i].n1 == pairs[j].n2)
+        triples.push_back(Triple{pairs[i].n2, pairs[i].n1, pairs[j].n1});
+      else if (pairs[i].n2 == pairs[j].n1)
+        triples.push_back(Triple{pairs[i].n1, pairs[i].n2, pairs[j].n2});
+      else if (pairs[i].n2 == pairs[j].n2)
+        triples.push_back(Triple{pairs[i].n1, pairs[i].n2, pairs[j].n1});
+    }
+  for (const Triple& triple : triples) {
+    Restraints::Angle angle;
+    angle.id1 = Restraints::AtomId{1, res.atoms[triple.n1].name};
+    angle.id2 = Restraints::AtomId{1, res.atoms[triple.n2].name};
+    angle.id3 = Restraints::AtomId{1, res.atoms[triple.n3].name};
+    double angle_rad = calculate_angle(res.atoms[triple.n1].pos,
+                                       res.atoms[triple.n2].pos,
+                                       res.atoms[triple.n3].pos);
+    angle.value = 0.01 * std::round(100 * deg(angle_rad));
+    angle.esd = 3.0;
+    cc->rt.angles.push_back(angle);
+  }
+  return cc;
+}
+
+Topo::ChainInfo::ChainInfo(ResidueSpan& subchain, const Chain& chain, const Entity* ent)
+  : chain_ref(chain) {
+  subchain_name = subchain.at(0).subchain;
+  res_infos.reserve(subchain.size());
+  if (ent) {
+    entity_id = ent->name;
+    polymer = ent->entity_type == EntityType::Polymer;
+    polymer_type = get_or_check_polymer_type(ent, subchain);
+  } else {
+    polymer = false;
+    polymer_type = PolymerType::Unknown;
+  }
+  for (Residue& res : subchain)
+    res_infos.emplace_back(&res);
+}
+
+// Add a ChemLink that restraints only bond length.
+static
+const std::string& add_auto_chemlink(MonLib& monlib,
+                                     const std::string& resname1, const std::string& aname1,
+                                     const std::string& resname2, const std::string& aname2,
+                                     double ideal_dist, double esd) {
+  ChemLink cl;
+  cl.side1.comp = resname1;
+  cl.side2.comp = resname2;
+  cl.id = resname1 + resname2;
+  cl.name = "auto-" + cl.id;
+  cl.rt.bonds.push_back({Restraints::AtomId{1, aname1},
+                         Restraints::AtomId{2, aname2},
+                         BondType::Unspec, false,
+                         ideal_dist, esd,
+                         ideal_dist, esd});
+  // ensure unique link id
+  size_t orig_len = cl.id.size();
+  for (int n = 0; monlib.get_link(cl.id) != nullptr; ++n)
+    cl.id.replace(orig_len, cl.id.size(), std::to_string(n));
+
+  auto it = monlib.links.emplace(cl.id, cl);
+  return it.first->first;
+}
+
+static const ChemLink* setup_link_if_matches(Topo::Link& link, const MonLib& monlib,
+                                             const std::string& atom1,
+                                             const std::string& atom2) {
+  bool invert;
+  const ChemLink* match = nullptr;
+  std::tie(match, invert, link.aliasing1, link.aliasing2) =
+    monlib.match_link(*link.res1, atom1, link.alt1, *link.res2, atom2, link.alt2);
+  if (match) {
+    link.link_id = match->id;
+    if (invert) {
+      std::swap(link.res1, link.res2);
+      std::swap(link.alt1, link.alt2);
+      std::swap(link.atom1_name_id, link.atom2_name_id);
+      std::swap(link.aliasing1, link.aliasing2);
+    }
+  }
+  return match;
+}
+
+static int atom_name_id(const std::string& s) {
+  int id = 0;
+  if (s.size() > 0)  // there is '\0' at the end
+    id = (s[0] << 24 | s[1] << 16);
+  if (s.size() > 2)
+    id |= (s[2] << 8 | s[3]);
+  return id | 0x20202020;
+}
+
+static void add_polymer_links(PolymerType polymer_type,
+                              const Topo::ResInfo& ri1,
+                              Topo::ResInfo& ri2,
+                              MonLib* monlib) {
+  Topo::Link link;
+  link.res1 = ri1.res;
+  link.res2 = ri2.res;
+  assert(&ri1 - &ri2 == link.res_distance());
+  bool groups_ok = (ri1.orig_chemcomp != nullptr && ri2.orig_chemcomp != nullptr);
+
+  if (is_polypeptide(polymer_type)) {
+    std::string c = "C";
+    std::string ca1 = "CA";
+    std::string n = "N";
+    std::string ca2 = "CA";
+    if (ri1.orig_chemcomp && !ChemComp::is_peptide_group(ri1.orig_chemcomp->group)) {
+      for (const ChemComp::Aliasing& aliasing : ri1.orig_chemcomp->aliases)
+        if (ChemComp::is_peptide_group(aliasing.group)) {
+          link.aliasing1 = &aliasing;
+          if (const std::string* ptr = aliasing.name_from_alias(c))
+            c = *ptr;
+          if (const std::string* ptr = aliasing.name_from_alias(ca1))
+            ca1 = *ptr;
+          break;
+        }
+      if (!link.aliasing1)
+        groups_ok = false;
+    }
+    ChemComp::Group n_terminus_group = ri2.orig_chemcomp ? ri2.orig_chemcomp->group
+                                                         : ChemComp::Group::Null;
+    if (ri2.orig_chemcomp && !ChemComp::is_peptide_group(ri2.orig_chemcomp->group)) {
+      for (const ChemComp::Aliasing& aliasing : ri2.orig_chemcomp->aliases)
+        if (ChemComp::is_peptide_group(aliasing.group)) {
+          link.aliasing2 = &aliasing;
+          n_terminus_group = aliasing.group;
+          if (const std::string* ptr = aliasing.name_from_alias(n))
+            n = *ptr;
+          if (const std::string* ptr = aliasing.name_from_alias(ca2))
+            ca2 = *ptr;
+          break;
+        }
+      if (!link.aliasing2)
+        groups_ok = false;
+    }
+    for (const Atom& a1 : ri1.res->atoms)
+      if (a1.name == c && a1.element == El::C) {
+        for (const Atom& a2 : ri2.res->atoms)
+          if (a2.name == n && a2.element == El::N &&
+              (a2.altloc == a1.altloc || a2.altloc == '\0' || a1.altloc == '\0') &&
+              in_peptide_bond_distance(&a1, &a2)) {
+            // One C-N pair of atoms can create here only one link.
+            // Ignoring artificial configuration of no-altloc C and N atoms,
+            // and CA atoms in 2+ conformations making both CIS and TRANS links.
+            link.alt1 = a1.altloc;
+            link.alt2 = a2.altloc;
+            link.atom1_name_id = atom_name_id(a1.name);
+            link.atom2_name_id = atom_name_id(a2.name);
+            if (groups_ok) {
+              // Deciding CIS/TRANS based on omega angle.
+              char alt = a1.altloc_or(a2.altloc_or('*'));
+              const Atom* ca1_atom = ri1.res->find_atom(ca1, alt, El::C);
+              const Atom* ca2_atom = ri2.res->find_atom(ca2, alt, El::C);
+              link.is_cis = is_peptide_bond_cis(ca1_atom, &a1, &a2, ca2_atom, 60.);
+              if (n_terminus_group == ChemComp::Group::PPeptide)
+                link.link_id = link.is_cis ? "PCIS" : "PTRANS";
+              else if (n_terminus_group == ChemComp::Group::MPeptide)
+                link.link_id = link.is_cis ? "NMCIS" : "NMTRANS";
+              else
+                link.link_id = link.is_cis ? "CIS" : "TRANS";
+            } else if (monlib) {
+              if (!setup_link_if_matches(link, *monlib, c, n))
+                link.link_id = add_auto_chemlink(*monlib,
+                                                 ri1.res->name, c,
+                                                 ri2.res->name, n,
+                                                 1.34, 0.04);
+            }
+            ri2.prev.push_back(link);
+          }
+      }
+
+  } else if (is_polynucleotide(polymer_type)) {
+    std::string o3p = "O3'";
+    std::string p = "P";
+    if (ri1.orig_chemcomp && !ChemComp::is_nucleotide_group(ri1.orig_chemcomp->group)) {
+      for (const ChemComp::Aliasing& aliasing : ri1.orig_chemcomp->aliases)
+        if (ChemComp::is_nucleotide_group(aliasing.group)) {
+          link.aliasing1 = &aliasing;
+          if (const std::string* o3p_ptr = aliasing.name_from_alias(o3p))
+            o3p = *o3p_ptr;
+          break;
+        }
+      if (!link.aliasing1)
+        groups_ok = false;
+    }
+    if (ri2.orig_chemcomp && !ChemComp::is_nucleotide_group(ri2.orig_chemcomp->group)) {
+      for (const ChemComp::Aliasing& aliasing : ri2.orig_chemcomp->aliases)
+        if (ChemComp::is_nucleotide_group(aliasing.group)) {
+          link.aliasing2 = &aliasing;
+          if (const std::string* p_ptr = aliasing.name_from_alias(p))
+            p = *p_ptr;
+          break;
+        }
+      if (!link.aliasing2)
+        groups_ok = false;
+    }
+    for (const Atom& a1 : ri1.res->atoms)
+      if (a1.name == o3p && a1.element == El::O) {
+        for (const Atom& a2 : ri2.res->atoms)
+          if (a2.name == p && a2.element == El::P &&
+              (a2.altloc == a1.altloc || a2.altloc == '\0' || a1.altloc == '\0') &&
+              in_nucleotide_bond_distance(&a1, &a2)) {
+            link.alt1 = a1.altloc;
+            link.alt2 = a2.altloc;
+            link.atom1_name_id = atom_name_id(a1.name);
+            link.atom2_name_id = atom_name_id(a2.name);
+            if (groups_ok) {
+              link.link_id = "p";
+            } else if (monlib) {
+              if (!setup_link_if_matches(link, *monlib, o3p, p))
+                link.link_id = add_auto_chemlink(*monlib,
+                                                 ri1.res->name, o3p,
+                                                 ri2.res->name, p,
+                                                 1.606, 0.02);
+            }
+            ri2.prev.push_back(link);
+          }
+    }
+  }
+
+  if (ri2.prev.empty()) {
+    link.link_id = "gap";
+    ri2.prev.push_back(link);
+  }
+}
+
+double Topo::ideal_chiral_abs_volume(const Chirality &ch) const {
+  const Restraints::Bond* bond_c1 = take_bond(ch.atoms[0], ch.atoms[1]);
+  const Restraints::Bond* bond_c2 = take_bond(ch.atoms[0], ch.atoms[2]);
+  const Restraints::Bond* bond_c3 = take_bond(ch.atoms[0], ch.atoms[3]);
+  const Restraints::Angle* angle_1c2 = take_angle(ch.atoms[1], ch.atoms[0], ch.atoms[2]);
+  const Restraints::Angle* angle_2c3 = take_angle(ch.atoms[2], ch.atoms[0], ch.atoms[3]);
+  const Restraints::Angle* angle_3c1 = take_angle(ch.atoms[3], ch.atoms[0], ch.atoms[1]);
+  if (bond_c1 && bond_c2 && bond_c3 && angle_1c2 && angle_2c3 && angle_3c1)
+    return chiral_abs_volume(bond_c1->value, bond_c2->value, bond_c3->value,
+                             angle_1c2->value, angle_2c3->value, angle_3c1->value);
+  return std::numeric_limits<double>::quiet_NaN();
+}
+
+std::vector<Topo::Rule> Topo::apply_restraints(const Restraints& rt,
+                                               Residue& res, Residue* res2, Asu asu,
+                                               char altloc1, char altloc2, bool require_alt) {
+  std::string altlocs;
+  if (altloc1 == '\0' && altloc2 == '\0') {
+    add_distinct_altlocs(res, altlocs);
+    if (res2)
+      add_distinct_altlocs(*res2, altlocs);
+  }
+  if (altlocs.empty())
+    altlocs += altloc1 != 0 ? altloc1 : altloc2;
+
+  std::vector<Rule> rules;
+  for (const Restraints::Bond& bond : rt.bonds)
+    for (char alt : altlocs)
+      if (Atom* at1 = bond.id1.get_from(res, res2, alt, altloc2))
+        if (Atom* at2 = bond.id2.get_from(res, res2, alt, altloc2)) {
+          bool with_alt = at1->altloc || at2->altloc;
+          if (with_alt || !require_alt) {
+            rules.push_back({RKind::Bond, bonds.size()});
+            bonds.push_back({&bond, {{at1, at2}}, asu});
+          }
+          if (!with_alt)
+            break;
+        }
+
+  if (only_bonds)
+    return rules;
+
+  for (const Restraints::Angle& angle : rt.angles)
+    for (char alt : altlocs)
+      if (Atom* at1 = angle.id1.get_from(res, res2, alt, altloc2))
+        if (Atom* at2 = angle.id2.get_from(res, res2, alt, altloc2))
+          if (Atom* at3 = angle.id3.get_from(res, res2, alt, altloc2)) {
+            bool with_alt = at1->altloc || at2->altloc || at3->altloc;
+            if (with_alt || !require_alt) {
+              rules.push_back({RKind::Angle, angles.size()});
+              angles.push_back({&angle, {{at1, at2, at3}}});
+            }
+            if (!with_alt)
+              break;
+          }
+  for (const Restraints::Torsion& tor : rt.torsions)
+    for (char alt : altlocs)
+      if (Atom* at1 = tor.id1.get_from(res, res2, alt, altloc2))
+        if (Atom* at2 = tor.id2.get_from(res, res2, alt, altloc2))
+          if (Atom* at3 = tor.id3.get_from(res, res2, alt, altloc2))
+            if (Atom* at4 = tor.id4.get_from(res, res2, alt, altloc2)) {
+              bool with_alt = at1->altloc || at2->altloc || at3->altloc || at4->altloc;
+              if (with_alt || !require_alt) {
+                rules.push_back({RKind::Torsion, torsions.size()});
+                torsions.push_back({&tor, {{at1, at2, at3, at4}}});
+              }
+              if (!with_alt)
+                break;
+        }
+  for (const Restraints::Chirality& chir : rt.chirs)
+    for (char alt : altlocs)
+      if (Atom* at1 = chir.id_ctr.get_from(res, res2, alt, altloc2))
+        if (Atom* at2 = chir.id1.get_from(res, res2, alt, altloc2))
+          if (Atom* at3 = chir.id2.get_from(res, res2, alt, altloc2))
+            if (Atom* at4 = chir.id3.get_from(res, res2, alt, altloc2)) {
+              bool with_alt = at1->altloc || at2->altloc || at3->altloc || at4->altloc;
+              if (with_alt || !require_alt) {
+                rules.push_back({RKind::Chirality, chirs.size()});
+                chirs.push_back({&chir, {{at1, at2, at3, at4}}});
+              }
+              if (!with_alt)
+                break;
+            }
+  for (const Restraints::Plane& plane : rt.planes)
+    for (char alt : altlocs) {
+      std::vector<Atom*> atoms;
+      bool with_alt = false;
+      for (const Restraints::AtomId& id : plane.ids)
+        if (Atom* atom = id.get_from(res, res2, alt, altloc2)) {
+          with_alt = with_alt || atom->altloc;
+          atoms.push_back(atom);
+        }
+      if (atoms.size() >= 4 && (with_alt || !require_alt)) {
+        rules.push_back({RKind::Plane, planes.size()});
+        planes.push_back({&plane, atoms});
+      }
+      if (!with_alt)
+        break;
+    }
+  return rules;
+}
+
+void Topo::apply_restraints_from_link(Link& link, const MonLib& monlib) {
+  if (link.link_id.empty() || link.link_id == "gap")
+    return;
+  const ChemLink* chem_link = monlib.get_link(link.link_id);
+  if (!chem_link) {
+    logger.err("ignoring link '", link.link_id, "' as it is not in the monomer library");
+    return;
+  }
+  const Restraints* rt = &chem_link->rt;
+  if (link.alt1 && link.alt2 && link.alt1 != link.alt2)
+    logger.err("LINK between different conformers: ", link.alt1, " (in ",
+               link.res1->name, ") and ", link.alt2, " (in ", link.res2->name, ").");
+  // aliases are a new feature - introduced in 2022
+  if (link.aliasing1 || link.aliasing2) {
+    std::unique_ptr<Restraints> rt_copy(new Restraints(*rt));
+    if (link.aliasing1)
+      for (const auto& p : link.aliasing1->related)
+        rt_copy->rename_atom(Restraints::AtomId{1, p.second}, p.first);
+    if (link.aliasing2)
+      for (const auto& p : link.aliasing2->related)
+        rt_copy->rename_atom(Restraints::AtomId{2, p.second}, p.first);
+    rt = rt_copy.get();
+    rt_storage.push_back(std::move(rt_copy));
+  }
+  link.link_rules = apply_restraints(*rt, *link.res1, link.res2, link.asu,
+                                     link.alt1, link.alt2, false);
+}
+
+// see comments above the declaration
+void Topo::initialize_refmac_topology(Structure& st, Model& model0,
+                                      MonLib& monlib, bool ignore_unknown_links) {
+  // initialize chain_infos
+  for (Chain& chain : model0.chains)
+    for (ResidueSpan& sub : chain.subchains()) {
+      // set Residue::group_idx which is used in Restraints::AtomId::get_from()
+      for (size_t i = 0; i != sub.size(); ++i) {
+        sub[i].group_idx = 0;
+        if (i != 0 && sub[i-1].seqid == sub[i].seqid)
+          sub[i].group_idx = sub[i-1].group_idx + 1;
+      }
+      const Entity* ent = st.get_entity_of(sub);
+      chain_infos.emplace_back(sub, chain, ent);
+    }
+
+  // add modifications from MODRES records (Refmac's extension)
+  for (const ModRes& modres : st.mod_residues)
+    if (!modres.mod_id.empty()) {
+      for (Topo::ChainInfo& chain_info : chain_infos)
+        if (chain_info.chain_ref.name == modres.chain_name) {
+          for (Topo::ResInfo& res_info : chain_info.res_infos)
+            if (*res_info.res == modres.res_id)
+              res_info.add_mod(modres.mod_id, nullptr, '\0');
+        }
+    }
+
+  // setup pointers to monomers and links in the polymer
+  for (ChainInfo& ci : chain_infos) {
+    for (ResInfo& ri : ci.res_infos) {
+      auto it = monlib.monomers.find(ri.res->name);
+      if (it != monlib.monomers.end())
+        ri.orig_chemcomp = &it->second;
+      // orig_chemcomp is left null for missing monomers
+    }
+    // setup polymer links
+    if (ci.polymer && !ci.res_infos.empty()) {
+      // handling of microheterogeneities makes it more complicated
+      // and it should be even more complex to handle partial bonding
+      auto prev_begin = ci.res_infos.begin();
+      auto prev_end = ci.group_end(prev_begin);
+      while (prev_end != ci.res_infos.end()) {
+        auto group_begin = prev_end;
+        auto group_end = ci.group_end(group_begin);
+        for (auto ri = group_begin; ri != group_end; ++ri)
+          for (auto prev_ri = prev_begin; prev_ri != prev_end; ++prev_ri) {
+            MonLib* monlib_ptr = ignore_unknown_links ? nullptr : &monlib;
+            add_polymer_links(ci.polymer_type, *prev_ri, *ri, monlib_ptr);
+          }
+        prev_begin = group_begin;
+        prev_end = group_end;
+      }
+    }
+  }
+
+  // add extra links
+  for (Connection& conn : st.connections)
+    if (conn.type != Connection::Hydrog) // ignoring hydrogen bonds
+      setup_connection(conn, model0, monlib, ignore_unknown_links);
+
+  // Add modifications from standard links. We do it here b/c polymer links
+  // could be disabled (link_id.clear()) in setup_connection().
+  for (ChainInfo& ci : chain_infos)
+    for (ResInfo& ri : ci.res_infos)
+      for (Link& prev : ri.prev)
+        if (const ChemLink* chem_link = monlib.get_link(prev.link_id)) {
+          ResInfo* ri_prev = &ri + prev.res_distance();
+          ri_prev->add_mod(chem_link->side1.mod, prev.aliasing1, prev.alt1);
+          ri.add_mod(chem_link->side2.mod, prev.aliasing2, prev.alt2);
+        }
+
+  // Apply modifications to monomer restraints
+  for (ChainInfo& chain_info : chain_infos)
+    for (ResInfo& ri : chain_info.res_infos) {
+      if (ri.orig_chemcomp) {
+        // The final ChemComp restraints that we'll use are made from
+        // original (_chem_comp) restraints with modifications (_chem_mod)
+        // applied. There is a corner case in which different conformations
+        // of the residue have different modifications applied.
+        bool has_mod_altlocs = false;
+        for (const Mod& mod : ri.mods)
+          if (mod.altloc != '\0')
+            has_mod_altlocs = true;
+        std::string altlocs;
+        if (has_mod_altlocs)
+          add_distinct_altlocs(*ri.res, altlocs);  // cf. apply_restraints
+        if (altlocs.empty())
+          altlocs += '\0';
+        for (char altloc : altlocs) {
+          // key for caching in Topo::cc_cache: ChemComp::name + modifications
+          std::string key = ri.orig_chemcomp->name;
+          for (const Mod& mod : ri.mods)
+            if (!mod.altloc || altloc == mod.altloc) {
+              key += char(1 + static_cast<int>(mod.alias));
+              key += mod.id;
+            }
+          auto it = cc_cache.find(key);
+          if (it != cc_cache.end()) {
+            ri.chemcomps.push_back({altloc, it->second.get()});
+          } else {  // it's not in cache yet - we need to add it
+            std::unique_ptr<ChemComp> cc_copy(new ChemComp(*ri.orig_chemcomp));
+            // apply modifications
+            for (const Mod& mod : ri.mods) {
+              if (!mod.altloc || altloc == mod.altloc) {
+                if (const ChemMod* chem_mod = monlib.get_mod(mod.id)) {
+                  try {
+                    chem_mod->apply_to(*cc_copy, mod.alias);
+                  } catch(std::runtime_error& e) {
+                    logger.err("failed to apply modification ", chem_mod->id,
+                               " to ", ri.res->name, ": ", e.what());
+                  }
+                } else {
+                  logger.err("modification not found: ", mod.id);
+                }
+              }
+            }
+            ri.chemcomps.push_back({altloc, cc_copy.get()});
+            cc_cache.emplace(key, std::move(cc_copy));
+          }
+        }
+        // Usually the same modifications are applied to all conformers.
+        // In such case reduce chemcomps to a single value.
+        if (ri.chemcomps.size() > 0 &&
+            std::all_of(ri.chemcomps.begin() + 1, ri.chemcomps.end(),
+              [&](const FinalChemComp& f) { return f.cc == ri.chemcomps[0].cc; })) {
+          ri.chemcomps.resize(1);
+          ri.chemcomps[0].altloc = '\0';
+        }
+      } else {  // orig_chemcomp not set - make ChemComp with ad-hoc restraints
+        // no cache - ad-hoc restraints are separate for each residue
+        cc_storage.emplace_back(make_chemcomp_with_restraints(*ri.res));
+        ri.chemcomps.push_back({'\0', cc_storage.back().get()});
+      }
+    }
+}
+
+void Topo::apply_all_restraints(const MonLib& monlib) {
+  bonds.clear();
+  angles.clear();
+  torsions.clear();
+  chirs.clear();
+  planes.clear();
+  rt_storage.clear();
+  for (ChainInfo& chain_info : chain_infos)
+    for (ResInfo& ri : chain_info.res_infos) {
+      // link restraints
+      for (Link& link : ri.prev)
+        apply_restraints_from_link(link, monlib);
+      // monomer restraints
+      auto it = ri.chemcomps.cbegin();
+      ri.monomer_rules = apply_restraints(it->cc->rt, *ri.res, nullptr, Asu::Same,
+                                          it->altloc, '\0', /*require_alt=*/false);
+      while (++it != ri.chemcomps.end()) {
+        auto rules = apply_restraints(it->cc->rt, *ri.res, nullptr, Asu::Same,
+                                      it->altloc, '\0', /*require_alt=*/true);
+        // calling reserve avoids bogus GCC warning -Wstringop-overflow
+        ri.monomer_rules.reserve(ri.monomer_rules.size() + rules.size());
+        vector_move_extend(ri.monomer_rules, std::move(rules));
+      }
+    }
+  for (Link& link : extras)
+    apply_restraints_from_link(link, monlib);
+}
+
+void Topo::create_indices() {
+  bond_index.clear();
+  for (Bond& bond : bonds) {
+    bond_index.emplace(bond.atoms[0], &bond);
+    if (bond.atoms[1] != bond.atoms[0])
+      bond_index.emplace(bond.atoms[1], &bond);
+  }
+  angle_index.clear();
+  for (Angle& ang : angles)
+    angle_index.emplace(ang.atoms[1], &ang);
+  torsion_index.clear();
+  for (Torsion& tor : torsions) {
+    torsion_index.emplace(tor.atoms[1], &tor);
+    if (tor.atoms[1] != tor.atoms[2])
+      torsion_index.emplace(tor.atoms[2], &tor);
+  }
+  plane_index.clear();
+  for (Plane& plane : planes)
+    for (Atom* atom : plane.atoms)
+      plane_index.emplace(atom, &plane);
+}
+
+Topo::Link* Topo::find_polymer_link(const AtomAddress& aa1, const AtomAddress& aa2) {
+  auto are_bonded = [&](const Link& link, const AtomAddress& a1, const AtomAddress& a2) {
+    return a1.res_id.matches_noseg(*link.res1) &&
+           a2.res_id.matches_noseg(*link.res2) &&
+           a1.altloc == link.alt1 &&
+           a2.altloc == link.alt2 &&
+           (a1.atom_name.empty() || atom_name_id(a1.atom_name) == link.atom1_name_id) &&
+           (a2.atom_name.empty() || atom_name_id(a2.atom_name) == link.atom2_name_id);
+  };
+  if (aa1.chain_name != aa2.chain_name)
+    return nullptr;
+  for (ChainInfo& ci : chain_infos)
+    if (aa1.chain_name == ci.chain_ref.name) {
+      for (ResInfo& ri : ci.res_infos)
+        for (Link& link : ri.prev) {
+          assert(link.res1 && link.res2);
+          if (are_bonded(link, aa1, aa2) || are_bonded(link, aa2, aa1))
+            return &link;
+        }
+    }
+  return nullptr;
+}
+
+// Tries to construct Topo::Link and append it to extras.
+// Side-effects: it may modify conn.link_id and add ChemLink to monlib.links.
+void Topo::setup_connection(Connection& conn, Model& model0, MonLib& monlib,
+                            bool ignore_unknown_links) {
+  if (conn.link_id == "gap") {
+    if (Link* polymer_link = find_polymer_link(conn.partner1, conn.partner2))
+      polymer_link->link_id.clear();  // disable polymer link
+    return;
+  }
+
+  Link extra;
+  CRA cra1 = model0.find_cra(conn.partner1, true);
+  CRA cra2 = model0.find_cra(conn.partner2, true);
+  if (!cra1.atom || !cra2.atom)
+    return;
+  extra.res1 = cra1.residue;
+  extra.res2 = cra2.residue;
+  extra.alt1 = conn.partner1.altloc;
+  extra.alt2 = conn.partner2.altloc;
+  extra.asu = conn.asu;
+
+  const ChemLink* match = nullptr;
+
+  // If we have link_id find ChemLink by name (and check if it matches).
+  if (!conn.link_id.empty()) {
+    match = monlib.get_link(conn.link_id);
+    if (!match) {
+      logger.err("link not found in monomer library: ", conn.link_id);
+      return;
+    }
+    if (match->rt.bonds.empty() ||
+        !monlib.link_side_matches_residue(match->side1, extra.res1->name, &extra.aliasing1) ||
+        !monlib.link_side_matches_residue(match->side2, extra.res2->name, &extra.aliasing2) ||
+        !atom_match_with_alias(match->rt.bonds[0].id1.atom,
+                               conn.partner1.atom_name, extra.aliasing1) ||
+        !atom_match_with_alias(match->rt.bonds[0].id2.atom,
+                               conn.partner2.atom_name, extra.aliasing2)) {
+      logger.err("link from the monomer library does not match: ", conn.link_id);
+      return;
+    }
+  } else {
+    // we don't have link_id - use the best matching link (if any)
+    match = setup_link_if_matches(extra, monlib,
+                                  conn.partner1.atom_name, conn.partner2.atom_name);
+    if (match)
+      conn.link_id = match->id;
+  }
+
+  // If a polymer link is also given in LINK/struct_conn,
+  // use only one of them. If LINK has explicit name (ccp4_link_id),
+  // or if it matches residue-specific link from monomer library, use it;
+  // otherwise, LINK is repetition of TRANS/CIS, so ignore LINK.
+  if (Link* polymer_link = find_polymer_link(conn.partner1, conn.partner2)) {
+    if (!conn.link_id.empty() ||  // conn has explicit link name
+        // polymer link was not really identified
+        cif::is_null(polymer_link->link_id) || polymer_link->link_id == "gap" ||
+        // conn is residue-specific
+        (match && !(match->side1.comp.empty() && match->side2.comp.empty())))
+      polymer_link->link_id.clear();  // disable polymer link, use conn
+    else
+      return;
+  }
+
+  if (match) {
+    extra.link_id = match->id;
+    // add modifications from the link
+    find_resinfo(extra.res1)->add_mod(match->side1.mod, extra.aliasing1, extra.alt1);
+    find_resinfo(extra.res2)->add_mod(match->side2.mod, extra.aliasing2, extra.alt2);
+  } else {
+    if (ignore_unknown_links)
+      return;
+    // create a new ChemLink and add it to the monomer library
+    double ideal_dist = monlib.find_ideal_distance(cra1, cra2);
+    extra.link_id = add_auto_chemlink(monlib,
+                                      extra.res1->name, conn.partner1.atom_name,
+                                      extra.res2->name, conn.partner2.atom_name,
+                                      ideal_dist, 0.02);
+  }
+  extras.push_back(extra);
+}
+
+void Topo::set_cispeps_in_structure(Structure& st) {
+  st.cispeps.clear();
+  if (chain_infos.empty())
+    return;
+  // model is not stored in Topo, let's determine it from chain_infos[0]
+  int model_num = 0;
+  for (const Model& model : st.models)
+    if (!model.chains.empty() &&
+        &model.chains[0] == &chain_infos[0].chain_ref)
+      model_num = model.num;
+  for (ChainInfo& chain_info : chain_infos)
+    for (ResInfo& res_info : chain_info.res_infos)
+      for (Link& link : res_info.prev)
+        if (link.is_cis) {
+          CisPep cp;
+          cp.model_num = model_num;
+          cp.partner_c = AtomAddress(chain_info.chain_ref.name, *link.res1, "", link.alt1);
+          cp.partner_n = AtomAddress(chain_info.chain_ref.name, *link.res2, "", link.alt2);
+          cp.only_altloc = link.alt1 ? link.alt1 : link.alt2;
+          for (const Rule& rule : link.link_rules)
+            if (rule.rkind == RKind::Torsion) {
+              const Torsion& tor = torsions[rule.index];
+              if (tor.restr->label == "omega") {
+                cp.reported_angle = tor.calculate();
+                break;
+              }
+            }
+          st.cispeps.push_back(cp);
+        }
+}
+
+namespace {
+
+void remove_hydrogens_from_atom(Topo::ResInfo* ri,
+                                       const std::string& atom_name, char alt) {
+  if (!ri)
+    return;
+  std::vector<Atom>& atoms = ri->res->atoms;
+  const Restraints& rt = ri->get_final_chemcomp(alt).rt;
+  for (auto it = atoms.end(); it-- != atoms.begin(); ) {
+    if (it->is_hydrogen() && is_same_conformer(it->altloc, alt)) {
+      const Restraints::AtomId* heavy = rt.first_bonded_atom(it->name);
+      if (heavy && heavy->atom == atom_name)
+        atoms.erase(it);
+    }
+  }
+}
+
+void set_cis_in_link(Topo::Link& link, bool is_cis) {
+  if (is_cis) {
+    if (ends_with(link.link_id, "TRANS"))
+      link.link_id.replace(link.link_id.size() - 5, 5, "CIS");
+  } else {
+    if (ends_with(link.link_id, "CIS"))
+      link.link_id.replace(link.link_id.size() - 3, 3, "TRANS");
+  }
+  link.is_cis = is_cis;
+}
+
+void force_cispeps(Topo& topo, bool single_model, const Model& model,
+                          const std::vector<CisPep>& cispeps) {
+  std::multimap<const Residue*, const CisPep*> cispep_index;
+  for (const CisPep& cp : cispeps) {
+    if (single_model || model.num == cp.model_num)
+      if (const Residue* res_n = model.find_cra(cp.partner_n).residue)
+        cispep_index.emplace(res_n, &cp);
+  }
+  for (Topo::ChainInfo& chain_info : topo.chain_infos)
+    for (Topo::ResInfo& res_info : chain_info.res_infos) {
+      auto range = cispep_index.equal_range(res_info.res);
+      for (Topo::Link& link : res_info.prev) {
+        bool is_cis = false;
+        for (auto i = range.first; i != range.second; ++i) {
+          const CisPep& cp = *i->second;
+          if (cp.partner_c.res_id.matches_noseg(*link.res1) &&
+              (cp.only_altloc == '\0' || cp.only_altloc == link.alt1
+                                      || cp.only_altloc == link.alt2))
+            is_cis = true;
+        }
+        if (is_cis != link.is_cis) {
+          set_cis_in_link(link, is_cis);
+          const std::string& ch_name = chain_info.chain_ref.name;
+          topo.logger.note("link between ", atom_str(ch_name, *link.res1, "", link.alt1),
+                           " and ", atom_str(ch_name, *link.res2, "", link.alt2),
+                           " forced to ", link.link_id);
+        }
+      }
+    }
+}
+
+struct Neigh {
+  char alt;
+  float occ;
+};
+using NeighMap = std::unordered_multimap<int, Neigh>;
+
+// Assumes no hydrogens in the residue.
+// Position and serial number are not assigned for new atoms.
+void add_hydrogens_without_positions(Topo::ResInfo& ri, const NeighMap& neighbor_altlocs) {
+  std::vector<Atom>& atoms = ri.res->atoms;
+  // Add H atom for each conformation (altloc) of the parent atom and its
+  // first neighbors.
+  for (size_t i = 0, size = atoms.size(); i != size; ++i) {
+    if (atoms[i].calc_flag == CalcFlag::NoHydrogen)
+      continue;
+    char parent_alt = atoms[i].altloc;
+    float parent_occ = atoms[i].occ;
+    std::map<char, float> altlocs; // altloc + occupancy
+    if (parent_alt == '\0') {
+      // We could have neighbor 1 with altlocs A,B and neighbor 2 with C,D.
+      // Or A,B and A,B,C. Or, neighbor 1 could have different occupancy
+      // of altloc A than neighbor 2. We don't want to check for all possible
+      // weird cases. Only ensure that the added H has total occupancy <= 1.
+      float occ_sum = 0;
+      auto range = neighbor_altlocs.equal_range(atoms[i].serial);
+      for (auto it = range.first; it != range.second; ++it) {
+        const Neigh& neigh = it->second;
+        if (altlocs.count(neigh.alt) == 0 && neigh.occ < 1.0f && occ_sum + neigh.occ <= 1.001f) {
+          occ_sum += neigh.occ;
+          altlocs.emplace(neigh.alt, neigh.occ);
+        }
+      }
+      if (occ_sum - parent_occ > 0.001f)
+        for (auto& it : altlocs)
+          it.second *= parent_occ;
+    }
+    if (altlocs.empty())
+      altlocs.emplace(parent_alt, parent_occ);
+    const ChemComp& cc = ri.get_final_chemcomp(parent_alt);
+    for (const Restraints::Bond& bond : cc.rt.bonds) {
+      // atoms may get re-allocated, so we can't set parent earlier
+      const Atom& parent = atoms[i];
+      assert(!parent.is_hydrogen());
+      const Restraints::AtomId* atom_id = bond.other(parent.name);
+      if (!atom_id)
+        continue;
+      auto it = cc.find_atom(atom_id->atom);
+      if (it == cc.atoms.end())
+        fail("inconsistent _chem_comp " + cc.name);
+      if (it->is_hydrogen()) {
+        gemmi::Atom atom;
+        atom.name = it->id;
+        atom.element = it->el;
+        // calc_flag will be changed to Calculated when the position is set
+        atom.calc_flag = CalcFlag::Dummy;
+        atom.b_iso = parent.b_iso;
+        for (auto alt_occ : altlocs) {
+          atom.altloc = alt_occ.first;
+          atom.occ = alt_occ.second;
+          atoms.push_back(atom);
+        }
+      }
+    }
+  }
+}
+
+NeighMap prepare_neighbor_altlocs(Topo& topo, const MonLib& monlib) {
+  // disable warnings here, so they are not printed twice
+  topo.logger.suspend();
+  // Prepare bonds. Fills topo.bonds, monomer_rules/link_rules and rt_storage,
+  // but they are all reset when apply_all_restraints() is called again.
+  topo.only_bonds = true;
+  topo.apply_all_restraints(monlib);
+  topo.only_bonds = false;
+  topo.logger.resume(); // re-enable warnings
+  NeighMap neighbors;
+  for (const Topo::Bond& bond : topo.bonds) {
+    const Atom* a1 = bond.atoms[0];
+    const Atom* a2 = bond.atoms[1];
+    if (a2->altloc)
+      neighbors.emplace(a1->serial, Neigh{a2->altloc, a2->occ});
+    if (a1->altloc && a1 != a2)
+      neighbors.emplace(a2->serial, Neigh{a1->altloc, a1->occ});
+  }
+  return neighbors;
+}
+
+}  // anonymous namespace
+
+std::unique_ptr<Topo>
+prepare_topology(Structure& st, MonLib& monlib, size_t model_index,
+                 HydrogenChange h_change, bool reorder,
+                 const Logger& logger, bool ignore_unknown_links, bool use_cispeps) {
+  std::unique_ptr<Topo> topo(new Topo);
+  topo->logger = logger;
+  if (model_index >= st.models.size())
+    fail("no such model index: " + std::to_string(model_index));
+  Model& model = st.models[model_index];
+  topo->initialize_refmac_topology(st, model, monlib, ignore_unknown_links);
+
+  if (use_cispeps)
+    force_cispeps(*topo, st.models.size() == 1, model, st.cispeps);
+
+  // remove hydrogens, or change deuterium to fraction, or nothing
+  // and then check atom names
+  for (Topo::ChainInfo& chain_info : topo->chain_infos)
+    for (Topo::ResInfo& ri : chain_info.res_infos) {
+      Residue& res = *ri.res;
+      if (h_change != HydrogenChange::NoChange && h_change != HydrogenChange::Shift
+          // don't re-add H's if we don't have chemical component description
+          && (ri.orig_chemcomp != nullptr || h_change == HydrogenChange::Remove)) {
+        // remove/add hydrogens
+        remove_hydrogens(res);
+      } else {
+        // Special handling of Deuterium - mostly for Refmac.
+        // Note: if the model has deuterium, it gets modified.
+        if (replace_deuterium_with_fraction(res)) {
+          // deuterium names usually differ from the names in dictionary
+          for (Atom& atom : res.atoms)
+            if (atom.name[0] == 'D' && atom.fraction != 0) {
+              const ChemComp& cc = ri.get_final_chemcomp(atom.altloc);
+              if (cc.find_atom(atom.name) == cc.atoms.end())
+                atom.name[0] = 'H';
+            }
+          st.has_d_fraction = true;
+        }
+      }
+      // check atom names
+      for (Atom& atom : res.atoms) {
+        const ChemComp& cc = ri.get_final_chemcomp(atom.altloc);
+        if (!cc.has_atom(atom.name)) {
+          std::string msg = "definition not found for "
+                          + atom_str(chain_info.chain_ref, *ri.res, atom);
+          if (ri.orig_chemcomp && ri.orig_chemcomp->has_atom(atom.name)) {
+            msg += " (linkage should remove this atom)";
+          } else {
+            auto it = cc.find_atom_by_old_name(atom.name);
+            if (it != cc.atoms.end())
+              cat_to(msg, " (replace ", atom.name, " with ", it->id, ')');
+          }
+          topo->logger.err(msg);
+        }
+      }
+    }
+
+  // add hydrogens
+  if (h_change == HydrogenChange::ReAdd ||
+      h_change == HydrogenChange::ReAddButWater ||
+      h_change == HydrogenChange::ReAddKnown) {
+    NeighMap neighbor_altlocs = prepare_neighbor_altlocs(*topo, monlib);
+    for (Topo::ChainInfo& chain_info : topo->chain_infos)
+      for (Topo::ResInfo& ri : chain_info.res_infos) {
+        Residue& res = *ri.res;
+        if (ri.orig_chemcomp != nullptr &&
+            (h_change == HydrogenChange::ReAdd || !res.is_water())) {
+          add_hydrogens_without_positions(ri, neighbor_altlocs);
+
+          // a special handling of HIS for compatibility with Refmac
+          if (res.name == "HIS") {
+            for (gemmi::Atom& atom : ri.res->atoms)
+              if (atom.name == "HD1" || atom.name == "HE2")
+                atom.occ = 0;
+          }
+        }
+      }
+  }
+
+  // sort atoms in residues
+  for (Topo::ChainInfo& chain_info : topo->chain_infos)
+    for (Topo::ResInfo& ri : chain_info.res_infos)
+      if (reorder && ri.orig_chemcomp) {
+        Residue& res = *ri.res;
+        const ChemComp& cc = *ri.orig_chemcomp;
+        for (Atom& atom : res.atoms) {
+          auto it = cc.find_atom(atom.name);
+          // If atom.name is not found (b/c it was added in a modification),
+          // the atom will be put after original atoms.
+          atom.serial = int(it - cc.atoms.begin()); // temporary, for sorting only
+        }
+        std::sort(res.atoms.begin(), res.atoms.end(), [](const Atom& a, const Atom& b) {
+                    return a.serial != b.serial ? a.serial < b.serial
+                                                : a.altloc < b.altloc;
+        });
+        // check for missing altloc
+        for (auto atom = res.atoms.begin(); atom + 1 < res.atoms.end(); ++atom)
+          if (atom->name == (atom + 1)->name && atom->altloc == '\0')
+            topo->logger.err("missing altloc in ", atom_str(chain_info.chain_ref, *ri.res, *atom));
+      }
+
+  // for atoms with ad-hoc links, for now we don't want hydrogens
+  if (!ignore_unknown_links && h_change != HydrogenChange::NoChange) {
+    auto remove_h_from_auto_links = [&](const Topo::Link& link) {
+      const ChemLink* cl = monlib.get_link(link.link_id);
+      if (cl && starts_with(cl->name, "auto-")) {
+        const Restraints::Bond& bond = cl->rt.bonds.at(0);
+        remove_hydrogens_from_atom(topo->find_resinfo(link.res1), bond.id1.atom, link.alt1);
+        remove_hydrogens_from_atom(topo->find_resinfo(link.res2), bond.id2.atom, link.alt2);
+      }
+    };
+    for (const Topo::ChainInfo& chain_info : topo->chain_infos)
+      for (const Topo::ResInfo& res_info : chain_info.res_infos)
+        for (const Topo::Link& link : res_info.prev)
+          remove_h_from_auto_links(link);
+    for (const Topo::Link& link : topo->extras)
+      remove_h_from_auto_links(link);
+  }
+
+  // fill Topo::bonds, angles, ... and ResInfo::monomer_rules, Links::link_rules
+  topo->apply_all_restraints(monlib);
+  // fill bond_index, angle_index, etc
+  topo->create_indices();
+
+  // the hydrogens added previously have positions not set
+  if (h_change != HydrogenChange::NoChange)
+    place_hydrogens_on_all_atoms(*topo);
+
+  if (h_change == HydrogenChange::ReAddKnown) {
+    // To leave only known hydrogens, we remove Hs with zero occupancy.
+    // As a side-effect, it removes any H atoms on zero-occupancy parents.
+    for (Chain& chain : model.chains)
+      for (Residue& res : chain.residues)
+        vector_remove_if(res.atoms, [](Atom& a) { return a.is_hydrogen() && a.occ == 0; });
+
+    // disable warnings here, so they are not printed twice
+    topo->logger.suspend();
+    // re-set restraints and indices
+    topo->apply_all_restraints(monlib);
+    topo->create_indices();
+    topo->logger.resume();
+  }
+
+  assign_serial_numbers(model);
+  return topo;
+}
+
+std::vector<AtomAddress> find_missing_atoms(const Topo& topo, bool including_hydrogen) {
+  std::vector<AtomAddress> ret;
+  for (const Topo::ChainInfo& chain_info : topo.chain_infos)
+    for (const Topo::ResInfo& ri : chain_info.res_infos) {
+      // check only the first conformation
+      const Topo::FinalChemComp& fcc = ri.chemcomps.at(0);
+      char altloc = fcc.altloc != '\0' ? fcc.altloc : '*';
+      for (const ChemComp::Atom& at : fcc.cc->atoms)
+        if ((including_hydrogen || !at.is_hydrogen()) &&
+            ri.res->find_atom(at.id, altloc) == nullptr)
+          ret.emplace_back(chain_info.chain_ref.name, *ri.res, at.id, fcc.altloc);
+    }
+  return ret;
+}
+
+}
diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 8d899bec1..eb04815f4 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -637,6 +637,12 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
     };
     ApplyPredictionRange(settings_prediction, experiment, latt);
     prediction_centring_ = settings_prediction.centering;
+    if (stills_window_ && !experiment.GetGoniometer().has_value()) {
+        settings_prediction.window_c0 = stills_window_->c0;
+        settings_prediction.window_ang = stills_window_->ang;
+        settings_prediction.window_bw = stills_window_->bw;
+        settings_prediction.window_q_scale = stills_window_->q_scale;
+    }
 
     // Online is bounded by what the image-buffer slot can carry, offline by the prediction limit; both
     // come from BraggPrediction so the cap, the prediction and the transport headroom cannot drift.
@@ -948,7 +954,7 @@ void IndexAndRefine::ScaleImage(DataMessage &msg, IntegrationOutcome& outcome) {
         return;
 
     auto scaling_start_time = std::chrono::steady_clock::now();
-    reindex_resolver->Resolve(outcome.reflections, outcome.latt);
+    outcome.reference_cc = reindex_resolver->Resolve(outcome.reflections, outcome.latt);
     auto scaling_end_time = std::chrono::steady_clock::now();
     msg.image_scale_time_s = std::chrono::duration<float>(scaling_end_time - scaling_start_time).count();
 }
diff --git a/image_analysis/IndexAndRefine.h b/image_analysis/IndexAndRefine.h
index 4ff2a5e01..5eaae7f43 100644
--- a/image_analysis/IndexAndRefine.h
+++ b/image_analysis/IndexAndRefine.h
@@ -90,6 +90,15 @@ struct FrameIndexerCalls {
     std::optional<IndexerResult> lattice_found;
 };
 
+// The half-width of a still's prediction window against resolution, sqrt(c0^2 + (ang d*)^2 + (bw |q_z|)^2)
+// (1/A, rad, relative), see IndexAndRefine::SetStillsWindow.
+struct StillsWindow {
+    float c0 = 0.0f;
+    float ang = 0.0f;
+    float bw = 0.0f;
+    float q_scale = 1.0f;   // centred on the excitation error of the reciprocal lattice scaled by this
+};
+
 class IndexAndRefine {
     // When false, the current image's result is still returned via the outgoing message, but the
     // whole-run integration_outcome vector is not retained (viewer live/interactive use, which never
@@ -144,6 +153,9 @@ class IndexAndRefine {
     // different error model (ISa 7.8 -> 3.6), post-refined the distance 119 um away, and the second
     // pass re-indexed 49 of 60 frames instead of 60.
     bool predict_all_centring_nodes_ = false;
+    // Stills: the excitation-error window every frame predicts through, as a curve in d* (see
+    // SetStillsWindow); empty, each frame predicts through twice its own profile radius.
+    std::optional<StillsWindow> stills_window_;
     // The lattice centring the last prediction actually ran in: 'P' unless a user-fixed space group
     // made it reject that group's centring absences. What a caller needs to know whether the
     // integration covers every node of the lattice - a P1 merge does.
@@ -223,6 +235,10 @@ public:
     void SetPredictionMosaicityOverride(std::vector<float> mosaicity_per_frame) {
         prediction_mosaicity_override_ = std::move(mosaicity_per_frame);
     }
+    // Stills: predict every frame through |dist_ewald| <= sqrt(c0^2 + (ang d*)^2 + (bw |q_z|)^2), a window
+    // that follows the run's rocking width, in place of twice the frame's own profile radius. Empty
+    // returns to the per-frame window.
+    void SetStillsWindow(std::optional<StillsWindow> w) { stills_window_ = w; }
     // Predict the centring-absent reflections too, even with a fixed space group - see the member.
     void PredictAllCentringNodes(bool on) { predict_all_centring_nodes_ = on; }
     // The centring prediction ran in - see the member.
diff --git a/image_analysis/IntegrationOutcome.h b/image_analysis/IntegrationOutcome.h
index a16f41957..2d1b37cc0 100644
--- a/image_analysis/IntegrationOutcome.h
+++ b/image_analysis/IntegrationOutcome.h
@@ -4,6 +4,7 @@
 #pragma once
 
 #include <algorithm>
+#include <vector>
 
 #include "../common/Reflection.h"
 #include "../common/CrystalLattice.h"
@@ -23,6 +24,9 @@ struct IntegrationOutcome {
     std::optional<int64_t> image_scale_cc_n;
     std::optional<float> image_scale_g;
     std::optional<float> image_scale_wedge_deg;
+    // Stills with a reference: the image's CC with it in each indexing it was offered, as indexed first
+    // (ReindexAmbiguityResolver::Resolve); empty otherwise.
+    std::vector<double> reference_cc;
 };
 
 // How far apart, in frames, two partials of one raw hkl may sit and still belong to the same rocking
diff --git a/image_analysis/MXAnalysisWithoutFPGA.cpp b/image_analysis/MXAnalysisWithoutFPGA.cpp
index e56230cd4..66976fc29 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.cpp
+++ b/image_analysis/MXAnalysisWithoutFPGA.cpp
@@ -535,8 +535,15 @@ void MXAnalysisWithoutFPGA::UpdateMaskResolution(const SpotFindingSettings &sett
 std::vector<Reflection> MXAnalysisWithoutFPGA::IntegrateOnImage(const std::vector<Reflection> &predicted,
                                                                 size_t npredicted, int64_t image_number) {
     const auto &modules = experiment.GetModules();
-    if (modules.empty())
-        return bragg_engine->Run(*preprocessor_buffer, predicted, npredicted, image_number);
+    const auto drop_shadow_clipped = [this](std::vector<Reflection> &reflections) {
+        DropShadowClipped(reflections, mask.GetMask(), static_cast<int>(experiment.GetXPixelsNumConv()),
+                          static_cast<int>(experiment.GetYPixelsNumConv()), experiment.GetBraggIntegrationSettings().GetR1());
+    };
+    if (modules.empty()) {
+        auto ret = bragg_engine->Run(*preprocessor_buffer, predicted, npredicted, image_number);
+        drop_shadow_clipped(ret);
+        return ret;
+    }
 
     // Predictions are where the reflections fall on the detector plane; the engine reads the image, so
     // each goes to where its panel put those pixels, and comes back to the plane once integrated. One in
@@ -557,6 +564,7 @@ std::vector<Reflection> MXAnalysisWithoutFPGA::IntegrateOnImage(const std::vecto
         on_image.push_back(r);
     }
     auto ret = bragg_engine->Run(*preprocessor_buffer, on_image, on_image.size(), image_number);
+    drop_shadow_clipped(ret);
     for (auto &r: ret) {
         const int64_t panel = modules.ModuleOfImagePixel(r.predicted_x, r.predicted_y);
         const auto [px, py] = modules.ImageToPlane(panel, r.predicted_x, r.predicted_y);
@@ -570,3 +578,26 @@ std::vector<Reflection> MXAnalysisWithoutFPGA::IntegrateOnImage(const std::vecto
     }
     return ret;
 }
+
+// A signal disk that lost pixels to the mask is otherwise kept, its profile fitted over the pixels that
+// remain. That holds for a gap or a dead pixel, which take nothing from their neighbours, but not for the
+// beam-stop shadow: the mask is drawn where the BACKGROUND is dimmed, and the Bragg signal's half-shadow
+// does not end where the background's does, so the rest of such a disk is attenuated too. Measured against
+// their symmetry mates, these observations came out 12-60 % low on the sweeps whose shadow edge crosses
+// busy low-resolution reflections (CCD and pixel detectors alike), and level with them elsewhere.
+void DropShadowClipped(std::vector<Reflection> &reflections, const std::vector<uint32_t> &mask,
+                       int W, int H, float r1) {
+    std::erase_if(reflections, [&](const Reflection &r) {
+        const int x0 = std::max(0, static_cast<int>(std::floor(r.predicted_x - r1)));
+        const int x1 = std::min(W - 1, static_cast<int>(std::ceil(r.predicted_x + r1)));
+        const int y0 = std::max(0, static_cast<int>(std::floor(r.predicted_y - r1)));
+        const int y1 = std::min(H - 1, static_cast<int>(std::ceil(r.predicted_y + r1)));
+        for (int y = y0; y <= y1; y++)
+            for (int x = x0; x <= x1; x++) {
+                const float dx = static_cast<float>(x) - r.predicted_x, dy = static_cast<float>(y) - r.predicted_y;
+                if (dx * dx + dy * dy < r1 * r1 && (mask[static_cast<size_t>(y) * W + x] & (1u << PixelMask::BeamStopPixelBit)))
+                    return true;
+            }
+        return false;
+    });
+}
diff --git a/image_analysis/MXAnalysisWithoutFPGA.h b/image_analysis/MXAnalysisWithoutFPGA.h
index 3d3b6e802..27cdff2e5 100644
--- a/image_analysis/MXAnalysisWithoutFPGA.h
+++ b/image_analysis/MXAnalysisWithoutFPGA.h
@@ -26,6 +26,12 @@
 class CudaStream;
 class AdaptiveSpotFinderGPU;
 
+// Leave out the reflections whose signal disk - radius r1 about the predicted position, in image
+// coordinates - reaches a pixel of the beam-stop shadow (PixelMask::BeamStopPixelBit of `mask`, a
+// width x height image).
+void DropShadowClipped(std::vector<Reflection> &reflections, const std::vector<uint32_t> &mask,
+                       int width, int height, float r1);
+
 // MXAnalysisWithoutFPGA is not thread safe - it has to owned by a single thread
 class MXAnalysisWithoutFPGA {
     const DiffractionExperiment &experiment;
diff --git a/image_analysis/WriteReflections.cpp b/image_analysis/WriteReflections.cpp
index fdfa111a8..3383f3c3f 100644
--- a/image_analysis/WriteReflections.cpp
+++ b/image_analysis/WriteReflections.cpp
@@ -2,6 +2,7 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include "WriteReflections.h"
+#include "geom_refinement/CellEsd.h"
 #include "scale_merge/Merge.h"
 #include "scale_merge/HKLKey.h"
 #include "scale_merge/TwinningAnalysis.h"
@@ -19,6 +20,7 @@
 #include <map>
 #include <memory>
 #include <tuple>
+#include <filesystem>
 #include <fstream>
 #include <iomanip>
 #include <sstream>
@@ -155,18 +157,38 @@ void AddProvenanceHistory(std::vector<std::string> &history, const OutputProvena
     add("Collected: ", provenance.collection_date);
 }
 
-// _entry, _cell and _symmetry.
+// An e.s.d. as written: "." for a parameter the symmetry fixes (its e.s.d. is zero), as SHELX's ZERR
+// writes 0 for it.
+std::string EsdStr(double esd, int decimals) {
+    return esd < CELL_ESD_FIXED ? std::string(".") : Fmt(esd, decimals);
+}
+
+// _entry, _cell (with the e.s.d.s where there are any, and the _cell_measurement they came from) and
+// _symmetry.
 void WriteBlockHeader(std::ostream &out, const std::string &entry_id, const UnitCell &unitCell,
-                      const gemmi::SpaceGroup &sg) {
+                      const gemmi::SpaceGroup &sg, const CellEsd *esd = nullptr) {
     out << "_entry.id   " << entry_id << "\n";
     out << "#\n";
     out << "_cell.entry_id     " << entry_id << "\n";
-    out << "_cell.length_a     " << Fmt(unitCell.a, 3) << "\n";
-    out << "_cell.length_b     " << Fmt(unitCell.b, 3) << "\n";
-    out << "_cell.length_c     " << Fmt(unitCell.c, 3) << "\n";
-    out << "_cell.angle_alpha  " << Fmt(unitCell.alpha, 2) << "\n";
-    out << "_cell.angle_beta   " << Fmt(unitCell.beta, 2) << "\n";
-    out << "_cell.angle_gamma  " << Fmt(unitCell.gamma, 2) << "\n";
+    out << "_cell.length_a     " << Fmt(unitCell.a, 4) << "\n";
+    out << "_cell.length_b     " << Fmt(unitCell.b, 4) << "\n";
+    out << "_cell.length_c     " << Fmt(unitCell.c, 4) << "\n";
+    out << "_cell.angle_alpha  " << Fmt(unitCell.alpha, 3) << "\n";
+    out << "_cell.angle_beta   " << Fmt(unitCell.beta, 3) << "\n";
+    out << "_cell.angle_gamma  " << Fmt(unitCell.gamma, 3) << "\n";
+    if (esd) {
+        out << "_cell.length_a_esd     " << EsdStr(esd->esd[0], 5) << "\n";
+        out << "_cell.length_b_esd     " << EsdStr(esd->esd[1], 5) << "\n";
+        out << "_cell.length_c_esd     " << EsdStr(esd->esd[2], 5) << "\n";
+        out << "_cell.angle_alpha_esd  " << EsdStr(esd->esd[3], 4) << "\n";
+        out << "_cell.angle_beta_esd   " << EsdStr(esd->esd[4], 4) << "\n";
+        out << "_cell.angle_gamma_esd  " << EsdStr(esd->esd[5], 4) << "\n";
+        out << "#\n";
+        out << "_cell_measurement.entry_id     " << entry_id << "\n";
+        out << "_cell_measurement.reflns_used  " << esd->reflections << "\n";
+        out << "_cell_measurement.theta_min    " << Fmt(esd->theta_min_deg, 2) << "\n";
+        out << "_cell_measurement.theta_max    " << Fmt(esd->theta_max_deg, 2) << "\n";
+    }
     out << "#\n";
     out << "_symmetry.entry_id               " << entry_id << "\n";
     out << "_symmetry.space_group_name_H-M  " << CifStr(sg.hm) << "\n";
@@ -270,7 +292,8 @@ void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
                            const TwinningAnalysisResult &twinning,
                            const OutputProvenance &provenance,
                            const std::string &filename,
-                           size_t nthreads) {
+                           size_t nthreads,
+                           const CellEsd *cell_esd) {
 
     std::ofstream out(filename);
     if (!out)
@@ -287,7 +310,7 @@ void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
     // ---------- data block ----------
     out << "data_sample" << "\n";
     out << "#\n";
-    WriteBlockHeader(out, entry_id, unitCell, sg);
+    WriteBlockHeader(out, entry_id, unitCell, sg, cell_esd);
 
     // ---------- _audit ----------
     out << "_audit.revision_id     1\n";
@@ -774,6 +797,63 @@ void WriteShelxHklReflections(const std::vector<ScaledFull> &fulls,
     });
 }
 
+void WriteShelxIns(const UnitCell &cell, const CellEsd *esd, const DiffractionExperiment &experiment,
+                   const std::string &title, const std::string &filename) {
+    const gemmi::SpaceGroup &sg = experiment.GetSpaceGroupOrP1();
+    const gemmi::GroupOps ops = sg.operations();
+    // LATT is the centring, positive where the group holds an inversion centre at the origin, which
+    // SHELX then generates itself - so only one of each -1 pair is listed (the proper rotations). A
+    // centring SHELX has no code for gets LATT -1 with every operator spelled out.
+    const std::string centrings = "PIRFABC";
+    const char centring = ops.find_centering();
+    const size_t latt_code = centring ? centrings.find(centring) : std::string::npos;
+    bool origin_inversion = false;
+    if (const gemmi::Op *inv = ops.find_by_rotation(gemmi::Op::inversion_rot()))
+        for (const auto &t : ops.cen_ops)
+            origin_inversion |= inv->tran == t;
+    const bool centro = latt_code != std::string::npos && origin_inversion;
+    int latt = latt_code != std::string::npos ? static_cast<int>(latt_code) + 1 : 1;
+    std::vector<gemmi::Op> symm;
+    for (const auto &op : latt_code != std::string::npos ? ops.sym_ops : ops.all_ops_sorted())
+        if (!(op == gemmi::Op::identity()) && !(centro && op.det_rot() < 0))
+            symm.push_back(op);
+
+    // SFAC and UNIT have to be the formula, which the diffraction does not tell: an organic one is put
+    // in its place at 18 A^3 per non-hydrogen atom, for the user to replace.
+    const int nonh = std::max(1, static_cast<int>(std::lround(gemmi::UnitCell(cell).volume / 18.0)));
+    const int n_c = std::max(1, static_cast<int>(std::lround(0.7 * nonh)));
+    const int n_n = std::max(1, static_cast<int>(std::lround(0.15 * nonh)));
+    const int n_o = std::max(1, nonh - n_c - n_n);
+
+    std::ofstream out(filename);
+    if (!out)
+        throw std::runtime_error("WriteShelxIns: cannot open " + filename);
+    char line[256];
+    out << "TITL " << title << " in " << sg.xhm() << "\n";
+    out << "REM Rugnux " << jfjoch_version() << ": CELL and ZERR from the data, SFAC/UNIT a placeholder"
+           " to replace with the formula\n";
+    std::snprintf(line, sizeof(line), "CELL %.5f %.5f %.5f %.5f %.4f %.4f %.4f\n", experiment.GetWavelength_A(),
+                  cell.a, cell.b, cell.c, cell.alpha, cell.beta, cell.gamma);
+    out << line;
+    // ZERR's first number is Z, the formula units in the cell: one per general position is assumed.
+    if (esd) {
+        std::snprintf(line, sizeof(line), "ZERR %d %.5f %.5f %.5f %.4f %.4f %.4f\n", ops.order(), esd->esd[0],
+                      esd->esd[1], esd->esd[2], esd->esd[3], esd->esd[4], esd->esd[5]);
+        out << line;
+    }
+    out << "LATT " << (centro ? latt : -latt) << "\n";
+    for (const auto &op : symm) {
+        std::string t = op.triplet();
+        for (auto &ch : t)
+            ch = static_cast<char>(std::toupper(static_cast<unsigned char>(ch)));
+        out << "SYMM " << t << "\n";
+    }
+    out << "SFAC C H N O\n";
+    out << "UNIT " << n_c << " " << n_c << " " << n_n << " " << n_o << "\n";
+    out << "HKLF 4\n";
+    out << "END\n";
+}
+
 namespace {
 
 // The detector position an observation is written at: a reflection too weak to have a measured
@@ -1233,4 +1313,6 @@ void WriteReflections(const std::vector<MergedReflection> &reflections,
         WriteShelxHklReflections(*scaled_fulls, filename + ".hkl", nthreads);
     else
         WriteShelxHklReflections(reflections, experiment, filename + ".hkl", nthreads);
+    WriteShelxIns(unitCell, nullptr, experiment, std::filesystem::path(filename).filename().string(),
+                  filename + ".ins");
 }
diff --git a/image_analysis/WriteReflections.h b/image_analysis/WriteReflections.h
index 1d9053fd8..b48b05018 100644
--- a/image_analysis/WriteReflections.h
+++ b/image_analysis/WriteReflections.h
@@ -14,6 +14,7 @@
 
 struct MergeStatistics;
 struct TwinningAnalysisResult;
+struct CellEsd;   // geom_refinement/CellEsd.h
 
 // The error model as it is reported, already formatted. `isa` is the whole-range 1/sqrt(a*b), the
 // same quantity XDS's ISa denotes, so a file written here is directly comparable with a CORRECT.LP;
@@ -36,8 +37,12 @@ struct OutputProvenance {
     std::string collection_date;   // as the input states it (NXmx /entry/start_time), ISO-8601
 };
 
+// An e.s.d. below this is a parameter the symmetry fixes: written "." in the mmCIF.
+constexpr double CELL_ESD_FIXED = 1e-9;
+
 // The merged reflections, their statistics and the experiment, as one PDBx/mmCIF data block.
 // nthreads: workers for the per-reflection row formatting, which is the bulk of the file.
+// cell_esd: the cell's e.s.d.s (_cell.*_esd, _cell_measurement), where there are any.
 void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
                            const UnitCell &unitCell,
                            const DiffractionExperiment &experiment,
@@ -46,7 +51,8 @@ void WriteMmcifReflections(const std::vector<MergedReflection> &reflections,
                            const TwinningAnalysisResult &twinning,
                            const OutputProvenance &provenance,
                            const std::string &filename,
-                           size_t nthreads);
+                           size_t nthreads,
+                           const CellEsd *cell_esd = nullptr);
 
 // The merged MTZ: H K L IMEAN SIGIMEAN [I(+) SIGI(+) I(-) SIGI(-)] F SIGF [F(+) SIGF(+) F(-) SIGF(-)]
 // FreeR_flag, one row per unique reflection in the CCP4 anomalous layout, the bracketed columns only where
@@ -75,6 +81,12 @@ void WriteShelxHklReflections(const std::vector<ScaledFull> &fulls,
                               const std::string &filename,
                               size_t nthreads);
 
+// The SHELX instruction file to go with the .hkl: TITL, CELL (at the wavelength), ZERR where the
+// e.s.d.s are known, LATT, SYMM, a placeholder SFAC/UNIT, HKLF 4, END - what SHELXT reads, and what
+// SHELXL's CIF takes the cell and its e.s.d.s from.
+void WriteShelxIns(const UnitCell &cell, const CellEsd *esd, const DiffractionExperiment &experiment,
+                   const std::string &title, const std::string &filename);
+
 // Unmerged observations in the column and batch-header layout POINTLESS writes: aimless, pointless,
 // careless and iotbx.merging_statistics all read that layout. H K L are the ASU indices and M/ISYM
 // recovers the index the reflection was measured at (which is what careless needs to see the crystal
diff --git a/image_analysis/beam_stop/SHADOW_FINDER.md b/image_analysis/beam_stop/SHADOW_FINDER.md
index 2f15a418d..0406eb6c3 100644
--- a/image_analysis/beam_stop/SHADOW_FINDER.md
+++ b/image_analysis/beam_stop/SHADOW_FINDER.md
@@ -206,15 +206,18 @@ beam-stop mask is an **offline** (Rugnux + viewer) feature and never goes to the
   than it went in - on one stills run the outer rings carried dim lobes over the detector's corners,
   sitting on the arm search's thresholds, so that the third decimal of the stated degree moved
   thousands of pixels in and out of the mask. So before the correction the mean projection is
+  pooled over 9 x 9 pixels (a sparse background otherwise leaves the sector medians at zero) and
   compared ring by ring with the profile a polarized source gives each 64 px band (each ring relative
   to its upper decile, each sector the brighter of itself and the one opposite, since a shadow is
   rarely on both sides; a band counted where three quarters of the azimuth are seen). The stated
   degree is applied in the plane the background follows when it follows one clearly - a correlation
-  above 0.5 and at least 0.3 of a fully polarized source's modulation - and as stated otherwise. Over
+  above 0.5 and at least 0.3 of a fully polarized source's modulation, but under twice it, which no
+  polarized source gives (a long-distance sweep's background carries such a harmonic from something
+  else) - and as stated otherwise. Over
   the rotation and stills corpora only the run whose plane lies along the image's y axis is turned; on
   every other run the correction, and so the mask, is what it was. An experiment that states no
   polarization is left uncorrected, as before. What was applied is read back with
-  `GetAppliedPolarization()`, and `rugnux`'s pre-scan writes it into the experiment, so the
+  `GetAppliedPolarization()` (and the correlation and scale it was decided on with `GetPlaneEvidence()`), and `rugnux`'s pre-scan writes it into the experiment, so the
   integration's correction follows the same plane: the plane is decided once, here.
 - **Unsigned saturation**: for unsigned images a detector-saturating reflection collides with the
   no-data sentinel and is skipped; harmless in practice (such reflections do not sit under the
diff --git a/image_analysis/beam_stop/ShadowFinder.cpp b/image_analysis/beam_stop/ShadowFinder.cpp
index 1081eb1bd..dd681d1b1 100644
--- a/image_analysis/beam_stop/ShadowFinder.cpp
+++ b/image_analysis/beam_stop/ShadowFinder.cpp
@@ -400,7 +400,7 @@ RingValues bin_by_ring(const Plane<float> &values, const Plane<char> &valid,
     return rv;
 }
 
-// The plane the background shows (PolarizationPlane): +1, -1, or 0 where it does not show one.
+// The plane the background shows, and what it is decided on (PolarizationPlane).
 // The degree of polarization cannot be told from the data, but the plane can, and it is not always the
 // one the experiment assumes - a detector mounted a quarter turn from another on the same kind of
 // beamline puts the suppressed direction along the image's other axis. Divided by the factor of the
@@ -408,8 +408,8 @@ RingValues bin_by_ring(const Plane<float> &values, const Plane<char> &valid,
 // then carried dim lobes over the detector's corners that sat on the arm search's thresholds, so that
 // the third decimal of p moved thousands of pixels in and out of the mask.
 // `mean` is the mean projection (W x H, NaN where unusable), compared ring by ring about the centre.
-float measured_plane(const std::vector<float> &mean, int W, int H, float centre_x, float centre_y,
-                     const float *det_matrix, float distance_px, size_t nthreads) {
+PlaneEvidence measured_plane(const std::vector<float> &mean, int W, int H, float centre_x, float centre_y,
+                             const float *det_matrix, float distance_px, size_t nthreads) {
     const int n_pixels = W * H;
     Plane<float> value(n_pixels);
     Plane<char> valid(n_pixels);
@@ -432,6 +432,23 @@ float measured_plane(const std::vector<float> &mean, int W, int H, float centre_
     const int max_radius = max_radius_atomic.load();
     const int n_bands = max_radius / HARMONIC_BAND_PX + 1;
 
+    // Pooled over a small box first, as the mask is (GetMask): a background of a fraction of a count per
+    // pixel per frame leaves most single pixels at zero over the frames read, and the sector medians below
+    // were then zero too, so that on a large photon-counting detector the plane could not be decided at all.
+    {
+        Plane<double> num(n_pixels);
+        Plane<int32_t> den(n_pixels);
+        for (int i = 0; i < n_pixels; i++) {
+            num[i] = valid[i] ? value[i] : 0.0;
+            den[i] = valid[i] ? 1 : 0;
+        }
+        const auto pooled_sum = box_sum(num, W, H, PLANE_POOL_PX, nthreads);
+        const auto pooled_count = box_sum(den, W, H, PLANE_POOL_PX, nthreads);
+        for (int i = 0; i < n_pixels; i++)
+            if (valid[i])
+                value[i] = static_cast<float>(pooled_sum[i] / pooled_count[i]);
+    }
+
     // Each ring is taken relative to its upper decile rather than its median: where a shadow covers
     // half of a ring the median sits on the shadow's edge and jumps from ring to ring.
     const RingValues rings = bin_by_ring(value, valid, radius, max_radius, nthreads);
@@ -713,6 +730,11 @@ std::optional<float> ShadowFinder::GetAppliedPolarization() const {
     return applied_polarization;
 }
 
+std::optional<shadow_finder::PlaneEvidence> ShadowFinder::GetPlaneEvidence() const {
+    std::unique_lock ul(m);
+    return plane_evidence;
+}
+
 std::vector<float> ShadowFinder::GetMeanProjection() const {
     std::unique_lock ul(m);
 #ifdef JFJOCH_USE_CUDA
@@ -739,6 +761,7 @@ std::vector<uint32_t> ShadowFinder::GetMask(size_t nthreads) const {
     if (nthreads == 0)
         nthreads = AvailableCpus();
     applied_polarization.reset();
+    plane_evidence.reset();
 #ifdef JFJOCH_USE_CUDA
     // Where every frame went to the device the mask is made there too, from the projection as it lies -
     // when it lies as the detector does (no panel table).
@@ -761,10 +784,9 @@ std::vector<uint32_t> ShadowFinder::GetMask(size_t nthreads) const {
         setup.gain = gain;
         setup.has_polarization = polarization.has_value();
         if (polarization) {
-            setup.polarization = PlaneApplied(*polarization,
-                                              measured_plane(gpu->MeanProjection(pixel_mask), width, height, beam_x,
-                                                             beam_y, setup.det_matrix,
-                                                             setup.distance_mm / setup.pixel_size_mm, nthreads));
+            plane_evidence = measured_plane(gpu->MeanProjection(pixel_mask), width, height, beam_x, beam_y,
+                                            setup.det_matrix, setup.distance_mm / setup.pixel_size_mm, nthreads);
+            setup.polarization = PlaneApplied(*polarization, plane_evidence->plane);
             applied_polarization = setup.polarization;
         }
         return gpu->Mask(setup, pixel_mask);
@@ -833,8 +855,9 @@ std::vector<uint32_t> ShadowFinder::MaskOn(const Projection &p, const std::vecto
                 projection[i] = valid_count[i] > 0 && known_mask[i] == 0
                                     ? static_cast<float>(static_cast<double>(sum_value[i]) / valid_count[i]) : NAN;
         });
-        polarization_applied = PlaneApplied(*polarization, measured_plane(projection, W, H, centre_x, centre_y,
-                                                                          det_matrix.data(), distance_px, nthreads));
+        plane_evidence = measured_plane(projection, W, H, centre_x, centre_y, det_matrix.data(), distance_px,
+                                        nthreads);
+        polarization_applied = PlaneApplied(*polarization, plane_evidence->plane);
         applied_polarization = polarization_applied;
     }
 
@@ -1255,7 +1278,7 @@ void HarmonicFit(const std::vector<double> &sector_median, int n_bands,
     }
 }
 
-float PolarizationPlane(const std::vector<double> &sector_median, const std::vector<float> &amplitude) {
+PlaneEvidence PolarizationPlane(const std::vector<double> &sector_median, const std::vector<float> &amplitude) {
     const int n_bands = static_cast<int>(amplitude.size());
     // The modulation is the same at phi and at phi + 180 deg; what shadows the detector rarely is - an
     // arm, a pin or a goniometer stands on one side of the beam - and shadows only darken. So each
@@ -1278,9 +1301,10 @@ float PolarizationPlane(const std::vector<double> &sector_median, const std::vec
     // A horizontally polarized source makes the background dim along lab x, c < 0, by more where the
     // modulation it can give is larger; a vertically polarized one makes it dim along lab y, c > 0. A
     // plane is taken only where the bands' harmonics follow its profile (PLANE_CORRELATION) and amount
-    // to a good part of what a fully polarized source gives (PLANE_MODULATION): a background with
-    // little modulation of its own decides nothing. With no modulation at all both are NaN, which
-    // decides nothing too.
+    // to a good part of what a fully polarized source gives (PLANE_MODULATION) without exceeding what any
+    // source can give (PLANE_MODULATION_MAX): a background with little modulation of its own decides
+    // nothing, and neither does one modulated by something else. With no modulation at all both are NaN,
+    // which decides nothing too.
     double ca = 0.0, cc = 0.0, aa = 0.0;
     for (int band = 0; band < n_bands; band++) {
         if (!seen_enough[band])
@@ -1289,13 +1313,16 @@ float PolarizationPlane(const std::vector<double> &sector_median, const std::vec
         cc += c[band] * c[band];
         aa += amplitude[band] * amplitude[band];
     }
-    const double correlation = ca / std::sqrt(cc * aa);
-    const double modulation = ca / aa;
-    if (correlation > PLANE_CORRELATION && modulation > PLANE_MODULATION)
-        return -1.0f;
-    if (correlation < -PLANE_CORRELATION && modulation < -PLANE_MODULATION)
-        return 1.0f;
-    return 0.0f;
+    PlaneEvidence evidence;
+    evidence.correlation = ca / std::sqrt(cc * aa);
+    evidence.modulation = ca / aa;
+    if (std::fabs(evidence.modulation) < PLANE_MODULATION_MAX) {
+        if (evidence.correlation > PLANE_CORRELATION && evidence.modulation > PLANE_MODULATION)
+            evidence.plane = -1.0f;
+        if (evidence.correlation < -PLANE_CORRELATION && evidence.modulation < -PLANE_MODULATION)
+            evidence.plane = 1.0f;
+    }
+    return evidence;
 }
 
 }   // namespace shadow_finder
diff --git a/image_analysis/beam_stop/ShadowFinder.h b/image_analysis/beam_stop/ShadowFinder.h
index 168c7087b..43e871491 100644
--- a/image_analysis/beam_stop/ShadowFinder.h
+++ b/image_analysis/beam_stop/ShadowFinder.h
@@ -16,6 +16,7 @@
 #include "../../common/DiffractionGeometry.h"
 #include "../../common/JFJochMessages.h"
 #include "../../common/PixelMask.h"
+#include "ShadowFinderInternal.h"
 #ifdef JFJOCH_USE_CUDA
 #include "ShadowAccumulatorGPU.h"
 #endif
@@ -63,6 +64,7 @@ class ShadowFinder {
     const std::optional<float> polarization;   // unset leaves the background as it was measured
     // What the last GetMask divided by: the stated degree, in the plane the background shows.
     mutable std::optional<float> applied_polarization;
+    mutable std::optional<shadow_finder::PlaneEvidence> plane_evidence;   // what that plane was decided on
     // Detector units per photon (BraggIntegrationSettings::PixelGain; 1 for counted photons). The
     // shadow is a ratio and does not see it, but the two tests made in counts do: how significant a
     // deficit is, and the count a pixel must reach to have recorded a reflection.
@@ -166,6 +168,8 @@ public:
     // background shows where it shows one clearly, and as stated otherwise. The run's other corrections
     // take it from here, so that the plane is decided once. Unset with no stated degree, or before GetMask.
     [[nodiscard]] std::optional<float> GetAppliedPolarization() const;
+    // What the last GetMask decided the plane on. Unset where GetAppliedPolarization is.
+    [[nodiscard]] std::optional<shadow_finder::PlaneEvidence> GetPlaneEvidence() const;
 
     // Mean counts per pixel over the frames added, NAN where nothing was counted. This is the
     // projection GetMask() tests, so anything else that wants the background before indexing
diff --git a/image_analysis/beam_stop/ShadowFinderInternal.h b/image_analysis/beam_stop/ShadowFinderInternal.h
index 47036e335..7295f4813 100644
--- a/image_analysis/beam_stop/ShadowFinderInternal.h
+++ b/image_analysis/beam_stop/ShadowFinderInternal.h
@@ -125,19 +125,34 @@ void HarmonicFit(const std::vector<double> &sector_median, int n_bands,
 // How closely, over the radial bands, the background's cos 2phi harmonic must follow the profile a
 // polarized source gives it (the correlation), and how large it must be against the profile of a fully
 // polarized source (the least-squares scale), before the plane is taken from the background rather
-// than as stated. On 46 rotation sweeps and 11 stills runs whose plane is horizontal, the largest values
-// towards the vertical plane are 0.48 and 0.18, the latter on a background with almost no modulation;
-// on a stills run whose plane lies along the image's y axis they are 0.998 and 0.47 - the scale reduced
-// there by the placeholder distance the pre-scan reads it at.
+// than as stated. Of 244 synchrotron rotation sweeps, all polarized horizontally, 216 show that plane
+// past both; apart from the one under PLANE_MODULATION_MAX the largest values towards the vertical plane
+// are 0.01 and 0.002, and on 11 sweeps from laboratory sources 0.43 and 0.14. On a stills run whose
+// plane lies along the image's y axis they are 0.998 and 0.47 - the scale reduced there by the
+// placeholder distance the pre-scan reads it at.
 inline constexpr double PLANE_CORRELATION = 0.5;
 inline constexpr double PLANE_MODULATION = 0.3;
+// No polarized source modulates the background by more than a fully polarized one does (a scale of 1). A
+// harmonic of twice that or more is not the source's: at a long distance, where polarization can move
+// the background by a few per cent at most, a sweep's background carried ten per cent along image y
+// (scale 2.9, correlation 0.66) on a horizontally polarized beamline. It decides nothing.
+inline constexpr double PLANE_MODULATION_MAX = 2.0;
+// The box the background is pooled over before the plane is measured, in pixels: the modulation changes
+// over hundreds of pixels, and pooling is what gives a sparse background a median that is not zero.
+inline constexpr int PLANE_POOL_PX = 9;
 
-// The plane the source is polarized in, as the background shows it: +1 for the plane containing lab x
-// (a horizontally polarized source), -1 for the plane turned by 90 degrees, 0 where the background does
-// not show one clearly. `sector_median` is laid
-// out as for HarmonicFit, each band's background relative to its rings; `amplitude[band]` is the
-// relative modulation a fully polarized source gives the band, sin^2 2theta / (1 + cos^2 2theta). See
-// GetMask.
-float PolarizationPlane(const std::vector<double> &sector_median, const std::vector<float> &amplitude);
+// The plane the source is polarized in, as the background shows it, and the two numbers it is decided on.
+struct PlaneEvidence {
+    float plane = 0.0f;        // +1 for the plane containing lab x (a horizontally polarized source), -1 for
+                               // the plane turned by 90 degrees, 0 where the background does not show one clearly
+    double correlation = NAN;  // of the bands' cos 2phi harmonic with a polarized source's profile
+    double modulation = NAN;   // the harmonic against a fully polarized source's (least-squares scale)
+                               // both positive towards the turned plane, negative towards lab x
+};
+
+// `sector_median` is laid out as for HarmonicFit, each band's background relative to its rings;
+// `amplitude[band]` is the relative modulation a fully polarized source gives the band,
+// sin^2 2theta / (1 + cos^2 2theta). See GetMask.
+PlaneEvidence PolarizationPlane(const std::vector<double> &sector_median, const std::vector<float> &amplitude);
 
 }   // namespace shadow_finder
diff --git a/image_analysis/bragg_prediction/BraggPrediction.cpp b/image_analysis/bragg_prediction/BraggPrediction.cpp
index a5aa7b7c5..e6f2d230a 100644
--- a/image_analysis/bragg_prediction/BraggPrediction.cpp
+++ b/image_analysis/bragg_prediction/BraggPrediction.cpp
@@ -154,8 +154,17 @@ int BraggPrediction::Calc(const DiffractionExperiment &experiment, const Crystal
                     const float bw_tol = kBandwidthCutoffSigmas * settings.bandwidth_sigma * std::fabs(recip_z);
                     radial_cutoff = std::sqrt(radial_cutoff * radial_cutoff + bw_tol * bw_tol);
                 }
+                float window_dist = dist_ewald_sphere;
+                if (settings.window_c0 > 0.0f || settings.window_ang > 0.0f || settings.window_bw > 0.0f) {
+                    const float wb = settings.window_bw * std::fabs(recip_z);
+                    radial_cutoff = std::sqrt(settings.window_c0 * settings.window_c0
+                                              + settings.window_ang * settings.window_ang * recip_sq + wb * wb);
+                    const float sc = settings.window_q_scale;
+                    const float Sc_x = sc * recip_x + S0.x, Sc_y = sc * recip_y + S0.y, Sc_z = sc * recip_z + S0.z;
+                    window_dist = std::fabs(std::sqrt(Sc_x * Sc_x + Sc_y * Sc_y + Sc_z * Sc_z) - one_over_wavelength);
+                }
 
-                if (dist_ewald_sphere <= radial_cutoff ) {
+                if (window_dist <= radial_cutoff) {
                     const float s0_p0 = S0.x * recip_x + S0.y * recip_y + S0.z * recip_z;
                     const float val = s0_sq * recip_sq - s0_p0 * s0_p0;
 
diff --git a/image_analysis/bragg_prediction/BraggPrediction.h b/image_analysis/bragg_prediction/BraggPrediction.h
index 2248e716c..f93ab8ef6 100644
--- a/image_analysis/bragg_prediction/BraggPrediction.h
+++ b/image_analysis/bragg_prediction/BraggPrediction.h
@@ -35,6 +35,16 @@ struct BraggPredictionSettings {
     // already the one the partiality applies to σ_M. CalcMosaicityXDS deconvolves the same term
     // out of the fitted σ_M, so it is not counted twice.
     float bandwidth_sigma = 0.0f;
+    // Stills: an excitation-error window that follows the rocking width against resolution,
+    // |dist_ewald| <= sqrt(window_c0^2 + (window_ang d*)^2 + (window_bw |q_z|)^2) (1/A, rad, relative). When
+    // any of the three is set it replaces ewald_dist_cutoff and the bandwidth term above; all zero leaves
+    // the prediction as it was.
+    float window_c0 = 0.0f;
+    float window_ang = 0.0f;
+    float window_bw = 0.0f;
+    // The window is centred where the rocking curve is: on the excitation error of the reciprocal lattice
+    // scaled by this (StillsPartialityRefine::MeasureRadialScale). dist_ewald stays the lattice's own.
+    float window_q_scale = 1.0f;
 };
 
 class BraggPrediction {
diff --git a/image_analysis/bragg_prediction/BraggPredictionGPU.cu b/image_analysis/bragg_prediction/BraggPredictionGPU.cu
index 09477cdbf..36871330b 100644
--- a/image_analysis/bragg_prediction/BraggPredictionGPU.cu
+++ b/image_analysis/bragg_prediction/BraggPredictionGPU.cu
@@ -114,7 +114,15 @@ namespace {
             const float bw_tol = kBandwidthCutoffSigmas * C.bandwidth_sigma * fabsf(recip_z);
             radial_cutoff = sqrtf(radial_cutoff * radial_cutoff + bw_tol * bw_tol);
         }
-        if (dist_ewald > radial_cutoff) return false;
+        float window_dist = dist_ewald;
+        if (C.window_c0 > 0.0f || C.window_ang > 0.0f || C.window_bw > 0.0f) {
+            const float wb = C.window_bw * fabsf(recip_z);
+            radial_cutoff = sqrtf(C.window_c0 * C.window_c0 + C.window_ang * C.window_ang * recip_sq + wb * wb);
+            const float sc = C.window_q_scale;
+            const float Scx = sc * recip_x + C.S0.x, Scy = sc * recip_y + C.S0.y, Scz = sc * recip_z + C.S0.z;
+            window_dist = fabsf(sqrtf(Scx * Scx + Scy * Scy + Scz * Scz) - C.one_over_wavelength);
+        }
+        if (window_dist > radial_cutoff) return false;
         float Srx = C.rot[0] * Sx + C.rot[1] * Sy + C.rot[2] * Sz;
         float Sry = C.rot[3] * Sx + C.rot[4] * Sy + C.rot[5] * Sz;
         float Srz = C.rot[6] * Sx + C.rot[7] * Sy + C.rot[8] * Sz;
@@ -241,6 +249,10 @@ int BraggPredictionGPU::Calc(const DiffractionExperiment &experiment,
     // Build constants on host
     KernelConsts hK = BuildKernelConsts(experiment, lattice, settings.high_res_A, settings.ewald_dist_cutoff,
                                         settings.centering, settings.bandwidth_sigma);
+    hK.window_c0 = settings.window_c0;
+    hK.window_ang = settings.window_ang;
+    hK.window_bw = settings.window_bw;
+    hK.window_q_scale = settings.window_q_scale;
     cudaMemcpyAsync(dK, &hK, sizeof(KernelConsts), cudaMemcpyHostToDevice, stream);
     cudaMemsetAsync(d_count, 0, sizeof(int), stream);
 
diff --git a/image_analysis/bragg_prediction/BraggPredictionGPU.h b/image_analysis/bragg_prediction/BraggPredictionGPU.h
index 5d75cf4e9..427b8d043 100644
--- a/image_analysis/bragg_prediction/BraggPredictionGPU.h
+++ b/image_analysis/bragg_prediction/BraggPredictionGPU.h
@@ -17,6 +17,7 @@ struct KernelConsts {
     float one_over_wavelength;
     float one_over_dmax_sq;
     float ewald_cutoff;
+    float window_c0, window_ang, window_bw, window_q_scale;   // the stills window curve; all zero: ewald_cutoff (see BraggPredictionSettings)
     float bandwidth_sigma;   // relative Δλ/λ (sigma); 0 = monochromatic
     // Angle-dependent sensor efficiency, reduced to the two per-dataset numbers the kernel needs:
     // the optical thickness at normal incidence and the absorbed fraction there. qe_a0 = 0 leaves
diff --git a/image_analysis/geom_refinement/CMakeLists.txt b/image_analysis/geom_refinement/CMakeLists.txt
index c655cf25f..397034851 100644
--- a/image_analysis/geom_refinement/CMakeLists.txt
+++ b/image_analysis/geom_refinement/CMakeLists.txt
@@ -34,6 +34,8 @@ ADD_LIBRARY(JFJochGeomRefinement STATIC
         GeometryRefiner.h
         LatticeReduction.cpp
         LatticeReduction.h
+        CellEsd.cpp
+        CellEsd.h
 )
 
 # fftw3f: BeamCenterFFT scores every candidate centre with one transform set (always fetched,
diff --git a/image_analysis/geom_refinement/CellEsd.cpp b/image_analysis/geom_refinement/CellEsd.cpp
new file mode 100644
index 000000000..1c7924d9b
--- /dev/null
+++ b/image_analysis/geom_refinement/CellEsd.cpp
@@ -0,0 +1,259 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "CellEsd.h"
+
+#include <algorithm>
+#include <cmath>
+
+#include "../../common/JFJochMath.h"
+#include "../../common/ParallelFor.h"
+
+namespace {
+    using Vec6 = Eigen::Matrix<double, 6, 1>;
+    // At most six parameters: fixed-capacity, so the per-observation products never touch the heap.
+    using VecK = Eigen::Matrix<double, Eigen::Dynamic, 1, 0, 6, 1>;
+    using MatK = Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, 0, 6, 6>;
+
+    // A symmetric matrix as (g11, g22, g33, g12, g13, g23) and back.
+    Vec6 ToVec6(const Eigen::Matrix3d &m) {
+        Vec6 v;
+        v << m(0, 0), m(1, 1), m(2, 2), m(0, 1), m(0, 2), m(1, 2);
+        return v;
+    }
+
+    Eigen::Matrix3d FromVec6(const Vec6 &v) {
+        Eigen::Matrix3d m;
+        m << v(0), v(3), v(4),
+             v(3), v(1), v(5),
+             v(4), v(5), v(2);
+        return m;
+    }
+
+    // h^T G h = hh . (g11, g22, g33, g12, g13, g23)
+    Vec6 IndexProducts(const CellObservation &o) {
+        const double h = o.h, k = o.k, l = o.l;
+        Vec6 v;
+        v << h * h, k * k, l * l, 2 * h * k, 2 * h * l, 2 * k * l;
+        return v;
+    }
+
+    double ToDeg(double rad) { return rad * 180.0 / PI; }
+}
+
+std::vector<Eigen::Matrix3d> MetricBasis(const gemmi::SpaceGroup &sg) {
+    // Project each of the six symmetric unit matrices onto the metrics the group leaves invariant,
+    // averaging R G R^T over the rotation parts, and keep an orthonormal basis of what comes out.
+    const gemmi::GroupOps ops = sg.operations();
+    std::vector<Eigen::Matrix3d> rots;
+    for (const gemmi::Op &op : ops.sym_ops) {
+        Eigen::Matrix3d r;
+        for (int i = 0; i < 3; i++)
+            for (int j = 0; j < 3; j++)
+                r(i, j) = static_cast<double>(op.rot[i][j]) / gemmi::Op::DEN;
+        rots.push_back(r);
+    }
+    Eigen::Matrix<double, 6, 6> projected;
+    for (int m = 0; m < 6; m++) {
+        Vec6 e = Vec6::Zero();
+        e(m) = 1.0;
+        const Eigen::Matrix3d g = FromVec6(e);
+        Eigen::Matrix3d sum = Eigen::Matrix3d::Zero();
+        for (const auto &r : rots)
+            sum += r * g * r.transpose();
+        projected.col(m) = ToVec6(sum / static_cast<double>(rots.size()));
+    }
+    Eigen::JacobiSVD<Eigen::Matrix<double, 6, 6>> svd(projected, Eigen::ComputeFullU);
+    std::vector<Eigen::Matrix3d> basis;
+    for (int m = 0; m < 6; m++)
+        if (svd.singularValues()(m) > 1e-8 * svd.singularValues()(0))
+            basis.push_back(FromVec6(svd.matrixU().col(m)));
+    return basis;
+}
+
+std::array<double, 6> CellFromReciprocalMetric(const Eigen::Matrix3d &gstar) {
+    const Eigen::Matrix3d g = gstar.inverse();
+    const double a = std::sqrt(g(0, 0)), b = std::sqrt(g(1, 1)), c = std::sqrt(g(2, 2));
+    return {a, b, c, ToDeg(std::acos(g(1, 2) / (b * c))), ToDeg(std::acos(g(0, 2) / (a * c))),
+            ToDeg(std::acos(g(0, 1) / (a * b)))};
+}
+
+std::array<double, 6> CellEsdFromCovariance(const std::vector<Eigen::Matrix3d> &basis, const Eigen::VectorXd &p,
+                                            const Eigen::MatrixXd &cov) {
+    Eigen::Matrix3d gstar = Eigen::Matrix3d::Zero();
+    for (size_t k = 0; k < basis.size(); k++)
+        gstar += p(k) * basis[k];
+    const Eigen::Matrix3d g = gstar.inverse();
+    const double len[3] = {std::sqrt(g(0, 0)), std::sqrt(g(1, 1)), std::sqrt(g(2, 2))};
+    // The angle opposite axis i lies between the other two, j and l: cos = G_jl / (len_j len_l).
+    const int pair[3][2] = {{1, 2}, {0, 2}, {0, 1}};
+
+    // Analytic derivatives of the six parameters with respect to each p_k: dG = -G dG* G.
+    Eigen::MatrixXd jac(6, static_cast<Eigen::Index>(basis.size()));
+    for (size_t k = 0; k < basis.size(); k++) {
+        const Eigen::Matrix3d dg = -g * basis[k] * g;
+        double dlen[3];
+        for (int i = 0; i < 3; i++) {
+            dlen[i] = dg(i, i) / (2.0 * len[i]);
+            jac(i, k) = dlen[i];
+        }
+        for (int i = 0; i < 3; i++) {
+            const int j = pair[i][0], l = pair[i][1];
+            const double cosv = g(j, l) / (len[j] * len[l]);
+            const double dcos = dg(j, l) / (len[j] * len[l]) - cosv * (dlen[j] / len[j] + dlen[l] / len[l]);
+            jac(3 + i, k) = ToDeg(-dcos / std::sqrt(1.0 - cosv * cosv));
+        }
+    }
+    const Eigen::MatrixXd cell_cov = jac * cov * jac.transpose();
+    std::array<double, 6> esd{};
+    // A parameter the symmetry fixes comes out at rounding level (1e-19), not at zero: make it zero.
+    for (int i = 0; i < 6; i++) {
+        esd[i] = std::sqrt(std::max(0.0, cell_cov(i, i)));
+        if (esd[i] < 1e-12)
+            esd[i] = 0.0;
+    }
+    return esd;
+}
+
+MetricFit FitReciprocalMetric(std::span<const CellObservation> obs, const std::vector<Eigen::Matrix3d> &basis) {
+    const int nparam = static_cast<int>(basis.size());
+    Eigen::Matrix<double, 6, Eigen::Dynamic, 0, 6, 6> v(6, nparam);
+    for (int k = 0; k < nparam; k++)
+        v.col(k) = ToVec6(basis[k]);
+
+    MetricFit fit;
+    fit.used.assign(obs.size(), true);
+    MatK normal;
+    double s2 = 0.0;
+    // Fit, reject the observations further than 4 sigma off it, fit again - until nothing changes.
+    for (int iter = 0; iter < 5; iter++) {
+        normal = MatK::Zero(nparam, nparam);
+        VecK rhs = VecK::Zero(nparam);
+        int64_t n = 0;
+        for (size_t i = 0; i < obs.size(); i++) {
+            if (!fit.used[i])
+                continue;
+            const double q2 = static_cast<double>(obs[i].q) * obs[i].q;
+            const VecK a = v.transpose() * IndexProducts(obs[i]);
+            normal.noalias() += a * a.transpose() / q2;   // weight 1/q^2 on q^2: one e.s.d. on q
+            rhs.noalias() += a;                            // a * q^2 / q^2
+            n++;
+        }
+        if (n < 10 * nparam + 10)
+            return {};
+        fit.p = normal.ldlt().solve(rhs);
+        double wr2 = 0.0;
+        std::vector<double> z(obs.size());
+        for (size_t i = 0; i < obs.size(); i++) {
+            const double q2 = static_cast<double>(obs[i].q) * obs[i].q;
+            const VecK a = v.transpose() * IndexProducts(obs[i]);
+            const double r = q2 - a.dot(fit.p);
+            z[i] = r * r / q2;
+            if (fit.used[i])
+                wr2 += z[i];
+        }
+        s2 = wr2 / static_cast<double>(n - nparam);
+        bool changed = false;
+        for (size_t i = 0; i < obs.size(); i++) {
+            const bool keep = z[i] <= 16.0 * s2;
+            changed |= keep != fit.used[i];
+            fit.used[i] = keep;
+        }
+        if (!changed)
+            break;
+    }
+    fit.cov = s2 * Eigen::MatrixXd(normal).inverse();
+    fit.ok = fit.p.allFinite() && fit.cov.allFinite();
+    return fit;
+}
+
+std::optional<CellEsd> EstimateCellEsd(std::span<const CellObservation> obs, const gemmi::SpaceGroup &sg,
+                                       double wavelength_A, int nblocks) {
+    const auto basis = MetricBasis(sg);
+    const MetricFit fit = FitReciprocalMetric(obs, basis);
+    if (!fit.ok)
+        return {};
+    const auto metric = [&basis](const Eigen::VectorXd &p) {
+        Eigen::Matrix3d g = Eigen::Matrix3d::Zero();
+        for (size_t k = 0; k < basis.size(); k++)
+            g += p(k) * basis[k];
+        return g;
+    };
+
+    CellEsd out;
+    out.esd_lsq = CellEsdFromCovariance(basis, fit.p, fit.cov);
+    const auto cell = CellFromReciprocalMetric(metric(fit.p));
+    out.fitted = UnitCell{static_cast<float>(cell[0]), static_cast<float>(cell[1]), static_cast<float>(cell[2]),
+                          static_cast<float>(cell[3]), static_cast<float>(cell[4]), static_cast<float>(cell[5])};
+
+    std::vector<int64_t> keys;
+    double q_min = INFINITY, q_max = 0.0;
+    int32_t frame_min = INT32_MAX, frame_max = INT32_MIN;
+    for (size_t i = 0; i < obs.size(); i++) {
+        if (!fit.used[i])
+            continue;
+        const auto &o = obs[i];
+        keys.push_back(((static_cast<int64_t>(o.h) + 1024) << 22) | ((static_cast<int64_t>(o.k) + 1024) << 11)
+                       | (static_cast<int64_t>(o.l) + 1024));
+        q_min = std::min(q_min, static_cast<double>(o.q));
+        q_max = std::max(q_max, static_cast<double>(o.q));
+        frame_min = std::min(frame_min, o.frame);
+        frame_max = std::max(frame_max, o.frame);
+    }
+    out.observations = static_cast<int64_t>(keys.size());
+    std::sort(keys.begin(), keys.end());
+    out.reflections = std::unique(keys.begin(), keys.end()) - keys.begin();
+    out.theta_min_deg = ToDeg(std::asin(std::min(1.0, wavelength_A * q_min / 2.0)));
+    out.theta_max_deg = ToDeg(std::asin(std::min(1.0, wavelength_A * q_max / 2.0)));
+
+    // The same fit on blocks of consecutive frames: the scatter of their cells, over sqrt(blocks).
+    // Least-squares cell e.s.d.s alone are too small: following Herbstein (2000) Acta Cryst. B56, 547-557
+    std::vector<std::array<double, 6>> block_cells;
+    const int64_t span = static_cast<int64_t>(frame_max) - frame_min + 1;
+    std::vector<std::vector<CellObservation>> block_obs(nblocks);
+    for (size_t i = 0; i < obs.size(); i++)
+        if (fit.used[i])
+            block_obs[(obs[i].frame - frame_min) * nblocks / span].push_back(obs[i]);
+    for (const auto &b : block_obs) {
+        const MetricFit bf = FitReciprocalMetric(b, basis);
+        if (bf.ok)
+            block_cells.push_back(CellFromReciprocalMetric(metric(bf.p)));
+    }
+    out.blocks = static_cast<int>(block_cells.size());
+    out.esd = out.esd_lsq;
+    if (out.blocks >= 4) {
+        std::array<double, 6> esd{};
+        for (int j = 0; j < 6; j++) {
+            double mean = 0.0;
+            for (const auto &c : block_cells)
+                mean += c[j] / out.blocks;
+            double var = 0.0;
+            for (const auto &c : block_cells)
+                var += (c[j] - mean) * (c[j] - mean) / (out.blocks - 1);
+            esd[j] = std::sqrt(var / out.blocks);
+            out.esd[j] = std::max(out.esd[j], esd[j]);
+        }
+        out.esd_blocks = esd;
+    }
+    return out;
+}
+
+std::vector<CellObservation> GatherCellObservations(const std::vector<IntegrationOutcome> &outcomes,
+                                                    size_t nthreads) {
+    std::vector<std::vector<CellObservation>> per_frame(outcomes.size());
+    ParallelFor(static_cast<int>(outcomes.size()), nthreads, [&](int f) {
+        const IntegrationOutcome &out = outcomes[f];
+        for (const auto &r : out.reflections) {
+            if (!r.observed || r.clipped || r.overloaded || r.on_ice_ring || !(r.sigma > 0.0f)
+                || !(r.I > 3.0f * r.sigma) || !std::isfinite(r.observed_x) || !std::isfinite(r.observed_y))
+                continue;
+            const float q = out.geom.DetectorToRecip(r.observed_x, r.observed_y).Length();
+            if (q > 0.0f)
+                per_frame[f].push_back(CellObservation{r.h, r.k, r.l, q, f});
+        }
+    });
+    std::vector<CellObservation> obs;
+    for (const auto &v : per_frame)
+        obs.insert(obs.end(), v.begin(), v.end());
+    return obs;
+}
diff --git a/image_analysis/geom_refinement/CellEsd.h b/image_analysis/geom_refinement/CellEsd.h
new file mode 100644
index 000000000..8a112d290
--- /dev/null
+++ b/image_analysis/geom_refinement/CellEsd.h
@@ -0,0 +1,84 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <array>
+#include <cstdint>
+#include <optional>
+#include <span>
+#include <vector>
+
+#include <Eigen/Dense>
+
+#include "../../common/UnitCell.h"
+#include "../IntegrationOutcome.h"
+#include "gemmi/symmetry.hpp"
+
+// The e.s.d.s of the unit cell, as SHELXL's ZERR and a CIF's _cell.*_esd ask for them.
+//
+// The cell is fitted to d-spacings: each strong integrated observation gives |q| = 1/d at its
+// observed centroid, which depends on the detector geometry alone (not on the orientation, nor on the
+// rotation angle), and q^2 = h^T G* h is LINEAR in the reciprocal metric tensor G*. So the fit is a
+// plain linear least squares in the components of G* the point group leaves free, and its covariance,
+// scaled by the goodness of fit, maps onto a, b, c, alpha, beta, gamma through the derivatives of the
+// cell with respect to G*. A length the group ties to another gets the same e.s.d., an angle it fixes
+// gets zero.
+//
+// Least-squares cell e.s.d.s are known to be too small (Herbstein (2000) Acta Cryst. B56, 547-557):
+// they see only the scatter of the centroids, not what changes over the sweep. The same fit is
+// therefore also made on blocks of consecutive frames, and the scatter of the block cells, over the
+// square root of their number, is the second estimate. The e.s.d. written is the larger of the two.
+
+// One observation: the Miller index in the setting of the cell, and |q| = 1/d at the observed
+// centroid, in 1/A.
+struct CellObservation {
+    int32_t h = 0, k = 0, l = 0;
+    float q = 0.0f;
+    int32_t frame = 0;
+};
+
+struct CellEsd {
+    std::array<double, 6> esd{};        // written: per parameter the larger of the two below
+    std::array<double, 6> esd_lsq{};    // least squares, scaled by the goodness of fit
+    std::optional<std::array<double, 6>> esd_blocks;   // block scatter / sqrt(blocks)
+    int blocks = 0;
+    int64_t observations = 0;           // observations in the fit, after rejection
+    int64_t reflections = 0;            // distinct h k l among them (_cell_measurement.reflns_used)
+    double theta_min_deg = 0.0;
+    double theta_max_deg = 0.0;
+    UnitCell fitted{};                  // the d-spacing fit's own cell, for comparison with the reported one
+};
+
+// Symmetric 3x3 matrices spanning the reciprocal metrics G* the point group of `sg` allows
+// (G* = R G* R^T for every rotation part R): 6 for triclinic down to 1 for cubic. Orthonormal as
+// 6-vectors (g11, g22, g33, g12, g13, g23).
+std::vector<Eigen::Matrix3d> MetricBasis(const gemmi::SpaceGroup &sg);
+
+// a, b, c (A) and alpha, beta, gamma (deg) of the reciprocal metric G*.
+std::array<double, 6> CellFromReciprocalMetric(const Eigen::Matrix3d &gstar);
+
+// The e.s.d.s of a, b, c, alpha, beta, gamma for G* = sum_k p_k basis_k with covariance cov(p).
+std::array<double, 6> CellEsdFromCovariance(const std::vector<Eigen::Matrix3d> &basis, const Eigen::VectorXd &p,
+                                            const Eigen::MatrixXd &cov);
+
+struct MetricFit {
+    bool ok = false;
+    Eigen::VectorXd p;
+    Eigen::MatrixXd cov;   // scaled by the goodness of fit
+    std::vector<bool> used;
+};
+
+// Weighted linear least squares of q^2 = h^T G* h, |q| taken at one constant e.s.d. (weight 1/q^2 on
+// q^2), with the observations further than 4 sigma off the fit rejected and the fit repeated.
+MetricFit FitReciprocalMetric(std::span<const CellObservation> obs, const std::vector<Eigen::Matrix3d> &basis);
+
+// Both estimates for observations in the setting of `sg`; blocks are cut by frame. Empty with too
+// few observations to fit.
+std::optional<CellEsd> EstimateCellEsd(std::span<const CellObservation> obs, const gemmi::SpaceGroup &sg,
+                                       double wavelength_A, int nblocks = 8);
+
+// The observations of a rotation run's integrated frames: observed, unclipped, unsaturated, off the
+// ice rings and I > 3 sigma.
+std::vector<CellObservation> GatherCellObservations(const std::vector<IntegrationOutcome> &outcomes,
+                                                    size_t nthreads);
diff --git a/image_analysis/indexing/CMakeLists.txt b/image_analysis/indexing/CMakeLists.txt
index 212810ce4..78675187f 100644
--- a/image_analysis/indexing/CMakeLists.txt
+++ b/image_analysis/indexing/CMakeLists.txt
@@ -27,18 +27,9 @@ ADD_LIBRARY(JFJochIndexing STATIC
 TARGET_LINK_LIBRARIES(JFJochIndexing JFJochCommon JFJochLatticeSearch)
 
 IF (JFJOCH_CUDA_AVAILABLE)
-    # A source archive carries no submodules, which is exactly what is wanted here: ffbidx's bundled
-    # eigen submodule must NOT be added, or it would add_subdirectory a second Eigen3::Eigen target.
-    # ffbidx instead resolves Eigen via the project-level Eigen3 (the find_package(Eigen3) at the top
-    # of image_analysis/CMakeLists.txt). The clone this replaces passed GIT_SUBMODULES "" to get the
-    # same tree.
-    FetchContent_Declare(
-            fast-indexer
-            URL https://github.com/paulscherrerinstitute/fast-feedback-indexer/archive/a94fd4f5c55289e70860feea358182d2072e02b5.tar.gz
-            URL_HASH SHA256=275590cb41db783b822b1c8403abc2b3c9986f3d98a1a7361fc0ad478ff466c0
-    )
-
-    FetchContent_MakeAvailable(fast-indexer)
+    # The fast-feedback indexer is vendored (fast_indexer_static); it takes Eigen from the project-level
+    # Eigen3 (the find_package(Eigen3) at the top of image_analysis/CMakeLists.txt).
+    ADD_SUBDIRECTORY(fast-feedback-indexer)
     TARGET_SOURCES(JFJochIndexing PRIVATE
             CUDAMemHelpers.h
             FFTIndexerGPU.cu FFTIndexerGPU.h
diff --git a/image_analysis/indexing/CUDAMemHelpers.h b/image_analysis/indexing/CUDAMemHelpers.h
index fcbe55d72..37de3fe94 100644
--- a/image_analysis/indexing/CUDAMemHelpers.h
+++ b/image_analysis/indexing/CUDAMemHelpers.h
@@ -108,6 +108,30 @@ public:
     cudaEvent_t get() const { return event_; }
 };
 
+// cudaStreamSynchronize with the waiting thread asleep: an event made with cudaEventBlockingSync, recorded on the
+// stream and waited for. cudaStreamSynchronize spins a core for the whole of the wait (the process's default
+// schedule), which on a card shared by several engines - refinement's weight trials - is a core per engine for
+// most of the run, taken from whatever else the host is doing. Made on the device of the streams it waits for;
+// one thread at a time.
+class StreamWaiter {
+    cudaEvent_t event_ = nullptr;
+public:
+    StreamWaiter() {
+        if (cudaEventCreateWithFlags(&event_, cudaEventBlockingSync | cudaEventDisableTiming) != cudaSuccess)
+            throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "Failed to create CUDA event");
+    }
+    ~StreamWaiter() {
+        if (event_) cudaEventDestroy(event_);
+    }
+    StreamWaiter(const StreamWaiter&) = delete;
+    StreamWaiter& operator=(const StreamWaiter&) = delete;
+
+    cudaError_t Wait(cudaStream_t stream) const {
+        const cudaError_t err = cudaEventRecord(event_, stream);
+        return err != cudaSuccess ? err : cudaEventSynchronize(event_);
+    }
+};
+
 // How much freed memory the pool keeps rather than returning it to the driver. Returning it puts the
 // next allocation straight back on the path this exists to avoid, so hold the per-worker engine
 // buffers; but the card also has to fit the merge, which asks for several gigabytes of its own after
diff --git a/image_analysis/indexing/fast-feedback-indexer/CMakeLists.txt b/image_analysis/indexing/fast-feedback-indexer/CMakeLists.txt
new file mode 100644
index 000000000..0fccd4b0d
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/CMakeLists.txt
@@ -0,0 +1,39 @@
+# The fast-feedback indexer (TORO, the GPU known-cell indexer behind FFBIDX), vendored from
+# https://github.com/paulscherrerinstitute/fast-feedback-indexer at commit a94fd4f5c55289e70860feea358182d2072e02b5,
+# BSD-3-Clause (LICENSE.md). Only the static library the build links is kept, with the rules upstream's
+# indexer/src/CMakeLists.txt gives it: its install, pkg-config, shared-library and C-API parts are left out,
+# version.h is written once rather than generated, and data/ holds the library's test spot lists that
+# FFBIDXIndexerCPU_MatchesGPU reads.
+
+SET(THREADS_PREFER_PTHREAD_FLAG ON)
+FIND_PACKAGE(Threads REQUIRED)
+FIND_PACKAGE(CUDAToolkit REQUIRED)
+IF (NOT DEFINED CMAKE_CUDA_ARCHITECTURES)
+    SET(CMAKE_CUDA_ARCHITECTURES "75;80")
+ENDIF()
+
+ADD_LIBRARY(fast_indexer_static STATIC
+        indexer_gpu.cu ffbidx/indexer_gpu.h
+        indexer.cpp
+        log.cpp
+        ffbidx/indexer.h
+        ffbidx/refine.h
+        ffbidx/log.h
+        ffbidx/exception.h
+        ffbidx/envvar.h
+        ffbidx/version.h)
+SET_TARGET_PROPERTIES(fast_indexer_static PROPERTIES CUDA_RUNTIME_LIBRARY Static)
+TARGET_COMPILE_FEATURES(fast_indexer_static PUBLIC cxx_std_17)
+TARGET_INCLUDE_DIRECTORIES(fast_indexer_static PUBLIC .)
+TARGET_LINK_LIBRARIES(fast_indexer_static
+        PRIVATE CUDA::cudart_static
+        PRIVATE Threads::Threads
+        PUBLIC Eigen3::Eigen)
+
+# indexer_gpu.cu includes CUB, which, like all of CCCL, stops with an #error under MSVC's traditional
+# preprocessor: the host compiler gets the conforming one for the CUDA sources, as upstream does. The
+# top-level CMakeLists.txt sets the same for every CUDA target; it is kept here so the library does not
+# depend on that.
+IF (MSVC)
+    TARGET_COMPILE_OPTIONS(fast_indexer_static PRIVATE $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=/Zc:preprocessor>)
+ENDIF()
diff --git a/image_analysis/indexing/fast-feedback-indexer/LICENSE.md b/image_analysis/indexing/fast-feedback-indexer/LICENSE.md
new file mode 100644
index 000000000..f9ab447d8
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/LICENSE.md
@@ -0,0 +1,22 @@
+The code in the **eigen** directory has it's own license
+* http://www.eigen.tuxfamily.org
+* https://www.mozilla.org/en-US/MPL/2.0
+
+Python has it's own license
+* https://docs.python.org/3/license.html#psf-license
+
+For the rest, the BSD-3-Clause applies.
+
+### BSD-3-Clause
+
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image0_local.txt b/image_analysis/indexing/fast-feedback-indexer/data/image0_local.txt
new file mode 100644
index 000000000..f36dbc646
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image0_local.txt
@@ -0,0 +1,298 @@
+36.9 0 0 4.83429e-15 78.95 0 4.83429e-15 4.83429e-15 78.95
+-0.055371 0.473773 -0.121095
+-0.0588781 0.465162 -0.116734
+0.426543 -0.0325397 -0.0961181
+0.0133439 -0.30226 -0.0468678
+0.344006 -0.160659 -0.0748791
+-0.197034 -0.0718448 -0.0222394
+-0.342727 -0.15456 -0.0733667
+0.458527 -0.0770242 -0.114664
+-0.0877891 -0.420758 -0.097085
+0.220288 -0.413958 -0.116761
+-0.0394481 -0.087645 -0.00462961
+0.276511 0.346708 -0.10371
+0.269925 -0.0869209 -0.0410498
+-0.441063 -0.0813343 -0.106217
+-0.475981 -0.0254935 -0.120914
+-0.279153 0.0684798 -0.0421984
+0.38077 0.0609531 -0.0773413
+-0.292215 -0.0951606 -0.0483936
+-0.00600919 -0.447577 -0.105775
+-0.00363741 -0.100819 -0.00510189
+-0.0746551 -0.102559 -0.00807855
+0.417675 -0.094881 -0.0963712
+-0.193093 -0.41505 -0.110928
+-0.459308 -0.0986124 -0.117214
+-0.366764 -0.310666 -0.12309
+-0.319698 -0.218012 -0.0779022
+0.384007 -0.106091 -0.0827852
+0.121547 -0.115845 -0.0141976
+0.0978358 -0.405263 -0.09105
+-0.383253 -0.10897 -0.0828074
+0.375311 -0.113327 -0.080055
+0.206502 -0.308821 -0.0715675
+-0.202333 -0.124625 -0.0286453
+0.370709 0.0744466 -0.0742396
+0.0477675 -0.46393 -0.115417
+-0.287502 -0.355031 -0.110452
+0.00823107 0.337017 -0.0585373
+-0.207954 -0.0855134 -0.0256066
+-0.331641 -0.276272 -0.0979536
+0.249489 0.238621 -0.0614824
+0.265879 -0.139562 -0.0461495
+0.0266054 -0.146353 -0.0111255
+-0.109113 -0.144518 -0.0165322
+0.0249291 -0.0289788 -0.000730884
+-0.0694774 -0.317386 -0.0542521
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image0_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image0_peakfinder8.txt
new file mode 100644
index 000000000..67bb6e02a
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image0_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image0_radial.txt
new file mode 100644
index 000000000..5f8d5c2c6
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image0_radial.txt
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image1_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image1_peakfinder8.txt
new file mode 100644
index 000000000..13a27a3eb
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image1_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image1_radial.txt
new file mode 100644
index 000000000..26a9f42b7
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image1_radial.txt
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image2_local.txt b/image_analysis/indexing/fast-feedback-indexer/data/image2_local.txt
new file mode 100644
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image2_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image2_peakfinder8.txt
new file mode 100644
index 000000000..005f62b9c
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image2_peakfinder8.txt
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image2_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image2_radial.txt
new file mode 100644
index 000000000..11e087886
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image2_radial.txt
@@ -0,0 +1,670 @@
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image3_local.txt b/image_analysis/indexing/fast-feedback-indexer/data/image3_local.txt
new file mode 100644
index 000000000..7ee46fe94
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image3_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image3_peakfinder8.txt
new file mode 100644
index 000000000..a81918adf
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image3_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image3_radial.txt
new file mode 100644
index 000000000..7d444f71f
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image3_radial.txt
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image4_local.txt b/image_analysis/indexing/fast-feedback-indexer/data/image4_local.txt
new file mode 100644
index 000000000..c75e2e060
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image4_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image4_peakfinder8.txt
new file mode 100644
index 000000000..1fc0f709a
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image4_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image4_radial.txt
new file mode 100644
index 000000000..562386d24
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image4_radial.txt
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image5_local.txt b/image_analysis/indexing/fast-feedback-indexer/data/image5_local.txt
new file mode 100644
index 000000000..9ccf5bae8
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image5_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image5_peakfinder8.txt
new file mode 100644
index 000000000..f69006201
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image5_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image5_radial.txt
new file mode 100644
index 000000000..20bc8fb21
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image5_radial.txt
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image6_local.txt b/image_analysis/indexing/fast-feedback-indexer/data/image6_local.txt
new file mode 100644
index 000000000..bc8b63e69
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image6_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image6_peakfinder8.txt
new file mode 100644
index 000000000..fd751cbf4
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image6_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image6_radial.txt
new file mode 100644
index 000000000..ab445ca30
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image6_radial.txt
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new file mode 100644
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image7_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image7_peakfinder8.txt
new file mode 100644
index 000000000..0564905f5
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image7_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image7_radial.txt
new file mode 100644
index 000000000..12bd2f434
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/data/image7_radial.txt
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image8_local.txt b/image_analysis/indexing/fast-feedback-indexer/data/image8_local.txt
new file mode 100644
index 000000000..f021b9ee1
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image8_peakfinder8.txt b/image_analysis/indexing/fast-feedback-indexer/data/image8_peakfinder8.txt
new file mode 100644
index 000000000..41cec02ab
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/data/image8_radial.txt b/image_analysis/indexing/fast-feedback-indexer/data/image8_radial.txt
new file mode 100644
index 000000000..903cba09f
--- /dev/null
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diff --git a/image_analysis/indexing/fast-feedback-indexer/ffbidx/envvar.h b/image_analysis/indexing/fast-feedback-indexer/ffbidx/envvar.h
new file mode 100644
index 000000000..df939c0f2
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/ffbidx/envvar.h
@@ -0,0 +1,89 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/ffbidx/envvar.h), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#ifndef FAST_FEEDBACK_ENVVAR_H
+#define FAST_FEEDBACK_ENVVAR_H
+
+#include <sstream>
+#include <stdexcept>
+#include <cstdlib>
+#include <functional>
+
+namespace fast_feedback {
+
+    template <typename result_type>
+    inline result_type envvar([[maybe_unused]] const char *name, [[maybe_unused]] std::function<result_type()> func)
+    {}
+
+    // throw std::invalid_argument, if value is not accepted
+    // return if_undefined() if undefined
+    template <>
+    inline bool envvar<bool>(const char* name, std::function<bool()> func)
+    {
+        static const std::vector<std::string> accepted = {"1", "true", "yes", "on", "0", "false", "no", "off"}; // [4] == "0"
+        char* varval = std::getenv(name);
+        if (varval != nullptr) {
+            unsigned i;
+            for (i=0u; i<accepted.size(); i++) {
+                if (accepted[i] == varval)
+                    goto found;
+            }
+            {
+                std::ostringstream oss;
+                oss << "illegal value for " << name << ": \"" << varval << "\" (use one of";
+                for (const auto& s : accepted)
+                    oss << " \"" << s << '\"';
+                oss << ')';
+                throw std::invalid_argument(oss.str());
+            }
+          found:
+            return i < 4u;
+        }
+        return func();
+    }
+
+    // throw std::invalid_argument, if value is not accepted
+    template <>
+    inline unsigned envvar<unsigned>(const char *name, std::function<unsigned()> func)
+    {
+        char* varval = std::getenv(name);
+        if (varval != nullptr) {
+            std::istringstream iss(varval);
+            unsigned val;
+            if (!(iss >> val) || !iss.eof()) {
+                std::ostringstream oss;
+                oss << "illegal value of type unsigned for " << name << ": " << varval;
+                throw std::invalid_argument(oss.str());
+            }
+            return val;
+        }
+        return func();
+    }
+
+} // namespace fast_feedback
+
+#endif // FAST_FEEDBACK_ENVVAR_H
diff --git a/image_analysis/indexing/fast-feedback-indexer/ffbidx/exception.h b/image_analysis/indexing/fast-feedback-indexer/ffbidx/exception.h
new file mode 100644
index 000000000..f478d9339
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/ffbidx/exception.h
@@ -0,0 +1,94 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/ffbidx/exception.h), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#ifndef FAST_FEEDBACK_EXCEPTION_H
+#define FAST_FEEDBACK_EXCEPTION_H
+
+#include <exception>
+#include <sstream>
+#include "envvar.h"
+
+namespace fast_feedback {
+
+    constexpr char INDEXER_VERBOSE_EXCEPTION[] = "INDEXER_VERBOSE_EXCEPTION";
+
+    struct exception : public std::exception {
+
+        std::string error_message;
+        const char* file_name;
+        unsigned line_number;
+
+        inline static bool verbose()
+        {
+            return envvar<bool>(INDEXER_VERBOSE_EXCEPTION, []()->bool{return false;});
+        }
+
+        inline static std::string verbosify(const std::string& message, const char* file, unsigned line)
+        {
+            if (verbose()) {
+                std::ostringstream oss;
+                oss << '(' << file << ':' << line << ") " << message;
+                return oss.str();
+            }
+            return message;
+        }
+
+        inline exception(const std::string& message, const char* file, unsigned line)
+            : error_message(verbosify(message, file, line)), file_name(file), line_number(line)
+        {}
+
+        inline exception(const exception&) = default;
+        inline exception(exception&&) = default;
+
+        inline exception& operator=(const exception&) = default;
+        inline exception& operator=(exception&&) = default;
+
+        inline ~exception() noexcept override
+        {}
+
+        inline const char* what() const noexcept override
+        {
+            return error_message.c_str();
+        }
+
+        template<typename T>
+        inline exception& operator<<(const T& data)
+        {
+            std::ostringstream oss;
+            oss << data;
+            error_message += oss.str();
+            return *this;
+        }
+
+    };
+
+}
+
+#define FF_EXCEPTION(msg) fast_feedback::exception(msg, __FILE__, __LINE__)
+#define FF_EXCEPTION_OBJ fast_feedback::exception{std::string{}, __FILE__, __LINE__}
+
+#endif
diff --git a/image_analysis/indexing/fast-feedback-indexer/ffbidx/indexer.h b/image_analysis/indexing/fast-feedback-indexer/ffbidx/indexer.h
new file mode 100644
index 000000000..404248cdb
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/ffbidx/indexer.h
@@ -0,0 +1,382 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/ffbidx/indexer.h), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#ifndef FAST_FEEDBACK_INDEXER_H
+#define FAST_FEEDBACK_INDEXER_H
+
+// Fast feedback indexer
+
+#include <stdexcept>
+#include <utility>
+#include <memory>
+#include <atomic>
+
+namespace fast_feedback {
+
+    // Input data for fast feedback indexer
+    //
+    // Input data consists of the (x,y,z) 3D space coordinates
+    // coordinates
+    // - of given unit cells        [0..3*n_cells[
+    // - of the spots               [0..n_spots[
+    // The origin is implicitly assumed to be part of the lattice.
+    template <typename float_type=float>
+    struct input final {
+        struct {
+            float_type* x;  // x coordinates, pinned memory
+            float_type* y;  // y coordinates, pinned memory
+            float_type* z;  // z coordinates, pinned memory
+        } cell;
+        struct {
+            float_type* x;  // x coordinates, pinned memory
+            float_type* y;  // y coordinates, pinned memory
+            float_type* z;  // z coordinates, pinned memory
+        } spot;
+        unsigned n_cells;   // number of given unit cells (must be before n_spots in memory, see copy_in())
+        unsigned n_spots;   // number of spots (must be after n_cells in memory, see copy_in())
+        bool new_cells;     // set to true if cells are new or have changed
+        bool new_spots;     // set to true if spots are new or have changed
+    };
+
+    // Output data for fast feedback indexer
+    //
+    // Output data consists of the (x,y,z) 3D space
+    // coordinates of the found unit cell vectors [0..3*n_cells[
+    //
+    // The coordinate arrays must be of size 3*n_cells at least,
+    // the score array at least of size n_cells
+    template <typename float_type=float>
+    struct output final {
+        float_type* x;      // x coordinates, pinned memory
+        float_type* y;      // y coordinates, pinned memory
+        float_type* z;      // z coordinates, pinned memory
+        float_type* score;  // per cell score, pinned memory
+        unsigned n_cells=1u;// number of unit cells
+    };
+
+    // Configuration setting for the fast feedback indexer runtime state
+    // These are used to determine GPU kernel grid sizes and calculation thresholds
+    // Memory must be pinned in order to be used as an argument for indexing
+    template <typename float_type=float>
+    struct config_runtime final {
+        float_type length_threshold=1e-9;       // threshold for determining equal vector length (|va| - threshold < |vb| < |va| + threshold)
+        float_type triml=0.001;                 // lower trim value for distance to nearest integer objective value - 0 < triml < trimh
+        float_type trimh=0.3;                   // higher trim value for distance to nearest integer objective value - triml < trimh < 0.5
+        float_type delta=0.1;                   // log2 curve position: score = log2(trim(dist(x)) + delta)
+        float_type dist1=0.2;                   // maximum distance to int for single coordinate
+        float_type dist3=0.15;                  // maximum distance to int for tripple coordinates
+        unsigned min_spots=6;                   // vector refinement: minimum number of spots to fit against (0: no refinement)
+        unsigned num_halfsphere_points=32*1024; // number of sample points on half sphere for finding vector candidates
+        unsigned num_angle_points=0;            // number of sample points in rotation space for finding cell candidates (0: auto)
+    };
+
+    // Configuration setting for the fast feedback indexer persistent state
+    // The persistent state determines static GPU memory consumtion
+    // Changing these parameters will cause reallocation of memory on the GPU
+    template <typename float_type=float>
+    struct config_persistent final {
+        unsigned max_output_cells=1;        // maximum number of output unit cells
+        unsigned max_input_cells=1;         // maximum number of input unit cells, (must be before max_spots in memory, see copy_in())
+        unsigned max_spots=200;             // maximum number of input spots, (must be after max_input_cells in memory, see copy_in())
+        unsigned num_candidate_vectors=32;  // number of candidate vectors (per input cell vector)
+        bool redundant_computations=false;  // compute candidates for all three cell vectors instead of just one
+    };
+
+    // Exception type for fast feedback indexer
+    struct indexer_error final : public std::runtime_error {};
+
+    // State ID to identify object private state
+    struct state_id final {
+        using type = unsigned;
+        static constexpr type null = 0u;    // instance identity usable to denote object instance without private state
+        static std::atomic<type> next;      // monotonically increasing atomic counter
+
+        // Allocate a new state identifier
+        static type alloc() noexcept
+        {
+            return next.fetch_add(1u);
+        }
+    };
+
+    // Indexer object
+    //
+    // Keeps persistent state, like GPU memory allocations.
+    template <typename float_type=float>
+    struct indexer final {
+        config_persistent<float_type> cpers;    // persistent configuration
+        const state_id::type state;             // object instance private state identifier
+
+        // Initialize this instance according to conf
+        static void init (indexer<float_type>& instance, const config_persistent<float_type>& conf);
+
+        // Drop this instance and its private state
+        static void drop (indexer<float_type>& instance);
+
+        // Create according to c
+        explicit inline indexer (const config_persistent<float_type>& c)
+            : state{state_id::alloc()}
+        { init(*this, c); }
+
+        // Create with default persistent config
+        inline indexer ()
+            : state{state_id::alloc()}
+        { init(*this, config_persistent<float_type>{}); }
+
+        // Create according to other.cpers
+        inline indexer (const indexer& other)
+            : state{state_id::alloc()}
+        { init(*this, other.cpers); }
+
+        // Reconfigure according to other.cpers
+        inline indexer& operator= (const indexer& other)
+        { if (other.state!=state) { drop(*this); init(*this, other.cpers); } return *this; }
+
+        // Take over others state
+        inline indexer (indexer&& other)
+            : cpers(std::move(other.cpers)), state(state_id::null)
+        {
+            std::swap(const_cast<state_id::type&>(state), const_cast<state_id::type&>(other.state));
+        }
+
+        // Take over others state
+        inline indexer& operator= (indexer&& other)
+        {
+            if (other.state != state) {
+                std::swap(cpers, other.cpers);
+                std::swap(const_cast<state_id::type&>(state), const_cast<state_id::type&>(other.state));
+            }
+            return *this;
+        }
+
+        // Drop if valid
+        inline ~indexer ()
+        {
+            if (state != state_id::null) {
+                drop(*this);
+                const_cast<state_id::type&>(state) = state_id::null;
+            }
+        }
+
+        // Run indexing asynchronously according to conf_rt on in data
+        // All coordinate data and the runtime config memory must be pinned.
+        // Before accessing output data, index_end() must be called.
+        // If callback is set, it will be called with the data argument as
+        // soon as the result is ready to be handled with index_end().
+        // The callback is not allowed to call any indexer method.
+        void index_start (const input<float_type>& in, output<float_type>& out, const config_runtime<float_type>& conf_rt,
+                          void(*callback)(void*)=nullptr, void* data=nullptr);
+        
+        // Finish indexing for output access
+        // Must follow an index_start() call if no callback was given to index_start().
+        // Must follow a callback() call if a callback was given to index_start().
+        void index_end (output<float_type>& out);
+
+        // Run indexing according to conf_rt on in data, put result into out data
+        // All coordinate data and the runtime config memory must be pinned
+        inline void index (const input<float_type>& in, output<float_type>& out, const config_runtime<float_type>& conf_rt)
+        {
+            index_start(in, out, conf_rt);
+            index_end(out);
+        }
+    };
+
+    // Pin allocated memory during the lifetime of this object
+    // Use this for already allocated unpinned memory
+    // Watch out when pinning memory that might move (like container data)
+    struct memory_pin final {
+        void* ptr;
+
+        // Nothing is pinned by default
+        inline memory_pin() noexcept
+            : ptr(nullptr)
+        {}
+
+        // Pin standard container content
+        // Make sure the container data is not moved during the lifetime of the pin
+        template<typename Container>
+        explicit inline memory_pin(const Container& container)
+            : ptr(nullptr)
+        {
+            void* mem_ptr = const_cast<Container&>(container).data();
+            pin(mem_ptr, container.size() * sizeof(typename Container::value_type));
+            ptr = mem_ptr;
+        }
+
+        // Raw memory pin
+        inline memory_pin(void* mem_ptr, std::size_t num_bytes)
+            : ptr(nullptr)
+        {
+            pin(mem_ptr, num_bytes);
+            ptr = mem_ptr;
+        }
+
+        // Take over pin from other
+        inline memory_pin(memory_pin&& other) noexcept
+            : ptr(nullptr)
+        {
+            std::swap(ptr, other.ptr);
+        }
+
+        // Take over pin from other
+        inline memory_pin& operator=(memory_pin&& other)
+        {
+            if (other.ptr != ptr) {
+                void* mem_ptr = nullptr;
+                std::swap(ptr, mem_ptr);
+                if (mem_ptr != nullptr)
+                    unpin(mem_ptr);
+                std::swap(ptr, other.ptr);
+            }
+            return *this;
+        }
+
+        // Unpin pinned memory if any
+        inline ~memory_pin()
+        {
+            if (ptr != nullptr) {
+                unpin(ptr);
+                ptr = nullptr;
+            }
+        }
+
+        memory_pin(const memory_pin&) = delete;
+        memory_pin& operator=(const memory_pin&) = delete;
+
+        // Pin on object
+        // Only works for objects without internally allocated extra memory
+        template<typename Object>
+        static inline memory_pin on(const Object& obj)
+        {
+            void* mem_ptr = const_cast<Object*>(&obj);
+            return memory_pin(mem_ptr, sizeof(obj));
+        }
+
+        // Pin on object underlying the pointer
+        // Only works for objects without internally allocated extra memory
+        template<typename Object>
+        static inline memory_pin on(const Object* obj_ptr)
+        {
+            void* mem_ptr = const_cast<Object*>(obj_ptr);
+            return memory_pin(mem_ptr, sizeof(*obj_ptr));
+        }
+
+        static void pin(void* ptr, std::size_t size);   // Raw memory pin
+        static void unpin(void* ptr);                   // Raw unpin
+    };
+
+    // Allocate pinned raw memory
+    void* alloc_pinned(std::size_t num_bytes);
+
+    // Deallocate pinned memory
+    void dealloc_pinned(void* ptr);
+
+    // Deleter for pinned smart pointers
+    // Calls destructor
+    template<typename T>
+    struct pinned_deleter final {
+        inline void operator()(T* ptr) const
+        {
+            if (ptr == nullptr)
+                return;
+            try {
+                ptr->~T();
+            } catch (...) {
+                try {
+                    dealloc_pinned(ptr);
+                } catch (...) {}    // ignore dealloc exception
+                throw;
+            }
+            dealloc_pinned(ptr);
+        }
+    };
+
+    // Specialized array version
+    template<typename T>
+    struct pinned_deleter<T[]> final {
+        inline void operator()(T ptr[]) const
+        {
+            pinned_deleter<T>{}(ptr);
+        }
+    };
+
+    // Pinned smart pointer
+    // Use this for memory allocated with alloc_pinned
+    template<typename T>
+    using pinned_ptr = std::unique_ptr<T, pinned_deleter<T>>;
+
+    // Allocate pinned object
+    // Calls default constructor
+    // This only works for objects that do not allocate internal extra memory
+    template<typename T>
+    inline pinned_ptr<T> alloc_pinned()
+    {
+        pinned_ptr<T> ptr{static_cast<T*>(alloc_pinned(sizeof(T)))};
+        new (ptr.get()) T;
+        return ptr;
+    }
+
+    // Check configuration consistency
+    // Throw exception with error message on detected inconsistency.
+    // Parameters can set separately to nullptr for a noop with respect
+    // to the particular parameter.
+    template<typename float_type=float>
+    void check_config(const config_persistent<float_type>* cpers, const config_runtime<float_type>* crt);
+
+    // Print config_persistent into stream
+    template<typename CharT, typename Traits, typename float_type=float>
+    inline auto& operator<<(std::basic_ostream<CharT, Traits>& out, const config_runtime<float_type>& crt)
+    {
+        out << "crt: length_threshold=" << crt.length_threshold
+            << " triml=" << crt.triml
+            << " trimh=" << crt.trimh
+            << " delta=" << crt.delta
+            << " dist1=" << crt.dist1
+            << " dist3=" << crt.dist3
+            << " min_spots=" << crt.min_spots
+            << " num_halfsphere_points=" << crt.num_halfsphere_points
+            << " num_angle_points=" << crt.num_angle_points;
+        return out;
+    }
+
+    // Print config_persistent into stream
+    template<typename CharT, typename Traits, typename float_type=float>
+    inline auto& operator<<(std::basic_ostream<CharT, Traits>& out, const config_persistent<float_type>& cpers)
+    {
+        out << "cpers: max_output_cells=" << cpers.max_output_cells
+            << " max_input_cells=" << cpers.max_input_cells
+            << " max_spots=" << cpers.max_spots
+            << " num_candidate_vectors=" << cpers.num_candidate_vectors
+            << " redundant_computations=" << cpers.redundant_computations;
+        return out;
+    }
+
+    // Throw exception if runtime problem is detected
+    void runtime_check();
+
+} // namespace fast_feedback
+
+#endif
diff --git a/image_analysis/indexing/fast-feedback-indexer/ffbidx/indexer_gpu.h b/image_analysis/indexing/fast-feedback-indexer/ffbidx/indexer_gpu.h
new file mode 100644
index 000000000..b10012b97
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/ffbidx/indexer_gpu.h
@@ -0,0 +1,74 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/ffbidx/indexer_gpu.h), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#ifndef INDEXER_GPU_H
+#define INDEXER_GPU_H
+
+#include "ffbidx/indexer.h"
+
+namespace gpu {
+   using namespace fast_feedback;
+
+   // GPU part of indexer::init
+   template <typename float_type>
+   void init (const indexer<float_type>& instance);
+
+   // GPU part of indexer::drop
+   template <typename float_type>
+   void drop (const indexer<float_type>& instance);
+
+   // GPU part of indexer::index_start
+   template <typename float_type>
+   void index_start (const indexer<float_type>& instance, const input<float_type>& in, output<float_type>& out, const config_runtime<float_type>& conf_rt,
+                     void(*callback)(void*), void* data);
+
+   // GPU part of indexer::index_end
+   template <typename float_type>
+   void index_end (const indexer<float_type>& instance, output<float_type>& out);
+
+   // Register host memory
+   void pin_memory(void* ptr, std::size_t size);
+
+   // Unregister host memory
+   void unpin_memory(void* ptr);
+
+   // Allocate pinned host memory
+   void* alloc_pinned(std::size_t num_bytes);
+
+   // Deallocate pinned host memory
+   void dealloc_pinned(void* ptr);
+   
+   // GPU version of check_config
+   template<typename float_type=float>
+   void check_config(const config_persistent<float_type>* cpers, const config_runtime<float_type>* crt);
+
+   // Check gpu runtime, throws exception on incompatibility
+   void runtime_check();
+
+} // namespace gpu
+
+#endif
diff --git a/image_analysis/indexing/fast-feedback-indexer/ffbidx/log.h b/image_analysis/indexing/fast-feedback-indexer/ffbidx/log.h
new file mode 100644
index 000000000..1f1968a19
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/ffbidx/log.h
@@ -0,0 +1,140 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/ffbidx/log.h), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#ifndef INDEXER_LOG_H
+#define INDEXER_LOG_H
+
+#include <iostream>
+#include <atomic>
+#include <mutex>
+#include <string>
+
+namespace fast_feedback {
+    namespace logger {
+        // Log levels
+        constexpr unsigned l_fatal = 0u;    // Log fatal errors
+        constexpr unsigned l_error = 1u;    // Log errors
+        constexpr unsigned l_warn = 2u;     // Log warnings
+        constexpr unsigned l_info = 3u;     // Log useful information
+        constexpr unsigned l_debug = 4u;    // Log debug information
+        constexpr unsigned l_undef = 10u;   // Undefined (only returned by get_init_log_level())
+
+        // Current log level, default is l_error
+        // Logging will react to changes dynamically
+        inline std::atomic<unsigned> level{l_error};
+
+        // Get string representation for log level
+        const char* level_to_string(unsigned log_level);
+
+        // Check if log level is active
+        template<unsigned log_level>
+        inline bool level_active() noexcept
+        {
+            return log_level <= level.load();
+        }
+
+        // Get common log output lock
+        std::mutex& lock() noexcept;
+
+        // Get version string
+        const char* get_version();
+
+        // Get log level from environment, if given
+        // Parses the environment variable INDEXER_LOG_LEVEL
+        // which should contain one of {"fatal", "error", "warn", "info", "debug"}
+        // If the variable is undefined, l_undef is returned.
+        unsigned get_init_log_level();
+
+        // Initalize log level using get_init_log_level()
+        // If the variable is undefined, the log level is not changed.
+        inline void init_log_level()
+        {
+            unsigned new_level = get_init_log_level();
+            if (new_level != l_undef)
+                level.store(new_level);
+        }
+
+        // Logger writes to clog
+        // Flushes only if log_level is l_fatal
+        template<unsigned log_level>
+        struct logger final {
+            inline logger()
+            {
+                init_log_level();
+            }
+        };
+
+        // For starting a stanza
+        inline struct stanza_type final {} stanza;
+
+        // Log output to clog
+        template<typename T, unsigned log_level>
+        inline logger<log_level>& operator<<(logger<log_level>& out, const T& value)
+        {
+            if (level_active<log_level>())
+                std::clog << value;
+            if constexpr (log_level == l_fatal) {
+                std::clog.flush();
+            }
+            return out;
+        }
+
+        // Start stanza
+        template<unsigned log_level>
+        inline logger<log_level>& operator<<(logger<log_level>& out, const stanza_type&)
+        {
+            if (level_active<log_level>())
+                std::clog << '(' << level_to_string(log_level) << ") ";
+            if constexpr (log_level == l_fatal) {
+                std::clog.flush();
+            }
+            return out;
+        }
+
+        #ifndef _INDEXER_LOG_IMPL_
+            // Logger objects
+            extern logger<l_fatal> fatal;
+            extern logger<l_error> error;
+            extern logger<l_warn> warn;
+            extern logger<l_info> info;
+            extern logger<l_debug> debug;
+        #endif
+
+        // TODO: imlement thread safe lock_guard<log_level> for logger<log_level>
+        // {
+        //  guard = logger << (create guard) blabla << blabla;
+        //  guard << blabla << blabla; (release guard)
+        // }
+    } // namespace logger
+} // namespace fast_feedback
+
+// Start and end locked logging conditional on logging level
+// This will hold the logger::lock()
+#define LOG_START(level) if (fast_feedback::logger::level_active<level>()) { std::lock_guard<std::mutex> logger_output_lock{fast_feedback::logger::lock()}; do
+#define LOG_END while(false); }
+
+#endif // INDEXER_LOG_H
diff --git a/image_analysis/indexing/fast-feedback-indexer/ffbidx/refine.h b/image_analysis/indexing/fast-feedback-indexer/ffbidx/refine.h
new file mode 100644
index 000000000..cc31b8a8d
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/ffbidx/refine.h
@@ -0,0 +1,1012 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/ffbidx/refine.h), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#ifndef INDEXER_REFINE_H
+#define INDEXER_REFINE_H
+
+#include <Eigen/Dense>
+#include <Eigen/LU>
+#include <numeric>
+#include <algorithm>
+#include "ffbidx/exception.h"
+#include "ffbidx/indexer.h"
+#include "ffbidx/log.h"
+
+namespace fast_feedback {
+    namespace refine {
+        // Provide convenience classes for the fast feedback indexer
+        // - indexer: calls the raw fast_feedback::indexer
+        // - indexer_ifss: calls indexer and refined the output cells
+        // - indexer_ifse: calls indexer and refines the output cells
+        //
+        // Like the raw indexer these indexers (idx) provide several call possibilities
+        //
+        // - synchronous: idx.index(..)
+        // - asynchronous: idx.index_start(.., callback, data)
+        //                      callback(data) by GPU <-- result is ready
+        //                 idx.index_end() <-- will do the refinement on CPU
+        //
+        // For multithreaded refinement use the base indexer, split the output cells into
+        // logical blocks, and let threads call the refine(..) static methods on individual
+        // output cell blocks.
+
+        using logger::stanza;
+
+        // Base indexer class for refinement
+        // - controlling all indexer data
+        // - getter/setter interface
+        // The origin is implicitly assumed to be part of the lattice
+        template<typename float_type=float>
+        class indexer {
+          protected:
+            fast_feedback::indexer<float_type> idx;                 // raw indexer
+            Eigen::MatrixX3<float_type> icells;                     // space for max_input_cells in real space
+            Eigen::MatrixX3<float_type> spots;                      // space for max_spots in reciprocal space
+            Eigen::MatrixX3<float_type> ocells;                     // max_output_cells coordinate container
+            Eigen::VectorX<float_type> scores;                      // output cell scores container
+            fast_feedback::input<float_type> input;                 // raw indexer input
+            fast_feedback::output<float_type> output;               // raw indexer output
+            fast_feedback::memory_pin pin_icells;                   // pin input cells container
+            fast_feedback::memory_pin pin_spots;                    // pin spots container
+            fast_feedback::memory_pin pin_ocells;                   // pin output cells container
+            fast_feedback::memory_pin pin_scores;                   // pin output cell scores container
+            fast_feedback::memory_pin pin_crt;                      // pin runtime config memory
+            fast_feedback::config_runtime<float_type> crt;          // raw indexer runtime config
+          public:
+            inline static void check_config (const fast_feedback::config_persistent<float_type>& cp,
+                                             const fast_feedback::config_runtime<float_type>& cr)
+            {
+                if (cp.max_input_cells <= 0u)
+                    throw FF_EXCEPTION("no input cells");
+                if (cp.max_output_cells <= 0)
+                    throw FF_EXCEPTION("no output cells");
+                if (cp.max_spots <= 0u)
+                    throw FF_EXCEPTION("no spots");
+                if (cp.num_candidate_vectors < 1u)
+                    throw FF_EXCEPTION("nonpositive number of candidate vectors");
+                if (cr.num_halfsphere_points < cp.num_candidate_vectors)
+                    throw FF_EXCEPTION("fewer half sphere sample points than required candidate vectors");
+                if ((cr.num_angle_points > 0u) && (cr.num_angle_points < cp.max_output_cells))
+                    throw FF_EXCEPTION("fewer angle sample points than required candidate cells");
+                if (cr.triml < float_type{0.f})
+                    throw FF_EXCEPTION("lower trim value < 0");
+                if (cr.triml > cr.trimh)
+                    throw FF_EXCEPTION("lower > higher trim value");
+                if (cr.trimh > float_type{.5f})
+                    throw FF_EXCEPTION("higher trim value > 0.5");
+                if (cr.delta <= float_type{.0})
+                    throw FF_EXCEPTION("nonpositive delta value");
+            }
+
+            // Create base indexer object
+            // - allocate (pinned) memory for all input and output data
+            // - store configuration
+            inline indexer (const fast_feedback::config_persistent<float_type>& cp,
+                            const fast_feedback::config_runtime<float_type>& cr)
+                : idx{cp},
+                  icells{cp.max_input_cells * 3u, 3u}, spots{cp.max_spots, 3u},
+                  ocells{3u * cp.max_output_cells, 3u}, scores{cp.max_output_cells},
+                  input{{&icells(0,0), &icells(0,1), &icells(0,2)}, {&spots(0,0), &spots(0,1), &spots(0,2)}, 0u, 0u, true, true},
+                  output{&ocells(0,0), &ocells(0,1), &ocells(0,2), scores.data(), idx.cpers.max_output_cells},
+                  pin_icells{icells}, pin_spots{spots},
+                  pin_ocells{ocells}, pin_scores{scores},
+                  pin_crt{fast_feedback::memory_pin::on(crt)},
+                  crt{cr}
+            {
+                check_config(cp, cr);
+            }
+
+            inline indexer (indexer&&) = default;
+            inline indexer& operator= (indexer&&) = default;
+            inline virtual ~indexer () = default;
+
+            indexer () = delete;
+            indexer (const indexer&) = delete;
+            indexer& operator= (const indexer&) = delete;
+
+            // Asynchronouly launch indexing operation on GPU
+            // - n_input_cells must be less than max_input_cells
+            // - n_spots must be less than max_spots
+            // - if callback is given, it will be called with data as the argument as soon as  index_end can be called
+            inline void index_start (unsigned n_input_cells, unsigned n_spots, void(*callback)(void*)=nullptr, void* data=nullptr)
+            {
+                if (n_input_cells == 0u) {
+                    input.new_cells = false;
+                } else {
+                    input.n_cells = n_input_cells;
+                    input.new_cells = true;
+                }
+                if (n_spots == 0u) {
+                    input.new_spots = false;
+                } else {
+                    input.n_spots = n_spots;
+                    input.new_spots = true;
+                }
+                idx.index_start(input, output, crt, callback, data);
+            }
+
+            // Finish indexing
+            // - index_start must have been called before this
+            inline virtual void index_end ()
+            {
+                idx.index_end(output);
+            }
+
+            // Synchronous indexing
+            // - n_input_cells must be less than max_input_cells
+            // - n_spots must be less than max_spots
+            inline void index (unsigned n_input_cells, unsigned n_spots)
+            {
+                index_start(n_input_cells, n_spots);
+                index_end();
+            }
+
+            // Reciprocal space spot access: spot i
+            inline float_type& spotX (unsigned i=0u) noexcept
+            { return spots(i, 0u); }
+
+            inline const float_type& spotX (unsigned i=0u) const noexcept
+            { return &spots(i, 0u); }
+
+            inline float_type& spotY (unsigned i=0u) noexcept
+            { return spots(i, 1u); }
+
+            inline const float_type& spotY (unsigned i=0u) const noexcept
+            { return spots(i, 1u); }
+
+            inline float_type& spotZ (unsigned i=0u) noexcept
+            { return spots(i, 2u); }
+
+            inline const float_type& spotZ (unsigned i=0u) const noexcept
+            { return spots(i, 2u); }
+
+            // Coords area designated for reciprocal space spots, fill top down
+            inline auto& spotM ()
+            { return spots; }
+
+            // Used coords area designated for reciprocal space spots
+            inline auto Spots ()
+            {
+                return spots.topRows(input.n_spots);
+            }
+
+            // Real space input cell access: cell i, vector j
+            inline float_type& iCellX (unsigned i=0u, unsigned j=0u) noexcept
+            { return icells(3u * i + j, 0u); }
+
+            inline const float_type& iCellX (unsigned i=0u, unsigned j=0u) const noexcept
+            { return icells(3u * i + j, 0u); }
+
+            inline float_type& iCellY (unsigned i=0u, unsigned j=0u) noexcept
+            { return icells(3u * i + j, 1u); }
+
+            inline const float_type& iCellY (unsigned i=0u, unsigned j=0u) const noexcept
+            { return icells(3u * i + j, 1u); }
+
+            inline float_type& iCellZ (unsigned i=0u, unsigned j=0u) noexcept
+            { return icells(3u * i + j, 2u); }
+
+            inline const float_type& iCellZ (unsigned i=0u, unsigned j=0u) const noexcept
+            { return icells(3u * i + j, 2u); }
+
+            // Coords area for real space input cell i
+            inline auto iCell (unsigned i=0u) noexcept
+            { return icells.block(3u * i, 0u, 3u, 3u); }
+
+            inline auto iCell (unsigned i=0u) const noexcept
+            { return icells.block(3u * i, 0u, 3u, 3u); }
+
+            // Coords area designated for real space input cells, fill cellwise bottom up
+            inline auto& iCellM () noexcept
+            { return icells; }
+
+            // Input size access
+            inline unsigned n_input_cells () const noexcept
+            { return input.n_cells; }
+
+            inline unsigned n_spots () const noexcept
+            { return input.n_spots; }
+
+            // Real space output cell access: cell i, vector j
+            inline float_type& oCellX (unsigned i=0u, unsigned j=0u) noexcept
+            { return ocells(3u * i + j, 0u); }
+
+            inline const float_type& oCellX (unsigned i=0u, unsigned j=0u) const noexcept
+            { return ocells(3u * i + j, 0u); }
+
+            inline float_type& oCellY (unsigned i=0u, unsigned j=0u) noexcept
+            { return ocells(3u * i + j, 1u); }
+
+            inline const float_type& oCellY (unsigned i=0u, unsigned j=0u) const noexcept
+            { return ocells(3u * i + j, 1u); }
+
+            inline float_type& oCellZ (unsigned i=0u, unsigned j=0u) noexcept
+            { return ocells(3u * i + j, 2u); }
+
+            inline const float_type& oCellZ (unsigned i=0u, unsigned j=0u) const noexcept
+            { return ocells(3u * i + j, 2u); }
+
+            // Real space output cell i
+            inline auto oCell (unsigned i) noexcept
+            { return ocells.block(3u * i, 0u, 3u, 3u); }
+
+            inline auto oCell (unsigned i) const noexcept
+            { return ocells.block(3u * i, 0u, 3u, 3u); }
+
+            // All output cells
+            inline auto& oCellM () noexcept
+            { return ocells; }
+
+            // Output cell score access: cell i
+            inline float_type& oScore (unsigned i=0u) noexcept
+            { return scores(i); }
+
+            inline const float_type& oScore (unsigned i=0u) const noexcept
+            { return scores(i); }
+
+            // All output scores
+            inline auto& oScoreV () noexcept
+            { return scores; }
+
+            // Dissect the base indexer score into two parts:
+            // - main score: number of spots within a distance of trimh to closest lattice point
+            // - sub score: exp2(sum[spots](log2(trim[triml..trimh](dist2int(dot(v,spot))) + delta)) / #spots) - delta
+            inline static std::pair<float_type, float_type> score_parts (float_type score) noexcept
+            {
+                float_type nsp = -std::floor(score);
+                float_type s = score + nsp;
+                return std::make_pair(nsp-1, s);
+            }
+
+            // Output size access
+            inline unsigned n_output_cells () const noexcept
+            { return output.n_cells; }
+
+            // Runtime configuration access
+            inline void length_threshold (float_type lt)
+            {
+                if (lt < float_type{.0f})
+                    throw FF_EXCEPTION("negative length threshold");
+                crt.length_threshold = lt;
+            }
+
+            inline float_type length_threshold () const noexcept
+            { return crt.length_threshold; }
+
+            inline void triml (float_type tl)
+            {
+                if (tl < float_type{0.f})
+                    throw FF_EXCEPTION("lower trim value < 0");
+                if (tl > crt.trimh)
+                    throw FF_EXCEPTION("lower > higher trim value");
+                crt.triml = tl;
+            }
+
+            inline float_type triml () const noexcept
+            {
+                return crt.triml;
+            }
+
+            inline void trimh (float_type th)
+            {
+                if (crt.triml > th)
+                    throw FF_EXCEPTION("lower > higher trim value");
+                if (th > float_type{.5f})
+                    throw FF_EXCEPTION("higher trim value > 0.5");
+                crt.trimh = th;
+            }
+
+            inline float_type trimh () const noexcept
+            {
+                return crt.trimh;
+            }
+
+            inline void delta (float_type d)
+            {
+                if (d <= float_type{.0})
+                    throw FF_EXCEPTION("nonnegative delta value");
+                crt.delta = d;
+            }
+
+            inline float_type delta () const noexcept
+            {
+                return crt.delta;
+            }
+
+            inline void dist1 (float_type d) noexcept
+            {
+                crt.dist1 = d;
+            }
+
+            inline float_type dist1 () const noexcept
+            {
+                return crt.dist1;
+            }
+
+            inline void dist3 (float_type d) noexcept
+            {
+                crt.dist3 = d;
+            }
+
+            inline float_type dist3 () const noexcept
+            {
+                return crt.dist3;
+            }
+
+            inline void min_spots1 (unsigned ms) noexcept
+            {
+                crt.min_spots = ms;
+            }
+
+            inline unsigned min_spots1 () const noexcept
+            { return crt.min_spots; }
+
+            inline void num_halfsphere_points (unsigned nhsp)
+            {
+                unsigned tmp = crt.num_halfsphere_points;
+                crt.num_halfsphere_points = nhsp;
+                try {
+                    check_config();
+                } catch (...) {
+                    crt.num_halfsphere_points = tmp;
+                    throw;
+                }
+            }
+
+            inline unsigned num_halfsphere_points () const noexcept
+            { return crt.num_halfsphere_points; }
+
+            inline void num_angle_points (unsigned nap)
+            {
+                unsigned tmp = crt.num_angle_points;
+                crt.num_angle_points = nap;
+                try {
+                    check_config();
+                } catch (...) {
+                    crt.num_angle_points = tmp;
+                    throw;
+                }
+            }
+
+            inline unsigned num_angle_points () const noexcept
+            { return crt.num_angle_points; }
+
+            inline const config_runtime<float_type>& conf_runtime () const noexcept
+            { return crt; }
+
+            // Persistent configuration access
+            // - to change the persistent config, create another indexer instance
+            inline unsigned max_output_cells () const noexcept
+            { return idx.cpers.max_output_cells; }
+
+            inline unsigned max_input_cells () const noexcept
+            { return idx.cpers.max_input_cells; }
+
+            inline unsigned max_spots () const noexcept
+            { return idx.cpers.max_spots; }
+
+            inline unsigned num_candidate_vectors () const noexcept
+            { return idx.cpers.num_candidate_vectors; }
+
+            inline bool redundant_computations () const noexcept
+            { return idx.cpers.redundant_computations; }
+
+            inline const config_persistent<float_type>& conf_persistent () const noexcept
+            { return idx.cpers; }
+        }; // indexer
+
+        // Iterative fit to selected spots refinement indexer extra config
+        template <typename float_type=float>
+        struct config_ifss final {
+            float_type threshold_contraction=.8;    // contract error threshold by this value in every iteration
+            float_type max_distance=.01;            // max distance to integer for inliers
+            unsigned min_spots=6;                   // minimum number of spots to fit against
+            unsigned max_iter=15;                   // max number of iterations
+        };
+
+        // Iterative fit to selected spots refinement indexer
+        template <typename float_type=float>
+        class indexer_ifss : public indexer<float_type> {
+            config_ifss<float_type> cifss;
+          public:
+            inline static void check_config (const config_ifss<float_type>& c)
+            {
+                if (c.threshold_contraction <= float_type{.0})
+                    throw FF_EXCEPTION("nonpositive threshold contraction");
+                if (c.threshold_contraction >= float_type{1.})
+                    throw FF_EXCEPTION("threshold contraction >= 1");
+                if (c.min_spots <= 3)
+                    throw FF_EXCEPTION("min spots <= 3");
+            }
+
+            inline indexer_ifss (const fast_feedback::config_persistent<float_type>& cp,
+                                const fast_feedback::config_runtime<float_type>& cr,
+                                const config_ifss<float_type>& c)
+                : indexer<float_type>{cp, cr}, cifss{c}
+            {
+                check_config(c);
+            }
+
+            inline indexer_ifss (indexer_ifss&&) = default;
+            inline indexer_ifss& operator= (indexer_ifss&&) = default;
+            inline ~indexer_ifss () override = default;
+
+            indexer_ifss () = delete;
+            indexer_ifss (const indexer_ifss&) = delete;
+            indexer_ifss& operator= (const indexer_ifss&) = delete;
+
+            // Refine cells
+            //
+            // This call splits cells into nblocks cell blocks to allow multithreaded cell refinement.
+            // All threads must use a common nblocks parameter and each thread an individual block parameter.
+            //
+            // input:
+            // - spots      spot reciprocal coordinates matrix
+            // - cells      output cells real space coordinates matrix like the one in the base indexer
+            // - scores     output cell scores matrix with scores coming from the base indexer
+            // - cpers      persistent config for the matrices
+            // - cifss      ifss config
+            // - block      which of the N cell blocks
+            // - nblocks    use N cell blocks
+            // output:
+            // - cells      the refined cells
+            // - scores     refined cell scores: largest distance of the min_spots closest to their approximated lattice points
+            template<typename MatX3, typename VecX>
+            inline static void refine (const Eigen::Ref<Eigen::MatrixX3<float_type>>& spots,
+                                       Eigen::DenseBase<MatX3>& cells,
+                                       Eigen::DenseBase<VecX>& scores,
+                                       const config_ifss<float_type>& cifss,
+                                       unsigned block=0, unsigned nblocks=1)
+            {
+                using namespace Eigen;
+                using Mx3 = MatrixX3<float_type>;
+                using M3 = Matrix3<float_type>;
+                const unsigned nspots = spots.rows();
+                const unsigned ncells = scores.rows();
+                VectorX<bool> below{nspots};
+                MatrixX3<bool> sel{nspots, 3u};
+                Mx3 resid{nspots, 3u};
+                Mx3 miller{nspots, 3u};
+                M3 cell;
+                const unsigned blocksize = (ncells + nblocks - 1u) / nblocks;
+                const unsigned startcell = block * blocksize;
+                const unsigned endcell = std::min(startcell + blocksize, ncells);
+                for (unsigned j=startcell; j<endcell; j++) {
+                    cell = cells.block(3u * j, 0u, 3u, 3u).transpose();  // cell: col vectors
+                    float_type threshold = indexer<float_type>::score_parts(scores[j]).second;
+                    resid = spots * cell;       // coordinates in system <cell>
+                    miller = round(resid.array());
+                    resid -= miller;
+                    if (threshold > cifss.max_distance) {
+                        below = (resid.rowwise().norm().array() < threshold);
+                        if (below.count() < cifss.min_spots)
+                            goto calc_score;
+                        threshold *= cifss.threshold_contraction;
+                        sel.colwise() = below;
+                        HouseholderQR<Mx3> qr{sel.select(spots, .0f)};
+                        cell = qr.solve(sel.select(miller, .0f));
+                    }
+                    for (unsigned niter=1; niter<cifss.max_iter && threshold>cifss.max_distance; niter++) {
+                        resid = (spots * cell) - miller;
+                        below = (resid.rowwise().norm().array() < threshold);
+                        if (below.count() < cifss.min_spots)
+                            break;
+                        threshold *= cifss.threshold_contraction;
+                        sel.colwise() = below;
+                        HouseholderQR<Mx3> qr{sel.select(spots, .0f)};
+                        cell = qr.solve(sel.select(miller, .0f));
+                    }
+                    calc_score: {
+                        ArrayX<float_type> dist = resid.rowwise().norm();
+                        if (dist.size() < cifss.min_spots) {
+                            scores(j) = float_type{1.};
+                        } else {
+                            auto nth = std::begin(dist) + (cifss.min_spots - 1);
+                            std::nth_element(std::begin(dist), nth, std::end(dist));
+                            scores(j) = *nth;
+                        }
+                    }
+                    cells.block(3u * j, 0u, 3u, 3u) = cell.transpose();
+                }
+            }
+
+            // Refined result
+            inline void index_end () override
+            {
+                indexer<float_type>::index_end();
+                refine(this->Spots(), this->ocells, this->scores, cifss);
+            }
+
+            // ifss configuration access
+            inline void threshold_contraction (float_type tc)
+            {
+                if (tc <= float_type{.0})
+                    throw FF_EXCEPTION("nonpositive threshold contraction");
+                if (tc >= float_type{1.})
+                    throw FF_EXCEPTION("threshold contraction >= 1");
+                cifss.threshold_contraction = tc;
+            }
+            
+            inline float_type threshold_contraction () const noexcept
+            { return cifss.threshold_contraction; }
+
+            inline void min_spots (unsigned ms)
+            {
+                if (ms <= 3)
+                    throw FF_EXCEPTION("min spots <= 3");
+                cifss.min_spots = ms;
+            }
+
+            inline unsigned min_spots () const noexcept
+            { return cifss.min_spots; }
+
+            inline void max_distance (float_type d) noexcept
+            { cifss.max_distance = d; }
+
+            inline float_type max_distance () const noexcept
+            { return cifss.max_distance; }
+            
+            inline void max_iter (unsigned n) noexcept
+            { cifss.max_iter = n; }
+
+            inline unsigned max_iter () const noexcept
+            { return cifss.max_iter; }
+
+            inline const config_ifss<float_type>& conf_ifss () const noexcept
+            { return cifss; }
+
+        }; // indexer_ifss
+
+        // Iterative fit to selected errors refinement indexer extra config
+        template <typename float_type=float>
+        struct config_ifse final {
+            float_type threshold_contraction=.8;    // contract error threshold by this value in every iteration
+            float_type max_distance=.01;            // max distance to integer for inliers
+            unsigned min_spots=6;                   // minimum number of spots to fit against
+            unsigned max_iter=15;                   // max number of iterations
+        };
+
+        // Iterative fit to selected errors refinement indexer
+        template <typename float_type=float>
+        class indexer_ifse : public indexer<float_type> {
+            config_ifse<float_type> cifse;
+          public:
+            inline static void check_config (const config_ifse<float_type>& c)
+            {
+                if (c.threshold_contraction <= float_type{.0})
+                    throw FF_EXCEPTION("nonpositive contraction speed");
+                if (c.min_spots <= 3)
+                    throw FF_EXCEPTION("min spots <= 3");
+            }
+
+            inline indexer_ifse (const fast_feedback::config_persistent<float_type>& cp,
+                          const fast_feedback::config_runtime<float_type>& cr,
+                          const config_ifse<float_type>& c)
+                : indexer<float_type>{cp, cr}, cifse{c}
+            {}
+
+            inline indexer_ifse (indexer_ifse&&) = default;
+            inline indexer_ifse& operator= (indexer_ifse&&) = default;
+            inline ~indexer_ifse () override = default;
+
+            indexer_ifse () = delete;
+            indexer_ifse (const indexer_ifse&) = delete;
+            indexer_ifse& operator= (const indexer_ifse&) = delete;
+
+            // Refine cells
+            //
+            // This call splits cells into nblocks cell blocks to allow multithreaded cell refinement.
+            // All threads must use a common nblocks parameter and each thread an individual block parameter.
+            //
+            // input:
+            // - spots      spot coordinate matrix
+            // - cells      output cells matrix like the one in the base indexer
+            // - scores     output cell scores matrix with scores coming from the base indexer
+            // - cpers      persistent config for the matrices
+            // - cifse      ifse config
+            // - block      which of the N cell blocks
+            // - nblocks    use N cell blocks
+            // output:
+            // - cells      the refined cells
+            // - scores     refined cell scores: largest distance of the min_spots closest to their approximated lattice points
+            template<typename MatX3, typename VecX>
+            inline static void refine (const Eigen::Ref<Eigen::MatrixX3<float_type>>& spots,
+                                       Eigen::DenseBase<MatX3>& cells,
+                                       Eigen::DenseBase<VecX>& scores,
+                                       const config_ifse<float_type>& cifse,
+                                       unsigned block=0, unsigned nblocks=1)
+            {
+                using namespace Eigen;
+                using Mx3 = MatrixX3<float_type>;
+                using M3 = Matrix3<float_type>;
+                const unsigned nspots = spots.rows();
+                const unsigned ncells = scores.rows();
+                VectorX<bool> below{nspots};
+                MatrixX3<bool> sel{nspots, 3u};
+                Mx3 resid{nspots, 3u};
+                Mx3 miller{nspots, 3u};
+                M3 cell;
+                const unsigned blocksize = (ncells + nblocks - 1u) / nblocks;
+                const unsigned startcell = block * blocksize;
+                const unsigned endcell = std::min(startcell + blocksize, ncells);
+                for (unsigned j=startcell; j<endcell; j++) {
+                    cell = cells.block(3u * j, 0u, 3u, 3u).transpose();  // cell: col vectors
+                    resid = spots * cell;   // coordinates in system <cell>
+                    miller = round(resid.array());
+                    resid -= miller;
+                    float_type threshold = indexer<float_type>::score_parts(scores[j]).second;
+                    for (unsigned niter=0; niter<cifse.max_iter && threshold>cifse.max_distance; niter++) {
+                        below = (resid.rowwise().norm().array() < threshold);
+                        if (below.count() < cifse.min_spots)
+                            break;
+                        threshold *= cifse.threshold_contraction;
+                        sel.colwise() = below;
+                        HouseholderQR<Mx3> qr{sel.select(spots, .0f)};
+                        cell -= qr.solve(sel.select(resid, .0f));
+                        resid = spots * cell;   // coordinates in system <cell>
+                        miller = round(resid.array());
+                        resid -= miller;
+                    }
+                    {
+                        ArrayX<float_type> dist = resid.rowwise().norm();
+                        if (dist.size() < cifse.min_spots) {
+                            scores(j) = float_type{1.};
+                        } else {
+                            auto nth = std::begin(dist) + (cifse.min_spots - 1);
+                            std::nth_element(std::begin(dist), nth, std::end(dist));
+                            scores(j) = *nth;
+                        }
+                    }
+                    cells.block(3u * j, 0u, 3u, 3u) = cell.transpose();
+                }
+            }
+
+            // Refined result
+            inline void index_end () override
+            {
+                indexer<float_type>::index_end();
+                refine(this->Spots(), this->ocells, this->scores, cifse);
+            }
+
+            // ifse configuration access
+            inline void threshold_contraction (float_type tc)
+            {
+                if (tc <= float_type{.0})
+                    throw FF_EXCEPTION("nonpositive threshold contraction");
+                if (tc >= float_type{1.})
+                    throw FF_EXCEPTION("threshold contraction >= 1");
+                cifse.threshold_contraction = tc;
+            }
+            
+            inline float_type threshold_contraction () const noexcept
+            { return cifse.threshold_contraction; }
+
+            inline float_type max_distance () const noexcept
+            { return cifse.max_distance; }
+            
+            inline void max_distance (float_type d) noexcept
+            { cifse.max_distance = d; }
+
+            inline void min_spots (unsigned ms)
+            {
+                if (ms <= 3)
+                    throw FF_EXCEPTION("min spots <= 3");
+                cifse.min_spots = ms;
+            }
+
+            inline unsigned min_spots () const noexcept
+            { return cifse.min_spots; }
+
+            inline void max_iter (unsigned n) noexcept
+            { cifse.max_iter = n; }
+
+            inline unsigned max_iter () const noexcept
+            { return cifse.max_iter; }
+
+            inline const config_ifse<float_type>& conf_ifse () const noexcept
+            { return cifse; }
+
+        }; // indexer_ifse
+
+        // Iterative fit to selected spots reciprocal refinement indexer extra config
+        template <typename float_type=float>
+        struct config_ifssr final {
+            float_type threshold_contraction=.8;    // contract error threshold by this value in every iteration
+            float_type max_distance=.00075;         // max distance to reciprocal spots for inliers
+            unsigned min_spots=8;                   // minimum number of spots to fit against
+            unsigned max_iter=32;                   // max number of iterations
+        };
+
+        // Iterative fit to selected spots refinement indexer
+        template <typename float_type=float>
+        class indexer_ifssr : public indexer<float_type> {
+            config_ifssr<float_type> cifssr;
+          public:
+            inline static void check_config (const config_ifssr<float_type>& c)
+            {
+                if (c.threshold_contraction <= float_type{.0})
+                    throw FF_EXCEPTION("nonpositive threshold contraction");
+                if (c.threshold_contraction >= float_type{1.})
+                    throw FF_EXCEPTION("threshold contraction >= 1");
+                if (c.min_spots <= 3)
+                    throw FF_EXCEPTION("min spots <= 3");
+            }
+
+            inline indexer_ifssr (const fast_feedback::config_persistent<float_type>& cp,
+                                  const fast_feedback::config_runtime<float_type>& cr,
+                                  const config_ifssr<float_type>& c)
+                : indexer<float_type>{cp, cr}, cifssr{c}
+            {
+                check_config(c);
+            }
+
+            inline indexer_ifssr (indexer_ifssr&&) = default;
+            inline indexer_ifssr& operator= (indexer_ifssr&&) = default;
+            inline ~indexer_ifssr () override = default;
+
+            indexer_ifssr () = delete;
+            indexer_ifssr (const indexer_ifssr&) = delete;
+            indexer_ifssr& operator= (const indexer_ifssr&) = delete;
+
+            // Refine cells
+            //
+            // This call splits cells into nblocks cell blocks to allow multithreaded cell refinement.
+            // All threads must use a common nblocks parameter and each thread an individual block parameter.
+            //
+            // input:
+            // - spots      spot reciprocal coordinates matrix
+            // - cells      output cells real space coordinates matrix like the one in the base indexer
+            // - scores     output cell scores matrix with scores coming from the base indexer
+            // - cpers      persistent config for the matrices
+            // - cifssr     ifssr config
+            // - block      which of the N cell blocks
+            // - nblocks    use N cell blocks
+            // output:
+            // - cells      the refined cells
+            // - scores     refined cell scores: largest distance of the min_spots closest to their approximated lattice points
+            template<typename MatX3, typename VecX>
+            inline static void refine (const Eigen::Ref<const Eigen::MatrixX3<float_type>>& spots,
+                                       Eigen::DenseBase<MatX3>& cells,
+                                       Eigen::DenseBase<VecX>& scores,
+                                       const config_ifssr<float_type>& cifssr,
+                                       unsigned block=0, unsigned nblocks=1)
+            {
+                using namespace Eigen;
+                using Mx3 = MatrixX3<float_type>;
+                using M3 = Matrix3<float_type>;
+                const unsigned nspots = spots.rows();
+                const unsigned ncells = scores.rows();
+                VectorX<bool> below{nspots};
+                MatrixX3<bool> sel{nspots, 3u};
+                Mx3 resid{nspots, 3u};
+                Mx3 miller{nspots, 3u};
+                M3 cell;
+                const unsigned blocksize = (ncells + nblocks - 1u) / nblocks;
+                const unsigned startcell = block * blocksize;
+                const unsigned endcell = std::min(startcell + blocksize, ncells);
+                for (unsigned j=startcell; j<endcell; j++) {
+                    if (nspots < cifssr.min_spots) {
+                        scores(j) = float_type{1.};
+                        continue;
+                    }
+                    cell = cells.block(3u * j, 0u, 3u, 3u).transpose(); // cell: col vectors
+                    const float_type scale = cell.colwise().norm().minCoeff();
+                    float_type threshold = indexer<float_type>::score_parts(scores[j]).second / scale;
+                    for (unsigned niter=1; niter<cifssr.max_iter && threshold>cifssr.max_distance; niter++) {
+                        miller = round((spots * cell).array());
+                        resid = miller * cell.inverse();    // reciprocal spots induced by <cell>
+                        resid -= spots;                     // distance between induced and given spots
+                        below = (resid.rowwise().norm().array() < threshold);
+                        if (below.count() < cifssr.min_spots)
+                            break;
+                        threshold *= cifssr.threshold_contraction;
+                        sel.colwise() = below;
+                        HouseholderQR<Mx3> qr{sel.select(spots, .0f)};
+                        cell = qr.solve(sel.select(miller, .0f));
+                    }
+                    {   // calc score
+                        ArrayX<float_type> dist = resid.rowwise().norm();
+                        auto nth = std::begin(dist) + (cifssr.min_spots - 1);
+                        std::nth_element(std::begin(dist), nth, std::end(dist));
+                        scores(j) = *nth;
+                    }
+                    cells.block(3u * j, 0u, 3u, 3u) = cell.transpose();
+                }
+            }
+
+            // Refined result
+            inline void index_end () override
+            {
+                indexer<float_type>::index_end();
+                refine(this->Spots(), this->ocells, this->scores, cifssr);
+            }
+
+            // ifss configuration access
+            inline void threshold_contraction (float_type tc)
+            {
+                if (tc <= float_type{.0})
+                    throw FF_EXCEPTION("nonpositive threshold contraction");
+                if (tc >= float_type{1.})
+                    throw FF_EXCEPTION("threshold contraction >= 1");
+                cifssr.threshold_contraction = tc;
+            }
+
+            inline float_type threshold_contraction () const noexcept
+            { return cifssr.threshold_contraction; }
+
+            inline void min_spots (unsigned ms)
+            {
+                if (ms <= 3)
+                    throw FF_EXCEPTION("min spots <= 3");
+                cifssr.min_spots = ms;
+            }
+
+            inline unsigned min_spots () const noexcept
+            { return cifssr.min_spots; }
+
+            inline void max_distance (float_type d) noexcept
+            { cifssr.max_distance = d; }
+
+            inline float_type max_distance () const noexcept
+            { return cifssr.max_distance; }
+
+            inline void max_iter (unsigned n) noexcept
+            { cifssr.max_iter = n; }
+
+            inline unsigned max_iter () const noexcept
+            { return cifssr.max_iter; }
+
+            inline const config_ifssr<float_type>& conf_ifssr () const noexcept
+            { return cifssr; }
+        }; // indexer_ifssr
+
+        // Return index for the best cell
+        template <typename VecX>
+        inline unsigned best_cell (const Eigen::DenseBase<VecX>& scores)
+        {
+            auto it = std::min_element(std::cbegin(scores), std::cend(scores));
+            return (unsigned)(it - std::cbegin(scores));
+        }
+
+        // Check if a cell looks like a viable unit cell for the spots
+        // - cell       cell in real space
+        // - spots      spots in reciprocal space
+        // - threshold  radius around approximated miller indices in primal space
+        //              or radius around spots in reciprocal space
+        // - min_spots  minimum number of spots within threshold
+        // - reciprocal take radius in reciprocal or primal space
+        template <typename Mat3, typename MatX3, typename float_type=typename Mat3::Scalar>
+        inline bool is_viable_cell (const Eigen::MatrixBase<Mat3>& cell,
+                                    const Eigen::MatrixBase<MatX3>& spots,
+                                    float_type threshold=.00075, unsigned min_spots=8u, bool reciprocal=true)
+        {
+            using M3x = Eigen::MatrixX3<float_type>;
+            M3x resid = spots * cell.transpose();
+            const M3x miller = round(resid.array());
+            if (reciprocal) {
+                resid = spots - miller * cell.transpose().inverse();
+            } else {
+                resid -= miller;
+            }
+            return (resid.rowwise().norm().array() < threshold).count() >= min_spots;
+        }
+
+        // Return indices of cells representing crystals
+        // Cell is considered a new crystal, if it differs by more than good n_spots
+        // to other crystalls
+        template <typename CellMat, typename SpotMat, typename VecX, typename float_type=typename CellMat::Scalar>
+        inline std::vector<unsigned> select_crystals (const Eigen::MatrixBase<CellMat>& cells,
+                                                      const Eigen::MatrixBase<SpotMat>& spots,
+                                                      const Eigen::DenseBase<VecX>& scores,
+                                                      float_type threshold=.00075, unsigned min_spots=8u,
+                                                      bool reciprocal=true)
+        {
+            using namespace Eigen;
+            using M3 = Matrix3f;
+            using Mx3 = MatrixX3<float_type>;
+            using Vx = VectorX<bool>;
+
+            std::vector<unsigned> crystals;
+            const unsigned n_cells = scores.size();
+            std::vector<unsigned> sorted(n_cells);
+
+            std::iota(std::begin(sorted), std::end(sorted), 0u);
+            std::sort(std::begin(sorted), std::end(sorted), [&scores](const unsigned& a, const unsigned&b) {
+                return scores[a] < scores[b];
+            });
+
+            auto spots_covered = [&cells, &spots, threshold, reciprocal](unsigned i) -> Vx {
+                M3 cell = cells.block(3u * i, 0u, 3u, 3u).transpose();
+                Mx3 resid = spots * cell;
+                const Mx3 miller = round(resid.array());
+                if (reciprocal) {
+                    resid = spots - miller * cell.inverse();
+                } else {
+                    resid -= miller;
+                }
+                return (resid.rowwise().norm().array() < threshold);
+            };
+
+            Vx allcover = spots_covered(sorted[0]);
+            if (allcover.count() < min_spots)
+                return crystals;
+            crystals.push_back(sorted[0]);
+
+            for (unsigned i=1u; i<n_cells; i++) {
+                Vx cellcover = spots_covered(sorted[i]);
+                const unsigned cnt = (cellcover.array() && !allcover.array()).count();
+                if (cnt < min_spots)
+                    continue;
+                allcover = allcover || cellcover;
+                crystals.push_back(sorted[i]);
+            }
+            return crystals;
+        }
+
+        // Make a lattice basis right handed
+        template <typename CellMat>
+        inline void make_right_handed (Eigen::MatrixBase<CellMat>& cell)
+        {
+            if (cell.determinant() < .0f)
+                cell = -cell;
+        }
+
+        // Compute a cell similarity score based on cell vector length
+        // It can be used for penalisation of cell scores for output cells dissimilar to an input cell
+        // max(0, m-t)**2, with m the maximum of the relative cell vector length differences plus the relative determinant difference
+        template <typename CellMatA, typename CellMatB, typename float_type=typename CellMatA::Scalar>
+        inline float_type cell_similarity (const Eigen::MatrixBase<CellMatA>& cellA, const Eigen::MatrixBase<CellMatB>& cellB, float_type threshold=.02f)
+        {
+            Eigen::Vector3<typename CellMatA::Scalar> vlen_a = cellA.rowwise().norm();
+            Eigen::Vector3<typename CellMatB::Scalar> vlen_b = cellB.rowwise().norm();
+            std::sort(std::begin(vlen_a), std::end(vlen_a));
+            std::sort(std::begin(vlen_b), std::end(vlen_b));
+            const float_type detA = cellA.determinant();
+            const float_type dD = std::abs((cellB.determinant() - detA) / detA);
+            float_type dL = .0f;
+            for (unsigned i=0; i<3u; i++)
+                dL = std::max(dL, std::abs(vlen_a[i] - vlen_b[i]) / vlen_a[i]);
+            const float_type score = dD + dL;
+            return std::max(float_type{.0f}, score * score - threshold);
+        }
+
+        // Make a string out of a configuration struct
+        template<typename config_type>
+        std::string conf2str(const config_type& conf)
+        {
+            std::ostringstream oss;
+            oss << "threshold_contraction=" << conf.threshold_contraction
+                << " max_distance=" << conf.max_distance
+                << " min_spots=" << conf.min_spots
+                << " max_iter=" << conf.max_iter;
+            return oss.str();
+        }
+
+    } // namespace refine
+} // namespace fast_feedback
+
+#endif // INDEXER_REFINE_H
diff --git a/image_analysis/indexing/fast-feedback-indexer/ffbidx/version.h b/image_analysis/indexing/fast-feedback-indexer/ffbidx/version.h
new file mode 100644
index 000000000..6ff6d08b8
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/ffbidx/version.h
@@ -0,0 +1,9 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5,
+// BSD-3-Clause - see LICENSE.md in this directory. Upstream generates this file from version.h.in at build
+// time; here it is written once with the pinned release and commit.
+#ifndef VERSION_H
+#define VERSION_H
+
+constexpr static auto version_string = "1.1.3-a94fd4f";
+
+#endif
diff --git a/image_analysis/indexing/fast-feedback-indexer/indexer.cpp b/image_analysis/indexing/fast-feedback-indexer/indexer.cpp
new file mode 100644
index 000000000..e465c2533
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/indexer.cpp
@@ -0,0 +1,103 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/indexer.cpp), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#include "ffbidx/exception.h"
+#include "ffbidx/indexer.h"
+#include "ffbidx/indexer_gpu.h"
+
+namespace fast_feedback {
+
+    std::atomic<state_id::type> state_id::next = static_cast<type>(state_id::null + 1u);
+
+    template <typename float_type>
+    void indexer<float_type>::init (indexer<float_type>& instance, const config_persistent<float_type>& conf)
+    {
+        if (instance.state == state_id::null)
+            throw FF_EXCEPTION("illegal initialisation of null state");
+        
+        instance.cpers = conf;
+        gpu::drop(instance);
+        gpu::init(instance);
+    }
+
+    template <typename float_type>
+    void indexer<float_type>::drop (indexer<float_type>& instance)
+    {
+        if (instance.state != state_id::null)
+            gpu::drop(instance);
+    }
+
+    template <typename float_type>
+    void indexer<float_type>::index_start(const input<float_type>& in, output<float_type>& out, const config_runtime<float_type>& conf_rt,
+                                          void(*callback)(void*), void* data)
+    {
+        gpu::index_start(*this, in, out, conf_rt, callback, data);
+    }
+
+    template <typename float_type>
+    void indexer<float_type>::index_end (output<float_type>& out)
+    {
+        gpu::index_end(*this, out);
+    }
+
+    void memory_pin::pin(void* ptr, std::size_t size)
+    {
+        gpu::pin_memory(ptr, size);
+    }
+
+    void memory_pin::unpin(void* ptr)
+    {
+        gpu::unpin_memory(ptr);
+    }
+
+    void* alloc_pinned(std::size_t num_bytes)
+    {
+        return gpu::alloc_pinned(num_bytes);
+    }
+
+    void dealloc_pinned(void* ptr)
+    {
+        gpu::dealloc_pinned(ptr);
+    }
+
+    template<typename float_type>
+    void check_config(const config_persistent<float_type>* cpers, const config_runtime<float_type>* crt)
+    {
+        gpu::check_config(cpers, crt);
+    }
+
+    void runtime_check()
+    {
+        gpu::runtime_check();
+    }
+
+    template void indexer<float>::init(indexer<float>&, const config_persistent<float>&);
+    template void indexer<float>::drop(indexer<float>&);
+    template void indexer<float>::index_start(const input<float>&, output<float>&, const config_runtime<float>&, void(*)(void*), void*);
+    template void indexer<float>::index_end(output<float>&);
+    template void check_config<float>(const config_persistent<float>*, const config_runtime<float>*);
+} // namespace fast_feedback
diff --git a/image_analysis/indexing/fast-feedback-indexer/indexer_gpu.cu b/image_analysis/indexing/fast-feedback-indexer/indexer_gpu.cu
new file mode 100644
index 000000000..5f44be5ed
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/indexer_gpu.cu
@@ -0,0 +1,2381 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/indexer_gpu.cu), BSD-3-Clause - see LICENSE.md in this directory.
+// Local modifications: a deterministic tie-break in the candidate ordering; the INDEXER_GPU_DEVICE environment
+// variable is not read (the indexer runs on the calling thread's current device, the one Jungfraujoch pins).
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#include <vector>
+#include <cstdlib>
+#include <sstream>
+#include <map>
+#include <memory>
+#include <chrono>
+#include <algorithm>
+#include <limits>
+#include <cassert>
+#include <cstring>
+#include <cub/block/block_radix_sort.cuh>
+#include "ffbidx/envvar.h"
+#include "ffbidx/exception.h"
+#include "ffbidx/log.h"
+#include "ffbidx/indexer_gpu.h"
+#include "cuda_runtime.h"
+
+namespace logger = fast_feedback::logger;
+using logger::stanza;
+
+namespace {
+
+    constexpr char INDEXER_GPU_DEBUG[] = "INDEXER_GPU_DEBUG";
+    constexpr unsigned n_threads = 1024;        // num cuda threads per block for find_candidates kernel
+    constexpr unsigned warp_size = 32;          // number of threads in a warp
+    constexpr unsigned mem_txn_unit = 32;       // minimum memory transaction unit (cache line sector)
+    constexpr unsigned all_lanes = 0xffffffff;  // mask for all lanes of a warp
+
+    template<typename float_type>
+    struct constant final {
+        // static constexpr float_type pi = 3.1415926535897932384628;
+        #pragma nv_diag_suppress 177 // suppress unused warning
+        [[maybe_unused]] static constexpr float_type pi2 = 6.2831853071795864769257;
+        #pragma nv_diag_suppress 177 // suppress unused warning
+        [[maybe_unused]] static constexpr float_type dl = 0.76393202250021030359082633; // 3 - sqrt(5), for spiral sample points on a half sphere
+        #pragma nv_diag_suppress 177 // suppress unused warning
+        [[maybe_unused]] static constexpr unsigned mem_txn_unit = ::mem_txn_unit / sizeof(float_type); // minimum memory transaction unit
+        static constexpr float_type eps = std::numeric_limits<float_type>::epsilon();
+    };
+
+    // NOTE: not allowed as member of constant
+    // (dl * 2^N) mod 2pi
+    template<typename float_type>
+    __constant__ static float_type dl2pNmod2pi[32] = {
+        0.76393202250021030359082633,   // N = 0
+        1.5278640450004206071816527,
+        3.0557280900008412143633053,
+        6.1114561800016824287266107,
+        5.9397270528237783805279346,
+        5.5962687984679702841305826,
+        4.9093522897563540913358776,
+        3.535519272333121705746469,
+        0.78785323748665693456765102,   // 8
+        1.575706474973313869135302,
+        3.1514129499466277382706041,
+        0.019640592713668999615921566,
+        0.039281185427337999231843132,
+        0.078562370854675998463686265,
+        0.15712474170935199692737253,
+        0.31424948341870399385474506,
+        0.62849896683740798770949012,   // 16
+        1.2569979336748159754189802,
+        2.5139958673496319508379605,
+        5.0279917346992639016759209,
+        3.7727981622189413264265548,
+        1.2624110172582961759278224,
+        2.5248220345165923518556449,
+        5.0496440690331847037112897,
+        3.8161028308867829304972927,    // 24
+        1.3490203545939793840692983,
+        2.6980407091879587681385967,
+        5.3960814183759175362771934,
+        4.5089775295722485956291,
+        2.7347697519649107143329137,
+        5.4695395039298214286658275,
+        4.6558937006800563804063691     // 31
+    };
+
+    std::atomic_bool gpu_debug_output{false};   // Print gpu debug output if true, set if INDEXER_GPU_DEBUG env var is set to true at indexer creation time
+
+    // Exception for cuda related errors
+    struct cuda_exception final : public fast_feedback::exception {
+
+        inline cuda_exception(cudaError_t error, const char* file, unsigned line)
+            : exception(std::string{}, file, line)
+        {
+            const char* error_name = cudaGetErrorName(error);
+            const char* error_string = cudaGetErrorString(error);
+            *this << '(' << error_name << ") " << error_string;
+        }
+
+    };
+
+    #define CU_EXCEPTION(err) cuda_exception(err, __FILE__, __LINE__)
+
+    #define CU_CHECK(err) {             \
+        cudaError_t error = (err);      \
+        if (error != cudaSuccess)       \
+            throw CU_EXCEPTION(error);  \
+    }
+
+    #define CU_CHECK_EXT(err)               \
+        switch (err) {                      \
+            case cudaSuccess:               \
+            case cudaErrorCudartUnloading:  \
+                break;;                     \
+            default:                        \
+                throw CU_EXCEPTION(err);    \
+        }
+
+    #define DEBUG_STREAM_SYNC(stream) { \
+        stream.sync();                  \
+    }
+
+    #define DEBUG_DEVICE_SYNC() {           \
+        CU_CHECK(cudaDeviceSynchronize());  \
+    }
+
+    // Cuda device infos
+    struct gpu_device final {
+        int id;
+        cudaDeviceProp prop;
+
+        static inline std::vector<gpu_device> list;             // Cuda device list
+        static inline std::atomic_bool cuda_initialized{false}; // Is the cuda runtime initialized?
+        static inline std::mutex init_lock;                     // Protect cuda runtime initalisation
+
+        // Check if cuda has been initialized
+        static void check_init()
+        {
+            if (! gpu_device::cuda_initialized.load())
+                throw FF_EXCEPTION("cuda runtime not initialized");
+        }
+
+        // Get the list of cuda devices
+        static void init()
+        {
+            if (cuda_initialized.load())
+                return;
+            
+            {
+                std::lock_guard<std::mutex> lock{init_lock};
+
+                if (cuda_initialized.load())
+                    return;
+            
+                int num_devices;
+                CU_CHECK(cudaGetDeviceCount(&num_devices));
+
+                list.resize(num_devices);
+                for (int dev=0; dev<num_devices; dev++) {
+                    gpu_device& device = list[dev];
+                    device.id = dev;
+                    CU_CHECK(cudaGetDeviceProperties(&device.prop, dev));
+                }
+
+                gpu_device::cuda_initialized.store(true);
+            }
+        }
+
+        // Get a CUDA device: the current device (local modification: no INDEXER_GPU_DEVICE override)
+        static int get()
+        {
+            int dev{-1};
+            CU_CHECK(cudaGetDevice(&dev));
+
+            LOG_START(logger::l_info) {
+                logger::info << stanza << "using GPU device " << dev << '\n';
+            } LOG_END;
+
+            return dev;
+        }
+
+        // Set current CUDA device
+        static void set(int dev)
+        {
+            if ((dev < 0) || (dev >= (int)list.size()))
+                throw FF_EXCEPTION_OBJ << "illegal value for GPU device";
+
+            auto compcap = list[dev].prop.major;    // COMPUTE CAPABILITY CHECK (__shuffle_sync requires >= 5.x)
+            if (compcap < 5)
+                throw FF_EXCEPTION_OBJ << "unsupported compute capability " << compcap << ".x (must be >= 5.x)";
+
+            CU_CHECK(cudaSetDevice(dev));
+        }
+    };
+
+    // Set GPU debug output if INDEXER_GPU_DEBUG is set to true
+    void gpu_debug_init()
+    {
+        bool debug = fast_feedback::envvar<bool>(INDEXER_GPU_DEBUG, []()->bool{return false;});
+        gpu_debug_output.store(debug);
+    }
+
+    // Deleter for device smart pointers
+    template<typename T>
+    struct gpu_deleter final {
+        void operator()(T* ptr) const
+        {
+            CU_CHECK_EXT(cudaFree(ptr));
+        }
+    };
+
+    // Device smart pointer
+    template<typename T>
+    using gpu_pointer = std::unique_ptr<T, gpu_deleter<T>>;
+
+    // Cuda event wrapper
+    template<unsigned flags=cudaEventDisableTiming>
+    struct gpu_event final {
+        cudaEvent_t event;
+
+        inline gpu_event()
+            : event{}
+        {}
+
+        gpu_event(const gpu_event&) = delete;
+        gpu_event& operator=(const gpu_event&) = delete;
+
+        gpu_event(gpu_event&& other)
+            : event{}
+        {
+            std::swap(other.event, event);
+        }
+
+        static void drop(cudaEvent_t& event)
+        {
+            if (event == cudaEvent_t{})
+                return;
+            CU_CHECK_EXT(cudaEventDestroy(event));
+            event = cudaEvent_t{};
+        }
+        
+        gpu_event& operator=(gpu_event&& other)
+        {
+            std::swap(other.event, event);
+            return *this;
+        }
+
+        inline ~gpu_event()
+        {
+            drop(event);
+        }
+
+        inline void init()
+        {
+            assert(event == cudaEvent_t{});
+            CU_CHECK(cudaEventCreateWithFlags(&event, flags));
+        }
+
+        inline void record(cudaStream_t stream=0)
+        {
+            assert(event != cudaEvent_t{});
+            CU_CHECK(cudaEventRecord(event, stream));
+        }
+
+        inline void sync()
+        {
+            assert(event != cudaEvent_t{});
+            CU_CHECK(cudaEventSynchronize(event));
+        }
+    };
+
+    template<unsigned flags>
+    static float gpu_timing(const gpu_event<flags>& start, const gpu_event<flags>& end)
+    {
+        static_assert(!(flags & cudaEventDisableTiming), "GPU timing measurement are only valid on events that don't have the cudaEventDisableTiming flag set");
+        assert(start.event != cudaEvent_t{});
+        assert(end.event != cudaEvent_t{});
+        float time;
+        CU_CHECK(cudaEventElapsedTime(&time, start.event, end.event));
+        return time;
+    }
+
+    // Cuda stream wrapper
+    struct gpu_stream final {
+        bool ready;                             // Is stream ready = initialized
+        cudaStream_t stream;                    // Cuda stream
+
+        // Return uninitialized stream
+        gpu_stream() noexcept
+            : ready{false}, stream{cudaStream_t{}}
+        {}
+
+        // Initialize stream with existing cuda stream
+        // The cuda stream given as argument will be managed by this object after the call,
+        // which basically means it should not be used afterwards.
+        gpu_stream(cudaStream_t s)
+            : ready{true}, stream{s}
+        {
+            unsigned int flags;
+            CU_CHECK(cudaStreamGetFlags(s, &flags));    // check that the s is initialized
+        }
+
+        // Move s into this
+        gpu_stream(gpu_stream&& s)
+            : ready{false}, stream{cudaStream_t{}}
+        {
+            std::swap(ready, s.ready);
+            std::swap(stream, s.stream);
+        }
+
+        // Move s into this
+        gpu_stream& operator=(gpu_stream&& s)
+        {
+            if (this != &s) {
+                if (ready) {
+                    CU_CHECK(cudaStreamDestroy(stream));
+                    ready = false;
+                }
+                std::swap(ready, s.ready);
+                std::swap(stream, s.stream);
+            }
+            return *this;
+        }
+
+        gpu_stream(const gpu_stream&) = delete;             // No copying
+        gpu_stream& operator=(const gpu_stream&) = delete;  // No copying
+
+        // Destroy this
+        ~gpu_stream()
+        {
+            release();
+        }
+
+        // Release and unititialize the cuda stream
+        // This is left in uninitialized state
+        void release()
+        {
+            if (ready) {
+                CU_CHECK_EXT(cudaStreamDestroy(stream));
+                ready = false;
+            }
+        }
+
+        // (Re)initialize the cuda stream
+        void init(unsigned int flags=cudaStreamDefault)
+        {
+            release();
+            CU_CHECK(cudaStreamCreateWithFlags(&stream, flags));
+            ready = true;
+        }
+
+        // Sync with cuda stream
+        void sync()
+        {
+            if (ready)
+                CU_CHECK(cudaStreamSynchronize(stream));
+        }
+
+        // Check for completion status
+        bool completed()
+        {
+            if (ready) {
+                auto error = cudaStreamQuery(stream);
+                switch (error) {
+                    case cudaSuccess:
+                        return true;
+                    case cudaErrorNotReady:
+                        return false;
+                    default:
+                        throw CU_EXCEPTION(error);
+                }
+            }
+            return true;
+        }
+
+        operator cudaStream_t&() noexcept { return stream; }    // Cast to cuda stream
+    };
+
+    // On GPU compact vector representation
+    template<typename float_type>
+    struct compact_vec final {
+        float_type x;
+        float_type y;
+        float_type z;
+    };
+
+    // On GPU data for indexer
+    template<typename float_type>
+    struct indexer_device_data final {
+        fast_feedback::config_persistent<float_type> cpers;
+        fast_feedback::config_runtime<float_type> crt;
+        fast_feedback::input<float_type> input;
+        fast_feedback::output<float_type> output;
+        float_type* candidate_length;           // Candidate vector groups length, [3 * max_input_cells]
+        float_type* candidate_value;            // Candidate vector objective function values, [3 * max_input_cells * num_candidate_vectors]
+        float_type* refined_candidates;         // Refined candidate coordinates in consecutive aligned tripples
+                                                // (x,y,z,gap; alignment = mem_txn_unit) [3 * max_input_cells * num_candidate_vectors * 3]
+        unsigned* candidate_sample;             // Sample number of candidate vectors, [3 * max_input_cells * num_candidate_vectors]
+        unsigned* cellvec_to_cand;              // Input cell vector to candidate group mapping, [3 * max_input_cells]
+        unsigned* cell_to_cellvec;              // Input cell to representing cell vector mapping, [max_input_cells]
+        unsigned* vec_cgrps;                    // Candidate vector groups of cell representing vectors, [max_input_cells]
+        unsigned* seq_block;                    // Per candidate vector group sequentializer for thread blocks (explicit init to 0, set to 0 in kernel after use)
+                                                //     First sequentializer is also used for candidate cell search
+    };
+
+    // Indexer GPU state representation on the Host side
+    //
+    // Candidate vector group = set of vectors with same length that are candidates for a unit cell vector
+    //
+    template<typename float_type>
+    struct indexer_gpu_state final {
+        using content_type = indexer_device_data<float_type>;
+        using key_type = fast_feedback::state_id::type;
+        using map_type = std::map<key_type, indexer_gpu_state>;
+        using config_persistent = fast_feedback::config_persistent<float_type>;
+        using config_runtime = fast_feedback::config_runtime<float_type>;
+        using memory_pin = fast_feedback::memory_pin;
+        using clock = std::chrono::high_resolution_clock;
+        using time_point = std::chrono::time_point<clock>;
+
+        gpu_pointer<content_type> data;                     // Indexer_device_data on GPU
+        gpu_pointer<float_type> elements;                   // Input/output vector elements of data on GPU
+        gpu_pointer<float_type> candidate_length;           // Candidate vector groups length values on GPU
+        gpu_pointer<float_type> candidate_value;            // Candidate vectors objective function values on GPU
+        gpu_pointer<float_type> refined_candidates;         // Refined candidate coordinates in consecutive aligned tripples on GPU
+        gpu_pointer<unsigned> candidate_sample;             // Sample number of candidate vectors on GPU
+        gpu_pointer<unsigned> cellvec_to_cand;              // Input cell vector to candidate group mapping on GPU
+        gpu_pointer<unsigned> cell_to_cellvec;              // Input cell to cell representing vector mapping on GPU
+        gpu_pointer<unsigned> vec_cgrps;                    // Candidate vector groups of cell representing vectors on GPU
+        gpu_pointer<unsigned> seq_block;                    // Thread block sequentializers on GPU
+        gpu_stream cuda_stream;                             // CUDA stream
+
+        // Temporary pinned space to transfer n_input_cells, n_output_cells, n_spots
+        fast_feedback::pinned_ptr<config_persistent> tmp;   // Pointer to make move construction simple
+
+        // Input cell coordinates on GPU pointing into elements
+        float_type* ix;
+        float_type* iy;
+        float_type* iz;
+
+        // Output cell coordinates and scores on GPU pointing into elements
+        float_type* ox;
+        float_type* oy;
+        float_type* oz;
+        float_type* cell_score;
+
+        // Last runtime config ang candidate group mapping properties for overhead and copy omission
+        config_runtime last_crt;
+        unsigned n_cand_groups = 0u;
+        unsigned n_vec_cgrps = 0u;
+        std::vector<unsigned> cell_candidate_h;
+        std::vector<unsigned> vec_cgrps_h;
+        std::vector<unsigned> candidate_idx_h;
+        std::vector<float_type> candidate_length_h;
+        memory_pin pin_cell_cand;
+        memory_pin pin_vec_grp;
+        memory_pin pin_cand_idx;
+        memory_pin pin_cand_len;
+
+        // Timings
+        gpu_event<cudaEventDefault> start;
+        gpu_event<cudaEventDefault> end;
+        time_point start_time{};
+
+        // GPU device
+        int device;
+
+        // Callback mode
+        bool callback_mode = false;
+
+        static std::mutex state_update; // Protect per indexer state map
+        static map_type dev_ptr;        // Per indexer state map
+
+        // Create hostside on GPU state representation with
+        // d        pointer to on GPU state
+        // e        on GPU input and output elements pointed to by d->elements
+        // cl       on GPU candidate lengths pointed to by d->candidate_length
+        // cv       on GPU candidate vector objective function values pointed to by d->candidate_value
+        // rc       on GPU refined candidates vector pointed to by d->refined_candidates
+        // cs       on GPU candidate vector sample numbers pointed to by d->candidate_sample
+        // v2c      on GPU input cell vector to candidate group mapping pointed to by d->cellvec_to_cand
+        // c2v      on GPU input cell to cell representing vector mapping pointed to by d->cell_to_cellvec
+        // vcgr     on GPU candidate groups of cell representing vectors pointed to by d->vec_cgrps
+        // sb       on GPU per candidate vector group/output cell block sequentializers pointed to by d->seq_block
+        // stream   GPU stream used for actions on this state
+        // x/y/zi   on GPU input pointers d->input.x / y / z
+        // x/y/z0   on GPU output pointers d->output.x / y / z
+        // score    on GPU per output cell scoring function values
+        // dev      cuda device number of the GPU holding this state
+        // cbm      host callback function is called when results are ready
+        indexer_gpu_state(gpu_pointer<content_type>&& d, gpu_pointer<float_type>&& e,
+                          gpu_pointer<float_type>&& cl, gpu_pointer<float_type>&& cv,
+                          gpu_pointer<float_type>&& rc,
+                          gpu_pointer<unsigned>&& cs, gpu_pointer<unsigned>&& v2c,
+                          gpu_pointer<unsigned>&& c2v, gpu_pointer<unsigned>&& vcgr,
+                          gpu_pointer<unsigned>&& sb, gpu_stream&& stream,
+                          float_type* xi, float_type* yi, float_type* zi,
+                          float_type* xo, float_type* yo, float_type* zo,
+                          float_type* scores, int dev, unsigned n_cells_in)
+            : data{std::move(d)}, elements{std::move(e)},
+              candidate_length{std::move(cl)}, candidate_value{std::move(cv)},
+              refined_candidates{std::move(rc)},
+              candidate_sample{std::move(cs)}, cellvec_to_cand{std::move(v2c)},
+              cell_to_cellvec{std::move(c2v)}, vec_cgrps{std::move(vcgr)},
+              seq_block{std::move(sb)}, cuda_stream{std::move(stream)},
+              ix{xi}, iy{yi}, iz{zi},
+              ox{xo}, oy{yo}, oz{zo},
+              cell_score{scores},
+              cell_candidate_h(n_cells_in), vec_cgrps_h(n_cells_in),
+              candidate_idx_h(3u * n_cells_in), candidate_length_h(3u * n_cells_in),
+              pin_cell_cand{cell_candidate_h},
+              pin_vec_grp{vec_cgrps_h},
+              pin_cand_idx{candidate_idx_h},
+              pin_cand_len{candidate_length_h},
+              device{dev}
+        {
+            tmp = fast_feedback::alloc_pinned<config_persistent>();
+            // Invalidate objects to help with overhead and copy omission
+            tmp->max_output_cells = -1u;
+            tmp->max_input_cells = -1u;
+            tmp->max_spots = -1u;
+            std::memset(static_cast<void*>(&last_crt), 0, sizeof(last_crt));
+        }
+
+        indexer_gpu_state() = default;                                      // Default with some uninitialized pointers
+        indexer_gpu_state(const indexer_gpu_state&) = delete;
+        indexer_gpu_state(indexer_gpu_state&&) = default;                   // Take over state representation
+        indexer_gpu_state& operator=(const indexer_gpu_state&) = delete;
+        indexer_gpu_state& operator=(indexer_gpu_state&&) = default;        // Take over state representation
+        ~indexer_gpu_state() = default;                                     // Drop on GPU state data
+
+        // Shortcut to get at reference
+        static inline indexer_gpu_state& ref(const key_type& id)
+        {
+            return dev_ptr[id];
+        }
+
+        // Shortcut to get at state data pointer
+        static inline gpu_pointer<content_type>& ptr(const key_type& id)
+        {
+            return ref(id).data;
+        }
+
+        // Shortcut to cuda stream
+        static inline gpu_stream& stream(const key_type& id)
+        {
+            return ref(id).cuda_stream;
+        }
+
+        // State exists
+        static inline bool exists(const key_type& id)
+        {
+            std::lock_guard<std::mutex> state_lock{state_update};
+            return dev_ptr.find(id) != std::end(dev_ptr);
+        }
+
+        // Drop state
+        static inline void drop(const key_type& id)
+        {
+            std::lock_guard<std::mutex> state_lock{state_update};
+            dev_ptr.erase(id);
+        }
+
+        // Copy runtime configuration to GPU
+        static inline void copy_crt(const key_type& state_id, const config_runtime& crt, cudaStream_t stream)
+        {
+            const auto crt_dp = &ptr(state_id)->crt;
+            CU_CHECK(cudaMemcpyAsync(crt_dp, &crt, sizeof(crt), cudaMemcpyHostToDevice, stream));
+            ref(state_id).last_crt = crt;
+            LOG_START(logger::l_debug) {
+                logger::debug << stanza << "copy runtime config data: " << &crt << "-->" << crt_dp << '\n';
+            } LOG_END;
+        }
+
+        // Copy input data to GPU
+        static inline void copy_in(const key_type& state_id, const config_persistent& cpers,
+                                   const fast_feedback::input<float_type>& input,
+                                   fast_feedback::output<float_type>& output,
+                                   cudaStream_t stream)
+        {
+            if (!input.new_cells && !input.new_spots)
+                return;
+
+            const auto& gpu_state = ref(state_id);
+            auto& pinned_tmp = const_cast<config_persistent&>(*gpu_state.tmp);
+            const auto& device_data = gpu_state.data;
+
+            output.n_cells = std::min(output.n_cells, cpers.max_output_cells);
+            if (pinned_tmp.max_output_cells != output.n_cells) {
+                pinned_tmp.max_output_cells = output.n_cells;
+                CU_CHECK(cudaMemcpyAsync(&device_data->output.n_cells, &pinned_tmp.max_output_cells, sizeof(output.n_cells), cudaMemcpyHostToDevice, stream));
+
+                LOG_START(logger::l_debug) {
+                    logger::debug << stanza << "copy " << output.n_cells << " cells(out)\n";
+                } LOG_END;
+            }
+
+            const auto n_input_cells = std::min(input.n_cells, cpers.max_input_cells);
+            const auto n_spots = std::min(input.n_spots, cpers.max_spots);
+            if ((pinned_tmp.max_input_cells != n_input_cells) ||
+                (pinned_tmp.max_spots != n_spots)) {
+                pinned_tmp.max_input_cells = n_input_cells;
+                pinned_tmp.max_spots = n_spots;
+                // NOTE: the following code assumes consecutive storage of two data members in pinned_tmp and in device_data->input
+                CU_CHECK(cudaMemcpyAsync(&device_data->input.n_cells, &pinned_tmp.max_input_cells, sizeof(n_input_cells) + sizeof(n_spots), cudaMemcpyHostToDevice, stream));
+
+                LOG_START(logger::l_debug) {
+                    logger::debug << stanza << "copy " << n_input_cells << " cells(in), " << n_spots << " spots\n";
+                } LOG_END;
+            }
+
+            if (input.new_cells && n_input_cells > 0u) {
+                const auto cell_sz = 3u * n_input_cells * sizeof(float_type);
+                CU_CHECK(cudaMemcpyAsync(gpu_state.ix, input.cell.x, cell_sz, cudaMemcpyHostToDevice, stream));
+                CU_CHECK(cudaMemcpyAsync(gpu_state.iy, input.cell.y, cell_sz, cudaMemcpyHostToDevice, stream));
+                CU_CHECK(cudaMemcpyAsync(gpu_state.iz, input.cell.z, cell_sz, cudaMemcpyHostToDevice, stream));
+                
+                LOG_START(logger::l_debug) {
+                    logger::debug << stanza << "copy (cells) "
+                                  << input.cell.x << "-->" << gpu_state.ix << ", "
+                                  << input.cell.y << "-->" << gpu_state.iy << ", "
+                                  << input.cell.z << "-->" << gpu_state.iz << '\n';
+                } LOG_END;
+            }
+
+            if (input.new_spots && n_spots > 0) {
+                const auto dst_offset = 3u * cpers.max_input_cells;
+                const auto spot_sz = n_spots * sizeof(float_type);
+                CU_CHECK(cudaMemcpyAsync(&gpu_state.ix[dst_offset], input.spot.x, spot_sz, cudaMemcpyHostToDevice, stream));
+                CU_CHECK(cudaMemcpyAsync(&gpu_state.iy[dst_offset], input.spot.y, spot_sz, cudaMemcpyHostToDevice, stream));
+                CU_CHECK(cudaMemcpyAsync(&gpu_state.iz[dst_offset], input.spot.z, spot_sz, cudaMemcpyHostToDevice, stream));
+
+                LOG_START(logger::l_debug) {
+                    logger::debug << stanza << "copy (spots) "
+                                  << input.cell.x << "-->" << &gpu_state.ix[3u * cpers.max_input_cells] << ", "
+                                  << input.cell.y << "-->" << &gpu_state.iy[3u * cpers.max_input_cells] << ", "
+                                  << input.cell.z << "-->" << &gpu_state.iz[3u * cpers.max_input_cells] << '\n';
+                } LOG_END;
+            }
+        }
+
+        static inline void init_cand(const key_type& state_id, const unsigned n_cand_groups, const unsigned n_vec_cgrps,
+                                     const config_persistent& cpers,
+                                     const std::vector<float_type>& cand_len, const std::vector<unsigned>& cand_idx,
+                                     const std::vector<unsigned>& cell_cand, const std::vector<unsigned>& vec_cgrps,
+                                     cudaStream_t stream)
+        {
+            const auto n_cand_vecs = n_cand_groups * cpers.num_candidate_vectors;
+            const auto& gpu_state = ref(state_id);
+
+            CU_CHECK(cudaMemcpyAsync(gpu_state.candidate_length.get(), cand_len.data(), n_cand_groups * sizeof(float_type), cudaMemcpyHostToDevice, stream));
+            CU_CHECK(cudaMemsetAsync(gpu_state.candidate_value.get(), 0, n_cand_vecs * sizeof(float_type), stream));
+            CU_CHECK(cudaMemcpyAsync(gpu_state.cellvec_to_cand.get(), cand_idx.data(), cand_idx.size() * sizeof(unsigned), cudaMemcpyHostToDevice, stream));
+            CU_CHECK(cudaMemcpyAsync(gpu_state.cell_to_cellvec.get(), cell_cand.data(), cell_cand.size() * sizeof(unsigned), cudaMemcpyHostToDevice, stream));
+            CU_CHECK(cudaMemcpyAsync(gpu_state.vec_cgrps.get(), vec_cgrps.data(), n_vec_cgrps * sizeof(unsigned), cudaMemcpyHostToDevice, stream));
+        }
+
+        // Copy output data from GPU
+        // This is a blocking call that synchronizes on stream
+        // Precondition: output.n_cells != 0
+        static inline void copy_out(const key_type& state_id, fast_feedback::output<float_type>& output, gpu_stream &stream)
+        {
+            const auto& gpu_state = ref(state_id);
+            const auto& device_data = gpu_state.data;
+            const auto cell_sz = 3u * output.n_cells * sizeof(float_type);
+
+            CU_CHECK(cudaMemcpyAsync(output.x, gpu_state.ox, cell_sz, cudaMemcpyDeviceToHost, stream));
+            CU_CHECK(cudaMemcpyAsync(output.y, gpu_state.oy, cell_sz, cudaMemcpyDeviceToHost, stream));
+            CU_CHECK(cudaMemcpyAsync(output.z, gpu_state.oz, cell_sz, cudaMemcpyDeviceToHost, stream));
+            CU_CHECK(cudaMemcpyAsync(output.score, gpu_state.cell_score, output.n_cells * sizeof(float_type), cudaMemcpyDeviceToHost, stream));
+            stream.sync();
+
+            LOG_START(logger::l_debug) {
+                logger::debug << stanza << "copy out: " << output.n_cells << " cells, elements=" << gpu_state.elements.get() << ": "
+                            << gpu_state.ox << "-->" << output.x << ", "
+                            << gpu_state.oy << "-->" << output.y << ", "
+                            << gpu_state.oz << "-->" << output.z << ", "
+                            << gpu_state.cell_score << "-->" << output.score << '\n';
+            } LOG_END;
+        }
+    };
+
+    // Calculate vector candidate groups
+    //   All input cell vectors are mapped to a candidate vector group that uniquely represents the length of the vector.
+    //   crt.length_threshold determines if two vectors are considered to have the same length.
+    // Input Args:
+    //   in        : indexing input
+    //   crt       : runtime configuration
+    //   n_cells_in: number of considered input cells
+    // Output Args:
+    //   cand_idx: input cell vector to candidate vector group mapping (preallocated size: 3 * n_cells_in)
+    //   cand_len: sorted candidate vector group length                (preallocated size: 3 * n_cells_in, initialized to: 0)
+    // Return:
+    //   number of candidate vector groups N ∈ [1 ... 3 * n_cells_in]
+    template <typename float_type>
+    unsigned calc_cand_groups(std::vector<unsigned>& cand_idx, std::vector<float_type>& cand_len,
+                              const fast_feedback::input<float_type>& in,
+                              const fast_feedback::config_runtime<float_type>& crt, const unsigned n_cells_in)
+    {
+        const unsigned n_vecs = 3u * n_cells_in;
+
+        if (cand_idx.size() < n_vecs)
+            throw FF_EXCEPTION("candidate index vector too small");
+        if (cand_len.size() < n_vecs)
+            throw FF_EXCEPTION("candidate length vector too small");
+        
+        // All vector lengths
+        for (unsigned i=0u; i<n_vecs; i++) {
+            const auto x = in.cell.x[i];
+            const auto y = in.cell.y[i];
+            const auto z = in.cell.z[i];
+            cand_len[i] = std::sqrt(x*x + y*y + z*z);
+        }
+
+        unsigned n_cand_groups{};
+        {   // Only keep elements that differ by more than length_threshold
+            std::sort(std::begin(cand_len), std::end(cand_len), std::greater<float_type>{});
+
+            const float_type l_threshold = crt.length_threshold;
+            LOG_START(logger::l_debug) {
+                logger::debug << stanza << "candidate_length =";
+                for (const auto& e : cand_len)
+                    logger::debug << ' ' << e;
+                logger::debug << ", threshold = " << l_threshold << '\n';                
+            } LOG_END;
+            
+            unsigned i=0, j=1;
+            do {
+                if ((cand_len[i] - cand_len[j]) < l_threshold) {
+                    LOG_START(logger::l_debug) {
+                        logger::debug << stanza << "  ignore " << cand_len[j] << '\n';
+                    } LOG_END;
+                } else if (++i != j) {
+                    cand_len[i] = cand_len[j];
+                }
+            } while(++j != n_vecs);
+            n_cand_groups = i + 1;
+            for (unsigned i=0u; i<n_vecs; i++) {
+                const auto x = in.cell.x[i];
+                const auto y = in.cell.y[i];
+                const auto z = in.cell.z[i];
+                float_type length = std::sqrt(x*x + y*y + z*z);
+                auto it = std::lower_bound(std::cbegin(cand_len), std::cbegin(cand_len) + n_cand_groups, length,
+                                        [l_threshold](const float_type& a, const float_type& l) -> bool {
+                                                return (a - l) >= l_threshold;
+                                        });
+                cand_idx[i] = it - std::cbegin(cand_len);
+            }
+        }
+        return n_cand_groups;
+    }
+
+    // Calculate a candidate vector for each cell
+    //   Chose a vector for every input cell. This vector will be used for the initial half-sphere brute force sampling step.
+    //   The algorithm relies on the decreasing order of the candidate group lengths and corresponding indices in cand_idx.
+    //   So a lower candidate vector group index in cand_idx means a longer vector.
+    // Input Args:
+    //   cand_idx: input cell vector to candidate vector group mapping (see ordering requirement above, size 3 * n_cells_in)
+    // Output Args:
+    //   cell_vec: cell to chosen input vector mapping (preallocated size: n_cells_in)
+    //   vec_cand: candidate groups of chosen input vectors (preallocated size: n_cells_in)
+    // Return:
+    //   Number of candidate groups for the chosen vectors
+    unsigned calc_cell_cand(std::vector<unsigned>& cell_vec, std::vector<unsigned>& vec_cand,
+                            const std::vector<unsigned>& cand_idx, const unsigned n_cells_in)
+    {
+        const unsigned n_vecs = 3u * n_cells_in;
+
+        if (cand_idx.size() < n_vecs)
+            throw FF_EXCEPTION("candidate index vector too small");
+        if (cell_vec.size() < n_cells_in)
+            throw FF_EXCEPTION("cell candidate vector too small");
+        if (vec_cand.size() < n_cells_in)
+            throw FF_EXCEPTION("candidate groups vector too small");
+
+        unsigned num_cand_grps = 0u;
+        unsigned vec = 0u;
+        for (unsigned cell=0u; cell<n_cells_in; cell++) {
+            unsigned cand = vec++;
+            for (unsigned v=1u; v<3u; vec++, v++) {
+                if (cand_idx[cand] > cand_idx[vec])
+                    cand = vec;
+            }
+            cell_vec[cell] = cand;
+            unsigned cand_grp = cand_idx[cand];
+            auto it = std::find(&vec_cand[0u], &vec_cand[num_cand_grps], cand_grp);
+            if (it == &vec_cand[num_cand_grps])
+                vec_cand[num_cand_grps++] = cand_grp;
+        }
+
+        return num_cand_grps;
+    }
+
+    template<> std::mutex indexer_gpu_state<float>::state_update{};
+    template<> indexer_gpu_state<float>::map_type indexer_gpu_state<float>::dev_ptr{};
+
+    template<typename float_type>
+    struct vec_cand_t final {
+        float_type value;   // objective function value
+        unsigned sample;    // sample point index
+    };
+
+    template<typename float_type>
+    struct cell_cand_t final {
+        constexpr static unsigned FLIPPED = 1u<<31;
+        float_type value;   // objective function value
+        unsigned vsample;   // sample point index, or plain candidate index
+        unsigned rsample;   // sample rotation angle index
+        unsigned cell_vec;  // cell vector index:
+                            // lower 31 bits: index
+                            // highest bit  : use flipped candidate vector
+    };
+
+    template<typename float_type>
+    using BlockRadixSort = cub::BlockRadixSort<float_type, n_threads, 1, unsigned>;
+
+    // -----------------------------------
+    //            GPU Auxiliary
+    // -----------------------------------
+
+    template<typename float_type>
+    struct util final {};
+
+    template<>
+    struct util<float> final {
+        __device__ __forceinline__ static float abs(const float val) noexcept
+        {
+            return fabsf(val);
+        }
+
+        __device__ __forceinline__ static float rint(const float val) noexcept
+        {
+            return rintf(val);
+        }
+
+        __device__ __forceinline__ static void sincos(const float angle,
+                                                      float* __restrict__ sine,
+                                                      float* __restrict__ cosine) noexcept
+        {
+            return sincosf(angle, sine, cosine);
+        }
+
+        // __device__ __forceinline__ static float cos(const float angle) noexcept
+        // {
+        //     return cosf(angle);
+        // }
+
+        __device__ __forceinline__ static float acos(const float x) noexcept
+        {
+            return acosf(x);
+        }
+
+        __device__ __forceinline__ static float log2(const float x) noexcept
+        {
+            return log2f(x);
+        }
+
+        __device__ __forceinline__ static float exp2(const float x) noexcept
+        {
+            return exp2f(x);
+        }
+
+        // x ^ y
+        // __device__ __forceinline__ static float pow(const float x, const float y) noexcept
+        // {
+        //     return powf(x, y);
+        // }
+
+        __device__ __forceinline__ static float sqrt(const float x) noexcept
+        {
+            return sqrtf(x);
+        }
+        
+        // __device__ __forceinline__ static float rem(const float x, const float y) noexcept
+        // {
+        //     return remainderf(x, y);
+        // }
+
+        __device__ __forceinline__ static float norm(const float x, const float y, const float z) noexcept
+        {   // sqrt(x*x + y*y + z*z)
+            return norm3df(x, y, z);
+        }
+
+        __device__ __forceinline__ static float rnorm(const float x, const float y, const float z) noexcept
+        {   // 1 / sqrt(x*x + y*y + z*z)
+            return rnorm3df(x, y, z);
+        }
+
+        __device__ __forceinline__ static float fma(const float x, const float y, const float z) noexcept
+        {   // x * y + z
+            return fmaf(x, y, z);
+        }
+
+        // __device__ __forceinline__ static void sincospi(const float a, float* sinp, float* cosp) noexcept
+        // {
+        //     sincospif(a, sinp, cosp);
+        // }
+
+        // __device__ __forceinline__ static float cospi(const float a) noexcept
+        // {
+        //     return cospif(a);
+        // }
+        
+        // __device__ __forceinline__ static void from_unsigned(float& f1, float& f2, const unsigned n) noexcept
+        // {
+        //     static constexpr unsigned nbits = 8u * sizeof(unsigned);
+        //     static constexpr unsigned mant_bits = std::numeric_limits<float>::digits;
+        //     static constexpr unsigned mask_upper = ((1u << mant_bits) - 1u) << (nbits - mant_bits);;
+        //     static constexpr unsigned mask_lower = ~mask_upper;
+
+        //     f1 = n & mask_upper;
+        //     f2 = n & mask_lower;
+        // }
+    };
+
+    // acquire block sequentializer in busy wait loop
+    __device__ __forceinline__ void seq_acquire(unsigned& __restrict__ seq) noexcept
+    {
+        while (atomicCAS(&seq, 0u, 1u) != 0u)
+            #if defined(__CUDA_ARCH__) && (__CUDA_ARCH__ >= 700)
+                __nanosleep(1)
+            #endif
+            ;
+    }
+
+    // release block sequentializer
+    __device__ __forceinline__ void seq_release(unsigned& __restrict__ seq) noexcept
+    {
+        __threadfence();
+        __stwt(&seq, 0u);
+    }
+    
+    // kahan sum
+    // (a, rest) = a + b + rest
+    template<typename float_type>
+    __device__ __forceinline__ void ksum(float_type& __restrict__ a,
+                                         float_type& __restrict__ rest,
+                                         const float_type b) noexcept
+    {
+        const float_type s = rest + b;
+        const float_type t = a;
+        a = t + s;
+        rest = s - (a - t);
+    }
+
+    // warpwise aggregate of float a in lane 0
+    __device__ __forceinline__ void reduce_add(float& __restrict__ a) noexcept
+    {
+        float r = .0f;
+        for (unsigned d=1; d<warp_size; d <<= 1u) {
+            const float b = __shfl_down_sync(all_lanes, a, d, d << 1u);
+            r = __shfl_down_sync(all_lanes, r, d, d << 1u);
+            ksum(a, r, b);
+        }
+    }
+
+    // warpwise aggregate of unsigned a in all lanes
+    __device__ __forceinline__ void reduce_add_broadcast(unsigned& __restrict__ a) noexcept
+    {
+        #if __CUDA_ARCH__ >= 800
+            a = __reduce_add_sync(all_lanes, a);
+        #else
+            for (unsigned d=1; d<warp_size; d <<= 1u)
+                a += __shfl_down_sync(all_lanes, a, d, d << 1u);
+            a = __shfl_sync(all_lanes, a, 0);
+        #endif
+    }
+
+    // max of a, b, c
+    template<typename float_type>
+    __device__ __forceinline__ float_type max3(const float_type a, const float_type b, const float_type c) noexcept
+    {
+        const float_type t = (a < b) ? b : a;
+        return (t < c) ? c : t;
+    }
+
+    // return value trimmed to the range [triml..trimh]
+    // assume triml <= trimh
+    template<typename float_type>
+    __device__ __forceinline__ float_type trim(const fast_feedback::config_runtime<float_type>& __restrict__ crt,
+                                               const float_type val) noexcept
+    {
+        return min(max(crt.triml, val), crt.trimh);
+    }
+
+    // return distance to nearest integer for value
+    // The function assumes that 0 <= triml <= trimh <= 0.5
+    template<typename float_type>
+    __device__ __forceinline__ float_type dist2int(const float_type val) noexcept
+    {
+        return util<float_type>::abs(val - util<float_type>::rint(val));
+    }
+
+    // a 🞄 a
+    template<typename float_type>
+    __device__ __forceinline__ float_type norm2(const float_type a[3]) noexcept
+    {
+        return util<float_type>::fma(a[0], a[0], util<float_type>::fma(a[1], a[1], a[2] * a[2]));
+    }
+
+    // a 🞄 b
+    template<typename float_type>
+    __device__ __forceinline__ float_type dot(const float_type a[3], const float_type b[3]) noexcept
+    {
+        return util<float_type>::fma(a[0], b[0], util<float_type>::fma(a[1], b[1], a[2] * b[2]));
+    }
+
+    // a = b X c
+    template<typename float_type>
+    __device__ __forceinline__ void cross(float_type a[3], const float_type b[3], const float_type c[3]) noexcept
+    {
+        a[0] = util<float_type>::fma(b[1], c[2], -b[2] * c[1]);
+        a[1] = util<float_type>::fma(b[2], c[0], -b[0] * c[2]);
+        a[2] = util<float_type>::fma(b[0], c[1], -b[1] * c[0]);
+    }
+    
+    // a = -a
+    template<typename float_type>
+    __device__ __forceinline__ void flip(float_type a[3]) noexcept
+    {
+        a[0] = -a[0];
+        a[1] = -a[1];
+        a[2] = -a[2];
+    }
+
+    // x = inv(A) * v; A in R^3 symmetric positive definite (only upper triangle is present)
+    // out: x
+    // in : A
+    // in : v
+    template<typename float_type>
+    __device__ __forceinline__ void sym_solve(float_type x[3], const float_type A[6], const float_type v[3]) noexcept
+    {
+        // A = [a b c]       0 1 2
+        //     [- d e]         3 4
+        //     [- - f]           5
+        // det_A = a*(d*f - e*e) - b*(b*f - c*e) + c*(b*e - c*d)
+        // A_inv = [[(d*f - e*e), -(b*f - c*e),  (b*e - c*d)],
+        //          [-          ,  (a*f - c*c), -(a*e - b*c)],
+        //          [-          , -           ,  (a*d - b*b)]] / det_A
+        // x = A_inv @ v
+
+        // A cofactors
+        const auto co00 = A[3]*A[5] - A[4]*A[4];
+        const auto co01 = A[1]*A[5] - A[2]*A[4];
+        const auto co02 = A[1]*A[4] - A[2]*A[3];
+
+        const auto co11 = A[0]*A[5] - A[2]*A[2];
+        const auto co12 = A[0]*A[4] - A[1]*A[2];
+
+        const auto co22 = A[0]*A[3] - A[1]*A[1];
+
+        // det = A[0]*co00 - A[1]*co01 + A[2]*co02
+        float_type t = A[0]*co00;
+        float_type r = 0.;
+        ksum(t, r, -A[1]*co01);
+        ksum(t, r, A[2]*co02);
+        const auto r_det_A = float_type{1.} / t;
+
+        // x[0] = (co00*v[0] - co01*v[1] + co02*v[2]) / det
+        t = co00*v[0];
+        r = 0.;
+        ksum(t, r, -co01*v[1]);
+        ksum(t, r, co02*v[2]);
+        x[0] = t * r_det_A;
+
+        // x[1] = (-co01*v[0] + co11*v[1] - co12*v[2]) / det
+        t = -co01*v[0];
+        r = 0.;
+        ksum(t, r, co11*v[1]);
+        ksum(t, r, -co12*v[2]);
+        x[1] = t * r_det_A;
+
+        // x[0] = (co02*v[0] - co12*v[1] + co22*v[2]) / det
+        t = co02*v[0];
+        r = 0.;
+        ksum(t, r, -co12*v[1]);
+        ksum(t, r, co22*v[2]);
+        x[2] = t * r_det_A;
+    }
+
+    // Calculate in a the unique unified mirroring vector that brings a to b if it exists
+    // Return unified mirroring vector in a, unified b in b, and length of b in l, and if the unique mirroring vector exists
+    // lb = |b|
+    // b = b / lb
+    // a = (a + l * b); a /= |a|
+    // l = lb
+    // pre: l = |a|
+    // post: result is false if and only if a is not unique (a and b collinear)
+    template<typename float_type>
+    __device__ __forceinline__ bool add_unify(float_type a[3], float_type b[3], float_type& __restrict__ l) noexcept
+    {
+        const float_type lb = util<float_type>::norm(b[0], b[1], b[2]);
+        for (unsigned i=0u; i<3u; i++) {
+            b[i] /= lb;
+            a[i] = util<float_type>::fma(l, b[i], a[i]);
+        }
+        l = lb;
+        const float_type f = util<float_type>::norm(a[0], a[1], a[2]);
+        if (f >= constant<float_type>::eps) {
+            for (unsigned i=0u; i<3u; i++)
+                a[i] /= f;
+            return true;
+        }
+        return false;
+    }
+
+    // Calculate a unit vector in a perpendicular to b and c
+    // a = b X c
+    // l = |a|
+    // a /= l
+    template<typename float_type>
+    __device__ __forceinline__ void perpendicular_unit(float_type a[3], const float_type b[3], const float_type c[3]) noexcept
+    {
+        cross(a, b, c);
+        const float_type f = util<float_type>::rnorm(a[0], a[1], a[2]);
+        for (unsigned i=0u; i<3u; i++)
+            a[i] *= f;
+    }
+
+    // Mirror a on axis represented by unit vector b
+    // a = 2 * (a 🞄 b) * b - a
+    // pre: |b| == 1
+    template<typename float_type>
+    __device__ __forceinline__ void mirror(float_type a[3], const float_type b[3]) noexcept
+    {
+        const float_type p2 = float_type{2.f} * dot(a, b);
+        for (unsigned i=0u; i<3u; i++)
+            a[i] = util<float_type>::fma(p2, b[i], -a[i]);
+    }
+
+    // laz = a 🞄 z      length af vector a projected to axis through z
+    // x = a - laz * z  projection of a to plane perpendicular to z
+    // x /= |x|         unit vector of projection
+    // laxy = a 🞄 x     length of projection 
+    // pre: |z| == 1
+    template<typename float_type>
+    __device__ __forceinline__ void project_unify(float_type x[3], const float_type a[3], const float_type z[3],
+                                                  float_type& __restrict__ laz,
+                                                  float_type& __restrict__ laxy) noexcept
+    {
+        laz = dot(a, z);
+        for (unsigned i=0u; i<3u; i++)
+            x[i] = util<float_type>::fma(-laz, z[i], a[i]);
+        const float_type f = util<float_type>::rnorm(x[0], x[1], x[2]);
+        for (unsigned i=0u; i<3u; i++)
+            x[i] *= f;
+        laxy = dot(a, x);
+    }
+
+    // Calculate vector a with z coordinate laz and with xy projection of length laxy and angle alpha
+    // a = laz * z + (cos(alpha) * x + sin(alpha) * y) * laxy
+    // pre x, y, z are of unit length and pairwise perpendicular
+    template<typename float_type>
+    __device__ __forceinline__ void rotate(float_type a[3],
+                                           const float_type x[3], const float_type y[3], const float_type z[3],
+                                           const float_type laz, const float_type laxy,
+                                           const float_type alpha) noexcept
+    {
+        float_type s, c;
+        util<float_type>::sincos(alpha, &s, &c);
+        for (unsigned i=0u; i<3u; i++)
+            a[i] = util<float_type>::fma(laz, z[i], (util<float_type>::fma(c, x[i], s * y[i]) * laxy));
+    }
+
+    // single threaded merge of block local sorted candidate vector array into global sorted candidate vector array
+    template<typename float_type>
+    __device__ __forceinline__ void merge_top_vecs(float_type* __restrict__ top_val,
+                                                   unsigned* __restrict__ top_sample,
+                                                   vec_cand_t<float_type>* __restrict__ cand,
+                                                   const unsigned n_cand) noexcept
+    {
+        // ---- python equivalent ----
+        // def a_top(A, B):
+        //     if A[-1] <= B[0]:
+        //         return
+        //     if B[-1] <= A[0]:
+        //         A[:] = B[:]
+        //         return
+        //     a, b0, b1, b2 = 0, 0, len(B)-1, len(B)-1
+        //     while a < len(A):
+        //         val = A[a]
+        //         if b1 < b2:
+        //             if val < B[b1]:
+        //                 B[b1] = val; b1 -= 1
+        //             if B[b0] < B[b2]:
+        //                 A[a] = B[b0]; b0 += 1
+        //             else:
+        //                 A[a] = B[b2]; b2 -= 1
+        //         else:
+        //             if val > B[b0]:
+        //                 if val < B[b1]:
+        //                     B[b1] = val; b1 -= 1
+        //                 else:
+        //                     A[a:] = B[b0:b0+len(A)-a]
+        //                     return
+        //                 A[a] = B[b0]; b0 += 1
+        //         a += 1
+        // ----------------------------
+        // Candidates are ordered by value, equal values by sample index: a total order, so the global top
+        // list is the same whatever order the blocks merge in (a value tie would otherwise go to the block
+        // that happened to merge first). The block-local lists are in this order already: the block's
+        // radix sort is stable and its samples ascend with the thread index.
+        auto less = [](float_type va, unsigned sa, float_type vb, unsigned sb) {
+            return va < vb || (va == vb && sa < sb);
+        };
+
+        if (!less(cand[0].value, cand[0].sample, top_val[n_cand-1], top_sample[n_cand-1]))
+            return;
+
+        if (!less(top_val[0], top_sample[0], cand[n_cand-1].value, cand[n_cand-1].sample)) {
+            for (unsigned i=0; i<n_cand; ++i) {
+                top_val[i] = cand[i].value;
+                top_sample[i] = cand[i].sample;
+            }
+            return;
+        }
+
+        unsigned top = 0;
+        unsigned cand0 = 0;
+        unsigned cand1 = n_cand - 1;
+        unsigned cand2 = n_cand - 1;
+
+        while (top < n_cand) {
+            auto val = top_val[top];
+            const unsigned val_sample = top_sample[top];
+            if (cand1 < cand2) {
+                if (less(val, val_sample, cand[cand1].value, cand[cand1].sample)) {
+                    cand[cand1].value = val;
+                    cand[cand1].sample = top_sample[top];
+                    --cand1;
+                }
+                if (less(cand[cand0].value, cand[cand0].sample, cand[cand2].value, cand[cand2].sample)) {
+                    top_val[top] = cand[cand0].value;
+                    top_sample[top] = cand[cand0].sample;
+                    ++cand0;
+                } else {
+                    top_val[top] = cand[cand2].value;
+                    top_sample[top] = cand[cand2].sample;
+                    --cand2;
+                }
+            } else if (less(cand[cand0].value, cand[cand0].sample, val, val_sample)) {
+                if (less(val, val_sample, cand[cand1].value, cand[cand1].sample)) {
+                    cand[cand1].value = val;
+                    cand[cand1].sample = top_sample[top];
+                    --cand1;
+                } else {
+                    for (; top<n_cand; ++top, ++cand0) {
+                        top_val[top] = cand[cand0].value;
+                        top_sample[top] = cand[cand0].sample;
+                    }
+                    return;
+                }
+                top_val[top] = cand[cand0].value;
+                top_sample[top] = cand[cand0].sample;
+                ++cand0;
+            }
+            ++top;
+        }
+    }
+
+    // Single threaded merge of block local sorted candidate cell array into global sorted output cell array.
+    // Misuse output cell vector as storage for { score[i]=value, x[i]=vsample, y[i]=rsample, z[i]=cell_vector_index }
+    // Run a separate kernel to expand vsample, rsample, cell_vector_index into cell vectors
+    template<typename float_type>
+    __device__ __forceinline__ void merge_top_cells(fast_feedback::output<float_type>& __restrict__ out,
+                                                    cell_cand_t<float_type>* __restrict__ cand,
+                                                    const unsigned n_cand) noexcept
+    {
+        // A total order, as in merge_top_vecs: equal values by cell vector (with its flip bit), candidate
+        // vector and rotation sample, so a tie does not go to whichever block merged first. Within a block
+        // only the rotation sample varies, and the block's stable radix sort leaves it ascending on ties.
+        auto key_less = [](unsigned ca, unsigned va, unsigned ra, unsigned cb, unsigned vb, unsigned rb) {
+            return ca != cb ? ca < cb : (va != vb ? va < vb : ra < rb);
+        };
+        auto out_key = [&](unsigned i, unsigned& c, unsigned& v, unsigned& r) {
+            c = *reinterpret_cast<unsigned*>(&out.z[3u * i]);
+            v = *reinterpret_cast<unsigned*>(&out.x[3u * i]);
+            r = *reinterpret_cast<unsigned*>(&out.y[3u * i]);
+        };
+        auto out_less_cand = [&](unsigned i, const cell_cand_t<float_type>& b) {
+            if (out.score[i] != b.value)
+                return out.score[i] < b.value;
+            unsigned c, v, r;
+            out_key(i, c, v, r);
+            return key_less(c, v, r, b.cell_vec, b.vsample, b.rsample);
+        };
+        auto cand_less_out = [&](const cell_cand_t<float_type>& a, unsigned i) {
+            if (a.value != out.score[i])
+                return a.value < out.score[i];
+            unsigned c, v, r;
+            out_key(i, c, v, r);
+            return key_less(a.cell_vec, a.vsample, a.rsample, c, v, r);
+        };
+        auto cand_less = [&](const cell_cand_t<float_type>& a, const cell_cand_t<float_type>& b) {
+            if (a.value != b.value)
+                return a.value < b.value;
+            return key_less(a.cell_vec, a.vsample, a.rsample, b.cell_vec, b.vsample, b.rsample);
+        };
+
+        if (!cand_less_out(cand[0], n_cand-1))
+            return;
+
+        if (!out_less_cand(0, cand[n_cand-1])) {
+            for (unsigned i=0u; i<n_cand; i++) {
+                out.score[i] = cand[i].value;
+                *reinterpret_cast<unsigned*>(&out.x[3u * i]) = cand[i].vsample;
+                *reinterpret_cast<unsigned*>(&out.y[3u * i]) = cand[i].rsample;
+                *reinterpret_cast<unsigned*>(&out.z[3u * i]) = cand[i].cell_vec;
+            }
+            return;
+        }
+
+        unsigned top = 0;
+        unsigned cand0 = 0;
+        unsigned cand1 = n_cand - 1;
+        unsigned cand2 = n_cand - 1;
+
+        while (top < n_cand) {
+            auto val = out.score[top];
+            if (cand1 < cand2) {
+                if (out_less_cand(top, cand[cand1])) {
+                    cand[cand1].value = val;
+                    cand[cand1].vsample = *reinterpret_cast<unsigned*>(&out.x[3u * top]);
+                    cand[cand1].rsample = *reinterpret_cast<unsigned*>(&out.y[3u * top]);
+                    cand[cand1].cell_vec = *reinterpret_cast<unsigned*>(&out.z[3u * top]);
+                    --cand1;
+                }
+                if (cand_less(cand[cand0], cand[cand2])) {
+                    out.score[top] = cand[cand0].value;
+                    *reinterpret_cast<unsigned*>(&out.x[3u * top]) = cand[cand0].vsample;
+                    *reinterpret_cast<unsigned*>(&out.y[3u * top]) = cand[cand0].rsample;
+                    *reinterpret_cast<unsigned*>(&out.z[3u * top]) = cand[cand0].cell_vec;
+                    ++cand0;
+                } else {
+                    out.score[top] = cand[cand2].value;
+                    *reinterpret_cast<unsigned*>(&out.x[3u * top]) = cand[cand2].vsample;
+                    *reinterpret_cast<unsigned*>(&out.y[3u * top]) = cand[cand2].rsample;
+                    *reinterpret_cast<unsigned*>(&out.z[3u * top]) = cand[cand2].cell_vec;
+                    --cand2;
+                }
+            } else if (cand_less_out(cand[cand0], top)) {
+                if (out_less_cand(top, cand[cand1])) {
+                    cand[cand1].value = val;
+                    cand[cand1].vsample = *reinterpret_cast<unsigned*>(&out.x[3u * top]);
+                    cand[cand1].rsample = *reinterpret_cast<unsigned*>(&out.y[3u * top]);
+                    cand[cand1].cell_vec = *reinterpret_cast<unsigned*>(&out.z[3u * top]);
+                    --cand1;
+                } else {
+                    for (; top<n_cand; ++top, ++cand0) {
+                        out.score[top] = cand[cand0].value;
+                        *reinterpret_cast<unsigned*>(&out.x[3u * top]) = cand[cand0].vsample;
+                        *reinterpret_cast<unsigned*>(&out.y[3u * top]) = cand[cand0].rsample;
+                        *reinterpret_cast<unsigned*>(&out.z[3u * top]) = cand[cand0].cell_vec;
+                    }
+                    return;
+                }
+                out.score[top] = cand[cand0].value;
+                *reinterpret_cast<unsigned*>(&out.x[3u * top]) = cand[cand0].vsample;
+                *reinterpret_cast<unsigned*>(&out.y[3u * top]) = cand[cand0].rsample;
+                *reinterpret_cast<unsigned*>(&out.z[3u * top]) = cand[cand0].cell_vec;
+                ++cand0;
+            }
+            ++top;
+        }
+    }
+
+    // Calculate sample point on half unit sphere
+    // sample_idx   index of sample point 0..n_samples
+    // n_samples    number of sampling points
+    // v            sample point coordinates on half unit sphere
+    template<typename float_type>
+    __device__ __forceinline__ void sample_point(const unsigned sample_idx, const unsigned n_samples, float_type v[3]) noexcept
+    {
+        // Version 2: Julia
+        // i = collect(0:np-1)
+        // dl = 3. - sqrt(5.)
+        // z = 1. .- i./(np-1)
+        // r = sqrt.(1. .- z .* z)
+        // l = i * dl
+        // x = cos.(l .* pi) .* r
+        // y = sin.(l .* pi) .* r
+
+        const float_type z = float_type{1.} - static_cast<float_type>(sample_idx) / (n_samples - 1);
+        const float_type r = util<float_type>::sqrt(float_type{1.} - z * z);
+
+        float_type l = .0;
+        {
+            float_type rest = .0;
+            static_assert(sizeof(unsigned) == 4, "assumption about sizeof(unsigned) violated");
+            for (unsigned i=0; i<32; i++) {
+                if (sample_idx & (1u << i))
+                    ksum(l, rest, dl2pNmod2pi<float_type>[i]);
+            }
+        }
+
+        float_type x, y;
+        util<float_type>::sincos(l, &y, &x);
+
+        v[0] = x * r;
+        v[1] = y * r;
+        v[2] = z;
+    }
+
+    // Get sample cell vectors a, b, and unified c
+    // z            (inout) sample cell vector c, maybe refined
+    // a            (out) sample cell vector a
+    // b            (out) sample cell vector b
+    // cx           input cell vectors x coordinates
+    // cy           input cell vectors y coordinates
+    // cz           input cell vectors z coordinates
+    // vlength      (inout) length of original cell vector c
+    // rsample      sample rotation angle index of sample cell [0 .. n_rsamples[
+    // n_rsamples   number of sample angles around sample cell vector c
+    // cell_vec     input cell vector index [0 .. 3*n_input_cells[
+    // post |z_out|=1, vlength=|z_in|
+    template<typename float_type>
+    __device__ __forceinline__ void sample_cell(float_type z[3], float_type a[3], float_type b[3],
+                                                const float_type* __restrict__ cx,
+                                                const float_type* __restrict__ cy,
+                                                const float_type* __restrict__ cz,                                                
+                                                float_type& __restrict__ vlength,
+                                                const unsigned rsample, const unsigned n_rsamples,
+                                                const unsigned cell_vec) noexcept
+    {
+        {   // Get input cell vectors a and b
+            const unsigned cell_base = cell_vec / 3u;
+            {
+                const unsigned idx = cell_base + (cell_vec + 1u) % 3u;
+                a[0] = cx[idx]; a[1] = cy[idx]; a[2] = cz[idx];
+            }
+            {
+                const unsigned idx = cell_base + (cell_vec + 2u) % 3u;
+                b[0] = cx[idx]; b[1] = cy[idx]; b[2] = cz[idx];
+            }
+        }
+        float_type t[3] = { cx[cell_vec], cy[cell_vec], cz[cell_vec] };
+        // Align cell to sample vector z by finding and mirroring on t
+        if (! add_unify(t, z, vlength))     // now z has unit length, vlength is it's original length
+            perpendicular_unit(t, z, a);
+        mirror(a, t);
+        mirror(b, t);
+        // Basis perpendicular to z and projections of a/b to z, xy
+        float_type x[3], laz, laxy;         // unit vector x, length of a projected to z and xy plane ⊥ v
+        float_type y[3], lbz, lbxy;         // unit vector y, length of b projected to z and xy plane ⊥ v
+        project_unify(x, a, z, laz, laxy);
+        project_unify(t, b, z, lbz, lbxy);
+        cross(y, z, x);
+        // Rotation around z for a, b
+        float_type delta = util<float_type>::acos(dot(t, x)); // angle delta between axy and bxy vectors
+        if (dot(t, y) < .0f)
+            delta = -delta;
+        const float_type alpha = rsample * constant<float_type>::pi2 / static_cast<float_type>(n_rsamples); // sample angle
+        rotate(a, x, y, z, laz, laxy, alpha);
+        rotate(b, x, y, z, lbz, lbxy, alpha + delta);
+    }
+
+    // Calculate combined score for single vector
+    // - pow(mul(s ∈ spots) trim[triml..trimh](dist2int(s 🞄 v * vlength)) + delta, 1/|spots|) - delta
+    // - negative number of spots within distance crt.trimh of an integer - 1 (to prevent negative scores)
+    // crt          runtime configuration with triml/h and delta
+    // v            unit vector in sample vector direction, |v| == 1
+    // vlength      sample vector length
+    // s{x,y,z}     spot coordinate pointers [n_spots]
+    // n_spots      number of spots
+    template<typename float_type>
+    __device__ __forceinline__ float_type sample1(const fast_feedback::config_runtime<float_type>& __restrict__ crt,
+                                                  const float_type v[3], const float_type vlength,
+                                                  const float_type* __restrict__ sx,
+                                                  const float_type* __restrict__ sy,
+                                                  const float_type* __restrict__ sz,
+                                                  const unsigned n_spots) noexcept
+    {
+        constexpr unsigned BATCH = 1u << 3;     // 2^n, with n=3
+        constexpr unsigned MASK = BATCH - 1u;   // lower n bits
+        float_type sval = float_type{0.f};
+        float_type sv = float_type{1.f};
+        unsigned n_good = 1u;                   // 1 too many to prevent positive numbers
+
+        const float_type delta = crt.delta;
+        unsigned i = 0u;
+        do {
+            const float_type s[3] = { sx[i], sy[i], sz[i] };
+            const float_type d = dist2int(vlength * dot(v, s));
+            n_good += (d < crt.dist1) ? 1u : 0u;
+            sv *= trim(crt, d) + delta;
+            if ((++i & MASK) == 0u) {
+                sval += util<float_type>::log2(sv);
+                sv = float_type{1.};
+            }
+        } while (i<n_spots);
+        if ((i & MASK) != 0u)
+            sval += util<float_type>::log2(sv);
+        return util<float_type>::exp2(sval / (float_type)n_spots) - delta - (float_type)n_good;
+    }
+
+    // Calculate combined score for cell
+    // - pow(mul(s ∈ spots) trim[triml..trimh](sqrt(sum[i=a,b,c](dist2int(s 🞄 vi / |vi|²)²))) + delta, 1/|spots|) - delta
+    // - negative number of spots within distance crt.trimh of an integer - 1 (to prevent negative scores)
+    // crt          runtime configuration with triml/h and delta
+    // z, a, b      sample vectors, z is c normalized
+    // s{x,y,z}     spot coordinate pointers [n_spots]
+    // lz           length of c
+    // n_spots      number of spots
+    template<typename float_type>
+    __device__ __forceinline__ float_type sample3(const fast_feedback::config_runtime<float_type>& __restrict__ crt,
+                                                  const float_type z[3], const float_type a[3], const float_type b[3],
+                                                  const float_type* __restrict__ sx,
+                                                  const float_type* __restrict__ sy,
+                                                  const float_type* __restrict__ sz,
+                                                  const float_type lz, const unsigned n_spots) noexcept
+    {
+        constexpr unsigned BATCH = 1u << 3;     // 2^n, with n=3
+        constexpr unsigned MASK = BATCH - 1u;   // lower n bits
+        float_type sval = float_type{1.f};
+        float_type sv = float_type{1.f};
+        unsigned n_good = 1u;                   // 1 too many to prevent positive numbers
+
+        const float_type delta = crt.delta;
+        unsigned i=0u;
+        do {
+            const float_type s[3] = { sx[i], sy[i], sz[i] };
+            const float_type dn = util<float_type>::norm(
+                dist2int(lz * dot(z, s)),
+                dist2int(dot(a, s)),
+                dist2int(dot(b, s))
+            );
+            n_good += (dn < crt.dist3) ? 1u : 0u;
+            sv *= trim(crt, dn) + delta;
+            if ((++i & MASK) == 0u) {
+                sval += util<float_type>::log2(sv);
+                sv = float_type{1.};
+            }
+        } while (i<n_spots);
+        if ((i & MASK) != 0u)
+            sval += util<float_type>::log2(sv);
+        return util<float_type>::exp2(sval / (float_type)n_spots) - delta - (float_type)n_good;
+    }
+
+    // -----------------------------------
+    //            GPU Kernels
+    // -----------------------------------
+
+    // single thread kernel
+    // kind 0-candidate vectors sampled + output cells (float)
+    //      1-candidate vectors refined
+    //      2-output cells (unsigned)
+    //      3-output cells (float)
+    template<typename float_type>
+    __global__ void gpu_debug_out(indexer_device_data<float_type>* __restrict__ data, const unsigned kind)
+    {
+        printf("### INDEXER_GPU_DEBUG (%u)\n", kind);
+        if (kind <= 1u) {
+            // Print out candidate vectors
+            unsigned ncg = 0u;
+            const unsigned ncv = data->cpers.num_candidate_vectors;
+            const unsigned n_cells_in  = data->input.n_cells;
+
+            if (kind == 0u) {
+                // Vector candidates sampled
+                const float_type* const __restrict__ cvp = data->candidate_value;
+                const unsigned* const __restrict__ csp = data->candidate_sample;
+                for (unsigned i=0u; i<n_cells_in; ++i) {
+                    printf("input cell%u rep %u, cgi:", i, data->cell_to_cellvec[i]);
+                    for (unsigned j=3*i; j<3*i+3; ++j) {
+                        unsigned cg = data->cellvec_to_cand[j];
+                        printf(" %u", cg);
+                        if (cg > ncg)
+                            ncg = cg;
+                    }
+                    printf("\n");
+                }
+
+                printf("redundant_comp=%u, rcgrps:", unsigned(data->cpers.redundant_computations));
+                for (unsigned i=0u; i<n_cells_in; ++i)
+                    printf(" %u", data->vec_cgrps[i]);
+                printf("\n");
+
+                for (unsigned i=0u; i<=ncg; ++i) {
+                    printf("cg%u:", i);
+                    auto cv = &cvp[i * ncv];
+                    auto cs = &csp[i * ncv];
+                    for (unsigned j=0; j<ncv; ++j) {
+                        printf(" %0.2f/%u", (float)cv[j], cs[j]);
+                    }
+                    printf("\n");
+                }
+            } else if (kind == 1u) { // kind == 1
+                // Vector candidates refined
+                const float_type* const __restrict__ rca = data->refined_candidates;
+                for (unsigned i=0u; i<(3u*n_cells_in); ++i) {
+                    unsigned cg = data->cellvec_to_cand[i];
+                    if (cg > ncg)
+                        ncg = cg;
+                }
+                for (unsigned i=0u; i<=ncg; ++i) {
+                    printf("cg%u:", i);
+                    for (unsigned j=0; j<ncv; ++j) {
+                        auto rc = &rca[((i * ncv) + j) * constant<float_type>::mem_txn_unit];
+                        printf(" (%0.2f,%0.2f,%0.2f)", (float)rc[0], (float)rc[1], (float)rc[2]);
+                    }
+                    printf("\n");
+                }
+                return;
+            }
+        } else {
+            const fast_feedback::output<float_type>& out = data->output;
+            const unsigned n_cells_out  = data->cpers.max_output_cells;
+            printf("output n_cells=%u\n", out.n_cells);
+            for (unsigned i=0u; i<n_cells_out; ++i) {
+                printf("output cell%u s=%f:\n", i, out.score[i]);
+                for (unsigned j=3u*i; j<3u*i+3u; ++j) {
+                    if (kind == 2u) {
+                        const unsigned cell_vec = *reinterpret_cast<unsigned*>(&out.z[j]);
+                        printf(" %u  %u  %u %s\n",
+                            *reinterpret_cast<unsigned*>(&out.x[j]),
+                            *reinterpret_cast<unsigned*>(&out.y[j]),
+                            cell_vec & ~cell_cand_t<float_type>::FLIPPED,
+                            cell_vec & cell_cand_t<float_type>::FLIPPED ? "flipped" : "");
+                    } else {
+                        printf(" %f  %f  %f\n", out.x[j], out.y[j], out.z[j]);
+                    }
+                }
+            }
+        }
+        printf("###\n");
+    }
+
+    // sample = blockDim.x * blockIdx.x + threadIdx.x
+    // for non-redundant (cpers.redundant_computations=false) calculations:
+    //      representing vector candidate group = blockIdx.y
+    // for redundant computations:
+    //      candidate group index = blockIdx.y
+    template<typename float_type>
+    __global__ void gpu_find_candidates(indexer_device_data<float_type>* __restrict__ data)
+    {
+        extern __shared__ double* shared_ptr[];
+
+        unsigned sample[1] = {blockDim.x * blockIdx.x + threadIdx.x};
+        const unsigned n_samples = data->crt.num_halfsphere_points;
+        const unsigned c_group = data->cpers.redundant_computations ? blockIdx.y : data->vec_cgrps[blockIdx.y];
+        float_type v[1] = {0.}; // objective function value for sample vector
+
+        if (*sample < n_samples) {                                   // calculate v
+            const float_type sl = data->candidate_length[c_group];  // sample vector length
+            float_type sv[3];                                       // unit vector in sample direction
+            sample_point(*sample, n_samples, sv);
+
+            const fast_feedback::input<float_type>& in = data->input;
+            const unsigned n_spots = in.n_spots;
+            *v = sample1(data->crt, sv, sl, in.spot.x, in.spot.y, in.spot.z, n_spots);
+        }
+
+        {   // sort within block {objective function value, sample} ascending by objective function value
+            auto sort_ptr = reinterpret_cast<typename BlockRadixSort<float_type>::TempStorage*>(shared_ptr);
+            BlockRadixSort<float_type>(*sort_ptr).Sort(v, sample);
+            __syncthreads();    // protect sort_ptr[] (it's in the same memory as cand_ptr)
+        }
+
+        const unsigned num_candidate_vectors = data->cpers.num_candidate_vectors;
+        auto cand_ptr = reinterpret_cast<vec_cand_t<float_type>*>(shared_ptr); // [num_candidate_vectors]
+        if (threadIdx.x < num_candidate_vectors)    // store top candidate vectors into cand_ptr
+            cand_ptr[threadIdx.x] = { *v, *sample };
+
+        if (num_candidate_vectors < warp_size) {    // wait for cand_ptr
+            if (threadIdx.x < warp_size)
+                __syncwarp();
+        } else
+            __syncthreads();
+
+        if (threadIdx.x == 0) { // merge block local into global result
+            auto value_ptr = &data->candidate_value[c_group * num_candidate_vectors];
+            auto sample_ptr = &data->candidate_sample[c_group * num_candidate_vectors];
+
+            seq_acquire(data->seq_block[c_group]);
+            merge_top_vecs(value_ptr, sample_ptr, cand_ptr, num_candidate_vectors);
+            seq_release(data->seq_block[c_group]);
+        }
+
+        // clear output cell scores
+        if (*sample < data->cpers.max_output_cells) {
+            data->output.score[*sample] = float_type{.0f};
+        }
+    }
+
+    // vector candidate index       = blockIdx.x
+    // vector candidate group index = blockIdx.y
+    // cuda thread block size = warp_size (32)
+    template<typename float_type>
+    __global__ void gpu_refine_cand(indexer_device_data<float_type>* __restrict__ data)
+    {
+        // # Python equivalent
+        // class Optimizer:
+        //     def __init__(self, reciprocal_spots, beta=[.3, .1, .03, .01]):
+        //         self.spots = reciprocal_spots   # spots in reciprocal space
+        //         self.beta = beta                # list of diminishing beta values
+        //         self.select = None              # spot selector boolean vector
+        //     def __call__(self, b):              # b: approximation column vector in nonreciprocal space
+        //         coord = self.spots @ b          # spot coordinates in nonreciprocal space
+        //         miller = np.round(coord)        # closest integer coordinates
+        //         for beta in self.beta:
+        //             coord = self.spots @ b
+        //             self.select = np.abs(coord - miller) < beta # index set: spots within distance beta of miller coordinate
+        //             if sum(self.select) < 6:
+        //                 return None
+        //             b = np.linalg.lstsq(self.spots[self.select,:], miller[self.select],rcond=-1)[0] # use least squares fit to selected spots for a better approximation vector
+        //         return b
+        static constexpr unsigned n_rounds = 4;
+        static constexpr float_type beta[n_rounds] = {.1, .05, .025, 0.01};         // beta values per round
+        const unsigned n_cand = gridDim.x;                                          // number of candidates per candidate group
+        const unsigned cand = blockIdx.x;                                           // candidate vector index (within candidate group)
+        const unsigned cand_grp = blockIdx.y;                                       // candidate group index
+        const unsigned n_vsamples = data->crt.num_halfsphere_points;                // total number of sample vectors
+        const unsigned vsample = data->candidate_sample[cand_grp * n_cand + cand];  // sample vector index
+        const float_type vlength = data->candidate_length[cand_grp];                // sample vector length
+        const fast_feedback::input<float_type>& in = data->input;                   // input data
+        const unsigned n_spots = in.n_spots;                                        // number of reciprocal spots
+        const float_type* sx = in.spot.x;
+        const float_type* sy = in.spot.y;                                           // reciprocal spot coordinates
+        const float_type* sz = in.spot.z;
+        float_type z0[3];                                                           // sample vector
+        float_type z[3];                                                            // refined sample vector
+        float_type STS[6] = {};                                                     // S.T @ S, i'th block (upper trinagle)
+        float_type STS_r[6] = {};                                                   // rest values
+        float_type STm[3] = {};                                                     // S.T @ m, i'th block
+        float_type STm_r[3] = {};                                                   // rest values
+
+        sample_point(vsample, n_vsamples, z);   // sample unit vector
+        for (unsigned i=0u; i<3u; i++) {
+            z[i] *= vlength;                    // refined sample vector
+            z0[i] = z[i];                       // sample vector
+        }
+
+        for (unsigned round=0; round<n_rounds; round++) {
+            {   // calculate miller indices and count good spots
+                const float_type b = beta[round];
+                unsigned good_spots = 0;
+                for (unsigned i=threadIdx.x; i<n_spots; i+= warp_size) {
+                    const float_type s[3] = { sx[i], sy[i], sz[i] };                    // spot i
+                    const float_type m = util<float_type>::rint(dot(s, z0));            // Miller index i
+                    const float_type d = std::abs(dot(s, z) - m);
+                    if (d >= b)
+                        continue;
+                    good_spots++;
+                    for (unsigned j=0u; j<3u; j++) {
+                        ksum(STm[j], STm_r[j], s[j] * m);
+                        for (unsigned k=j; k<3u; k++) {
+                            unsigned l = (j<<1u) - (j>>1u) + k;
+                            ksum(STS[l], STS_r[l], s[j]*s[k]);
+                        }
+                    }
+                }
+
+                reduce_add_broadcast(good_spots);
+
+                if (good_spots < data->crt.min_spots)
+                    break;
+            }
+
+            for (unsigned j=0u; j<3u; j++) {
+                reduce_add(STm[j]);
+                for (unsigned k=j; k<3u; k++)
+                    reduce_add(STS[(j<<1u)-(j>>1u)+k]);
+            }
+
+            if (threadIdx.x == 0)
+                sym_solve(z, STS, STm);
+
+            for (unsigned j=0u; j<3u; j++)
+                z[j] = __shfl_sync(all_lanes, z[j], 0);
+        }
+
+        if (threadIdx.x == 0) {
+            float_type* refined_candidate = &data->refined_candidates[(cand_grp * n_cand + cand) * constant<float_type>::mem_txn_unit];
+            for (unsigned i=0u; i<3u; i++)
+                refined_candidate[i] = z[i];
+        }
+    }
+
+    // sample rotation angle index = blockDim.x * blockIdx.x + threadIdx.x
+    // for non-redundant (cpers.redundant_computations=false) calculations:
+    //      input cell index = blockIdx.y
+    // for redundant computations:
+    //      cell vector index = blockIdx.y
+    // vector candidate index = blockIdx.z / 2
+    // flipped candidate = blockIdx.z & 1
+    template<typename float_type>
+    __global__ void gpu_find_cells(indexer_device_data<float_type>* __restrict__ data)
+    {
+        extern __shared__ double* shared_ptr[];
+
+        const unsigned n_vsamples = data->crt.num_halfsphere_points;
+        unsigned rsample = blockIdx.x * blockDim.x + threadIdx.x;
+        const unsigned cell_vec = data->cpers.redundant_computations ? blockIdx.y : data->cell_to_cellvec[blockIdx.y];
+        const unsigned cand = blockIdx.z / 2u;
+        const bool flipped = blockIdx.z & 1;    // use flipped candidate vector?
+        const unsigned cand_grp = data->cellvec_to_cand[cell_vec];
+        const unsigned n_cand = data->cpers.num_candidate_vectors;
+        const unsigned vsample = data->candidate_sample[cand_grp * n_cand + cand];
+        float_type vabc=.0f;    // accumulated sample values for a, b, c cell vectors
+
+        { // calculate vabc for vsample/rsample/
+            const fast_feedback::input<float_type>& __restrict__ in = data->input;
+            const unsigned n_rsamples = gridDim.x * blockDim.x;
+            float_type vlength = data->candidate_length[cand_grp];
+            float_type z[3], a[3], b[3];
+
+            if (data->crt.min_spots != 0) {
+                const float_type* const __restrict__ refined_candidate = &data->refined_candidates[(cand_grp * n_cand + cand) * constant<float_type>::mem_txn_unit];
+                for (unsigned i=0u; i<3u; i++)
+                    z[i] = refined_candidate[i];
+            } else {
+                sample_point(vsample, n_vsamples, z);
+                for (unsigned i=0u; i<3u; i++)
+                    z[i] *= vlength;
+            }
+            // z = (refined) rotated cell vector, vlength = original cell vector length
+            if (flipped)
+                flip(z);
+
+            sample_cell(z, a, b, in.cell.x, in.cell.y, in.cell.z, vlength, rsample, n_rsamples, cell_vec);
+            // z unified, vlength has it's original length
+
+            const unsigned n_spots = in.n_spots;
+            vabc = sample3(data->crt, z, a, b, in.spot.x, in.spot.y, in.spot.z, vlength, n_spots);
+        }
+
+        // Get best output cells for block
+        {   // sort within block {objective function value, sample} ascending by objective function value
+            float_type key[1] = {vabc};
+            unsigned val[1] = {rsample};
+            {
+                auto sort_ptr = reinterpret_cast<typename BlockRadixSort<float_type>::TempStorage*>(shared_ptr);
+                BlockRadixSort<float_type>(*sort_ptr).Sort(key, val);
+            }
+            vabc = *key;
+            rsample = *val;
+            __syncthreads();                // protect sort_ptr[] (it's in the same memory as cand_ptr)
+        }
+
+        const unsigned n_output_cells = data->output.n_cells;
+        auto __restrict__ cand_ptr = reinterpret_cast<cell_cand_t<float_type>*>(shared_ptr); // [output.n_cells]
+        if (threadIdx.x < n_output_cells) { // store top candidate cells into cand_ptr
+            if (data->crt.min_spots != 0) {
+                cand_ptr[threadIdx.x] = { vabc, cand, rsample, flipped ? (cell_vec | cell_cand_t<float_type>::FLIPPED) : cell_vec };
+            } else {
+                cand_ptr[threadIdx.x] = { vabc, vsample, rsample, flipped ? (cell_vec | cell_cand_t<float_type>::FLIPPED) : cell_vec };
+            }
+        }
+
+        if (n_output_cells < warp_size) {   // wait for cand_ptr
+            if (threadIdx.x < warp_size)
+                __syncwarp();
+        } else
+            __syncthreads();
+
+        if (threadIdx.x == 0) {             // merge block local into global result
+            seq_acquire(data->seq_block[0]);
+            merge_top_cells(data->output, cand_ptr, n_output_cells);
+            seq_release(data->seq_block[0]);
+        }
+    }
+
+    // expand {cand, rsample, cell_vec} to coordinates of unit cell vectors
+    // threadIdx.x = output cell index
+    // n_rsamples   number of rotation angle samples rounded up to n_threads (must match n_rsamples in gpu_find_cells)
+    template<typename float_type>
+    __global__ void gpu_expand_cells(indexer_device_data<float_type>* __restrict__ data, const unsigned n_rsamples)
+    {
+        const fast_feedback::input<float_type>& __restrict__ in = data->input;
+        fast_feedback::output<float_type>& __restrict__ out = data->output;
+        float_type* __restrict__ ox = out.x;
+        float_type* __restrict__ oy = out.y;
+        float_type* __restrict__ oz = out.z;
+        const unsigned cell_base = 3u * threadIdx.x;
+        const unsigned rsample = *reinterpret_cast<unsigned*>(&oy[cell_base]);
+        const unsigned cell_vec = *reinterpret_cast<unsigned*>(&oz[cell_base]) & ~cell_cand_t<float_type>::FLIPPED;
+        const bool flipped = *reinterpret_cast<unsigned*>(&oz[cell_base]) & cell_cand_t<float_type>::FLIPPED;
+        const unsigned cand_grp = data->cellvec_to_cand[cell_vec];
+        const unsigned n_cand = data->cpers.num_candidate_vectors;
+        float_type vlength = data->candidate_length[cand_grp];
+        float_type z[3], a[3], b[3];
+
+        if (data->crt.min_spots != 0) {
+            const unsigned cand = *reinterpret_cast<unsigned*>(&ox[cell_base]);
+            const float_type* const __restrict__ refined_candidate = &data->refined_candidates[(cand_grp * n_cand + cand) * constant<float_type>::mem_txn_unit];
+            for (unsigned i=0u; i<3u; i++)
+                z[i] = refined_candidate[i];
+        } else {
+            const unsigned vsample = *reinterpret_cast<unsigned*>(&ox[cell_base]);
+            const unsigned n_vsamples = data->crt.num_halfsphere_points;
+            sample_point(vsample, n_vsamples, z);
+            for (unsigned i=0u; i<3u; i++)
+                z[i] *= vlength;
+        }
+        if (flipped)
+            flip(z);
+        // z = rotated cell vector
+
+        sample_cell(z, a, b, in.cell.x, in.cell.y, in.cell.z, vlength, rsample, n_rsamples, cell_vec);
+
+        const unsigned iz = cell_vec % 3u;
+        const unsigned ia = (iz + 1u) % 3u;
+        const unsigned ib = (iz + 2u) % 3u;
+        ox[cell_base + iz] = z[0] * vlength;
+        ox[cell_base + ia] = a[0];
+        ox[cell_base + ib] = b[0];
+        oy[cell_base + iz] = z[1] * vlength;
+        oy[cell_base + ia] = a[1];
+        oy[cell_base + ib] = b[1];
+        oz[cell_base + iz] = z[2] * vlength;
+        oz[cell_base + ia] = a[2];
+        oz[cell_base + ib] = b[2];
+    }
+
+    // Test PTX compatibility
+    // Flip bit zero of *int_ptr with a single cuda thread
+    __global__ void gpu_ptx_compatibility_test(int* int_ptr)
+    {
+        *int_ptr ^= 1;
+    }
+
+} // anonymous namespace
+
+namespace gpu {
+
+    template <typename float_type>
+    void init (const indexer<float_type>& instance)
+    {
+        using gpu_state = indexer_gpu_state<float_type>;
+        using device_data = indexer_device_data<float_type>;
+
+        gpu_device::init();
+        gpu_debug_init();
+
+        const auto state_id = instance.state;
+        if (gpu_state::exists(state_id))
+            throw FF_EXCEPTION("instance illegal reinitialisation");
+
+        const auto& cpers = instance.cpers;
+
+        if (cpers.num_candidate_vectors < 1u)
+            throw FF_EXCEPTION("nonpositive number of candidate vectors");
+        if (instance.cpers.num_candidate_vectors > n_threads)
+            throw FF_EXCEPTION("fewer threads in a block than candidate vectors");
+
+        device_data* data = nullptr;
+        float_type* candidate_length = nullptr;
+        float_type* candidate_value = nullptr;
+        float_type* refined_candidates = nullptr;
+        unsigned* candidate_sample = nullptr;
+        unsigned* cellvec_to_cand = nullptr;
+        unsigned* cell_to_cellvec = nullptr;
+        unsigned* vec_cgrps = nullptr;
+        unsigned* sequentializers = nullptr;
+        float_type* elements = nullptr;
+        float_type* ix;
+        float_type* iy;
+        float_type* iz;
+        float_type* ox;
+        float_type* oy;
+        float_type* oz;
+        float_type* scores;
+
+        int dev = gpu_device::get();
+        gpu_device::set(dev);
+
+        {
+            gpu_stream stream;
+            stream.init();      // new cuda stream
+
+            CU_CHECK(cudaMalloc(&data, sizeof(device_data)));
+            gpu_pointer<device_data> data_ptr{data};
+        
+            {
+                std::size_t vector_dimension = std::max(3 * cpers.max_input_cells, cpers.max_output_cells);
+                CU_CHECK(cudaMalloc(&sequentializers, vector_dimension * sizeof(unsigned)));
+            }
+
+            gpu_pointer<unsigned> sequentializers_ptr{sequentializers};
+            {   // initialize sequentializers
+                std::size_t vector_dimension = 3 * cpers.max_input_cells;
+                CU_CHECK(cudaMemsetAsync(sequentializers, 0, vector_dimension * sizeof(unsigned), stream));
+            }
+
+            {
+                std::size_t vector_dimension = 10 * cpers.max_output_cells + 9 * cpers.max_input_cells + 3 * cpers.max_spots;
+                CU_CHECK(cudaMalloc(&elements, vector_dimension * sizeof(float_type)));
+            }
+            gpu_pointer<float_type> element_ptr{elements};
+
+            {
+                std::size_t vector_dimension = 3 * cpers.max_input_cells;
+                CU_CHECK(cudaMalloc(&candidate_length, vector_dimension * sizeof(float_type)));
+            }
+            gpu_pointer<float_type> candidate_length_ptr{candidate_length};
+
+            {
+                std::size_t vector_dimension = 3 * cpers.num_candidate_vectors * cpers.max_input_cells;
+                CU_CHECK(cudaMalloc(&candidate_value, vector_dimension * sizeof(float_type)));
+            }
+            gpu_pointer<float_type> candidate_value_ptr{candidate_value};
+
+            {
+                static_assert(mem_txn_unit >= 3 * sizeof(float_type));
+                std::size_t vector_dimension = constant<float_type>::mem_txn_unit * 3 * cpers.num_candidate_vectors * cpers.max_input_cells;
+                CU_CHECK(cudaMalloc(&refined_candidates, vector_dimension * sizeof(float_type)));
+            }
+            gpu_pointer<float_type> refined_candidates_ptr{refined_candidates};
+
+            {
+                std::size_t vector_dimension = 3 * cpers.num_candidate_vectors * cpers.max_input_cells;
+                CU_CHECK(cudaMalloc(&candidate_sample, vector_dimension * sizeof(unsigned)));
+            }
+            gpu_pointer<unsigned> candidate_sample_ptr{candidate_sample};
+
+            {
+                std::size_t vector_dimension = 3 * cpers.max_input_cells;
+                CU_CHECK(cudaMalloc(&cellvec_to_cand, vector_dimension * sizeof(unsigned)));
+            }
+            gpu_pointer<unsigned> v2c_ptr{cellvec_to_cand};
+
+            {
+                std::size_t vector_dimension = cpers.max_input_cells;
+                CU_CHECK(cudaMalloc(&cell_to_cellvec, vector_dimension * sizeof(unsigned)));
+            }
+            gpu_pointer<unsigned> c2v_ptr{cell_to_cellvec};
+
+            {
+                std::size_t vector_dimension = cpers.max_input_cells;
+                CU_CHECK(cudaMalloc(&vec_cgrps, vector_dimension * sizeof(unsigned)));
+            }
+            gpu_pointer<unsigned> vcgrp_ptr{vec_cgrps};
+
+            std::size_t dim = cpers.max_output_cells;
+            scores = elements;
+
+            ox = elements + dim;
+            dim = 3 * cpers.max_output_cells;
+            oy = ox + dim;
+            oz = oy + dim;
+
+            ix = oz + dim;
+            dim = 3 * cpers.max_input_cells + cpers.max_spots;
+            iy = ix + dim;
+            iz = iy + dim;
+
+            {
+                std::lock_guard<std::mutex> state_lock{gpu_state::state_update};
+                gpu_state::ref(state_id) = gpu_state{std::move(data_ptr), std::move(element_ptr),
+                                                     std::move(candidate_length_ptr), std::move(candidate_value_ptr),
+                                                     std::move(refined_candidates_ptr),
+                                                     std::move(candidate_sample_ptr), std::move(v2c_ptr),
+                                                     std::move(c2v_ptr), std::move(vcgrp_ptr),
+                                                     std::move(sequentializers_ptr), std::move(stream),
+                                                     ix, iy, iz,
+                                                     ox, oy, oz,
+                                                     scores, dev,
+                                                     cpers.max_input_cells};
+            }
+
+            LOG_START(logger::l_debug) {
+                logger::debug << stanza << "init id=" << state_id << " on " << dev << ", data=" << data << '\n'
+                              << stanza << "  cand len=" << candidate_length << ", val=" << candidate_value << ", smpl=" << candidate_sample << '\n'
+                              << stanza << "  vec2cand=" << cellvec_to_cand << ", cell2vec=" << cell_to_cellvec << ", vec_cgrp=" << vec_cgrps << '\n'
+                              << stanza << "  seq=" << sequentializers << ", elements=" << elements << ", score=" << scores << '\n'
+                              << stanza << "  refcand=" << refined_candidates << '\n'
+                              << stanza << "    ox=" << ox << ", oy=" << oy << ", oz=" << oz << '\n'
+                              << stanza << "    ix=" << ix << ", iy=" << iy << ", iz=" << iz << '\n';
+            } LOG_END;
+        }
+
+        {
+            const unsigned so = 3 * cpers.max_input_cells; // spot offset
+            device_data _data{cpers, fast_feedback::config_runtime<float_type>{},
+                              fast_feedback::input<float_type>{{ix, iy, iz}, {&ix[so], &iy[so], &iz[so]}, 0, 0, true, true},
+                              fast_feedback::output<float_type>{ox, oy, oz, scores, 0},
+                              candidate_length, candidate_value,
+                              refined_candidates,
+                              candidate_sample, cellvec_to_cand,
+                              cell_to_cellvec, vec_cgrps,
+                              sequentializers};
+            auto pin_data = memory_pin::on(_data);
+            CU_CHECK(cudaMemcpyAsync(data, &_data, sizeof(_data), cudaMemcpyHostToDevice, gpu_state::stream(state_id)));
+        }
+    }
+
+    // Drop state if any
+    template <typename float_type>
+    void drop (const indexer<float_type>& instance)
+    {
+        using gpu_state = indexer_gpu_state<float_type>;
+
+        gpu_device::init();
+        gpu_state::drop(instance.state);
+    }
+
+    // Run indexer asynchronously
+    template <typename float_type>
+    void index_start (const indexer<float_type>& instance, const input<float_type>& in, output<float_type>& out, const config_runtime<float_type>& conf_rt,
+                      void(*host_callback)(void*), void* callback_data)
+    {
+        using gpu_state = indexer_gpu_state<float_type>;
+        using clock = std::chrono::high_resolution_clock;
+
+        gpu_device::check_init();
+        auto state_id = instance.state;
+        auto& state = gpu_state::ref(state_id);
+
+        gpu_device::set(state.device);
+
+        bool timing = logger::level_active<logger::l_info>();
+        if (timing) {
+            state.start_time = clock::now();
+            state.start.init();
+            state.end.init();
+        }
+
+        const bool crt_changed = (std::memcmp(&conf_rt, &state.last_crt, sizeof(conf_rt)) != 0);
+        const bool lth_changed = (state.last_crt.length_threshold != conf_rt.length_threshold);
+
+        // Check input/output (*TODO*: merge this with check_config() for consistency)
+        const auto n_cells_in = std::min(in.n_cells, instance.cpers.max_input_cells);
+        const auto n_cells_out = out.n_cells;
+        if (n_cells_in <= 0u)
+            throw FF_EXCEPTION("no given input cells");
+        if (n_cells_out <= 0)
+            throw FF_EXCEPTION("no output cells");
+        if (in.n_spots <= 0u)
+            throw FF_EXCEPTION("no spots");
+        if (conf_rt.num_halfsphere_points < instance.cpers.num_candidate_vectors)
+            throw FF_EXCEPTION("fewer halfsphere sample points than required candidate vectors");
+        if ((conf_rt.num_angle_points > 0u) && (conf_rt.num_angle_points < instance.cpers.max_output_cells))
+            throw FF_EXCEPTION("fewer angle sample points than required candidate cells");
+        if (conf_rt.delta <= .0f)
+            throw FF_EXCEPTION("nonpositive delta value in runtime configuration");
+        if (conf_rt.triml >= conf_rt.trimh)
+            throw FF_EXCEPTION("lower trim value bigger than higher trim value");
+        if (conf_rt.triml < .0f)
+            throw FF_EXCEPTION("negative lower trim value");
+        if ((conf_rt.min_spots != 0) && (conf_rt.min_spots < 4))
+            throw FF_EXCEPTION("minimum number of spots to fit vectors against too low");
+        if (n_cells_out > n_threads)
+            throw FF_EXCEPTION("fewer threads in a block than output cells");
+        if (instance.cpers.max_output_cells < out.n_cells)
+            throw FF_EXCEPTION("more output cells requested than the configured maximum");
+        
+        gpu_stream& stream = gpu_state::stream(state_id);
+
+        LOG_START(logger::l_debug) {
+            logger::debug << stanza << "index on " << state.device << ", n_cells = " << n_cells_in << "(in:" << (in.new_cells?"new":"old") << ")/"
+                                    << n_cells_out << "(out), n_spots = " << in.n_spots << ':' << (in.new_spots?"new":"old") << '\n';
+        } LOG_END;
+
+        if (crt_changed)
+            gpu_state::copy_crt(state_id, conf_rt, stream);
+            
+        if (in.new_cells || lth_changed) {
+            // Calculate input vector candidate groups
+            std::fill(std::begin(state.candidate_length_h), std::end(state.candidate_length_h), float_type{}); // need to sort
+            state.n_cand_groups = calc_cand_groups(state.candidate_idx_h, state.candidate_length_h, in, conf_rt, n_cells_in);
+            state.n_vec_cgrps = calc_cell_cand(state.cell_candidate_h, state.vec_cgrps_h, state.candidate_idx_h, n_cells_in);
+            gpu_state::init_cand(state_id, state.n_cand_groups, state.n_vec_cgrps, instance.cpers,
+                                 state.candidate_length_h, state.candidate_idx_h, state.cell_candidate_h, state.vec_cgrps_h, stream);
+
+            LOG_START(logger::l_debug) {
+                logger::debug << stanza << "  candidate_idx =";
+                for (const auto& e : state.candidate_idx_h)
+                    logger::debug << ' ' << e;
+                logger::debug << ", n_cand_groups = " << state.n_cand_groups << '\n';
+                logger::debug << stanza << "cell_candidates =";
+                for (const auto& e : state.cell_candidate_h)
+                    logger::debug << ' ' << e;
+                logger::debug << ", vec_cgrps =";
+                for (unsigned i=0u; i<state.n_vec_cgrps; i++)
+                    logger::debug << ' ' << state.vec_cgrps_h[i];
+                logger::debug << ", n_vec_cgrps = " << state.n_vec_cgrps << '\n';
+            } LOG_END;
+        }
+
+        bool dbg_flag = gpu_debug_output.load();
+        {   // find vector candidates
+            const unsigned n_samples = conf_rt.num_halfsphere_points;
+            const dim3 n_blocks((n_samples + n_threads - 1) / n_threads,                                            // samples
+                                instance.cpers.redundant_computations ? state.n_cand_groups : state.n_vec_cgrps);   // number of (cell representing vector) candidate groups
+            const unsigned shared_sz = std::max(instance.cpers.num_candidate_vectors * sizeof(vec_cand_t<float_type>),
+                                                sizeof(typename BlockRadixSort<float_type>::TempStorage));
+            gpu_state::copy_in(state_id, instance.cpers, in, out, stream);
+            if (timing)
+                state.start.record(stream);
+            gpu_find_candidates<float_type><<<n_blocks, n_threads, shared_sz, stream>>>(gpu_state::ptr(state_id).get());
+            CU_CHECK(cudaPeekAtLastError());
+            if (dbg_flag)
+                gpu_debug_out<float_type><<<1, 1, 0, stream>>>(gpu_state::ptr(state_id).get(), 0u);
+        }
+        if (conf_rt.min_spots != 0) { // refine vectors
+            const dim3 n_blocks{
+                instance.cpers.num_candidate_vectors,                                               // x: number of canditate vectors (per candidate group)
+                instance.cpers.redundant_computations ? state.n_cand_groups : state.n_vec_cgrps     // y: number of (cell representing vector) candidate groups
+            };
+            gpu_refine_cand<float_type><<<n_blocks, warp_size, 0, stream>>>(gpu_state::ptr(state_id).get());
+            CU_CHECK(cudaPeekAtLastError());
+            if (dbg_flag)
+                gpu_debug_out<float_type><<<1, 1, 0, stream>>>(gpu_state::ptr(state_id).get(), 1u);
+        }
+        {   // find cells
+            const unsigned n_xblocks = (conf_rt.num_angle_points == 0u ?
+                                            (2.5 * std::sqrt(conf_rt.num_halfsphere_points) + n_threads - 1.) / n_threads // 2*pi*r^2 (half sphere) --> 2*pi*r (circumference)
+                                           :(conf_rt.num_angle_points + n_threads - 1u) / n_threads);
+            const dim3 n_blocks(n_xblocks,                                                              // rotation samples
+                                instance.cpers.redundant_computations ? 3u * n_cells_in : n_cells_in,   // num cell vectors / num cells
+                                2u * instance.cpers.num_candidate_vectors);                             // num cand vecs (original/flipped)
+            const unsigned shared_sz = std::max(n_cells_out * sizeof(cell_cand_t<float_type>),
+                                                sizeof(typename BlockRadixSort<float_type>::TempStorage));
+            gpu_find_cells<float_type><<<n_blocks, n_threads, shared_sz, stream>>>(gpu_state::ptr(state_id).get());
+            CU_CHECK(cudaPeekAtLastError());
+            if (dbg_flag)
+                gpu_debug_out<float_type><<<1, 1, 0, stream>>>(gpu_state::ptr(state_id).get(), 2u);
+            gpu_expand_cells<float_type><<<1, n_cells_out, 0, stream>>>(gpu_state::ptr(state_id).get(), n_xblocks * n_threads);
+            CU_CHECK(cudaPeekAtLastError());
+            if (dbg_flag)
+                gpu_debug_out<float_type><<<1, 1, 0, stream>>>(gpu_state::ptr(state_id).get(), 3u);
+            if (timing)
+                state.end.record(stream);
+        }
+        if (host_callback != nullptr) {
+            state.callback_mode = true;
+            CU_CHECK(cudaLaunchHostFunc(stream, host_callback, callback_data));
+        } else
+            state.callback_mode = false;
+    }
+
+    template <typename float_type>
+    void index_end (const indexer<float_type>& instance, output<float_type>& out)
+    {
+        using gpu_state = indexer_gpu_state<float_type>;
+        using clock = std::chrono::high_resolution_clock;
+        using duration = std::chrono::duration<double, std::milli>;
+        using time_point = std::chrono::time_point<clock>;
+
+        auto state_id = instance.state;
+        auto& state = gpu_state::ref(state_id);
+
+        gpu_device::set(state.device);
+        gpu_stream& stream = state.cuda_stream;
+        state.callback_mode = false;
+
+        gpu_state::copy_out(state_id, out, stream); // synchronizes on stream
+        if (logger::level_active<logger::l_info>()) {
+            time_point end = clock::now();
+            duration elapsed = end - state.start_time;
+            LOG_START(logger::l_info) {
+                logger::info << stanza << "indexing_time: " << elapsed.count() << "ms\n";
+                logger::info << stanza << "kernel_time: " << gpu_timing(state.start, state.end) << "ms\n";
+            } LOG_END;
+        }
+    }
+
+    // Raw memory pin
+    void pin_memory(void* ptr, std::size_t size)
+    {
+        CU_CHECK(cudaHostRegister(ptr, size, cudaHostRegisterDefault));
+    }
+
+    // Raw memory unpin
+    void unpin_memory(void* ptr)
+    {
+        CU_CHECK_EXT(cudaHostUnregister(ptr));
+    }
+
+    void* alloc_pinned(std::size_t num_bytes)
+    {
+        void* ptr;
+        CU_CHECK(cudaHostAlloc(&ptr, num_bytes, cudaHostAllocDefault));
+        return ptr;
+    }
+
+    void dealloc_pinned(void* ptr)
+    {
+        CU_CHECK_EXT(cudaFreeHost(ptr));
+    }
+
+    template<typename float_type>
+    void check_config(const config_persistent<float_type>* cpers, const config_runtime<float_type>* crt)
+    {
+        if (cpers) {
+            if (cpers->max_input_cells <= 0u)
+                throw FF_EXCEPTION("max_input_cells <= 0");
+            if (cpers->max_output_cells <= 0u)
+                throw FF_EXCEPTION("max_output_cells <= 0");
+            if (cpers->max_output_cells > n_threads)
+                throw FF_EXCEPTION("fewer threads in a block than output cells");
+            if (cpers->max_spots <= 0u)
+                throw FF_EXCEPTION("max_spots <= 0");
+            if (cpers->num_candidate_vectors <= 0u)
+                throw FF_EXCEPTION("num_candidate_vectors <= 0");
+        }
+        if (crt) {
+            if (crt->delta <= .0f)
+                throw FF_EXCEPTION("nonpositive delta value in runtime configuration");
+            if (crt->triml >= crt->trimh)
+                throw FF_EXCEPTION("lower trim value bigger than higher trim value");
+            if (crt->triml < .0f)
+                throw FF_EXCEPTION("negative lower trim value");
+            if ((crt->min_spots != 0) && (crt->min_spots < 4))
+                throw FF_EXCEPTION("minimum number of spots to fit vectors against too low");
+        }
+        if (crt && cpers) {
+            if (crt->num_halfsphere_points < cpers->num_candidate_vectors)
+                throw FF_EXCEPTION("fewer halfsphere sample points than required candidate vectors");
+            if ((crt->num_angle_points > 0u) && (crt->num_angle_points < cpers->max_output_cells))
+                throw FF_EXCEPTION("fewer angle sample points than required candidate cells");
+        }
+    }
+
+    // Check compatibility between driver and runtime,
+    // throw an exception if incompatibility is detected
+    void runtime_check()
+    {
+        // check compatibility between reported driver and runtime versions
+        int driver=0, runtime=0;
+        CU_CHECK(cudaDriverGetVersion(&driver));
+        CU_CHECK(cudaRuntimeGetVersion(&runtime));
+        logger::debug << stanza << "CUDA version check: driver=" << driver << ", runtime=" << runtime << '\n';
+        if (driver < runtime)
+            throw FF_EXCEPTION("CUDA driver version is older than the runtime version");
+
+        // call dummy compatibility test kernel that flips bit 0, with one CUDA thread
+        int* dummy, data=0;
+        CU_CHECK(cudaMalloc(&dummy, sizeof(int)));
+        gpu_pointer<int> gpu_ptr(dummy);
+        CU_CHECK(cudaMemcpy(dummy, &data, sizeof(int), cudaMemcpyHostToDevice));
+        gpu_ptx_compatibility_test<<<1,1>>>(dummy);
+        CU_CHECK(cudaMemcpy(&data, dummy, sizeof(int), cudaMemcpyDeviceToHost));
+        if (data != 1)
+            throw FF_EXCEPTION("PTX compatibility test failed");
+    }
+
+    template void init<float> (const indexer<float>&);
+    template void drop<float> (const indexer<float>&);
+    template void index_start<float> (const indexer<float>&, const input<float>&, output<float>&, const config_runtime<float>&, void(*)(void*), void*);
+    template void index_end<float> (const indexer<float>&, output<float>&);
+    template void check_config<float> (const config_persistent<float>*, const config_runtime<float>*);
+} // namespace gpu
+
+extern "C" {
+    int _num_gpus()
+    {
+        int ngpus = 0;
+        if (cudaGetDeviceCount(&ngpus) != cudaSuccess)
+            return -1;
+        return ngpus;
+    }
+
+    int _select_gpu(int gpu)
+    {
+        if (cudaSetDevice(gpu) != cudaSuccess)
+            return -1;
+        return 0;
+    }
+}
diff --git a/image_analysis/indexing/fast-feedback-indexer/log.cpp b/image_analysis/indexing/fast-feedback-indexer/log.cpp
new file mode 100644
index 000000000..d151ea1dd
--- /dev/null
+++ b/image_analysis/indexing/fast-feedback-indexer/log.cpp
@@ -0,0 +1,120 @@
+// Vendored from https://github.com/paulscherrerinstitute/fast-feedback-indexer, commit a94fd4f5c55289e70860feea358182d2072e02b5
+// (indexer/src/log.cpp), BSD-3-Clause - see LICENSE.md in this directory.
+/*
+Copyright 2022 Paul Scherrer Institute
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+------------------------
+
+Author: hans-christian.stadler@psi.ch
+*/
+
+#define _INDEXER_LOG_IMPL_
+
+#include <map>
+#include <sstream>
+#include "ffbidx/log.h"
+#include "ffbidx/exception.h"
+
+namespace {
+
+    #include "ffbidx/version.h"
+
+    using namespace fast_feedback::logger;
+
+    const std::map<std::string, unsigned> string_to_level = {
+        {"fatal", l_fatal},
+        {"error", l_error},
+        {"warn", l_warn},
+        {"info", l_info},
+        {"debug", l_debug}
+    };
+
+    // Protect log output
+    std::mutex logging_output_lock;
+
+    constexpr char INDEXER_LOG_LEVEL[] = "INDEXER_LOG_LEVEL";
+
+    inline bool initialized = false;
+
+} // namespace
+
+namespace fast_feedback {
+    namespace logger {
+
+        const char* get_version()
+        {
+            return version_string;
+        }
+
+        unsigned get_init_log_level()
+        {
+            unsigned level = l_undef;
+            char* l_string = std::getenv(INDEXER_LOG_LEVEL);
+            if (l_string != nullptr) {
+                auto entry = string_to_level.find(l_string);
+                if (entry == string_to_level.end()) {
+                    std::ostringstream oss;
+                    for (const auto& e : string_to_level)
+                        oss << e.first << ", ";
+                    std::string levels_list = oss.str();
+                    levels_list.erase(levels_list.size() - 2);
+                    throw FF_EXCEPTION_OBJ << "illegal value for " << INDEXER_LOG_LEVEL << ": " << l_string << " (should be in [" << levels_list << "])\n";
+                }
+                level = entry->second;
+            }
+            if (!initialized && (level >= l_info) && (level <= l_debug)) {
+                initialized = true;
+                std::lock_guard logger_output_lock{lock()};
+                std::clog << "(version) " << get_version() << '\n';
+            }
+            return level;
+        }
+
+        const char* level_to_string(unsigned log_level)
+        {
+            switch (log_level) {
+                case l_fatal:
+                    return "fatal";
+                case l_error:
+                    return "error";
+                case l_warn:
+                    return "warn";
+                case l_info:
+                    return "info";
+                case l_debug:
+                    return "debug";
+            }
+
+            return "undef";
+        }
+        
+        std::mutex& lock() noexcept
+        {
+            return logging_output_lock;
+        }
+
+        logger<l_fatal> fatal;
+        logger<l_error> error;
+        logger<l_warn> warn;
+        logger<l_info> info;
+        logger<l_debug> debug;
+
+    } // namespace logger
+} // namespace fast_feedback
diff --git a/image_analysis/scale_merge/AnisotropyAnalysis.cpp b/image_analysis/scale_merge/AnisotropyAnalysis.cpp
index 28f840900..94249e410 100644
--- a/image_analysis/scale_merge/AnisotropyAnalysis.cpp
+++ b/image_analysis/scale_merge/AnisotropyAnalysis.cpp
@@ -337,8 +337,23 @@ namespace {
             }
     }
 
+    // The hemisphere direction nearest to s, -1 for s = 0.
+    int NearestDirection(const gemmi::Vec3 &s, const std::vector<gemmi::Vec3> &dirs) {
+        const double len = s.length();
+        if (!(len > 0))
+            return -1;
+        const gemmi::Vec3 unit(s.x / len, s.y / len, s.z / len);
+        int best = 0;
+        double best_dot = -1.0;
+        for (int j = 0; j < N_DIRECTIONS; ++j) {
+            const double dot = std::fabs(unit.dot(dirs[j]));
+            if (dot > best_dot) { best_dot = dot; best = j; }
+        }
+        return best;
+    }
+
     Cells BuildCells(const std::vector<Usable> &refl, const gemmi::UnitCell &cell,
-                     const gemmi::SpaceGroup *sg, int n_shells) {
+                     const gemmi::SpaceGroup *sg, int n_shells, size_t nthreads) {
         Cells c;
         c.n_shells = n_shells;
         const std::vector<gemmi::Op> ops = sg ? sg->operations().sym_ops : std::vector<gemmi::Op>{gemmi::Op::identity()};
@@ -353,26 +368,32 @@ namespace {
         std::vector<int32_t> raw_cell, raw_cluster;
         std::vector<float> raw_value;
 
+        // The direction of each copy (-1 for the origin), on all threads; the cells are filled below in
+        // reflection order, as one loop would fill them.
+        const auto copy_s = [&](const Usable &r, const gemmi::Op &op) {
+            const gemmi::Op::Miller m = op.apply_to_hkl(r.hkl);
+            gemmi::Vec3 s = cell.frac.mat.left_multiply(gemmi::Vec3(m[0], m[1], m[2]));
+            if (s.z < 0)
+                s = gemmi::Vec3(-s.x, -s.y, -s.z);
+            return s;
+        };
+        const size_t n_taken = (refl.size() + stride - 1) / stride;
+        std::vector<int> direction(n_taken * ops.size());
+        ParallelChunks(static_cast<int>(n_taken), nthreads, [&](int lo, int hi) {
+            for (int t = lo; t < hi; ++t)
+                for (size_t o = 0; o < ops.size(); ++o)
+                    direction[t * ops.size() + o] = NearestDirection(copy_s(refl[t * stride], ops[o]), dirs);
+        });
+
         std::vector<std::pair<int, gemmi::Vec3>> hits;      // (cell, s) of this reflection's copies
         for (size_t i = 0; i < refl.size(); i += stride) {
             const auto &r = refl[i];
             hits.clear();
-            for (const auto &op : ops) {
-                const gemmi::Op::Miller m = op.apply_to_hkl(r.hkl);
-                gemmi::Vec3 s = cell.frac.mat.left_multiply(gemmi::Vec3(m[0], m[1], m[2]));
-                if (s.z < 0)
-                    s = gemmi::Vec3(-s.x, -s.y, -s.z);
-                const double len = s.length();
-                if (!(len > 0))
+            for (size_t o = 0; o < ops.size(); ++o) {
+                const int best = direction[i / stride * ops.size() + o];
+                if (best < 0)
                     continue;
-                const gemmi::Vec3 unit(s.x / len, s.y / len, s.z / len);
-                int best = 0;
-                double best_dot = -1.0;
-                for (int j = 0; j < N_DIRECTIONS; ++j) {
-                    const double dot = std::fabs(unit.dot(dirs[j]));
-                    if (dot > best_dot) { best_dot = dot; best = j; }
-                }
-                hits.emplace_back(r.shell * N_DIRECTIONS + best, s);
+                hits.emplace_back(r.shell * N_DIRECTIONS + best, copy_s(r, ops[o]));
             }
             // A reflection contributes to a cell ONCE however many of its symmetry copies land there, so
             // a cell's standard error counts independent measurements.
@@ -920,7 +941,7 @@ namespace {
     // de-duplicated: two observations of the same reflection recorded on different frames are two
     // measurements, and the difference between them is exactly the signal this arm is after.
     Cells BuildObservationCells(const std::vector<AnisotropyObservation> &obs, const gemmi::UnitCell &cell,
-                                const gemmi::SpaceGroup *sg, int n_shells) {
+                                const gemmi::SpaceGroup *sg, int n_shells, size_t nthreads) {
         Cells c;
         c.n_shells = n_shells;
         const HKLKeyGenerator key(/*merge_friedel=*/true, sg ? *sg : *gemmi::find_spacegroup_by_number(1));
@@ -939,7 +960,8 @@ namespace {
         }
         if (order.empty())
             return c;
-        std::sort(order.begin(), order.end());
+        // The index makes the pairs a total order, so any sort leaves the same one.
+        ParallelSort(order.begin(), order.end(), nthreads, std::less<>());
         int32_t n_clusters = 1;
         for (size_t i = 1; i < order.size(); ++i)
             if (order[i].first != order[i - 1].first)
@@ -987,21 +1009,24 @@ namespace {
         raw_cell.reserve(kept.size());
         raw_value.reserve(kept.size());
         raw_cluster.reserve(kept.size());
-        for (size_t i = 0; i < kept.size(); ++i) {
-            const auto &o = obs[kept[i]];
+        const auto obs_s = [&](const AnisotropyObservation &o) {
             gemmi::Vec3 s = cell.frac.mat.left_multiply(gemmi::Vec3(o.h, o.k, o.l));
             if (s.z < 0)
                 s = gemmi::Vec3(-s.x, -s.y, -s.z);
-            const double len = s.length();
-            if (!(len > 0))
+            return s;
+        };
+        // The directions on all threads, the sums below in observation order.
+        std::vector<int> direction(kept.size());
+        ParallelChunks(static_cast<int>(kept.size()), nthreads, [&](int lo, int hi) {
+            for (int i = lo; i < hi; ++i)
+                direction[i] = NearestDirection(obs_s(obs[kept[i]]), dirs);
+        });
+        for (size_t i = 0; i < kept.size(); ++i) {
+            const auto &o = obs[kept[i]];
+            const int best = direction[i];
+            if (best < 0)
                 continue;
-            const gemmi::Vec3 unit(s.x / len, s.y / len, s.z / len);
-            int best = 0;
-            double best_dot = -1.0;
-            for (int j = 0; j < N_DIRECTIONS; ++j) {
-                const double dot = std::fabs(unit.dot(dirs[j]));
-                if (dot > best_dot) { best_dot = dot; best = j; }
-            }
+            const gemmi::Vec3 s = obs_s(o);
             const int cid = shell[i] * N_DIRECTIONS + best;
             sum[cid] += o.I;
             sumsq[cid] += static_cast<double>(o.I) * o.I;
@@ -1029,12 +1054,12 @@ namespace {
     SystematicFloor MeasureSystematicFloor(const std::vector<AnisotropyObservation> &obs,
                                            const gemmi::UnitCell &cell, const gemmi::SpaceGroup *sg,
                                            const std::vector<Tensor> &full,
-                                           const std::vector<Tensor> &forbidden) {
+                                           const std::vector<Tensor> &forbidden, size_t nthreads) {
         SystematicFloor out;
         const int q = static_cast<int>(forbidden.size());
         if (q == 0 || obs.empty())
             return out;
-        const Cells cells = BuildObservationCells(obs, cell, sg, N_SHELLS);
+        const Cells cells = BuildObservationCells(obs, cell, sg, N_SHELLS, nthreads);
         if (cells.mu.empty())
             return out;
         const TensorFit fit = FitTensor(cells, full, true);
@@ -1292,7 +1317,7 @@ AnisotropyResult AnalyzeAnisotropy(const std::vector<MergedReflection> &merged,
     if (refl.size() < static_cast<size_t>(MIN_CELLS * MIN_CELL_REFLECTIONS))
         return result;
 
-    const Cells cells = BuildCells(refl, cell, space_group, N_SHELLS);
+    const Cells cells = BuildCells(refl, cell, space_group, N_SHELLS, run.nthreads);
     const TensorFit constrained = FitTensor(cells, allowed, true);
     if (!constrained.ok)
         return result;
@@ -1347,7 +1372,7 @@ AnisotropyResult AnalyzeAnisotropy(const std::vector<MergedReflection> &merged,
         result.shape_stable = true;
         for (int alt : {8, 16}) {
             const auto alt_refl = SelectReflections(merged, cell, space_group, alt);
-            const Cells alt_cells = BuildCells(alt_refl, cell, space_group, alt);
+            const Cells alt_cells = BuildCells(alt_refl, cell, space_group, alt, run.nthreads);
             const TensorFit alt_fit = FitTensor(alt_cells, allowed, false);
             if (!alt_fit.ok) {
                 result.shape_stable = false;
@@ -1404,7 +1429,7 @@ AnisotropyResult AnalyzeAnisotropy(const std::vector<MergedReflection> &merged,
         refuse("the systematic-error scale can only be measured on unmerged observations, and none were "
                "available for this merge");
     } else {
-        const SystematicFloor sys = MeasureSystematicFloor(unmerged, cell, space_group, full, forbidden);
+        const SystematicFloor sys = MeasureSystematicFloor(unmerged, cell, space_group, full, forbidden, run.nthreads);
         result.n_observations = sys.n_observations;
         result.forbidden_z = sys.forbidden_z;
         if (!sys.ok) {
@@ -1513,7 +1538,7 @@ gemmi::Mat33 AnisotropyPriorHKL(const std::vector<MergedReflection> &merged, con
     const auto refl = SelectReflections(merged, cell, space_group, N_SHELLS);
     if (refl.size() < static_cast<size_t>(MIN_CELLS * MIN_CELL_REFLECTIONS))
         return AnisotropyTensorHKL(result, cell);
-    const Eigen3 axes = Decompose(FitTensor(BuildCells(refl, cell, space_group, N_SHELLS), allowed, true).b);
+    const Eigen3 axes = Decompose(FitTensor(BuildCells(refl, cell, space_group, N_SHELLS, 1), allowed, true).b);
     for (int n = 0; n < 3; ++n) {
         result.eigenvalue[n] = axes.value[n];
         for (int j = 0; j < 3; ++j)
diff --git a/image_analysis/scale_merge/AnisotropyAnalysis.h b/image_analysis/scale_merge/AnisotropyAnalysis.h
index a5bd8a18a..ca91ddb43 100644
--- a/image_analysis/scale_merge/AnisotropyAnalysis.h
+++ b/image_analysis/scale_merge/AnisotropyAnalysis.h
@@ -180,6 +180,8 @@ struct AnisotropyRunInfo {
     bool dose_term_in_scale_model = true;
     // The run's measured radiation damage (MergeStatistics::radiation_damage_delta_b), for the caution.
     double radiation_damage_relative_b = NAN;
+    // Workers for the cell assignment and the observation sort; the result is the same at any count.
+    size_t nthreads = 1;
 };
 
 AnisotropyResult AnalyzeAnisotropy(const std::vector<MergedReflection> &merged,
diff --git a/image_analysis/scale_merge/CMakeLists.txt b/image_analysis/scale_merge/CMakeLists.txt
index 0fd093890..e3340bce4 100644
--- a/image_analysis/scale_merge/CMakeLists.txt
+++ b/image_analysis/scale_merge/CMakeLists.txt
@@ -29,6 +29,8 @@ ADD_LIBRARY(JFJochScaleMerge
         SphericalHarmonicSurface.h
         ReindexAmbiguity.cpp
         ReindexAmbiguity.h
+        ReferenceFreeReindex.cpp
+        ReferenceFreeReindex.h
         CrystalSetting.cpp
         CrystalSetting.h
         TranslationalNCS.cpp
diff --git a/image_analysis/scale_merge/CellPopulation.cpp b/image_analysis/scale_merge/CellPopulation.cpp
index 601708b4e..d4d7f7fe1 100644
--- a/image_analysis/scale_merge/CellPopulation.cpp
+++ b/image_analysis/scale_merge/CellPopulation.cpp
@@ -74,6 +74,15 @@ std::pair<double, double> GivenCellPopulation(const std::vector<double> &relativ
         if (smooth[i] <= 0 || (i > 0 && smooth[i - 1] > smooth[i]) || (i + 1 < nbins && smooth[i + 1] >= smooth[i]))
             continue;
         const int left = valley(i, -1), right = valley(i, +1);
+        // A population is its highest peak: a stray frame or two in its tail is a local maximum too, and
+        // with no valley of its own its range is the whole population - or, where the tail runs out
+        // before any valley, everything, two forms included.
+        bool highest = true;
+        for (int j = left < 0 ? 0 : left; j <= (right < 0 ? nbins - 1 : right); j++)
+            if (smooth[j] > smooth[i])
+                highest = false;
+        if (!highest)
+            continue;
         const double low = left < 0 ? -everything : lo + (left + 0.5) * bin;
         const double high = right < 0 ? everything : lo + (right + 0.5) * bin;
         size_t count = 0;
diff --git a/image_analysis/scale_merge/CentreOfSymmetry.cpp b/image_analysis/scale_merge/CentreOfSymmetry.cpp
index 5a77ae794..a7faebf74 100644
--- a/image_analysis/scale_merge/CentreOfSymmetry.cpp
+++ b/image_analysis/scale_merge/CentreOfSymmetry.cpp
@@ -2,17 +2,25 @@
 // SPDX-License-Identifier: GPL-3.0-only
 
 #include "CentreOfSymmetry.h"
+#include "../../common/ParallelFor.h"
 
 #include <algorithm>
 #include <array>
 #include <cmath>
 #include <cstdint>
-#include <map>
 #include <random>
+#include <unordered_map>
 
 namespace {
     using Hkl = std::array<int, 3>;
 
+    struct HklHash {
+        size_t operator()(const Hkl& h) const {
+            return std::hash<uint64_t>{}((uint64_t(uint32_t(h[0])) << 42) ^ (uint64_t(uint32_t(h[1])) << 21)
+                                         ^ uint64_t(uint32_t(h[2])));
+        }
+    };
+
     struct Refl {
         Hkl hkl;
         double I, sigma, d;
@@ -76,15 +84,13 @@ namespace {
 
     // Uniform, exponential and normal deviates written out rather than taken from <random>'s
     // distributions, whose output the standard leaves to the implementation: the decision this feeds
-    // must be the same on every platform. mt19937_64 itself is fully specified.
-    struct Deviates {
-        std::mt19937_64 engine{20261004};
-        double Uniform() { return (static_cast<double>(engine() >> 11) + 0.5) * 0x1.0p-53; }
-        double Exponential() { return -std::log(Uniform()); }
-        double Normal() {   // Box-Muller, one of the pair
-            return std::sqrt(-2.0 * std::log(Uniform())) * std::cos(2.0 * 3.14159265358979323846 * Uniform());
-        }
-    };
+    // must be the same on every platform. mt19937_64 itself is fully specified. Each takes the
+    // generator's raw outputs, in the order it uses them.
+    double Uniform(uint64_t x) { return (static_cast<double>(x >> 11) + 0.5) * 0x1.0p-53; }
+    double Exponential(uint64_t x) { return -std::log(Uniform(x)); }
+    double Normal(uint64_t x1, uint64_t x2) {   // Box-Muller, one of the pair
+        return std::sqrt(-2.0 * std::log(Uniform(x1))) * std::cos(2.0 * 3.14159265358979323846 * Uniform(x2));
+    }
 
     CentreStatistic Calibrated(double measured, double acentric, double centric) {
         return {measured, acentric, centric,
@@ -95,7 +101,7 @@ namespace {
 // Following Howells, Phillips & Rogers (1950) Acta Cryst. 3, 210-214 (N(z)), and Padilla & Yeates
 // (2003) Acta Cryst. D59, 1124-1130 (the L-test, read here against its centric value 2/pi).
 CentreOfSymmetryResult AnalyzeCentreOfSymmetry(const std::vector<MergedReflection>& merged,
-                                               const gemmi::SpaceGroup& space_group) {
+                                               const gemmi::SpaceGroup& space_group, size_t nthreads) {
     CentreOfSymmetryResult out;
     const gemmi::GroupOps gops = space_group.operations();
 
@@ -114,7 +120,9 @@ CentreOfSymmetryResult AnalyzeCentreOfSymmetry(const std::vector<MergedReflectio
 
     // Fold onto the Laue class: one weighted mean per orbit, keyed by the orbit's largest member.
     struct Acc { double w = 0.0, wI = 0.0, d = 0.0; };
-    std::map<Hkl, Acc> folded;
+    // Hashed: the order the orbits come out in does not matter, the sort below puts them in one.
+    std::unordered_map<Hkl, Acc, HklHash> folded;
+    folded.reserve(merged.size());
     for (const auto& r : merged) {
         if (!std::isfinite(r.I) || !std::isfinite(r.sigma) || !(r.sigma > 0.0f) || !(r.d > 0.0f))
             continue;
@@ -157,7 +165,8 @@ CentreOfSymmetryResult AnalyzeCentreOfSymmetry(const std::vector<MergedReflectio
 
     // The two classes, in resolution order.
     std::vector<size_t> general, control;
-    std::map<Hkl, size_t> general_index;
+    std::unordered_map<Hkl, size_t, HklHash> general_index;
+    general_index.reserve(refl.size());
     for (size_t i = 0; i < refl.size(); ++i) {
         const gemmi::Op::Miller hkl{{refl[i].hkl[0], refl[i].hkl[1], refl[i].hkl[2]}};
         const gemmi::Op::Miller minus{{-hkl[0], -hkl[1], -hkl[2]}};
@@ -220,22 +229,32 @@ CentreOfSymmetryResult AnalyzeCentreOfSymmetry(const std::vector<MergedReflectio
     const Stats g = ClassStats(I, general), c = ClassStats(I, control);
     const double l = MeanAbsL(I, pairs);
 
-    Deviates dev;
+    std::mt19937_64 engine{20261004};
     Stats sim_g[2], sim_c[2];
     double sim_l[2] = {0.0, 0.0};
     std::vector<double> I_sim(refl.size());
+    std::vector<uint64_t> raw;
     for (int centric = 0; centric < 2; ++centric)
         for (int rep = 0; rep < SIMULATION_REPEATS; ++rep) {
-            for (size_t i = 0; i < refl.size(); ++i) {
-                double x;
-                if (centric) {
-                    const double z = dev.Normal();
-                    x = z * z;
-                } else {
-                    x = dev.Exponential();
+            // A reflection takes 4 draws (centric: two normals) or 3 (acentric: an exponential and a
+            // normal), drawn here in reflection order and turned into intensities on all threads.
+            const size_t per = centric ? 4 : 3;
+            raw.resize(refl.size() * per);
+            for (auto& x : raw)
+                x = engine();
+            ParallelChunks(static_cast<int>(refl.size()), nthreads, [&](int lo, int hi) {
+                for (int i = lo; i < hi; ++i) {
+                    const uint64_t* u = &raw[i * per];
+                    double x;
+                    if (centric) {
+                        const double z = Normal(u[0], u[1]);
+                        x = z * z;
+                    } else {
+                        x = Exponential(u[0]);
+                    }
+                    I_sim[i] = mean_true[i] * x + Normal(u[per - 2], u[per - 1]) * sigma[i];
                 }
-                I_sim[i] = mean_true[i] * x + dev.Normal() * sigma[i];
-            }
+            });
             const Stats sg = ClassStats(I_sim, general), sc = ClassStats(I_sim, control);
             sim_g[centric].e2m1 += sg.e2m1 / SIMULATION_REPEATS;
             sim_g[centric].nz01 += sg.nz01 / SIMULATION_REPEATS;
diff --git a/image_analysis/scale_merge/CentreOfSymmetry.h b/image_analysis/scale_merge/CentreOfSymmetry.h
index 19c794248..29bceaa9c 100644
--- a/image_analysis/scale_merge/CentreOfSymmetry.h
+++ b/image_analysis/scale_merge/CentreOfSymmetry.h
@@ -51,4 +51,4 @@ struct CentreOfSymmetryResult {
 // `merged` is a merge in any group of the Laue class of `space_group` (P1 included); it is folded onto
 // that Laue class here. Reflections `space_group` extinguishes are left out.
 CentreOfSymmetryResult AnalyzeCentreOfSymmetry(const std::vector<MergedReflection>& merged,
-                                               const gemmi::SpaceGroup& space_group);
+                                               const gemmi::SpaceGroup& space_group, size_t nthreads = 1);
diff --git a/image_analysis/scale_merge/ErrorModel.cpp b/image_analysis/scale_merge/ErrorModel.cpp
index 77999d826..a129cc3cf 100644
--- a/image_analysis/scale_merge/ErrorModel.cpp
+++ b/image_analysis/scale_merge/ErrorModel.cpp
@@ -121,6 +121,7 @@ bool ErrorModelUpdate(const std::vector<double> &bs2, const std::vector<double>
         if (!(Ass > 0.0)) return false;
         a_new = std::clamp(Bs / Ass, 0.25, 100.0);
         b2_new = 0.0;
+        fit.b_resolved = false;
     } else {
         if (!(det > 1e-10 * Ass * AII)) return false;
         const double a_fit = (Bs * AII - BI * AsI) / det;
@@ -130,13 +131,18 @@ bool ErrorModelUpdate(const std::vector<double> &bs2, const std::vector<double>
         // Leverage is not enough: b^2 can have it and still come out at zero within its own error,
         // and 1/b then reads the noise in b as an I/sigma. The standard error of b^2 comes from the
         // bins' own scatter about the fitted line; this only decides what is printed.
+        // Nor is a standard error enough when a sits on a bound: the b^2 reported beside a clamped a
+        // is not the solution of any fit. A bin whose median deviation lies far below the others' -
+        // observations that repeat their mates to the bit - takes the whole fit through its 1/bd2^2
+        // weight and pulls both terms towards zero; a stops at its bound, b^2 does not, and 1/b of
+        // the remainder reads as an I/sigma in the thousands or millions.
         double chi = 0.0;
         for (int bin = 0; bin < n_bins; ++bin) {
             if (!(bd2[bin] > 0.0)) continue;
             const double r = (bd2[bin] - a_fit * bs2[bin] - b2_fit * bI2[bin]) / bd2[bin];
             chi += r * r;
         }
-        fit.b_resolved = b2_fit >= 2.0 * std::sqrt(chi / (n_bins - 2) * Ass / det);
+        fit.b_resolved = a_new == a_fit && b2_fit >= 2.0 * std::sqrt(chi / (n_bins - 2) * Ass / det);
     }
     const bool settled = std::fabs(a_new - a) <= 1e-4 * a && std::fabs(b2_new - b2) <= 1e-4 * b2;
     a = a_new;
diff --git a/image_analysis/scale_merge/ErrorModel.h b/image_analysis/scale_merge/ErrorModel.h
index 34ceb4a4b..d6ee315ec 100644
--- a/image_analysis/scale_merge/ErrorModel.h
+++ b/image_analysis/scale_merge/ErrorModel.h
@@ -35,7 +35,8 @@ struct ErrorModelFit {
     bool active = false;       // the pool was large enough to fit
     double a = 1.0, b2 = 0.0;
     bool b_measured = true;    // false: no bin reached where b could be seen; b is held at 0
-    bool b_resolved = true;    // b^2 stood clear of two of its standard errors
+    bool b_resolved = true;    // b^2 stood clear of two of its standard errors, with a inside its bounds
+                               // and b measured; the only state in which 1/b is reported as ISa
 };
 
 // Scratch: the partitioned copy of the pool (reused between calls to save the allocation), with the rank
diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index 16bfa0fcd..f422a2cb6 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -62,7 +62,6 @@ MergeOnTheFly::MergeOnTheFly(const DiffractionExperiment &x)
       scaling_settings(x.GetScalingSettings()),
       indexing_settings(x.GetIndexingSettings()),
       high_resolution_limit(scaling_settings.GetHighResolutionLimit_A()),
-      low_resolution_limit(scaling_settings.GetLowResolutionLimit_A()),
       // A min-image-CC of 0 (the default) means "no limit": leave the optional
       // empty so the per-image CC cut is inactive. Otherwise a 0.0 threshold
       // would silently drop every image with a non-positive per-image CC.
@@ -73,7 +72,8 @@ MergeOnTheFly::MergeOnTheFly(const DiffractionExperiment &x)
       capture_coeff(scaling_settings.GetCaptureUncertaintyCoeff()),
       generator(scaling_settings.GetMergeFriedel(), space_group),
       reject_outliers(scaling_settings.GetOutlierRejectNsigma() > 0.0),
-      reject_nsigma(scaling_settings.GetOutlierRejectNsigma()) {
+      reject_nsigma(scaling_settings.GetOutlierRejectNsigma()),
+      stills(!x.IsRotationIndexing()) {
 }
 
 MergeOnTheFly &MergeOnTheFly::ReferenceCell(const std::optional<UnitCell> &cell) {
@@ -89,7 +89,7 @@ size_t MergeOnTheFly::Contributions(const IntegrationOutcome &outcome, std::vect
 
         if (r.image_scale_corr <= 0.0 || !std::isfinite(r.image_scale_corr))
             continue;
-        if (!AcceptReflection(r, high_resolution_limit, low_resolution_limit))
+        if (!AcceptReflection(r, high_resolution_limit, std::nullopt))
             continue;
         if (exclude_ice_rings && r.on_ice_ring)
             continue;
@@ -245,6 +245,7 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
     error_model_a = 1.0;
     error_model_b = 0.0;
     error_model_chi2 = 0.0;
+    error_model_b_resolved = true;
     error_model_mean_I.clear();
     reject_median_I.clear();
     reject_up = 0.0;
@@ -267,7 +268,7 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
                     continue;
                 if (r.image_scale_corr <= 0.0 || !std::isfinite(r.image_scale_corr))
                     continue;
-                if (!AcceptReflection(r, high_resolution_limit, low_resolution_limit))
+                if (!AcceptReflection(r, high_resolution_limit, std::nullopt))
                     continue;
                 if (exclude_ice_rings && r.on_ice_ring)
                     continue;
@@ -414,12 +415,34 @@ void MergeOnTheFly::RefineErrorModel(const std::vector<IntegrationOutcome> &outc
     const double det = Ass * AII - AsI * AsI;
     if (!(det > 1e-10 * Ass * AII))
         return;
-    const double a  = std::clamp((Bs * AII - BI * AsI) / det, 0.25, 100.0);
-    const double b2 = std::max((Ass * BI - AsI * Bs) / det, 0.0);
+    const double a_fit = (Bs * AII - BI * AsI) / det;
+    const double b2_fit = (Ass * BI - AsI * Bs) / det;
+    const double a  = std::clamp(a_fit, 0.25, 100.0);
+    const double b2 = std::max(b2_fit, 0.0);
+    // Whether 1/b can be reported as ISa, decided as the rotation fit decides it (ErrorModelUpdate):
+    // b^2 two of its standard errors clear of zero, the error from the bins' scatter about the line,
+    // and a inside its bounds - beside a clamped a the b^2 above is not the solution of any fit, and
+    // it is a near-zero-scatter bin that puts a on its bound (see the weight floor above).
+    double chi = 0.0;
+    for (int bin = 0; bin < n_bins; ++bin) {
+        if (!(bd2[bin] > 0.0)) continue;
+        const double r = (bd2[bin] - a_fit * bs2[bin] - b2_fit * bI2[bin]) / bd2[bin];
+        chi += r * r;
+    }
+    error_model_b_resolved = a == a_fit && b2_fit >= 2.0 * std::sqrt(chi / (n_bins - 2) * Ass / det);
 
     error_model_a = a;
     error_model_b = std::sqrt(b2);
     error_model_active = true;
+    // A still's observations of one reflection spread by their partiality and per-crystal scale, not by a
+    // multiplicative factor about the median: many read near zero, so the spread of ln(I / median) is
+    // wide and the band drawn from it lets through even a powder grain or a neighbour's spot at hundreds
+    // of sigma. The error model's b is that spread measured as it is, so stills test the plain band of
+    // n sigma about the median.
+    if (stills) {
+        reject_up = reject_nsigma * error_model_b;
+        reject_down = reject_nsigma * error_model_b;
+    }
 
     // Achieved goodness of fit: the median of the per-observation dev2/(a*sigma^2 + (b*<I>)^2). That
     // ratio is chi-square(1)-distributed (median 0.4549) when the sigmas are correct, so normalize by
@@ -641,7 +664,9 @@ MergeStatistics MergeOnTheFly::MergeStats(const std::vector<MergedReflection> &m
 
     auto d_min_limit_A = d_min_override.has_value()
         ? d_min_override : scaling_settings.GetHighResolutionLimit_A();
-    auto d_max_limit_A = scaling_settings.GetLowResolutionLimit_A();
+    // The low-resolution limit bounds the scale fit, not the merge (ScalingSettings), so the statistics
+    // run to the coarsest reflection unless a range is declared.
+    std::optional<double> d_max_limit_A;
     if (declared_range) {
         d_min_limit_A = declared_range->d_min;
         d_max_limit_A = std::isfinite(declared_range->d_max)
@@ -841,6 +866,7 @@ MergeStatistics MergeOnTheFly::MergeStats(const std::vector<MergedReflection> &m
 
     MergeStatistics out;
     out.shells.resize(n_shells);
+    out.n_observations_rejected = reject_count;
 
     for (int s = 0; s < n_shells; ++s) {
         const auto &sa = acc[s];
diff --git a/image_analysis/scale_merge/Merge.h b/image_analysis/scale_merge/Merge.h
index 6c8ca78a7..bea32cae1 100644
--- a/image_analysis/scale_merge/Merge.h
+++ b/image_analysis/scale_merge/Merge.h
@@ -288,7 +288,6 @@ class MergeOnTheFly {
 
     std::optional<UnitCell> reference_cell;
     std::optional<double> high_resolution_limit;
-    std::optional<double> low_resolution_limit;
     std::optional<double> image_cc_limit;
     // Apply image_cc_limit in Mask(). One flag for the whole engine, not a per-call argument, so the
     // merge, the error model and MergeStats can never disagree about which images are in.
@@ -317,6 +316,7 @@ class MergeOnTheFly {
     double error_model_a = 1.0;
     double error_model_b = 0.0;
     double error_model_chi2 = 0.0;   // achieved median reduced chi^2 (~1.0 = honestly calibrated sigmas)
+    bool   error_model_b_resolved = true;   // as ErrorModelFit::b_resolved; 1/b is reported as ISa only then
     // The (b*I)^2 term uses the reflection's *mean* intensity (constant over its
     // observations), so it inflates sigma without biasing the inverse-variance weights -
     // using the per-observation I_i instead would over-weight down-fluctuated points.
@@ -334,9 +334,10 @@ class MergeOnTheFly {
     double reject_nsigma = 6.0;
     std::unordered_map<uint64_t, float> reject_median_I;
     // The asymmetric band of OutlierBand.h: exp(+-n s) - 1 about the reflection mean, s the spread of
-    // ln(I / median) measured on this merge's observations.
+    // ln(I / median) measured on this merge's observations; on stills n b, the linear band.
     double reject_up = 0.0, reject_down = 0.0;
     size_t reject_count = 0;
+    bool stills = false;
 
     bool Mask(const IntegrationOutcome &outcome) const;
 
@@ -366,6 +367,7 @@ public:
     [[nodiscard]] double ErrorModelA() const { return error_model_a; }
     [[nodiscard]] double ErrorModelB() const { return error_model_b; }
     [[nodiscard]] double ErrorModelChi2() const { return error_model_chi2; }
+    [[nodiscard]] bool   ErrorModelBResolved() const { return error_model_b_resolved; }
 
     // Outlier rejection (driven by ScalingSettings::GetOutlierRejectNsigma) reports its count.
     [[nodiscard]] size_t RejectedCount() const { return reject_count; }
diff --git a/image_analysis/scale_merge/ReferenceFreeReindex.cpp b/image_analysis/scale_merge/ReferenceFreeReindex.cpp
new file mode 100644
index 000000000..f23cc3689
--- /dev/null
+++ b/image_analysis/scale_merge/ReferenceFreeReindex.cpp
@@ -0,0 +1,452 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "ReferenceFreeReindex.h"
+
+#include <algorithm>
+#include <array>
+#include <cstdint>
+#include <numbers>
+#include <random>
+#include <unordered_map>
+
+#include "HKLKey.h"
+#include "ReindexAmbiguity.h"
+#include "../../common/CrystalLattice.h"
+#include "../../common/ParallelFor.h"
+
+namespace {
+    constexpr size_t MIN_REFLECTIONS = 20;
+    constexpr int RESOLUTION_BINS = 20;
+    constexpr int RESTARTS = 4;
+    constexpr int MAX_SWEEPS = 100;
+    constexpr double DECIDED_SIGMA = 3.0;
+    // Two fits closer than this (a 0.1% difference of one axis, squared) are the same fit.
+    constexpr double METRIC_TIE = 1e-6;
+
+    double CellDistance(const UnitCell &u, const UnitCell &ref) {
+        const auto rel = [](double v, double r) { return (v - r) / r; };
+        const auto ang = [](double v, double r) { return (v - r) * std::numbers::pi / 180.0; };
+        return rel(u.a, ref.a) * rel(u.a, ref.a) + rel(u.b, ref.b) * rel(u.b, ref.b)
+               + rel(u.c, ref.c) * rel(u.c, ref.c) + ang(u.alpha, ref.alpha) * ang(u.alpha, ref.alpha)
+               + ang(u.beta, ref.beta) * ang(u.beta, ref.beta) + ang(u.gamma, ref.gamma) * ang(u.gamma, ref.gamma);
+    }
+
+    double Median(std::vector<double> v) {
+        if (v.empty())
+            return NAN;
+        std::nth_element(v.begin(), v.begin() + v.size() / 2, v.end());
+        return v[v.size() / 2];
+    }
+}
+
+MetricAnchors AnchorOnCells(const std::vector<IntegrationOutcome> &outcomes, const UnitCell &cell,
+                            const std::vector<gemmi::Op> &ops) {
+    std::vector<gemmi::Op> indexings{gemmi::Op::identity()};
+    indexings.insert(indexings.end(), ops.begin(), ops.end());
+    const size_t K = indexings.size();
+
+    // How much better an image's own refined cell fits the run's cell as indexed than after indexing g.
+    const auto cell_preference = [&](const IntegrationOutcome &o, size_t g) {
+        return CellDistance(ReindexLattice(o.latt, indexings[g]).GetUnitCell(), cell)
+               - CellDistance(o.latt.GetUnitCell(), cell);
+    };
+    // Which indexings the cells decide: those the indexed images' cells prefer the identity over (a tie
+    // counting half) for at least METRIC_DECIDED of them.
+    MetricAnchors out;
+    std::vector<bool> decided(K, false);
+    for (size_t g = 1; g < K; ++g) {
+        double prefer = 0, n = 0;
+        for (const auto &o : outcomes) {
+            if (o.reflections.empty())
+                continue;
+            const double p = cell_preference(o, g);
+            prefer += std::fabs(p) < METRIC_TIE ? 0.5 : p > 0 ? 1.0 : 0.0;
+            n += 1;
+        }
+        out.metric_preference.push_back(n > 0 ? prefer / n : 0.5);
+        decided[g] = out.metric_preference.back() >= METRIC_DECIDED;
+    }
+    // Where the cells decide an indexing, an image whose own cell prefers the identity stays as indexed.
+    out.allowed.assign(outcomes.size() * K, 1);
+    for (size_t o = 0; o < outcomes.size(); ++o)
+        for (size_t g = 1; g < K; ++g)
+            if (decided[g] && !outcomes[o].reflections.empty() && cell_preference(outcomes[o], g) >= METRIC_TIE)
+                out.allowed[o * K + g] = 0;
+    return out;
+}
+
+ReferenceAnchorResult AnchorReferenceReindex(std::vector<IntegrationOutcome> &outcomes, const UnitCell &cell,
+                                             const std::vector<gemmi::Op> &ops) {
+    std::vector<gemmi::Op> indexings{gemmi::Op::identity()};
+    indexings.insert(indexings.end(), ops.begin(), ops.end());
+    const size_t K = indexings.size();
+    // The indexing best correlated with the reference among those open: the one as indexed unless another
+    // beats it; a score that is not finite never wins (the rule of the per-image resolver).
+    const auto best = [&](const std::vector<double> &cc, const uint8_t *open) {
+        size_t b = 0;
+        for (size_t g = 1; g < K; ++g)
+            if (open[g] && std::isfinite(cc[g]) && (!std::isfinite(cc[b]) || cc[g] > cc[b]))
+                b = g;
+        return b;
+    };
+    const std::vector<uint8_t> all_open(K, 1);
+
+    // Each image back in the indexing it was indexed in.
+    std::vector<size_t> by_reference(outcomes.size(), 0);
+    for (size_t o = 0; o < outcomes.size(); ++o) {
+        auto &out = outcomes[o];
+        if (out.reference_cc.size() != K)
+            continue;
+        by_reference[o] = best(out.reference_cc, all_open.data());
+        if (by_reference[o] != 0)
+            ReindexImage(out.reflections, out.latt, indexings[by_reference[o]].inverse());
+    }
+
+    const MetricAnchors anchors = AnchorOnCells(outcomes, cell, ops);
+    ReferenceAnchorResult result;
+    result.metric_preference = anchors.metric_preference;
+    for (size_t o = 0; o < outcomes.size(); ++o) {
+        auto &out = outcomes[o];
+        if (out.reference_cc.size() != K)
+            continue;
+        const size_t g = best(out.reference_cc, &anchors.allowed[o * K]);
+        result.overruled += g != by_reference[o];
+        if (g != 0)
+            ReindexImage(out.reflections, out.latt, indexings[g]);
+        out.reference_cc.clear();   // the scores were for the indexing as indexed, which is no longer known
+    }
+    return result;
+}
+
+ReferenceFreeReindexResult ResolveReindexReferenceFree(std::vector<IntegrationOutcome> &outcomes,
+                                                       const DiffractionExperiment &x,
+                                                       const UnitCell &cell,
+                                                       const std::vector<gemmi::Op> &all_ops,
+                                                       size_t nthreads, bool apply) {
+    ReferenceFreeReindexResult out;
+    out.choice.assign(outcomes.size(), -1);
+
+    if (all_ops.empty())
+        return out;
+    const auto &s = x.GetScalingSettings();
+    const gemmi::SpaceGroup &sg = x.GetSpaceGroupOrP1();
+    std::vector<gemmi::Op> indexings{gemmi::Op::identity()};
+    indexings.insert(indexings.end(), all_ops.begin(), all_ops.end());
+    const int K = static_cast<int>(indexings.size());
+
+    const MetricAnchors anchors = AnchorOnCells(outcomes, cell, all_ops);
+    out.metric_preference = anchors.metric_preference;
+
+    const auto accept = [&](const Reflection &r) {
+        return !r.on_ice_ring && AcceptReflection(r, s.GetHighResolutionLimit_A(), s.GetLowResolutionLimit_A())
+               && r.partiality >= s.GetMinPartiality() && r.partiality > 0.0f
+               && std::isfinite(r.I) && std::isfinite(r.sigma) && r.sigma > 0.0f;
+    };
+    const auto corrected = [](const Reflection &r) {
+        return static_cast<double>(r.I) * (r.prescaling_corr * r.qe_corr * r.flight_corr) / r.partiality;
+    };
+
+    // What each image has to offer: how many reflections, how fine, and how far its indices reach in
+    // any of the indexings (which sizes the index table below).
+    const int n_out = static_cast<int>(outcomes.size());
+    std::vector<size_t> count(n_out, 0);
+    std::vector<std::array<int, 3>> reach(n_out, {0, 0, 0});
+    std::vector<double> s3_max(n_out, 0.0);
+    ParallelFor(n_out, nthreads, [&](int o) {
+        for (const auto &r : outcomes[o].reflections) {
+            if (!accept(r))
+                continue;
+            ++count[o];
+            s3_max[o] = std::max(s3_max[o], 1.0 / (static_cast<double>(r.d) * r.d * r.d));
+            for (const auto &op : indexings) {
+                const auto h = op.apply_to_hkl({{r.h, r.k, r.l}});
+                for (int i = 0; i < 3; ++i)
+                    reach[o][i] = std::max(reach[o][i], std::abs(h[i]));
+            }
+        }
+    });
+
+    // The crystals: images with enough reflections, in image order.
+    std::vector<int> crystal_outcome;
+    std::vector<size_t> begin{0};
+    std::array<int, 3> bound{0, 0, 0};
+    double s3_top = 0.0;
+    for (int o = 0; o < n_out; ++o) {
+        if (count[o] < MIN_REFLECTIONS)
+            continue;
+        crystal_outcome.push_back(o);
+        begin.push_back(begin.back() + count[o]);
+        for (int i = 0; i < 3; ++i)
+            bound[i] = std::max(bound[i], reach[o][i]);
+        s3_top = std::max(s3_top, s3_max[o]);
+    }
+    const int N = static_cast<int>(crystal_outcome.size());
+    if (N < 2)
+        return out;
+
+    // The indexings each crystal may take (AnchorOnCells): a crystal its own cell anchors is one of those
+    // the others are decided against.
+    std::vector<uint8_t> allowed(static_cast<size_t>(N) * K);
+    std::vector<bool> free(N, false);
+    for (int c = 0; c < N; ++c)
+        for (int g = 0; g < K; ++g) {
+            allowed[c * K + g] = anchors.allowed[crystal_outcome[c] * K + g];
+            free[c] = free[c] || (g > 0 && allowed[c * K + g]);
+        }
+    out.crystals = std::count(free.begin(), free.end(), true);
+    if (out.crystals == 0)
+        return out;
+    const size_t nnz = begin.back();
+
+    // The mean intensity in shells of equal reciprocal volume over the whole run, so that a crystal's
+    // intensities are compared after the fall-off with resolution, which every indexing shares, is out.
+    const auto bin_of = [&](const Reflection &r) {
+        const double s3 = 1.0 / (static_cast<double>(r.d) * r.d * r.d);
+        return std::min(RESOLUTION_BINS - 1, static_cast<int>(RESOLUTION_BINS * s3 / s3_top));
+    };
+    std::vector<std::array<double, 2 * RESOLUTION_BINS>> bin_part(N);
+    ParallelFor(N, nthreads, [&](int c) {
+        auto &b = bin_part[c];
+        b.fill(0.0);
+        for (const auto &r : outcomes[crystal_outcome[c]].reflections)
+            if (accept(r)) {
+                b[bin_of(r)] += corrected(r);
+                b[RESOLUTION_BINS + bin_of(r)] += 1.0;
+            }
+    });
+    std::array<double, RESOLUTION_BINS> bin_mean{};
+    {
+        std::array<double, 2 * RESOLUTION_BINS> total{};
+        for (const auto &b : bin_part)   // in crystal order: the same sum at any thread count
+            for (int i = 0; i < 2 * RESOLUTION_BINS; ++i)
+                total[i] += b[i];
+        for (int i = 0; i < RESOLUTION_BINS; ++i)
+            bin_mean[i] = total[RESOLUTION_BINS + i] > 0 ? total[i] / total[RESOLUTION_BINS + i] : 1.0;
+        if (std::any_of(bin_mean.begin(), bin_mean.end(), [](double m) { return !(m > 0.0); }))
+            for (auto &m : bin_mean)
+                m = 1.0;   // a shell with a non-positive mean: compare raw intensities instead
+    }
+
+    // Every index any indexing can produce, mapped to a dense number of its reflection in the
+    // asymmetric unit (Friedel mates together: the anomalous difference would only add noise here).
+    const HKLKeyGenerator key_gen(/*merge_friedel=*/true, sg);
+    const int dh = 2 * bound[0] + 1, dk = 2 * bound[1] + 1, dl = 2 * bound[2] + 1;
+    const auto entry = [&](int h, int k, int l) {
+        return (static_cast<size_t>(h + bound[0]) * dk + (k + bound[1])) * dl + (l + bound[2]);
+    };
+    std::vector<uint64_t> table_key(static_cast<size_t>(dh) * dk * dl);
+    ParallelFor(dh, nthreads, [&](int ih) {
+        for (int k = -bound[1]; k <= bound[1]; ++k)
+            for (int l = -bound[2]; l <= bound[2]; ++l)
+                table_key[entry(ih - bound[0], k, l)] = key_gen(ih - bound[0], k, l).pack();
+    });
+    std::vector<int32_t> table(table_key.size());
+    int32_t n_keys = 0;
+    {
+        std::unordered_map<uint64_t, int32_t> dense;
+        for (size_t i = 0; i < table_key.size(); ++i) {
+            const auto [it, inserted] = dense.try_emplace(table_key[i], n_keys);
+            n_keys += inserted;
+            table[i] = it->second;
+        }
+    }
+    table_key = {};
+
+    // Each crystal's intensities, divided by the shell mean and standardised within the crystal (the
+    // unknown scale and offset of an image drop out), and where each lands in every indexing. Each is
+    // weighted by how much of it is signal: a standardised intensity has unit variance, of which its
+    // measurement error takes (sigma / sd)^2, so a weak or barely recorded reflection counts for little.
+    std::vector<float> z(nnz);
+    std::vector<std::vector<int32_t>> key(K, std::vector<int32_t>(nnz));
+    ParallelFor(N, nthreads, [&](int c) {
+        std::vector<double> err;
+        size_t j = begin[c];
+        double sum = 0, sum2 = 0;
+        for (const auto &r : outcomes[crystal_outcome[c]].reflections) {
+            if (!accept(r))
+                continue;
+            const double v = corrected(r) / bin_mean[bin_of(r)];
+            z[j] = static_cast<float>(v);
+            err.push_back(r.sigma * (r.prescaling_corr * r.qe_corr * r.flight_corr) / r.partiality
+                          / bin_mean[bin_of(r)]);
+            sum += v;
+            sum2 += v * v;
+            for (int g = 0; g < K; ++g) {
+                const auto h = indexings[g].apply_to_hkl({{r.h, r.k, r.l}});
+                key[g][j] = table[entry(h[0], h[1], h[2])];
+            }
+            ++j;
+        }
+        const double n = static_cast<double>(begin[c + 1] - begin[c]);
+        const double mean = sum / n;
+        const double sd = std::sqrt(std::max(0.0, sum2 / n - mean * mean));
+        for (size_t i = begin[c]; i < begin[c + 1]; ++i) {
+            const double e = err[i - begin[c]] / sd;
+            z[i] = sd > 0 ? static_cast<float>((z[i] - mean) / sd / (1.0 + e * e)) : 0.0f;
+        }
+    });
+    table = {};
+
+    // Following Brehm & Diederichs (2014) Acta Cryst. D70, 101-109: each crystal in turn takes the
+    // indexing in which it agrees best with all the others, until none changes. Agreement is the sum
+    // over all pairs of crystals of the products of their standardised intensities on common
+    // reflections, which is the dot product of a crystal with the sum of all the others - so a pass over
+    // the crystals costs one pass over the reflections, not one per pair of crystals. The sum of all
+    // pairs only ever grows, so it ends; a few starts are made and the one that ends highest is kept.
+    std::vector<double> M(n_keys);
+    const auto add = [&](int c, int g, double sign) {
+        for (size_t i = begin[c]; i < begin[c + 1]; ++i)
+            M[key[g][i]] += sign * z[i];
+    };
+    const auto dot = [&](int c, int g) {
+        double d = 0;
+        for (size_t i = begin[c]; i < begin[c + 1]; ++i)
+            d += z[i] * M[key[g][i]];
+        return d;
+    };
+    std::vector<int> best_choice;
+    double best_objective = -1.0;
+    for (int restart = 0; restart < RESTARTS; ++restart) {
+        std::vector<int> choice(N, 0);
+        std::mt19937 rng(restart);
+        if (restart > 0)
+            for (int c = 0; c < N; ++c) {
+                const int g = static_cast<int>(rng() % K);
+                choice[c] = allowed[c * K + g] ? g : 0;
+            }
+        std::fill(M.begin(), M.end(), 0.0);
+        for (int c = 0; c < N; ++c)
+            add(c, choice[c], 1.0);
+        int sweeps = 0;
+        // Run until a pass moves no more than one crystal in a thousand: what still moves then are crystals
+        // too weak to be decided either way.
+        for (int changed = N; changed > N / 1000 && sweeps < MAX_SWEEPS; ++sweeps) {
+            changed = 0;
+            for (int c = 0; c < N; ++c) {
+                add(c, choice[c], -1.0);
+                int best = choice[c];
+                double best_dot = dot(c, best);
+                for (int g = 0; g < K; ++g) {
+                    if (g == choice[c] || !allowed[c * K + g])
+                        continue;
+                    const double d = dot(c, g);
+                    if (d > best_dot) {
+                        best_dot = d;
+                        best = g;
+                    }
+                }
+                changed += best != choice[c];
+                choice[c] = best;
+                add(c, best, 1.0);
+            }
+        }
+        double objective = 0;
+        for (double m : M)
+            objective += m * m;
+        if (objective > best_objective) {
+            best_objective = objective;
+            best_choice = choice;
+            out.sweeps = sweeps;
+        }
+    }
+
+    // How clearly each crystal is decided: its CC with the mean of all the other crystals, in the chosen
+    // indexing and in the best other one, and the difference of the two in sigma (Fisher's z; each CC
+    // on n reflections has an error of 1/sqrt(n - 3), and the two are nearly independent).
+    std::fill(M.begin(), M.end(), 0.0);
+    std::vector<double> C(n_keys, 0.0);
+    for (int c = 0; c < N; ++c)
+        for (size_t i = begin[c]; i < begin[c + 1]; ++i) {
+            M[key[best_choice[c]][i]] += z[i];
+            C[key[best_choice[c]][i]] += 1.0;
+        }
+    std::vector<double> sigma(N, NAN), cc_chosen(N, NAN), cc_other(N, NAN);
+    ParallelFor(N, nthreads, [&](int c) {
+        std::vector<double> cc(K, NAN);
+        std::vector<double> n_used(K, 0.0);
+        for (int g = 0; g < K; ++g) {
+            double sx = 0, sy = 0, sxx = 0, syy = 0, sxy = 0, n = 0;
+            for (size_t i = begin[c]; i < begin[c + 1]; ++i) {
+                const int32_t k = key[g][i];
+                const double own = g == best_choice[c] ? 1.0 : 0.0;
+                const double cnt = C[k] - own;
+                if (cnt <= 0)
+                    continue;
+                const double xv = z[i], yv = (M[k] - own * z[i]) / cnt;
+                sx += xv; sy += yv; sxx += xv * xv; syy += yv * yv; sxy += xv * yv; n += 1;
+            }
+            const double vx = sxx - sx * sx / n, vy = syy - sy * sy / n;
+            if (n > 3 && vx > 0 && vy > 0) {
+                cc[g] = std::clamp((sxy - sx * sy / n) / std::sqrt(vx * vy), -0.999, 0.999);
+                n_used[g] = n;
+            }
+        }
+        const int g0 = best_choice[c];
+        int other = -1;
+        for (int g = 0; g < K; ++g)
+            if (g != g0 && allowed[c * K + g] && std::isfinite(cc[g]) && (other < 0 || cc[g] > cc[other]))
+                other = g;
+        if (!std::isfinite(cc[g0]) || other < 0)
+            return;
+        cc_chosen[c] = cc[g0];
+        cc_other[c] = cc[other];
+        sigma[c] = (std::atanh(cc[g0]) - std::atanh(cc[other]))
+                   * std::sqrt((std::min(n_used[g0], n_used[other]) - 3.0) / 2.0);
+    });
+    std::vector<double> sig, ccc, cco;
+    for (int c = 0; c < N; ++c)
+        if (free[c] && std::isfinite(sigma[c])) {
+            sig.push_back(sigma[c]);
+            ccc.push_back(cc_chosen[c]);
+            cco.push_back(cc_other[c]);
+        }
+    out.median_sigma = Median(sig);
+    out.cc_chosen = Median(ccc);
+    out.cc_other = Median(cco);
+    if (!sig.empty())
+        out.decided_fraction = static_cast<double>(std::count_if(sig.begin(), sig.end(), [](double v) {
+            return v > DECIDED_SIGMA; })) / static_cast<double>(sig.size());
+
+    // Any consistent answer relabelled as a whole by one of the indexings is as consistent: take the
+    // one that leaves the most crystals where they are - unless the cells decide an indexing, in which
+    // case the crystals they anchor fix the whole. Two indexings are the same for the merge when they
+    // send a general reflection to the same reflection of the asymmetric unit.
+    const std::array<int, 3> general{2, 5, 11};
+    const auto same = [&](const gemmi::Op::Miller &a, const gemmi::Op::Miller &b) {
+        return key_gen(a[0], a[1], a[2]) == key_gen(b[0], b[1], b[2]);
+    };
+    const auto composed = [&](int global, int g) {   // indexing g, then the overall relabel
+        return indexings[global].apply_to_hkl(indexings[g].apply_to_hkl(general));
+    };
+    int global = 0;
+    size_t global_kept = 0;
+    const bool anchored = std::any_of(out.metric_preference.begin(), out.metric_preference.end(),
+                                      [](double p) { return p >= METRIC_DECIDED; });
+    for (int h = 0; h < (anchored ? 1 : K); ++h) {
+        size_t kept = 0;
+        for (int c = 0; c < N; ++c)
+            kept += same(composed(h, best_choice[c]), general);
+        if (kept > global_kept) {
+            global_kept = kept;
+            global = h;
+        }
+    }
+    for (int c = 0; c < N; ++c) {
+        int final_g = best_choice[c];
+        for (int g = 0; g < K; ++g)
+            if (same(composed(global, best_choice[c]), indexings[g].apply_to_hkl(general))) {
+                final_g = g;
+                break;
+            }
+        out.choice[crystal_outcome[c]] = final_g;
+        if (final_g == 0)
+            continue;
+        ++out.reindexed;
+        if (apply) {
+            auto &o = outcomes[crystal_outcome[c]];
+            ReindexImage(o.reflections, o.latt, indexings[final_g]);
+        }
+    }
+    return out;
+}
diff --git a/image_analysis/scale_merge/ReferenceFreeReindex.h b/image_analysis/scale_merge/ReferenceFreeReindex.h
new file mode 100644
index 000000000..2527b1d54
--- /dev/null
+++ b/image_analysis/scale_merge/ReferenceFreeReindex.h
@@ -0,0 +1,77 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <cmath>
+#include <cstdint>
+#include <vector>
+
+#include "gemmi/symmetry.hpp"
+
+#include "../../common/DiffractionExperiment.h"
+#include "../IntegrationOutcome.h"
+
+// Serial stills with no reference: every crystal is indexed in one of the indexings its lattice allows
+// (the identity and the twin-law operators of ReindexAmbiguityOperators), at random. Which one each
+// crystal is in is decided from the data alone, by putting each crystal into the indexing in which it
+// agrees best with all the others. The overall choice among the equivalent consistent answers is the
+// one that moves the fewest crystals.
+//
+// An operator is only an ambiguity where the crystal's own lattice cannot tell the indexings apart. Where
+// the cell is merely close to a more symmetric one (two axes a few per cent apart, say), the crystals'
+// refined cells already say which axis is which, and the indexer has used that. For such an operator a
+// crystal whose cell prefers the indexing it came in stays there, as an anchor, and only the others are
+// decided by the intensities.
+// An operator whose reindexed cell is the worse fit to the run's cell for at least this share of the
+// crystals is one the cells decide. For a true (merohedral) ambiguity the two fits are equal and the
+// share is a half.
+constexpr double METRIC_DECIDED = 0.9;
+
+// Which indexings each image's own refined cell leaves open. Indexing g is the image as indexed for g = 0
+// and after ops[g - 1] otherwise; `cell` is the run's cell. An operator the cells decide is closed to
+// every image whose cell fits `cell` better as indexed; everything else is open.
+struct MetricAnchors {
+    std::vector<double> metric_preference;   // per operator: share of the images whose refined cell is
+                                             // closer to `cell` as indexed than after the operator
+    std::vector<uint8_t> allowed;            // allowed[o * (ops.size() + 1) + g]: indexing g open to image o
+};
+MetricAnchors AnchorOnCells(const std::vector<IntegrationOutcome> &outcomes, const UnitCell &cell,
+                            const std::vector<gemmi::Op> &ops);
+
+// With a reference - a reference MTZ or intensities from the model - each image has been put, image by
+// image, into the indexing that correlates best with it (ReindexAmbiguityResolver, which leaves the scores in
+// IntegrationOutcome::reference_cc, over the same `ops`). The reference knows nothing of the cells, so
+// here the cells have their say first, as above: an image its own cell anchors keeps that indexing,
+// and the reference decides among the indexings left open to the others.
+struct ReferenceAnchorResult {
+    std::vector<double> metric_preference;   // as in MetricAnchors
+    size_t overruled = 0;                    // images the reference had put into an indexing their cell
+                                             // excludes, now in the best open one instead
+};
+ReferenceAnchorResult AnchorReferenceReindex(std::vector<IntegrationOutcome> &outcomes, const UnitCell &cell,
+                                             const std::vector<gemmi::Op> &ops);
+
+struct ReferenceFreeReindexResult {
+    size_t crystals = 0;           // crystals that took part (enough reflections to say anything, and an
+                                   // indexing their own cell leaves open)
+    size_t reindexed = 0;          // of them, put into an indexing other than the one they came in
+    double median_sigma = NAN;     // per crystal, how far its chosen indexing beats the best other one
+                                   // in agreement with the rest of the merge, in sigma; the median
+    double decided_fraction = NAN; // share of the crystals for which that margin is over 3 sigma
+    double cc_chosen = NAN;        // median CC of a crystal with the merge of all the others, as chosen
+    double cc_other = NAN;         // ... and in the best other indexing
+    std::vector<double> metric_preference;   // per operator: share of crystals whose refined cell is
+                                             // closer to `cell` as indexed than after the operator
+    int sweeps = 0;                // passes over the crystals until (almost) none changed (the start kept)
+    std::vector<int> choice;       // per outcome: -1 did not take part, 0 kept, k reindexed by ops[k - 1]
+};
+
+// `cell` is the run's cell, `ops` its twin-law operators (identity excluded). With apply = false nothing is changed - the
+// result then says how many crystals the data alone would put into another indexing than they are in,
+// which, after a reference has resolved them, is the disagreement with the reference.
+ReferenceFreeReindexResult ResolveReindexReferenceFree(std::vector<IntegrationOutcome> &outcomes,
+                                                       const DiffractionExperiment &x,
+                                                       const UnitCell &cell,
+                                                       const std::vector<gemmi::Op> &ops,
+                                                       size_t nthreads, bool apply);
diff --git a/image_analysis/scale_merge/ReindexAmbiguity.cpp b/image_analysis/scale_merge/ReindexAmbiguity.cpp
index 61783520c..42486ce0f 100644
--- a/image_analysis/scale_merge/ReindexAmbiguity.cpp
+++ b/image_analysis/scale_merge/ReindexAmbiguity.cpp
@@ -266,18 +266,23 @@ double ReindexAmbiguityResolver::ReferenceCC(std::span<const Reflection> reflect
 
 // Serial stills index each crystal in one of the merohedrally-equivalent hands at random; pick, for this
 // image alone, the reindexing whose intensities correlate best with the external reference and apply it.
-void ReindexAmbiguityResolver::Resolve(std::span<Reflection> reflections, CrystalLattice &latt) const {
+std::vector<double> ReindexAmbiguityResolver::Resolve(std::span<Reflection> reflections, CrystalLattice &latt) const {
     if (ops.empty())
-        return;
+        return {};
 
-    const BestReindex best = PickBestReindex(
-        ReferenceCC(reflections, gemmi::Op::identity()), ops,
-        [&](const gemmi::Op &op) { return ReferenceCC(reflections, op); });
-    if (best.is_identity)
-        return;
+    std::vector<double> cc{ReferenceCC(reflections, gemmi::Op::identity())};
+    const BestReindex best = PickBestReindex(cc[0], ops, [&](const gemmi::Op &op) {
+        cc.push_back(ReferenceCC(reflections, op));
+        return cc.back();
+    });
+    if (!best.is_identity)
+        ReindexImage(reflections, latt, best.op);
+    return cc;
+}
 
+void ReindexImage(std::span<Reflection> reflections, CrystalLattice &latt, const gemmi::Op &op) {
     for (auto &r : reflections) {
-        const gemmi::Op::Miller h = best.op.apply_to_hkl({{r.h, r.k, r.l}});
+        const gemmi::Op::Miller h = op.apply_to_hkl({{r.h, r.k, r.l}});
         r.h = h[0]; r.k = h[1]; r.l = h[2];
     }
     // Everything after this - the sublattice relabel, the partiality post-refinement - predicts a spot
@@ -285,5 +290,5 @@ void ReindexAmbiguityResolver::Resolve(std::span<Reflection> reflections, Crysta
     // axes, a frame relabelled by an operator that is only a near-symmetry of the lattice was put
     // through the sublattice relabel a second time, and its reflections came out at indices finer
     // than anything measured.
-    latt = ReindexLattice(latt, best.op);
+    latt = ReindexLattice(latt, op);
 }
diff --git a/image_analysis/scale_merge/ReindexAmbiguity.h b/image_analysis/scale_merge/ReindexAmbiguity.h
index 773011342..57346d18d 100644
--- a/image_analysis/scale_merge/ReindexAmbiguity.h
+++ b/image_analysis/scale_merge/ReindexAmbiguity.h
@@ -21,7 +21,8 @@
 // Resolving the indexing ("alternative indexing" / reindexing) ambiguity: when the lattice symmetry
 // is higher than the crystal Laue symmetry (merohedral / pseudo-merohedral), a crystal can be validly
 // indexed in several ways related by reindexing operators. The right one is picked by agreement with a
-// reference (reference-MTZ intensities or a model), so no reference-free ambigator (cosym) is needed.
+// reference (reference-MTZ intensities or a model); serial stills without one are made consistent from
+// the data alone (ReferenceFreeReindex.h).
 //
 // This is distinct from the screw-axis / enantiomorph ambiguity (P4_1 vs P4_3): that leaves the merged
 // intensities unchanged, so it is never resolved here — it is adopted from the reference/model.
@@ -39,6 +40,10 @@ std::vector<gemmi::Op> ReindexAmbiguityOperators(const UnitCell &cell, const gem
 // R^-1 times the old ones, so h' (a*, b*, c*)' is the same reciprocal vector as h (a*, b*, c*).
 CrystalLattice ReindexLattice(const CrystalLattice &latt, const gemmi::Op &op);
 
+// One image put into another indexing: its reflections relabelled by `op` and its lattice moved onto the
+// same axes, so that a spot's new index still predicts it where it was measured.
+void ReindexImage(std::span<Reflection> reflections, CrystalLattice &latt, const gemmi::Op &op);
+
 std::vector<MergedReflection> ReindexReflections(const std::vector<MergedReflection> &merged,
                                                  const gemmi::Op &op);
 
@@ -133,9 +138,11 @@ public:
     // The reference must be an external, correctly-handed dataset (not the data's own running merge).
     ReindexAmbiguityResolver(const DiffractionExperiment &x, const std::vector<MergedReflection> &reference);
 
-    // Reindex this image's reflections in place into the hand best-correlated with the reference (done
-    // once per image, for good). No-op when there is no ambiguity.
+    // Reindex this image's reflections in place into the hand best-correlated with the reference. No-op
+    // when there is no ambiguity.
     // Relabels the image's reflections and moves its lattice onto the same axes, so that a spot's new
-    // index still predicts it where it was measured.
-    void Resolve(std::span<Reflection> reflections, CrystalLattice &latt) const;
+    // index still predicts it where it was measured. Returns the CC in each indexing, as indexed first and
+    // then the operators of ReindexAmbiguityOperators(cell, space group) - empty when there are none -
+    // for AnchorReferenceReindex to revisit the choice once the whole run's cells are known.
+    std::vector<double> Resolve(std::span<Reflection> reflections, CrystalLattice &latt) const;
 };
diff --git a/image_analysis/scale_merge/RotationScaleMerge.cpp b/image_analysis/scale_merge/RotationScaleMerge.cpp
index 4761d0954..b1722648c 100644
--- a/image_analysis/scale_merge/RotationScaleMerge.cpp
+++ b/image_analysis/scale_merge/RotationScaleMerge.cpp
@@ -350,7 +350,7 @@ RotationScaleMerge::RotationScaleMerge(const DiffractionExperiment &experiment,
     const auto s = x.GetScalingSettings();
     min_partiality = s.GetMinPartiality();
     d_min_limit = s.GetHighResolutionLimit_A();
-    d_max_limit = s.GetLowResolutionLimit_A();
+    d_max_scale = s.GetLowResolutionLimit_A();
     merge_friedel = s.GetMergeFriedel();
     capture_uncertainty_coeff = s.GetCaptureUncertaintyCoeff();
     min_captured_fraction = s.GetMinCapturedFraction();
@@ -408,23 +408,38 @@ RotationScaleMerge::RotationScaleMerge(const DiffractionExperiment &experiment,
 // the scaling and the sweep ledger to judge as they judge any other. Only from the ends inward: a frame
 // inside the sweep without beam is news, and is left to the ledger too. A frame with nothing integrated
 // on it (missing from disk, not processed) is walked past and not counted.
-std::pair<int, int> TrimBlankSweepEnds(std::vector<IntegrationOutcome> &outcomes, size_t nthreads) {
+namespace {
     constexpr double BLANK_TAIL_SIGMA = 3.0;
+}
+
+SweepEndTally TallySweepEnd(const IntegrationOutcome &outcome) {
+    SweepEndTally t;
+    for (const auto &r : outcome.reflections) {
+        if (std::isfinite(r.I) && std::isfinite(r.sigma) && r.sigma > 0.0f) {
+            t.upper += r.I > BLANK_TAIL_SIGMA * r.sigma;
+            t.lower += r.I < -BLANK_TAIL_SIGMA * r.sigma;
+        }
+        if (std::isfinite(r.bkg)) { t.bkg_sum += r.bkg; ++t.bkg_n; }
+    }
+    return t;
+}
+
+std::pair<int, int> TrimBlankSweepEnds(std::vector<IntegrationOutcome> &outcomes, size_t nthreads) {
+    std::vector<SweepEndTally> tally(outcomes.size());
+    ParallelFor(static_cast<int>(outcomes.size()), nthreads, [&](int f) { tally[f] = TallySweepEnd(outcomes[f]); });
+    return TrimBlankSweepEnds(outcomes, tally);
+}
+
+std::pair<int, int> TrimBlankSweepEnds(std::vector<IntegrationOutcome> &outcomes,
+                                       const std::vector<SweepEndTally> &tally) {
     const int n = static_cast<int>(outcomes.size());
     std::vector<int64_t> upper(n, 0), lower(n, 0);
     std::vector<double> bkg(n, 0.0);
-    ParallelFor(n, nthreads, [&](int f) {
-        double bkg_sum = 0.0;
-        int64_t bkg_n = 0;
-        for (const auto &r : outcomes[f].reflections) {
-            if (std::isfinite(r.I) && std::isfinite(r.sigma) && r.sigma > 0.0f) {
-                upper[f] += r.I > BLANK_TAIL_SIGMA * r.sigma;
-                lower[f] += r.I < -BLANK_TAIL_SIGMA * r.sigma;
-            }
-            if (std::isfinite(r.bkg)) { bkg_sum += r.bkg; ++bkg_n; }
-        }
-        if (bkg_n > 0) bkg[f] = bkg_sum / bkg_n;
-    });
+    for (int f = 0; f < n; ++f) {
+        upper[f] = tally[f].upper;
+        lower[f] = tally[f].lower;
+        if (tally[f].bkg_n > 0) bkg[f] = tally[f].bkg_sum / tally[f].bkg_n;
+    }
     std::vector<double> excess, tails, background;
     for (int f = 0; f < n; ++f)
         if (!outcomes[f].reflections.empty()) {
@@ -606,7 +621,7 @@ void RotationScaleMerge::IngestHost() {
     // genuinely share (h,k,l) and image_number: the predictor emits both intersections of a
     // reflection's rotation circle with the Ewald sphere, and near the blind region the two are close
     // enough in angle that both land on the same frame. Without a final key their relative order was
-    // whatever the sort happened to produce, and the combine reads it - it takes on_ice from the first
+    // whatever the sort happened to produce, and the combine reads it - it takes unscaled from the first
     // member of an event, and its per-event sums are floating point. Ordering them by arrival makes
     // the result independent of the sort algorithm, which is what lets the order be reproduced by a
     // faster one.
@@ -733,8 +748,9 @@ void RotationScaleMerge::IngestHost() {
 #ifdef JFJOCH_USE_CUDA
 // The resident path's ingest. The reflections go to the card frame by frame, and the card measures the
 // per-frame background, sorts, cuts the raw-hkl runs and drops what the resolution range excludes
-// (RotationScaleMergeGPU::IngestUpload .. IngestSort); once the scaling is known to fit, they go to the
-// card a second time for the observations the cut kept (IngestObservations) - the observations, the runs
+// (RotationScaleMergeGPU::IngestUpload .. IngestSort); once the scaling is known to fit, the observations
+// the cut kept are taken from them on the card, or from a second upload where the first could not stay
+// (IngestObservations) - the observations, the runs
 // and the order of each that BuildInRangeObservations lays down on the host, to the bit, and left where
 // the device pipeline reads them. The geometry smoothing then runs here on what the card hands back.
 void RotationScaleMerge::IngestOnDevice() {
@@ -755,7 +771,7 @@ void RotationScaleMerge::IngestOnDevice() {
     std::vector<double> mean_bkg(n_frames);
     gpu_->IngestMeanBackground(mean_bkg.data());
     MeasureIncidentFlux(mean_bkg);
-    const int n = gpu_->IngestSort(d_min_limit, d_max_limit);
+    const int n = gpu_->IngestSort(d_min_limit, std::nullopt);
     n_partials_obs = n;
     RotationScaleMergeGPU::IngestLayout layout;
     gpu_->IngestGetLayout(layout);
@@ -775,11 +791,16 @@ void RotationScaleMerge::IngestOnDevice() {
     // ends before a single observation is on it.
     if (ScaleOnCPUWhereTooLarge())
         return;
+    std::unique_ptr<TimingMark> sub_mark;
+    auto sub = [&](const char *n) { sub_mark.reset(); sub_mark = std::make_unique<TimingMark>(*logger, std::string("rsm/i ") + n); };
+    sub("observations");
     auto pos = std::make_shared<ObsPosition>();
     pos->px.resize(n); pos->py.resize(n);
-    gpu_->IngestObservations(refl.data(), count.data(), nthreads, frame_flux.data(), pos->px.data(), pos->py.data());
+    gpu_->IngestObservations(refl.data(), count.data(), nthreads, frame_flux.data(),
+                             d_max_scale ? static_cast<float>(*d_max_scale) : INFINITY, pos->px.data(), pos->py.data());
     obs_position = std::move(pos);
 
+    sub("geometry");
     const SmoothedGeometry sg = SmoothedFrameGeometry();
     int64_t n_resolved = 0;
     if (sg.half > 0) {
@@ -813,6 +834,7 @@ void RotationScaleMerge::IngestOnDevice() {
     // SmoothMosaicityAndPartiality on the card: the events relaid, the mosaicity smoothed here, the
     // partiality recomputed from it. RockingEventFrames reads the corr as integrated, so it is taken
     // before the recompute moves it.
+    sub("partiality");
     const auto gon = x.GetGoniometer();
     if (const double increment_deg = gon ? gon->GetIncrement_deg() : 0.0; std::fabs(increment_deg) > 0.0) {
         int64_t n_events = 0, n_relaid = 0;
@@ -997,7 +1019,7 @@ void RotationScaleMerge::IngestDevice(const RotationScaleMerge *observations_fro
                     fbuf[3][i] = o.partiality; fbuf[4][i] = r.zeta; fbuf[5][i] = o.corr;
                     fbuf[6][i] = r.bkg; fbuf[7][i] = r.var_bkg; fbuf[8][i] = r.image_number;
                     fbuf[9][i] = r.d;
-                    flags[i] = static_cast<uint8_t>((r.on_ice_ring ? 1 : 0) | (ClippedFlags(r) << 1));   // SetObsFlags
+                    flags[i] = static_cast<uint8_t>(Unscaled(r) | (ClippedFlags(r) << 1));   // SetObsFlags
                 }
             });
             constexpr F fields[NFLOAT] = {F::I, F::Sigma, F::PrescalingCorr, F::Partiality,
@@ -1042,7 +1064,7 @@ void RotationScaleMerge::IngestDevice(const RotationScaleMerge *observations_fro
 void RotationScaleMerge::BuildInRangeObservations(std::unique_ptr<SortKey[]> &keys, int n_obs,
                                                   const SmoothedGeometry &sg) {
     const int n_run = static_cast<int>(rawrun_start.size());
-    const bool limited = d_min_limit.has_value() || d_max_limit.has_value();
+    const bool limited = d_min_limit.has_value();
 
     std::vector<uint8_t> keep_run(n_run, 1);
     // Filled once, with the value the branch below actually wants: a resolution-limited run used to
@@ -1053,7 +1075,7 @@ void RotationScaleMerge::BuildInRangeObservations(std::unique_ptr<SortKey[]> &ke
             for (int r = lo; r < hi; ++r) {
                 const float d = rawrun_d[r];
                 const bool in_range = std::isfinite(d) && d > 0.0f
-                        && !(d_min_limit && d < *d_min_limit) && !(d_max_limit && d > *d_max_limit);
+                        && !(d_min_limit && d < *d_min_limit);
                 keep_run[r] = in_range ? 1 : 0;
                 if (!in_range) continue;
                 const int p0 = rawrun_start[r], p1 = p0 + rawrun_count[r];
@@ -1555,7 +1577,6 @@ int RotationScaleMerge::ComputeAsuGroups(const HKLKeyGenerator &keygen) {
             const float d = rawrun_d[r];   // resolution is a per-raw-hkl property (all its partials share d)
             if (!std::isfinite(d) || d <= 0.0f) continue;
             if (d_min_limit && d < *d_min_limit) continue;
-            if (d_max_limit && d > *d_max_limit) continue;
             key[r] = keygen(rawrun_h[r], rawrun_k[r], rawrun_l[r]).pack();
             eligible[r] = 1;
         }
@@ -3208,19 +3229,27 @@ void RotationScaleMerge::MeasureBatchDeltaCCHalf(int n_groups) {
         std::vector<Sums> d;
         std::vector<int32_t> touched;
     };
-    const int n_workers = static_cast<int>(std::clamp<size_t>(nthreads, 1, 8));
+    // A worker's scratch is as long as the merge, so it is made on first use, by the worker: the
+    // workers a measurement does not need cost nothing, and the ones it does zero theirs side by side.
+    const int n_workers = static_cast<int>(std::clamp<size_t>(std::min<size_t>(nthreads, n_batch), 1, 16));
     std::vector<RangeScratch> scratch(n_workers);
-    for (auto &sc : scratch)
-        sc.d.assign(n_groups, Sums{});
+    auto scratch_of = [&](int t) -> RangeScratch & {
+        if (scratch[t].d.empty()) scratch[t].d.assign(n_groups, Sums{});
+        return scratch[t];
+    };
+    // Each worker takes a range of the reflections and walks every observation for them, so a
+    // reflection's sums are added in observation order whatever the split: the one serial sum.
     auto build_totals = [&]() {
-        std::fill(tot.begin(), tot.end(), Sums{});
-        for (int i = 0; i < n_full; ++i) {
-            const int g = obs_group[i];
-            if (g < 0 || frame_rejected[obs_frame[i]]) continue;
-            Sums &t = tot[g];
-            t.n += 1; t.s1 += obs_I[i]; t.s2 += obs_I[i] * obs_I[i];
-            t.w += obs_info[i];
-        }
+        ParallelChunks(n_groups, nthreads, [&](int g0, int g1) {
+            std::fill(tot.begin() + g0, tot.begin() + g1, Sums{});
+            for (int i = 0; i < n_full; ++i) {
+                const int g = obs_group[i];
+                if (g < g0 || g >= g1 || frame_rejected[obs_frame[i]]) continue;
+                Sums &t = tot[g];
+                t.n += 1; t.s1 += obs_I[i]; t.s2 += obs_I[i] * obs_I[i];
+                t.w += obs_info[i];
+            }
+        });
     };
 
     // delta-CC1/2 of the frames [f0, f1]. delta_cc is the difference in CC units, which is what a user
@@ -3283,9 +3312,10 @@ void RotationScaleMerge::MeasureBatchDeltaCCHalf(int n_groups) {
         return r;
     };
     auto measure = [&](int f0, int f1) {
-        accumulate(scratch[0], f0, f1);
-        const RangeDelta r = evaluate(scratch[0]);
-        clear(scratch[0]);
+        RangeScratch &sc = scratch_of(0);
+        accumulate(sc, f0, f1);
+        const RangeDelta r = evaluate(sc);
+        clear(sc);
         return r;
     };
     // Every range in `ranges`, side by side. Ranges that start on the same frame are one chain, measured
@@ -3305,7 +3335,7 @@ void RotationScaleMerge::MeasureBatchDeltaCCHalf(int n_groups) {
         std::vector<RangeDelta> out(ranges.size());
         std::atomic<int> next_chain{0};
         parallel_detail::RunTasks(std::min(n_workers, n_chain), [&](int t) {
-            RangeScratch &sc = scratch[t];
+            RangeScratch &sc = scratch_of(t);
             for (int c = next_chain++; c < n_chain; c = next_chain++) {
                 int added_to = ranges[sorted[chain_start[c]]].first - 1;
                 for (size_t k = chain_start[c]; k < chain_start[c + 1]; ++k) {
@@ -3978,11 +4008,11 @@ void RotationScaleMerge::ApplyCellSurface(const std::vector<int32_t> &cell, int
                                           const SphericalHarmonicBasis *sh_basis) {
     // An observation on an ice ring is excluded from scaling, as the run's log says: its background is
     // the ring's, uneven round the azimuth, so it would teach a surface the ring rather than the
-    // detector. The `Is > 0` filter the fit once had hid this omission by dropping the over-subtracted
+    // detector. So is one coarser than the scale fit's low-resolution limit (Unscaled). The `Is > 0` filter the fit once had hid this omission by dropping the over-subtracted
     // half of those observations.
     auto usable = [&](const Obs &o) {
         return o.group >= 0 && o.corr > 0.0f && std::isfinite(o.corr) && o.partiality >= min_partiality
-               && !o.on_ice;
+               && !o.unscaled;
     };
     // The observations any of the passes below can use, in fulls order, with the four fields those
     // passes read copied out beside them. Around twenty passes follow, and each one used to reach back
@@ -4713,7 +4743,7 @@ void RotationScaleMerge::Combine() {
             float peak_frame = partials[ev[i]].r->image_number;
             float peak_px = partials[ev[i]].r->predicted_x, peak_py = partials[ev[i]].r->predicted_y;
             float peak_partiality = -1.0f;
-            const bool on_ice = partials[ev[i]].r->on_ice_ring;
+            const uint8_t unscaled = Unscaled(*partials[ev[i]].r);
             uint8_t flags = 0;
             for (size_t m = i; m < kk; ++m) flags |= ClippedFlags(*partials[ev[m]].r);
             // A saturated pixel anywhere in the rocking curve means its brightest part was not measured:
@@ -4797,7 +4827,7 @@ void RotationScaleMerge::Combine() {
             full.image_number = peak_frame;
             full.px = peak_px; full.py = peak_py;
             full.frame = peak_outcome;
-            full.on_ice = on_ice ? 1 : 0;
+            full.unscaled = unscaled;
             full.clipped = clipped ? 1 : 0;
             full.group = group;   // the raw hkl's ASU group for the current space group (<0 = absent)
             out.push_back(full);
@@ -4933,7 +4963,7 @@ void RotationScaleMerge::ComputePerFrameCC(const std::vector<double> &partial_gr
             const PartialObs &o = partials[i];
             const Reflection &r = *o.r;
             const int g = partial_group[i];
-            if (r.on_ice_ring) continue;
+            if (Unscaled(r)) continue;
             if (g < 0) continue;
             if (o.partiality < min_partiality) continue;
             if (!std::isfinite(r.I) || !std::isfinite(o.corr) || o.corr <= 0.0f) continue;
@@ -5028,7 +5058,7 @@ RotationScaleMerge::Result RotationScaleMerge::MergeAndStats(int n_groups, bool
     // A full is usable for the merge / error model if it passes AddImage's filters (with the current
     // ice context).
     auto usable_merge = [&](const Obs &o) {
-        return UsableFull(o) && !(for_search && o.on_ice);
+        return UsableFull(o) && !(for_search && o.unscaled);
     };
 
     // The em-stats / samples / merge-accumulate / R_meas reductions run on the resident, scaled fulls
@@ -5731,7 +5761,7 @@ RotationScaleMerge::Result RotationScaleMerge::MergeAndStats(int n_groups, bool
                         // MergeOnTheFly does on the stills path): the intensity is still merged and written,
                         // the flag only lets a consumer that must not read ring signal as crystal signal -
                         // the CC1/2 resolution-cutoff fit - leave it out.
-                        if (o.on_ice) a.on_ice = true;
+                        if (o.unscaled & UNSCALED_ICE) a.on_ice = true;
                         if (!std::isfinite(a.d) && std::isfinite(o.d) && o.d > 0.0f) a.d = o.d;
                     }
                 }
@@ -6551,8 +6581,7 @@ RotationScaleMerge::Result RotationScaleMerge::MergeAndStats(int n_groups, bool
     // infinite d_max - when no limit was declared. Reflections the beam stop, a mask or the limit ate
     // then count as missing. The high end stays the finest d reached. See MergeStats in Merge.cpp.
     const float d_min_pad = sd_min * 0.999f;
-    const float d_max_declared = d_max_limit ? static_cast<float>(*d_max_limit)
-                                             : std::numeric_limits<float>::infinity();
+    const float d_max_declared = std::numeric_limits<float>::infinity();
     // The innermost shell is labelled by the bound it reaches, except when that bound is infinite
     // and the coarsest reflection measured is the only finite thing to say.
     const float d_max_label = std::isfinite(d_max_declared) ? d_max_declared : sd_max;
@@ -6605,7 +6634,7 @@ RotationScaleMerge::Result RotationScaleMerge::MergeAndStats(int n_groups, bool
                 pool.push_back(s);
         error_model_active = false;   // a pool too small to fit leaves no model, not the run's own
         fit_error_model(pool);
-        if (error_model_active)
+        if (error_model_active && error_model_b_resolved)
             result.reference_isa = ToXdsErrorModel(error_model_a, error_model_b).isa;
     }
 
@@ -6798,7 +6827,7 @@ RotationScaleMerge::Result RotationScaleMerge::RunArm(bool scale_partials, bool
         frame_scaled_scratch.assign(n_frames, 1);
         partial_loop.converged = true;
     } else if (!scaled_on_gpu) {
-        const PartialLoopKey key{Group().xhm(), merge_friedel, d_min_limit, d_max_limit,
+        const PartialLoopKey key{Group().xhm(), merge_friedel, d_min_limit, d_max_scale,
                                  min_partiality, smooth_window, scaling_iter};
         const auto memo = std::find_if(partial_loop_memos.begin(), partial_loop_memos.end(),
                                        [&](const PartialLoopMemo &m) { return m.key == key; });
@@ -6872,7 +6901,7 @@ RotationScaleMerge::Result RotationScaleMerge::RunArm(bool scale_partials, bool
             // model needs zeta > 0.
             auto fitted_obs = [&](int i) {
                 const PartialObs &o = partials[i];
-                return partial_group[i] >= 0 && !o.r->on_ice_ring && o.partiality >= min_partiality
+                return partial_group[i] >= 0 && !Unscaled(*o.r) && o.partiality >= min_partiality
                        && std::isfinite(o.r->zeta) && o.r->zeta > 0.0f;
             };
             const int n_fit_frames = static_cast<int>(frame_start.size());
@@ -7171,7 +7200,7 @@ RotationScaleMerge::Result RotationScaleMerge::RunArm(bool scale_partials, bool
         FullsStaging &st = fulls_staging;
         st.Resize(nf);
         gpu_->GetFulls(st.run.data(), st.I.data(), st.sigma.data(), st.d.data(),
-                       st.image_number.data(), st.frame.data(), st.on_ice.data(), st.clipped.data(),
+                       st.image_number.data(), st.frame.data(), st.unscaled.data(), st.clipped.data(),
                        st.group.data());
         gpu_->GetFullsPeak(st.peak.data());
         const ObsPosition &pos = *obs_position;
@@ -7188,7 +7217,7 @@ RotationScaleMerge::Result RotationScaleMerge::RunArm(bool scale_partials, bool
                 o.corr = scaled_fulls_on_gpu ? st.corr[i] : 1.0f;
                 o.image_number = st.image_number[i]; o.frame = st.frame[i];
                 o.px = pos.px[st.peak[i]]; o.py = pos.py[st.peak[i]];
-                o.on_ice = st.on_ice[i]; o.clipped = st.clipped[i]; o.group = st.group[i];
+                o.unscaled = st.unscaled[i]; o.clipped = st.clipped[i]; o.group = st.group[i];
                 // A full has no rocking geometry of its own and carries no background; the combine on
                 // the device does not produce these, and a reused buffer would keep the last chain's.
                 o.zeta = 0.0f; o.delta_phi = 0.0f; o.bkg = 0.0f;
@@ -7244,7 +7273,7 @@ RotationScaleMerge::Result RotationScaleMerge::RunArm(bool scale_partials, bool
         // The partials' filters for the Unity model, which needs no zeta, and whose coefficient is the
         // mean itself: the partiality is folded into the full, and prescaling_corr is 1.
         auto fitted_full = [&](const Obs &o) {
-            return o.group >= 0 && !o.on_ice && o.partiality >= min_partiality;
+            return o.group >= 0 && !o.unscaled && o.partiality >= min_partiality;
         };
         std::vector<int32_t> fit_start(n_frames + 1, 0);
         ParallelFor(n_frames, nthreads, [&](int f) {
diff --git a/image_analysis/scale_merge/RotationScaleMerge.h b/image_analysis/scale_merge/RotationScaleMerge.h
index 4ef64c4fb..6291bdf1e 100644
--- a/image_analysis/scale_merge/RotationScaleMerge.h
+++ b/image_analysis/scale_merge/RotationScaleMerge.h
@@ -67,7 +67,17 @@ template <class T> using FillVector = std::vector<T, DefaultInitAllocator<T>>;
 // Stills use the per-image ScaleOnTheFly (fixed partiality) instead.
 //
 // Before any of it: TrimBlankSweepEnds clears the reflections of the frames at either end of the sweep
-// that the beam never reached, and returns how many it cleared at the start and at the end.
+// that the beam never reached, and returns how many it cleared at the start and at the end. It decides
+// on each frame's SweepEndTally, one walk over the frame's reflections in their order; a caller walking
+// them anyway for something else hands the tallies over, the other form makes them on all threads.
+struct SweepEndTally {
+    int64_t upper = 0, lower = 0;   // reflections standing above / below zero by more than the tail sigma
+    double bkg_sum = 0.0;
+    int64_t bkg_n = 0;
+};
+SweepEndTally TallySweepEnd(const IntegrationOutcome &outcome);
+std::pair<int, int> TrimBlankSweepEnds(std::vector<IntegrationOutcome> &outcomes,
+                                       const std::vector<SweepEndTally> &tally);
 std::pair<int, int> TrimBlankSweepEnds(std::vector<IntegrationOutcome> &outcomes, size_t nthreads);
 
 class RotationScaleMerge {
@@ -248,6 +258,10 @@ public:
     // The copy does not write its per-frame scales back (WriteBackPerFrameScale does).
     [[nodiscard]] std::unique_ptr<RotationScaleMerge> CloneIngest(int device, Logger &log) const;
 
+    // The per-frame scale choice the first merge that is not a search makes (see Run), from a copy that made
+    // that merge in this engine's place: the merges after it keep it, as they would on this engine.
+    void TakeScalePartialsChoice(const RotationScaleMerge &from) { scale_partials_choice = from.scale_partials_choice; }
+
     // The card memory an engine may hold during a merge, the device helpers its merge calls included:
     // what a caller goes by when it decides whether a second engine fits beside one already on the
     // card. Call after IngestHost(). It counts what the ingest knows - the observations, the rocking
@@ -338,7 +352,7 @@ private:
         float px, py;   // predicted detector position (for the absorption surface; CPU path only)
         float image_number;   // fractional frame position (for 3D-combine contiguity)
         int32_t frame;        // index of the outcome whose per-frame scale G applies to this obs
-        uint8_t on_ice;
+        uint8_t unscaled;     // UNSCALED_ICE | UNSCALED_LOW_RES: kept out of the scale fit, still merged
         uint8_t clipped;      // OBS_CLIPPED | OBS_OVERLOADED (Reflection::clipped / ::overloaded); a full
                               // is clipped if any of its partials is, and an overloaded event is no full
         float corr;           // image_scale_corr (working; updated by scaling)
@@ -362,6 +376,14 @@ private:
     static uint8_t ClippedFlags(const Reflection &r) {
         return (r.clipped ? OBS_CLIPPED : 0) | (r.overloaded ? OBS_OVERLOADED : 0);
     }
+    // Why an observation stays out of the scale fit (Obs::unscaled), with the bit values the device flags
+    // use: it sits on an ice ring, whose background is the ring's, or it is coarser than the scale fit's
+    // low-resolution limit (ScalingSettings::low_resolution_limit_A). Either is still merged and written.
+    static constexpr uint8_t UNSCALED_ICE = 1;
+    static constexpr uint8_t UNSCALED_LOW_RES = 8;
+    uint8_t Unscaled(const Reflection &r) const {
+        return (r.on_ice_ring ? UNSCALED_ICE : 0) | (d_max_scale && r.d > *d_max_scale ? UNSCALED_LOW_RES : 0);
+    }
 
     // One leverage-corrected error-model sample per usable full: its counting variance at the group's
     // mean, that mean squared, its squared deviation from the mean - and the resolution it sits at,
@@ -410,7 +432,9 @@ private:
     int n_frames = 0;
     double min_partiality = 0.02;
     std::optional<double> d_min_limit;
-    std::optional<double> d_max_limit;
+    // The low-resolution limit of the scale FIT. Coarser observations are merged and written, but a
+    // handful of them on a large cell can bend the whole scale model (Unscaled).
+    std::optional<double> d_max_scale;
     bool merge_friedel = true;
     double capture_uncertainty_coeff = 0.0;
     double min_captured_fraction = 0.0;
@@ -566,12 +590,12 @@ private:
     struct FullsStaging {
         FillVector<int32_t> run, peak, frame, group;
         FillVector<float> I, sigma, d, image_number, corr, var_bkg, var_per_I, capture;
-        FillVector<uint8_t> on_ice, clipped;
+        FillVector<uint8_t> unscaled, clipped;
         void Resize(int n) {
             run.resize(n); peak.resize(n); frame.resize(n); group.resize(n);
             I.resize(n); sigma.resize(n); d.resize(n); image_number.resize(n); corr.resize(n);
             var_bkg.resize(n); var_per_I.resize(n); capture.resize(n);
-            on_ice.resize(n); clipped.resize(n);
+            unscaled.resize(n); clipped.resize(n);
         }
     };
     FullsStaging fulls_staging;
diff --git a/image_analysis/scale_merge/RotationScaleMergeGPU.cu b/image_analysis/scale_merge/RotationScaleMergeGPU.cu
index e14faab8b..08c795305 100644
--- a/image_analysis/scale_merge/RotationScaleMergeGPU.cu
+++ b/image_analysis/scale_merge/RotationScaleMergeGPU.cu
@@ -61,11 +61,14 @@ namespace {
     struct alignas(16) ObsRecord { float I, sigma, partiality, prescaling_corr; };   // floats 0, 1, 2, 3
 
     // A partial's flags, one byte: on an ice ring, then RotationScaleMerge::OBS_CLIPPED and
-    // OBS_OVERLOADED one bit up. A full's on_ice byte is 0 or OBS_ON_ICE_FLAG, so the kernels shared by
-    // the two read either the same way.
+    // OBS_OVERLOADED one bit up, then coarser than the scale fit's low-resolution limit. The two that keep
+    // an observation out of the scale fit are OBS_UNSCALED, and a full's unscaled byte holds those of its
+    // partials, so the kernels shared by the two read either the same way.
     constexpr uint8_t OBS_ON_ICE_FLAG = 1;
     constexpr uint8_t OBS_CLIPPED_FLAG = 2;
     constexpr uint8_t OBS_OVERLOADED_FLAG = 4;
+    constexpr uint8_t OBS_LOW_RES_FLAG = 8;
+    constexpr uint8_t OBS_UNSCALED = OBS_ON_ICE_FLAG | OBS_LOW_RES_FLAG;
 
     // An observation's frame. The fulls carry theirs (frame); the partials lie in frame order, so theirs
     // is the last frame starting at or before them in the frame CSR (start, n_frames entries) - an empty
@@ -131,10 +134,10 @@ namespace {
     // where the observation is not one the reference is built from (the host RunArm says why, where it fills ScalingFit).
     __device__ __forceinline__ bool ScaleCoeff(int i, double min_partiality, const int32_t *__restrict__ group,
                                                const ObsRecord &o, const float *__restrict__ zeta,
-                                               const uint8_t *__restrict__ on_ice,
+                                               const uint8_t *__restrict__ unscaled,
                                                const double *__restrict__ group_mean, float &coeff) {
         const int g = group[i];
-        if (!((g >= 0) && !(on_ice[i] & OBS_ON_ICE_FLAG) && isfinite(zeta[i]) && zeta[i] > 0.0f && o.partiality >= min_partiality))
+        if (!((g >= 0) && !(unscaled[i] & OBS_UNSCALED) && isfinite(zeta[i]) && zeta[i] > 0.0f && o.partiality >= min_partiality))
             return false;
         const double mean = group_mean[g];
         if (!isfinite(mean)) return false;
@@ -155,7 +158,7 @@ namespace {
                                        const int32_t *__restrict__ frame_count,
                                        const int32_t *__restrict__ perm, double min_partiality,
                                        const int32_t *__restrict__ group, const ObsRecord *__restrict__ obs,
-                                       const float *__restrict__ zeta, const uint8_t *__restrict__ on_ice,
+                                       const float *__restrict__ zeta, const uint8_t *__restrict__ unscaled,
                                        const double *__restrict__ group_mean, long min_obs,
                                        double *__restrict__ g, uint8_t *__restrict__ scaled,
                                        double *__restrict__ info) {
@@ -173,7 +176,7 @@ namespace {
             const int a = perm ? perm[i] : i;
             const ObsRecord o = obs[a];
             float coeff_f;
-            if (!ScaleCoeff(a, min_partiality, group, o, zeta, on_ice, group_mean, coeff_f)) continue;
+            if (!ScaleCoeff(a, min_partiality, group, o, zeta, unscaled, group_mean, coeff_f)) continue;
             ++cnt_local;
             const double coeff = coeff_f;
             const double w = SafeInvD(o.sigma, 1.0);
@@ -214,7 +217,7 @@ namespace {
         double sx = 0, sy = 0, sx2 = 0, sy2 = 0, sxy = 0;
         long nl = 0;
         for (int i = lo + threadIdx.x; i < hi; i += blockDim.x) {
-            if (flags[i] & OBS_ON_ICE_FLAG) continue;
+            if (flags[i] & OBS_UNSCALED) continue;
             const int g = group[i];
             if (g < 0) continue;
             const ObsRecord o = obs[i];
@@ -329,7 +332,7 @@ namespace {
         const int32_t *rr_offset;           // emit pass: per-run base offset into the fulls arrays
         int32_t *f_run, *f_peak, *f_frame, *f_group;
         float *f_I, *f_sigma, *f_d, *f_img, *f_var_bkg, *f_var_per_I, *f_capture;
-        uint8_t *f_on_ice, *f_clipped;
+        uint8_t *f_unscaled, *f_clipped;
     };
 
     // One thread's raw-hkl run: split its usable partials (already in image_number order within the run)
@@ -381,7 +384,7 @@ namespace {
                 return double(p.obs[i].I) + n_bkg * (double(p.bkg[i]) - pooled_bkg);
             };
 
-            // Pass B: seed F (inverse-variance mean of pooled_I*corr), plus peak / d / on_ice / partiality.
+            // Pass B: seed F (inverse-variance mean of pooled_I*corr), plus peak / d / unscaled / partiality.
             double sum_w = 0.0, sum_wI = 0.0, sum_partiality = 0.0;
             float d = NAN;
             const int first = p.perm[ev_start];
@@ -389,7 +392,7 @@ namespace {
             float peak_frame = p.image_number[first];
             int peak_obs = first;
             float peak_partiality = -1.0f;
-            const bool on_ice = p.flags[first] & OBS_ON_ICE_FLAG;
+            const uint8_t unscaled = p.flags[first] & OBS_UNSCALED;
             uint8_t flags = 0;
             for (int m = ev_start; m <= ev_end; ++m) flags |= p.flags[p.perm[m]];
             // An overloaded event is not a measurement of the reflection; see the host combine.
@@ -466,7 +469,7 @@ namespace {
                 p.f_img[o] = peak_frame;
                 p.f_peak[o] = peak_obs;
                 p.f_frame[o] = peak_outcome;
-                p.f_on_ice[o] = on_ice ? 1 : 0;
+                p.f_unscaled[o] = unscaled;
                 p.f_clipped[o] = clipped ? 1 : 0;
                 p.f_group[o] = group;
             }
@@ -586,13 +589,13 @@ namespace {
 
     // Per full: 1 if it gives a term (all, even frame, odd frame) - the host's `usable(o) && cell >= 0`.
     // A full's partiality is 1 (the combine sets it so on both paths).
-    __global__ void SurfaceKeepKernel(int n, const int32_t *group, const float *corr, const uint8_t *on_ice,
+    __global__ void SurfaceKeepKernel(int n, const int32_t *group, const float *corr, const uint8_t *unscaled,
                                       const int32_t *frame, const int32_t *cell, double min_partiality,
                                       int32_t *keep, int32_t *keep_even, int32_t *keep_odd) {
         const int i = blockIdx.x * blockDim.x + threadIdx.x;
         if (i >= n) return;
         const float c = corr[i];
-        const bool k = group[i] >= 0 && c > 0.0f && isfinite(c) && 1.0f >= min_partiality && !on_ice[i]
+        const bool k = group[i] >= 0 && c > 0.0f && isfinite(c) && 1.0f >= min_partiality && !unscaled[i]
                        && cell[i] >= 0;
         const bool odd = frame[i] & 1;
         keep[i] = k; keep_even[i] = k && !odd; keep_odd[i] = k && odd;
@@ -699,7 +702,7 @@ namespace {
         const float *I, *sigma, *corr, *d, *reject_median, *var_bkg, *var_per_I, *capture;
         const float *reject_var_add;   // per group: the shell's measured share of dI^2/4
         const int32_t *group, *frame;
-        const uint8_t *on_ice, *frame_cell_ok, *half;
+        const uint8_t *unscaled, *frame_cell_ok, *half;
         const uint8_t *hand, *has_hands;   // per-full Bijvoet hand; per-group "two hands to split"
         const int32_t *gperm, *gstart, *gcount;
         const double *em_mean, *merged_I, *cc_factor;
@@ -727,7 +730,7 @@ namespace {
         if (!p.frame_cell_ok[p.frame[i]]) return false;
         const float c = p.corr[i];
         if (!(c > 0.0f) || !isfinite(c)) return false;
-        if (p.for_search && p.on_ice[i]) return false;
+        if (p.for_search && p.unscaled[i]) return false;
         if (FULL_PARTIALITY < p.min_partiality) return false;
         const float I_corr = p.I[i] * c, sigma_corr = p.sigma[i] * c;
         return isfinite(I_corr) && isfinite(sigma_corr) && sigma_corr > 0.0f;
@@ -982,7 +985,7 @@ namespace {
                 swI += wI; sw += w;
                 if (half) { swIh1 += wI; swh1 += w; swht1 += wt; ++nh1; }
                 else { swIh0 += wI; swh0 += w; swht0 += wt; ++nh0; }
-                if (p.on_ice[i]) onice = 1;   // see the host merge loop
+                if (p.unscaled[i] & OBS_ON_ICE_FLAG) onice = 1;   // see the host merge loop
                 if (!isfinite(dd) && isfinite(p.d[i]) && p.d[i] > 0.0f) dd = p.d[i];
             }
             p.a_swI[g] = swI; p.a_sw[g] = sw; p.a_swIh0[g] = swIh0; p.a_swIh1[g] = swIh1;
@@ -1295,7 +1298,7 @@ struct RotationScaleMergeGPU::Impl {
     // run: the raw-hkl run a full is of; peak: the partial its position is taken from
     CudaDevicePtr<int32_t> f_run, f_peak, f_frame, f_group;
     CudaDevicePtr<float> f_I, f_sigma, f_d, f_img, f_var_bkg, f_var_per_I, f_capture;
-    CudaDevicePtr<uint8_t> f_on_ice, f_clipped;
+    CudaDevicePtr<uint8_t> f_unscaled, f_clipped;
     // scale-fulls (Unity model, kept resident): all-ones partiality/zeta and records with partiality and
     // prescaling_corr 1, so the shared scaling kernels yield coeff=mean, plus the working corr and the
     // fulls frame/group CSRs (built on the host from the small f_frame/f_group key arrays, over the
@@ -1327,9 +1330,16 @@ struct RotationScaleMergeGPU::Impl {
     CudaDevicePtr<int32_t> in_new_idx;
     int in_n_keep = 0;
     CudaDevicePtr<float> in_dphi;
-    // The reflections of the ingest's frames, through two pinned buffers of whole frames, each filled on
-    // all threads while the other is on its way to the card; take(cnt, base, src) takes cnt of them,
-    // the first being reflection base, apart on the card.
+    // Every reflection as uploaded, kept on the card from the upload to the extract where the copy fits
+    // beside the ingest's peak (IngestUpload), so that the reflections cross the bus once; empty where
+    // it does not, and the extract stages them a second time.
+    CudaDevicePtr<Reflection> in_refl;
+    // The reflections of the ingest's frames, through two pinned buffers of whole frames (kept from the
+    // upload to the extract, which may stage them again), each filled on all threads while the other
+    // is on its way to the card; take(cnt, base, src) takes cnt of them, the first being reflection
+    // base, apart on the card.
+    CudaHostPtr<Reflection> in_stage[2];
+    int in_stage_cap = 0;
     template <typename Take>
     void StageReflections(const Reflection *const *refl, const int32_t *count, size_t nthreads, Take take);
     RotationScaleMergeGPU::IngestLayout in_layout;
@@ -1426,7 +1436,7 @@ void RotationScaleMergeGPU::Impl::ReleaseFulls() {
     n_fulls = 0;
     f_run = {}; f_peak = {}; f_frame = {}; f_group = {};
     f_I = {}; f_sigma = {}; f_d = {}; f_img = {};
-    f_var_bkg = {}; f_var_per_I = {}; f_capture = {}; f_on_ice = {}; f_clipped = {};
+    f_var_bkg = {}; f_var_per_I = {}; f_capture = {}; f_unscaled = {}; f_clipped = {};
     f_corr = {}; f_zeta = {}; f_obs = {};
     f_frame_perm = {}; f_frame_start = {}; f_frame_count = {};
     f_gperm = {}; f_gstart = {}; f_gcount = {};
@@ -1647,7 +1657,7 @@ void RotationScaleMergeGPU::MergeEmSamples(bool for_search, double min_partialit
     p.for_search = d.merge_for_search;
     p.I = d.f_I.get(); p.sigma = d.f_sigma.get(); p.corr = d.f_corr.get();
     p.d = d.f_d.get(); p.group = d.f_group.get(); p.frame = d.f_frame.get();
-    p.on_ice = d.f_on_ice.get(); p.frame_cell_ok = d.frame_cell_ok.get();
+    p.unscaled = d.f_unscaled.get(); p.frame_cell_ok = d.frame_cell_ok.get();
     p.gperm = d.f_gperm.get(); p.gstart = d.f_gstart.get(); p.gcount = d.f_gcount.get();
     p.em_mean = d.m_em_mean.get(); p.sw = sw.get(); p.swI = swI.get();
     p.em_mean_out = d.m_em_mean.get(); p.cnt = cnt.get();
@@ -1730,7 +1740,7 @@ void RotationScaleMergeGPU::MergeAccum(double error_model_a, double error_model_
     p.reject_var_add = var_add.get();
     p.I = d.f_I.get(); p.sigma = d.f_sigma.get(); p.corr = d.f_corr.get();
     p.d = d.f_d.get(); p.group = d.f_group.get(); p.frame = d.f_frame.get();
-    p.on_ice = d.f_on_ice.get(); p.frame_cell_ok = d.frame_cell_ok.get();
+    p.unscaled = d.f_unscaled.get(); p.frame_cell_ok = d.frame_cell_ok.get();
     p.half = d_half.get();
     p.var_bkg = d.f_var_bkg.get(); p.var_per_I = d.f_var_per_I.get(); p.capture = d.f_capture.get();
     p.gperm = d.f_gperm.get(); p.gstart = d.f_gstart.get(); p.gcount = d.f_gcount.get();
@@ -1825,7 +1835,7 @@ void RotationScaleMergeGPU::MergeBijvoetExcess(double error_model_a, double erro
     p.n_groups = ng; p.min_partiality = d.merge_min_part; p.for_search = d.merge_for_search;
     p.I = d.f_I.get(); p.sigma = d.f_sigma.get(); p.corr = d.f_corr.get();
     p.d = d.f_d.get(); p.group = d.f_group.get(); p.frame = d.f_frame.get();
-    p.on_ice = d.f_on_ice.get(); p.frame_cell_ok = d.frame_cell_ok.get();
+    p.unscaled = d.f_unscaled.get(); p.frame_cell_ok = d.frame_cell_ok.get();
     p.gperm = d.f_gperm.get(); p.gstart = d.f_gstart.get(); p.gcount = d.f_gcount.get();
     p.hand = d.m_hand.get(); p.has_hands = d.m_has_hands.get();
     p.error_model_a = error_model_a; p.error_model_b = error_model_b; p.error_model_active = 1;
@@ -1857,7 +1867,7 @@ void RotationScaleMergeGPU::MergeGroupScatter(double *sum, double *sum_sq, doubl
     p.n_groups = ng; p.min_partiality = d.merge_min_part; p.for_search = d.merge_for_search;
     p.I = d.f_I.get(); p.sigma = d.f_sigma.get(); p.corr = d.f_corr.get();
     p.d = d.f_d.get(); p.group = d.f_group.get(); p.frame = d.f_frame.get();
-    p.on_ice = d.f_on_ice.get(); p.frame_cell_ok = d.frame_cell_ok.get();
+    p.unscaled = d.f_unscaled.get(); p.frame_cell_ok = d.frame_cell_ok.get();
     p.gperm = d.f_gperm.get(); p.gstart = d.f_gstart.get(); p.gcount = d.f_gcount.get();
     p.em_mean = d.m_em_mean.get(); p.var_bkg = d.f_var_bkg.get(); p.var_per_I = d.f_var_per_I.get();
     p.capture = d.f_capture.get();
@@ -1884,7 +1894,7 @@ void RotationScaleMergeGPU::MergeHalves(uint64_t *obs_key, uint8_t *half) {
     p.n_groups = ng; p.min_partiality = d.merge_min_part; p.for_search = d.merge_for_search;
     p.I = d.f_I.get(); p.sigma = d.f_sigma.get(); p.corr = d.f_corr.get();
     p.d = d.f_d.get(); p.group = d.f_group.get(); p.frame = d.f_frame.get();
-    p.on_ice = d.f_on_ice.get(); p.frame_cell_ok = d.frame_cell_ok.get();
+    p.unscaled = d.f_unscaled.get(); p.frame_cell_ok = d.frame_cell_ok.get();
     p.gperm = d.f_gperm.get(); p.gstart = d.f_gstart.get(); p.gcount = d.f_gcount.get();
 
     const int obs_blocks = std::min(65535, (nf + BLK - 1) / BLK);
@@ -2041,7 +2051,7 @@ int RotationScaleMergeGPU::Combine(const int32_t *rawrun_group, double min_parti
     d.f_I = d.Alloc<float>(nf); d.f_sigma = d.Alloc<float>(nf);
     d.f_d = d.Alloc<float>(nf); d.f_img = d.Alloc<float>(nf);
     d.f_var_bkg = d.Alloc<float>(nf); d.f_var_per_I = d.Alloc<float>(nf); d.f_capture = d.Alloc<float>(nf);
-    d.f_on_ice = d.Alloc<uint8_t>(nf); d.f_clipped = d.Alloc<uint8_t>(nf);
+    d.f_unscaled = d.Alloc<uint8_t>(nf); d.f_clipped = d.Alloc<uint8_t>(nf);
     d.f_corr = d.Alloc<float>(nf);
     d.f_zeta = d.Alloc<float>(nf);
     d.f_obs = d.Alloc<ObsRecord>(nf);
@@ -2052,7 +2062,7 @@ int RotationScaleMergeGPU::Combine(const int32_t *rawrun_group, double min_parti
     p.f_frame = d.f_frame.get(); p.f_group = d.f_group.get();
     p.f_I = d.f_I.get(); p.f_sigma = d.f_sigma.get(); p.f_d = d.f_d.get(); p.f_img = d.f_img.get();
     p.f_var_bkg = d.f_var_bkg.get(); p.f_var_per_I = d.f_var_per_I.get(); p.f_capture = d.f_capture.get();
-    p.f_on_ice = d.f_on_ice.get(); p.f_clipped = d.f_clipped.get();
+    p.f_unscaled = d.f_unscaled.get(); p.f_clipped = d.f_clipped.get();
     if (d.n_fulls > 0) {
         CombineKernel<true><<<blocks, BLK, 0, impl_->s()>>>(p);
         CudaCheck(cudaGetLastError(), "combine emit launch");
@@ -2062,7 +2072,7 @@ int RotationScaleMergeGPU::Combine(const int32_t *rawrun_group, double min_parti
 }
 
 void RotationScaleMergeGPU::GetFulls(int32_t *run, float *I, float *sigma, float *d,
-                                     float *image_number, int32_t *frame, uint8_t *on_ice,
+                                     float *image_number, int32_t *frame, uint8_t *unscaled,
                                      uint8_t *clipped, int32_t *group) const {
     DeviceGuard guard(impl_->device, impl_->available);
     const auto &dd = *impl_;
@@ -2075,7 +2085,7 @@ void RotationScaleMergeGPU::GetFulls(int32_t *run, float *I, float *sigma, float
     dl(group, dd.f_group.get(), n * sizeof(int32_t));
     dl(I, dd.f_I.get(), n * sizeof(float)); dl(sigma, dd.f_sigma.get(), n * sizeof(float));
     dl(d, dd.f_d.get(), n * sizeof(float)); dl(image_number, dd.f_img.get(), n * sizeof(float));
-    dl(on_ice, dd.f_on_ice.get(), n * sizeof(uint8_t));
+    dl(unscaled, dd.f_unscaled.get(), n * sizeof(uint8_t));
     dl(clipped, dd.f_clipped.get(), n * sizeof(uint8_t));
 }
 
@@ -2111,7 +2121,7 @@ void RotationScaleMergeGPU::FitFullsScale(double min_partiality) {
         d.f_obs.get(), d.f_corr.get(), d.group_mean.get());
     CudaCheck(cudaGetLastError(), "ReduceGroupMeansKernel launch");
     FitPerFrameGKernel<<<d.n_frames, BLK, 0, impl_->s()>>>(d.n_frames, d.f_frame_start.get(), d.f_frame_count.get(),
-        d.f_frame_perm.get(), min_partiality, d.f_group.get(), d.f_obs.get(), d.f_zeta.get(), d.f_on_ice.get(),
+        d.f_frame_perm.get(), min_partiality, d.f_group.get(), d.f_obs.get(), d.f_zeta.get(), d.f_unscaled.get(),
         d.group_mean.get(), 1L, d.g.get(), d.scaled.get(), d.info.get());
     CudaCheck(cudaGetLastError(), "scale fulls launch");
     CudaCheck(cudaStreamSynchronize(impl_->s()), "scale fulls sync");
@@ -2250,7 +2260,7 @@ int RotationScaleMergeGPU::SurfaceBuildTerms(const int32_t *cell, const float *c
         keep = d.Alloc<int32_t>(std::max(1, nf)); even = d.Alloc<int32_t>(std::max(1, nf));
         odd = d.Alloc<int32_t>(std::max(1, nf));
         if (nf > 0) {
-            SurfaceKeepKernel<<<(nf + BLK - 1) / BLK, BLK, 0, st>>>(nf, d.f_group.get(), d_corr.get(), d.f_on_ice.get(),
+            SurfaceKeepKernel<<<(nf + BLK - 1) / BLK, BLK, 0, st>>>(nf, d.f_group.get(), d_corr.get(), d.f_unscaled.get(),
                 d.f_frame.get(), d_cell.get(), min_partiality, keep.get(), even.get(), odd.get());
             CudaCheck(cudaGetLastError(), "surface keep launch");
         }
@@ -2509,8 +2519,9 @@ namespace {
 
     struct IngestArrays {
         ObsRecord *obs;
-        float *zeta, *corr, *bkg, *var_bkg, *image_number, *d, *dphi;
+        float *zeta, *corr, *bkg, *var_bkg, *image_number, *d, *dphi, *px, *py;
         uint8_t *flags;
+        float d_max_scale;        // coarser than this is kept out of the scale fit (OBS_LOW_RES_FLAG)
         const int32_t *new_idx;   // the cut's place of each reflection (an exclusive prefix over the kept)
         int n, n_keep;            // reflections and observations
     };
@@ -2537,8 +2548,10 @@ namespace {
         a.image_number[i] = r.image_number;
         a.d[i] = r.d;
         a.dphi[i] = r.delta_phi_deg;
+        a.px[i] = r.predicted_x;
+        a.py[i] = r.predicted_y;
         a.flags[i] = (r.on_ice_ring ? OBS_ON_ICE_FLAG : 0) | (r.clipped ? OBS_CLIPPED_FLAG : 0)
-                     | (r.overloaded ? OBS_OVERLOADED_FLAG : 0);
+                     | (r.overloaded ? OBS_OVERLOADED_FLAG : 0) | (r.d > a.d_max_scale ? OBS_LOW_RES_FLAG : 0);
     }
 
 
@@ -2838,13 +2851,18 @@ void RotationScaleMergeGPU::Impl::StageReflections(const Reflection *const *refl
     for (int o = 0; o < n_frames; ++o)
         max_count = std::max(max_count, count[o]);
     // Where the card reads host memory directly (gpu_direct_host_read()), the kernel takes the pinned
-    // buffer apart in place, without the upload.
+    // buffer apart in place, without the upload. Where the reflections stay resident (in_refl), each
+    // buffer goes to its place in the copy instead of a staging buffer of its own on the card.
     constexpr size_t STAGE_BYTES = 64 << 20;
     const bool direct = gpu_direct_host_read();
     const int cap = std::max(static_cast<int>(STAGE_BYTES / sizeof(Reflection)), max_count);
-    CudaHostPtr<Reflection> stage[2] = {CudaHostPtr<Reflection>(cap), CudaHostPtr<Reflection>(cap)};
+    if (cap > in_stage_cap) {
+        in_stage[0] = CudaHostPtr<Reflection>(cap);
+        in_stage[1] = CudaHostPtr<Reflection>(cap);
+        in_stage_cap = cap;
+    }
     CudaDevicePtr<Reflection> staged[2];
-    if (!direct) {
+    if (!direct && !in_refl) {
         staged[0] = Alloc<Reflection>(cap);
         staged[1] = Alloc<Reflection>(cap);
     }
@@ -2859,7 +2877,7 @@ void RotationScaleMergeGPU::Impl::StageReflections(const Reflection *const *refl
         const int cnt = in_src_start[f1] - base;
         if (in_flight[b])
             CudaCheck(cudaEventSynchronize(copied[b]), "staging buffer");
-        Reflection *dst = stage[b].get();
+        Reflection *dst = in_stage[b].get();
         ParallelFor(f1 - f0, nthreads, [&](int fo) {
             const int o = f0 + fo;
             std::copy(refl[o], refl[o] + count[o], dst + (in_src_start[o] - base));
@@ -2867,10 +2885,11 @@ void RotationScaleMergeGPU::Impl::StageReflections(const Reflection *const *refl
         if (cnt > 0) {
             const Reflection *src = dst;
             if (!direct) {
-                CudaCheck(cudaMemcpyAsync(staged[b].get(), dst, size_t(cnt) * sizeof(Reflection),
-                                          cudaMemcpyHostToDevice, s()), "upload reflections");
+                Reflection *to = in_refl ? in_refl.get() + base : staged[b].get();
+                CudaCheck(cudaMemcpyAsync(to, dst, size_t(cnt) * sizeof(Reflection), cudaMemcpyHostToDevice, s()),
+                          "upload reflections");
                 CudaCheck(cudaEventRecord(copied[b], s()), "upload reflections");
-                src = staged[b].get();
+                src = to;
             }
             in_flight[b] = true;
             take(cnt, base, src);
@@ -2900,9 +2919,18 @@ void RotationScaleMergeGPU::IngestUpload(int n_frames, const Reflection *const *
         ThrowTooLargeForGPU(n);
     // See AllocObservations: these are the first of the scaling's buffers.
     cuda_trim_allocation_pool();
+    const int na = std::max(1, n);
+    // The reflections stay on the card until the observations are taken from them where that copy and
+    // the ingest's own peak beside it (67 bytes per reflection, see RotationScaleMerge::DeviceBytes)
+    // fit a quarter of the card - decided on the card's total, so the answer does not depend on the
+    // moment, and with room for a second engine's ingest beside this one. Not where the card reads
+    // the host's memory in place: there the copy would be the upload it saves.
+    constexpr size_t INGEST_PEAK_BYTES_PER_REFLECTION = 67;
+    d.in_refl = {};
+    if (!gpu_direct_host_read() && size_t(n) * (sizeof(Reflection) + INGEST_PEAK_BYTES_PER_REFLECTION) <= total_bytes / 4)
+        d.in_refl = d.Alloc<Reflection>(na);
     // Only what the sort and the cut read; the observations are taken from the reflections once the cut
     // has decided which they are (IngestObservations), so the two are never on the card together.
-    const int na = std::max(1, n);
     d.in_img = d.Alloc<float>(na); d.in_d = d.Alloc<float>(na); d.in_bkg = d.Alloc<float>(na);
     d.in_key = d.Alloc<uint64_t>(na);
     const IngestKeys a{d.in_img.get(), d.in_d.get(), d.in_bkg.get(), d.in_key.get()};
@@ -3117,34 +3145,38 @@ void RotationScaleMergeGPU::IngestGetLayout(IngestLayout &out) const {
 }
 
 void RotationScaleMergeGPU::IngestObservations(const Reflection *const *refl, const int32_t *count, size_t nthreads,
-                                               const double *frame_flux, float *px, float *py) {
+                                               const double *frame_flux, float d_max_scale, float *px, float *py) {
     DeviceGuard guard(impl_->device, impl_->available);
     auto &d = *impl_;
     const int n_keep = d.in_n_keep;
+    const int nka = std::max(1, n_keep);
     d.AllocObservations(n_keep);
-    d.in_dphi = d.Alloc<float>(std::max(1, n_keep));
+    d.in_dphi = d.Alloc<float>(nka);
+    // The predicted positions, which only the fulls' and only on the host read, go there straight away.
+    CudaDevicePtr<float> dev_px = d.Alloc<float>(nka), dev_py = d.Alloc<float>(nka);
+    const int n = d.in_src_start[d.n_frames];
     const IngestArrays a{d.obs.get(), d.zeta.get(), d.corr.get(), d.bkg.get(), d.var_bkg.get(), d.image_number.get(),
-                         d.d_obs.get(), d.in_dphi.get(), d.flags.get(), d.in_new_idx.get(),
-                         d.in_src_start[d.n_frames], n_keep};
-    d.StageReflections(refl, count, nthreads, [&](int cnt, int base, const Reflection *src) {
+                         d.d_obs.get(), d.in_dphi.get(), dev_px.get(), dev_py.get(), d.flags.get(), d_max_scale,
+                         d.in_new_idx.get(), n, n_keep};
+    const auto extract = [&](int cnt, int base, const Reflection *src) {
         IngestExtractKernel<<<(cnt + BLK - 1) / BLK, BLK, 0, d.s()>>>(cnt, base, src, a);
         CudaCheck(cudaGetLastError(), "IngestExtractKernel launch");
-    });
-    // The predicted positions, which only the fulls' and only on the host read, stay there.
-    const int n = d.in_src_start[d.n_frames];
-    std::vector<int32_t> new_idx(n);
-    if (n > 0)
-        CopyAndWait(new_idx.data(), d.in_new_idx.get(), size_t(n) * sizeof(int32_t), cudaMemcpyDeviceToHost, d.s(),
-                    "download places");
+    };
+    if (d.in_refl) {
+        if (n > 0)
+            extract(n, 0, d.in_refl.get());
+        CudaCheck(cudaStreamSynchronize(d.s()), "extract reflections");
+        d.in_refl = {};
+    } else {
+        d.StageReflections(refl, count, nthreads, extract);
+    }
     d.in_new_idx = {};
-    ParallelFor(d.n_frames, nthreads, [&](int o) {
-        for (int j = 0; j < count[o]; ++j) {
-            const int src = d.in_src_start[o] + j, i = new_idx[src];
-            if ((src + 1 < n ? new_idx[src + 1] : n_keep) == i) continue;
-            px[i] = refl[o][j].predicted_x;
-            py[i] = refl[o][j].predicted_y;
-        }
-    });
+    d.in_stage[0] = {}; d.in_stage[1] = {}; d.in_stage_cap = 0;
+    if (n_keep > 0) {
+        CopyAndWait(px, dev_px.get(), size_t(n_keep) * sizeof(float), cudaMemcpyDeviceToHost, d.s(), "download positions");
+        CopyAndWait(py, dev_py.get(), size_t(n_keep) * sizeof(float), cudaMemcpyDeviceToHost, d.s(), "download positions");
+    }
+    dev_px = {}; dev_py = {};
 
     // The kept observations are in frame order, as the reflections were (IngestSort laid out the CSR).
     CudaDevicePtr<double> flux;
diff --git a/image_analysis/scale_merge/RotationScaleMergeGPU.h b/image_analysis/scale_merge/RotationScaleMergeGPU.h
index b479fe174..eb69648e2 100644
--- a/image_analysis/scale_merge/RotationScaleMergeGPU.h
+++ b/image_analysis/scale_merge/RotationScaleMergeGPU.h
@@ -61,7 +61,8 @@ public:
     // The steps below build, from the reflections, exactly the observations and raw-hkl runs that
     // RotationScaleMerge::BuildInRangeObservations builds on the host, and leave them where the uploads
     // above and SetRawRuns would: the reflections are sorted and cut on the card, and cross the bus
-    // twice - once for what the sort and the cut read, once for the observations the cut kept.
+    // once where their copy fits beside the ingest (IngestUpload), else twice - once for what the sort
+    // and the cut read, once for the observations the cut kept.
 
     // The reflections of n_frames frames, frame o's count[o] of them at refl[o], uploaded in frame order;
     // what the sort, the cut and the background below read is kept per reflection.
@@ -88,8 +89,9 @@ public:
     // its order, each with its deterministic correction divided by its frame's flux (length n_frames).
     // px/py (length IngestSort's count) receive each observation's predicted position, which is not
     // kept on the card (GetFullsPeak).
+    // d_max_scale: observations coarser than this are flagged to stay out of the scale fit (INFINITY: none).
     void IngestObservations(const Reflection *const *refl, const int32_t *count, size_t nthreads,
-                            const double *frame_flux, float *px, float *py);
+                            const double *frame_flux, float d_max_scale, float *px, float *py);
     // The ingest's geometry smoothing, on the observations IngestSort left (RotationScaleMerge::IngestOnDevice):
     // each delta_phi re-solved against its frame's smoothed lattice where the frame has one - recip holds
     // a*, b*, c* per frame (9 floats), ok which frames, and the goniometer frame as SmoothedGeometry
@@ -240,7 +242,7 @@ public:
     // of. The working corr is downloaded separately by GetFullsCorr (it is only meaningful after the
     // fulls scaling; otherwise the caller sets it).
     void GetFulls(int32_t *run, float *I, float *sigma, float *d,
-                  float *image_number, int32_t *frame, uint8_t *on_ice, uint8_t *clipped,
+                  float *image_number, int32_t *frame, uint8_t *unscaled, uint8_t *clipped,
                   int32_t *group) const;
 
     // Download the observation each full's predicted detector position is that of (its peak partial),
diff --git a/image_analysis/scale_merge/ScaleOnTheFly.cpp b/image_analysis/scale_merge/ScaleOnTheFly.cpp
index 823b42706..5cce4b17d 100644
--- a/image_analysis/scale_merge/ScaleOnTheFly.cpp
+++ b/image_analysis/scale_merge/ScaleOnTheFly.cpp
@@ -31,45 +31,57 @@ namespace {
         return 1.0 / x;
     }
 
+    // The scatter of a still about its scale model is not counting noise: the strong reflections of a frame
+    // scatter by tens of percent (partiality, orientation, the crystal itself), far beyond their counting
+    // sigma. Measured in counting sigmas alone, every strong reflection is an outlier to the robust fit and
+    // the scale is decided by the weak ones. So the fit's variance carries a model error proportional to
+    // the predicted intensity. Its size barely matters (0.1-1.0 all fit alike); its presence does.
+    constexpr double SCALE_MODEL_ERROR = 0.3;
+
     // One reflection reduced to the 1-D scale fit: predicted intensity is G * coeff (coeff is constant
-    // while B is fixed), measured is Iobs, weighted by 1/sigma.
+    // while B is fixed), measured is Iobs; sigma2 its measured variance, var_bkg the background part of it.
     struct ScaleObs {
         double coeff;
         double Iobs;
-        double weight;
+        double sigma2;
+        double var_bkg;
     };
 
-    // Robust per-image scale: minimise sum_i Cauchy_k( weight_i (G*coeff_i - Iobs_i) ) over G >= 0. The
-    // model is linear in G, so this M-estimate is a few reweighted-least-squares steps (each a closed-form
-    // weighted ratio) - the same objective the Ceres path solves, without a per-image problem/autodiff/
-    // trust-region. Seeded from the plain weighted-LS solution; Cauchy weight is 1/(1 + (res/k)^2).
-    double SolveScaleIRLS(const std::vector<ScaleObs> &obs, double robust_k) {
-        auto weighted_scale = [&obs](auto robust_weight) {
-            double num = 0.0, den = 0.0;
-            for (const auto &o: obs) {
-                const double rw = robust_weight(o);
-                const double w2 = o.weight * o.weight;
-                num += rw * w2 * o.coeff * o.Iobs;
-                den += rw * w2 * o.coeff * o.coeff;
-            }
-            return den > 0.0 ? num / den : NAN;
-        };
+    // The variance of an observation at the model m = G * coeff: background, the counting noise of m and
+    // the model error.
+    double ModelVariance(const ScaleObs &o, double G) {
+        const double m = G * o.coeff;
+        return o.var_bkg + std::max(0.0, m) + SCALE_MODEL_ERROR * SCALE_MODEL_ERROR * m * m;
+    }
 
-        double G = weighted_scale([](const ScaleObs &) { return 1.0; });
-        if (!std::isfinite(G))
+    // Robust per-image scale: minimise sum_i Cauchy_k( (G*coeff_i - Iobs_i) / sqrt(var_i(G)) ) over G >= 0.
+    // The model is linear in G, so this M-estimate is a few reweighted-least-squares steps (each a
+    // closed-form weighted ratio), the variances re-evaluated at each step's G. Seeded from the plain
+    // least-squares solution weighted by the measured variances; Cauchy weight is 1/(1 + (res/k)^2).
+    double SolveScaleIRLS(const std::vector<ScaleObs> &obs, double robust_k) {
+        double num = 0.0, den = 0.0;
+        for (const auto &o: obs) {
+            num += o.coeff * o.Iobs / o.sigma2;
+            den += o.coeff * o.coeff / o.sigma2;
+        }
+        if (!(den > 0.0) || !std::isfinite(num / den))
             return 1.0;
-        G = std::max(0.0, G);
+        double G = std::max(0.0, num / den);
 
         const double k2 = robust_k * robust_k;
         for (int iter = 0; iter < 30; ++iter) {
-            const double G_prev = G;
-            const double G_next = weighted_scale([&](const ScaleObs &o) {
-                const double res = o.weight * (G * o.coeff - o.Iobs);
-                return 1.0 / (1.0 + res * res / k2);
-            });
-            if (!std::isfinite(G_next))
+            num = den = 0.0;
+            for (const auto &o: obs) {
+                const double var = ModelVariance(o, G);
+                const double res = G * o.coeff - o.Iobs;
+                const double w = 1.0 / (var + res * res / k2);   // Cauchy weight / var
+                num += w * o.coeff * o.Iobs;
+                den += w * o.coeff * o.coeff;
+            }
+            if (!(den > 0.0) || !std::isfinite(num / den))
                 break;
-            G = std::max(0.0, G_next);
+            const double G_prev = G;
+            G = std::max(0.0, num / den);
             if (std::abs(G - G_prev) <= 1e-7 * std::max(G, 1.0))
                 break;
         }
@@ -118,7 +130,11 @@ void ScaleOnTheFly::Scale(IntegrationOutcome &integration_outcome) const {
             if (it == reference_data.end())
                 continue;
             const double coeff = r.partiality * SafeInv(r.prescaling_corr * r.qe_corr * r.flight_corr, 1.0) * it->second;
-            obs.push_back({coeff, static_cast<double>(r.I), SafeInv(r.sigma, 1.0)});
+            const double sigma2 = static_cast<double>(r.sigma) * r.sigma;
+            if (!(sigma2 > 0.0) || !std::isfinite(sigma2))
+                continue;
+            const double var_bkg = std::isfinite(r.var_bkg) && r.var_bkg > 0.0f ? r.var_bkg : sigma2;
+            obs.push_back({coeff, static_cast<double>(r.I), sigma2, var_bkg});
         }
 
         if (obs.size() < MIN_REFLECTIONS) {
diff --git a/image_analysis/scale_merge/SearchSpaceGroup.cpp b/image_analysis/scale_merge/SearchSpaceGroup.cpp
index 6cf37304d..92b7a3bb1 100644
--- a/image_analysis/scale_merge/SearchSpaceGroup.cpp
+++ b/image_analysis/scale_merge/SearchSpaceGroup.cpp
@@ -144,9 +144,21 @@ namespace {
         if (CenteringAbsent(gops, hkl))
             return REFL_CENTRING_ABSENT;
         const uint8_t zone = static_cast<uint8_t>((MirrorZoneOf(mirrors, hkl) + 1) << 4);
-        if (gops.is_systematically_absent(hkl))
+        // gemmi's is_systematically_absent and epsilon_factor_without_centering in one pass over the
+        // operators: both ask which of them fix hkl. The absence test adds each centring vector to a
+        // fixing operator's translation, but no centring vector shifts the phase of this reflection
+        // (above), so the operator's own translation decides, as it does for one with none.
+        const gemmi::Op::Miller denh = {{gemmi::Op::DEN * hkl[0], gemmi::Op::DEN * hkl[1], gemmi::Op::DEN * hkl[2]}};
+        int epsilon = 0;
+        bool absent = false;
+        for (const gemmi::Op& op : gops.sym_ops)
+            if (op.apply_to_hkl_without_division(hkl) == denh) {
+                ++epsilon;
+                absent |= gemmi::GroupOps::has_phase_shift(op.tran, hkl);
+            }
+        if (absent)
             return REFL_ABSENT | zone;
-        return REFL_PRESENT | zone | (gops.epsilon_factor_without_centering(hkl) > 1 ? REFL_ON_AXIS : 0);
+        return REFL_PRESENT | zone | (epsilon > 1 ? REFL_ON_AXIS : 0);
     }
 
     // The zone a mirror fixes, named the way a crystallographer names it - "h0l" for the mirror
diff --git a/image_analysis/scale_merge/StillsPartialityRefine.cpp b/image_analysis/scale_merge/StillsPartialityRefine.cpp
index 401c8882d..6096da7f4 100644
--- a/image_analysis/scale_merge/StillsPartialityRefine.cpp
+++ b/image_analysis/scale_merge/StillsPartialityRefine.cpp
@@ -22,6 +22,9 @@ namespace {
     constexpr size_t MIN_FIT_REFLECTIONS = 20;
     constexpr double kRadToDeg = 180.0 / 3.14159265358979323846;
 
+    // Model error of the per-crystal scale fit, as a fraction of the predicted intensity - ScaleOnTheFly's.
+    constexpr double SCALE_MODEL_ERROR = 0.3;
+
     double SafeInv(double x, double fallback) {
         if (!std::isfinite(x) || x == 0.0)
             return fallback;
@@ -30,18 +33,52 @@ namespace {
 
     // One accepted reflection reduced to the physical partiality fit: the base reciprocal vector q (crystal
     // frame at the stored per-image orientation), the reference full intensity, the measured intensity, the
-    // reciprocal of the prescaling correction (the factor that turns a true intensity back into counts)
-    // and the weight. dist_ewald / partiality are recomputed from q under the refined tilt.
+    // reciprocal of the prescaling correction (the factor that turns a true intensity back into counts),
+    // the measured variance and its background part, and the weight the tilt is refined with.
+    // dist_ewald / partiality are recomputed from q under the refined tilt.
     struct FitObs {
         double qx, qy, qz;
         double Iref;
         double Iobs;
         double inv_corr;     // 1 / (prescaling_corr * qe_corr * flight_corr)
-        double weight;       // 1 / sigma
+        double sigma2;
+        double var_bkg;
+        double weight;       // 1 / sqrt(variance at the current model), set with each G
     };
 
+    // The variance of an observation at the model m: background, the counting noise of m and the model error.
+    double ModelVariance(const FitObs &o, double m) {
+        return o.var_bkg + std::max(0.0, m) + SCALE_MODEL_ERROR * SCALE_MODEL_ERROR * m * m;
+    }
+
     double VecLen(double x, double y, double z) { return std::sqrt(x * x + y * y + z * z); }
 
+    // The rocking width sigma^2 at a reflection of resolution d* (and |q_z|, for the bandwidth term): the
+    // run's table where there is one - linear in d* between its shells, held beyond the outermost - else
+    // the three-term formula.
+    struct Width {
+        double gamma0, gamma_e, bw;
+        const std::vector<double> *table_dstar = nullptr, *table_s = nullptr;
+
+        double Sigma2(double dstar, double qz) const {
+            if (table_dstar && !table_dstar->empty()) {
+                const auto &x = *table_dstar;
+                const auto &y = *table_s;
+                double s = y.front();
+                if (dstar >= x.back())
+                    s = y.back();
+                else if (dstar > x.front()) {
+                    const size_t i = std::upper_bound(x.begin(), x.end(), dstar) - x.begin();
+                    s = y[i - 1] + (dstar - x[i - 1]) / (x[i] - x[i - 1]) * (y[i] - y[i - 1]);
+                }
+                return s * s;
+            }
+            const double sig_ang = gamma_e * dstar;
+            const double sbw = bw * std::fabs(qz);
+            return gamma0 * gamma0 + sig_ang * sig_ang + sbw * sbw;
+        }
+    };
+
     // Analytic partiality for a reflection whose base reciprocal vector is q, tilted by (psi_x, psi_y).
     // Mirrors BraggPrediction: dist_ewald = |S| - 1/lambda with S = q_rot + S0, and
     // p = exp(-dist_ewald^2 / 2 sigma^2), sigma^2 = gamma0^2 + (gamma_e*d*)^2 + (bw*|q_z|)^2 - three
@@ -52,7 +89,7 @@ namespace {
     double ComputeP(double qx, double qy, double qz,
                     double psi_x, double psi_y,
                     double s0x, double s0y, double s0z, double inv_lambda,
-                    double gamma0, double gamma_e, double bw) {
+                    const Width &width) {
         double aa[3] = {psi_x, psi_y, 0.0};
         double q[3] = {qx, qy, qz};
         double qr[3];
@@ -60,9 +97,7 @@ namespace {
         const double Sx = qr[0] + s0x, Sy = qr[1] + s0y, Sz = qr[2] + s0z;
         const double de = std::sqrt(Sx * Sx + Sy * Sy + Sz * Sz) - inv_lambda;
         const double dstar = std::sqrt(qr[0] * qr[0] + qr[1] * qr[1] + qr[2] * qr[2]);
-        const double sig_ang = gamma_e * dstar;
-        const double sbw = bw * std::fabs(qr[2]);
-        const double sig2 = gamma0 * gamma0 + sig_ang * sig_ang + sbw * sbw;
+        const double sig2 = width.Sigma2(dstar, qr[2]);
         if (!(sig2 > 0.0))
             return 1.0;
         return std::exp(-0.5 * de * de / sig2);
@@ -72,9 +107,8 @@ namespace {
     // their plain moment of de is u = W^2 / 3, and the intensity-weighted moment m of a Gaussian of width
     // s cut at +-W is u * g(a), a = W / s, with g(a) = 3/a^2 (1 - 2 a phi(a) / erf(a / sqrt 2)): 1 for a
     // curve much wider than the window, s^2 / u for a much narrower one. Solves g(a) = m / u for s^2 by
-    // bisection (g falls with a). A curve wider than the window cannot be measured through it, so it is
-    // taken as wide as the window (a = 1).
-    double UntruncatedVariance(double m, double u) {
+    // bisection (g falls with a). A curve wider than the window cannot be measured through it: empty.
+    std::optional<double> UntruncatedVariance(double m, double u) {
         auto g = [](double a) {
             const double phi = std::exp(-0.5 * a * a) / std::sqrt(2.0 * 3.14159265358979323846);
             return 3.0 / (a * a) * (1.0 - 2.0 * a * phi / std::erf(a / std::sqrt(2.0)));
@@ -82,7 +116,7 @@ namespace {
         const double t = m / u;
         double lo = 1.0, hi = 50.0;
         if (!(t < g(lo)))
-            return 3.0 * u;
+            return std::nullopt;
         for (int i = 0; i < 60; ++i) {
             const double mid = 0.5 * (lo + hi);
             (g(mid) > t ? lo : hi) = mid;
@@ -91,36 +125,32 @@ namespace {
         return 3.0 * u / (a * a);
     }
 
-    // Robust per-crystal scale G (linear in G given the model coefficients), identical objective to
-    // ScaleOnTheFly::SolveScaleIRLS: minimise sum Cauchy_k( w (G*coeff - Iobs) ) over G >= 0.
-    double SolveScaleIRLS(const std::vector<double> &coeff, const std::vector<double> &Iobs,
-                          const std::vector<double> &weight, double robust_k) {
-        auto weighted_scale = [&](auto robust_weight) {
-            double num = 0.0, den = 0.0;
-            for (size_t i = 0; i < coeff.size(); ++i) {
-                const double rw = robust_weight(i);
-                const double w2 = weight[i] * weight[i];
-                num += rw * w2 * coeff[i] * Iobs[i];
-                den += rw * w2 * coeff[i] * coeff[i];
-            }
-            return den > 0.0 ? num / den : NAN;
-        };
-
-        double G = weighted_scale([](size_t) { return 1.0; });
-        if (!std::isfinite(G))
+    // Robust per-crystal scale G (linear in G given the model coefficients), the objective of
+    // ScaleOnTheFly::SolveScaleIRLS: minimise sum Cauchy_k( (G*coeff - Iobs) / sqrt(var(G*coeff)) ) over G >= 0,
+    // the variances re-evaluated at each step's G.
+    double SolveScaleIRLS(const std::vector<FitObs> &obs, const std::vector<double> &coeff, double robust_k) {
+        double num = 0.0, den = 0.0;
+        for (size_t i = 0; i < obs.size(); ++i) {
+            num += coeff[i] * obs[i].Iobs / obs[i].sigma2;
+            den += coeff[i] * coeff[i] / obs[i].sigma2;
+        }
+        if (!(den > 0.0) || !std::isfinite(num / den))
             return 1.0;
-        G = std::max(0.0, G);
+        double G = std::max(0.0, num / den);
 
         const double k2 = robust_k * robust_k;
         for (int iter = 0; iter < 30; ++iter) {
-            const double G_prev = G;
-            const double G_next = weighted_scale([&](size_t i) {
-                const double res = weight[i] * (G * coeff[i] - Iobs[i]);
-                return 1.0 / (1.0 + res * res / k2);
-            });
-            if (!std::isfinite(G_next))
+            num = den = 0.0;
+            for (size_t i = 0; i < obs.size(); ++i) {
+                const double res = G * coeff[i] - obs[i].Iobs;
+                const double w = 1.0 / (ModelVariance(obs[i], G * coeff[i]) + res * res / k2);
+                num += w * coeff[i] * obs[i].Iobs;
+                den += w * coeff[i] * coeff[i];
+            }
+            if (!(den > 0.0) || !std::isfinite(num / den))
                 break;
-            G = std::max(0.0, G_next);
+            const double G_prev = G;
+            G = std::max(0.0, num / den);
             if (std::abs(G - G_prev) <= 1e-7 * std::max(G, 1.0))
                 break;
         }
@@ -143,16 +173,14 @@ namespace {
     // ComputeP with the tilt given as its rotation matrix.
     struct TiltModel {
         double s0x, s0y, s0z, inv_lambda;
-        double gamma0, gamma_e, bw;
+        Width width;
 
         double P(const std::array<double, 9> &R, const FitObs &o) const {
             const double qx = R[0] * o.qx + R[1] * o.qy + R[2] * o.qz;
             const double qy = R[3] * o.qx + R[4] * o.qy + R[5] * o.qz;
             const double qz = R[6] * o.qx + R[7] * o.qy + R[8] * o.qz;
             const double de = VecLen(qx + s0x, qy + s0y, qz + s0z) - inv_lambda;
-            const double sig_ang = gamma_e * VecLen(qx, qy, qz);
-            const double sbw = bw * std::fabs(qz);
-            const double sig2 = gamma0 * gamma0 + sig_ang * sig_ang + sbw * sbw;
+            const double sig2 = width.Sigma2(VecLen(qx, qy, qz), qz);
             if (!(sig2 > 0.0))
                 return 1.0;
             return std::exp(-0.5 * de * de / sig2);
@@ -247,7 +275,8 @@ StillsPartialityRefine::StillsPartialityRefine(const DiffractionExperiment &x)
 
 double StillsPartialityRefine::RefineOne(IntegrationOutcome &outcome,
                                          const std::map<HKLKey, double> &reference,
-                                         const std::optional<RunWidth> &run_width) const {
+                                         const std::optional<RunWidth> &run_width,
+                                         double radial_scale) const {
     if (outcome.reflections.empty())
         return 0.0;
 
@@ -258,8 +287,8 @@ double StillsPartialityRefine::RefineOne(IntegrationOutcome &outcome,
     const double inv_lambda = 1.0 / outcome.geom.GetWavelength_A();
 
     auto base_q = [&](const Reflection &r) {
-        return Astar * static_cast<float>(r.h) + Bstar * static_cast<float>(r.k)
-               + Cstar * static_cast<float>(r.l);
+        return (Astar * static_cast<float>(r.h) + Bstar * static_cast<float>(r.k)
+                + Cstar * static_cast<float>(r.l)) * static_cast<float>(radial_scale);
     };
 
     // Collect the reflections that constrain the fit (accepted, non-ice, finite, present in the reference).
@@ -284,6 +313,8 @@ double StillsPartialityRefine::RefineOne(IntegrationOutcome &outcome,
             .Iref = it->second,
             .Iobs = static_cast<double>(r.I),
             .inv_corr = SafeInv(r.prescaling_corr * r.qe_corr * r.flight_corr, 1.0),
+            .sigma2 = static_cast<double>(r.sigma) * r.sigma,
+            .var_bkg = std::isfinite(r.var_bkg) && r.var_bkg > 0.0f ? r.var_bkg : static_cast<double>(r.sigma) * r.sigma,
             .weight = SafeInv(r.sigma, 1.0),
         });
 
@@ -337,28 +368,31 @@ double StillsPartialityRefine::RefineOne(IntegrationOutcome &outcome,
         gamma_e = std::max(run_width->gamma_e, 1e-9);
         bw = run_width->bandwidth_sigma;
     }
+    const Width width{.gamma0 = gamma0, .gamma_e = gamma_e, .bw = bw,
+                      .table_dstar = run_width ? &run_width->table_dstar : nullptr,
+                      .table_s = run_width ? &run_width->table_s : nullptr};
 
     double psi[2] = {0.0, 0.0};
     double G = 1.0;
 
     const TiltModel model{.s0x = S0.x, .s0y = S0.y, .s0z = S0.z, .inv_lambda = inv_lambda,
-                          .gamma0 = gamma0, .gamma_e = gamma_e, .bw = bw};
+                          .width = width};
     const bool refine_tilt = obs.size() >= settings_.min_reflections;
     const int inner = refine_tilt ? settings_.inner_iterations : 1;
 
     for (int it = 0; it < inner; ++it) {
-        // (1) Solve G given the current partialities.
-        std::vector<double> coeff(obs.size()), Iobs(obs.size()), weight(obs.size());
+        // (1) Solve G given the current partialities, and weight the tilt fit by the variances at that model.
+        std::vector<double> coeff(obs.size());
         for (size_t j = 0; j < obs.size(); ++j) {
             const double p = ComputeP(obs[j].qx, obs[j].qy, obs[j].qz, psi[0], psi[1],
-                                      S0.x, S0.y, S0.z, inv_lambda, gamma0, gamma_e, bw);
+                                      S0.x, S0.y, S0.z, inv_lambda, width);
             coeff[j] = p * obs[j].inv_corr * obs[j].Iref;
-            Iobs[j] = obs[j].Iobs;
-            weight[j] = obs[j].weight;
         }
-        G = SolveScaleIRLS(coeff, Iobs, weight, settings_.robust_k);
+        G = SolveScaleIRLS(obs, coeff, settings_.robust_k);
         if (!(G > 0.0) || !std::isfinite(G))
             return 0.0;
+        for (size_t j = 0; j < obs.size(); ++j)
+            obs[j].weight = 1.0 / std::sqrt(ModelVariance(obs[j], G * coeff[j]));
 
         if (!refine_tilt)
             break;
@@ -370,23 +404,12 @@ double StillsPartialityRefine::RefineOne(IntegrationOutcome &outcome,
             break;
     }
 
-    // Keep what the crystal came in with. This refinement is on by default, so a crystal the tilt model
-    // happens to suit WORSE than the fixed partiality it replaces must not be made worse by it - and
-    // whether it suits is only known once the corrections are written and the CC re-measured.
-    const auto cc_before = outcome.image_scale_cc;
-    const auto g_before = outcome.image_scale_g;
-    std::vector<std::pair<float, float>> before;   // partiality, image_scale_corr
-    before.reserve(outcome.reflections.size());
-    for (const auto &r: outcome.reflections)
-        before.emplace_back(r.partiality, r.image_scale_corr);
-
     // Write the refined partiality + scale correction onto every reflection of the crystal (not only the
     // fit subset), so the merge sees a consistent model. image_scale_corr = prescaling_corr * qe_corr * flight_corr /
     // (partiality * G), the same composition ScaleOnTheFly writes.
     for (auto &r: outcome.reflections) {
         const Coord q = base_q(r);
-        const double p = ComputeP(q.x, q.y, q.z, psi[0], psi[1], S0.x, S0.y, S0.z, inv_lambda,
-                                  gamma0, gamma_e, bw);
+        const double p = ComputeP(q.x, q.y, q.z, psi[0], psi[1], S0.x, S0.y, S0.z, inv_lambda, width);
         r.partiality = static_cast<float>(p);
         const float corr = r.prescaling_corr * r.qe_corr * r.flight_corr;
         const double denom = p * G;
@@ -402,20 +425,6 @@ double StillsPartialityRefine::RefineOne(IntegrationOutcome &outcome,
     const auto [cc, cc_n] = ImageReferenceCC(outcome.reflections, reference, hkl_key_generator_,
                                              d_min_limit_, d_max_limit_, min_partiality_);
 
-    // Adopt the refined model only if it correlates with the reference at least as well as the model it
-    // replaces. Rejecting puts the crystal back exactly as it arrived, which is the same state a
-    // crystal with too few reflections to fit ends in. A CC that cannot be measured at all counts as
-    // worse, not as no opinion: ImageReferenceCC returns NaN when too few reflections clear the
-    // partiality cut, which is precisely what a refinement that collapsed the partialities produces -
-    // and adopting it would leave image_scale_cc NaN, on which --min-image-cc drops the image outright.
-    if (cc_before.has_value() && std::isfinite(*cc_before) && !(std::isfinite(cc) && cc >= *cc_before)) {
-        for (size_t i = 0; i < outcome.reflections.size(); ++i) {
-            outcome.reflections[i].partiality = before[i].first;
-            outcome.reflections[i].image_scale_corr = before[i].second;
-        }
-        outcome.image_scale_g = g_before;
-        return 0.0;   // nothing adopted, so no tilt to report
-    }
     outcome.image_scale_cc = cc;
     outcome.image_scale_cc_n = cc_n;
 
@@ -423,8 +432,67 @@ double StillsPartialityRefine::RefineOne(IntegrationOutcome &outcome,
     return tilt_deg;
 }
 
+double StillsPartialityRefine::MeasureRadialScale(const std::vector<IntegrationOutcome> &outcomes,
+                                                  const std::optional<UnitCell> &reference_cell,
+                                                  double radial_scale) const {
+    // A scale of the reciprocal lattice - a wavelength, or a cell, a little off - leaves every spot where
+    // it was (positions fix only lambda d*), but moves each reflection's excitation error by
+    // eps lambda d*^2 / 2 for q -> (1 + eps) q, so the run's rocking curve sits off zero by an amount
+    // growing as d*^2. The prediction window is symmetric in de, so the intensity-weighted mean de of a
+    // shell is that offset, and a line through the origin in lambda d*^2 / 2 gives eps. A window that cuts
+    // an off-centre curve pulls the mean toward zero, so the caller iterates from the scale found.
+    const auto &indexing = experiment_.GetIndexingSettings();
+    struct Point { double x, de, w; };
+    std::vector<Point> pts;
+    double max_x = 0.0;
+    for (const auto &o: outcomes) {
+        if (!o.image_scale_g || !(*o.image_scale_g > 0.0))
+            continue;
+        if (reference_cell && !o.latt.GetUnitCell().is_close(*reference_cell, indexing.GetUnitCellDistTolerance(),
+                                                               indexing.GetUnitCellAngleTolerance_deg()))
+            continue;
+        const Coord S0 = o.geom.GetScatteringVector();
+        const double inv_lambda = 1.0 / o.geom.GetWavelength_A();
+        for (const auto &r: o.reflections) {
+            if (r.on_ice_ring || !AcceptReflection(r, d_min_limit_, d_max_limit_) || !(r.d > 0.0f))
+                continue;
+            const double w = r.I * r.prescaling_corr * r.qe_corr * r.flight_corr / *o.image_scale_g;
+            if (!std::isfinite(w))
+                continue;
+            const Coord q = (o.latt.Astar() * static_cast<float>(r.h) + o.latt.Bstar() * static_cast<float>(r.k)
+                             + o.latt.Cstar() * static_cast<float>(r.l)) * static_cast<float>(radial_scale);
+            const double x = 0.5 / (inv_lambda * r.d * r.d);
+            pts.push_back({x, VecLen(q.x + S0.x, q.y + S0.y, q.z + S0.z) - inv_lambda, w});
+            max_x = std::max(max_x, x);
+        }
+    }
+    constexpr int N_SHELLS = 8;
+    if (pts.size() < 100 * N_SHELLS)
+        return radial_scale;
+    std::array<double, N_SHELLS> sw{}, swde{}, swx{};
+    for (const auto &p: pts) {
+        const int b = std::min(N_SHELLS - 1, static_cast<int>(p.x / max_x * N_SHELLS));
+        sw[b] += p.w;
+        swde[b] += p.w * p.de;
+        swx[b] += p.w * p.x;
+    }
+    double sxy = 0.0, sxx = 0.0;
+    for (int b = 0; b < N_SHELLS; ++b) {
+        if (!(sw[b] > 0.0))
+            continue;
+        const double x = swx[b] / sw[b], y = swde[b] / sw[b];
+        sxy += sw[b] * x * y;
+        sxx += sw[b] * x * x;
+    }
+    if (!(sxx > 0.0) || !std::isfinite(sxy))
+        return radial_scale;
+    // the slope is eps, removed by scaling q by (1 - eps)
+    return radial_scale * (1.0 - sxy / sxx);
+}
+
 std::optional<StillsPartialityRefine::RunWidth> StillsPartialityRefine::MeasureRunWidth(
-        const std::vector<IntegrationOutcome> &outcomes, const std::optional<UnitCell> &reference_cell) const {
+        const std::vector<IntegrationOutcome> &outcomes, const std::optional<UnitCell> &reference_cell,
+        double radial_scale, const RunWidth *window_width) const {
     // The rocking width measured on the crystals rather than on the prediction window. A lattice point
     // sits anywhere across the window with equal likelihood, while what it records is I_full * p(de), so
     // the intensity-weighted second moment of the excitation error, sum I de^2 / sum I, is the width s^2
@@ -433,8 +501,22 @@ std::optional<StillsPartialityRefine::RunWidth> StillsPartialityRefine::MeasureR
     // instead the window's own (W^2 / 3). Measured in shells of d*^2 over the whole run, where the
     // intensities of thousands of crystals average out, and fitted as s^2 = gamma0^2 + gamma_e^2 d*^2 +
     // (bandwidth_sigma lambda d*^2 / 2)^2.
+    //
+    // Each frame predicts through a window of its own (twice its profile radius), and these differ by an
+    // order of magnitude within a run. Pooled, the frames with the widest windows decide both moments, and
+    // the correction then reads their window: on a run whose windows are mostly narrower than the curve at
+    // high resolution, the pooled measurement came out as the window at every resolution, a width constant
+    // in d* that is several times too wide at low resolution. So within a shell the frames are taken in
+    // WINDOW_GROUPS groups of similar window, each measured against its own, and the shell's width is the
+    // median of the groups whose curve is narrower than their window; a shell where no group can see the
+    // curve is left out.
+    //
+    // A frame's window is the largest excitation error it predicted where it predicted through one width.
+    // Predicted through the run's width (window_width), the window is its formula at the reflection's own
+    // resolution: the frame's largest excitation error is then the high-resolution window, and taken as the
+    // window of its low-resolution reflections it put them in the wrong group.
     const auto &indexing = experiment_.GetIndexingSettings();
-    struct Point { double x, de2, w, var_w; };
+    struct Point { double x, de2, w, var_w, window; };
     std::vector<Point> pts;
     for (const auto &o: outcomes) {
         if (!o.image_scale_g || !(*o.image_scale_g > 0.0))
@@ -442,6 +524,10 @@ std::optional<StillsPartialityRefine::RunWidth> StillsPartialityRefine::MeasureR
         if (reference_cell && !o.latt.GetUnitCell().is_close(*reference_cell, indexing.GetUnitCellDistTolerance(),
                                                                indexing.GetUnitCellAngleTolerance_deg()))
             continue;
+        float frame_window = 0.0f;   // the largest excitation error the frame predicted
+        for (const auto &r: o.reflections)
+            if (std::isfinite(r.dist_ewald))
+                frame_window = std::max(frame_window, std::fabs(r.dist_ewald));
         for (const auto &r: o.reflections) {
             if (r.on_ice_ring || !AcceptReflection(r, d_min_limit_, d_max_limit_))
                 continue;
@@ -449,40 +535,135 @@ std::optional<StillsPartialityRefine::RunWidth> StillsPartialityRefine::MeasureR
             const double w = r.I * corr, sigma_w = r.sigma * corr;
             if (!std::isfinite(w) || !std::isfinite(sigma_w) || !std::isfinite(r.dist_ewald) || !(r.d > 0.0f))
                 continue;
-            pts.push_back({1.0 / (static_cast<double>(r.d) * r.d),
-                           static_cast<double>(r.dist_ewald) * r.dist_ewald, w, sigma_w * sigma_w});
+            // The excitation error the window was cut in is the prediction's; the curve's is taken at the
+            // run's radial scale (MeasureRadialScale), recomputed from the lattice when that is not one.
+            double de = r.dist_ewald;
+            if (radial_scale != 1.0) {
+                const Coord q = (o.latt.Astar() * static_cast<float>(r.h) + o.latt.Bstar() * static_cast<float>(r.k)
+                                 + o.latt.Cstar() * static_cast<float>(r.l)) * static_cast<float>(radial_scale);
+                const Coord S0 = o.geom.GetScatteringVector();
+                de = VecLen(q.x + S0.x, q.y + S0.y, q.z + S0.z) - 1.0 / o.geom.GetWavelength_A();
+            }
+            double window = frame_window;
+            if (window_width) {
+                // the formula at the reflection's d*, its bandwidth term at |q_z| = lambda d*^2 / 2
+                const double dstar = 1.0 / r.d;
+                const double a = window_width->gamma_e * dstar;
+                const double b = window_width->bandwidth_sigma * o.geom.GetWavelength_A() * dstar * dstar / 2.0;
+                window = std::sqrt(window_width->gamma0 * window_width->gamma0 + a * a + b * b);
+            }
+            pts.push_back({1.0 / (static_cast<double>(r.d) * r.d), de * de, w, sigma_w * sigma_w, window});
         }
     }
     constexpr size_t N_SHELLS = 8;
+    constexpr size_t WINDOW_GROUPS = 4;
     if (pts.size() < 100 * N_SHELLS)
         return std::nullopt;
     std::sort(pts.begin(), pts.end(), [](const Point &a, const Point &b) { return a.x < b.x; });
 
     Logger logger("StillsPartialityRefine");
-    // A shell's moment is no better than the summed intensity it is weighted by, so a shell is used only
-    // where that sum is measured to 10 % (sum I / sigma(sum I) >= 10): the shells beyond the diffraction
-    // limit, where the sum is noise and can even be negative, say nothing about the width.
+    // A group's moment is no better than the summed intensity it is weighted by, so a group is used only
+    // where that sum is measured to 10 % (sum I / sigma(sum I) >= 10): beyond the diffraction limit the
+    // sum is noise and can even be negative, and says nothing about the width.
     constexpr double MIN_SHELL_SIGNAL = 10.0;
+    // The width of the points [lo, hi) of pts (sorted by d*): the median of the window groups' widths.
+    auto shell_width = [&](size_t lo, size_t hi) -> std::optional<double> {
+        std::vector<Point> shell(pts.begin() + lo, pts.begin() + hi);
+        std::sort(shell.begin(), shell.end(), [](const Point &a, const Point &b) { return a.window < b.window; });
+        std::vector<double> widths;
+        for (size_t g = 0; g < WINDOW_GROUPS; ++g) {
+            const size_t glo = g * shell.size() / WINDOW_GROUPS, ghi = (g + 1) * shell.size() / WINDOW_GROUPS;
+            double sw = 0.0, svar = 0.0, swde2 = 0.0, sde2 = 0.0;
+            for (size_t i = glo; i < ghi; ++i) {
+                sw += shell[i].w;
+                svar += shell[i].var_w;
+                swde2 += shell[i].w * shell[i].de2;
+                sde2 += shell[i].de2;
+            }
+            if (!(sw >= MIN_SHELL_SIGNAL * std::sqrt(svar)) || !(swde2 > 0.0))
+                continue;
+            if (const auto v = UntruncatedVariance(swde2 / sw, sde2 / static_cast<double>(ghi - glo)))
+                widths.push_back(*v);
+        }
+        if (widths.empty())
+            return std::nullopt;
+        std::sort(widths.begin(), widths.end());
+        const size_t m = widths.size();
+        return m % 2 ? widths[m / 2] : 0.5 * (widths[m / 2 - 1] + widths[m / 2]);
+    };
+
+    // For the three-term formula (the prediction window): shells of equal count in d*^2.
     std::vector<double> sx, sy;
     for (size_t k = 0; k < N_SHELLS; ++k) {
-        double sw = 0.0, svar = 0.0, swde2 = 0.0, sde2 = 0.0, sumx = 0.0;
         const size_t lo = k * pts.size() / N_SHELLS, hi = (k + 1) * pts.size() / N_SHELLS;
-        for (size_t i = lo; i < hi; ++i) {
-            sw += pts[i].w;
-            svar += pts[i].var_w;
-            swde2 += pts[i].w * pts[i].de2;
-            sde2 += pts[i].de2;
-            sumx += pts[i].x;
-        }
-        const double n = static_cast<double>(hi - lo);
-        if (!(sw >= MIN_SHELL_SIGNAL * std::sqrt(svar)) || !(swde2 > 0.0))
+        const auto y = shell_width(lo, hi);
+        if (!y)
             continue;
-        const double x = sumx / n, y = UntruncatedVariance(swde2 / sw, sde2 / n);
+        double sumx = 0.0;
+        for (size_t i = lo; i < hi; ++i)
+            sumx += pts[i].x;
+        const double x = sumx / static_cast<double>(hi - lo);
         sx.push_back(x);
-        sy.push_back(y);
-        logger.Debug("Stills rocking width at d = {:.2f} A: {:.2e} 1/A ({:.3f} deg), I/sigma {:.0f}", 1.0 / std::sqrt(x),
-                     std::sqrt(y), std::sqrt(y / x) * kRadToDeg, sw / std::sqrt(svar));
+        sy.push_back(*y);
+        logger.Debug("Stills rocking width at d = {:.2f} A: {:.2e} 1/A ({:.3f} deg)",
+                     1.0 / std::sqrt(x), std::sqrt(*y), std::sqrt(*y / x) * kRadToDeg);
     }
+
+    // For the partiality: shells of equal width in d*, kept as a table. Equal-count shells crowd where
+    // the reflections are - on a run predicting ~1000 reflections a frame, all eight sat at 3.8-1.8 A, so
+    // the low-resolution width was the formula's extrapolation, and the three-term fit flipped between
+    // forms with the number of frames (to a pure bandwidth at 50k frames). Measured where it is used and
+    // interpolated, the width needs no form. A wider curve at finer resolution is the physics (every term
+    // grows with d*), so the table is made non-decreasing (pool adjacent violators, weighted by the
+    // shells' summed signal).
+    std::vector<double> table_dstar, table_s, table_weight;
+    {
+        const double lo_d = std::sqrt(pts.front().x), hi_d = std::sqrt(pts.back().x);
+        size_t lo = 0;
+        for (size_t k = 0; k < N_SHELLS; ++k) {
+            const double edge = lo_d + (hi_d - lo_d) * static_cast<double>(k + 1) / N_SHELLS;
+            size_t hi = lo;
+            while (hi < pts.size() && (k + 1 == N_SHELLS || std::sqrt(pts[hi].x) < edge))
+                ++hi;
+            double sw = 0.0, svar = 0.0, sds = 0.0;
+            for (size_t i = lo; i < hi; ++i) {
+                sw += pts[i].w;
+                svar += pts[i].var_w;
+                sds += std::sqrt(pts[i].x);
+            }
+            if (hi - lo >= 400 && sw >= MIN_SHELL_SIGNAL * std::sqrt(svar))
+                if (const auto y = shell_width(lo, hi)) {
+                    table_dstar.push_back(sds / static_cast<double>(hi - lo));
+                    table_s.push_back(std::sqrt(*y));
+                    table_weight.push_back(sw / std::sqrt(svar));
+                }
+            lo = hi;
+        }
+        std::vector<double> block_s, block_w;
+        std::vector<size_t> block_n;
+        for (size_t i = 0; i < table_s.size(); ++i) {
+            block_s.push_back(table_s[i]);
+            block_w.push_back(table_weight[i]);
+            block_n.push_back(1);
+            while (block_s.size() > 1 && block_s[block_s.size() - 2] > block_s.back()) {
+                const size_t j = block_s.size() - 2;
+                block_s[j] = (block_s[j] * block_w[j] + block_s.back() * block_w.back()) / (block_w[j] + block_w.back());
+                block_w[j] += block_w.back();
+                block_n[j] += block_n.back();
+                block_s.pop_back();
+                block_w.pop_back();
+                block_n.pop_back();
+            }
+        }
+        table_s.clear();
+        for (size_t j = 0; j < block_s.size(); ++j)
+            table_s.insert(table_s.end(), block_n[j], block_s[j]);
+        if (table_dstar.size() < 3) {
+            table_dstar.clear();
+            table_s.clear();
+        }
+    }
+
     if (sx.size() < 3)
         return std::nullopt;
 
@@ -525,14 +706,22 @@ std::optional<StillsPartialityRefine::RunWidth> StillsPartialityRefine::MeasureR
         return std::nullopt;
     // The d*^4 term is a bandwidth: its radial smear bw |q_z|, with |q_z| = lambda d*^2 / 2 on the sphere.
     const RunWidth width{.gamma0 = std::sqrt(best[0]), .gamma_e = std::sqrt(best[1]),
-                         .bandwidth_sigma = 2.0 * std::sqrt(best[2]) / experiment_.GetWavelength_A()};
+                         .bandwidth_sigma = 2.0 * std::sqrt(best[2]) / experiment_.GetWavelength_A(),
+                         .radial_scale = radial_scale, .table_dstar = table_dstar, .table_s = table_s};
     logger.Info("Stills rocking width measured: {:.2e} 1/A + {:.3f} deg angular + {:.4f} bandwidth (FWHM)",
                 width.gamma0, width.gamma_e * kRadToDeg, width.bandwidth_sigma * 2.3548);
+    std::string table;
+    for (size_t i = 0; i < table_dstar.size(); ++i)
+        table += fmt::format(" {:.2f} A {:.2e}", 1.0 / table_dstar[i], table_s[i]);
+    logger.Info("Stills rocking width for the partiality, against resolution (1/A):{}",
+                table.empty() ? " none, the formula is used" : table);
     return width;
 }
 
 double StillsPartialityRefine::Run(std::vector<IntegrationOutcome> &outcomes, size_t nthreads,
-                                   const std::optional<UnitCell> &reference_cell) const {
+                                   const std::optional<UnitCell> &reference_cell,
+                                   const std::optional<RunWidth> &given_width,
+                                   std::optional<RunWidth> *used_width) const {
     const auto &indexing = experiment_.GetIndexingSettings();
     auto merged_crystal = [&](const IntegrationOutcome &o) {
         return !reference_cell || o.latt.GetUnitCell().is_close(*reference_cell,
@@ -544,7 +733,22 @@ double StillsPartialityRefine::Run(std::vector<IntegrationOutcome> &outcomes, si
     nthreads = std::max<size_t>(1, nthreads);
 
     double last_mean_tilt = 0.0;
-    const auto run_width = MeasureRunWidth(outcomes, reference_cell);
+    // Where the frames were predicted through a curve measured before the image pass, the partialities use
+    // that same curve. Measured again here, through windows that follow it, the width reads narrower at low
+    // resolution (its constant term falls to about zero), and the merge it gave moved R-free against the
+    // models by up to +-0.015 per run in both directions, where the one curve moved it by at most +0.008.
+    std::optional<RunWidth> run_width = given_width;
+    if (!run_width) {
+        double radial_scale = 1.0;
+        for (int i = 0; i < 3; ++i)
+            radial_scale = MeasureRadialScale(outcomes, reference_cell, radial_scale);
+        Logger("StillsPartialityRefine").Info("Stills rocking curve centre: reciprocal lattice scaled by {:+.2e}",
+                                              radial_scale - 1.0);
+        run_width = MeasureRunWidth(outcomes, reference_cell, radial_scale);
+    }
+    const double radial_scale = run_width ? run_width->radial_scale : 1.0;
+    if (used_width)
+        *used_width = run_width;
 
     for (int outer = 0; outer < settings_.outer_iterations; ++outer) {
         // Reference full intensities from the current corrections.
@@ -560,7 +764,7 @@ double StillsPartialityRefine::Run(std::vector<IntegrationOutcome> &outcomes, si
         auto worker = [&]() {
             size_t i = next.fetch_add(1);
             while (i < outcomes.size()) {
-                const double t = merged_crystal(outcomes[i]) ? RefineOne(outcomes[i], reference, run_width) : 0.0;
+                const double t = merged_crystal(outcomes[i]) ? RefineOne(outcomes[i], reference, run_width, radial_scale) : 0.0;
                 if (t > 0.0) {
                     double prev = tilt_sum.load();
                     while (!tilt_sum.compare_exchange_weak(prev, prev + t)) {}
diff --git a/image_analysis/scale_merge/StillsPartialityRefine.h b/image_analysis/scale_merge/StillsPartialityRefine.h
index a3600f0ca..9ba83f1bd 100644
--- a/image_analysis/scale_merge/StillsPartialityRefine.h
+++ b/image_analysis/scale_merge/StillsPartialityRefine.h
@@ -7,6 +7,7 @@
 #include <vector>
 
 #include "../../common/DiffractionExperiment.h"
+#include "../../common/StillsRunWidth.h"
 #include "../IntegrationOutcome.h"
 #include "HKLKey.h"
 
@@ -45,20 +46,34 @@ public:
 
     explicit StillsPartialityRefine(const DiffractionExperiment &x);
 
+    // The run's rocking width (common/StillsRunWidth.h): the three-term formula, which the prediction
+    // window uses, and the table in d* the partiality uses where it is not empty; measured from the
+    // intensity-weighted excitation errors with the reciprocal lattice scaled by radial_scale (the curve's
+    // centre, MeasureRadialScale); empty when the run has too few reflections to measure it.
+    using RunWidth = StillsRunWidth;
+
     // Refine all crystals in place. Returns the mean |dpsi| applied (degrees), for diagnostics.
     // Only the crystals whose cell is close to reference_cell (all without one) are refined and make the
-    // reference: the others are not merged.
+    // reference: the others are not merged. The partiality width is run_width where one is given (the
+    // width the frames were predicted with), else measured here (MeasureRunWidth); the one used is put in
+    // used_width where that is given.
     double Run(std::vector<IntegrationOutcome> &outcomes, size_t nthreads,
-               const std::optional<UnitCell> &reference_cell) const;
-
-    // The run's rocking width, sigma^2 = gamma0^2 + (gamma_e d*)^2 + (bandwidth_sigma |q_z|)^2 (1/A, rad,
-    // relative), measured from the intensity-weighted excitation errors; empty when the run has too
-    // few reflections to measure it.
-    struct RunWidth {
-        double gamma0, gamma_e, bandwidth_sigma;
-    };
+               const std::optional<UnitCell> &reference_cell,
+               const std::optional<RunWidth> &run_width = std::nullopt,
+               std::optional<RunWidth> *used_width = nullptr) const;
+    // window: the width the frames were predicted through (|dist_ewald| <= k times its formula at the
+    // reflection's d*), where they were; without one each frame's window is taken as the largest excitation
+    // error it predicted.
     std::optional<RunWidth> MeasureRunWidth(const std::vector<IntegrationOutcome> &outcomes,
-                                            const std::optional<UnitCell> &reference_cell) const;
+                                            const std::optional<UnitCell> &reference_cell,
+                                            double radial_scale = 1.0,
+                                            const RunWidth *window = nullptr) const;
+
+    // The run's radial scale of the reciprocal lattice (a wavelength or cell scale the spot positions cannot
+    // see), measured from where the rocking curve is centred against d*^2: one step from radial_scale, so
+    // call it a few times. Returns radial_scale unchanged when the run has too few reflections.
+    double MeasureRadialScale(const std::vector<IntegrationOutcome> &outcomes,
+                              const std::optional<UnitCell> &reference_cell, double radial_scale) const;
 
 private:
     const DiffractionExperiment experiment_;
@@ -72,5 +87,5 @@ private:
     // Refine one crystal against the reference map; returns |dpsi| in degrees (0 if skipped).
     double RefineOne(IntegrationOutcome &outcome,
                      const std::map<HKLKey, double> &reference,
-                     const std::optional<RunWidth> &run_width) const;
+                     const std::optional<RunWidth> &run_width, double radial_scale) const;
 };
diff --git a/image_analysis/structure_refinement/CMakeLists.txt b/image_analysis/structure_refinement/CMakeLists.txt
index 62ac58f77..d9cf337f4 100644
--- a/image_analysis/structure_refinement/CMakeLists.txt
+++ b/image_analysis/structure_refinement/CMakeLists.txt
@@ -16,7 +16,52 @@ ADD_LIBRARY(JFJochStructureRefinement STATIC
         $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:ModelStructureFactorsGPU.cu>
         ModelStructureFactorsGPU.h ModelStructureFactorsGPUEngine.h
         $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:ModelScaleGPU.cu> ModelScaleGPU.h
-        SigmaA.cpp SigmaA.h)
+        SigmaA.cpp SigmaA.h
+        MonomerLibrary.cpp MonomerLibrary.h
+        RefinementMath.h RefinementMinimiser.h
+        RefinementRestraints.cpp RefinementRestraints.h
+        RefinementXray.cpp RefinementXray.h
+        Refinement.cpp Refinement.h
+        DensityBlobs.cpp DensityBlobs.h
+        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:RefinementGPU.cpp>
+        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:RefinementGPU.cu>
+        RefinementGPU.h RefinementGPUEngine.h
+        ${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp)
+
+# The subset of the CCP4 Monomer Library that refinement restrains with (monomers/, chosen by
+# monomers/update_monomers.py), carried in the binary so that nothing is read from disk: every .cif of the
+# directory as a string, cut into pieces of at most 12000 characters - under the 16380 a single literal may
+# hold with MSVC - which MonomerLibrary.cpp joins again. A .cif added or edited re-runs the configure.
+FILE(GLOB MONOMER_CIFS ${CMAKE_CURRENT_SOURCE_DIR}/monomers/*.cif)
+SET_PROPERTY(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS ${MONOMER_CIFS} ${CMAKE_CURRENT_SOURCE_DIR}/monomers)
+SET(monomer_source "// Generated from image_analysis/structure_refinement/monomers by its CMakeLists.txt - do not edit.\n")
+STRING(APPEND monomer_source "#include \"MonomerLibrary.h\"\n\n")
+SET(monomer_table "")
+SET(monomer_count 0)
+FOREACH(cif ${MONOMER_CIFS})
+    GET_FILENAME_COMPONENT(cif_name ${cif} NAME)
+    FILE(READ ${cif} text)
+    STRING(LENGTH "${text}" text_length)
+    SET(pieces "")
+    SET(n_pieces 0)
+    SET(offset 0)
+    WHILE(offset LESS text_length)
+        STRING(SUBSTRING "${text}" ${offset} 12000 piece)
+        STRING(APPEND pieces "R\"MONLIB(${piece})MONLIB\",\n")
+        MATH(EXPR offset "${offset} + 12000")
+        MATH(EXPR n_pieces "${n_pieces} + 1")
+    ENDWHILE()
+    STRING(APPEND monomer_source "static const char *const file_${monomer_count}[] = {\n${pieces}};\n")
+    STRING(APPEND monomer_table "    {\"${cif_name}\", file_${monomer_count}, ${n_pieces}},\n")
+    MATH(EXPR monomer_count "${monomer_count} + 1")
+ENDFOREACH()
+STRING(APPEND monomer_source "\nextern const EmbeddedMonomerFile embedded_monomer_files[] = {\n${monomer_table}};\n")
+STRING(APPEND monomer_source "extern const size_t embedded_monomer_file_count = ${monomer_count};\n")
+# Written only when it changed, so a configure does not rebuild the library.
+FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp.tmp "${monomer_source}")
+CONFIGURE_FILE(${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp.tmp
+               ${CMAKE_CURRENT_BINARY_DIR}/MonomerLibraryData.cpp COPYONLY)
+TARGET_INCLUDE_DIRECTORIES(JFJochStructureRefinement PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
 
 # JFJochIndexing for CUDAMemHelpers.h and, under CUDA, to put cuFFT (RigidBodyGPU.cu) after these
 # objects on the link line.
diff --git a/image_analysis/structure_refinement/DensityBlobs.cpp b/image_analysis/structure_refinement/DensityBlobs.cpp
new file mode 100644
index 000000000..b2a9b7fb9
--- /dev/null
+++ b/image_analysis/structure_refinement/DensityBlobs.cpp
@@ -0,0 +1,131 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "DensityBlobs.h"
+
+#include <algorithm>
+#include <cmath>
+
+#include "gemmi/blob.hpp"
+#include "gemmi/neighbor.hpp"
+
+namespace {
+
+constexpr double CUTOFF_SIGMA = 3.0;
+constexpr double PEAK_SIGMA = 4.0;
+// Closer than this to a model atom, the density is the model's own atom out of place.
+constexpr double MODEL_ERROR_DISTANCE = 1.6;
+// Waters and ions sit at least this far from the model's atoms.
+constexpr double CONTACT_MIN = 2.2;
+// An ion's peak, in sigma, where the anomalous map gives no help (with two metal-like contacts); an anomalous
+// peak this high says heavier than water on its own.
+constexpr double ION_PEAK_SIGMA = 8.0;
+constexpr double ION_ANOMALOUS_SIGMA = 4.0;
+// The smallest blob called ligand-like, A^3, and at low resolution one and a half of the resolution's spheres: at
+// high resolution a strong single atom's blob already spans several of them.
+constexpr double LIGAND_MIN_VOLUME = 8.0;
+
+bool Polar(const gemmi::Element &el) {
+    return el == gemmi::El::N || el == gemmi::El::O;
+}
+
+}  // namespace
+
+const char *DensityBlobKindName(DensityBlob::Kind kind) {
+    switch (kind) {
+        case DensityBlob::Kind::Water: return "WATER";
+        case DensityBlob::Kind::Ion: return "ION";
+        case DensityBlob::Kind::Ligand: return "LIGAND";
+        case DensityBlob::Kind::ModelError: return "MODEL_ERROR";
+        case DensityBlob::Kind::Unassigned: break;
+    }
+    return "UNASSIGNED";
+}
+
+DensityBlobsMessage DensityBlobsToMessage(const std::vector<DensityBlob> &blobs) {
+    DensityBlobsMessage m;
+    for (const DensityBlob &b : blobs) {
+        m.kind.emplace_back(DensityBlobKindName(b.kind));
+        m.x.push_back(b.centroid.x);
+        m.y.push_back(b.centroid.y);
+        m.z.push_back(b.centroid.z);
+        m.peak_sigma.push_back(b.peak_sigma);
+        m.volume.push_back(b.volume);
+        m.score.push_back(b.score);
+        m.nearest_atom.push_back(b.nearest_atom);
+        m.nearest_atom_distance.push_back(b.nearest_atom_distance);
+        m.polar_contacts.push_back(b.polar_contacts);
+        m.metal_contacts.push_back(b.metal_contacts);
+        m.anomalous_sigma.push_back(b.anomalous_sigma);
+    }
+    return m;
+}
+
+// Following Coot's unmodelled blobs, Emsley et al. (2010) Acta Cryst. D66, 486-501
+std::vector<DensityBlob> FindDensityBlobs(const gemmi::Grid<float> &difference, double rms, const gemmi::Structure &model,
+                                          double d_min, const gemmi::Grid<float> *anomalous, double anomalous_rms) {
+    std::vector<DensityBlob> out;
+    if (!(rms > 0) || model.models.empty())
+        return out;
+    gemmi::Grid<float> map = difference;
+    for (float &v : map.data)
+        v = static_cast<float>(v / rms);
+    gemmi::BlobCriteria criteria;
+    criteria.cutoff = CUTOFF_SIGMA;
+    criteria.min_volume = 0.0;
+    criteria.min_score = 0.0;
+    criteria.min_peak = PEAK_SIGMA;
+    const std::vector<gemmi::Blob> blobs = gemmi::find_blobs_by_flood_fill(map, criteria);
+
+    gemmi::Model copy = model.models[0];
+    gemmi::UnitCell cell = map.unit_cell;
+    cell.set_cell_images_from_spacegroup(map.spacegroup);
+    gemmi::NeighborSearch ns(copy, cell, 5.0);
+    ns.populate(false);
+    // A single atom's blob at this resolution: a sphere of half the resolution's radius.
+    const double atom_volume = 4.0 / 3.0 * 3.14159265358979 * std::pow(0.5 * d_min, 3);
+
+    for (const gemmi::Blob &b : blobs) {
+        DensityBlob d;
+        d.peak_sigma = b.peak_value;
+        d.volume = b.volume;
+        d.score = b.score;
+        d.centroid = b.centroid;
+        // the copy of the blob beside the atom nearest to it
+        if (gemmi::NeighborSearch::Mark *m = ns.find_nearest_atom(b.centroid, 12.0)) {
+            const gemmi::CRA cra = m->to_cra(copy);
+            const gemmi::FTransform t = ns.get_image_transformation(m->image_idx);
+            const gemmi::Fractional fc = cell.fractionalize(b.centroid);
+            const gemmi::Fractional fi = t.apply(cell.fractionalize(cra.atom->pos));
+            const gemmi::Fractional shifted(fc.x - std::round(fc.x - fi.x), fc.y - std::round(fc.y - fi.y),
+                                            fc.z - std::round(fc.z - fi.z));
+            d.centroid = cell.orthogonalize(gemmi::FTransform(t.inverse()).apply(shifted));
+            d.nearest_atom_distance = d.centroid.dist(cra.atom->pos);
+            d.nearest_atom = cra.atom->name + " " + cra.residue->name + " " + cra.chain->name +
+                             cra.residue->seqid.str();
+        } else
+            d.nearest_atom_distance = INFINITY;
+        ns.for_each(d.centroid, '\0', 3.4, [&](gemmi::NeighborSearch::Mark &m, double dist_sq) {
+            const double r = std::sqrt(dist_sq);
+            if (Polar(m.element) && r >= 2.4)
+                d.polar_contacts++;
+            if ((Polar(m.element) || m.element == gemmi::El::S) && r >= 1.8 && r <= 2.6)
+                d.metal_contacts++;
+        });
+        if (anomalous != nullptr && anomalous_rms > 0)
+            d.anomalous_sigma = anomalous->interpolate_value(b.peak_pos) / anomalous_rms;
+
+        if (d.nearest_atom_distance < MODEL_ERROR_DISTANCE)
+            d.kind = DensityBlob::Kind::ModelError;
+        else if (d.nearest_atom_distance >= 1.8 &&
+                 (d.anomalous_sigma >= ION_ANOMALOUS_SIGMA || (d.metal_contacts >= 2 && d.peak_sigma >= ION_PEAK_SIGMA)))
+            d.kind = DensityBlob::Kind::Ion;
+        else if (d.volume > std::max(1.5 * atom_volume, LIGAND_MIN_VOLUME) && d.nearest_atom_distance >= CONTACT_MIN)
+            d.kind = DensityBlob::Kind::Ligand;
+        else if (d.nearest_atom_distance >= CONTACT_MIN && d.polar_contacts >= 1)
+            d.kind = DensityBlob::Kind::Water;
+        out.push_back(d);
+    }
+    std::sort(out.begin(), out.end(), [](const DensityBlob &a, const DensityBlob &b) { return a.score > b.score; });
+    return out;
+}
diff --git a/image_analysis/structure_refinement/DensityBlobs.h b/image_analysis/structure_refinement/DensityBlobs.h
new file mode 100644
index 000000000..499aa37af
--- /dev/null
+++ b/image_analysis/structure_refinement/DensityBlobs.h
@@ -0,0 +1,46 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include "gemmi/grid.hpp"
+#include "gemmi/model.hpp"
+
+#include "../../common/JFJochMessages.h"
+
+// What a model leaves unexplained: the connected regions of positive mFo-DFc density above a cutoff ("blobs"),
+// each placed beside the model, measured and given a likely reading - a water, an ion, something ligand-sized,
+// or an error of the model itself (a misplaced or missing atom, an alternative conformation).
+//
+// The readings are rules on what is measured, meant to point a person at the density, not to identify a
+// compound: a blob called LIGAND is density of ligand size and shape where the model has nothing, which a
+// buffer molecule or an unmodelled side chain can be as well as the compound that was soaked.
+struct DensityBlob {
+    enum class Kind { Water, Ion, Ligand, ModelError, Unassigned };
+    Kind kind = Kind::Unassigned;
+    gemmi::Position centroid;        // the copy nearest the model
+    double peak_sigma = 0;           // the highest point, in the map's rms
+    double volume = 0;               // A^3 above the cutoff
+    double score = 0;                // the density above the cutoff integrated, sigma A^3
+    double nearest_atom_distance = 0;
+    std::string nearest_atom;        // e.g. "OG1 THR A42"
+    int polar_contacts = 0;          // N or O of the model at 2.4-3.4 A
+    int metal_contacts = 0;          // N, O or S of the model at 1.8-2.6 A
+    double anomalous_sigma = 0;      // the anomalous difference map at the peak, 0 where there is none
+};
+
+const char *DensityBlobKindName(DensityBlob::Kind kind);
+
+// The blobs as the end message carries them to the writer, for <prefix>_blobs.json.
+DensityBlobsMessage DensityBlobsToMessage(const std::vector<DensityBlob> &blobs);
+
+// The blobs of `difference` (an mFo-DFc map of the whole cell, rms `rms`) above 3 sigma that peak above 4 sigma,
+// strongest (by score) first. `model`: what the map was made from, in the map's cell. `anomalous`: the anomalous
+// difference map on any grid of the same cell, or null. Following the flood fill of Coot's unmodelled blobs as
+// gemmi implements it (find_blobs_by_flood_fill).
+std::vector<DensityBlob> FindDensityBlobs(const gemmi::Grid<float> &difference, double rms, const gemmi::Structure &model,
+                                          double d_min, const gemmi::Grid<float> *anomalous = nullptr,
+                                          double anomalous_rms = 0);
diff --git a/image_analysis/structure_refinement/ModelDensityGPU.cu b/image_analysis/structure_refinement/ModelDensityGPU.cu
index 30bd7dd38..a60879d06 100644
--- a/image_analysis/structure_refinement/ModelDensityGPU.cu
+++ b/image_analysis/structure_refinement/ModelDensityGPU.cu
@@ -4,6 +4,7 @@
 #include "ModelDensityGPU.h"
 
 #include <algorithm>
+#include <climits>
 #include <cmath>
 
 #include <cub/cub.cuh>
@@ -21,6 +22,7 @@ constexpr int BRICK = 8;                  // the gather's bricks are BRICK^3 gri
 constexpr int GATHER_TILE = 128;           // atoms staged in shared memory at a time
 constexpr int MAX_BRICKS_PER_AXIS = 16;   // an atom's box touches at most this many bricks along an axis
 constexpr int THREADS = 256;
+constexpr int SORT_ATOMS = 4096;          // a brick's atoms are sorted in shared memory up to this many
 
 __device__ __forceinline__ int imod(int a, int n) {
     const int r = a % n;
@@ -64,58 +66,97 @@ __device__ void atom_bricks(const float4 &pos, const int *box, int nu, int nv, i
     nbw = axis_bricks(__float2int_rn(pos.z), box[2], nw, bw);
 }
 
-__global__ void count_pairs_kernel(const float4 *pos, const int *box, int n, int nu, int nv, int nw, int *count,
-                                   int *overflow) {
+// How many atoms touch each brick: integer atomics, whose sum does not depend on their order.
+__global__ void count_bricks_kernel(const float4 *pos, const int *box, int n, int nu, int nv, int nw, int *brick_count) {
     const int i = blockIdx.x * blockDim.x + threadIdx.x;
-    if (i > n)
+    if (i >= n)
         return;
-    if (i == n) {
-        count[n] = 0;   // so the exclusive scan's last entry is the total
-        return;
-    }
     int bu[MAX_BRICKS_PER_AXIS], bv[MAX_BRICKS_PER_AXIS], bw[MAX_BRICKS_PER_AXIS], a, b, c;
     atom_bricks(pos[i], box + 3 * i, nu, nv, nw, bu, a, bv, b, bw, c);
-    if (a < 0 || b < 0 || c < 0) {
-        *overflow = 1;
-        a = b = c = 0;
-    }
-    count[i] = a * b * c;
+    const int nbu = (nu + BRICK - 1) / BRICK, nbv = (nv + BRICK - 1) / BRICK;
+    for (int k = 0; k < c; k++)
+        for (int j = 0; j < b; j++)
+            for (int l = 0; l < a; l++)
+                atomicAdd(brick_count + bu[l] + nbu * (bv[j] + nbv * bw[k]), 1);
 }
 
-// The (brick, atom) pairs, atom-major: sorted stably by brick, each brick's atoms stay in model order.
-__global__ void fill_pairs_kernel(const float4 *pos, const int *box, int n, int nu, int nv, int nw,
-                                  const int *offset, int *key, int *value) {
+// Each atom into the segments of the bricks it touches, at whatever place in the segment the atomic hands out:
+// the order within a brick is settled by order_bricks_kernel.
+__global__ void fill_bricks_kernel(const float4 *pos, const int *box, int n, int nu, int nv, int nw,
+                                   const int *brick_start, int *brick_fill, int *pair_atom) {
     const int i = blockIdx.x * blockDim.x + threadIdx.x;
     if (i >= n)
         return;
     int bu[MAX_BRICKS_PER_AXIS], bv[MAX_BRICKS_PER_AXIS], bw[MAX_BRICKS_PER_AXIS], a, b, c;
     atom_bricks(pos[i], box + 3 * i, nu, nv, nw, bu, a, bv, b, bw, c);
     const int nbu = (nu + BRICK - 1) / BRICK, nbv = (nv + BRICK - 1) / BRICK;
-    int o = offset[i];
     for (int k = 0; k < c; k++)
         for (int j = 0; j < b; j++)
             for (int l = 0; l < a; l++) {
-                key[o] = bu[l] + nbu * (bv[j] + nbv * bw[k]);
-                value[o] = i;
-                o++;
+                const int brick = bu[l] + nbu * (bv[j] + nbv * bw[k]);
+                pair_atom[brick_start[brick] + atomicAdd(brick_fill + brick, 1)] = i;
             }
 }
 
-__global__ void brick_ranges_kernel(const int *key, int npairs, int *start, int *end) {
-    const int i = blockIdx.x * blockDim.x + threadIdx.x;
-    if (i >= npairs)
+// Each brick's atoms into model order, one block per brick: a bitonic sort of the segment in shared memory,
+// padded to a power of two, for the bricks of up to SORT_ATOMS atoms. A larger brick is ranked instead: an
+// atom's place is the number of the brick's atoms with a lower index (an atom is in a brick once), counted
+// against the segment staged a tile at a time, a pair staying with one thread through the tiles.
+__global__ void order_bricks_kernel(const int *unordered, const int *brick_start, int *rank, int *pair_atom) {
+    const int brick = blockIdx.x;
+    const int s = brick_start[brick], e = brick_start[brick + 1], k = e - s;
+    __shared__ int keys[SORT_ATOMS];
+    if (k <= SORT_ATOMS) {
+        int n = 1;
+        while (n < k)
+            n <<= 1;
+        for (int t = threadIdx.x; t < n; t += THREADS)
+            keys[t] = t < k ? unordered[s + t] : INT_MAX;
+        __syncthreads();
+        for (int size = 2; size <= n; size <<= 1)
+            for (int stride = size >> 1; stride > 0; stride >>= 1) {
+                for (int t = threadIdx.x; t < n / 2; t += THREADS) {
+                    const int i = 2 * t - (t & (stride - 1)), j = i + stride;
+                    const int a = keys[i], b = keys[j];
+                    if ((a > b) == ((i & size) == 0)) {
+                        keys[i] = b;
+                        keys[j] = a;
+                    }
+                }
+                __syncthreads();
+            }
+        for (int t = threadIdx.x; t < k; t += THREADS)
+            pair_atom[s + t] = keys[t];
         return;
-    const int k = key[i];
-    if (i == 0 || key[i - 1] != k)
-        start[k] = i;
-    if (i == npairs - 1 || key[i + 1] != k)
-        end[k] = i + 1;
+    }
+    for (int c = s; c < e; c += THREADS) {
+        const int m = min(THREADS, e - c);
+        __syncthreads();
+        if (threadIdx.x < m)
+            keys[threadIdx.x] = unordered[c + threadIdx.x];
+        __syncthreads();
+        for (int p = s + threadIdx.x; p < e; p += THREADS) {
+            const int atom = unordered[p];
+            int below = 0;
+            for (int q = 0; q < m; q++)
+                below += keys[q] < atom;
+            rank[p] = (c == s ? 0 : rank[p]) + below;
+        }
+    }
+    for (int p = s + threadIdx.x; p < e; p += THREADS)
+        pair_atom[s + rank[p]] = unordered[p];
 }
 
-// An atom's box as the gather tests it: its first point, unwrapped (c - d) and wrapped into the grid, and its
-// width less one (2 d), along each axis; and its centre in grid units.
-struct GatherBox {
-    int lo[3], first[3], span[3];
+// What the gather needs of one staged atom: its isotropic Gaussians (an anisotropic atom's matrices are read
+// from the atoms in global memory), and its box as the brick sees it - a bit per point of the brick along each
+// axis for whether the point is in the box, and for the points that are, what gemmi's box offset makes of them:
+// the point's unwrapped box index is base + t, less n where t reaches wrap.
+struct GatherAtom {
+    float a[5], b[5];
+    float occ, max_r2;
+    int index, aniso;
+    int masks;         // bits 0-7: u, 8-15: v, 16-23: w
+    int base[3], wrap[3];
     float nctr[3];
 };
 
@@ -137,51 +178,61 @@ __global__ void gather_kernel(const ModelDensityAtom *atoms, const float4 *pos,
     const int nbu = (g.nu + BRICK - 1) / BRICK, nbv = (g.nv + BRICK - 1) / BRICK;
     const int brick = blockIdx.x;
     const int s = brick_start[brick], e = brick_end[brick];   // s == e: an empty brick, written as zeros
-    const int u = (brick % nbu) * BRICK + threadIdx.x, v = (brick / nbu % nbv) * BRICK + threadIdx.y,
-              w = (brick / (nbu * nbv)) * BRICK + threadIdx.z;
+    const int origin[3] = {(brick % nbu) * BRICK, (brick / nbu % nbv) * BRICK, (brick / (nbu * nbv)) * BRICK};
+    const int tu = threadIdx.x, tv = threadIdx.y, tw = threadIdx.z;
+    const int u = origin[0] + tu, v = origin[1] + tv, w = origin[2] + tw;
     const bool inside = u < g.nu && v < g.nv && w < g.nw;
-    const int tid = threadIdx.x + BRICK * (threadIdx.y + BRICK * threadIdx.z);
+    const int tid = tu + BRICK * (tv + BRICK * tw);
     const int n3[3] = {g.nu, g.nv, g.nw};
 
-    constexpr int WORDS = sizeof(ModelDensityAtom) / sizeof(int);
-    __shared__ int sh_index[GATHER_TILE];
-    __shared__ ModelDensityAtom sh_atom[GATHER_TILE];
-    __shared__ GatherBox sh_box[GATHER_TILE];
+    __shared__ GatherAtom sh[GATHER_TILE];
     float acc = 0.0f;
     for (int c = s; c < e; c += GATHER_TILE) {
         const int m = min(GATHER_TILE, e - c);
         __syncthreads();
         if (tid < m) {
             const int a = pair_atom[c + tid];
-            sh_index[tid] = a;
+            const ModelDensityAtom &at = atoms[a];
             const float4 p = pos[a];
             const float nctr[3] = {p.x, p.y, p.z};
-            GatherBox &b = sh_box[tid];
+            GatherAtom &r = sh[tid];
+            for (int q = 0; q < 5; q++) {
+                r.a[q] = at.a[q];
+                r.b[q] = at.b[q][0];
+            }
+            r.occ = at.occ;
+            r.max_r2 = at.max_r2;
+            r.index = a;
+            r.aniso = at.aniso;
+            r.masks = 0;
             for (int k = 0; k < 3; k++) {
                 const int d = box[3 * a + k];
-                b.lo[k] = __float2int_rn(nctr[k]) - d;
-                b.first[k] = imod(b.lo[k], n3[k]);
-                b.span[k] = 2 * d;
-                b.nctr[k] = nctr[k];
+                const int lo = __float2int_rn(nctr[k]) - d, first = imod(lo, n3[k]), span = 2 * d;
+                const int m0 = box_offset(origin[k], first, n3[k]);
+                for (int t = 0; t < BRICK; t++) {
+                    const int mt = m0 + t;
+                    if ((mt < n3[k] ? mt : mt - n3[k]) <= span)
+                        r.masks |= 1 << (8 * k + t);
+                }
+                r.base[k] = lo + m0;
+                r.wrap[k] = n3[k] - m0;
+                r.nctr[k] = nctr[k];
             }
         }
         __syncthreads();
-        for (int i = tid; i < m * WORDS; i += BRICK * BRICK * BRICK)
-            reinterpret_cast<int *>(sh_atom)[i] = reinterpret_cast<const int *>(atoms + sh_index[i / WORDS])[i % WORDS];
-        __syncthreads();
         if (!inside)
             continue;
         for (int k = 0; k < m; k++) {
-            const GatherBox &b = sh_box[k];
-            const int mu = box_offset(u, b.first[0], g.nu), mv = box_offset(v, b.first[1], g.nv),
-                      mw = box_offset(w, b.first[2], g.nw);
-            if (mu > b.span[0] || mv > b.span[1] || mw > b.span[2])
+            const GatherAtom &at = sh[k];
+            if (!((at.masks >> tu) & (at.masks >> (8 + tv)) & (at.masks >> (16 + tw)) & 1))
                 continue;
-            const ModelDensityAtom &at = sh_atom[k];
+            const int pu = at.base[0] + tu - (tu >= at.wrap[0] ? g.nu : 0);
+            const int pv = at.base[1] + tv - (tv >= at.wrap[1] ? g.nv : 0);
+            const int pw = at.base[2] + tw - (tw >= at.wrap[2] ? g.nw : 0);
             // f = centre - (u, v, w) in the box's own (unwrapped) indices, then in A, as the CPU walks it
-            const float fx = b.nctr[0] - static_cast<float>(b.lo[0] + mu);
-            const float fy = b.nctr[1] - static_cast<float>(b.lo[1] + mv);
-            const float fz = b.nctr[2] - static_cast<float>(b.lo[2] + mw);
+            const float fx = at.nctr[0] - static_cast<float>(pu);
+            const float fy = at.nctr[1] - static_cast<float>(pv);
+            const float fz = at.nctr[2] - static_cast<float>(pw);
             const float z = g.m22 * fz;
             const float y = g.m11 * fy + g.m12 * fz;
             const float yz = y * y + z * z;
@@ -192,10 +243,10 @@ __global__ void gather_kernel(const ModelDensityAtom *atoms, const float4 *pos,
             float density = 0.0f;
             if (!at.aniso) {
                 for (int q = 0; q < 5; q++)
-                    density += at.a[q] * expapprox(fmaxf(at.b[q][0] * r2, -88.f));
+                    density += at.a[q] * expapprox(fmaxf(at.b[q] * r2, -88.f));
             } else {
                 for (int q = 0; q < 5; q++) {
-                    const float *bq = at.b[q];
+                    const float *bq = atoms[at.index].b[q];
                     // gemmi's SMat33::r_u_r(), in its order
                     const float rur = x * x * bq[0] + y * y * bq[1] + z * z * bq[2] +
                                       2 * (x * y * bq[3] + x * z * bq[4] + y * z * bq[5]);
@@ -213,15 +264,12 @@ int blocks(size_t n) {
     return static_cast<int>((n + THREADS - 1) / THREADS);
 }
 
-// cub's temporary storage for the pair scan and sort at the capacity.
-size_t CubBytes(size_t atoms, size_t pairs) {
-    size_t scan = 0, sort = 0;
+// cub's temporary storage for the scan over the bricks.
+size_t CubBytes(size_t bricks) {
+    size_t scan = 0;
     cuda_err(cub::DeviceScan::ExclusiveSum(nullptr, scan, static_cast<int *>(nullptr), static_cast<int *>(nullptr),
-                                           static_cast<int>(atoms + 1)));
-    cuda_err(cub::DeviceRadixSort::SortPairs(nullptr, sort, static_cast<int *>(nullptr), static_cast<int *>(nullptr),
-                                             static_cast<int *>(nullptr), static_cast<int *>(nullptr),
-                                             static_cast<int>(pairs)));
-    return std::max(scan, sort);
+                                           static_cast<int>(bricks + 1)));
+    return scan;
 }
 
 }  // namespace
@@ -238,24 +286,27 @@ size_t ModelDensityGPU::Bricks(int nu, int nv, int nw) {
     return static_cast<size_t>((nu + BRICK - 1) / BRICK) * ((nv + BRICK - 1) / BRICK) * ((nw + BRICK - 1) / BRICK);
 }
 
-std::vector<int> ModelDensityGPU::Boxes(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms) {
+void ModelDensityGPU::Boxes(const ModelDensityGrid &grid, const ModelDensityAtom *atoms, size_t n, int *box) {
     const int n3[3] = {grid.nu, grid.nv, grid.nw};
     double spacing[3];
     for (int k = 0; k < 3; k++)
         spacing[k] = 1.0 / (n3[k] * std::sqrt(grid.frac[3 * k] * grid.frac[3 * k] + grid.frac[3 * k + 1] * grid.frac[3 * k + 1] +
                                               grid.frac[3 * k + 2] * grid.frac[3 * k + 2]));
-    std::vector<int> box(3 * atoms.size());
-    for (size_t i = 0; i < atoms.size(); i++)
+    for (size_t i = 0; i < n; i++)
         for (int k = 0; k < 3; k++)
             box[3 * i + k] = static_cast<int>(std::ceil(atoms[i].radius / spacing[k]));
+}
+
+std::vector<int> ModelDensityGPU::Boxes(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms) {
+    std::vector<int> box(3 * atoms.size());
+    Boxes(grid, atoms.data(), atoms.size(), box.data());
     return box;
 }
 
-size_t ModelDensityGPU::PairBound(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms) {
-    const std::vector<int> box = Boxes(grid, atoms);
+size_t ModelDensityGPU::PairBound(const ModelDensityGrid &grid, const int *box, size_t n) {
     const int n3[3] = {grid.nu, grid.nv, grid.nw};
     size_t pairs = 0;
-    for (size_t i = 0; i < atoms.size(); i++) {
+    for (size_t i = 0; i < n; i++) {
         size_t product = 1;
         for (int k = 0; k < 3; k++)
             product *= AxisBrickBound(box[3 * i + k], n3[k]);
@@ -264,48 +315,63 @@ size_t ModelDensityGPU::PairBound(const ModelDensityGrid &grid, const std::vecto
     return pairs;
 }
 
-bool ModelDensityGPU::Supports(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms) {
+size_t ModelDensityGPU::PairBound(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms) {
     const std::vector<int> box = Boxes(grid, atoms);
+    return PairBound(grid, box.data(), atoms.size());
+}
+
+bool ModelDensityGPU::Supports(const ModelDensityGrid &grid, const int *box, size_t n) {
     const int n3[3] = {grid.nu, grid.nv, grid.nw};
-    for (size_t i = 0; i < box.size(); i++)
+    for (size_t i = 0; i < 3 * n; i++)
         if (2 * box[i] + 1 > n3[i % 3] || AxisBrickBound(box[i], n3[i % 3]) > MAX_BRICKS_PER_AXIS)
             return false;
     return true;
 }
 
+bool ModelDensityGPU::Supports(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms) {
+    const std::vector<int> box = Boxes(grid, atoms);
+    return Supports(grid, box.data(), atoms.size());
+}
+
 size_t ModelDensityGPU::DeviceBytes(size_t max_atoms, size_t max_pairs, size_t max_bricks) {
-    const size_t na = max_atoms + 1;
-    return na * (sizeof(ModelDensityAtom) + 3 * sizeof(int) + 2 * sizeof(int)) + 4 * max_pairs * sizeof(int) +
-           2 * max_bricks * sizeof(int) + CubBytes(na, max_pairs + 1);
+    const size_t na = max_atoms + 1, nb = max_bricks + 1;
+    return na * (sizeof(ModelDensityAtom) + 3 * sizeof(int)) + 3 * max_pairs * sizeof(int) + 3 * nb * sizeof(int) +
+           CubBytes(nb);
 }
 
 ModelDensityGPU::ModelDensityGPU(cudaStream_t stream, size_t max_atoms_, size_t max_pairs_, size_t max_bricks_)
     : stream(stream), max_atoms(max_atoms_), max_pairs(max_pairs_), max_bricks(max_bricks_) {
     const auto sync = CudaAlloc::Synchronous;
-    const size_t na = std::max<size_t>(max_atoms, 1), np = std::max<size_t>(max_pairs, 1),
-                 nb = std::max<size_t>(max_bricks, 1);
+    const size_t na = std::max<size_t>(max_atoms, 1), np = std::max<size_t>(max_pairs, 1), nb = max_bricks + 1;
     atoms = CudaDevicePtr<ModelDensityAtom>(na, sync);
     box = CudaDevicePtr<int>(3 * na, sync);
-    overflow = CudaDevicePtr<int>(1, sync);
-    count = CudaDevicePtr<int>(na + 1, sync);
-    offset = CudaDevicePtr<int>(na + 1, sync);
-    key = CudaDevicePtr<int>(np, sync);
-    value = CudaDevicePtr<int>(np, sync);
-    key_sorted = CudaDevicePtr<int>(np, sync);
-    value_sorted = CudaDevicePtr<int>(np, sync);
+    brick_count = CudaDevicePtr<int>(nb, sync);
     brick_start = CudaDevicePtr<int>(nb, sync);
-    brick_end = CudaDevicePtr<int>(nb, sync);
-    cub_bytes = CubBytes(na, np);
+    brick_fill = CudaDevicePtr<int>(nb, sync);
+    unordered = CudaDevicePtr<int>(np, sync);
+    rank = CudaDevicePtr<int>(np, sync);
+    pair_atom = CudaDevicePtr<int>(np, sync);
+    cub_bytes = CubBytes(nb);
     cub_temp = CudaDevicePtr<char>(std::max<size_t>(cub_bytes, 1), sync);
+    host_box = CudaHostPtr<int>(3 * na);
 }
 
 void ModelDensityGPU::SetAtoms(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atom_list) {
-    if (atom_list.size() > max_atoms || Bricks(grid.nu, grid.nv, grid.nw) > max_bricks)
+    SetAtoms(grid, atom_list.data(), atom_list.size());
+}
+
+void ModelDensityGPU::SetAtoms(const ModelDensityGrid &grid, const ModelDensityAtom *atom_list, size_t n) {
+    if (n > max_atoms || Bricks(grid.nu, grid.nv, grid.nw) > max_bricks)
         throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "model density: grid or atoms over the reserve");
+    // The boxes into the pinned staging buffer, so that their copy and the atoms' (pinned where the caller keeps
+    // them so) go up by DMA instead of through the driver's staging of pageable memory.
+    Boxes(grid, atom_list, n, host_box);
     // An atom whose box is wider than the cell would reach a point through more than one image, which
     // gemmi's box walk adds and the gather's box test does not; such a cell is left to the CPU.
-    if (!Supports(grid, atom_list))
+    if (!Supports(grid, host_box, n))
         throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "model density: an atom wider than the cell");
+    if (PairBound(grid, host_box, n) > max_pairs)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "model density: gather pairs over the reserve");
     geom.nu = grid.nu;
     geom.nv = grid.nv;
     geom.nw = grid.nw;
@@ -317,50 +383,37 @@ void ModelDensityGPU::SetAtoms(const ModelDensityGrid &grid, const std::vector<M
     geom.m11 = static_cast<float>(grid.orth[4] * inv_n[1]);
     geom.m12 = static_cast<float>(grid.orth[5] * inv_n[2]);
     geom.m22 = static_cast<float>(grid.orth[8] * inv_n[2]);
-    const std::vector<int> b = Boxes(grid, atom_list);
-    n_atoms = static_cast<int>(atom_list.size());
+    n_atoms = static_cast<int>(n);
     if (n_atoms > 0) {
-        cuda_err(cudaMemcpyAsync(atoms, atom_list.data(), atom_list.size() * sizeof(ModelDensityAtom),
-                                 cudaMemcpyHostToDevice, stream));
-        cuda_err(cudaMemcpyAsync(box, b.data(), b.size() * sizeof(int), cudaMemcpyHostToDevice, stream));
+        cuda_err(cudaMemcpyAsync(atoms, atom_list, n * sizeof(ModelDensityAtom), cudaMemcpyHostToDevice, stream));
+        cuda_err(cudaMemcpyAsync(box, host_box, 3 * n * sizeof(int), cudaMemcpyHostToDevice, stream));
     }
-    // The uploads read host vectors that end with this call.
+    // The uploads read the caller's atoms, which it may change once this returns.
     cuda_err(cudaStreamSynchronize(stream));
 }
 
 void ModelDensityGPU::Compute(const float4 *d_pos, float *d_grid) {
-    cuda_err(cudaMemsetAsync(overflow, 0, sizeof(int), stream));
-    count_pairs_kernel<<<blocks(n_atoms + 1), THREADS, 0, stream>>>(d_pos, box, n_atoms, geom.nu, geom.nv, geom.nw,
-                                                                    count, overflow);
-    cuda_err(cudaGetLastError());
-    size_t temp = cub_bytes;
-    cuda_err(cub::DeviceScan::ExclusiveSum(cub_temp.get(), temp, count.get(), offset.get(), n_atoms + 1, stream));
-    int npairs = 0;
-    int over = 0;
-    cuda_err(cudaMemcpyAsync(&npairs, offset.get() + n_atoms, sizeof(int), cudaMemcpyDeviceToHost, stream));
-    cuda_err(cudaMemcpyAsync(&over, overflow.get(), sizeof(int), cudaMemcpyDeviceToHost, stream));
-    cuda_err(cudaStreamSynchronize(stream));
-    if (over)
-        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "model density: an atom's box over the bricks per axis");
-    if (static_cast<size_t>(npairs) > max_pairs)
-        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "model density: gather pairs over the reserve");
-    fill_pairs_kernel<<<blocks(n_atoms), THREADS, 0, stream>>>(d_pos, box, n_atoms, geom.nu, geom.nv, geom.nw,
-                                                               offset, key, value);
-    cuda_err(cudaGetLastError());
+    // Counted per brick, scanned, filled, and each brick put in model order: nothing comes back to the host, so
+    // the launches queue straight through (and record into a CUDA graph). The bricks' atoms end up as a stable
+    // sort of the atom-major pairs by brick would leave them.
     const int nb = static_cast<int>(Bricks(geom.nu, geom.nv, geom.nw));
-    int bits = 1;
-    while ((1 << bits) < nb)
-        bits++;
-    temp = cub_bytes;
-    cuda_err(cub::DeviceRadixSort::SortPairs(cub_temp.get(), temp, key.get(), key_sorted.get(), value.get(),
-                                             value_sorted.get(), npairs, 0, bits, stream));
-    cuda_err(cudaMemsetAsync(brick_start, 0, nb * sizeof(int), stream));
-    cuda_err(cudaMemsetAsync(brick_end, 0, nb * sizeof(int), stream));
-    if (npairs > 0) {
-        brick_ranges_kernel<<<blocks(npairs), THREADS, 0, stream>>>(key_sorted, npairs, brick_start, brick_end);
+    cuda_err(cudaMemsetAsync(brick_count, 0, (nb + 1) * sizeof(int), stream));
+    cuda_err(cudaMemsetAsync(brick_fill, 0, nb * sizeof(int), stream));
+    if (n_atoms > 0) {
+        count_bricks_kernel<<<blocks(n_atoms), THREADS, 0, stream>>>(d_pos, box, n_atoms, geom.nu, geom.nv, geom.nw,
+                                                                     brick_count);
         cuda_err(cudaGetLastError());
     }
-    gather_kernel<<<nb, dim3(BRICK, BRICK, BRICK), 0, stream>>>(atoms, d_pos, box, value_sorted, brick_start, brick_end,
-                                                                geom, d_grid);
+    size_t temp = cub_bytes;
+    cuda_err(cub::DeviceScan::ExclusiveSum(cub_temp.get(), temp, brick_count.get(), brick_start.get(), nb + 1, stream));
+    if (n_atoms > 0) {
+        fill_bricks_kernel<<<blocks(n_atoms), THREADS, 0, stream>>>(d_pos, box, n_atoms, geom.nu, geom.nv, geom.nw,
+                                                                    brick_start, brick_fill, unordered);
+        cuda_err(cudaGetLastError());
+    }
+    order_bricks_kernel<<<nb, THREADS, 0, stream>>>(unordered, brick_start, rank, pair_atom);
+    cuda_err(cudaGetLastError());
+    gather_kernel<<<nb, dim3(BRICK, BRICK, BRICK), 0, stream>>>(atoms, d_pos, box, pair_atom, brick_start,
+                                                                brick_start.get() + 1, geom, d_grid);
     cuda_err(cudaGetLastError());
 }
diff --git a/image_analysis/structure_refinement/ModelDensityGPU.h b/image_analysis/structure_refinement/ModelDensityGPU.h
index d46941ab7..855ecd4d7 100644
--- a/image_analysis/structure_refinement/ModelDensityGPU.h
+++ b/image_analysis/structure_refinement/ModelDensityGPU.h
@@ -49,23 +49,32 @@ public:
     // gemmi's box around each atom (MakeAtomBox, ModelGrid.cpp): the points within ceil(radius / spacing)
     // of the nearest one along each axis, three per atom.
     static std::vector<int> Boxes(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms);
+    static void Boxes(const ModelDensityGrid &grid, const ModelDensityAtom *atoms, size_t n, int *box);
     // (brick, atom) pairs of the gather over at most.
     static size_t PairBound(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms);
+    static size_t PairBound(const ModelDensityGrid &grid, const int *box, size_t n);
     // Whether the gather reproduces gemmi's box walk on this grid: every atom's box narrower than the cell,
     // so that no point is reached by two images of one atom.
     static bool Supports(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms);
+    static bool Supports(const ModelDensityGrid &grid, const int *box, size_t n);
 
     ModelDensityGPU(cudaStream_t stream, size_t max_atoms, size_t max_pairs, size_t max_bricks);
 
-    // The grid and the atoms' densities. Throws if they are over the capacity or if !Supports().
+    // The grid and the atoms' densities. Throws if they are over the capacity or if !Supports(). The atoms are
+    // read until the call returns; from pinned memory (PinnedVector) they go up by DMA.
     void SetAtoms(const ModelDensityGrid &grid, const std::vector<ModelDensityAtom> &atoms);
+    void SetAtoms(const ModelDensityGrid &grid, const ModelDensityAtom *atoms, size_t n);
 
     // The density into d_grid (nu * nv * nw floats, every point written). d_pos: each atom's centre in
     // grid units - its fractional position times the grid size, as the CPU's DensityBox holds it, not
-    // wrapped into the cell - in the order SetAtoms() got them; w is not read. Waits on the stream once,
-    // for the number of (brick, atom) pairs.
+    // wrapped into the cell - in the order SetAtoms() got them; w is not read. Queued on the stream, nothing
+    // waited for: the pairs are built in buffers of a fixed shape, so this records into a CUDA graph.
     void Compute(const float4 *d_pos, float *d_grid);
 
+    // The densities and the boxes of the atoms last set, on the device, for a kernel that walks the same boxes.
+    const ModelDensityAtom *DeviceAtoms() const { return atoms; }
+    const int *DeviceBoxes() const { return box; }
+
     // What the gather kernel needs of the grid.
     struct Geometry {
         int nu, nv, nw;
@@ -81,8 +90,10 @@ private:
 
     CudaDevicePtr<ModelDensityAtom> atoms;
     CudaDevicePtr<int> box;
-    CudaDevicePtr<int> overflow;          // an atom's box over MAX_BRICKS_PER_AXIS
-    CudaDevicePtr<int> count, offset, key, value, key_sorted, value_sorted, brick_start, brick_end;
+    CudaHostPtr<int> host_box;            // the boxes' staging buffer, pinned
+    // per brick its atoms counted, where its segment starts (max_bricks + 1: the last entry the total) and how
+    // far it is filled; per pair the atom as the fill placed it, its rank in the brick, and in model order
+    CudaDevicePtr<int> brick_count, brick_start, brick_fill, unordered, rank, pair_atom;
     CudaDevicePtr<char> cub_temp;
     size_t cub_bytes = 0;
 };
diff --git a/image_analysis/structure_refinement/ModelMaskGPU.cu b/image_analysis/structure_refinement/ModelMaskGPU.cu
index 627da9aa8..d4fc89bb5 100644
--- a/image_analysis/structure_refinement/ModelMaskGPU.cu
+++ b/image_analysis/structure_refinement/ModelMaskGPU.cu
@@ -206,12 +206,15 @@ __global__ void shrink_edges(const float *mask, int *edge, const int3 *stencil,
     edge[i] = is_edge;
 }
 
-// The stencil is symmetric (an offset and its negative are the same distance), so a macromolecule point
-// that an edge point reaches is one that reaches an edge point.
+// The stencil is symmetric (an offset and its negative are the same distance), so a macromolecule point within
+// it of an edge point is one an edge point reaches: each edge point marks its stencil as solvent. The edge points
+// are a thin shell, so this visits far fewer points than asking every macromolecule point for an edge within
+// reach; every write is the same store of 1, made only to points the edge pass did not change, so the mask is
+// the same bit for bit (a solvent point written again stays 1).
 __global__ void shrink_margin(float *mask, const int *edge, const int3 *stencil, int n_stencil, int nu, int nv, int nw) {
     const size_t n = static_cast<size_t>(nu) * nv * nw;
     const size_t i = blockIdx.x * static_cast<size_t>(blockDim.x) + threadIdx.x;
-    if (i >= n || mask[i] >= 1.0f)
+    if (i >= n || !edge[i])
         return;
     const int u = static_cast<int>(i % nu);
     const int v = static_cast<int>((i / nu) % nv);
@@ -220,10 +223,7 @@ __global__ void shrink_margin(float *mask, const int *edge, const int3 *stencil,
         const size_t j = wrap(u + stencil[k].x, nu)
                          + static_cast<size_t>(nu) * (wrap(v + stencil[k].y, nv)
                                                       + static_cast<size_t>(nv) * wrap(w + stencil[k].z, nw));
-        if (edge[j]) {
-            mask[i] = 1.0f;
-            return;
-        }
+        mask[j] = 1.0f;
     }
 }
 
diff --git a/image_analysis/structure_refinement/ModelScaleGPU.cu b/image_analysis/structure_refinement/ModelScaleGPU.cu
index f26a72744..bfa19dce9 100644
--- a/image_analysis/structure_refinement/ModelScaleGPU.cu
+++ b/image_analysis/structure_refinement/ModelScaleGPU.cu
@@ -25,6 +25,8 @@ constexpr int THREADS = 128;
 constexpr int BLOCKS = 48;
 constexpr int SLOTS = 36;      // 1 + 28 + 7: the WSSR, the lower half of J^T J and J^T r for 7 parameters
 constexpr int MAX_FITS = 88;   // FitModelScale's coarse pass, the larger of its two
+constexpr int MAX_ROBUST_FITS = 32;   // FitModelScale's fine pass, at most 5 x 5 points
+constexpr int ROBUST_ROUNDS = 4;      // as ModelScaling.cpp
 
 // What a launch sums over the points for one fit.
 constexpr int MODE_ISOTROPIC = 0;  // fit_isotropic_b_approximately(): sx, sy, sxx, sxy, n
@@ -54,7 +56,7 @@ __global__ void solvent_amplitudes(const double *__restrict__ stol2, const float
 template <int NA>
 __global__ void scale_sums(const int *__restrict__ hkl, const double *__restrict__ stol2,
                            const float *__restrict__ fobs, const unsigned char *__restrict__ strong,
-                           const float *__restrict__ f_abs_all, int n,
+                           const float *__restrict__ f_abs_all, const float *__restrict__ weight_all, int n,
                            const ModelScaleFitState *__restrict__ fits, Constraints c, double *__restrict__ partial) {
     constexpr int NS = 1 + NA * (NA + 1) / 2 + NA;   // WSSR, J^T J lower half, J^T r
     const ModelScaleFitState f = fits[blockIdx.y];
@@ -105,10 +107,12 @@ __global__ void scale_sums(const int *__restrict__ hkl, const double *__restrict
         const float r_u_r_f = fx * fx * uf[0] + fy * fy * uf[1] + fz * fz * uf[2]
                               + 2 * (fx * fy * uf[3] + fx * fz * uf[4] + fy * fz * uf[5]);
         const float k_aniso = expf(-0.25f * r_u_r_f);
+        // the robust fit's weight (ModelScaling.cpp, ComputeLMMatrices and ComputeWSSR multiply by it)
+        const double w = f.weighted ? weight_all[static_cast<size_t>(f.column) * n + i] : 1.0;
         if (f.mode == MODE_WSSR) {
             const float value = f_abs * static_cast<float>(f.k_overall * k_aniso);
             const double dy = fo - value;
-            acc[0] += dy * dy;
+            acc[0] += dy * dy * w;
             continue;
         }
 
@@ -124,13 +128,13 @@ __global__ void scale_sums(const int *__restrict__ hkl, const double *__restrict
             dy_da[j] = r[0] * du[0] + r[1] * du[1] + r[2] * du[2] + r[3] * du[3] + r[4] * du[4] + r[5] * du[5];
         }
         const double dy = fo - y;
-        acc[0] += dy * dy;
+        acc[0] += dy * dy * w;
         int s = 1;
         for (int j = 0; j < NA; j++)
             for (int k = 0; k <= j; k++)
-                acc[s++] += dy_da[j] * dy_da[k];
+                acc[s++] += dy_da[j] * dy_da[k] * w;
         for (int j = 0; j < NA; j++)
-            acc[s++] += dy * dy_da[j];
+            acc[s++] += dy * dy_da[j] * w;
     }
 
     // The block's sum of each slot the mode fills: a fixed shuffle tree within each warp, then the warps
@@ -155,6 +159,75 @@ __global__ void scale_sums(const int *__restrict__ hkl, const double *__restrict
     }
 }
 
+// The robust fit's residuals |Fo - value| of each fit (blockIdx.y) at its parameters, compute_value() as in MODE_R.
+__global__ void robust_residuals(const int *__restrict__ hkl, const float *__restrict__ fobs,
+                                 const float *__restrict__ f_abs_all, int n,
+                                 const ModelScaleFitState *__restrict__ fits, float *__restrict__ residual) {
+    const ModelScaleFitState f = fits[blockIdx.y];
+    const float *f_abs_fit = f_abs_all + static_cast<size_t>(f.column) * n;
+    for (int i = blockIdx.x * THREADS + threadIdx.x; i < n; i += BLOCKS * THREADS) {
+        const double hx = hkl[3 * i], hy = hkl[3 * i + 1], hz = hkl[3 * i + 2];
+        const double *u = f.b_star;
+        const double r_u_r = hx * hx * u[0] + hy * hy * u[1] + hz * hz * u[2]
+                             + 2 * (hx * hy * u[3] + hx * hz * u[4] + hy * hz * u[5]);
+        const float value = f_abs_fit[i] * static_cast<float>(f.k_overall * exp(-0.25 * r_u_r));
+        residual[static_cast<size_t>(f.column) * n + i] = fabsf(fobs[i] - value);
+    }
+}
+
+// The robust fit's weights 1 / sqrt(1 + (r / c)^2) from the residuals (ModelScaling.cpp, RobustReweight); a fit
+// whose c is not positive keeps its weights.
+__global__ void robust_weights(const float *__restrict__ residual, int n, const ModelScaleFitState *__restrict__ fits,
+                               float *__restrict__ weight) {
+    const ModelScaleFitState f = fits[blockIdx.y];
+    if (!(f.c > 0))
+        return;
+    const size_t row = static_cast<size_t>(f.column) * n;
+    for (int i = blockIdx.x * THREADS + threadIdx.x; i < n; i += BLOCKS * THREADS) {
+        const double q = residual[row + i] / f.c;
+        weight[row + i] = static_cast<float>(1.0 / sqrt(1.0 + q * q));
+    }
+}
+
+// The robust fit's c of each fit (blockIdx.x): the median of its residuals, the element std::nth_element puts at
+// n / 2, by radix selection - the residuals are not negative, so their order is that of their bits as unsigned
+// integers, and four passes find those bits a byte at a time. The counts are of integers: the same answer
+// whatever order the threads take.
+__global__ void residual_median(const float *__restrict__ residual, int n, const ModelScaleFitState *__restrict__ fits,
+                                double *__restrict__ c) {
+    __shared__ unsigned int count[256];
+    __shared__ unsigned int prefix, rank;
+    const float *r = residual + static_cast<size_t>(fits[blockIdx.x].column) * n;
+    if (threadIdx.x == 0) {
+        prefix = 0;
+        rank = n / 2;
+    }
+    for (int shift = 24; shift >= 0; shift -= 8) {
+        for (int b = threadIdx.x; b < 256; b += blockDim.x)
+            count[b] = 0;
+        __syncthreads();
+        // the bits above this byte, which the residuals counted must share with the median
+        const unsigned int high = shift == 24 ? 0 : 0xffffffffu << (shift + 8);
+        for (int i = threadIdx.x; i < n; i += blockDim.x) {
+            const unsigned int u = __float_as_uint(r[i]);
+            if ((u & high) == prefix)
+                atomicAdd(&count[(u >> shift) & 255], 1u);
+        }
+        __syncthreads();
+        if (threadIdx.x == 0) {
+            unsigned int b = 0;
+            while (rank >= count[b]) {
+                rank -= count[b];
+                b++;
+            }
+            prefix |= b << shift;
+        }
+        __syncthreads();
+    }
+    if (threadIdx.x == 0)
+        c[blockIdx.x] = __uint_as_float(prefix);
+}
+
 // Each fit's block partials summed in block order.
 __global__ void sum_blocks(const double *__restrict__ partial, double *__restrict__ sums) {
     const int s = threadIdx.x;
@@ -303,6 +376,10 @@ struct ModelScaleGPU::LevMarRun {
     }
 };
 
+size_t ModelScaleGPU::RobustBytes(size_t max_points) {
+    return 2 * MAX_ROBUST_FITS * max_points * sizeof(float) + MAX_ROBUST_FITS * sizeof(double);
+}
+
 size_t ModelScaleGPU::DeviceBytes(size_t max_points) {
     return max_points * (3 * sizeof(int) + sizeof(double) + sizeof(float) + sizeof(unsigned char))
            + MAX_FITS * max_points * sizeof(float)
@@ -368,22 +445,28 @@ const double *ModelScaleGPU::Reduce(int nfits) {
             c.row[j][k] = static_cast<float>(constraints_[j][k]);
     const dim3 grid(BLOCKS, nfits);
     switch (n_params_) {
-        case 2: scale_sums<2><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, n_, fits_, c, partial_); break;
-        case 3: scale_sums<3><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, n_, fits_, c, partial_); break;
-        case 4: scale_sums<4><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, n_, fits_, c, partial_); break;
-        case 5: scale_sums<5><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, n_, fits_, c, partial_); break;
-        case 6: scale_sums<6><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, n_, fits_, c, partial_); break;
-        case 7: scale_sums<7><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, n_, fits_, c, partial_); break;
+        case 2: scale_sums<2><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, weight_, n_, fits_, c, partial_); break;
+        case 3: scale_sums<3><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, weight_, n_, fits_, c, partial_); break;
+        case 4: scale_sums<4><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, weight_, n_, fits_, c, partial_); break;
+        case 5: scale_sums<5><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, weight_, n_, fits_, c, partial_); break;
+        case 6: scale_sums<6><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, weight_, n_, fits_, c, partial_); break;
+        case 7: scale_sums<7><<<grid, THREADS, 0, stream_>>>(hkl_, stol2_, fobs_, strong_, f_abs_, weight_, n_, fits_, c, partial_); break;
         default: throw std::logic_error("ModelScaleGPU: unexpected number of parameters");
     }
     cuda_err(cudaGetLastError());
     sum_blocks<<<nfits, SLOTS, 0, stream_>>>(partial_, sums_);
     cuda_err(cudaGetLastError());
     cuda_err(cudaMemcpyAsync(host_sums_, sums_, nfits * SLOTS * sizeof(double), cudaMemcpyDeviceToHost, stream_));
-    cuda_err(cudaStreamSynchronize(stream_));
+    Wait();
     return host_sums_;
 }
 
+void ModelScaleGPU::Wait() {
+    cudaError_t err;
+    while ((err = cudaStreamQuery(stream_)) == cudaErrorNotReady) {}
+    cuda_err(err);
+}
+
 // fit_isotropic_b_approximately() then fit_parameters() for every fit in `fits`, which start from the
 // k_overall and b_star they hold, and are left holding the answer.
 void ModelScaleGPU::FitBatch(const float2 *d_fcmol, const float2 *d_fmask, std::vector<ModelScaleFitState> &fits) {
@@ -414,7 +497,11 @@ void ModelScaleGPU::FitBatch(const float2 *d_fcmol, const float2 *d_fmask, std::
         const double b[6] = {elem(0, 0), elem(1, 1), elem(2, 2), elem(0, 1), elem(0, 2), elem(1, 2)};
         std::copy(b, b + 6, fits[i].b_star);
     }
+    LevMarBatch(fits);
+}
 
+void ModelScaleGPU::LevMarBatch(std::vector<ModelScaleFitState> &fits) {
+    const size_t nfits = fits.size();
     // get_parameters() and set_parameters() with k_sol and b_sol fixed
     const int na = n_params_;
     auto get_parameters = [&](const ModelScaleFitState &f) {
@@ -459,6 +546,49 @@ void ModelScaleGPU::FitBatch(const float2 *d_fcmol, const float2 *d_fmask, std::
         set_parameters(fits[i], runs[i].Result());
 }
 
+// ModelScaling.cpp's robust rounds of each fit: the residuals at its parameters, their median taken once as c,
+// the weights, and gemmi's Levenberg-Marquardt again from where the fit stands. The median is the element
+// std::nth_element puts at n / 2, as there.
+void ModelScaleGPU::RobustBatch(std::vector<ModelScaleFitState> &fits) {
+    const size_t nfits = fits.size();
+    if (nfits > static_cast<size_t>(MAX_ROBUST_FITS))
+        throw std::logic_error("ModelScaleGPU: too many robust fits in one launch");
+    if (!weight_) {
+        weight_ = CudaDevicePtr<float>(MAX_ROBUST_FITS * max_points_);
+        residual_ = CudaDevicePtr<float>(MAX_ROBUST_FITS * max_points_);
+        median_ = CudaDevicePtr<double>(MAX_ROBUST_FITS);
+        host_median_ = CudaHostPtr<double>(MAX_ROBUST_FITS);
+    }
+    for (size_t i = 0; i < nfits; i++) {
+        fits[i].column = static_cast<int>(i);
+        fits[i].weighted = 0;
+        fits[i].c = 0;
+    }
+    const dim3 grid(BLOCKS, static_cast<unsigned>(nfits));
+    for (int round = 0; round < ROBUST_ROUNDS; round++) {
+        UploadFits(fits);
+        robust_residuals<<<grid, THREADS, 0, stream_>>>(hkl_, fobs_, f_abs_, n_, fits_, residual_);
+        cuda_err(cudaGetLastError());
+        if (round == 0) {
+            residual_median<<<static_cast<unsigned>(nfits), 1024, 0, stream_>>>(residual_, n_, fits_, median_);
+            cuda_err(cudaGetLastError());
+            cuda_err(cudaMemcpyAsync(host_median_, median_, nfits * sizeof(double), cudaMemcpyDeviceToHost, stream_));
+            Wait();
+            for (size_t i = 0; i < nfits; i++)
+                fits[i].c = host_median_[i];
+            UploadFits(fits);
+        }
+        robust_weights<<<grid, THREADS, 0, stream_>>>(residual_, n_, fits_, weight_);
+        cuda_err(cudaGetLastError());
+        Wait();   // host_fits_ is written again below
+        for (ModelScaleFitState &f : fits)
+            f.weighted = f.c > 0;
+        LevMarBatch(fits);
+    }
+    for (ModelScaleFitState &f : fits)
+        f.weighted = 0;
+}
+
 ModelScaleParams ModelScaleGPU::Fit(const float2 *d_fcmol, const float2 *d_fmask, double k_sol, double b_sol) {
     ModelScaleParams out;
     if (n_ == 0)
@@ -473,7 +603,8 @@ ModelScaleParams ModelScaleGPU::Fit(const float2 *d_fcmol, const float2 *d_fmask
 // FitModelScale's grid (ModelScaling.cpp, default ModelScaleBox with b_sol up to b_hi): a coarse pass
 // over the box and a finer one around its winner, every grid point its own fit, the winner the lowest
 // finite R in grid order. The fits of a pass run together, one launch per Levenberg-Marquardt step.
-ModelSolventFit ModelScaleGPU::FitSolvent(const float2 *d_fcmol, const float2 *d_fmask, double b_hi) {
+ModelSolventFit ModelScaleGPU::FitSolvent(const float2 *d_fcmol, const float2 *d_fmask, double b_hi, bool robust,
+                                          double k_start, double b_start) {
     ModelSolventFit out;
     if (n_ < 20)
         return out;
@@ -483,8 +614,10 @@ ModelSolventFit ModelScaleGPU::FitSolvent(const float2 *d_fcmol, const float2 *d
     const double k_lo = 0.10, k_hi = 0.60, b_lo = 10.0;   // ModelScaleBox{}
     const double b_step = std::max(10.0, (b_hi - b_lo) / 7.0);
     double best_r = -1;
-    auto try_points = [&](std::vector<ModelScaleFitState> &fits) {
+    auto try_points = [&](std::vector<ModelScaleFitState> &fits, bool robust_pass) {
         FitBatch(d_fcmol, d_fmask, fits);
+        if (robust_pass)
+            RobustBatch(fits);
         for (auto &f : fits)
             f.mode = MODE_R;
         const double *r = Sums(fits);
@@ -505,19 +638,26 @@ ModelSolventFit ModelScaleGPU::FitSolvent(const float2 *d_fcmol, const float2 *d
         return ModelScaleFitState{1.0, {0, 0, 0, 0, 0, 0}, ks, bs, 0, 0};
     };
 
-    std::vector<ModelScaleFitState> coarse;
-    for (double ks = k_lo; ks <= k_hi + 1e-9; ks += 0.05)
-        for (double bs = b_lo; bs <= b_hi + 1e-9; bs += b_step)
-            coarse.push_back(point(ks, bs));
-    try_points(coarse);
-    const double k0 = out.k_sol, b0 = out.b_sol;
+    double k0 = k_start, b0 = b_start;
+    if (k0 < 0) {
+        std::vector<ModelScaleFitState> coarse;
+        for (double ks = k_lo; ks <= k_hi + 1e-9; ks += 0.05)
+            for (double bs = b_lo; bs <= b_hi + 1e-9; bs += b_step)
+                coarse.push_back(point(ks, bs));
+        try_points(coarse, false);
+        k0 = out.k_sol;
+        b0 = out.b_sol;
+    }
     const double k_hi2 = std::min(k_hi, k0 + 0.05);
     const double b_hi2 = std::min(b_hi, b0 + b_step);
     std::vector<ModelScaleFitState> fine;
     for (double ks = std::max(k_lo, k0 - 0.05); ks <= k_hi2 + 1e-9; ks += 0.025)
         for (double bs = std::max(b_lo, b0 - b_step); bs <= b_hi2 + 1e-9; bs += b_step / 2.0)
             fine.push_back(point(ks, bs));
-    try_points(fine);
+    // a robust fit takes the fine pass robustly, the coarse winner included (as FitModelScale)
+    if (robust)
+        best_r = -1;
+    try_points(fine, robust);
     out.r = best_r;
     return out;
 }
diff --git a/image_analysis/structure_refinement/ModelScaleGPU.h b/image_analysis/structure_refinement/ModelScaleGPU.h
index 3906b5c53..178508864 100644
--- a/image_analysis/structure_refinement/ModelScaleGPU.h
+++ b/image_analysis/structure_refinement/ModelScaleGPU.h
@@ -36,6 +36,8 @@ struct ModelScaleFitState {
     double k_sol, b_sol;
     int mode;
     int column;   // the fit's row of |Fcalc + solvent| on the device
+    int weighted; // the robust fit's weights (row `column`) multiply the WSSR and J^T J, J^T r; 0: weight 1
+    double c;     // the robust fit's scale of the residuals (ModelScaling.cpp, RobustReweight)
 };
 
 class ModelScaleGPU {
@@ -59,7 +61,13 @@ public:
     // FitModelScale (ModelScaling.cpp) with the default box, b_sol up to b_hi: the same grid, the same
     // winner. Throws ModelScaleGPUTooFewReflections where FitModelScale would chain the grid points
     // (five or fewer reflections for the isotropic fit).
-    ModelSolventFit FitSolvent(const float2 *d_fcmol, const float2 *d_fmask, double b_hi = 80.0);
+    // robust: the fine pass by robust least squares, as FitModelScale with ModelScaleBox::robust - the
+    // reweighting on the device, the median of each fit's first residuals included.
+    // k_start, b_start: ModelScaleBox's - the fine pass around them, no coarse pass (negative: as FitModelScale).
+    ModelSolventFit FitSolvent(const float2 *d_fcmol, const float2 *d_fmask, double b_hi = 80.0,
+                               bool robust = false, double k_start = -1, double b_start = -1);
+    // What a robust FitSolvent takes on the card beyond DeviceBytes(), reserved at its first call.
+    static size_t RobustBytes(size_t max_points);
 
 private:
     struct LevMarRun;
@@ -70,8 +78,16 @@ private:
     // The sums of the first `nfits` uploaded fits over all points, one row of SLOTS doubles per fit, on
     // the host.
     const double *Reduce(int nfits);
+    // The stream's queued work done, polled for: a fit's launches are short and the host waits for every one
+    // of them, so sleeping until the device raises the wake-up (set_gpu_blocking_sync) would cost more than
+    // the work itself.
+    void Wait();
     const double *Sums(const std::vector<ModelScaleFitState> &fits);
     void FitBatch(const float2 *d_fcmol, const float2 *d_fmask, std::vector<ModelScaleFitState> &fits);
+    // gemmi's Levenberg-Marquardt for every fit in `fits` from the parameters it holds.
+    void LevMarBatch(std::vector<ModelScaleFitState> &fits);
+    // The robust rounds of a batch FitBatch() has fitted: reweight, fit again, ROBUST_ROUNDS times.
+    void RobustBatch(std::vector<ModelScaleFitState> &fits);
 
     cudaStream_t stream_;
     size_t max_points_;
@@ -91,4 +107,7 @@ private:
     CudaDevicePtr<double> sums_;              // per fit, per slot
     CudaHostPtr<ModelScaleFitState> host_fits_;
     CudaHostPtr<double> host_sums_;
+    CudaDevicePtr<float> weight_, residual_;  // the robust fit's, per fit of a batch, per point
+    CudaDevicePtr<double> median_;            // the robust fit's c, per fit of a batch
+    CudaHostPtr<double> host_median_;
 };
diff --git a/image_analysis/structure_refinement/ModelScaling.cpp b/image_analysis/structure_refinement/ModelScaling.cpp
index 6a099189b..0b7688974 100644
--- a/image_analysis/structure_refinement/ModelScaling.cpp
+++ b/image_analysis/structure_refinement/ModelScaling.cpp
@@ -25,6 +25,8 @@
 
 namespace {
 
+constexpr int ROBUST_ROUNDS = 4;   // reweightings of the robust fit (ModelScaleBox::robust)
+
 // gemmi::Scaling<float> as a grid point fits it: the same starting point, parameters, model values,
 // derivatives and R. The solvent pair is fixed there, so |Fcalc + k_sol exp(-b_sol s^2) Fmask| of a
 // reflection is the same at every evaluation of the solver; it is taken once per grid point here rather than
@@ -35,8 +37,9 @@ struct FixedSolventFit {
         gemmi::Miller hkl;
         float fobs;
         float fcalc_abs;   // std::abs(Scaling::get_fcalc(p))
+        double weight = 1.0;   // 1, but for the robust fit's reweighting (RobustReweight)
         double get_y() const { return fobs; }
-        double get_weight() const { return 1.0; }
+        double get_weight() const { return weight; }
     };
     const std::vector<gemmi::Vec6> &constraint_matrix;
     double k_overall = 1.0;
@@ -61,7 +64,7 @@ struct FixedSolventFit {
             // Scaling::get_fcalc() at (k_sol, b_sol)
             const std::complex<float> fcalc =
                 s.use_solvent ? p.fcmol + (float) (k_sol * std::exp(-b_sol * p.stol2)) * p.fmask : p.fcmol;
-            points[i] = {p.hkl, p.fobs, std::abs(fcalc)};
+            points[i] = {p.hkl, p.fobs, std::abs(fcalc), 1.0};
             if (p.fobs < 1 || p.fobs < p.sigma)  // skip weak reflections
                 continue;
             double fcalc_abs = points[i].fcalc_abs;
@@ -138,6 +141,28 @@ struct FixedSolventFit {
     }
 };
 
+// The robust fit's weights at the current parameters: each reflection's residual r = |Fo| - |F_model| weighted by
+// 1 / sqrt(1 + (r / c)^2), with c the median |r| of the unweighted fit. Iterated, the weighted least squares then
+// minimises sum c^2 2 (sqrt(1 + (r / c)^2) - 1) - quadratic for the bulk of the reflections and linear for the few
+// a model fits badly (a beam-stop shadow, an ice ring, a missing part of the model), which least squares would
+// otherwise let set the scale of all the rest.
+// Following Huber (1964) Ann. Math. Statist. 35, 73-101 for the M-estimator, as iteratively reweighted least squares
+// The smooth (pseudo-Huber) loss of Charbonnier et al. (1997) IEEE Trans. Image Process. 6, 298-311
+void RobustReweight(FixedSolventFit &fit, double &c) {
+    std::vector<double> r(fit.points.size());
+    for (size_t i = 0; i < fit.points.size(); i++)
+        r[i] = std::fabs(fit.points[i].fobs - fit.compute_value(fit.points[i]));
+    if (c <= 0) {
+        std::vector<double> sorted = r;
+        std::nth_element(sorted.begin(), sorted.begin() + sorted.size() / 2, sorted.end());
+        c = sorted[sorted.size() / 2];
+    }
+    if (c <= 0)
+        return;
+    for (size_t i = 0; i < fit.points.size(); i++)
+        fit.points[i].weight = 1.0 / std::sqrt(1.0 + gemmi::sq(r[i] / c));
+}
+
 // R-factor of the current parameters over the fitted reflections. This is what the grid is
 // selected on, and it is the quantity the scale exists to make small.
 double RFactor(const FixedSolventFit &fit) {
@@ -171,16 +196,17 @@ double ComputeLMMatrices(const FixedSolventFit &fit, const double *kaniso, doubl
         const double k = kaniso ? kaniso[i] : std::exp(-0.25 * fit.b_star.r_u_r(gemmi::Vec3(p.hkl)));
         double y = fit.compute_value_and_derivatives<NA>(p, k, dy_da);
         double dy_sig = p.get_y() - y;
+        const double w = p.get_weight();
         for (int j = 0; j != NA; ++j) {
             const bool used = dy_da[j] != 0;
             for (int k = 0; k < NA; ++k) {
-                const double a = dy_da[j] * dy_da[k];
+                const double a = dy_da[j] * dy_da[k] * w;
                 alpha[NA * j + k] += used ? a : 0.0;
             }
-            const double b = dy_sig * dy_da[j];
+            const double b = dy_sig * dy_da[j] * w;
             beta[j] += used ? b : 0.0;
         }
-        wssr += gemmi::sq(dy_sig);
+        wssr += gemmi::sq(dy_sig) * w;
     }
     // The upper half of alpha is the lower half's mirror, as in gemmi.
     for (int j = 1; j < NA; j++)
@@ -198,8 +224,8 @@ double ComputeWSSR(const FixedSolventFit &fit, std::vector<double> &kaniso) {
     for (size_t i = 0; i < fit.points.size(); ++i) {
         const auto &p = fit.points[i];
         kaniso[i] = std::exp(-0.25 * fit.b_star.r_u_r(p.hkl));
-        // FixedSolventFit::compute_value(), weight 1
-        wssr += gemmi::sq(p.get_y() - p.fcalc_abs * (float) (fit.k_overall * kaniso[i]));
+        // FixedSolventFit::compute_value()
+        wssr += gemmi::sq(p.get_y() - p.fcalc_abs * (float) (fit.k_overall * kaniso[i])) * p.get_weight();
     }
     return (double) wssr;
 }
@@ -343,10 +369,18 @@ ModelScaleReport FitModelScale(gemmi::Scaling<float> &scaling, ModelScaleBox box
     // The scale the walk stands at, which a point starts from only where the data give it no start of its own.
     double k_last = scaling.k_overall;
     gemmi::SMat33<double> b_last = scaling.b_star;
-    auto fit_point = [&scaling](FixedSolventFit &fit, PointFit &pf, double k_start,
-                                const gemmi::SMat33<double> &b_start) {
+    bool robust_pass = false;               // the fine pass of a robust fit (ModelScaleBox::robust)
+    auto fit_point = [&scaling, &robust_pass](FixedSolventFit &fit, PointFit &pf, double k_start,
+                                              const gemmi::SMat33<double> &b_start) {
         fit.Start(scaling, pf.k_sol, pf.b_sol, k_start, b_start);
         LevMarFit(fit);                      // k_overall + anisotropic B only
+        if (robust_pass) {
+            double c = 0;
+            for (int round = 0; round < ROBUST_ROUNDS; round++) {
+                RobustReweight(fit, c);
+                LevMarFit(fit);
+            }
+        }
         pf.r = RFactor(fit);
         pf.k_overall = fit.k_overall;
         pf.b_star = fit.b_star;
@@ -394,15 +428,26 @@ ModelScaleReport FitModelScale(gemmi::Scaling<float> &scaling, ModelScaleBox box
     // 10 A^2, or in eight values where the box is wider than the default, so a raised ceiling costs
     // no more grid points.
     const double b_step = std::max(10.0, (box.b_hi - box.b_lo) / 7.0);
-    std::vector<PointFit> coarse;
-    for (double ks = box.k_lo; ks <= box.k_hi + 1e-9; ks += 0.05)
-        for (double bs = box.b_lo; bs <= box.b_hi + 1e-9; bs += b_step)
-            coarse.push_back(PointFit{ks, bs});
-    try_points(coarse);
-    const double k0 = best_k_sol, b0 = best_b_sol;
+    double k0 = box.k_start, b0 = box.b_start;
+    if (k0 < 0) {
+        std::vector<PointFit> coarse;
+        for (double ks = box.k_lo; ks <= box.k_hi + 1e-9; ks += 0.05)
+            for (double bs = box.b_lo; bs <= box.b_hi + 1e-9; bs += b_step)
+                coarse.push_back(PointFit{ks, bs});
+        try_points(coarse);
+        k0 = best_k_sol;
+        b0 = best_b_sol;
+    }
     const double k_hi2 = std::min(box.k_hi, k0 + 0.05);
     const double b_hi2 = std::min(box.b_hi, b0 + b_step);
     std::vector<PointFit> fine;
+    // A robust fit takes the fine pass robustly: each of its points, and the coarse winner again, by robust least
+    // squares - the coarse pass only finds where to look.
+    if (box.robust) {
+        robust_pass = true;
+        fitted.clear();
+        best_r = -1;
+    }
     for (double ks = std::max(box.k_lo, k0 - 0.05); ks <= k_hi2 + 1e-9; ks += 0.025)
         for (double bs = std::max(box.b_lo, b0 - b_step); bs <= b_hi2 + 1e-9; bs += b_step / 2.0)
             fine.push_back(PointFit{ks, bs});
@@ -431,15 +476,26 @@ double SolventBMax(const gemmi::Model &model) {
 }
 
 #ifdef JFJOCH_USE_CUDA
+// A fit is a chain of small launches, each waited for by the host's Levenberg-Marquardt: on a card shared with
+// long kernels (refinement's trials side by side) every wait would queue behind them, so the stream goes first.
+int HighestStreamPriority() {
+    int least = 0, greatest = 0;
+    cudaDeviceGetStreamPriorityRange(&least, &greatest);
+    return greatest;
+}
+
 struct ModelScaleGPUPool::Engine {
     CudaStream stream;
     ModelScaleGPU scale;
     CudaDevicePtr<float2> fcalc, fmask;
-    explicit Engine(size_t max_points) : scale(stream, max_points), fcalc(max_points), fmask(max_points) {}
+    explicit Engine(size_t max_points)
+        : stream(cudaStreamNonBlocking, HighestStreamPriority()), scale(stream, max_points), fcalc(max_points),
+          fmask(max_points) {}
 };
 
-size_t ModelScaleGPUPool::DeviceBytes(size_t max_points, size_t engines) {
-    return engines * (ModelScaleGPU::DeviceBytes(max_points) + 2 * max_points * sizeof(float2));
+size_t ModelScaleGPUPool::DeviceBytes(size_t max_points, size_t engines, bool robust) {
+    return engines * (ModelScaleGPU::DeviceBytes(max_points) + 2 * max_points * sizeof(float2) +
+                      (robust ? ModelScaleGPU::RobustBytes(max_points) : 0));
 }
 
 ModelScaleGPUPool::ModelScaleGPUPool(int device, size_t max_points, size_t engines)
@@ -460,7 +516,8 @@ ModelScaleGPUPool::~ModelScaleGPUPool() {
     set_gpu(current);
 }
 
-ModelScaleReport ModelScaleGPUPool::Fit(gemmi::Scaling<float> &scaling, double b_hi, size_t nthreads) {
+ModelScaleReport ModelScaleGPUPool::Fit(gemmi::Scaling<float> &scaling, double b_hi, size_t nthreads, bool robust,
+                                        double k_start, double b_start) {
     const size_t n = scaling.points.size();
     std::vector<std::array<int, 3>> hkl(n);
     std::vector<double> stol2(n);
@@ -503,11 +560,11 @@ ModelScaleReport ModelScaleGPUPool::Fit(gemmi::Scaling<float> &scaling, double b
         if (cudaMemcpyAsync(e->fcalc, fc.data(), n * sizeof(float2), cudaMemcpyHostToDevice, e->stream) != cudaSuccess
             || cudaMemcpyAsync(e->fmask, fm.data(), n * sizeof(float2), cudaMemcpyHostToDevice, e->stream) != cudaSuccess)
             throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "ModelScaleGPUPool: the upload failed");
-        fit = e->scale.FitSolvent(e->fcalc, e->fmask, b_hi);
+        fit = e->scale.FitSolvent(e->fcalc, e->fmask, b_hi, robust, k_start, b_start);
     } catch (const ModelScaleGPUTooFewReflections &) {
         set_gpu(current);
         release();
-        return FitModelScale(scaling, {.b_hi = b_hi}, nthreads);
+        return FitModelScale(scaling, {.b_hi = b_hi, .robust = robust, .k_start = k_start, .b_start = b_start}, nthreads);
     } catch (...) {
         set_gpu(current);
         release();
diff --git a/image_analysis/structure_refinement/ModelScaling.h b/image_analysis/structure_refinement/ModelScaling.h
index a3d465e85..8630d62f9 100644
--- a/image_analysis/structure_refinement/ModelScaling.h
+++ b/image_analysis/structure_refinement/ModelScaling.h
@@ -31,6 +31,12 @@
 struct ModelScaleBox {
     double k_lo = 0.10, k_hi = 0.60;
     double b_lo = 10.0, b_hi = 80.0;
+    // The overall scale and anisotropic B of the points of the fine pass by robust least squares
+    // (ModelScaling.cpp, RobustReweight) rather than plain least squares on |F|: what refinement scores a model with.
+    bool robust = false;
+    // Where a fit of the model as it was a moment ago found the solvent: the fine pass around (k_start, b_start)
+    // without the coarse pass. Negative: the coarse pass finds where to look.
+    double k_start = -1, b_start = -1;
 };
 
 // The b_sol ceiling for `model`: 80 A^2, or twice the model's mean atomic B where that is higher.
@@ -60,15 +66,19 @@ ModelScaleReport FitModelScale(gemmi::Scaling<float> &scaling, ModelScaleBox box
 class ModelScaleGPUPool {
 public:
     // What `engines` engines for fits of up to `max_points` reflections take on the card.
-    static size_t DeviceBytes(size_t max_points, size_t engines);
+    static size_t DeviceBytes(size_t max_points, size_t engines, bool robust = false);
     // On `device`. Throws JFJochException on a CUDA failure.
     ModelScaleGPUPool(int device, size_t max_points, size_t engines);
     ~ModelScaleGPUPool();
 
-    // FitModelScale(scaling, {.b_hi = b_hi}, nthreads). Where FitModelScale would walk the grid point to
-    // point (five or fewer reflections for the isotropic start), it is FitModelScale on the host. Safe to
-    // call from several threads. Throws JFJochException on a CUDA failure.
-    ModelScaleReport Fit(gemmi::Scaling<float> &scaling, double b_hi, size_t nthreads);
+    // FitModelScale(scaling, {.b_hi = b_hi, .robust = robust}, nthreads). Where FitModelScale would walk the
+    // grid point to point (five or fewer reflections for the isotropic start), it is FitModelScale on the host.
+    // Safe to call from several threads. Throws JFJochException on a CUDA failure. The robust fit's reweighting
+    // runs on the device; it is FitModelScale's robust fit to rounding (float residuals and weights, the
+    // anisotropic factor of the steps in float), deterministic run to run.
+    // k_start, b_start: ModelScaleBox's.
+    ModelScaleReport Fit(gemmi::Scaling<float> &scaling, double b_hi, size_t nthreads, bool robust = false,
+                         double k_start = -1, double b_start = -1);
     // What the pool holds on the card.
     size_t Bytes() const { return DeviceBytes(max_points_, engines_.size()); }
 
diff --git a/image_analysis/structure_refinement/MonomerLibrary.cpp b/image_analysis/structure_refinement/MonomerLibrary.cpp
new file mode 100644
index 000000000..3c55b8fb3
--- /dev/null
+++ b/image_analysis/structure_refinement/MonomerLibrary.cpp
@@ -0,0 +1,96 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "MonomerLibrary.h"
+
+#include <algorithm>
+#include <cstring>
+#include <vector>
+
+#include "gemmi/numb.hpp"       // as_number
+#include "gemmi/read_cif.hpp"   // read_cif_from_memory
+
+// Generated by CMakeLists.txt from monomers/*.cif (MonomerLibraryData.cpp in the build tree).
+extern const EmbeddedMonomerFile embedded_monomer_files[];
+extern const size_t embedded_monomer_file_count;
+
+namespace {
+
+struct MetalRow {
+    gemmi::El metal, ligand;
+    int coordination;
+    double distance, std;
+    int count;
+};
+
+struct EmbeddedLibrary {
+    gemmi::MonLib monlib;
+    std::vector<MetalRow> metals;   // metals.cif
+};
+
+EmbeddedLibrary ReadEmbeddedMonomerLibrary() {
+    EmbeddedLibrary lib;
+    gemmi::MonLib &monlib = lib.monlib;
+    for (size_t i = 0; i < embedded_monomer_file_count; i++) {
+        const EmbeddedMonomerFile &f = embedded_monomer_files[i];
+        std::string text;
+        for (size_t k = 0; k < f.n_pieces; k++)
+            text += f.pieces[k];
+        gemmi::cif::Document doc = gemmi::read_cif_from_memory(text.data(), text.size(), f.name);
+        if (std::strcmp(f.name, "ener_lib.cif") == 0)
+            monlib.ener_lib.read(doc);
+        else if (std::strcmp(f.name, "metals.cif") == 0) {
+            for (const auto &row : doc.blocks.at(0).find("_metal_coordination.",
+                                                         {"metal", "ligand", "coordination", "distance", "std", "count"}))
+                lib.metals.push_back({gemmi::find_element(row[0].c_str()), gemmi::find_element(row[1].c_str()),
+                                      gemmi::cif::as_int(row[2]), gemmi::cif::as_number(row[3]),
+                                      gemmi::cif::as_number(row[4]), gemmi::cif::as_int(row[5])});
+        } else
+            monlib.read_monomer_doc(doc);
+    }
+    return lib;
+}
+
+const EmbeddedLibrary &Library() {
+    static const EmbeddedLibrary lib = ReadEmbeddedMonomerLibrary();
+    return lib;
+}
+
+}  // namespace
+
+const gemmi::MonLib &EmbeddedMonomerLibrary() {
+    return Library().monlib;
+}
+
+bool EmbeddedMetalDistance(gemmi::El metal, gemmi::El ligand, int coordination, double &distance, double &sigma) {
+    // the rows of the pair resting on enough sites: the nearest at or below the coordination and above it
+    const MetalRow *lo = nullptr, *hi = nullptr;
+    for (const MetalRow &r : Library().metals) {
+        if (r.metal != metal || r.ligand != ligand || r.count < METAL_MIN_SITES)
+            continue;
+        if (r.coordination <= coordination && (lo == nullptr || r.coordination > lo->coordination))
+            lo = &r;
+        if (r.coordination > coordination && (hi == nullptr || r.coordination < hi->coordination))
+            hi = &r;
+    }
+    if (lo == nullptr && hi == nullptr)
+        return false;
+    if (lo != nullptr && (lo->coordination == coordination || hi == nullptr)) {
+        distance = lo->distance;
+        sigma = lo->std;
+    } else if (lo == nullptr) {
+        distance = hi->distance;
+        sigma = hi->std;
+    } else {
+        // between two coordination numbers: linear in the coordination
+        const double t = static_cast<double>(coordination - lo->coordination) / (hi->coordination - lo->coordination);
+        distance = lo->distance + t * (hi->distance - lo->distance);
+        sigma = lo->std + t * (hi->std - lo->std);
+    }
+    sigma = std::max(sigma, METAL_MIN_SIGMA);
+    return true;
+}
+
+bool InEmbeddedMonomerLibrary(const std::string &code) {
+    return EmbeddedMonomerLibrary().monomers.count(code) > 0;
+}
diff --git a/image_analysis/structure_refinement/MonomerLibrary.h b/image_analysis/structure_refinement/MonomerLibrary.h
new file mode 100644
index 000000000..a856f7430
--- /dev/null
+++ b/image_analysis/structure_refinement/MonomerLibrary.h
@@ -0,0 +1,35 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <cstddef>
+#include <string>
+
+#include "gemmi/monlib.hpp"
+
+// The restraint dictionary refinement uses: the subset of the CCP4 Monomer Library (Vagin et al. 2004,
+// LGPL-3.0) carried in the binary - the standard amino acids and nucleotides, the common modified RNA nucleotides,
+// their links and modifications, the common cofactors (NAD(P)(H), FAD, FMN, hemes, SAM/SAH), a few other ligands
+// and additives, water and ions; monomers/update_monomers.py holds the list. Parsed from memory once per process;
+// no file is read.
+const gemmi::MonLib &EmbeddedMonomerLibrary();
+
+// The ideal distance and its sigma of a bond from a metal ion to a donor atom (O, N, S) at a site of `coordination`
+// donors, from the library's statistics of metal sites (metals.json, embedded as monomers/metals.cif). Only rows
+// resting on at least METAL_MIN_SITES sites count: the row of that coordination number, else the two nearest
+// below and above it interpolated linearly, else the nearest one; the sigma is the row's standard deviation, at
+// least METAL_MIN_SIGMA. False where the pair has no such row.
+constexpr int METAL_MIN_SITES = 20;
+constexpr double METAL_MIN_SIGMA = 0.02;   // A
+bool EmbeddedMetalDistance(gemmi::El metal, gemmi::El ligand, int coordination, double &distance, double &sigma);
+
+// Whether `code` (a residue name) has a description in it.
+bool InEmbeddedMonomerLibrary(const std::string &code);
+
+// One .cif of monomers/, as CMakeLists.txt embeds it: its name and its text in pieces.
+struct EmbeddedMonomerFile {
+    const char *name;
+    const char *const *pieces;
+    size_t n_pieces;
+};
diff --git a/image_analysis/structure_refinement/Refinement.cpp b/image_analysis/structure_refinement/Refinement.cpp
new file mode 100644
index 000000000..86a4d72a8
--- /dev/null
+++ b/image_analysis/structure_refinement/Refinement.cpp
@@ -0,0 +1,1560 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "Refinement.h"
+
+#include <algorithm>
+#include <chrono>
+#include <future>
+#include <map>
+#include <optional>
+#include <cmath>
+#include <numeric>
+#include <random>
+#include <thread>
+#include <unordered_map>
+
+#include <ceres/gradient_problem.h>
+#include <ceres/gradient_problem_solver.h>
+#include <ceres/jet.h>
+#include <ceres/rotation.h>
+
+#include "gemmi/fourier.hpp"   // get_size_for_hkl, get_f_phi_on_grid
+#include "gemmi/it92.hpp"
+#include "gemmi/modify.hpp"    // remove_hydrogens
+#include "gemmi/scaling.hpp"
+#include "gemmi/stats.hpp"     // calculate_data_statistics
+
+#include "../../common/JFJochException.h"
+#include "../../common/JFJochMath.h"
+#include "../../common/Logger.h"
+#include "../../common/ParallelFor.h"
+#include "ModelFFT.h"
+#include "ModelScaling.h"
+#include "RefinementMath.h"
+#include "RefinementMinimiser.h"
+#include "RefinementXray.h"
+#ifdef JFJOCH_USE_CUDA
+#include "../../common/CUDAWrapper.h"
+#include "RefinementGPU.h"
+#endif
+
+namespace {
+
+constexpr double B_FLOOR = 2.0;      // A^2: no atom's B goes below it
+// nor above twice the model's largest B, within these bounds (the GPU's gather is reserved for it)
+constexpr double B_CEILING_MIN = 100.0, B_CEILING_MAX = 300.0;
+// How far below the smallest B of the model a macro-cycle's B refinement may take an atom; the blur of the
+// cycle is chosen for that.
+constexpr double B_STEP_DOWN = 10.0;
+constexpr double REPULSION_MARGIN = 0.5;   // A: pairs this much beyond their contact distance are listed too
+// The geometry the weight is chosen within (Afonine et al. 2012 select among weights by R-free with the
+// geometry held to a target in the same way).
+constexpr double MAX_RMSD_BONDS = 0.02, MAX_RMSD_ANGLES = 2.0;
+// R-free differences smaller than this do not decide between two weights: the tighter geometry is taken.
+constexpr double R_FREE_TIE = 0.001;
+// The minimiser (RefinementMinimiser): a solve stops where an iteration lowers the target by less than this,
+// relative; the most a position (A) or a B (A^2) moves in the first trial of a line search.
+constexpr double MINIMISER_F_TOLERANCE = 1e-7;
+constexpr double MAX_STEP_XYZ = 0.3, MAX_STEP_B = 10.0;
+
+// The figure of merit of the likelihood, <cos(dphi)>, at X = 2 Fo D Fc / var: I1(X)/I0(X) for an acentric
+// reflection, tanh(X / 2) for a centric one.
+// Following Murshudov, Vagin & Dodson (1997) Acta Cryst. D53, 240-255
+double Fom(double x, bool centric) {
+    double log_i0 = 0, ratio = 0;
+    refine_math::BesselI0I1(x, log_i0, ratio);
+    return centric ? std::tanh(0.5 * x) : ratio;
+}
+
+std::string Joined(const std::vector<std::string> &names) {
+    std::string out;
+    for (const std::string &n : names)
+        out += (out.empty() ? "" : " ") + n;
+    return out;
+}
+
+std::vector<gemmi::Atom *> AtomList(gemmi::Model &model) {
+    std::vector<gemmi::Atom *> atoms;
+    for (gemmi::Chain &ch : model.chains)
+        for (gemmi::Residue &r : ch.residues)
+            for (gemmi::Atom &a : r.atoms)
+                atoms.push_back(&a);
+    return atoms;
+}
+
+// The model as refinement takes it: the first model only, without hydrogens and atoms of unknown element,
+// every B isotropic (an anisotropic one becomes its equivalent isotropic B) and inside the allowed range.
+gemmi::Structure PrepareModel(const gemmi::Structure &placed, const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg) {
+    gemmi::Structure st = placed;
+    st.models.resize(1);
+    st.cell = cell;
+    st.spacegroup_hm = sg.xhm();
+    gemmi::remove_hydrogens(st.models[0]);
+    for (gemmi::Chain &ch : st.models[0].chains)
+        for (gemmi::Residue &r : ch.residues) {
+            std::erase_if(r.atoms, [](const gemmi::Atom &a) { return a.element == gemmi::El::X; });
+            for (gemmi::Atom &a : r.atoms) {
+                if (a.aniso.nonzero()) {
+                    a.b_iso = static_cast<float>(gemmi::u_to_b() * a.aniso.trace() / 3.0);
+                    a.aniso = {0, 0, 0, 0, 0, 0};
+                }
+                a.b_iso = static_cast<float>(std::clamp<double>(a.b_iso, B_FLOOR, B_CEILING_MAX));
+            }
+        }
+    gemmi::remove_empty_children(st);
+    st.setup_cell_images();
+    return st;
+}
+
+// What every stage works on: the model, the reflections, the engine and the row model of the cycle.
+struct Context {
+    gemmi::Structure st;
+    std::vector<gemmi::Atom *> atoms;
+    gemmi::UnitCell cell;
+    const gemmi::SpaceGroup *sg = nullptr;
+    double d_min = 0;
+    RefinementReflections refl;
+    std::unique_ptr<RefinementEngine> engine;
+    std::unique_ptr<BulkSolventMask> mask;
+#ifdef JFJOCH_USE_CUDA
+    std::unique_ptr<ModelScaleGPUPool> scale_gpu;
+#endif
+    size_t nthreads = 1;
+    // the likelihood fit's: all of the run's, also in a trial's slot - the slots refit at the same time, the GPU
+    // idles meanwhile, and the bins they queue on the shared worker pool are fitted by whichever thread is free
+    size_t ml_threads = 1;
+    int device = -1;            // the engine's GPU
+    size_t engine_bytes = 0;    // and what it holds there
+    XrayRowModel rows;
+    std::vector<std::complex<float>> fcalc, fmask;
+    double k_sol = 0, b_sol = 0;
+    // where the last Refit()'s solvent grid ended (before MoveOverallB()): the next one's fine pass is around it
+    // (negative: the next one searches the whole box)
+    double grid_k_sol = -1, grid_b_sol = -1;
+    double k_overall = 0;
+    gemmi::SMat33<double> b_star{0, 0, 0, 0, 0, 0};
+    double b_floor = B_FLOOR;   // the cycle's lowest allowed B
+    double b_ceiling = B_CEILING_MAX;
+    // Riding hydrogens: per atom the parent it rides on (-1: none), and where it sits from the parent.
+    std::vector<int> rider_parent;
+    std::vector<int> rider_start, rider_index;   // SetRiderParents()
+    std::vector<gemmi::Position> rider_offset;
+    int evaluations = 0;
+    const std::atomic<bool> *cancel = nullptr;   // RefinementSettings::cancel
+
+    bool Cancelled() const { return cancel != nullptr && cancel->load(std::memory_order_relaxed); }
+
+    gemmi::Model &Model() { return st.models[0]; }
+
+    // The riders' parents, and per parent its riders in index order (rider_start, rider_index: CSR over the atoms).
+    void SetRiderParents(const std::vector<int> &parents) {
+        rider_parent = parents;
+        rider_start.assign(atoms.size() + 1, 0);
+        for (int p : rider_parent)
+            if (p >= 0)
+                rider_start[p + 1]++;
+        for (size_t i = 0; i < atoms.size(); i++)
+            rider_start[i + 1] += rider_start[i];
+        rider_index.resize(rider_start.back());
+        std::vector<int> fill(rider_start.begin(), rider_start.end() - 1);
+        for (size_t i = 0; i < rider_parent.size(); i++)
+            if (rider_parent[i] >= 0)
+                rider_index[fill[rider_parent[i]]++] = static_cast<int>(i);
+    }
+    // The hydrogens moved with their parents, at the offsets they were last placed at, and given their B.
+    void MoveRiders() {
+        const int n = static_cast<int>(rider_parent.size());
+        ParallelChunks(n, ThreadsForWork(n, nthreads, 16384), [&](int lo, int hi) {
+            for (int i = lo; i < hi; i++)
+                if (rider_parent[i] >= 0) {
+                    atoms[i]->pos = atoms[rider_parent[i]]->pos + rider_offset[i];
+                    atoms[i]->b_iso = atoms[rider_parent[i]]->b_iso;
+                }
+        });
+    }
+    // What the target says of a hydrogen is said of its parent: each parent takes its riders in index order, as
+    // the serial walk over the atoms added them (a rider has no riders of its own).
+    void FoldRiders(std::vector<std::array<double, 4>> &g) const {
+        const int n = static_cast<int>(rider_parent.size());
+        ParallelChunks(n, ThreadsForWork(n, nthreads, 16384), [&](int lo, int hi) {
+            for (int i = lo; i < hi; i++)
+                for (int r = rider_start[i]; r < rider_start[i + 1]; r++)
+                    for (int c = 0; c < 4; c++)
+                        g[i][c] += g[rider_index[r]][c];
+        });
+    }
+
+    std::vector<std::array<double, 4>> XyzB() const {
+        std::vector<std::array<double, 4>> out(atoms.size());
+        for (size_t i = 0; i < atoms.size(); i++)
+            out[i] = {atoms[i]->pos.x, atoms[i]->pos.y, atoms[i]->pos.z, atoms[i]->b_iso};
+        return out;
+    }
+    std::vector<gemmi::Position> Positions() const {
+        std::vector<gemmi::Position> out;
+        for (const gemmi::Atom *a : atoms)
+            out.push_back(a->pos);
+        return out;
+    }
+    void SetPositions(const std::vector<gemmi::Position> &p) {
+        for (size_t i = 0; i < atoms.size(); i++)
+            atoms[i]->pos = p[i];
+    }
+    std::vector<double> B() const {
+        std::vector<double> out;
+        for (const gemmi::Atom *a : atoms)
+            out.push_back(a->b_iso);
+        return out;
+    }
+    void SetB(const std::vector<double> &b) {
+        for (size_t i = 0; i < atoms.size(); i++)
+            atoms[i]->b_iso = static_cast<float>(b[i]);
+    }
+
+    // What Refit() fitted, to start another context from without fitting it again.
+    struct Fit {
+        double b_floor = B_FLOOR;
+        double k_sol = 0, b_sol = 0, k_overall = 0;
+        gemmi::SMat33<double> b_star{0, 0, 0, 0, 0, 0};
+        XrayRowModel rows;
+        double grid_k_sol = -1, grid_b_sol = -1;
+    };
+    Fit Fitted() const { return {b_floor, k_sol, b_sol, k_overall, b_star, rows, grid_k_sol, grid_b_sol}; }
+    // Refit() as it was where `fit` was taken, for the atoms as they were there.
+    void Restore(const Fit &fit) {
+        b_floor = fit.b_floor;
+        engine->SetBlur(RefinementBlur(cell, *sg, d_min, b_floor));
+        k_sol = fit.k_sol;
+        b_sol = fit.b_sol;
+        k_overall = fit.k_overall;
+        b_star = fit.b_star;
+        rows = fit.rows;
+        grid_k_sol = fit.grid_k_sol;
+        grid_b_sol = fit.grid_b_sol;
+        engine->SetRowModel(rows);
+    }
+    // The next Refit() from nothing an earlier one found: the whole solvent box, the likelihood from the moments.
+    void ForgetStarts() {
+        grid_k_sol = grid_b_sol = -1;
+        rows.bin_d.clear();
+    }
+
+    // A new macro-cycle: the blur for the B the cycle may reach, the bulk-solvent mask of the model as it is,
+    // the scale and the solvent fitted to the working set, and the likelihood's parameters from the free set.
+    // Returns the R-factors of the model as it stands.
+    RFactors Refit() {
+        const RefinementStage stage("refit");
+        double b_min = b_ceiling;
+        for (const gemmi::Atom *a : atoms)
+            b_min = std::min<double>(b_min, a->b_iso);
+        b_floor = std::max(B_FLOOR, b_min - B_STEP_DOWN);
+        engine->SetBlur(RefinementBlur(cell, *sg, d_min, b_floor));
+        {
+            const RefinementStage s1("refit.fcalc");
+            engine->Fcalc(Model(), fcalc);
+        }
+        {
+            const RefinementStage s2("refit.fmask");
+            // the GPU engine masks on the same grid as BulkSolventMask (bit for bit but at points on an atom's
+            // radius, ModelMaskGPU.h)
+            if (engine->OnGPU())
+                engine->Fmask(Model(), fmask);
+            else
+                mask->Fmask(Model(), refl.hkl, fmask);
+        }
+        std::optional<RefinementStage> s3("refit.scale");
+
+        gemmi::AsuData<std::complex<float>> fc, fm;
+        gemmi::AsuData<gemmi::ValueSigma<float>> fo;
+        fc.unit_cell_ = fm.unit_cell_ = fo.unit_cell_ = cell;
+        fc.spacegroup_ = fm.spacegroup_ = fo.spacegroup_ = sg;
+        for (size_t m = 0; m < refl.Size(); m++) {
+            fc.v.push_back({refl.hkl[m], fcalc[m]});
+            fm.v.push_back({refl.hkl[m], fmask[m]});
+            if (!refl.free[m])
+                fo.v.push_back({refl.hkl[m], {refl.fo[m], 1.0f}});
+        }
+        gemmi::Scaling<float> scaling(cell, sg);
+        scaling.use_solvent = true;
+        scaling.prepare_points(fc, fo, &fm);
+        // the scale of the score: by robust least squares (ModelScaleBox::robust)
+#ifdef JFJOCH_USE_CUDA
+        if (scale_gpu)
+            scale_gpu->Fit(scaling, SolventBMax(Model()), nthreads, true, grid_k_sol, grid_b_sol);
+        else
+#endif
+            FitModelScale(scaling, {.b_hi = SolventBMax(Model()), .robust = true, .k_start = grid_k_sol,
+                                    .b_start = grid_b_sol}, nthreads);
+        s3.reset();
+        k_sol = grid_k_sol = scaling.k_sol;
+        b_sol = grid_b_sol = scaling.b_sol;
+        k_overall = scaling.k_overall;
+        b_star = scaling.b_star;
+        rows.k_total.resize(refl.Size());
+        rows.fmask.resize(refl.Size());
+        std::vector<std::complex<float>> fmodel(refl.Size());
+        for (size_t m = 0; m < refl.Size(); m++) {
+            rows.k_total[m] = static_cast<float>(scaling.get_overall_scale_factor(refl.hkl[m]));
+            rows.fmask[m] = static_cast<float>(scaling.get_solvent_scale(cell.calculate_stol_sq(refl.hkl[m]))) * fmask[m];
+            fmodel[m] = rows.k_total[m] * (fcalc[m] + rows.fmask[m]);
+        }
+        {
+            const RefinementStage s4("refit.ml");
+            EstimateLikelihoodParameters(refl, fmodel, rows, ml_threads);
+        }
+        engine->SetRowModel(rows);
+        return ComputeRFactors(refl, fmodel);
+    }
+
+    // The overall isotropic B of the last Refit() moved into the atoms, and into the solvent's B so that F_model stays
+    // as it is (but where an atom meets a bound of B): left in the scale, it and the atoms' B drift against each
+    // other as the B factors are refined - and the B restraints, in proportion to B, depend on which holds it.
+    // As phenix.refine moves the overall B into the atoms (Afonine et al. (2012) Acta Cryst. D68, 352-367)
+    void MoveOverallB() {
+        const gemmi::Mat33 b = cell.orth.mat.multiply(b_star.as_mat33()).multiply(cell.orth.mat.transpose());
+        const double b_iso = (b[0][0] + b[1][1] + b[2][2]) / 3.0;
+        double b_min = b_ceiling;
+        for (size_t i = 0; i < atoms.size(); i++)
+            if (rider_parent.empty() || rider_parent[i] < 0) {
+                atoms[i]->b_iso = static_cast<float>(std::clamp(atoms[i]->b_iso + b_iso, B_FLOOR, b_ceiling));
+                b_min = std::min<double>(b_min, atoms[i]->b_iso);
+            }
+        MoveRiders();
+        b_floor = std::max(B_FLOOR, b_min - B_STEP_DOWN);
+        engine->SetBlur(RefinementBlur(cell, *sg, d_min, b_floor));
+        // b_iso I in Cartesian is b_iso F F^T in the reciprocal basis
+        const gemmi::Mat33 f = cell.frac.mat.multiply(cell.frac.mat.transpose());
+        b_star = {b_star.u11 - b_iso * f[0][0], b_star.u22 - b_iso * f[1][1], b_star.u33 - b_iso * f[2][2],
+                  b_star.u12 - b_iso * f[0][1], b_star.u13 - b_iso * f[0][2], b_star.u23 - b_iso * f[1][2]};
+        b_sol += b_iso;
+        for (size_t m = 0; m < refl.Size(); m++) {
+            rows.k_total[m] *= static_cast<float>(std::exp(b_iso * refl.inv_d2[m] / 4.0));
+            rows.fmask[m] *= static_cast<float>(std::exp(-b_iso * refl.inv_d2[m] / 4.0));
+        }
+        engine->SetRowModel(rows);
+    }
+
+    // Every term of the score of the atoms as they are, at the scale, the solvent and the likelihood parameters
+    // of the last Refit().
+    RefinementScore Score() {
+        const std::vector<std::complex<float>> fmodel = FModel();
+        RefinementScore sc;
+        sc.k_overall = k_overall;
+        sc.k_sol = k_sol;
+        sc.b_sol = b_sol;
+        sc.mask_spacing = mask->Spacing();
+        // b_star is in the reciprocal basis (exp(-h^T b_star h / 4)); in Cartesian B = O b_star O^T
+        const gemmi::Mat33 b = cell.orth.mat.multiply(b_star.as_mat33()).multiply(cell.orth.mat.transpose());
+        sc.b_iso = (b[0][0] + b[1][1] + b[2][2]) / 3.0;
+        sc.b_aniso = {b[0][0] - sc.b_iso, b[1][1] - sc.b_iso, b[2][2] - sc.b_iso, b[0][1], b[0][2], b[1][2]};
+        const RFactors r = ComputeRFactors(refl, fmodel);
+        sc.r_work = r.r_work;
+        sc.r_free = r.r_free;
+        sc.n_work = r.n_work;
+        sc.n_free = r.n_free;
+        sc.nll_work = sc.nll_free = 0;
+        double fom_sum = 0;
+        int fom_n = 0;
+        for (size_t m = 0; m < refl.Size(); m++) {
+            double dfc = 0;
+            const double fc = std::abs(fmodel[m]);
+            const double nll = refine_math::AmplitudeNegLogLikelihood<double>(refl.fo[m], fc, rows.d[m], rows.var[m],
+                                                                             refl.centric[m], dfc);
+            (refl.free[m] ? sc.nll_free : sc.nll_work) += nll;
+            // the figure of merit of the same likelihood, over the working reflections
+            const double x = 2.0 * refl.fo[m] * rows.d[m] * fc / rows.var[m];
+            if (!refl.free[m]) {
+                fom_sum += Fom(x, refl.centric[m]);
+                fom_n++;
+            }
+        }
+        sc.fom = fom_n > 0 ? fom_sum / fom_n : NAN;
+        for (int p : rider_parent)
+            sc.hydrogens += p >= 0;
+        constexpr int SHELLS = 20;
+        double s_lo = refl.inv_d2[0], s_hi = refl.inv_d2[0];
+        for (double s2 : refl.inv_d2) {
+            s_lo = std::min(s_lo, s2);
+            s_hi = std::max(s_hi, s2);
+        }
+        std::vector<std::array<double, 4>> sums(SHELLS, {0, 0, 0, 0});
+        sc.shells.resize(SHELLS);
+        for (int k = 0; k < SHELLS; k++) {
+            sc.shells[k].d_max = 1.0 / std::sqrt(s_lo + (s_hi - s_lo) * k / SHELLS);
+            sc.shells[k].d_min = 1.0 / std::sqrt(s_lo + (s_hi - s_lo) * (k + 1) / SHELLS);
+        }
+        for (size_t m = 0; m < refl.Size(); m++) {
+            const int k = std::min(SHELLS - 1, static_cast<int>((refl.inv_d2[m] - s_lo) / (s_hi - s_lo) * SHELLS));
+            const int f = refl.free[m] ? 2 : 0;
+            sums[k][f] += std::fabs(refl.fo[m] - std::abs(fmodel[m]));
+            sums[k][f + 1] += refl.fo[m];
+            (refl.free[m] ? sc.shells[k].n_free : sc.shells[k].n_work)++;
+        }
+        for (int k = 0; k < SHELLS; k++) {
+            if (sums[k][1] > 0)
+                sc.shells[k].r_work = sums[k][0] / sums[k][1];
+            if (sums[k][3] > 0)
+                sc.shells[k].r_free = sums[k][2] / sums[k][3];
+        }
+        return sc;
+    }
+
+    // The X-ray target's curvature in each atom's B, up to one factor (CalibrateBCurvature): the likelihood's
+    // curvature in |F_model| of the cycle, 2 (k_total D)^2 / var, summed in resolution shells, against the atom's own
+    // part of it, (s^2 / 4)^2 f(s)^2 exp(-B s^2 / 2). A hydrogen's is its parent's.
+    std::vector<double> XrayBCurvatureShape() const {
+        constexpr int SHELLS = 32;
+        double s2_max = 0;
+        for (double s2 : refl.inv_d2)
+            s2_max = std::max(s2_max, s2);
+        std::vector<double> w(SHELLS, 0), s2_sum(SHELLS, 0);
+        std::vector<int> n(SHELLS, 0);
+        for (size_t m = 0; m < refl.Size(); m++) {
+            if (refl.free[m])
+                continue;
+            const int k = std::min(SHELLS - 1, static_cast<int>(refl.inv_d2[m] / s2_max * SHELLS));
+            const double kd = rows.k_total[m] * rows.d[m];
+            w[k] += 2.0 * kd * kd / rows.var[m];
+            s2_sum[k] += refl.inv_d2[m];
+            n[k]++;
+        }
+        std::map<std::pair<int, signed char>, std::vector<double>> f2;   // per element and charge, per shell
+        std::vector<double> shape(atoms.size(), 0.0);
+        for (size_t i = 0; i < atoms.size(); i++) {
+            const gemmi::Atom &a = *atoms[i];
+            std::vector<double> &f = f2[{static_cast<int>(a.element.elem), a.charge}];
+            if (f.empty()) {
+                const auto &coef = gemmi::IT92<double>::get(a.element, a.charge, a.serial);
+                f.resize(SHELLS, 0);
+                for (int k = 0; k < SHELLS; k++)
+                    if (n[k] > 0)
+                        f[k] = std::pow(coef.calculate_sf(s2_sum[k] / n[k] / 4.0), 2);
+            }
+            for (int k = 0; k < SHELLS; k++)
+                if (n[k] > 0) {
+                    const double s2 = s2_sum[k] / n[k];
+                    shape[i] += w[k] * f[k] * a.occ * a.occ * std::exp(-a.b_iso * s2 / 2.0) * s2 * s2 / 16.0;
+                }
+        }
+        for (size_t i = 0; i < rider_parent.size(); i++)
+            if (rider_parent[i] >= 0)
+                shape[rider_parent[i]] += shape[i];
+        return shape;
+    }
+
+    // The factor that turns XrayBCurvatureShape() into the X-ray target's curvature: its second derivative along a
+    // random +-1 direction of the B factors of `params`, by central differences of the gradient, over what the shape
+    // predicts for it.
+    double CalibrateBCurvature(const std::vector<int> &params, const std::vector<double> &shape) {
+        constexpr double EPS = 0.5;   // A^2
+        const std::vector<double> b0 = B();
+        std::mt19937 rng(7);
+        std::vector<double> v(params.size());
+        for (double &x : v)
+            x = rng() % 2 == 0 ? 1.0 : -1.0;
+        std::array<std::vector<std::array<double, 4>>, 2> g;
+        for (int side = 0; side < 2; side++) {
+            for (size_t k = 0; k < params.size(); k++)
+                atoms[params[k]]->b_iso = static_cast<float>(b0[params[k]] + (side == 0 ? EPS : -EPS) * v[k]);
+            MoveRiders();
+            engine->Evaluate(Model(), &g[side]);
+            FoldRiders(g[side]);
+        }
+        SetB(b0);
+        MoveRiders();
+        double num = 0, den = 0;
+        for (size_t k = 0; k < params.size(); k++) {
+            num += v[k] * (g[0][params[k]][3] - g[1][params[k]][3]) / (2 * EPS);
+            den += shape[params[k]];
+        }
+        return den > 0 ? std::max(num / den, 0.0) : 0.0;
+    }
+
+    // F_model with the cycle's scale and solvent, for the atoms as they are now.
+    std::vector<std::complex<float>> FModel() {
+        engine->Fcalc(Model(), fcalc);
+        std::vector<std::complex<float>> fmodel(refl.Size());
+        for (size_t m = 0; m < refl.Size(); m++)
+            fmodel[m] = rows.k_total[m] * (fcalc[m] + rows.fmask[m]);
+        return fmodel;
+    }
+};
+
+ceres::GradientProblemSolver::Options SolverOptions(int iterations) {
+    ceres::GradientProblemSolver::Options options;
+    options.line_search_direction_type = ceres::LBFGS;
+    options.max_num_iterations = iterations;
+    options.function_tolerance = 1e-7;
+    options.gradient_tolerance = 1e-10;
+    options.parameter_tolerance = 1e-9;
+    options.logging_type = ceres::SILENT;
+    return options;
+}
+
+// SolverOptions(iterations) that stop at the next iteration, where the minimiser stands, once ctx is cancelled.
+class CancelCheck : public ceres::IterationCallback {
+public:
+    explicit CancelCheck(const Context &ctx) : ctx_(ctx) {}
+    ceres::CallbackReturnType operator()(const ceres::IterationSummary &) override {
+        return ctx_.Cancelled() ? ceres::SOLVER_TERMINATE_SUCCESSFULLY : ceres::SOLVER_CONTINUE;
+    }
+    ceres::GradientProblemSolver::Options Options(int iterations) const {
+        ceres::GradientProblemSolver::Options options = SolverOptions(iterations);
+        options.callbacks.push_back(const_cast<CancelCheck *>(this));
+        return options;
+    }
+
+private:
+    const Context &ctx_;
+};
+
+// The positions or the B factors of the refinable atoms, against w times the X-ray target plus a restraint set
+// (minimised by RefinementMinimiser).
+class AtomTarget {
+public:
+    enum class Mode { Xyz, B };
+    AtomTarget(Context &ctx, Mode mode, const std::vector<int> &param_atoms, double weight, int restraint_set)
+        : ctx_(ctx), mode_(mode), param_atoms_(param_atoms), weight_(weight), restraint_set_(restraint_set) {}
+
+    // The parameters of the atoms as they are: x y z per atom, or B per atom.
+    std::vector<double> Get() const {
+        std::vector<double> p;
+        for (int i : param_atoms_) {
+            const gemmi::Atom &a = *ctx_.atoms[i];
+            if (mode_ == Mode::Xyz) {
+                p.push_back(a.pos.x);
+                p.push_back(a.pos.y);
+                p.push_back(a.pos.z);
+            } else
+                p.push_back(a.b_iso);
+        }
+        return p;
+    }
+    // The atoms set to the parameters, their riders with them.
+    void Set(const double *p) const {
+        const int n = static_cast<int>(param_atoms_.size());
+        ParallelChunks(n, ThreadsForWork(n, ctx_.nthreads, 16384), [&](int lo, int hi) {
+            for (int k = lo; k < hi; k++) {
+                gemmi::Atom &a = *ctx_.atoms[param_atoms_[k]];
+                if (mode_ == Mode::Xyz)
+                    a.pos = gemmi::Position(p[3 * k], p[3 * k + 1], p[3 * k + 2]);
+                else
+                    a.b_iso = static_cast<float>(std::clamp(p[k], ctx_.b_floor, ctx_.b_ceiling));
+            }
+        });
+        ctx_.MoveRiders();
+    }
+    // the most a parameter moves in the first trial of a line search
+    double MaxStep() const { return mode_ == Mode::Xyz ? MAX_STEP_XYZ : MAX_STEP_B; }
+
+    bool Evaluate(const double *p, double *cost, double *gradient) const {
+        const RefinementStage stage(mode_ == Mode::Xyz ? "eval.xyz" : "eval.b");
+        Set(p);
+        ctx_.evaluations++;
+        std::vector<std::array<double, 4>> &gx = gx_, &gr = gr_;
+        double xray = 0, restraints = 0;
+        {
+            const RefinementStage s1("eval.engine");
+            xray = ctx_.engine->EvaluateWithRestraints(ctx_.Model(), restraint_set_, gradient != nullptr ? &gx : nullptr,
+                                                       gradient != nullptr ? &gr : nullptr, restraints);
+        }
+        *cost = weight_ * xray + restraints;
+        if (gradient == nullptr)
+            return std::isfinite(*cost);
+        ctx_.FoldRiders(gx);
+        const int n = static_cast<int>(param_atoms_.size());
+        ParallelChunks(n, ThreadsForWork(n, ctx_.nthreads, 16384), [&](int lo, int hi) {
+            for (int k = lo; k < hi; k++) {
+                const int i = param_atoms_[k];
+                if (mode_ == Mode::Xyz)
+                    for (int c = 0; c < 3; c++)
+                        gradient[3 * k + c] = weight_ * gx[i][c] + gr[i][c];
+                else {
+                    // held at a bound, B does not move further out: by the whole target, restraints included
+                    const double g = weight_ * gx[i][3] + gr[i][3];
+                    const bool held = (p[k] <= ctx_.b_floor && g > 0) || (p[k] >= ctx_.b_ceiling && g < 0);
+                    gradient[k] = held ? 0.0 : g;
+                }
+            }
+        });
+        return std::isfinite(*cost);
+    }
+
+private:
+    Context &ctx_;
+    Mode mode_;
+    const std::vector<int> &param_atoms_;
+    double weight_;
+    int restraint_set_;
+    // the gradients per atom, kept from evaluation to evaluation (7 MB each on a large model: made anew, their
+    // pages fault in every time)
+    mutable std::vector<std::array<double, 4>> gx_, gr_;
+};
+
+// The minimiser's diagonal for the B factors of `param_atoms` (RefinementMinimiser::SetDiagonal): weight times the
+// X-ray target's curvature in B plus the B restraints', each element at least a thousandth of the median. The
+// positions take none: their restraints' curvature is that of stiff bonds and angles, which move atoms together, so
+// as a diagonal it slows rather than scales the minimiser.
+std::vector<double> BDiagonal(const std::vector<double> &xray, const std::vector<double> &restraints,
+                              const std::vector<int> &param_atoms, double weight) {
+    std::vector<double> h;
+    for (int i : param_atoms)
+        h.push_back(weight * xray[i] + restraints[i]);
+    std::vector<double> sorted = h;
+    std::nth_element(sorted.begin(), sorted.begin() + sorted.size() / 2, sorted.end());
+    const double floor = std::max(1e-3 * sorted[sorted.size() / 2], 1e-12);
+    for (double &v : h)
+        v = std::max(v, floor);
+    return h;
+}
+
+// `minimiser` carries its memory from the call before; `diagonal` is the curvature it scales the steps by (none: 1).
+void Minimise(Context &ctx, const AtomTarget &target, int iterations, RefinementMinimiser &minimiser,
+              std::vector<double> diagonal = {}) {
+    std::vector<double> p = target.Get();
+    if (p.empty())
+        return;
+    minimiser.SetDiagonal(diagonal.empty() ? std::vector<double>(p.size(), 1.0) : std::move(diagonal));
+    minimiser.Minimise([&](const std::vector<double> &x, double &f, std::vector<double> &g) {
+                           return target.Evaluate(x.data(), &f, g.data());
+                       },
+                       p, iterations, MINIMISER_F_TOLERANCE, target.MaxStep(), [&]() { return ctx.Cancelled(); });
+    target.Set(p.data());   // where the minimiser ended, not where its last line search probed
+}
+
+// Groups of atoms that move as rigid bodies (one per chain) against the X-ray target: per body an angle-axis
+// rotation about its centroid, scaled by its rms radius so that a unit moves a typical atom by an angstrom as a
+// unit of translation does, then a translation.
+class RigidBodiesTarget : public ceres::FirstOrderFunction {
+public:
+    RigidBodiesTarget(Context &ctx, const std::vector<std::vector<int>> &bodies)
+        : ctx_(ctx), bodies_(bodies), base_(ctx.Positions()) {
+        for (const std::vector<int> &b : bodies) {
+            gemmi::Position c;
+            for (int i : b)
+                c += base_[i];
+            c *= 1.0 / static_cast<double>(b.size());
+            double r2 = 0;
+            for (int i : b)
+                r2 += c.dist_sq(base_[i]);
+            centre_.push_back(c);
+            radius_.push_back(std::max(1.0, std::sqrt(r2 / static_cast<double>(b.size()))));
+        }
+    }
+    int NumParameters() const override { return static_cast<int>(6 * bodies_.size()); }
+
+    bool Evaluate(const double *q, double *cost, double *gradient) const override {
+        const RefinementStage stage("eval.rigid");
+        Place(q);
+        ctx_.evaluations++;
+        std::vector<std::array<double, 4>> g;
+        *cost = ctx_.engine->Evaluate(ctx_.Model(), gradient != nullptr ? &g : nullptr);
+        if (gradient == nullptr)
+            return std::isfinite(*cost);
+        using Jet = ceres::Jet<double, 3>;
+        for (size_t b = 0; b < bodies_.size(); b++) {
+            const Jet aa[3] = {Jet(q[6 * b] / radius_[b], 0), Jet(q[6 * b + 1] / radius_[b], 1),
+                               Jet(q[6 * b + 2] / radius_[b], 2)};
+            double dq[6] = {0, 0, 0, 0, 0, 0};
+            for (int i : bodies_[b]) {
+                const gemmi::Position d = base_[i] - centre_[b];
+                const Jet p[3] = {Jet(d.x), Jet(d.y), Jet(d.z)};
+                Jet rp[3];
+                ceres::AngleAxisRotatePoint(aa, p, rp);
+                for (int c = 0; c < 3; c++) {
+                    for (int k = 0; k < 3; k++)
+                        dq[k] += g[i][c] * rp[c].v[k] / radius_[b];
+                    dq[3 + c] += g[i][c];
+                }
+            }
+            std::copy(dq, dq + 6, gradient + 6 * b);
+        }
+        return std::isfinite(*cost);
+    }
+
+    void Place(const double *q) const {
+        for (size_t b = 0; b < bodies_.size(); b++) {
+            const double aa[3] = {q[6 * b] / radius_[b], q[6 * b + 1] / radius_[b], q[6 * b + 2] / radius_[b]};
+            for (int i : bodies_[b]) {
+                const gemmi::Position d = base_[i] - centre_[b];
+                const double p[3] = {d.x, d.y, d.z};
+                double rp[3];
+                ceres::AngleAxisRotatePoint(aa, p, rp);
+                ctx_.atoms[i]->pos = gemmi::Position(rp[0] + centre_[b].x + q[6 * b + 3], rp[1] + centre_[b].y + q[6 * b + 4],
+                                                     rp[2] + centre_[b].z + q[6 * b + 5]);
+            }
+        }
+    }
+
+private:
+    Context &ctx_;
+    const std::vector<std::vector<int>> &bodies_;
+    std::vector<gemmi::Position> base_;
+    std::vector<gemmi::Position> centre_;
+    std::vector<double> radius_;
+};
+
+// One B shift per group of atoms (a residue), against the X-ray target.
+class GroupBTarget : public ceres::FirstOrderFunction {
+public:
+    GroupBTarget(Context &ctx, const std::vector<std::vector<int>> &groups)
+        : ctx_(ctx), groups_(groups), base_(ctx.B()) {}
+    int NumParameters() const override { return static_cast<int>(groups_.size()); }
+
+    bool Evaluate(const double *q, double *cost, double *gradient) const override {
+        const RefinementStage stage("eval.group_b");
+        Place(q);
+        ctx_.evaluations++;
+        std::vector<std::array<double, 4>> g;
+        *cost = ctx_.engine->Evaluate(ctx_.Model(), gradient != nullptr ? &g : nullptr);
+        if (gradient != nullptr)
+            for (size_t k = 0; k < groups_.size(); k++) {
+                gradient[k] = 0;
+                for (int i : groups_[k]) {
+                    const double b = base_[i] + q[k];
+                    if (b > ctx_.b_floor && b < ctx_.b_ceiling)
+                        gradient[k] += g[i][3];
+                }
+            }
+        return std::isfinite(*cost);
+    }
+
+    void Place(const double *q) const {
+        for (size_t k = 0; k < groups_.size(); k++)
+            for (int i : groups_[k])
+                ctx_.atoms[i]->b_iso = static_cast<float>(std::clamp(base_[i] + q[k], ctx_.b_floor, ctx_.b_ceiling));
+    }
+
+private:
+    Context &ctx_;
+    const std::vector<std::vector<int>> &groups_;
+    std::vector<double> base_;
+};
+
+// The placement stage: rigid bodies, then group B.
+void RefinePlacement(Context &ctx, bool group_b, RefinementResult &result) {
+    const RefinementStage stage("placement");
+    std::vector<std::vector<int>> bodies, groups;
+    size_t i = 0;
+    for (const gemmi::Chain &ch : ctx.Model().chains) {
+        std::vector<int> body;
+        for (const gemmi::Residue &r : ch.residues) {
+            std::vector<int> group;
+            for (size_t k = 0; k < r.atoms.size(); k++, i++) {
+                group.push_back(static_cast<int>(i));
+                if (!r.is_water())
+                    body.push_back(static_cast<int>(i));
+            }
+            groups.push_back(group);
+        }
+        // A chain of a few atoms (an ion, a ligand of its own chain) stays where it is.
+        if (body.size() >= 50)
+            bodies.push_back(body);
+    }
+    // Each step is kept only where it lowers R-free beyond the tie: a deposited model was refined atom by atom
+    // already, and moving its chains or shifting its B factors residue by residue then only makes it worse.
+    RFactors before = ctx.Refit();
+    if (!bodies.empty()) {
+        const std::vector<gemmi::Position> pos0 = ctx.Positions();
+        std::vector<double> q(6 * bodies.size(), 0.0);
+        auto target = std::make_unique<RigidBodiesTarget>(ctx, bodies);
+        RigidBodiesTarget *rb = target.get();
+        ceres::GradientProblem problem(std::move(target));
+        ceres::GradientProblemSolver::Summary summary;
+        const CancelCheck cancel_check(ctx);
+        ceres::Solve(cancel_check.Options(30), problem, q.data(), &summary);
+        rb->Place(q.data());
+        const RFactors after = ctx.Refit();
+        if (after.r_free < before.r_free - R_FREE_TIE) {
+            result.rigid_bodies = static_cast<int>(bodies.size());
+            before = after;
+        } else {
+            ctx.SetPositions(pos0);
+            before = ctx.Refit();
+        }
+    }
+    if (group_b) {
+        const std::vector<double> b0 = ctx.B();
+        std::vector<double> q(groups.size(), 0.0);
+        auto target = std::make_unique<GroupBTarget>(ctx, groups);
+        GroupBTarget *gb = target.get();
+        ceres::GradientProblem problem(std::move(target));
+        ceres::GradientProblemSolver::Summary summary;
+        const CancelCheck cancel_check(ctx);
+        ceres::Solve(cancel_check.Options(30), problem, q.data(), &summary);
+        gb->Place(q.data());
+        result.group_b = ctx.Refit().r_free < before.r_free - R_FREE_TIE;
+        if (!result.group_b)
+            ctx.SetB(b0);
+    }
+}
+
+// The X-ray weight that balances the two gradients: the norm of the geometry's gradient (taken on the model
+// shaken by 0.1 A, where a refined model's geometry would have none) over the norm of the X-ray target's.
+// Following Brunger, Karplus & Petsko (1989) Acta Cryst. A45, 50-61, as phenix.refine starts its weight search
+// (Afonine et al. (2012) Acta Cryst. D68, 352-367)
+double BalancedWeight(Context &ctx, const std::vector<int> &refinable) {
+    std::vector<std::array<double, 4>> gx, gr;
+    ctx.engine->Evaluate(ctx.Model(), &gx);
+    std::vector<std::array<double, 4>> xyzb = ctx.XyzB();
+    std::mt19937 rng(1);
+    std::normal_distribution<double> shake(0.0, 0.1);
+    for (std::array<double, 4> &a : xyzb)
+        for (int c = 0; c < 3; c++)
+            a[c] += shake(rng);
+    ctx.engine->EvaluateRestraints(0, xyzb, &gr);
+    double nx = 0, ng = 0;
+    for (int i : refinable)
+        for (int c = 0; c < 3; c++) {
+            nx += gx[i][c] * gx[i][c];
+            ng += gr[i][c] * gr[i][c];
+        }
+    return nx > 0 ? std::sqrt(ng / nx) : 1.0;
+}
+
+// The B factors' X-ray weight that balances the two gradients, as BalancedWeight() does for the positions: the B
+// similarity's gradient on the model with its B shaken by 20% (a flat B, as a model may come, gives none) over the
+// X-ray target's.
+double BalancedADPWeight(Context &ctx, const RestraintSet &b_restraints, const std::vector<int> &refinable) {
+    std::vector<std::array<double, 4>> gx;
+    ctx.engine->Evaluate(ctx.Model(), &gx);
+    ctx.FoldRiders(gx);
+    std::vector<std::array<double, 4>> xyzb = ctx.XyzB();
+    std::mt19937 rng(2);
+    std::normal_distribution<double> shake(0.0, 0.2);
+    for (std::array<double, 4> &a : xyzb)
+        a[3] *= std::exp(shake(rng));
+    std::vector<std::array<double, 4>> gr(xyzb.size(), {0, 0, 0, 0});
+    EvaluateRestraints(b_restraints, xyzb, &gr);
+    double nx = 0, ng = 0;
+    for (int i : refinable) {
+        nx += gx[i][3] * gx[i][3];
+        ng += gr[i][3] * gr[i][3];
+    }
+    return nx > 0 ? std::sqrt(ng / nx) : 1.0;
+}
+
+// The model's map coefficients and its difference map, weighted by the refinement's own likelihood: m its figure
+// of merit and D its D (2mFo - DFc, mFo - DFc).
+// Following Read (1986) Acta Cryst. A42, 140-149
+void MakeMaps(Context &ctx, const std::vector<MergedReflection> &merged, double wavelength_A, RefinementResult &result) {
+    const RefinementStage stage("maps");
+    ctx.Refit();
+    const std::vector<std::complex<float>> fmodel = ctx.FModel();
+    const gemmi::GroupOps gops = ctx.sg->operations();
+    std::vector<double> fom(ctx.refl.Size());
+    double fom_sum = 0;
+    int fom_n = 0;
+    for (size_t m = 0; m < ctx.refl.Size(); m++) {
+        const double x = 2.0 * ctx.refl.fo[m] * ctx.rows.d[m] * std::abs(fmodel[m]) / ctx.rows.var[m];
+        fom[m] = Fom(x, ctx.refl.centric[m]);
+        if (!ctx.refl.free[m]) {
+            fom_sum += fom[m];
+            fom_n++;
+        }
+    }
+    result.mean_fom = fom_n > 0 ? fom_sum / fom_n : 0;
+
+    auto maps = std::make_shared<ModelMaps>();
+    MtzTable &mtz = maps->coefficients;
+    mtz.space_group_name = ctx.sg->xhm();
+    mtz.unit_cell = UnitCell{static_cast<float>(ctx.cell.a), static_cast<float>(ctx.cell.b), static_cast<float>(ctx.cell.c),
+                             static_cast<float>(ctx.cell.alpha), static_cast<float>(ctx.cell.beta),
+                             static_cast<float>(ctx.cell.gamma)};
+    mtz.datasets = {{"HKL_base", "HKL_base", "HKL_base", 0.0f},
+                    {"refinement", "refinement", "refinement", static_cast<float>(wavelength_A)}};
+    const std::pair<const char *, char> columns[] = {{"H", 'H'}, {"K", 'H'}, {"L", 'H'}, {"FP", 'F'}, {"FC", 'F'},
+                                                     {"PHIC", 'P'}, {"FWT", 'F'}, {"PHWT", 'P'}, {"DELFWT", 'F'},
+                                                     {"PHDELWT", 'P'}, {"FOM", 'W'}, {"FREE", 'I'}};
+    for (const auto &[label, type] : columns)
+        mtz.columns.push_back({label, type, type == 'H' ? 0 : 1, {}});
+    gemmi::AsuData<std::complex<float>> diff;
+    diff.unit_cell_ = ctx.cell;
+    diff.spacegroup_ = ctx.sg;
+    for (size_t m = 0; m < ctx.refl.Size(); m++) {
+        const double fo = ctx.refl.fo[m], fc = std::abs(fmodel[m]);
+        const double mw = fom[m], d = ctx.rows.d[m];
+        const double fwt = ctx.refl.centric[m] ? mw * fo : 2 * mw * fo - d * fc;
+        const double delfwt = mw * fo - d * fc;
+        const double phi = std::arg(fmodel[m]);
+        double phi_deg = phi * 180.0 / PI;
+        if (phi_deg < 0)
+            phi_deg += 360.0;
+        const float row[] = {static_cast<float>(ctx.refl.hkl[m][0]), static_cast<float>(ctx.refl.hkl[m][1]),
+                             static_cast<float>(ctx.refl.hkl[m][2]), static_cast<float>(fo), static_cast<float>(fc),
+                             static_cast<float>(phi_deg), static_cast<float>(fwt), static_cast<float>(phi_deg),
+                             static_cast<float>(delfwt), static_cast<float>(phi_deg), static_cast<float>(mw),
+                             ctx.refl.free[m] ? 0.0f : 1.0f};
+        for (size_t c = 0; c < mtz.columns.size(); c++)
+            mtz.columns[c].values.push_back(row[c]);
+        diff.v.push_back({ctx.refl.hkl[m], std::polar(static_cast<float>(delfwt), static_cast<float>(phi))});
+    }
+    result.maps = maps;
+    // The difference map beside the anomalous one below: neither reads the other.
+    std::future<void> difference_map = std::async(std::launch::async, [&diff, &result] {
+        const std::array<int, 3> size = gemmi::get_size_for_hkl(diff, {{0, 0, 0}}, 3.0);
+        result.difference_map = std::make_shared<gemmi::Grid<float>>(MapFromFPhi(gemmi::get_f_phi_on_grid<float>(diff, size, true)));
+        result.difference_map_rms = gemmi::calculate_data_statistics(result.difference_map->data).rms;
+    });
+
+    // The anomalous difference map: F(+) - F(-) on the model's phase turned back by 90 degrees, read on the +
+    // rows of an anomalous merge only (as model validation reads it).
+    // Following ANODE, Thorn & Sheldrick (2011) J. Appl. Cryst. 44, 1285-1287
+    const gemmi::ReciprocalAsu asu(ctx.sg);
+    std::map<gemmi::Miller, float> danom;
+    for (const MergedReflection &r : merged) {
+        if (!std::isfinite(r.F_plus) || !std::isfinite(r.F_minus))
+            continue;
+        const gemmi::Miller h{{r.h, r.k, r.l}};
+        if (gops.is_reflection_centric(h))
+            continue;
+        const auto [hasu, plus] = asu.to_asu_sign(h, gops);
+        if (plus)
+            danom[hasu] = r.F_plus - r.F_minus;
+    }
+    if (!danom.empty()) {
+        gemmi::AsuData<std::complex<float>> anom;
+        anom.unit_cell_ = ctx.cell;
+        anom.spacegroup_ = ctx.sg;
+        for (size_t m = 0; m < ctx.refl.Size(); m++) {
+            const auto it = danom.find(ctx.refl.hkl[m]);
+            if (it != danom.end())
+                anom.v.push_back({ctx.refl.hkl[m], it->second * std::polar(1.0f, static_cast<float>(std::arg(fmodel[m]) - PI / 2))});
+        }
+        if (!anom.v.empty()) {
+            result.anomalous_map = std::make_shared<gemmi::Grid<float>>(
+                MapFromFPhi(gemmi::get_f_phi_on_grid<float>(anom, gemmi::get_size_for_hkl(anom, {{0, 0, 0}}, 3.0), true)));
+            result.anomalous_map_rms = gemmi::calculate_data_statistics(result.anomalous_map->data).rms;
+        }
+    }
+    difference_map.get();
+}
+
+// The engine for the model as it is now: on the GPU where it is wanted and takes the case within its budget,
+// on the CPU otherwise.
+void MakeEngine(Context &ctx, bool gpu, const RefinementSettings &settings, Logger &logger) {
+    const RefinementStage stage("engine");
+    ctx.engine.reset();
+#ifdef JFJOCH_USE_CUDA
+    ctx.scale_gpu.reset();
+    if (gpu && get_gpu_count() > 0) {
+        try {
+            const int device = get_gpu();
+            const size_t card = get_gpu_total_memory(device);
+            const size_t usable = card / 5 * 4;
+            const size_t budget = usable > settings.gpu_resident_bytes ? usable - settings.gpu_resident_bytes : 0;
+            size_t bytes = 0;
+            ctx.engine = MakeRefinementEngineGPU(device, ctx.cell, *ctx.sg, ctx.d_min, ctx.refl, ctx.Model(),
+                                                 ctx.b_ceiling, budget, &bytes, settings.nthreads);
+            ctx.device = device;
+            ctx.engine_bytes = bytes;
+            if (ctx.engine) {
+                ctx.scale_gpu = std::make_unique<ModelScaleGPUPool>(device, ctx.refl.Size(), 1);
+                logger.Debug("Refinement: GPU engine {:.2f} GB of a {:.2f} GB budget (scale pool {:.2f} GB)", bytes / 1e9,
+                             budget / 1e9, ModelScaleGPUPool::DeviceBytes(ctx.refl.Size(), 1, true) / 1e9);
+            } else
+                logger.Info("Refinement: on the CPU - the GPU cannot take this case or {:.1f} GB is over its budget",
+                            bytes / 1e9);
+        } catch (const JFJochException &e) {
+            logger.Warning("Refinement: the GPU failed ({}), on the CPU", e.what());
+            ctx.engine.reset();
+            ctx.scale_gpu.reset();
+        }
+    }
+#else
+    (void) gpu;
+    (void) logger;
+#endif
+    if (!ctx.engine)
+        ctx.engine = MakeRefinementEngineCPU(ctx.cell, *ctx.sg, ctx.d_min, ctx.refl, settings.nthreads);
+}
+
+// The riding hydrogens placed on their parents as they are, and the offsets and B they ride with.
+void PlaceRiders(Context &ctx, RefinementTopology &topo) {
+    const RefinementStage stage("riders");
+    PlaceRidingHydrogens(topo);
+    ctx.rider_offset.assign(ctx.atoms.size(), gemmi::Position());
+    for (size_t i = 0; i < ctx.atoms.size(); i++)
+        if (ctx.rider_parent[i] >= 0) {
+            ctx.rider_offset[i] = ctx.atoms[i]->pos - ctx.atoms[ctx.rider_parent[i]]->pos;
+            ctx.atoms[i]->b_iso = ctx.atoms[ctx.rider_parent[i]]->b_iso;
+        }
+}
+
+// The geometry and the repulsions of the model as it is.
+RestraintSet RestraintsNow(Context &ctx, const RefinementTopology &topo) {
+    const RefinementStage stage("repulsions");
+    RestraintSet set = topo.geometry;
+    set.Append(topo.metal_bonds);
+    set.Append(BuildRepulsions(topo, ctx.Model(), ctx.cell, *ctx.sg, REPULSION_MARGIN, ctx.nthreads));
+    set.Finalize(ctx.atoms.size());
+    return set;
+}
+
+// The B similarity of the model as it is: bonded and angle-related pairs, and atoms in contact.
+RestraintSet BRestraintsNow(Context &ctx, const RefinementTopology &topo) {
+    const RefinementStage stage("b_restraints");
+    RestraintSet set = topo.adp;
+    set.Append(BuildBContacts(topo, ctx.Model(), ctx.cell, *ctx.sg, ctx.nthreads));
+    set.Finalize(ctx.atoms.size());
+    return set;
+}
+
+// Where a weight trial runs: a model with its topology and its engine.
+struct TrialSlot {
+    Context *ctx;
+    RefinementTopology *topo;
+};
+
+// A slot of its own beside the main one.
+struct OwnSlot {
+    Context ctx;
+    RefinementTopology topo;
+};
+
+// A copy of the model as it was before the topology was made (the same topology comes out of it, hydrogens
+// included), with an engine of the main one's kind - a GPU's on `device`. Null where the card cannot make one.
+std::unique_ptr<OwnSlot> MakeOwnSlot(const gemmi::Structure &before_topology, const Context &main, int device,
+                                     size_t nthreads, const RefinementSettings &settings) {
+    auto slot = std::make_unique<OwnSlot>();
+    Context &ctx = slot->ctx;
+    ctx.st = before_topology;
+    ctx.cell = main.cell;
+    ctx.sg = main.sg;
+    ctx.d_min = main.d_min;
+    ctx.refl = main.refl;
+    ctx.nthreads = nthreads;
+    ctx.ml_threads = settings.nthreads;
+    ctx.cancel = main.cancel;
+    ctx.b_ceiling = main.b_ceiling;
+    ctx.mask = std::make_unique<BulkSolventMask>(ctx.cell, *ctx.sg, ctx.d_min, nthreads);
+    slot->topo = BuildRefinementTopology(ctx.st, settings.riding_hydrogens);
+    ctx.atoms = AtomList(ctx.Model());
+    ctx.SetRiderParents(slot->topo.rider_parent);
+#ifdef JFJOCH_USE_CUDA
+    if (main.engine->OnGPU()) {
+        try {
+            ctx.engine = MakeRefinementEngineGPU(device, ctx.cell, *ctx.sg, ctx.d_min, ctx.refl, ctx.Model(),
+                                                 ctx.b_ceiling, SIZE_MAX, nullptr, nthreads);
+            if (!ctx.engine)
+                return nullptr;
+            ctx.scale_gpu = std::make_unique<ModelScaleGPUPool>(device, ctx.refl.Size(), 1);
+        } catch (const std::exception &) {
+            return nullptr;
+        }
+        ctx.device = device;
+    }
+#else
+    (void) device;
+#endif
+    if (!ctx.engine)
+        ctx.engine = MakeRefinementEngineCPU(ctx.cell, *ctx.sg, ctx.d_min, ctx.refl, nthreads);
+    ctx.engine->SetRestraints(1, slot->topo.adp);
+    return slot;
+}
+
+// The devices of the slots beside the main one, `wanted` of them at most: the GPUs in turn from the main
+// engine's, each taking engines while they fit in its budget. The slots beyond one per card go to the cards the
+// ladder's long trials (those refining B) leave free: RunTrials gives the long trials to the first slots, one
+// card each, so a short trial then shares a card with a short one, not with a long one. -1 for each one on the
+// CPU, where the main one and those beside it are no more than the threads.
+std::vector<int> OwnSlotDevices(const Context &main, int wanted, const RefinementSettings &settings) {
+#ifdef JFJOCH_USE_CUDA
+    if (main.engine->OnGPU()) {
+        const int n = get_gpu_count();
+        const int longest = static_cast<int>(settings.weight_ladder.size()) *
+                            static_cast<int>(std::count_if(settings.adp_ladder.begin(), settings.adp_ladder.end(),
+                                                           [](double adp) { return adp > 0; }));
+        const int free = n - longest;   // cards without a long trial, after the first slots' cards
+        // a slot's engine and its scale pool, the robust fit's buffers included
+        const size_t slot_bytes = main.engine_bytes + ModelScaleGPUPool::DeviceBytes(main.refl.Size(), 1, true);
+        std::vector<size_t> used(n, 0);
+        used[main.device] = slot_bytes;
+        std::vector<int> devices;
+        for (int k = 1; k <= wanted; k++) {
+            const int d = (k < n || free <= 0) ? (main.device + k) % n : (main.device + longest + (k - n) % free) % n;
+            const size_t usable = get_gpu_total_memory(d) / 5 * 4;
+            const size_t budget = usable > settings.gpu_resident_bytes ? usable - settings.gpu_resident_bytes : 0;
+            if (used[d] + slot_bytes <= budget) {
+                used[d] += slot_bytes;
+                devices.push_back(d);
+            }
+        }
+        return devices;
+    }
+#endif
+    // on the CPU, no more trials at once than threads: each slot is a model, a topology and an engine of its own
+    const int beside = std::min(wanted, static_cast<int>(settings.nthreads) - 1);
+    return std::vector<int>(std::max(beside, 0), -1);
+}
+
+// One weight trial: `cycles` macro-cycles from pos0 and b0, of the positions at X-ray weight w and, where adp_w is
+// not 0, the B factors at X-ray weight adp_w. `fit`: what was fitted at pos0 and b0 already, null to fit it here.
+struct TrialOutcome {
+    RefinementWeightTrial trial;
+    std::vector<gemmi::Position> pos;
+    std::vector<double> b;
+    Context::Fit fit;   // the scale, the solvent and the likelihood's parameters fitted where it ended
+    std::string line;   // what the log says of it
+    bool ran = false;   // false: left out, the refinement cancelled before it
+};
+
+TrialOutcome RunTrial(TrialSlot slot, const std::vector<int> &refinable, const std::vector<gemmi::Position> &pos0,
+                      const std::vector<double> &b0, const Context::Fit *fit, double w, double adp_w, int cycles,
+                      const RefinementSettings &settings) {
+    Context &ctx = *slot.ctx;
+    RefinementTopology &topo = *slot.topo;
+    const RefinementStage stage(adp_w > 0 ? "rung.b" : "rung.xyz");
+    ctx.SetPositions(pos0);
+    ctx.SetB(b0);
+    // the positions and the B factors in turn, each with a memory of its own kept from macro-cycle to macro-cycle
+    const AtomTarget xyz(ctx, AtomTarget::Mode::Xyz, refinable, w, 0), b(ctx, AtomTarget::Mode::B, refinable, adp_w, 1);
+    RefinementMinimiser xyz_minimiser(20, ctx.nthreads), b_minimiser(20, ctx.nthreads);
+    double xray_scale = 0;
+    for (int cycle = 0; cycle < cycles && !ctx.Cancelled(); cycle++) {
+        PlaceRiders(ctx, topo);
+        if (cycle == 0 && fit != nullptr)
+            ctx.Restore(*fit);
+        else {
+            // a trial starts from nothing the slot's previous trial left
+            if (cycle == 0)
+                ctx.ForgetStarts();
+            ctx.Refit();
+        }
+        if (adp_w > 0)
+            ctx.MoveOverallB();
+        {
+            const RestraintSet set = RestraintsNow(ctx, topo);
+            const RefinementStage s1("set_restraints");
+            ctx.engine->SetRestraints(0, set);
+        }
+        {
+            const RefinementStage s2("minimise.xyz");
+            Minimise(ctx, xyz, settings.xyz_iterations, xyz_minimiser);
+        }
+        if (adp_w > 0) {
+            const RestraintSet b_set = BRestraintsNow(ctx, topo);
+            ctx.engine->SetRestraints(1, b_set);
+            std::vector<double> xray = ctx.XrayBCurvatureShape();
+            if (cycle == 0)
+                xray_scale = ctx.CalibrateBCurvature(refinable, xray);
+            for (double &x : xray)
+                x *= xray_scale;
+            const RefinementStage s3("minimise.b");
+            Minimise(ctx, b, settings.b_iterations, b_minimiser,
+                     BDiagonal(xray, BRestraintCurvature(b_set, ctx.XyzB()), refinable, adp_w));
+        }
+    }
+    PlaceRiders(ctx, topo);
+    TrialOutcome out;
+    RefinementWeightTrial &t = out.trial;
+    t.weight = w;
+    t.adp_weight = adp_w;
+    const RFactors rf = ctx.Refit();
+    t.r_work = rf.r_work;
+    t.r_free = rf.r_free;
+    {
+        const RefinementStage s1("measure");
+        t.geometry = MeasureGeometry(topo.geometry,
+                                     BuildRepulsions(topo, ctx.Model(), ctx.cell, *ctx.sg, 0.0, ctx.nthreads), ctx.XyzB(),
+                                     &topo.metal_bonds);
+    }
+    t.within_bounds = t.geometry.rmsd_bonds <= MAX_RMSD_BONDS && t.geometry.rmsd_angles <= MAX_RMSD_ANGLES;
+    out.line = fmt::format("X-ray weight {:.3g}, B {}: R-work {:.4f}, R-free {:.4f}, rmsd bonds {:.4f} A, "
+                           "angles {:.2f} deg{}{}",
+                           w, adp_w > 0 ? fmt::format("refined at weight {:.3g}", adp_w) : std::string("held"),
+                           rf.r_work, rf.r_free, t.geometry.rmsd_bonds, t.geometry.rmsd_angles,
+                           t.geometry.metal_bonds > 0 ? fmt::format(", metal bonds {:.3f} A", t.geometry.rmsd_metal)
+                                                      : std::string(),
+                           t.within_bounds ? "" : " (geometry out of bounds)");
+    out.pos = ctx.Positions();
+    out.b = ctx.B();
+    out.fit = ctx.Fitted();
+    out.ran = true;
+    return out;
+}
+
+// The trials (w, adp_w) side by side, the longest to the slots first and each slot's trials in turn on a thread of
+// its own (on its GPU), returned in the order given. Every trial starts from pos0 and b0 and takes nothing from the
+// one before it in its slot, so the outcome is the same for any number of slots.
+std::vector<TrialOutcome> RunTrials(const std::vector<TrialSlot> &trial_slots,
+                                    const std::vector<std::pair<double, double>> &trials,
+                                    const std::vector<int> &refinable, const std::vector<gemmi::Position> &pos0,
+                                    const std::vector<double> &b0, const Context::Fit *fit, int cycles,
+                                    const RefinementSettings &settings) {
+    std::vector<TrialOutcome> out(trials.size());
+    std::vector<std::exception_ptr> errors(trial_slots.size());
+    // the threads shared among the slots that run (the outcome does not depend on how many each has)
+    const size_t running = std::min(trial_slots.size(), trials.size());
+    for (size_t s = 0; s < running; s++)
+        trial_slots[s].ctx->nthreads = std::max<size_t>(1, settings.nthreads / running);
+    // The trials that refine B are the longest: they go to the slots first, so that two of them share a slot (or a
+    // card) only where the slots are fewer than they are; the first slots are on cards of their own (OwnSlotDevices).
+    std::vector<size_t> order(trials.size());
+    std::iota(order.begin(), order.end(), 0);
+    std::stable_sort(order.begin(), order.end(),
+                     [&](size_t a, size_t b) { return (trials[a].second > 0) > (trials[b].second > 0); });
+    auto run_slot = [&](size_t s) {
+        try {
+#ifdef JFJOCH_USE_CUDA
+            const ScopedGpuPin pin(trial_slots[s].ctx->device >= 0 ? trial_slots[s].ctx->device : get_gpu());
+#endif
+            for (size_t j = s; j < trials.size(); j += trial_slots.size())
+                if (const size_t i = order[j]; !trial_slots[s].ctx->Cancelled())
+                    out[i] = RunTrial(trial_slots[s], refinable, pos0, b0, fit, trials[i].first, trials[i].second,
+                                      cycles, settings);
+        } catch (...) {
+            errors[s] = std::current_exception();
+        }
+    };
+    std::vector<std::thread> threads;
+    for (size_t s = 1; s < std::min(trial_slots.size(), trials.size()); s++)
+        threads.emplace_back(run_slot, s);
+    run_slot(0);
+    for (std::thread &t : threads)
+        t.join();
+    for (const std::exception_ptr &e : errors)
+        if (e)
+            std::rethrow_exception(e);
+    return out;
+}
+
+}  // namespace
+
+RefinementResult RefineModel(const gemmi::Structure &placed, const std::vector<MergedReflection> &merged,
+                             const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double wavelength_A,
+                             Logger &logger, const RefinementSettings &settings) {
+    const auto start = std::chrono::steady_clock::now();
+    RefinementResult result;
+    Context ctx;
+    ctx.st = PrepareModel(placed, cell, sg);
+    ctx.cell = cell;
+    ctx.sg = &sg;
+    ctx.nthreads = settings.nthreads;
+    ctx.ml_threads = settings.nthreads;
+    ctx.cancel = settings.cancel;
+    ctx.atoms = AtomList(ctx.Model());
+    result.atoms = static_cast<int>(ctx.atoms.size());
+    double b_max = 0;
+    for (const gemmi::Atom *a : ctx.atoms)
+        b_max = std::max<double>(b_max, a->b_iso);
+    ctx.b_ceiling = std::clamp(2 * b_max, B_CEILING_MIN, B_CEILING_MAX);
+    if (ctx.atoms.empty()) {
+        result.failure_reason = "the model has no atoms";
+        return result;
+    }
+    double max_inv_d2 = 0;
+    for (const MergedReflection &r : merged)
+        if (std::isfinite(r.F) && r.d > 0)
+            max_inv_d2 = std::max(max_inv_d2, 1.0 / (double(r.d) * r.d));
+    if (max_inv_d2 <= 0) {
+        result.failure_reason = "no amplitudes";
+        return result;
+    }
+    // just past the finest reflection, so that prepare_asu_data()'s strict limit keeps it
+    ctx.d_min = 0.999 / std::sqrt(max_inv_d2);
+    result.d_min = 1.0 / std::sqrt(max_inv_d2);
+    ctx.refl = PrepareRefinementReflections(merged, cell, sg, ctx.d_min);
+    if (ctx.refl.Size() < 100) {
+        result.failure_reason = "too few reflections";
+        return result;
+    }
+
+    ctx.mask = std::make_unique<BulkSolventMask>(cell, sg, ctx.d_min, settings.nthreads);
+
+    // The dictionary's view of the model, and its hydrogens riding on their parents from the start, so that the
+    // model is scored as the restrained stage refines it.
+    const bool restrained = settings.restrained || settings.score_only;
+    // The weight trials' slots start from a copy of the model as it is before the topology is made.
+    const gemmi::Structure before_topology = ctx.st;
+    RefinementTopology topo;
+    if (restrained) {
+        std::optional<RefinementStage> topo_stage("topology");
+        topo = BuildRefinementTopology(ctx.st, settings.riding_hydrogens);
+        topo_stage.reset();
+        ctx.atoms = AtomList(ctx.Model());
+        ctx.SetRiderParents(topo.rider_parent);
+        PlaceRiders(ctx, topo);
+    }
+
+    MakeEngine(ctx, settings.gpu, settings, logger);
+    result.on_gpu = ctx.engine->OnGPU();
+
+    RFactors r = ctx.Refit();
+    result.n_work = r.n_work;
+    result.n_free = r.n_free;
+    result.r_work_start = r.r_work;
+    result.r_free_start = r.r_free;
+    result.score_start = ctx.Score();
+    logger.Info("Refinement: {} atoms ({} riding hydrogens), {} reflections to {:.2f} A ({} free), on the {}; as given "
+                "R-work {:.4f}, R-free {:.4f}; k_sol {:.3f}, b_sol {:.1f}, overall B {:.1f}, mask grid {:.2f} A",
+                ctx.atoms.size(), result.score_start.hydrogens, ctx.refl.Size(), result.d_min, r.n_free,
+                result.on_gpu ? "GPU" : "CPU", r.r_work, r.r_free, ctx.k_sol, ctx.b_sol, result.score_start.b_iso,
+                result.score_start.mask_spacing);
+
+    // The maps, the blobs and the model of where the refinement ended.
+    auto finish = [&]() {
+        MakeMaps(ctx, merged, wavelength_A, result);
+        {
+            const RefinementStage stage("blobs");
+            result.blobs = FindDensityBlobs(*result.difference_map, result.difference_map_rms, ctx.st, result.d_min,
+                                            result.anomalous_map.get(), result.anomalous_map_rms);
+        }
+        result.k_sol = ctx.k_sol;
+        result.b_sol = ctx.b_sol;
+        result.model = std::make_shared<gemmi::Structure>(ctx.st);
+        result.ok = true;
+        result.seconds = std::chrono::duration<double>(std::chrono::steady_clock::now() - start).count();
+    };
+    if (settings.score_only) {
+        result.score_start.hkl = ctx.refl.hkl;
+        result.score_start.fcalc = ctx.fcalc;
+        result.score_start.fmask = ctx.rows.fmask;
+        result.score_start.k_total = ctx.rows.k_total;
+        result.score_start.d = ctx.rows.d;
+        result.score_start.var = ctx.rows.var;
+        result.r_work_placement = result.r_work_start;
+        result.r_free_placement = result.r_free_start;
+        result.restrained_residues = topo.restrained_residues;
+        result.fixed_residues = topo.fixed_residues;
+        result.fixed_names = topo.fixed_names;
+        result.geometry_start = MeasureGeometry(topo.geometry, BuildRepulsions(topo, ctx.Model(), cell, sg, 0.0),
+                                                ctx.XyzB(), &topo.metal_bonds);
+        finish();
+        const GeometryStatistics &g = result.geometry_start;
+        logger.Info("Refinement: the model scored only; geometry rmsd bonds {:.4f} A (rmsZ {:.2f}, {} bonds), metal "
+                    "bonds {:.4f} A (rmsZ {:.2f}, {}; {} links made), both {:.4f} A; angles {:.2f} deg (rmsZ {:.2f})",
+                    g.rmsd_bonds, g.rmsz_bonds, g.bonds, g.rmsd_metal, g.rmsz_metal, g.metal_bonds, topo.metal_links,
+                    g.RmsdAllBonds(), g.rmsd_angles, g.rmsz_angles);
+        return result;
+    }
+
+    // The trials run side by side, as many at a time as the longest set of them has and the cards take engines:
+    // on the main model and engine, and on copies with engines of their own; each with a share of the threads. The
+    // copies are made while the placement runs: they start from the model as it was before the topology was made
+    // and take nothing from the main context that the placement changes.
+    int wanted = static_cast<int>(std::max({settings.weight_ladder.size() * settings.adp_ladder.size(),
+                                            settings.final_ladder.size(), size_t{3}}));
+    if (settings.max_trials_at_once > 0)
+        wanted = std::min(wanted, static_cast<int>(settings.max_trials_at_once));
+    const std::vector<int> devices = settings.restrained ? OwnSlotDevices(ctx, wanted - 1, settings) : std::vector<int>();
+    const size_t slot_threads = std::max<size_t>(1, settings.nthreads / (devices.size() + 1));
+    std::vector<std::unique_ptr<OwnSlot>> own(devices.size());
+    std::vector<std::thread> slot_builders;
+    // joined before the slots are taken, or here where the placement throws
+    struct JoinAll {
+        std::vector<std::thread> &threads;
+        ~JoinAll() {
+            for (std::thread &t : threads)
+                if (t.joinable())
+                    t.join();
+        }
+    } join_slot_builders{slot_builders};
+    for (size_t k = 0; k < devices.size(); k++)
+        slot_builders.emplace_back([&, k]() {
+#ifdef JFJOCH_USE_CUDA
+            const ScopedGpuPin pin(devices[k] >= 0 ? devices[k] : get_gpu());
+#endif
+            // a slot that cannot be made is left out, as where the card cannot take its engine
+            try {
+                own[k] = MakeOwnSlot(before_topology, ctx, devices[k], slot_threads, settings);
+            } catch (const std::exception &e) {
+                logger.Warning("Refinement: a trial slot could not be made ({}), the trials share fewer", e.what());
+            }
+        });
+
+    RefinePlacement(ctx, settings.group_b, result);
+    if (restrained)
+        PlaceRiders(ctx, topo);
+    r = ctx.Refit();
+    result.r_work_placement = r.r_work;
+    result.r_free_placement = r.r_free;
+    logger.Info("Refinement, placement ({} rigid bodies kept, B per residue {}): R-work {:.4f}, R-free {:.4f}",
+                result.rigid_bodies, result.group_b ? "kept" : "not kept", r.r_work, r.r_free);
+
+    if (settings.restrained) {
+        ctx.Refit();
+        result.restrained_residues = topo.restrained_residues;
+        result.fixed_residues = topo.fixed_residues;
+        result.fixed_names = topo.fixed_names;
+        std::vector<int> refinable;
+        for (size_t i = 0; i < ctx.atoms.size(); i++)
+            if (topo.refinable[i])
+                refinable.push_back(static_cast<int>(i));
+        result.refined_atoms = static_cast<int>(refinable.size());
+        logger.Info("Refinement: {} residues restrained, {} held fixed{}; {} bonds, {} metal bonds ({} links made), {} "
+                    "angles, {} torsions, {} chiral volumes, {} planes",
+                    topo.restrained_residues, topo.fixed_residues,
+                    topo.fixed_names.empty() ? std::string() : " (" + Joined(topo.fixed_names) + ")",
+                    topo.bonds, topo.metal_bonds.records.size(), topo.metal_links, topo.angles, topo.torsions, topo.chirals, topo.planes);
+
+        ctx.engine->SetRestraints(1, topo.adp);
+        {
+            const RestraintSet set = RestraintsNow(ctx, topo);
+            ctx.engine->SetRestraints(0, set);
+            RestraintSet repulsions = BuildRepulsions(topo, ctx.Model(), cell, sg, 0.0, ctx.nthreads);
+            result.geometry_start = MeasureGeometry(topo.geometry, repulsions, ctx.XyzB(), &topo.metal_bonds);
+        }
+        double w0 = 0, adp_w0 = 0;
+        {
+            const RefinementStage stage("balanced_weight");
+            w0 = BalancedWeight(ctx, refinable);
+            adp_w0 = BalancedADPWeight(ctx, BRestraintsNow(ctx, topo), refinable);
+        }
+        logger.Info("Refinement: geometry as given rmsd bonds {:.4f} A, angles {:.2f} deg, {} clashes; balanced X-ray "
+                    "weights {:.3g} (positions), {:.3g} (B)", result.geometry_start.rmsd_bonds,
+                    result.geometry_start.rmsd_angles, result.geometry_start.clashes, w0, adp_w0);
+
+        const std::vector<gemmi::Position> pos0 = ctx.Positions();
+        const std::vector<double> b0 = ctx.B();
+
+        std::optional<RefinementStage> slot_stage("slots");
+        for (std::thread &t : slot_builders)
+            t.join();
+        const size_t main_threads = ctx.nthreads;
+        ctx.nthreads = slot_threads;
+        std::vector<TrialSlot> trial_slots{{&ctx, &topo}};
+        for (const std::unique_ptr<OwnSlot> &o : own)
+            if (o)
+                trial_slots.push_back({&o->ctx, &o->topo});
+        slot_stage.reset();
+        logger.Debug("Refinement: {} weight trials at a time", trial_slots.size());
+
+        // A trial displaces another only where its geometry is within bounds and its R-free lower by more than the
+        // tie.
+        auto displaces = [](const RefinementWeightTrial &t, const RefinementWeightTrial &b) {
+            return t.within_bounds && (!b.within_bounds || t.r_free < b.r_free - R_FREE_TIE);
+        };
+        // Of a set of trials, the one kept: they come in order of trust, the first kept unless a later one displaces
+        // it. -1: none ran.
+        auto choose = [&](std::vector<TrialOutcome> &outcomes, const char *stage) {
+            int best = -1;
+            for (size_t k = 0; k < outcomes.size(); k++) {
+                const TrialOutcome &o = outcomes[k];
+                if (!o.ran)
+                    continue;
+                logger.Info("Refinement, {}: {}", stage, o.line);
+                result.trials.push_back(o.trial);
+                if (best < 0 || displaces(o.trial, outcomes[best].trial))
+                    best = static_cast<int>(k);
+            }
+            return best;
+        };
+        const double w_max = w0 * settings.max_weight;
+
+        // 1. The weights from the placed model: the ladder's rungs, tighter geometry first, each with the B factors
+        //    held and refined at their own balanced weight.
+        std::vector<std::pair<double, double>> ladder;
+        for (double rung : settings.weight_ladder)
+            for (double adp : settings.adp_ladder)
+                ladder.emplace_back(w0 * rung, adp_w0 * adp);
+        std::vector<TrialOutcome> outcomes = RunTrials(trial_slots, ladder, refinable, pos0, b0, nullptr,
+                                                       settings.macro_cycles, settings);
+        int k = choose(outcomes, "ladder");
+        TrialOutcome state;
+        if (k >= 0)
+            state = std::move(outcomes[k]);
+
+        // 2. The trajectory: steps of a few macro-cycles from where the last one ended, each trying the weights as they
+        //    are and, in turn, the positions' X-ray weight halved and doubled (halved: the geometry loosens as the
+        //    model improves at one weight, until it leaves the bounds) and the B factors' divided and multiplied by
+        //    four.
+        //    A step is taken while it lowers R-free or R-work by more than the tie and its R-free stays within the tie
+        //    of the best so far; the trajectory ends at its best step (on a deposited model, whose free set it was
+        //    fitted to, R-work falls while R-free rises, and it ends where it began).
+        TrialOutcome best = state;
+        // The trials of the step that went from the best so far: the final ladder goes from there too, and a trial
+        // of the same weights from the same model is the same computation.
+        std::vector<TrialOutcome> from_best;
+        bool state_is_best = true;
+        for (int step = 0; step < settings.max_steps && state.ran && !ctx.Cancelled(); step++) {
+            const double w = state.trial.weight, adp = state.trial.adp_weight;
+            std::vector<std::pair<double, double>> trials = {{w, adp}};
+            if (step % 2 == 1 && adp > 0) {
+                trials.emplace_back(w, adp / 4);
+                trials.emplace_back(w, 4 * adp);
+            } else {
+                trials.emplace_back(w / 2, adp);
+                if (2 * w <= w_max)
+                    trials.emplace_back(2 * w, adp);
+            }
+            outcomes = RunTrials(trial_slots, trials, refinable, state.pos, state.b, &state.fit, settings.macro_cycles,
+                                 settings);
+            if (state_is_best)
+                from_best = outcomes;
+            k = choose(outcomes, fmt::format("step {}", step + 1).c_str());
+            if (k < 0)
+                break;
+            const RefinementWeightTrial &t = outcomes[k].trial;
+            const bool gains = displaces(t, state.trial) || (t.within_bounds && t.r_work < state.trial.r_work - R_FREE_TIE);
+            if (!gains || !(t.within_bounds && t.r_free < best.trial.r_free + R_FREE_TIE))
+                break;
+            state = std::move(outcomes[k]);
+            state_is_best = displaces(state.trial, best.trial);
+            if (state_is_best) {
+                best = state;
+                from_best.clear();
+            }
+        }
+        state = std::move(best);
+
+        // 3. The final weights: a short ladder from where the trajectory ended, tighter geometry first, its choice
+        //    kept where it displaces that. A rung the step from there tried already is taken from that step.
+        if (state.ran && !ctx.Cancelled()) {
+            const double w = state.trial.weight, adp = state.trial.adp_weight;
+            std::vector<std::pair<double, double>> trials;
+            for (double f : settings.final_ladder)
+                if (w * f <= w_max)
+                    trials.emplace_back(w * f, adp);
+            outcomes.assign(trials.size(), TrialOutcome());
+            std::vector<std::pair<double, double>> missing;
+            for (size_t i = 0; i < trials.size(); i++) {
+                for (const TrialOutcome &o : from_best)
+                    if (o.ran && o.trial.weight == trials[i].first && o.trial.adp_weight == trials[i].second)
+                        outcomes[i] = o;
+                if (!outcomes[i].ran)
+                    missing.push_back(trials[i]);
+            }
+            std::vector<TrialOutcome> ran = RunTrials(trial_slots, missing, refinable, state.pos, state.b, &state.fit,
+                                                      settings.macro_cycles, settings);
+            for (size_t i = 0, m = 0; i < trials.size(); i++)
+                if (!outcomes[i].ran)
+                    outcomes[i] = std::move(ran[m++]);
+            k = choose(outcomes, "final");
+            // The main slot's fit as it stands where its last rung ran on it, for the maps' Refit() to start from
+            // (the solvent grid and the likelihood's D) whether the rung ran or was taken from the step.
+            const size_t main_last = (trials.size() - 1) / trial_slots.size() * trial_slots.size();
+            if (outcomes[main_last].ran)
+                ctx.Restore(outcomes[main_last].fit);
+            if (k >= 0 && displaces(outcomes[k].trial, state.trial))
+                state = std::move(outcomes[k]);
+        }
+        for (size_t s = 1; s < trial_slots.size(); s++)
+            ctx.evaluations += trial_slots[s].ctx->evaluations;
+        ctx.nthreads = main_threads;
+        if (state.ran) {
+            ctx.SetPositions(state.pos);
+            ctx.SetB(state.b);
+            PlaceRiders(ctx, topo);
+            result.restrained = true;
+            result.weight = state.trial.weight;
+            result.adp_weight = state.trial.adp_weight;
+            result.r_work = state.trial.r_work;
+            result.r_free = state.trial.r_free;
+            result.geometry = state.trial.geometry;
+        } else
+            ctx.Refit();   // no trial ran: the model as placed, its scale and solvent for the maps
+    }
+    result.cancelled = ctx.Cancelled();
+    if (result.cancelled)
+        logger.Warning("Refinement: cancelled, {} weight trials ran", result.trials.size());
+
+    finish();
+    logger.Info("Refinement: done in {:.1f} s, {} target evaluations{}", result.seconds, ctx.evaluations,
+                result.restrained ? fmt::format("; R-work {:.4f}, R-free {:.4f}, weight {:.3g}", result.r_work,
+                                                result.r_free, result.weight)
+                                  : std::string());
+    RefinementStage::Log(logger);
+    return result;
+}
diff --git a/image_analysis/structure_refinement/Refinement.h b/image_analysis/structure_refinement/Refinement.h
new file mode 100644
index 000000000..f9eadd055
--- /dev/null
+++ b/image_analysis/structure_refinement/Refinement.h
@@ -0,0 +1,160 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <array>
+#include <atomic>
+#include <cmath>
+#include <complex>
+#include <memory>
+#include <string>
+#include <vector>
+
+#include "gemmi/grid.hpp"
+#include "gemmi/model.hpp"
+#include "gemmi/symmetry.hpp"
+#include "gemmi/unitcell.hpp"
+
+#include "../../common/Reflection.h"   // MergedReflection
+#include "DensityBlobs.h"
+#include "ModelValidation.h"           // ModelMaps
+#include "RefinementRestraints.h"      // GeometryStatistics
+
+class Logger;
+
+// Refinement of an atomic model already placed against the data (ValidateAgainstModel's placed model, or a
+// molecular-replacement placement), in two stages:
+//
+// 1. Placement: each chain as a rigid body, then one B shift per residue, each kept only where it lowers
+//    R-free. Needs no dictionary.
+// 2. Restrained: every atom's position and isotropic B, against the maximum-likelihood amplitude target with
+//    the geometry the dictionary describes (MonomerLibrary.h: bonds, angles, planes, chiral volumes,
+//    torsions, repulsions; B similarity of bonded atoms and of atoms in contact, in proportion to B). Residues
+//    it does not describe are held fixed and stay in the structure factors and the bulk-solvent mask. The
+//    weights of the X-ray term against the geometry and against the B similarity, and whether to refine the B
+//    factors, are chosen by R-free among trials whose geometry stays within bounds: a ladder from the placed
+//    model, then a trajectory of steps that each try the weights as they are and changed, from where the last
+//    step ended, until no step gains; then a short final ladder.
+//
+// The library reads and writes nothing: the model and the reflections come in, the refined model, the
+// statistics and the map coefficients go out. Nothing it finds feeds back into processing decisions.
+struct RefinementSettings {
+    bool restrained = true;          // stage 2; false stops after the placement stage
+    bool score_only = false;         // only score the model as given (RefinementResult::score_start), no stage
+    bool group_b = true;             // the placement stage's B shift per residue
+    int macro_cycles = 2;            // per weight trial, from the model the trial starts from
+    int xyz_iterations = 30;         // L-BFGS iterations per macro-cycle
+    int b_iterations = 20;
+    // The first trials, from the placed model: the positions' X-ray weight, times the gradient-balanced one
+    // (BalancedWeight), each with the B factors' X-ray weight their own balanced one times each of adp_ladder (0: B
+    // held).
+    std::vector<double> weight_ladder = {1.0 / 1024, 1.0 / 128, 1.0 / 16};
+    std::vector<double> adp_ladder = {0.0, 1.0};
+    // Then at most this many steps of the trajectory, each a set of trials from where the last one ended,
+    int max_steps = 8;
+    // and the final trials from where it ended, at its weights times each of these;
+    std::vector<double> final_ladder = {0.5, 1.0, 2.0};
+    double max_weight = 1.0 / 8;     // the positions' X-ray weight at most, times the balanced one
+    bool riding_hydrogens = true;    // the dictionary's hydrogens added, riding on their parents
+    bool gpu = true;
+    size_t nthreads = 1;
+    size_t gpu_resident_bytes = 0;   // held on the card by what runs beside
+    // The most weight trials run side by side, 0 for as many as the ladders and the cards take; the result does not
+    // depend on it (1 runs them one after another, as a check of that).
+    size_t max_trials_at_once = 0;
+    // Set by the caller (from any thread) to cut a running refinement short: checked between the minimiser's
+    // iterations and before every weight trial. The trials that ran are chosen among as usual, those that did not
+    // are left out (RefinementResult::cancelled); cut before the first trial, the model is the placement's.
+    const std::atomic<bool> *cancel = nullptr;
+};
+
+// R by resolution: one of RefinementScore's shells, equal in width in 1/d^2 between the coarsest and the
+// finest reflection.
+struct RefinementShell {
+    double d_max = 0, d_min = 0;
+    int n_work = 0, n_free = 0;
+    double r_work = NAN, r_free = NAN;
+};
+
+// What scoring a model against the data gives, every term of it: the model's structure factors are
+// F_model = k_overall exp(-s^T B s / 4) (Fcalc + k_sol exp(-b_sol s^2 / 4) Fmask), the scale and the solvent
+// fitted to the working reflections; R-work and R-free; and the likelihood target, -ln L summed over the
+// working and over the free reflections, at D and the variance estimated from the free set.
+struct RefinementScore {
+    double k_overall = 0;
+    double b_iso = 0;                // the overall B: a third of the trace of B (Cartesian, A^2)
+    std::array<double, 6> b_aniso{}; // B less b_iso: B11 B22 B33 B12 B13 B23 (Cartesian, A^2)
+    double k_sol = 0, b_sol = 0;
+    double mask_spacing = 0;         // A, the grid the solvent mask is drawn on
+    double r_work = NAN, r_free = NAN;
+    int n_work = 0, n_free = 0;
+    double nll_work = NAN, nll_free = NAN;
+    double fom = NAN;                // the likelihood's mean figure of merit, working reflections
+    int hydrogens = 0;               // riding hydrogens in the model scored
+    std::vector<RefinementShell> shells;
+    // Per reflection, with settings.score_only only: the atoms' Fcalc, the solvent's k_sol exp(-b_sol s^2/4) Fmask
+    // and k_overall exp(-s^T B s / 4), in the order of `hkl`, and the likelihood's parameters.
+    std::vector<gemmi::Miller> hkl;
+    std::vector<std::complex<float>> fcalc, fmask;
+    std::vector<float> k_total;
+    std::vector<float> d, var;       // the likelihood's D and variance (epsilon beta + sigma^2)
+};
+
+// One rung of the weight ladder.
+struct RefinementWeightTrial {
+    double weight = 0;               // the X-ray term's weight
+    double adp_weight = 0;           // the B refinement's X-ray weight; 0: the B factors were held
+    double r_work = 1, r_free = 1;
+    GeometryStatistics geometry;
+    bool within_bounds = false;      // the geometry bounds the choice is made inside
+};
+
+struct RefinementResult {
+    bool ok = false;
+    std::string failure_reason;
+    bool on_gpu = false;
+    double seconds = 0;
+    double d_min = 0;
+    int n_work = 0, n_free = 0;
+
+    // The model as given, scaled to these reflections (B made isotropic; the dictionary's hydrogens riding
+    // where the restrained stage runs or the model is only scored), and every term of that score.
+    double r_work_start = 1, r_free_start = 1;
+    RefinementScore score_start;
+    // After the placement stage.
+    int rigid_bodies = 0;            // the chains moved as rigid bodies, where that was kept
+    bool group_b = false;            // the B shift per residue was kept
+    double r_work_placement = 1, r_free_placement = 1;
+    // After the restrained stage (NaN where it did not run).
+    bool restrained = false;
+    bool cancelled = false;          // cut short by RefinementSettings::cancel
+    double r_work = NAN, r_free = NAN;
+    double weight = 0;
+    double adp_weight = 0;           // 0: the B factors kept as placed
+    std::vector<RefinementWeightTrial> trials;
+    GeometryStatistics geometry_start, geometry;
+
+    int atoms = 0, refined_atoms = 0;
+    int restrained_residues = 0, fixed_residues = 0;
+    std::vector<std::string> fixed_names;
+    double k_sol = 0, b_sol = 0;
+    double mean_fom = 0;
+
+    std::shared_ptr<gemmi::Structure> model;   // the refined model, in the data's cell and frame
+    std::shared_ptr<ModelMaps> maps;           // its 2mFo-DFc and mFo-DFc coefficients (as _maps.mtz holds them)
+    // The mFo-DFc map of the refined model and its rms, for finding what it leaves unexplained (DensityBlobs.h).
+    std::shared_ptr<gemmi::Grid<float>> difference_map;
+    double difference_map_rms = 0;
+    // The anomalous difference map on the refined model's phases, where the merge kept the Bijvoet pairs.
+    std::shared_ptr<gemmi::Grid<float>> anomalous_map;
+    double anomalous_map_rms = 0;
+    // What the refined model leaves unexplained in the difference map (FindDensityBlobs).
+    std::vector<DensityBlob> blobs;
+};
+
+// `placed`: the model in the data's cell and space group. `merged`: the merge, with French-Wilson amplitudes
+// and free flags, in the same group.
+RefinementResult RefineModel(const gemmi::Structure &placed, const std::vector<MergedReflection> &merged,
+                             const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double wavelength_A,
+                             Logger &logger, const RefinementSettings &settings);
diff --git a/image_analysis/structure_refinement/RefinementGPU.cpp b/image_analysis/structure_refinement/RefinementGPU.cpp
new file mode 100644
index 000000000..dc886f577
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementGPU.cpp
@@ -0,0 +1,359 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "RefinementGPU.h"
+
+#include <algorithm>
+#include <cmath>
+#include <optional>
+
+#include "gemmi/dencalc.hpp"
+#include "gemmi/it92.hpp"
+#include "gemmi/solmask.hpp"   // SolventMasker, refmac_radius_for_bulk_solvent
+
+#include "../../common/ParallelFor.h"
+#include "RefinementGPUEngine.h"
+
+namespace {
+
+using Table = gemmi::IT92<float>;
+
+// One atom's density as the gather takes it, isotropic, with `blur`.
+ModelDensityAtom DensityAtom(const gemmi::Atom &atom, double b_iso, const gemmi::DensityCalculator<Table, float> &dc) {
+    using CReal = Table::Coef::coef_type;
+    const auto &coef = Table::get(atom.element, atom.charge, atom.serial);
+    const CReal b = static_cast<CReal>(b_iso + dc.blur);
+    const auto precal = coef.precalculate_density_iso(b, 0.0f);
+    const double radius = dc.estimate_radius(precal, b);
+    ModelDensityAtom a{};
+    a.occ = atom.occ;
+    a.aniso = 0;
+    a.radius = static_cast<float>(radius);
+    a.max_r2 = static_cast<float>(radius * radius);
+    for (int k = 0; k < 5; k++) {
+        a.a[k] = precal.a[k];
+        a.b[k][0] = precal.b[k];
+    }
+    return a;
+}
+
+std::vector<const gemmi::Atom *> Atoms(const gemmi::Model &model) {
+    std::vector<const gemmi::Atom *> atoms;
+    for (const gemmi::Chain &ch : model.chains)
+        for (const gemmi::Residue &r : ch.residues)
+            for (const gemmi::Atom &a : r.atoms)
+                atoms.push_back(&a);
+    return atoms;
+}
+
+// Whether `atoms` is Atoms(model) still: as many atoms, the first and the last the same ones.
+bool SameAtoms(const gemmi::Model &model, const std::vector<const gemmi::Atom *> &atoms) {
+    size_t n = 0;
+    const gemmi::Atom *first = nullptr, *last = nullptr;
+    for (const gemmi::Chain &ch : model.chains)
+        for (const gemmi::Residue &r : ch.residues)
+            if (!r.atoms.empty()) {
+                if (first == nullptr)
+                    first = &r.atoms.front();
+                last = &r.atoms.back();
+                n += r.atoms.size();
+            }
+    return n > 0 && n == atoms.size() && first == atoms.front() && last == atoms.back();
+}
+
+// The engine's single-precision gradient into the caller's doubles, element by element in parallel: bit for bit
+// the serial loop's.
+void Widen(const std::array<float, 4> *from, size_t n, std::vector<std::array<double, 4>> &to, size_t nthreads) {
+    to.resize(n);
+    ParallelChunks(static_cast<int>(n), ThreadsForWork(n, nthreads, 16384), [&](int lo, int hi) {
+        for (int i = lo; i < hi; i++)
+            to[i] = {from[i][0], from[i][1], from[i][2], from[i][3]};
+    });
+}
+
+class RefinementEngineGPU : public RefinementEngine {
+public:
+    RefinementEngineGPU(int device, const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min,
+                        const RefinementReflections &refl, const gemmi::Model &model, double b_max, size_t nthreads)
+        : device_(device), cell_(cell), sg_(sg), d_min_(d_min), nthreads_(nthreads) {
+        const gemmi::Grid<float> grid = RigidBodyZoneGrid(cell, sg, d_min);
+        setup_.grid.nu = grid.nu;
+        setup_.grid.nv = grid.nv;
+        setup_.grid.nw = grid.nw;
+        for (int i = 0; i < 3; i++)
+            for (int j = 0; j < 3; j++) {
+                setup_.grid.orth[3 * i + j] = cell.orth.mat[i][j];
+                setup_.grid.frac[3 * i + j] = cell.frac.mat[i][j];
+            }
+        setup_.volume = cell.volume;
+        // the mask on a grid of its own, as BulkSolventMask has it
+        const gemmi::Grid<float> mask_grid = BulkSolventMask::MaskGrid(cell, sg, d_min);
+        setup_.mask_grid = setup_.grid;
+        setup_.mask_grid.nu = mask_grid.nu;
+        setup_.mask_grid.nv = mask_grid.nv;
+        setup_.mask_grid.nw = mask_grid.nw;
+        const gemmi::GroupOps gops = sg.operations();
+        setup_.den = gemmi::Op::DEN;
+        setup_.centring = static_cast<double>(gops.cen_ops.size());
+        for (const gemmi::Op &op : gops.sym_ops) {
+            std::array<int, 12> o{};
+            for (int i = 0; i < 3; i++) {
+                for (int j = 0; j < 3; j++)
+                    o[3 * i + j] = op.rot[i][j];
+                o[9 + i] = op.tran[i];
+            }
+            setup_.sym_ops.push_back(o);
+        }
+        for (const gemmi::Op::Tran &cen : gops.cen_ops)
+            for (const gemmi::Op &op : gops.sym_ops) {
+                ModelMaskOp m{};
+                for (int i = 0; i < 3; i++) {
+                    for (int j = 0; j < 3; j++)
+                        m.rot[3 * i + j] = static_cast<double>(op.rot[i][j]) / gemmi::Op::DEN;
+                    m.tran[i] = static_cast<double>(op.tran[i] + cen[i]) / gemmi::Op::DEN;
+                }
+                setup_.mask_ops.push_back(m);
+            }
+        for (size_t m = 0; m < refl.Size(); m++) {
+            setup_.rows.push_back({refl.hkl[m][0], refl.hkl[m][1], refl.hkl[m][2]});
+            setup_.inv_d2.push_back(refl.inv_d2[m]);
+            setup_.fo.push_back(refl.fo[m]);
+            setup_.work.push_back(!refl.free[m]);
+            setup_.centric.push_back(refl.centric[m]);
+        }
+
+        // The adjoint of the composition on cuFFT's half-u spectrum: the term of row m and operator o, at
+        // k = hR, goes to k where k_u > 0, conjugated to -k where k_u < 0, and to both on the planes k_u = 0
+        // and k_u = nu/2, which hold their own Friedel mates.
+        const int nu = grid.nu, nv = grid.nv, nw = grid.nw;
+        auto point = [&](int ku, int kv, int kw) {
+            return ku + (nu / 2 + 1) * (gemmi::modulo(kv, nv) + nv * gemmi::modulo(kw, nw));
+        };
+        std::vector<std::pair<int, int>> entries;
+        const int n_ops = static_cast<int>(gops.sym_ops.size());
+        for (size_t m = 0; m < refl.Size(); m++)
+            for (int o = 0; o < n_ops; o++) {
+                const gemmi::Miller k = gops.sym_ops[o].apply_to_hkl(refl.hkl[m]);
+                const int term = (static_cast<int>(m) * n_ops + o) * 2;
+                if (k[0] > 0 && 2 * k[0] != nu)
+                    entries.emplace_back(point(k[0], k[1], k[2]), term);
+                else if (k[0] < 0 && -2 * k[0] != nu)
+                    entries.emplace_back(point(-k[0], -k[1], -k[2]), term + 1);
+                else {
+                    const int ku = std::abs(k[0]);
+                    entries.emplace_back(point(ku, k[1], k[2]), term);
+                    entries.emplace_back(point(ku, -k[1], -k[2]), term + 1);
+                }
+            }
+        std::stable_sort(entries.begin(), entries.end(),
+                         [](const auto &a, const auto &b) { return a.first < b.first; });
+        for (size_t e = 0; e < entries.size(); e++) {
+            if (e == 0 || entries[e].first != entries[e - 1].first) {
+                setup_.scatter_point.push_back(entries[e].first);
+                setup_.scatter_start.push_back(static_cast<int>(e));
+            }
+            setup_.scatter_term.push_back(entries[e].second);
+        }
+        setup_.scatter_start.push_back(static_cast<int>(entries.size()));
+
+        // The gather's reserve for every atom at b_max with the largest blur a refinement sets (B down to 0).
+        dc_ = Calculator(RefinementBlur(cell, sg, d_min, 0.0));
+        std::vector<ModelDensityAtom> widest;
+        for (const gemmi::Atom *a : Atoms(model))
+            widest.push_back(DensityAtom(*a, b_max, dc_));
+        setup_.max_atoms = widest.size();
+        setup_.max_pairs = ModelDensityGPU::PairBound(setup_.grid, widest);
+        supported_ = !setup_.rows.empty() && ModelDensityGPU::Supports(setup_.grid, widest) &&
+                     setup_.mask_ops.size() <= ModelMaskGPU::MAX_OPS;
+        if (supported_) {
+            fft_work_ = RefinementGPUEngine::FFTWorkBytes(device, setup_);
+            // the restraints: about thirty records and slots per atom
+            bytes_ = RefinementGPUEngine::DeviceBytes(setup_, fft_work_, 30 * widest.size(), 60 * widest.size());
+        }
+    }
+
+    bool Supported() const { return supported_; }
+    size_t Bytes() const { return bytes_; }
+    void Reserve() { engine_ = std::make_unique<RefinementGPUEngine>(device_, setup_, fft_work_); }
+
+    void SetBlur(double blur) override {
+        dc_ = Calculator(blur);
+        last_b_.clear();
+        engine_->SetBlur(blur);
+    }
+
+    void SetRowModel(const XrayRowModel &rows) override {
+        std::vector<std::array<float, 2>> fmask(rows.fmask.size());
+        for (size_t m = 0; m < fmask.size(); m++)
+            fmask[m] = {rows.fmask[m].real(), rows.fmask[m].imag()};
+        engine_->SetRowModel(rows.k_total, fmask, rows.d, rows.var);
+    }
+
+    bool OnGPU() const override { return true; }
+
+    void Fcalc(const gemmi::Model &model, std::vector<std::complex<float>> &f) override {
+        SetAtoms(model);
+        std::vector<std::array<float, 2>> out;
+        engine_->Fcalc(out);
+        f.resize(out.size());
+        for (size_t m = 0; m < out.size(); m++)
+            f[m] = {out[m][0], out[m][1]};
+    }
+
+    void Fmask(const gemmi::Model &model, std::vector<std::complex<float>> &f) override {
+        const gemmi::SolventMasker masker(gemmi::AtomicRadiiSet::Refmac);
+        std::vector<ModelMaskAtom> mask_atoms;
+        for (const gemmi::Atom *a : Atoms(model)) {
+            if ((masker.ignore_hydrogen && a->is_hydrogen()) || (masker.ignore_zero_occupancy_atoms && a->occ <= 0))
+                continue;
+            const gemmi::Fractional f0 = cell_.fractionalize(a->pos);
+            double frac[3] = {f0.x, f0.y, f0.z};
+            for (double &x : frac) {
+                x -= std::floor(x);
+                if (x >= 1.0)
+                    x = 0.0;
+            }
+            mask_atoms.push_back({frac[0], frac[1], frac[2],
+                                  masker.constant_r + masker.rprobe +
+                                      gemmi::refmac_radius_for_bulk_solvent(a->element.elem)});
+        }
+        std::vector<std::array<float, 2>> out;
+        engine_->Fmask(mask_atoms, out);
+        f.resize(out.size());
+        for (size_t m = 0; m < out.size(); m++)
+            f[m] = {out[m][0], out[m][1]};
+    }
+
+    double Evaluate(const gemmi::Model &model, std::vector<std::array<double, 4>> *grad) override {
+        SetAtoms(model);
+        double value = 0;
+        {
+            const RefinementStage stage("gpu.evaluate");
+            value = engine_->Evaluate(grad != nullptr);
+        }
+        if (grad != nullptr)
+            Widen(engine_->HostGradient(), atom_ptrs_.size(), *grad, nthreads_);
+        return value;
+    }
+
+    double EvaluateWithRestraints(const gemmi::Model &model, int which, std::vector<std::array<double, 4>> *grad,
+                                  std::vector<std::array<double, 4>> *restraint_grad, double &restraints) override {
+        SetAtoms(model);
+        double value = 0;
+        {
+            const RefinementStage stage("gpu.evaluate");
+            value = engine_->EvaluateWithRestraints(grad != nullptr, which, [&](std::array<float, 4> *x) {
+                for (size_t i = 0; i < atom_ptrs_.size(); i++) {
+                    const gemmi::Atom &a = *atom_ptrs_[i];
+                    x[i] = {static_cast<float>(a.pos.x), static_cast<float>(a.pos.y), static_cast<float>(a.pos.z), a.b_iso};
+                }
+            }, restraint_grad != nullptr, restraints);
+        }
+        if (grad != nullptr)
+            Widen(engine_->HostGradient(), atom_ptrs_.size(), *grad, nthreads_);
+        if (restraint_grad != nullptr)
+            Widen(engine_->HostRestraintGradient(), atom_ptrs_.size(), *restraint_grad, nthreads_);
+        return value;
+    }
+
+    void SetRestraints(int which, const RestraintSet &set) override {
+        engine_->SetRestraints(which, set.records, set.plane_atoms, set.slot_start, set.slot_index, set.n_slots);
+    }
+
+    double EvaluateRestraints(int which, const std::vector<std::array<double, 4>> &xyzb,
+                              std::vector<std::array<double, 4>> *grad) override {
+        std::vector<std::array<float, 4>> x(xyzb.size()), g;
+        for (size_t i = 0; i < xyzb.size(); i++)
+            x[i] = {static_cast<float>(xyzb[i][0]), static_cast<float>(xyzb[i][1]), static_cast<float>(xyzb[i][2]),
+                    static_cast<float>(xyzb[i][3])};
+        double value = 0;
+        {
+            const RefinementStage stage("gpu.restraints");
+            value = engine_->EvaluateRestraints(which, x, grad != nullptr ? &g : nullptr);
+        }
+        if (grad != nullptr) {
+            grad->resize(g.size());
+            for (size_t i = 0; i < g.size(); i++)
+                (*grad)[i] = {g[i][0], g[i][1], g[i][2], g[i][3]};
+        }
+        return value;
+    }
+
+private:
+    gemmi::DensityCalculator<Table, float> Calculator(double blur) const {
+        gemmi::DensityCalculator<Table, float> dc;
+        dc.d_min = d_min_;
+        dc.rate = 1.5;
+        dc.grid.unit_cell = cell_;
+        dc.grid.spacegroup = &sg_;
+        dc.blur = blur;
+        dc.cutoff = REFINEMENT_DENSITY_CUTOFF;
+        return dc;
+    }
+
+    // The atoms' grid positions to the device, and their densities where some B moved (made again only for the
+    // atoms whose B moved).
+    void SetAtoms(const gemmi::Model &model) {
+        std::optional<RefinementStage> stage("gpu.atoms_host");
+        // the pointers kept from the last call where the model is the same one still (its context's own)
+        if (!SameAtoms(model, atom_ptrs_))
+            atom_ptrs_ = Atoms(model);
+        const std::vector<const gemmi::Atom *> &atoms = atom_ptrs_;
+        const int n = static_cast<int>(atoms.size());
+        if (last_b_.size() != atoms.size()) {
+            last_b_.assign(atoms.size(), NAN);
+            atoms_.resize(atoms.size());
+            pos_.resize(atoms.size());
+        }
+        changed_.assign(atoms.size(), 0);
+        const int n3[3] = {setup_.grid.nu, setup_.grid.nv, setup_.grid.nw};
+        ParallelChunks(n, ThreadsForWork(atoms.size(), nthreads_, 4096), [&](int lo, int hi) {
+            for (int i = lo; i < hi; i++) {
+                if (!(atoms[i]->b_iso == last_b_[i])) {
+                    atoms_[i] = DensityAtom(*atoms[i], atoms[i]->b_iso, dc_);
+                    last_b_[i] = atoms[i]->b_iso;
+                    changed_[i] = 1;
+                }
+                const gemmi::Fractional f = cell_.fractionalize(atoms[i]->pos);
+                pos_[i] = {static_cast<float>(f.x * n3[0]), static_cast<float>(f.y * n3[1]), static_cast<float>(f.z * n3[2]), 0};
+            }
+        });
+        stage.reset();
+        const RefinementStage upload("gpu.upload");
+        if (std::find(changed_.begin(), changed_.end(), 1) != changed_.end())
+            engine_->SetDensities(atoms_.data(), atoms_.size());
+        engine_->SetPositions(pos_.data(), pos_.size());
+    }
+
+    int device_;
+    gemmi::UnitCell cell_;
+    const gemmi::SpaceGroup &sg_;
+    double d_min_;
+    size_t nthreads_;
+    RefinementGPUSetup setup_;
+    gemmi::DensityCalculator<Table, float> dc_;
+    bool supported_ = false;
+    size_t fft_work_ = 0, bytes_ = 0;
+    std::unique_ptr<RefinementGPUEngine> engine_;
+    std::vector<const gemmi::Atom *> atom_ptrs_;   // the model's atoms at the last SetAtoms()
+    std::vector<float> last_b_;
+    PinnedVector<ModelDensityAtom> atoms_;   // pinned: a B rung sends them every evaluation (37 MB on a large model)
+    PinnedVector<std::array<float, 4>> pos_;
+    std::vector<char> changed_;
+};
+
+}  // namespace
+
+std::unique_ptr<RefinementEngine> MakeRefinementEngineGPU(int device, const gemmi::UnitCell &cell,
+                                                          const gemmi::SpaceGroup &sg, double d_min,
+                                                          const RefinementReflections &refl,
+                                                          const gemmi::Model &model, double b_max, size_t budget,
+                                                          size_t *device_bytes, size_t nthreads) {
+    auto engine = std::make_unique<RefinementEngineGPU>(device, cell, sg, d_min, refl, model, b_max, nthreads);
+    if (device_bytes != nullptr)
+        *device_bytes = engine->Bytes();
+    if (!engine->Supported() || engine->Bytes() > budget)
+        return nullptr;
+    engine->Reserve();
+    return engine;
+}
diff --git a/image_analysis/structure_refinement/RefinementGPU.cu b/image_analysis/structure_refinement/RefinementGPU.cu
new file mode 100644
index 000000000..90d9672ec
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementGPU.cu
@@ -0,0 +1,922 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "RefinementGPUEngine.h"
+
+#include <algorithm>
+#include <string>
+
+#include <cub/cub.cuh>
+#include <cufft.h>
+
+#include "../../common/JFJochException.h"
+#include "../indexing/CUDAMemHelpers.h"
+
+namespace {
+
+void cuda_err(cudaError_t val) {
+    if (val != cudaSuccess)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, cudaGetErrorString(val));
+}
+
+void cufft_err(cufftResult val) {
+    if (val != CUFFT_SUCCESS)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "cuFFT error " + std::to_string(static_cast<int>(val)));
+}
+
+constexpr int THREADS = 256;
+constexpr int WARP = 32;
+constexpr double FOUR_PI2 = 4 * refine_math::PI * refine_math::PI;
+
+int blocks(size_t n) {
+    return static_cast<int>((n + THREADS - 1) / THREADS);
+}
+
+__device__ __forceinline__ int imod(int a, int n) {
+    const int r = a % n;
+    return r < 0 ? r + n : r;
+}
+
+// gemmi's unsafe_expapprox(), as ModelDensityGPU.cu has it.
+__device__ __forceinline__ float expapprox(float x) {
+    const float val = 12102203.1615614f * x + 1065353216.f;
+    const int vali = static_cast<int>(val);
+    const float a = __int_as_float(vali & 0x7F800000);
+    const float b = __int_as_float((vali & 0x7FFFFF) | 0x3F800000);
+    return a * (0.509871020f + b * (0.312146713f + b * (0.166617139f + b * (-2.190619930e-3f + b * 1.3555747234e-2f))));
+}
+
+// exp(+2 pi i h.t) for h.t = ht / den, exact for the fractions a translation is made of.
+__device__ __forceinline__ void op_phase(int ht, int den, double &c, double &s) {
+    sincospi(2.0 * ht / den, &s, &c);
+}
+
+// The phases of every h.t the rows and operators make, as a table over the integer h.t from `min`: the hot
+// kernels read it in place of op_phase() - the same function at the same argument, so the same bits.
+__global__ void phase_table_kernel(int min, int count, int den, double2 *phase) {
+    const int i = blockIdx.x * blockDim.x + threadIdx.x;
+    if (i >= count)
+        return;
+    double s, c;
+    op_phase(min + i, den, c, s);
+    phase[i] = make_double2(c, s);
+}
+
+// F of the atoms at each row, composed from the half-u transform of one copy (ModelStructureFactorsGPU.cu's
+// compose_kernel), and with `evaluate` the target's term of a working row and the coefficient
+// conj(dT/dF) n_cen unblur the gradient's map is made of. `ops` holds each operator's rotation in whole
+// units and its translation in units of 1 / den.
+__global__ void compose_target_kernel(const float2 *f1, float norm, int nu, int nv, int nw, const int *ops, int n_ops,
+                                      const double2 *phase, int phase_min, const int *row_hkl, const double *row_scale,
+                                      int rows, bool evaluate, const float *k_total, const float2 *fmask,
+                                      const float *ml_d, const float *ml_var, const float *fo, const char *work,
+                                      const char *centric, float2 *f, double *nll, float2 *coef) {
+    const int m = blockIdx.x * blockDim.x + threadIdx.x;
+    if (m >= rows)
+        return;
+    const int h[3] = {row_hkl[3 * m], row_hkl[3 * m + 1], row_hkl[3 * m + 2]};
+    double sr = 0, si = 0;
+    for (int o = 0; o < n_ops; o++) {
+        const int *rot = ops + 12 * o, *tran = rot + 9;
+        int k[3];
+        for (int i = 0; i < 3; i++)
+            k[i] = rot[i] * h[0] + rot[3 + i] * h[1] + rot[6 + i] * h[2];
+        const bool conj = k[0] < 0;
+        if (conj)
+            for (int i = 0; i < 3; i++)
+                k[i] = -k[i];
+        const float2 out = f1[k[0] + static_cast<size_t>(nu / 2 + 1) * (imod(k[1], nv) + static_cast<size_t>(nv) * imod(k[2], nw))];
+        const double vr = out.x * norm, vi = (conj ? out.y : -out.y) * norm;
+        const double2 p = phase[h[0] * tran[0] + h[1] * tran[1] + h[2] * tran[2] - phase_min];
+        sr += p.x * vr - p.y * vi;
+        si += p.x * vi + p.y * vr;
+    }
+    const double scale = row_scale[m];
+    sr *= scale;
+    si *= scale;
+    f[m] = make_float2(static_cast<float>(sr), static_cast<float>(si));
+    if (!evaluate)
+        return;
+    double term = 0, cr = 0, ci = 0;
+    if (work[m]) {
+        const double k = k_total[m];
+        const double mr = k * (sr + fmask[m].x), mi = k * (si + fmask[m].y);
+        const double fc = sqrt(mr * mr + mi * mi);
+        double dfc = 0;
+        term = refine_math::AmplitudeNegLogLikelihood<double>(fo[m], fc, ml_d[m], ml_var[m], centric[m], dfc);
+        if (fc > 0) {
+            // dT/dF = k dT/d|F_model| F_model / |F_model|; the coefficient is its conjugate times the scale
+            const double g = k * dfc / fc * scale;
+            cr = g * mr;
+            ci = -g * mi;
+        }
+    }
+    nll[m] = term;
+    coef[m] = make_float2(static_cast<float>(cr), static_cast<float>(ci));
+}
+
+// The gradient's coefficients on the half-u spectrum: each point the sum, in order, of the terms
+// (coef[row] exp(2 pi i h.t_op)) / 2 that land on it, conjugated where they land as a Friedel mate. A term is
+// its row * 2 + conj, and its phase the table's entry at term_phase.
+__global__ void scatter_kernel(const float2 *coef, const double2 *phase, const int *point, const int *start,
+                               const int *term, const int *term_phase, int points, float2 *spectrum) {
+    const int s = blockIdx.x * blockDim.x + threadIdx.x;
+    if (s >= points)
+        return;
+    double sr = 0, si = 0;
+    for (int e = start[s]; e < start[s + 1]; e++) {
+        const int t = term[e];
+        const bool conj = t & 1;
+        const int m = t >> 1;
+        const double2 p = phase[term_phase[e]];
+        const double ar = 0.5 * (coef[m].x * p.x - coef[m].y * p.y), ai = 0.5 * (coef[m].x * p.y + coef[m].y * p.x);
+        sr += ar;
+        si += conj ? -ai : ai;
+    }
+    spectrum[point[s]] = make_float2(static_cast<float>(sr), static_cast<float>(si));
+}
+
+// F_mask at each row, read at h directly (ModelStructureFactorsGPU.cu's fmask_kernel).
+__global__ void fmask_kernel(const float2 *fm, float norm, const int *row_hkl, int rows, int nu, int nv, int nw,
+                             float2 *fmask) {
+    const int m = blockIdx.x * blockDim.x + threadIdx.x;
+    if (m >= rows)
+        return;
+    int h = row_hkl[3 * m], k = row_hkl[3 * m + 1], l = row_hkl[3 * m + 2];
+    const bool conj = h < 0;
+    if (conj) {
+        h = -h;
+        k = -k;
+        l = -l;
+    }
+    const float2 out = fm[h + static_cast<size_t>(nu / 2 + 1) * (imod(k, nv) + static_cast<size_t>(nv) * imod(l, nw))];
+    const float re = out.x * norm, im = -out.y * norm;
+    fmask[m] = make_float2(re, conj ? -im : im);
+}
+
+// dT/d(x, y, z, B) of every atom: the derivative map summed against the derivatives of the atom's density over
+// its box, one warp per atom, the lanes' sums added in a fixed tree. The box, the points within the radius and
+// their offsets from the centre are the density gather's (ModelDensityGPU.cu).
+__global__ void atom_gradient_kernel(const ModelDensityAtom *atoms, const float4 *pos, const int *box, int n,
+                                     ModelDensityGPU::Geometry g, const float *map, float map_scale, float4 *grad) {
+    const int a = (blockIdx.x * blockDim.x + threadIdx.x) / WARP;
+    const int lane = threadIdx.x % WARP;
+    if (a >= n)
+        return;
+    const ModelDensityAtom at = atoms[a];
+    const float4 p = pos[a];
+    const float nctr[3] = {p.x, p.y, p.z};
+    // the box's first point, unwrapped and wrapped into the grid; a box is narrower than the cell (Supports())
+    int lo[3], first[3], span[3];
+    const int n3[3] = {g.nu, g.nv, g.nw};
+    for (int k = 0; k < 3; k++) {
+        lo[k] = __float2int_rn(nctr[k]) - box[3 * a + k];
+        first[k] = imod(lo[k], n3[k]);
+        span[k] = 2 * box[3 * a + k] + 1;
+    }
+    const int total = span[0] * span[1] * span[2];
+    // the lane's points t = lane, lane + WARP, ... as (iu, iv, iw) in the box, stepped on without dividing
+    int iu = lane % span[0], iv = lane / span[0] % span[1], iw = lane / (span[0] * span[1]);
+    const int step_u = WARP % span[0], step_v = WARP / span[0];
+    auto next = [&]() {
+        iu += step_u;
+        iv += step_v;
+        if (iu >= span[0]) {
+            iu -= span[0];
+            iv++;
+        }
+        while (iv >= span[1]) {
+            iv -= span[1];
+            iw++;
+        }
+    };
+    float gx = 0, gy = 0, gz = 0, gb = 0;
+    for (int t = lane; t < total; t += WARP, next()) {
+        const int u = lo[0] + iu, v = lo[1] + iv, w = lo[2] + iw;
+        const float fx = nctr[0] - static_cast<float>(u);
+        const float fy = nctr[1] - static_cast<float>(v);
+        const float fz = nctr[2] - static_cast<float>(w);
+        const float z = g.m22 * fz;
+        const float y = g.m11 * fy + g.m12 * fz;
+        const float x = g.m00 * fx + (g.m01 * fy + g.m02 * fz);
+        const float r2 = (y * y + z * z) + x * x;
+        if (r2 > at.max_r2)
+            continue;
+        const int mu = first[0] + iu, mv = first[1] + iv, mw = first[2] + iw;
+        const float value = map[(mu < g.nu ? mu : mu - g.nu) +
+                                static_cast<size_t>(g.nu) * ((mv < g.nv ? mv : mv - g.nv) +
+                                                             static_cast<size_t>(g.nv) * (mw < g.nw ? mw : mw - g.nw))];
+        float dr2 = 0, db = 0;
+        for (int q = 0; q < 5; q++) {
+            const float b = at.b[q][0];
+            const float e = at.a[q] * expapprox(fmaxf(b * r2, -88.f));
+            dr2 += e * b;
+            db += e * b * (1.5f + b * r2);
+        }
+        gx += value * dr2 * x;
+        gy += value * dr2 * y;
+        gz += value * dr2 * z;
+        gb += value * db;
+    }
+    for (int off = WARP / 2; off > 0; off /= 2) {
+        gx += __shfl_down_sync(0xffffffff, gx, off);
+        gy += __shfl_down_sync(0xffffffff, gy, off);
+        gz += __shfl_down_sync(0xffffffff, gz, off);
+        gb += __shfl_down_sync(0xffffffff, gb, off);
+    }
+    if (lane == 0) {
+        const float s = 2.0f * at.occ * map_scale;
+        grad[a] = make_float4(s * gx, s * gy, s * gz, at.occ * map_scale * gb / static_cast<float>(FOUR_PI2));
+    }
+}
+
+using V3f = refine_math::V3<float>;
+
+__device__ V3f xyz(const float4 *p, int i) {
+    const float4 q = p[i];
+    return {q.x, q.y, q.z};
+}
+
+// Every restraint's E, and its gradient into its slots, one thread per restraint.
+__global__ void restraint_kernel(const RestraintRecord *records, int n, const int *plane_atoms, const float4 *xyzb,
+                                 float4 *contrib, double *energy) {
+    const int i = blockIdx.x * blockDim.x + threadIdx.x;
+    if (i >= n)
+        return;
+    const RestraintRecord &r = records[i];
+    V3f g[4] = {};
+    int na = 0;
+    float e = 0;
+    switch (static_cast<RestraintKind>(r.kind)) {
+        case RestraintKind::Bond:
+            e = refine_math::BondTerm(xyz(xyzb, r.atom[0]), xyz(xyzb, r.atom[1]), r.ideal, r.sigma, g);
+            na = 2;
+            break;
+        case RestraintKind::Angle:
+            e = refine_math::AngleTerm(xyz(xyzb, r.atom[0]), xyz(xyzb, r.atom[1]), xyz(xyzb, r.atom[2]), r.ideal,
+                                       r.sigma, g);
+            na = 3;
+            break;
+        case RestraintKind::Torsion:
+            e = refine_math::TorsionTerm(xyz(xyzb, r.atom[0]), xyz(xyzb, r.atom[1]), xyz(xyzb, r.atom[2]),
+                                         xyz(xyzb, r.atom[3]), r.ideal, r.sigma, r.period, g);
+            na = 4;
+            break;
+        case RestraintKind::Chiral:
+            e = refine_math::ChiralTerm(xyz(xyzb, r.atom[0]), xyz(xyzb, r.atom[1]), xyz(xyzb, r.atom[2]),
+                                        xyz(xyzb, r.atom[3]), r.ideal, r.sigma, g);
+            na = 4;
+            break;
+        case RestraintKind::Repulsion: {
+            const V3f q = xyz(xyzb, r.atom[1]);
+            const V3f image{r.rot[0] * q.x + r.rot[1] * q.y + r.rot[2] * q.z + r.tran[0],
+                            r.rot[3] * q.x + r.rot[4] * q.y + r.rot[5] * q.z + r.tran[1],
+                            r.rot[6] * q.x + r.rot[7] * q.y + r.rot[8] * q.z + r.tran[2]};
+            e = refine_math::RepulsionTerm(xyz(xyzb, r.atom[0]), image, r.ideal, r.sigma, g);
+            const V3f gi = g[1];
+            g[1] = {r.rot[0] * gi.x + r.rot[3] * gi.y + r.rot[6] * gi.z,
+                    r.rot[1] * gi.x + r.rot[4] * gi.y + r.rot[7] * gi.z,
+                    r.rot[2] * gi.x + r.rot[5] * gi.y + r.rot[8] * gi.z};
+            na = 2;
+            break;
+        }
+        case RestraintKind::Plane: {
+            V3f px[RefinementGPUEngine::MAX_PLANE_ATOMS], pg[RefinementGPUEngine::MAX_PLANE_ATOMS];
+            const int m = r.atom[1];
+            for (int k = 0; k < m; k++)
+                px[k] = xyz(xyzb, plane_atoms[r.atom[0] + k]);
+            e = refine_math::PlaneTerm(px, m, r.sigma, pg);
+            for (int k = 0; k < m; k++)
+                contrib[r.slot + k] = make_float4(pg[k].x, pg[k].y, pg[k].z, 0.0f);
+            break;
+        }
+        case RestraintKind::BSimilarity: {
+            float gi = 0, gj = 0;
+            e = refine_math::BSimilarityTerm(xyzb[r.atom[0]].w, xyzb[r.atom[1]].w, r.sigma, gi, gj);
+            contrib[r.slot] = make_float4(0, 0, 0, gi);
+            contrib[r.slot + 1] = make_float4(0, 0, 0, gj);
+            break;
+        }
+    }
+    for (int k = 0; k < na; k++)
+        contrib[r.slot + k] = make_float4(g[k].x, g[k].y, g[k].z, 0.0f);
+    energy[i] = e;
+}
+
+// Each atom's restraint gradient: its slots summed in order.
+__global__ void slot_gather_kernel(const float4 *contrib, const int *start, const int *index, int n, float4 *grad) {
+    const int a = blockIdx.x * blockDim.x + threadIdx.x;
+    if (a >= n)
+        return;
+    float4 s = make_float4(0, 0, 0, 0);
+    for (int k = start[a]; k < start[a + 1]; k++) {
+        const float4 c = contrib[index[k]];
+        s.x += c.x;
+        s.y += c.y;
+        s.z += c.z;
+        s.w += c.w;
+    }
+    grad[a] = s;
+}
+
+CudaFFTShape ForwardShape(const ModelDensityGrid &g) {
+    return {.n = {g.nw, g.nv, g.nu}, .idist = g.nu * g.nv * g.nw, .odist = (g.nu / 2 + 1) * g.nv * g.nw,
+            .type = CUFFT_R2C};
+}
+
+bool SameGrid(const ModelDensityGrid &a, const ModelDensityGrid &b) {
+    return a.nu == b.nu && a.nv == b.nv && a.nw == b.nw;
+}
+
+CudaFFTShape InverseShape(const ModelDensityGrid &g) {
+    return {.n = {g.nw, g.nv, g.nu}, .idist = (g.nu / 2 + 1) * g.nv * g.nw, .odist = g.nu * g.nv * g.nw,
+            .type = CUFFT_C2R};
+}
+
+class DeviceGuard {
+public:
+    explicit DeviceGuard(int device) {
+        cuda_err(cudaGetDevice(&previous_));
+        cuda_err(cudaSetDevice(device));
+    }
+    ~DeviceGuard() { cudaSetDevice(previous_); }
+    DeviceGuard(const DeviceGuard &) = delete;
+    DeviceGuard &operator=(const DeviceGuard &) = delete;
+
+private:
+    int previous_ = 0;
+};
+
+size_t GridPoints(const ModelDensityGrid &g) {
+    return static_cast<size_t>(g.nu) * g.nv * g.nw;
+}
+
+size_t ComplexPoints(const ModelDensityGrid &g) {
+    return static_cast<size_t>(g.nu / 2 + 1) * g.nv * g.nw;
+}
+
+template <typename T>
+void Upload(CudaDevicePtr<T> &dst, const std::vector<T> &src, cudaStream_t stream) {
+    if (!src.empty())
+        cuda_err(cudaMemcpyAsync(dst, src.data(), src.size() * sizeof(T), cudaMemcpyHostToDevice, stream));
+}
+
+// A device buffer of at least n elements, kept between calls and grown when it is too small.
+template <typename T>
+void Ensure(CudaDevicePtr<T> &p, size_t &capacity, size_t n) {
+    if (n <= capacity && p)
+        return;
+    capacity = std::max<size_t>(n, 1);
+    p = CudaDevicePtr<T>(capacity, CudaAlloc::Synchronous);
+}
+
+// h.t of a row and an operator, in units of 1 / den.
+int HT(const std::array<int, 3> &h, const std::array<int, 12> &op) {
+    return h[0] * op[9] + h[1] * op[10] + h[2] * op[11];
+}
+
+// The range of h.t over the rows and operators: the phase table's.
+void PhaseRange(const RefinementGPUSetup &setup, int &min, int &max) {
+    min = max = 0;
+    for (const auto &h : setup.rows)
+        for (const auto &op : setup.sym_ops) {
+            const int ht = HT(h, op);
+            min = std::min(min, ht);
+            max = std::max(max, ht);
+        }
+}
+
+// cub's temporary storage to reduce n doubles.
+size_t ReduceBytes(size_t n) {
+    size_t bytes = 0;
+    cuda_err(cub::DeviceReduce::Sum(nullptr, bytes, static_cast<double *>(nullptr), static_cast<double *>(nullptr),
+                                    static_cast<int>(std::max<size_t>(n, 1))));
+    return bytes;
+}
+
+// The engine's wait on its stream, polling: an evaluation is a millisecond or a few, and where a slot has a
+// card to itself the wake-up of a sleeping thread is on the critical path of every one of them.
+class StreamPoller {
+public:
+    cudaError_t Wait(cudaStream_t stream) const {
+        cudaError_t err;
+        while ((err = cudaStreamQuery(stream)) == cudaErrorNotReady) {}
+        return err;
+    }
+};
+
+// What a function queues on a stream, recorded once as a CUDA graph and replayed from then on: the same
+// launches in the same order, so the same bits, without the host between them. Recorded again where `key`
+// differs from the recording's (another shape: the atoms, a gradient asked or not, another restraint set).
+// Where the stream cannot be captured the function is run as it is, every time.
+class RecordedLaunches {
+public:
+    RecordedLaunches() = default;
+    RecordedLaunches(const RecordedLaunches &) = delete;
+    RecordedLaunches &operator=(const RecordedLaunches &) = delete;
+    ~RecordedLaunches() {
+        if (exec_ != nullptr)
+            cudaGraphExecDestroy(exec_);
+    }
+
+    void Launch(cudaStream_t stream, long key, const std::function<void()> &queue) {
+        if (direct_) {
+            queue();
+            return;
+        }
+        if (exec_ == nullptr || key != key_) {
+            if (exec_ != nullptr)
+                cuda_err(cudaGraphExecDestroy(exec_));
+            exec_ = nullptr;
+            cudaGraph_t graph = nullptr;
+            cuda_err(cudaStreamBeginCapture(stream, cudaStreamCaptureModeThreadLocal));
+            try {
+                queue();
+            } catch (const JFJochException &) {
+                cudaStreamEndCapture(stream, &graph);
+                if (graph != nullptr)
+                    cudaGraphDestroy(graph);
+                cudaGetLastError();
+                direct_ = true;
+                queue();
+                return;
+            }
+            cuda_err(cudaStreamEndCapture(stream, &graph));
+            cuda_err(cudaGraphInstantiate(&exec_, graph, 0));
+            cuda_err(cudaGraphDestroy(graph));
+            key_ = key;
+        }
+        cuda_err(cudaGraphLaunch(exec_, stream));
+    }
+
+private:
+    cudaGraphExec_t exec_ = nullptr;
+    long key_ = 0;
+    bool direct_ = false;
+};
+
+}  // namespace
+
+struct RefinementGPUEngineImpl {
+    struct Restraints {
+        int records = 0, atoms = 0;
+        size_t cap_records = 0, cap_planes = 0, cap_start = 0, cap_index = 0, cap_slots = 0, cap_reduce = 0,
+               cap_atoms = 0, cap_xyzb = 0, reduce_bytes = 0;
+        CudaDevicePtr<RestraintRecord> rec;
+        CudaDevicePtr<int> plane_atoms, slot_start, slot_index;
+        CudaDevicePtr<float4> contrib, xyzb, grad;
+        CudaDevicePtr<double> energy, sum;
+        CudaDevicePtr<char> reduce_temp;
+        int version = 0;   // counts SetRestraints(): a recording of the set is of one version
+        RecordedLaunches launches;
+    };
+
+    RefinementGPUSetup setup;
+    size_t work_bytes;
+    int device = 0;
+    CudaStream stream;
+    StreamPoller waiter;   // the engine's waits on the stream, polled
+    int n_atoms = 0;
+
+    CudaDevicePtr<float4> pos;
+    // What comes back, pinned, so that a copy back queues without waiting: the X-ray target and the restraints'
+    // sums, their gradients, and the restraints' positions going up.
+    CudaHostPtr<double> host_sums;
+    CudaHostPtr<float4> host_grad, host_xyzb, host_restraint_grad;
+    CudaDevicePtr<ModelMaskAtom> mask_atoms;
+    CudaDevicePtr<float> grid;
+    CudaDevicePtr<float2> spectrum;
+    CudaDevicePtr<char> fft_work;
+    // The mask's grid, spectrum and transform where its grid is not the structure factors' (grid, spectrum,
+    // forward otherwise).
+    CudaDevicePtr<float> mask_grid;
+    CudaDevicePtr<float2> mask_spectrum;
+    CudaDevicePtr<int> ops, row_hkl;
+    CudaDevicePtr<double> row_scale;
+    CudaDevicePtr<float> k_total, ml_d, ml_var, fo;
+    CudaDevicePtr<float2> fmask_scaled, f, fm, coef;
+    CudaDevicePtr<char> work, centric;
+    CudaDevicePtr<double> nll, nll_sum;
+    CudaDevicePtr<char> reduce_temp;
+    size_t reduce_bytes = 0;
+    CudaDevicePtr<int> scatter_point, scatter_start, scatter_term, scatter_phase;
+    CudaDevicePtr<double2> phase;   // exp(2 pi i h.t) over the integer h.t from phase_min
+    int phase_min = 0;
+    CudaDevicePtr<float4> grad;
+    std::unique_ptr<ModelDensityGPU> density;
+    std::unique_ptr<ModelMaskGPU> mask;
+    CudaFFTPlan forward, inverse, mask_forward;
+    ModelDensityGPU::Geometry geom{};
+    Restraints restraints[2];
+    RecordedLaunches evaluate;   // QueueEvaluate() recorded
+
+    RefinementGPUEngineImpl(int dev, const RefinementGPUSetup &s, size_t fft_work_bytes) : setup(s), work_bytes(fft_work_bytes), device(dev) {
+        const auto sync = CudaAlloc::Synchronous;
+        const size_t na = std::max<size_t>(setup.max_atoms, 1), nr = std::max<size_t>(setup.rows.size(), 1);
+        pos = CudaDevicePtr<float4>(na, sync);
+        host_sums = CudaHostPtr<double>(2);
+        host_grad = CudaHostPtr<float4>(na);
+        host_xyzb = CudaHostPtr<float4>(na);
+        host_restraint_grad = CudaHostPtr<float4>(na);
+        mask_atoms = CudaDevicePtr<ModelMaskAtom>(na, sync);
+        grad = CudaDevicePtr<float4>(na, sync);
+        grid = CudaDevicePtr<float>(GridPoints(setup.grid), sync);
+        spectrum = CudaDevicePtr<float2>(ComplexPoints(setup.grid), sync);
+        fft_work = CudaDevicePtr<char>(std::max<size_t>(work_bytes, 1), sync);
+        ops = CudaDevicePtr<int>(std::max<size_t>(12 * setup.sym_ops.size(), 1), sync);
+        row_hkl = CudaDevicePtr<int>(3 * nr, sync);
+        row_scale = CudaDevicePtr<double>(nr, sync);
+        k_total = CudaDevicePtr<float>(nr, sync);
+        ml_d = CudaDevicePtr<float>(nr, sync);
+        ml_var = CudaDevicePtr<float>(nr, sync);
+        fo = CudaDevicePtr<float>(nr, sync);
+        fmask_scaled = CudaDevicePtr<float2>(nr, sync);
+        f = CudaDevicePtr<float2>(nr, sync);
+        fm = CudaDevicePtr<float2>(nr, sync);
+        coef = CudaDevicePtr<float2>(nr, sync);
+        work = CudaDevicePtr<char>(nr, sync);
+        centric = CudaDevicePtr<char>(nr, sync);
+        nll = CudaDevicePtr<double>(nr, sync);
+        nll_sum = CudaDevicePtr<double>(1, sync);
+        reduce_bytes = ReduceBytes(nr);
+        reduce_temp = CudaDevicePtr<char>(std::max<size_t>(reduce_bytes, 1), sync);
+        scatter_point = CudaDevicePtr<int>(std::max<size_t>(setup.scatter_point.size(), 1), sync);
+        scatter_start = CudaDevicePtr<int>(std::max<size_t>(setup.scatter_start.size(), 1), sync);
+        scatter_term = CudaDevicePtr<int>(std::max<size_t>(setup.scatter_term.size(), 1), sync);
+        scatter_phase = CudaDevicePtr<int>(std::max<size_t>(setup.scatter_term.size(), 1), sync);
+        int phase_max = 0;
+        PhaseRange(setup, phase_min, phase_max);
+        const int phase_count = phase_max - phase_min + 1;
+        phase = CudaDevicePtr<double2>(phase_count, sync);
+        density = std::make_unique<ModelDensityGPU>(stream, setup.max_atoms, setup.max_pairs,
+                                                    ModelDensityGPU::Bricks(setup.grid.nu, setup.grid.nv, setup.grid.nw));
+        mask = std::make_unique<ModelMaskGPU>(stream, GridPoints(setup.mask_grid));
+        ModelMaskGrid mg;
+        mg.nu = setup.mask_grid.nu;
+        mg.nv = setup.mask_grid.nv;
+        mg.nw = setup.mask_grid.nw;
+        std::copy(setup.mask_grid.orth, setup.mask_grid.orth + 9, mg.orth);
+        mg.volume = setup.volume;
+        mask->SetGrid(mg, setup.mask_ops);
+        if (!SameGrid(setup.mask_grid, setup.grid)) {
+            mask_grid = CudaDevicePtr<float>(GridPoints(setup.mask_grid), sync);
+            mask_spectrum = CudaDevicePtr<float2>(ComplexPoints(setup.mask_grid), sync);
+        }
+
+        // the rotations in whole units (gemmi's are den times an integer matrix), the translations as given
+        std::vector<int> flat_ops;
+        for (const auto &o : setup.sym_ops) {
+            for (int i = 0; i < 9; i++)
+                flat_ops.push_back(o[i] / setup.den);
+            flat_ops.insert(flat_ops.end(), o.begin() + 9, o.end());
+        }
+        std::vector<int> hkl;
+        for (const auto &h : setup.rows)
+            hkl.insert(hkl.end(), h.begin(), h.end());
+        // each scatter term as row * 2 + conj, and its phase's place in the table
+        const int n_ops = static_cast<int>(setup.sym_ops.size());
+        std::vector<int> term, term_phase;
+        for (const int t : setup.scatter_term) {
+            const int m = (t >> 1) / n_ops, o = (t >> 1) % n_ops;
+            term.push_back(m * 2 + (t & 1));
+            term_phase.push_back(HT(setup.rows[m], setup.sym_ops[o]) - phase_min);
+        }
+        Upload(ops, flat_ops, stream);
+        Upload(row_hkl, hkl, stream);
+        Upload(fo, setup.fo, stream);
+        Upload(work, setup.work, stream);
+        Upload(centric, setup.centric, stream);
+        Upload(scatter_point, setup.scatter_point, stream);
+        Upload(scatter_start, setup.scatter_start, stream);
+        Upload(scatter_term, term, stream);
+        Upload(scatter_phase, term_phase, stream);
+        phase_table_kernel<<<blocks(phase_count), THREADS, 0, stream>>>(phase_min, phase_count, setup.den, phase);
+        cuda_err(cudaGetLastError());
+
+        const double inv_n[3] = {1.0 / setup.grid.nu, 1.0 / setup.grid.nv, 1.0 / setup.grid.nw};
+        geom.nu = setup.grid.nu;
+        geom.nv = setup.grid.nv;
+        geom.nw = setup.grid.nw;
+        geom.m00 = static_cast<float>(setup.grid.orth[0] * inv_n[0]);
+        geom.m01 = static_cast<float>(setup.grid.orth[1] * inv_n[1]);
+        geom.m02 = static_cast<float>(setup.grid.orth[2] * inv_n[2]);
+        geom.m11 = static_cast<float>(setup.grid.orth[4] * inv_n[1]);
+        geom.m12 = static_cast<float>(setup.grid.orth[5] * inv_n[2]);
+        geom.m22 = static_cast<float>(setup.grid.orth[8] * inv_n[2]);
+
+        forward = CudaFFTPlan(ForwardShape(setup.grid), stream, fft_work);
+        inverse = CudaFFTPlan(InverseShape(setup.grid), stream, fft_work);
+        if (!SameGrid(setup.mask_grid, setup.grid))
+            mask_forward = CudaFFTPlan(ForwardShape(setup.mask_grid), stream, fft_work);
+        if (forward.WorkBytes() > work_bytes || inverse.WorkBytes() > work_bytes ||
+            (mask_grid.get() != nullptr && mask_forward.WorkBytes() > work_bytes))
+            throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "refinement: cuFFT work area over the reserve");
+        cuda_err(cudaStreamSynchronize(stream));
+    }
+
+    ~RefinementGPUEngineImpl() { cudaStreamSynchronize(stream); }
+
+    float Norm() const { return static_cast<float>(setup.volume / static_cast<double>(GridPoints(setup.grid))); }
+    float MaskNorm() const {
+        return static_cast<float>(setup.volume / static_cast<double>(GridPoints(setup.mask_grid)));
+    }
+
+    // The atoms' density on the grid and its transform into the spectrum.
+    void Transform() {
+        density->Compute(pos, grid);
+        cufft_err(forward.R2C(grid, reinterpret_cast<cufftComplex *>(spectrum.get())));
+    }
+
+    void Compose(bool evaluate) {
+        const int rows = static_cast<int>(setup.rows.size());
+        if (rows == 0)
+            return;
+        compose_target_kernel<<<blocks(rows), THREADS, 0, stream>>>(
+            spectrum, Norm(), setup.grid.nu, setup.grid.nv, setup.grid.nw, ops, static_cast<int>(setup.sym_ops.size()),
+            phase, phase_min, row_hkl, row_scale, rows, evaluate, k_total, fmask_scaled, ml_d, ml_var, fo, work, centric,
+            f, nll, coef);
+        cuda_err(cudaGetLastError());
+    }
+
+    // The X-ray target into host_sums[0] and, with `grad`, its gradient into host_grad: queued, not waited for.
+    void QueueEvaluate(bool grad) {
+        const int rows = static_cast<int>(setup.rows.size());
+        Transform();
+        Compose(true);
+        if (rows > 0) {
+            size_t temp = reduce_bytes;
+            cuda_err(cub::DeviceReduce::Sum(reduce_temp.get(), temp, nll.get(), nll_sum.get(), rows, stream));
+            cuda_err(cudaMemcpyAsync(host_sums.get(), nll_sum, sizeof(double), cudaMemcpyDeviceToHost, stream));
+        }
+        if (grad) {
+            const ModelDensityGrid &g = setup.grid;
+            cuda_err(cudaMemsetAsync(spectrum, 0, ComplexPoints(g) * sizeof(float2), stream));
+            const int points = static_cast<int>(setup.scatter_point.size());
+            if (points > 0) {
+                scatter_kernel<<<blocks(points), THREADS, 0, stream>>>(coef, phase, scatter_point, scatter_start,
+                                                                       scatter_term, scatter_phase, points, spectrum);
+                cuda_err(cudaGetLastError());
+            }
+            cufft_err(inverse.C2R(reinterpret_cast<cufftComplex *>(spectrum.get()), this->grid));
+            if (n_atoms > 0) {
+                const size_t threads = static_cast<size_t>(n_atoms) * WARP;
+                atom_gradient_kernel<<<blocks(threads), THREADS, 0, stream>>>(density->DeviceAtoms(), pos,
+                                                                              density->DeviceBoxes(), n_atoms, geom,
+                                                                              this->grid, Norm(), this->grad);
+                cuda_err(cudaGetLastError());
+                cuda_err(cudaMemcpyAsync(host_grad.get(), this->grad, n_atoms * sizeof(float4), cudaMemcpyDeviceToHost,
+                                         stream));
+            }
+        }
+    }
+
+    // Restraint set `which` at host_xyzb into host_sums[1] and, with `grad`, its gradient into
+    // host_restraint_grad: queued, not waited for.
+    void QueueRestraints(int which, bool grad) {
+        Restraints &r = restraints[which];
+        if (r.atoms > 0)
+            cuda_err(cudaMemcpyAsync(r.xyzb, host_xyzb.get(), r.atoms * sizeof(float4), cudaMemcpyHostToDevice, stream));
+        if (r.records > 0) {
+            restraint_kernel<<<blocks(r.records), THREADS, 0, stream>>>(r.rec, r.records, r.plane_atoms, r.xyzb, r.contrib,
+                                                                        r.energy);
+            cuda_err(cudaGetLastError());
+            size_t temp = r.reduce_bytes;
+            cuda_err(cub::DeviceReduce::Sum(r.reduce_temp.get(), temp, r.energy.get(), r.sum.get(), r.records, stream));
+            cuda_err(cudaMemcpyAsync(host_sums.get() + 1, r.sum, sizeof(double), cudaMemcpyDeviceToHost, stream));
+        }
+        if (grad && r.atoms > 0) {
+            if (r.records > 0) {
+                slot_gather_kernel<<<blocks(r.atoms), THREADS, 0, stream>>>(r.contrib, r.slot_start, r.slot_index,
+                                                                            r.atoms, r.grad);
+                cuda_err(cudaGetLastError());
+            } else
+                cuda_err(cudaMemsetAsync(r.grad, 0, r.atoms * sizeof(float4), stream));
+            cuda_err(cudaMemcpyAsync(host_restraint_grad.get(), r.grad, r.atoms * sizeof(float4), cudaMemcpyDeviceToHost,
+                                     stream));
+        }
+    }
+
+    // QueueEvaluate() and QueueRestraints() as their recordings (the sums that no launch writes zeroed here, on
+    // the host, so that a replay finds them so).
+    void LaunchEvaluate(bool grad) {
+        host_sums[0] = 0;
+        evaluate.Launch(stream, 2L * n_atoms + (grad ? 1 : 0), [&]() { QueueEvaluate(grad); });
+    }
+
+    void LaunchRestraints(int which, bool grad) {
+        Restraints &r = restraints[which];
+        host_sums[1] = 0;
+        r.launches.Launch(stream, 2L * r.version + (grad ? 1 : 0), [&]() { QueueRestraints(which, grad); });
+    }
+};
+
+namespace {
+
+void CopyOut(const float4 *from, int n, std::vector<std::array<float, 4>> &to) {
+    to.resize(n);
+    std::copy(reinterpret_cast<const std::array<float, 4> *>(from), reinterpret_cast<const std::array<float, 4> *>(from) + n,
+              to.begin());
+}
+
+}  // namespace
+
+size_t RefinementGPUEngine::FFTWorkBytes(int device, const RefinementGPUSetup &setup) {
+    DeviceGuard guard(device);
+    size_t bytes = std::max(CudaFFTPlan::WorkBytes(ForwardShape(setup.grid)),
+                            CudaFFTPlan::WorkBytes(InverseShape(setup.grid)));
+    if (!SameGrid(setup.mask_grid, setup.grid))
+        bytes = std::max(bytes, CudaFFTPlan::WorkBytes(ForwardShape(setup.mask_grid)));
+    return bytes;
+}
+
+size_t RefinementGPUEngine::DeviceBytes(const RefinementGPUSetup &s, size_t fft_work_bytes, size_t max_records,
+                                        size_t max_slots) {
+    const size_t na = s.max_atoms + 1, nr = s.rows.size() + 1;
+    size_t bytes = na * (2 * sizeof(float4) + 3 * sizeof(int) + sizeof(ModelMaskAtom) + sizeof(ModelDensityAtom));
+    bytes += GridPoints(s.grid) * sizeof(float) + ComplexPoints(s.grid) * sizeof(float2) + fft_work_bytes;
+    bytes += nr * (3 * sizeof(int) + 2 * sizeof(double) + 4 * sizeof(float) + 4 * sizeof(float2) + 2);
+    bytes += (s.scatter_point.size() + s.scatter_start.size() + 2 * s.scatter_term.size()) * sizeof(int);
+    int phase_min = 0, phase_max = 0;
+    PhaseRange(s, phase_min, phase_max);
+    bytes += static_cast<size_t>(phase_max - phase_min + 1) * sizeof(double2);
+    bytes += ModelDensityGPU::DeviceBytes(s.max_atoms, s.max_pairs, ModelDensityGPU::Bricks(s.grid.nu, s.grid.nv, s.grid.nw));
+    bytes += ModelMaskGPU::DeviceBytes(GridPoints(s.mask_grid));
+    if (!SameGrid(s.mask_grid, s.grid))
+        bytes += GridPoints(s.mask_grid) * sizeof(float) + ComplexPoints(s.mask_grid) * sizeof(float2);
+    // the two restraint sets of SetRestraints(), each up to these
+    bytes += 2 * (max_records * (sizeof(RestraintRecord) + sizeof(double)) + max_slots * (sizeof(float4) + sizeof(int)) +
+                  na * (2 * sizeof(float4) + sizeof(int)));
+    return bytes;
+}
+
+RefinementGPUEngine::RefinementGPUEngine(int device, const RefinementGPUSetup &setup, size_t fft_work_bytes) {
+    DeviceGuard guard(device);
+    impl_ = std::make_unique<RefinementGPUEngineImpl>(device, setup, fft_work_bytes);
+}
+
+RefinementGPUEngine::~RefinementGPUEngine() {
+    if (impl_) {
+        DeviceGuard guard(impl_->device);
+        impl_.reset();
+    }
+}
+
+void RefinementGPUEngine::SetBlur(double blur) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    std::vector<double> scale(e.setup.rows.size());
+    for (size_t m = 0; m < scale.size(); m++)
+        scale[m] = e.setup.centring * std::exp(blur * 0.25 * e.setup.inv_d2[m]);
+    Upload(e.row_scale, scale, e.stream);
+    cuda_err(e.waiter.Wait(e.stream));
+}
+
+void RefinementGPUEngine::SetRowModel(const std::vector<float> &k_total, const std::vector<std::array<float, 2>> &fmask,
+                                      const std::vector<float> &d, const std::vector<float> &var) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    Upload(e.k_total, k_total, e.stream);
+    if (!fmask.empty())
+        cuda_err(cudaMemcpyAsync(e.fmask_scaled, fmask.data(), fmask.size() * sizeof(float2), cudaMemcpyHostToDevice,
+                                 e.stream));
+    Upload(e.ml_d, d, e.stream);
+    Upload(e.ml_var, var, e.stream);
+    cuda_err(e.waiter.Wait(e.stream));
+}
+
+void RefinementGPUEngine::SetDensities(const ModelDensityAtom *atoms, size_t n) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    if (n > e.setup.max_atoms)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "refinement: atoms over the reserve");
+    e.density->SetAtoms(e.setup.grid, atoms, n);
+    e.n_atoms = static_cast<int>(n);
+}
+
+void RefinementGPUEngine::SetPositions(const std::array<float, 4> *pos, size_t n) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    if (static_cast<int>(n) != e.n_atoms)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "refinement: positions do not match the atoms");
+    if (n > 0)
+        cuda_err(cudaMemcpyAsync(e.pos, pos, n * sizeof(float4), cudaMemcpyHostToDevice, e.stream));
+}
+
+void RefinementGPUEngine::Fcalc(std::vector<std::array<float, 2>> &f) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    e.Transform();
+    e.Compose(false);
+    f.resize(e.setup.rows.size());
+    if (!f.empty())
+        cuda_err(cudaMemcpyAsync(f.data(), e.f, f.size() * sizeof(float2), cudaMemcpyDeviceToHost, e.stream));
+    cuda_err(e.waiter.Wait(e.stream));
+}
+
+void RefinementGPUEngine::Fmask(const std::vector<ModelMaskAtom> &mask_atoms, std::vector<std::array<float, 2>> &f) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    if (mask_atoms.size() > e.setup.max_atoms)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "refinement: mask atoms over the reserve");
+    if (!mask_atoms.empty())
+        cuda_err(cudaMemcpyAsync(e.mask_atoms, mask_atoms.data(), mask_atoms.size() * sizeof(ModelMaskAtom),
+                                 cudaMemcpyHostToDevice, e.stream));
+    const bool own = e.mask_grid.get() != nullptr;
+    float *grid = own ? e.mask_grid.get() : e.grid.get();
+    float2 *spectrum = own ? e.mask_spectrum.get() : e.spectrum.get();
+    e.mask->Compute(e.mask_atoms, static_cast<int>(mask_atoms.size()), grid);
+    cufft_err((own ? e.mask_forward : e.forward).R2C(grid, reinterpret_cast<cufftComplex *>(spectrum)));
+    const int rows = static_cast<int>(e.setup.rows.size());
+    f.resize(rows);
+    if (rows > 0) {
+        const ModelDensityGrid &g = e.setup.mask_grid;
+        fmask_kernel<<<blocks(rows), THREADS, 0, e.stream>>>(spectrum, e.MaskNorm(), e.row_hkl, rows, g.nu, g.nv, g.nw,
+                                                             e.fm);
+        cuda_err(cudaGetLastError());
+        cuda_err(cudaMemcpyAsync(f.data(), e.fm, rows * sizeof(float2), cudaMemcpyDeviceToHost, e.stream));
+    }
+    cuda_err(e.waiter.Wait(e.stream));
+}
+
+double RefinementGPUEngine::Evaluate(bool grad) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    e.LaunchEvaluate(grad);
+    cuda_err(e.waiter.Wait(e.stream));
+    return e.host_sums[0];
+}
+
+const std::array<float, 4> *RefinementGPUEngine::HostGradient() const {
+    return reinterpret_cast<const std::array<float, 4> *>(impl_->host_grad.get());
+}
+
+const std::array<float, 4> *RefinementGPUEngine::HostRestraintGradient() const {
+    return reinterpret_cast<const std::array<float, 4> *>(impl_->host_restraint_grad.get());
+}
+
+double RefinementGPUEngine::EvaluateWithRestraints(bool grad, int which,
+                                                   const std::function<void(std::array<float, 4> *)> &xyzb,
+                                                   bool restraint_grad, double &restraints) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    RefinementGPUEngineImpl::Restraints &r = e.restraints[which];
+    if (r.atoms != e.n_atoms)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "refinement: restraint atoms do not match");
+    e.LaunchEvaluate(grad);
+    xyzb(reinterpret_cast<std::array<float, 4> *>(e.host_xyzb.get()));
+    e.LaunchRestraints(which, restraint_grad);
+    cuda_err(e.waiter.Wait(e.stream));
+    restraints = e.host_sums[1];
+    return e.host_sums[0];
+}
+
+void RefinementGPUEngine::SetRestraints(int which, const std::vector<RestraintRecord> &records,
+                                        const std::vector<int> &plane_atoms, const std::vector<int> &slot_start,
+                                        const std::vector<int> &slot_index, int n_slots) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    RefinementGPUEngineImpl::Restraints &r = e.restraints[which];
+    for (const RestraintRecord &rec : records)
+        if (rec.kind == static_cast<int>(RestraintKind::Plane) && rec.atom[1] > MAX_PLANE_ATOMS)
+            throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "refinement: a plane of too many atoms");
+    r.records = static_cast<int>(records.size());
+    r.atoms = static_cast<int>(slot_start.empty() ? 0 : slot_start.size() - 1);
+    Ensure(r.rec, r.cap_records, records.size());
+    Ensure(r.energy, r.cap_reduce, records.size());
+    Ensure(r.plane_atoms, r.cap_planes, plane_atoms.size());
+    Ensure(r.slot_start, r.cap_start, slot_start.size());
+    Ensure(r.slot_index, r.cap_index, slot_index.size());
+    Ensure(r.contrib, r.cap_slots, static_cast<size_t>(n_slots));
+    Ensure(r.xyzb, r.cap_xyzb, r.atoms);
+    Ensure(r.grad, r.cap_atoms, r.atoms);
+    if (!r.sum)
+        r.sum = CudaDevicePtr<double>(1, CudaAlloc::Synchronous);
+    const size_t bytes = ReduceBytes(r.cap_reduce);
+    if (!r.reduce_temp || bytes > r.reduce_bytes) {
+        r.reduce_bytes = bytes;
+        r.reduce_temp = CudaDevicePtr<char>(std::max<size_t>(bytes, 1), CudaAlloc::Synchronous);
+    }
+    Upload(r.rec, records, e.stream);
+    Upload(r.plane_atoms, plane_atoms, e.stream);
+    Upload(r.slot_start, slot_start, e.stream);
+    Upload(r.slot_index, slot_index, e.stream);
+    r.version++;
+    cuda_err(e.waiter.Wait(e.stream));
+}
+
+double RefinementGPUEngine::EvaluateRestraints(int which, const std::vector<std::array<float, 4>> &xyzb,
+                                               std::vector<std::array<float, 4>> *grad) {
+    RefinementGPUEngineImpl &e = *impl_;
+    DeviceGuard guard(e.device);
+    RefinementGPUEngineImpl::Restraints &r = e.restraints[which];
+    if (static_cast<int>(xyzb.size()) != r.atoms)
+        throw JFJochException(JFJochExceptionCategory::GPUCUDAError, "refinement: restraint atoms do not match");
+    // the staging buffer free again
+    cuda_err(e.waiter.Wait(e.stream));
+    std::copy(xyzb.begin(), xyzb.end(), reinterpret_cast<std::array<float, 4> *>(e.host_xyzb.get()));
+    e.LaunchRestraints(which, grad != nullptr);
+    cuda_err(e.waiter.Wait(e.stream));
+    if (grad != nullptr)
+        CopyOut(e.host_restraint_grad, r.atoms, *grad);
+    return e.host_sums[1];
+}
diff --git a/image_analysis/structure_refinement/RefinementGPU.h b/image_analysis/structure_refinement/RefinementGPU.h
new file mode 100644
index 000000000..764454679
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementGPU.h
@@ -0,0 +1,24 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+// Restrained refinement's targets on a GPU (CUDA builds only): the RefinementEngine of RefinementXray.h with
+// everything per evaluation on the device - the atoms' density (ModelDensityGPU's gather), its transform, the
+// symmetry composed in reciprocal space, the likelihood target, the derivative map by the inverse transform
+// of the target's derivatives and every atom's gradient read off it, and the geometry restraints. The host
+// passes positions in and gets one value and one gradient per atom back.
+
+#include <memory>
+
+#include "RefinementXray.h"
+
+// The engine for refining `model` against `refl` on `device`, or null where the GPU cannot take this case (an
+// atom's box wider than the cell, too many symmetry operators) or its memory is over `budget` bytes.
+// `b_max`: the largest B an atom may reach, which the gather's reserve is sized for. Throws JFJochException on a
+// CUDA failure. `nthreads`: the host threads that work out the atoms' densities.
+std::unique_ptr<RefinementEngine> MakeRefinementEngineGPU(int device, const gemmi::UnitCell &cell,
+                                                          const gemmi::SpaceGroup &sg, double d_min,
+                                                          const RefinementReflections &refl,
+                                                          const gemmi::Model &model, double b_max, size_t budget,
+                                                          size_t *device_bytes = nullptr, size_t nthreads = 1);
diff --git a/image_analysis/structure_refinement/RefinementGPUEngine.h b/image_analysis/structure_refinement/RefinementGPUEngine.h
new file mode 100644
index 000000000..4b8c86d7c
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementGPUEngine.h
@@ -0,0 +1,93 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+// The device half of restrained refinement on a GPU (RefinementGPU.h, CUDA builds only). The host half works
+// out with gemmi everything that depends on the cell, the group and the reflections; this half grids the atoms,
+// transforms, composes the symmetry, evaluates the likelihood target, takes its derivative back to every atom
+// by the FFT method, and evaluates the geometry restraints. Every kernel is deterministic - gathers and fixed
+// reduction trees, no floating-point atomics - so the same input gives the same bits on every run.
+
+#include <array>
+#include <cstddef>
+#include <functional>
+#include <memory>
+#include <vector>
+
+#include "ModelDensityGPU.h"
+#include "ModelMaskGPU.h"
+#include "RefinementMath.h"
+
+// Everything an engine needs that does not depend on the atoms.
+struct RefinementGPUSetup {
+    ModelDensityGrid grid;                     // the structure-factor grid, u fastest
+    ModelDensityGrid mask_grid;                // the bulk-solvent mask's (BulkSolventMask::MaskGrid), u fastest
+    double volume = 0;
+    std::vector<std::array<int, 12>> sym_ops;  // gemmi's Op: rot row-major and tran, in units of 1 / den
+    int den = 24;
+    double centring = 1;                       // the number of centring vectors
+    std::vector<ModelMaskOp> mask_ops;         // every operator with every centring vector
+    std::vector<std::array<int, 3>> rows;      // the reflections, in the order their numbers come back
+    std::vector<double> inv_d2;
+    std::vector<float> fo;
+    std::vector<char> work, centric;
+    // The adjoint of the composition, as a gather: the half-u spectrum points the gradient's coefficients
+    // land on (ascending), and for each the terms (row * ops + op) * 2 + conj adding to it, in order.
+    std::vector<int> scatter_point, scatter_start, scatter_term;
+    size_t max_atoms = 0, max_pairs = 0;
+};
+
+struct RefinementGPUEngineImpl;
+
+class RefinementGPUEngine {
+public:
+    static size_t DeviceBytes(const RefinementGPUSetup &setup, size_t fft_work_bytes, size_t max_records,
+                              size_t max_slots);
+    static size_t FFTWorkBytes(int device, const RefinementGPUSetup &setup);
+
+    RefinementGPUEngine(int device, const RefinementGPUSetup &setup, size_t fft_work_bytes);
+    ~RefinementGPUEngine();
+
+    // n_cen exp(blur s^2 / 4) per reflection: prepare_asu_data()'s unblur.
+    void SetBlur(double blur);
+    // Per macro-cycle: F_model = k_total (F + fmask), and the likelihood's D and variance.
+    void SetRowModel(const std::vector<float> &k_total, const std::vector<std::array<float, 2>> &fmask,
+                     const std::vector<float> &d, const std::vector<float> &var);
+
+    // The atoms' densities, as ModelStructureFactorsGPU takes them (the boxes of ModelDensityGPU::Boxes() made
+    // from them): called again only where some atom's density changed. Read until the call returns; from pinned
+    // memory they go up by DMA.
+    void SetDensities(const ModelDensityAtom *atoms, size_t n);
+    // The atoms' grid positions (fractional times the grid size, not wrapped), in the order of SetDensities():
+    // read until the next evaluation returns, so from a pinned buffer the copy goes up by DMA.
+    void SetPositions(const std::array<float, 4> *pos, size_t n);
+    // F of the atoms at the rows.
+    void Fcalc(std::vector<std::array<float, 2>> &f);
+    // The bulk-solvent mask's F at the rows (the mask atoms fractional, wrapped), on the mask's own grid.
+    void Fmask(const std::vector<ModelMaskAtom> &mask_atoms, std::vector<std::array<float, 2>> &f);
+    // -ln L over the working rows for the atoms last set and, with `grad`, dT/d(x, y, z, B) per atom into
+    // HostGradient().
+    double Evaluate(bool grad);
+    // The gradients of the last evaluation, in the engine's pinned buffers: valid until the next one.
+    const std::array<float, 4> *HostGradient() const;
+    const std::array<float, 4> *HostRestraintGradient() const;
+
+    // Restraint set `which` (0 or 1), as RestraintSet holds it.
+    void SetRestraints(int which, const std::vector<RestraintRecord> &records, const std::vector<int> &plane_atoms,
+                       const std::vector<int> &slot_start, const std::vector<int> &slot_index, int n_slots);
+    // The sum of E of set `which` at `xyzb` (x, y, z, B per atom) and dE/d(x, y, z, B) per atom.
+    double EvaluateRestraints(int which, const std::vector<std::array<float, 4>> &xyzb,
+                              std::vector<std::array<float, 4>> *grad);
+    // Evaluate() and EvaluateRestraints() in one submission with one wait: the X-ray target is queued first, and
+    // `xyzb` writes the restraints' x, y, z, B of every atom while the device works on it. The gradients into
+    // HostGradient() and HostRestraintGradient().
+    double EvaluateWithRestraints(bool grad, int which, const std::function<void(std::array<float, 4> *)> &xyzb,
+                                  bool restraint_grad, double &restraints);
+
+    // The most atoms of a plane restraint the kernel takes.
+    static constexpr int MAX_PLANE_ATOMS = 32;
+
+private:
+    std::unique_ptr<RefinementGPUEngineImpl> impl_;
+};
diff --git a/image_analysis/structure_refinement/RefinementMath.h b/image_analysis/structure_refinement/RefinementMath.h
new file mode 100644
index 000000000..af87c6bc6
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementMath.h
@@ -0,0 +1,280 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+// The per-term arithmetic of restrained refinement (Refinement.h), written once for the CPU and the GPU:
+// the maximum-likelihood amplitude target of one reflection and the geometry restraints, each with its
+// derivatives. Plain functions on plain numbers, so the CUDA engine (RefinementGPU.cu) and the CPU path
+// (RefinementXray.cpp, RefinementRestraints.cpp) evaluate the same expressions.
+
+#include <cmath>
+
+#if defined(__CUDACC__)
+#define REFINE_HD __host__ __device__
+#else
+#define REFINE_HD
+#endif
+
+// What a restraint is, for the evaluators on either side (RefinementRestraints.h builds them).
+enum class RestraintKind : int { Bond = 0, Angle, Torsion, Chiral, Plane, Repulsion, BSimilarity };
+
+// One restraint. E = ((value - ideal) / sigma)^2, summed over a set (BSimilarity: sigma is kappa, BSimilarityTerm).
+struct RestraintRecord {
+    int kind = 0;
+    int atom[4] = {0, 0, 0, 0};   // Plane: atom[0] the first of its atoms in plane_atoms, atom[1] their number
+    float ideal = 0;              // A, degrees, A^3 (chiral) or A (repulsion: the contact distance)
+    float sigma = 1;
+    int period = 0;               // Torsion
+    int slot = 0;                 // the first of its gradient slots, one per atom
+    // Repulsion: where the second atom is, as the image x' = rot x + tran of its position (Cartesian);
+    // the identity elsewhere.
+    float rot[9] = {1, 0, 0, 0, 1, 0, 0, 0, 1};
+    float tran[3] = {0, 0, 0};
+};
+
+namespace refine_math {
+
+constexpr double PI = 3.14159265358979323846;
+constexpr double DEG = PI / 180.0;
+
+// ln I0(x) and I1(x)/I0(x) for x >= 0, from the polynomial approximations of Abramowitz & Stegun (1964),
+// Handbook of Mathematical Functions, 9.8.1-9.8.4 (relative error below 2e-7); for large x through the
+// exponentially scaled form, so nothing overflows.
+template <typename T>
+REFINE_HD inline void BesselI0I1(T x, T &log_i0, T &i1_over_i0) {
+    if (x < T(3.75)) {
+        const T t = (x / T(3.75)) * (x / T(3.75));
+        const T i0 = T(1.0) + t * (T(3.5156229) + t * (T(3.0899424) + t * (T(1.2067492) +
+                     t * (T(0.2659732) + t * (T(0.0360768) + t * T(0.0045813))))));
+        const T i1 = x * (T(0.5) + t * (T(0.87890594) + t * (T(0.51498869) + t * (T(0.15084934) +
+                     t * (T(0.02658733) + t * (T(0.00301532) + t * T(0.00032411)))))));
+        log_i0 = log(i0);
+        i1_over_i0 = i1 / i0;
+    } else {
+        const T t = T(3.75) / x;
+        // sqrt(x) exp(-x) I0(x) and sqrt(x) exp(-x) I1(x)
+        const T s0 = T(0.39894228) + t * (T(0.01328592) + t * (T(0.00225319) + t * (T(-0.00157565) +
+                     t * (T(0.00916281) + t * (T(-0.02057706) + t * (T(0.02635537) + t * (T(-0.01647633) +
+                     t * T(0.00392377))))))));
+        const T s1 = T(0.39894228) + t * (T(-0.03988024) + t * (T(-0.00362018) + t * (T(0.00163801) +
+                     t * (T(-0.01031555) + t * (T(0.02282967) + t * (T(-0.02895312) + t * (T(0.01787654) +
+                     t * T(-0.00420059))))))));
+        log_i0 = x + log(s0) - T(0.5) * log(x);
+        i1_over_i0 = s1 / s0;
+    }
+}
+
+// The likelihood of one observed amplitude given the model amplitude Fc - the Rice distribution for an
+// acentric reflection, its centric counterpart otherwise - with D the fraction of the model that is
+// right and var the variance the rest of the structure and the measurement leave (epsilon beta plus the
+// observation's own sigma^2). Returns -ln L without the terms that depend on neither Fc nor the
+// parameters, and sets d(-ln L)/dFc.
+// Following Pannu & Read (1996) Acta Cryst. A52, 659-668 and Murshudov, Vagin & Dodson (1997) Acta Cryst.
+// D53, 240-255
+template <typename T>
+REFINE_HD inline T AmplitudeNegLogLikelihood(T fo, T fc, T d, T var, bool centric, T &dfc) {
+    if (!centric) {
+        const T x = T(2.0) * d * fo * fc / var;
+        T log_i0, ratio;
+        BesselI0I1(x, log_i0, ratio);
+        dfc = (T(2.0) * d * d * fc - ratio * T(2.0) * d * fo) / var;
+        return log(var) + (fo * fo + d * d * fc * fc) / var - log_i0;
+    }
+    const T x = d * fo * fc / var;
+    // ln cosh x = x + ln(1 + exp(-2x)) - ln 2 for x >= 0
+    const T log_cosh = x + log(T(1.0) + exp(T(-2.0) * x)) - T(0.6931471805599453);
+    dfc = (d * d * fc - tanh(x) * d * fo) / var;
+    return T(0.5) * log(var) + (fo * fo + d * d * fc * fc) / (T(2.0) * var) - log_cosh;
+}
+
+// --- geometry restraints: E = ((value - ideal) / sigma)^2 and dE/dx for each atom ---
+
+template <typename T>
+struct V3 {
+    T x, y, z;
+};
+
+template <typename T> REFINE_HD inline V3<T> operator-(V3<T> a, V3<T> b) { return {a.x - b.x, a.y - b.y, a.z - b.z}; }
+template <typename T> REFINE_HD inline V3<T> operator+(V3<T> a, V3<T> b) { return {a.x + b.x, a.y + b.y, a.z + b.z}; }
+template <typename T> REFINE_HD inline V3<T> operator*(T s, V3<T> a) { return {s * a.x, s * a.y, s * a.z}; }
+template <typename T> REFINE_HD inline T Dot(V3<T> a, V3<T> b) { return a.x * b.x + a.y * b.y + a.z * b.z; }
+template <typename T> REFINE_HD inline V3<T> Cross(V3<T> a, V3<T> b) {
+    return {a.y * b.z - a.z * b.y, a.z * b.x - a.x * b.z, a.x * b.y - a.y * b.x};
+}
+template <typename T> REFINE_HD inline T Norm(V3<T> a) { return sqrt(Dot(a, a)); }
+
+// A bond length.
+template <typename T>
+REFINE_HD inline T BondTerm(V3<T> a, V3<T> b, T ideal, T sigma, V3<T> g[2]) {
+    const V3<T> d = a - b;
+    const T len = Norm(d);
+    const T r = (len - ideal) / sigma;
+    const T f = len > T(0) ? T(2.0) * r / (sigma * len) : T(0);
+    g[0] = f * d;
+    g[1] = (-f) * d;
+    return r * r;
+}
+
+// A bond angle at b, ideal and sigma in degrees.
+template <typename T>
+REFINE_HD inline T AngleTerm(V3<T> a, V3<T> b, V3<T> c, T ideal, T sigma, V3<T> g[3]) {
+    const V3<T> u = a - b, v = c - b;
+    const T lu = Norm(u), lv = Norm(v);
+    const V3<T> cr = Cross(u, v);
+    const T theta = atan2(Norm(cr), Dot(u, v));
+    const T s = T(DEG);
+    const T r = (theta - ideal * s) / (sigma * s);
+    // dtheta/du = (cos(theta) u/|u| - v/|v|) / (|u| sin(theta)), and the same with u and v swapped
+    const T sin_t = fmax(sin(theta), T(1e-6)), cos_t = cos(theta);
+    const T f = T(2.0) * r / (sigma * s);
+    const V3<T> du = (T(1.0) / (lu * sin_t)) * ((cos_t / lu) * u - (T(1.0) / lv) * v);
+    const V3<T> dv = (T(1.0) / (lv * sin_t)) * ((cos_t / lv) * v - (T(1.0) / lu) * u);
+    g[0] = f * du;
+    g[2] = f * dv;
+    g[1] = (-f) * (du + dv);
+    return r * r;
+}
+
+// The dihedral angle p0-p1-p2-p3 in radians, and its derivatives with respect to the four positions.
+// Following Blondel & Karplus (1996) J. Comput. Chem. 17, 1132-1141
+template <typename T>
+REFINE_HD inline T Dihedral(V3<T> p0, V3<T> p1, V3<T> p2, V3<T> p3, V3<T> d[4]) {
+    const V3<T> b1 = p1 - p0, b2 = p2 - p1, b3 = p3 - p2;
+    const V3<T> m = Cross(b1, b2), n = Cross(b2, b3);
+    const T lb2 = Norm(b2);
+    const T mm = fmax(Dot(m, m), T(1e-12)), nn = fmax(Dot(n, n), T(1e-12));
+    const T phi = atan2(lb2 * Dot(b1, n), Dot(m, n));
+    d[0] = (-lb2 / mm) * m;
+    d[3] = (lb2 / nn) * n;
+    const T bb = lb2 * lb2;
+    const T p = Dot(b1, b2) / bb, q = Dot(b3, b2) / bb;
+    d[1] = (-(T(1.0) + p)) * d[0] + q * d[3];
+    d[2] = (-T(1.0)) * (d[0] + d[1] + d[3]);
+    return phi;
+}
+
+// A torsion restrained to ideal (degrees) modulo 360/period; period 0 is read as 1.
+template <typename T>
+REFINE_HD inline T TorsionTerm(V3<T> p0, V3<T> p1, V3<T> p2, V3<T> p3, T ideal, T sigma, int period, V3<T> g[4]) {
+    V3<T> d[4];
+    const T phi = Dihedral(p0, p1, p2, p3, d) / T(DEG);
+    const T step = T(360.0) / T(period > 0 ? period : 1);
+    T delta = phi - ideal;
+    delta -= step * floor(delta / step + T(0.5));
+    const T r = delta / sigma;
+    const T f = T(2.0) * r / (sigma * T(DEG));
+    for (int i = 0; i < 4; i++)
+        g[i] = f * d[i];
+    return r * r;
+}
+
+// A chiral volume (c the centre): (a1 - c) . ((a2 - c) x (a3 - c)).
+template <typename T>
+REFINE_HD inline T ChiralTerm(V3<T> c, V3<T> a1, V3<T> a2, V3<T> a3, T ideal, T sigma, V3<T> g[4]) {
+    const V3<T> x1 = a1 - c, x2 = a2 - c, x3 = a3 - c;
+    const T vol = Dot(x1, Cross(x2, x3));
+    const T r = (vol - ideal) / sigma;
+    const T f = T(2.0) * r / sigma;
+    g[1] = f * Cross(x2, x3);
+    g[2] = f * Cross(x3, x1);
+    g[3] = f * Cross(x1, x2);
+    g[0] = (-T(1.0)) * (g[1] + g[2] + g[3]);
+    return r * r;
+}
+
+// A repulsion below the contact distance d0 (none above it).
+template <typename T>
+REFINE_HD inline T RepulsionTerm(V3<T> a, V3<T> b, T d0, T sigma, V3<T> g[2]) {
+    const V3<T> d = a - b;
+    const T len = Norm(d);
+    if (len >= d0 || len <= T(0)) {
+        g[0] = g[1] = V3<T>{0, 0, 0};
+        return T(0);
+    }
+    const T r = (d0 - len) / sigma;
+    const T f = T(-2.0) * r / (sigma * len);
+    g[0] = f * d;
+    g[1] = (-f) * d;
+    return r * r;
+}
+
+// Two atoms' B alike in proportion to their size: the symmetric Kullback-Leibler divergence of two isotropic
+// Gaussians of variances B_i and B_j over kappa^2 (up to a factor), E = (B_i - B_j)^2 / (kappa^2 B_i B_j) - a
+// difference restraint whose sigma is kappa sqrt(B_i B_j). Sets dE/dB_i and dE/dB_j.
+// Following Murshudov et al. (2011) Acta Cryst. D67, 355-367 (the Kullback-Leibler form of the ADP restraints)
+template <typename T>
+REFINE_HD inline T BSimilarityTerm(T bi, T bj, T kappa, T &gi, T &gj) {
+    const T k2 = kappa * kappa, d = bi - bj;
+    gi = d * (bi + bj) / (k2 * bi * bi * bj);
+    gj = -d * (bi + bj) / (k2 * bi * bj * bj);
+    return d * d / (k2 * bi * bj);
+}
+
+// The unit eigenvector of the smallest eigenvalue of a symmetric 3x3 matrix (a00 a11 a22 a01 a02 a12), by
+// cyclic Jacobi rotations.
+template <typename T>
+REFINE_HD inline V3<T> SmallestEigenvector(const T m_in[6]) {
+    T a[3][3] = {{m_in[0], m_in[3], m_in[4]}, {m_in[3], m_in[1], m_in[5]}, {m_in[4], m_in[5], m_in[2]}};
+    T v[3][3] = {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}};
+    for (int sweep = 0; sweep < 12; sweep++)
+        for (int p = 0; p < 2; p++)
+            for (int q = p + 1; q < 3; q++) {
+                if (fabs(a[p][q]) < T(1e-30))
+                    continue;
+                const T theta = (a[q][q] - a[p][p]) / (T(2.0) * a[p][q]);
+                const T t = (theta >= 0 ? T(1.0) : T(-1.0)) / (fabs(theta) + sqrt(theta * theta + T(1.0)));
+                const T c = T(1.0) / sqrt(t * t + T(1.0)), s = t * c;
+                for (int k = 0; k < 3; k++) {
+                    const T akp = a[k][p], akq = a[k][q];
+                    a[k][p] = c * akp - s * akq;
+                    a[k][q] = s * akp + c * akq;
+                }
+                for (int k = 0; k < 3; k++) {
+                    const T apk = a[p][k], aqk = a[q][k];
+                    a[p][k] = c * apk - s * aqk;
+                    a[q][k] = s * apk + c * aqk;
+                }
+                for (int k = 0; k < 3; k++) {
+                    const T vkp = v[k][p], vkq = v[k][q];
+                    v[k][p] = c * vkp - s * vkq;
+                    v[k][q] = s * vkp + c * vkq;
+                }
+            }
+    int i = 0;
+    if (a[1][1] < a[i][i])
+        i = 1;
+    if (a[2][2] < a[i][i])
+        i = 2;
+    return {v[0][i], v[1][i], v[2][i]};
+}
+
+// A plane: the distances of n atoms from their least-squares plane. The plane is optimal, so the
+// derivative of each atom's distance carries no term from the plane moving: dE/dx_i = 2 (n.(x_i - c)) n / sigma^2.
+template <typename T>
+REFINE_HD inline T PlaneTerm(const V3<T> *x, int n, T sigma, V3<T> *g) {
+    V3<T> c{0, 0, 0};
+    for (int i = 0; i < n; i++)
+        c = c + x[i];
+    c = (T(1.0) / T(n)) * c;
+    T m[6] = {0, 0, 0, 0, 0, 0};
+    for (int i = 0; i < n; i++) {
+        const V3<T> d = x[i] - c;
+        m[0] += d.x * d.x;
+        m[1] += d.y * d.y;
+        m[2] += d.z * d.z;
+        m[3] += d.x * d.y;
+        m[4] += d.x * d.z;
+        m[5] += d.y * d.z;
+    }
+    const V3<T> nv = SmallestEigenvector(m);
+    T e = 0;
+    for (int i = 0; i < n; i++) {
+        const T r = Dot(nv, x[i] - c) / sigma;
+        e += r * r;
+        g[i] = (T(2.0) * r / sigma) * nv;
+    }
+    return e;
+}
+
+}  // namespace refine_math
diff --git a/image_analysis/structure_refinement/RefinementMinimiser.h b/image_analysis/structure_refinement/RefinementMinimiser.h
new file mode 100644
index 000000000..1a19b2677
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementMinimiser.h
@@ -0,0 +1,211 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <algorithm>
+#include <cmath>
+#include <deque>
+#include <functional>
+#include <vector>
+
+#include "../../common/ParallelFor.h"
+
+// Limited-memory BFGS whose memory outlives one call, so that a refinement's macro-cycles - each a few dozen
+// iterations on a target whose scale and likelihood parameters were refitted in between - go on from what the
+// earlier ones learnt of the curvature instead of starting each from a steepest-descent step. The initial inverse
+// Hessian is a diagonal the caller gives (SetDiagonal: an estimate of the Hessian's diagonal, so that a parameter
+// with ten times the curvature of another takes a tenth of its step), scaled each iteration by the latest pair
+// (Oren-Shanno in that metric). The line search backtracks from the full step to sufficient decrease.
+// Following Nocedal (1980) Math. Comp. 35, 773-782 and Liu & Nocedal (1989) Math. Program. 45, 503-528
+class RefinementMinimiser {
+public:
+    // f(x, g): the target at x, and its gradient in g (sized as x); false where it cannot be evaluated there.
+    using Target = std::function<bool(const std::vector<double> &x, double &f, std::vector<double> &g)>;
+
+    // `nthreads`: the threads the sweeps over the parameters run on (the dot products stay serial chains).
+    explicit RefinementMinimiser(size_t memory = 20, size_t nthreads = 1) : memory_(memory), nthreads_(nthreads) {}
+
+    // Forget the pairs (the target changed beyond what the memory still describes, e.g. another weight).
+    void Reset() {
+        s_.clear();
+        y_.clear();
+        sy_.clear();
+    }
+    // The estimated diagonal of the Hessian; every element > 0.
+    void SetDiagonal(std::vector<double> h) { h_ = std::move(h); }
+
+    struct Outcome {
+        int iterations = 0;
+        int evaluations = 0;
+        double f_start = 0, f_end = 0;
+    };
+
+    // At most `iterations` iterations from x (x is where it ended); stops early where an iteration lowers f by
+    // less than `f_tolerance` relative to |f|, or `stop` says so (checked before every iteration). `max_step`, in
+    // the parameters' units, is the most any parameter moves in the first trial of a line search.
+    Outcome Minimise(const Target &target, std::vector<double> &x, int iterations, double f_tolerance, double max_step,
+                     const std::function<bool()> &stop = nullptr) {
+        const size_t n = x.size();
+        if (h_.size() != n)
+            h_.assign(n, 1.0);
+        Outcome out;
+        double f = 0;
+        std::vector<double> g(n), d(n), x_new(n), g_new(n);
+        if (!target(x, f, g))
+            return out;
+        out.evaluations++;
+        out.f_start = out.f_end = f;
+        for (int it = 0; it < iterations; it++) {
+            if (stop && stop())
+                break;
+            Direction(g, d);
+            double gd = Dot(g, d);
+            if (!(gd < 0)) {   // not a descent direction: the memory no longer fits, start again from the diagonal
+                Reset();
+                Direction(g, d);
+                gd = Dot(g, d);
+                if (!(gd < 0))
+                    break;
+            }
+            double d_max = 0;
+            for (double v : d)
+                d_max = std::max(d_max, std::fabs(v));
+            double alpha = d_max > max_step ? max_step / d_max : 1.0;
+            double f_new = 0;
+            bool accepted = false;
+            for (int ls = 0; ls < 10; ls++) {
+                Sweep(n, [&](size_t k) { x_new[k] = x[k] + alpha * d[k]; });
+                const bool ok = target(x_new, f_new, g_new);
+                out.evaluations++;
+                if (ok && f_new <= f + 1e-4 * alpha * gd) {
+                    accepted = true;
+                    break;
+                }
+                // the minimum of the quadratic through f, its slope and f_new, kept within [0.1, 0.5] of the step
+                const double q = ok ? -gd * alpha * alpha / (2.0 * (f_new - f - gd * alpha)) : 0.1 * alpha;
+                alpha = std::clamp(q, 0.1 * alpha, 0.5 * alpha);
+            }
+            if (!accepted)
+                break;
+            // the pair's vectors are the ones the memory last let go, where it did: made anew, their pages fault in
+            std::vector<double> s = std::move(spare_s_), y = std::move(spare_y_);
+            s.resize(n);
+            y.resize(n);
+            Sweep(n, [&](size_t k) {
+                s[k] = x_new[k] - x[k];
+                y[k] = g_new[k] - g[k];
+            });
+            const double sy = Dot(s, y);
+            if (sy > 1e-10 * std::sqrt(Dot(s, s) * Dot(y, y))) {
+                s_.push_back(std::move(s));
+                y_.push_back(std::move(y));
+                sy_.push_back(sy);
+                if (s_.size() > memory_) {
+                    spare_s_ = std::move(s_.front());
+                    spare_y_ = std::move(y_.front());
+                    s_.pop_front();
+                    y_.pop_front();
+                    sy_.pop_front();
+                }
+            } else {
+                spare_s_ = std::move(s);
+                spare_y_ = std::move(y);
+            }
+            const double decrease = f - f_new;
+            x.swap(x_new);
+            g.swap(g_new);
+            f = f_new;
+            out.iterations++;
+            out.f_end = f;
+            if (decrease <= f_tolerance * std::max(std::fabs(f), 1.0))
+                break;
+        }
+        return out;
+    }
+
+private:
+    static double Dot(const std::vector<double> &a, const std::vector<double> &b) {
+        double s = 0;
+        for (size_t k = 0; k < a.size(); k++)
+            s += a[k] * b[k];
+        return s;
+    }
+
+    // fn(k) for every k below n on the threads, each element on its own: the serial loop's bits.
+    template <typename Fn>
+    void Sweep(size_t n, Fn fn) const {
+        ParallelChunks(static_cast<int>(n), ThreadsForWork(n, nthreads_), [&](int lo, int hi) {
+            for (int k = lo; k < hi; k++)
+                fn(static_cast<size_t>(k));
+        });
+    }
+
+    // d = -H g by the two-loop recursion, H0 = gamma diag(1/h). Every dot product is a serial chain of n
+    // additions, so each sweep over the parameters takes the next pair's dot product while it applies the
+    // previous pair's update to q - the same operations on each element in the same order as a sweep for
+    // each would do, with the update's memory traffic hidden under the chain.
+    void Direction(const std::vector<double> &g, std::vector<double> &d) const {
+        const size_t n = g.size(), m = s_.size();
+        std::vector<double> &q = q_;   // kept from call to call: made anew, its pages fault in every time
+        q.assign(g.begin(), g.end());
+        std::vector<double> a(m), rho(m);
+        for (size_t i = 0; i < m; i++)
+            rho[i] = 1.0 / sy_[i];
+        double dot = m > 0 ? Dot(s_[m - 1], q) : 0.0, yhy = 0.0;
+        for (size_t i = m; i-- > 0;) {
+            a[i] = rho[i] * dot;
+            const double ai = a[i];
+            const double *y = y_[i].data();
+            dot = 0.0;
+            if (i > 0) {
+                const double *s = s_[i - 1].data();
+                for (size_t k = 0; k < n; k++) {
+                    q[k] -= ai * y[k];
+                    dot += s[k] * q[k];
+                }
+            } else {
+                const double *yl = y_[m - 1].data();
+                for (size_t k = 0; k < n; k++) {
+                    q[k] -= ai * y[k];
+                    yhy += yl[k] * yl[k] / h_[k];
+                }
+            }
+        }
+        const double gamma = m > 0 ? sy_[m - 1] / yhy : 1.0;
+        if (m > 0) {
+            const double *y = y_[0].data();
+            for (size_t k = 0; k < n; k++) {
+                q[k] *= gamma / h_[k];
+                dot += y[k] * q[k];
+            }
+        } else
+            for (size_t k = 0; k < n; k++)
+                q[k] *= gamma / h_[k];
+        for (size_t i = 0; i < m; i++) {
+            // b on its own and (a[i] - b) in the loop, as before: written as a[i] - rho[i] * dot the compiler
+            // contracts it into a fused multiply-add, and the bits change
+            const double b = rho[i] * dot;
+            const double *s = s_[i].data();
+            dot = 0.0;
+            if (i + 1 < m) {
+                const double *y = y_[i + 1].data();
+                for (size_t k = 0; k < n; k++) {
+                    q[k] += s[k] * (a[i] - b);
+                    dot += y[k] * q[k];
+                }
+            } else
+                for (size_t k = 0; k < n; k++)
+                    q[k] += s[k] * (a[i] - b);
+        }
+        for (size_t k = 0; k < n; k++)
+            d[k] = -q[k];
+    }
+
+    size_t memory_, nthreads_;
+    std::deque<std::vector<double>> s_, y_;
+    std::deque<double> sy_;   // s.y of each pair, as taken when it was kept
+    std::vector<double> spare_s_, spare_y_;   // the pair the memory last let go, for the next one to reuse
+    mutable std::vector<double> q_;           // Direction()'s working vector
+    std::vector<double> h_;
+};
diff --git a/image_analysis/structure_refinement/RefinementRestraints.cpp b/image_analysis/structure_refinement/RefinementRestraints.cpp
new file mode 100644
index 000000000..61239cbfe
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementRestraints.cpp
@@ -0,0 +1,751 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "RefinementRestraints.h"
+
+#include <algorithm>
+#include <cmath>
+#include <functional>
+#include <set>
+#include <unordered_map>
+
+#include "gemmi/neighbor.hpp"
+#include "gemmi/polyheur.hpp"   // setup_entities
+#include "gemmi/riding_h.hpp"   // place_hydrogens_on_all_atoms
+#include "gemmi/topo.hpp"
+
+#include "../../common/ParallelFor.h"
+#include "MonomerLibrary.h"
+#include "RefinementMath.h"
+
+using refine_math::V3;
+
+namespace {
+
+constexpr float CHIRAL_SIGMA = 0.2f;                  // A^3
+constexpr float REPULSION_SIGMA = 0.2f;               // A
+constexpr float HBOND_CONTACT = 2.6f;                 // A
+constexpr float METAL_CONTACT = 1.9f;                 // A, to N, O or S
+// B similarity (BSimilarityTerm's kappa: sigma = kappa sqrt(B_i B_j)): main chain and the rest, for bonded pairs and
+// pairs bonded to a common atom - REFMAC's logs list sigma near 0.1 B for main-chain bonded pairs from B 11 to 140
+// A^2, the ratios between the classes are those of the fixed sigmas this replaced (1.5, 2.0, 3.0, 4.5 A^2, i.e. these
+// at B = 15) - and atoms in contact, waters among them, that no bond or angle relates.
+constexpr float B_KAPPA_MAIN_BOND = 0.1f, B_KAPPA_MAIN_ANGLE = 0.133f;
+constexpr float B_KAPPA_SIDE_BOND = 0.2f, B_KAPPA_SIDE_ANGLE = 0.3f;
+constexpr float B_KAPPA_CONTACT = 0.5f;
+constexpr double B_CONTACT_DISTANCE = 4.0;           // A
+
+bool IsMainChain(const gemmi::Atom &a) {
+    static const std::set<std::string> names = {"N", "CA", "C", "O", "OXT", "P", "OP1", "OP2", "O5'", "C5'",
+                                                "C4'", "C3'", "O3'"};
+    return names.count(a.name) > 0;
+}
+
+bool IsMetal(const gemmi::Element &el) {
+    return el.is_metal();
+}
+
+// The radius van der Waals contacts are made of, without hydrogens: the dictionary's for the atom's
+// energy type, or an element's typical value where the residue is not described.
+float VdwRadius(const gemmi::MonLib &monlib, const std::string &resname, const gemmi::Atom &a) {
+    auto cc = monlib.monomers.find(resname);
+    if (cc != monlib.monomers.end()) {
+        auto it = cc->second.find_atom(a.name);
+        if (it != cc->second.atoms.end()) {
+            auto e = monlib.ener_lib.atoms.find(it->chem_type);
+            if (e != monlib.ener_lib.atoms.end() && std::isfinite(e->second.vdw_radius))
+                return static_cast<float>(e->second.vdw_radius);
+        }
+    }
+    switch (a.element.elem) {
+        case gemmi::El::C: return 1.70f;
+        case gemmi::El::N: return 1.55f;
+        case gemmi::El::O: return 1.52f;
+        case gemmi::El::S: return 1.80f;
+        case gemmi::El::P: return 1.80f;
+        default: return 1.70f;
+    }
+}
+
+bool CanHydrogenBond(const gemmi::MonLib &monlib, const std::string &resname, const gemmi::Atom &a) {
+    if (a.element != gemmi::El::N && a.element != gemmi::El::O)
+        return false;
+    auto cc = monlib.monomers.find(resname);
+    if (cc != monlib.monomers.end()) {
+        auto it = cc->second.find_atom(a.name);
+        if (it != cc->second.atoms.end()) {
+            auto e = monlib.ener_lib.atoms.find(it->chem_type);
+            if (e != monlib.ener_lib.atoms.end())
+                return e->second.hb_type == 'D' || e->second.hb_type == 'A' || e->second.hb_type == 'B' ||
+                       e->second.hb_type == 'H';
+        }
+    }
+    return true;   // N or O of an undescribed residue
+}
+
+V3<double> At(const std::vector<std::array<double, 4>> &xyzb, int i) {
+    return {xyzb[i][0], xyzb[i][1], xyzb[i][2]};
+}
+
+V3<double> Image(const RestraintRecord &r, V3<double> p) {
+    return {r.rot[0] * p.x + r.rot[1] * p.y + r.rot[2] * p.z + r.tran[0],
+            r.rot[3] * p.x + r.rot[4] * p.y + r.rot[5] * p.z + r.tran[1],
+            r.rot[6] * p.x + r.rot[7] * p.y + r.rot[8] * p.z + r.tran[2]};
+}
+
+// The gradient at an image back on the atom it is an image of: rot^T g.
+V3<double> FromImage(const RestraintRecord &r, V3<double> g) {
+    return {r.rot[0] * g.x + r.rot[3] * g.y + r.rot[6] * g.z,
+            r.rot[1] * g.x + r.rot[4] * g.y + r.rot[7] * g.z,
+            r.rot[2] * g.x + r.rot[5] * g.y + r.rot[8] * g.z};
+}
+
+// The bonds the dictionary gives a metal atom within its own residue: none for an ion, four for a heme's iron.
+int DictionaryMetalBonds(const gemmi::MonLib &monlib, const gemmi::CRA &metal) {
+    auto cc = monlib.monomers.find(metal.residue->name);
+    if (cc == monlib.monomers.end())
+        return 0;
+    int n = 0;
+    for (const gemmi::Restraints::Bond &b : cc->second.rt.bonds)
+        n += b.id1.atom == metal.atom->name || b.id2.atom == metal.atom->name;
+    return n;
+}
+
+bool IsMetalDonor(const gemmi::Element &el) {
+    return el == gemmi::El::O || el == gemmi::El::N || el == gemmi::El::S;
+}
+
+// The modification a donor's residue takes when it binds a metal: the proton the bond replaces, as the
+// library's own ZN-HISND, ZN-HISNE and ZN-CYS links have it.
+std::string MetalDonorModification(const std::string &resname, const std::string &atom) {
+    if (resname == "HIS" && atom == "ND1")
+        return "DEL-HD1";
+    if (resname == "HIS" && atom == "NE2")
+        return "DEL-HE2";
+    if (resname == "CYS" && atom == "SG")
+        return "CYSmod1";
+    return "";
+}
+
+// The model's LINK / struct_conn records between a metal atom (an ion, or the iron of a heme) and an O, N or S
+// that no link of the dictionary describes (its ZN-CYS, ZN-HISND, ZN-HISNE, FE-CYS, FE-HISND and FE-HISNE are
+// taken as they are): a link of one bond is made for each in `monlib`, at the distance of the library's statistics
+// of metal sites (EmbeddedMetalDistance) for the two elements and the site's coordination - the number of records
+// between the metal and an O, N or S, plus the bonds its own residue's dictionary gives it (a heme's four pyrrole
+// N) - and the record is pointed at it, so that prepare_topology() restrains it like any other link.
+// Only the bond: no angles at the metal. Sites are taken from the records alone, as REFMAC takes links from
+// the coordinate file; a contact without a record stays a repulsion (BuildRepulsions, METAL_CONTACT).
+// Records to a symmetry mate are left out, as every bond to a symmetry mate is (BuildRefinementTopology).
+// Returns the number of links made.
+// Distances as surveyed by Harding (2001) Acta Cryst. D57, 401-411 and (2006) Acta Cryst. D62, 678-682,
+// and for Mg, Na and K at nucleic acids by Leonarski, D'Ascenzo & Auffinger (2017) Nucleic Acids Res. 45, 987-1004
+int AddMetalLinks(gemmi::Structure &st, gemmi::MonLib &monlib) {
+    gemmi::Model &model = st.models.at(0);
+    struct Site {
+        gemmi::Connection *conn;
+        gemmi::CRA metal, donor;
+        bool metal_first;   // the metal is partner1
+    };
+    std::vector<Site> sites;
+    std::unordered_map<const gemmi::Atom *, int> coordination;
+    for (gemmi::Connection &conn : st.connections) {
+        gemmi::CRA a = model.find_cra(conn.partner1, true), b = model.find_cra(conn.partner2, true);
+        if (!a.atom || !b.atom)
+            continue;
+        const bool a_metal = IsMetal(a.atom->element), b_metal = IsMetal(b.atom->element);
+        if (a_metal == b_metal)
+            continue;
+        const gemmi::CRA &metal = a_metal ? a : b, &donor = a_metal ? b : a;
+        if (!IsMetalDonor(donor.atom->element))
+            continue;
+        // the site's coordination: every record of the metal, a symmetry mate's or one the dictionary describes too
+        if (coordination.count(metal.atom) == 0)
+            coordination[metal.atom] = DictionaryMetalBonds(monlib, metal);
+        coordination[metal.atom]++;
+        if (!conn.link_id.empty() || conn.asu == gemmi::Asu::Different ||
+            std::get<0>(monlib.match_link(*a.residue, a.atom->name, conn.partner1.altloc, *b.residue, b.atom->name,
+                                          conn.partner2.altloc)) != nullptr)
+            continue;
+        sites.push_back({&conn, metal, donor, a_metal});
+    }
+    int made = 0;
+    for (const Site &site : sites) {
+        double distance = 0, sigma = 0;
+        if (!EmbeddedMetalDistance(site.metal.atom->element.elem, site.donor.atom->element.elem,
+                                   coordination[site.metal.atom], distance, sigma))
+            continue;
+        const gemmi::Connection &conn = *site.conn;
+        gemmi::ChemLink link;
+        link.side1.comp = conn.partner1.res_id.name;
+        link.side2.comp = conn.partner2.res_id.name;
+        (site.metal_first ? link.side2 : link.side1).mod =
+            MetalDonorModification(site.donor.residue->name, site.donor.atom->name);
+        link.id = "metal-" + std::to_string(made);
+        link.name = link.id;
+        link.rt.bonds.push_back({gemmi::Restraints::AtomId{1, conn.partner1.atom_name},
+                                 gemmi::Restraints::AtomId{2, conn.partner2.atom_name},
+                                 gemmi::BondType::Metal, false, distance, sigma, distance, sigma});
+        monlib.links.emplace(link.id, link);
+        site.conn->link_id = link.id;
+        made++;
+    }
+    return made;
+}
+
+}  // namespace
+
+void RestraintSet::Add(RestraintRecord r, int n_atoms_of_r) {
+    r.slot = n_slots;
+    n_slots += n_atoms_of_r;
+    records.push_back(r);
+}
+
+void RestraintSet::Append(const RestraintSet &other) {
+    const int plane_offset = static_cast<int>(plane_atoms.size());
+    for (RestraintRecord r : other.records) {
+        r.slot += n_slots;
+        if (r.kind == static_cast<int>(RestraintKind::Plane))
+            r.atom[0] += plane_offset;
+        records.push_back(r);
+    }
+    plane_atoms.insert(plane_atoms.end(), other.plane_atoms.begin(), other.plane_atoms.end());
+    n_slots += other.n_slots;
+}
+
+void RestraintSet::Finalize(size_t n_atoms) {
+    slot_atom.assign(n_slots, -1);
+    for (const RestraintRecord &r : records) {
+        if (r.kind == static_cast<int>(RestraintKind::Plane)) {
+            for (int k = 0; k < r.atom[1]; k++)
+                slot_atom[r.slot + k] = plane_atoms[r.atom[0] + k];
+        } else {
+            const int n = r.kind == static_cast<int>(RestraintKind::Bond) ||
+                                  r.kind == static_cast<int>(RestraintKind::Repulsion) ||
+                                  r.kind == static_cast<int>(RestraintKind::BSimilarity) ? 2
+                          : r.kind == static_cast<int>(RestraintKind::Angle) ? 3 : 4;
+            for (int k = 0; k < n; k++)
+                slot_atom[r.slot + k] = r.atom[k];
+        }
+    }
+    slot_start.assign(n_atoms + 1, 0);
+    for (int a : slot_atom)
+        if (a >= 0)
+            slot_start[a + 1]++;
+    for (size_t a = 0; a < n_atoms; a++)
+        slot_start[a + 1] += slot_start[a];
+    slot_index.assign(slot_start[n_atoms], 0);
+    std::vector<int> fill(slot_start.begin(), slot_start.end() - 1);
+    for (int s = 0; s < n_slots; s++)
+        if (slot_atom[s] >= 0)
+            slot_index[fill[slot_atom[s]]++] = s;
+}
+
+double RestraintValue(const RestraintSet &set, const RestraintRecord &r, const std::vector<std::array<double, 4>> &xyzb) {
+    V3<double> g[4];
+    switch (static_cast<RestraintKind>(r.kind)) {
+        case RestraintKind::Bond:
+            return refine_math::Norm(At(xyzb, r.atom[0]) - At(xyzb, r.atom[1]));
+        case RestraintKind::Angle: {
+            const V3<double> u = At(xyzb, r.atom[0]) - At(xyzb, r.atom[1]), v = At(xyzb, r.atom[2]) - At(xyzb, r.atom[1]);
+            return std::atan2(refine_math::Norm(refine_math::Cross(u, v)), refine_math::Dot(u, v)) / refine_math::DEG;
+        }
+        case RestraintKind::Torsion:
+            return refine_math::Dihedral(At(xyzb, r.atom[0]), At(xyzb, r.atom[1]), At(xyzb, r.atom[2]),
+                                         At(xyzb, r.atom[3]), g) / refine_math::DEG;
+        case RestraintKind::Chiral: {
+            const V3<double> c = At(xyzb, r.atom[0]);
+            return refine_math::Dot(At(xyzb, r.atom[1]) - c,
+                                    refine_math::Cross(At(xyzb, r.atom[2]) - c, At(xyzb, r.atom[3]) - c));
+        }
+        case RestraintKind::Repulsion:
+            return refine_math::Norm(At(xyzb, r.atom[0]) - Image(r, At(xyzb, r.atom[1])));
+        case RestraintKind::BSimilarity:
+            return xyzb[r.atom[0]][3] - xyzb[r.atom[1]][3];
+        case RestraintKind::Plane:
+            break;
+    }
+    (void) set;
+    return NAN;
+}
+
+double EvaluateRestraints(const RestraintSet &set, const std::vector<std::array<double, 4>> &xyzb,
+                          std::vector<std::array<double, 4>> *grad) {
+    double sum = 0;
+    std::vector<V3<double>> px, pg;
+    for (const RestraintRecord &r : set.records) {
+        V3<double> g[4] = {};
+        int n = 0;
+        double e = 0;
+        const double ideal = r.ideal, sigma = r.sigma;
+        switch (static_cast<RestraintKind>(r.kind)) {
+            case RestraintKind::Bond:
+                e = refine_math::BondTerm(At(xyzb, r.atom[0]), At(xyzb, r.atom[1]), ideal, sigma, g);
+                n = 2;
+                break;
+            case RestraintKind::Angle:
+                e = refine_math::AngleTerm(At(xyzb, r.atom[0]), At(xyzb, r.atom[1]), At(xyzb, r.atom[2]), ideal, sigma, g);
+                n = 3;
+                break;
+            case RestraintKind::Torsion:
+                e = refine_math::TorsionTerm(At(xyzb, r.atom[0]), At(xyzb, r.atom[1]), At(xyzb, r.atom[2]),
+                                             At(xyzb, r.atom[3]), ideal, sigma, r.period, g);
+                n = 4;
+                break;
+            case RestraintKind::Chiral:
+                e = refine_math::ChiralTerm(At(xyzb, r.atom[0]), At(xyzb, r.atom[1]), At(xyzb, r.atom[2]),
+                                            At(xyzb, r.atom[3]), ideal, sigma, g);
+                n = 4;
+                break;
+            case RestraintKind::Repulsion:
+                e = refine_math::RepulsionTerm(At(xyzb, r.atom[0]), Image(r, At(xyzb, r.atom[1])), ideal, sigma, g);
+                g[1] = FromImage(r, g[1]);
+                n = 2;
+                break;
+            case RestraintKind::Plane: {
+                const int m = r.atom[1];
+                px.resize(m);
+                pg.resize(m);
+                for (int k = 0; k < m; k++)
+                    px[k] = At(xyzb, set.plane_atoms[r.atom[0] + k]);
+                e = refine_math::PlaneTerm(px.data(), m, sigma, pg.data());
+                if (grad != nullptr)
+                    for (int k = 0; k < m; k++) {
+                        std::array<double, 4> &d = (*grad)[set.plane_atoms[r.atom[0] + k]];
+                        d[0] += pg[k].x;
+                        d[1] += pg[k].y;
+                        d[2] += pg[k].z;
+                    }
+                break;
+            }
+            case RestraintKind::BSimilarity: {
+                double gi = 0, gj = 0;
+                e = refine_math::BSimilarityTerm(xyzb[r.atom[0]][3], xyzb[r.atom[1]][3], sigma, gi, gj);
+                if (grad != nullptr) {
+                    (*grad)[r.atom[0]][3] += gi;
+                    (*grad)[r.atom[1]][3] += gj;
+                }
+                break;
+            }
+        }
+        sum += e;
+        if (grad != nullptr)
+            for (int k = 0; k < n; k++) {
+                std::array<double, 4> &d = (*grad)[r.atom[k]];
+                d[0] += g[k].x;
+                d[1] += g[k].y;
+                d[2] += g[k].z;
+            }
+    }
+    return sum;
+}
+
+std::vector<double> BRestraintCurvature(const RestraintSet &set, const std::vector<std::array<double, 4>> &xyzb) {
+    std::vector<double> h(xyzb.size(), 0.0);
+    for (const RestraintRecord &r : set.records)
+        if (r.kind == static_cast<int>(RestraintKind::BSimilarity)) {
+            // d2E/dB_i^2 of BSimilarityTerm = 2 B_j / (kappa^2 B_i^3)
+            const double bi = xyzb[r.atom[0]][3], bj = xyzb[r.atom[1]][3], k2 = double(r.sigma) * r.sigma;
+            h[r.atom[0]] += 2.0 * bj / (k2 * bi * bi * bi);
+            h[r.atom[1]] += 2.0 * bi / (k2 * bj * bj * bj);
+        }
+    return h;
+}
+
+RefinementTopology BuildRefinementTopology(gemmi::Structure &st, bool hydrogens) {
+    RefinementTopology out;
+    gemmi::Model &model = st.models.at(0);
+    out.monlib = std::make_shared<gemmi::MonLib>(EmbeddedMonomerLibrary());
+    gemmi::MonLib &monlib = *out.monlib;
+    gemmi::setup_entities(st);
+    out.metal_links = AddMetalLinks(st, monlib);
+    gemmi::Logger quiet;   // missing atoms and unknown residues are what the fixed residues report
+    quiet.threshold = 0;
+    out.topo = gemmi::prepare_topology(st, monlib, 0,
+                                       hydrogens ? gemmi::HydrogenChange::ReAddButWater : gemmi::HydrogenChange::NoChange,
+                                       /*reorder=*/false, quiet, /*ignore_unknown_links=*/true, /*use_cispeps=*/true);
+    gemmi::Topo *topo = out.topo.get();
+
+    // the atoms as they are now, hydrogens added
+    std::unordered_map<const gemmi::Atom *, int> index;
+    std::vector<const gemmi::Residue *> residue_of;
+    for (const gemmi::Chain &ch : model.chains)
+        for (const gemmi::Residue &r : ch.residues)
+            for (const gemmi::Atom &a : r.atoms) {
+                index[&a] = static_cast<int>(residue_of.size());
+                residue_of.push_back(&r);
+            }
+    const size_t n = residue_of.size();
+    out.refinable.assign(n, 0);
+    out.vdw_radius.assign(n, 1.7f);
+    out.hbond.assign(n, 0);
+    out.metal.assign(n, 0);
+    out.altloc.assign(n, 0);
+    out.element.assign(n, gemmi::El::X);
+    out.rider_parent.assign(n, -1);
+    for (const gemmi::Topo::Bond &b : topo->bonds)
+        for (int k = 0; k < 2; k++)
+            if (b.atoms[k]->is_hydrogen() && !b.atoms[1 - k]->is_hydrogen())
+                out.rider_parent[index.at(b.atoms[k])] = index.at(b.atoms[1 - k]);
+    // A hydrogen gemmi could not place, or with no parent, scatters nothing.
+    for (gemmi::Chain &ch : model.chains)
+        for (gemmi::Residue &r : ch.residues)
+            for (gemmi::Atom &a : r.atoms)
+                if (a.is_hydrogen() && (out.rider_parent[index.at(&a)] < 0 || !std::isfinite(a.pos.x))) {
+                    a.occ = 0;
+                    out.rider_parent[index.at(&a)] = -1;
+                    if (!std::isfinite(a.pos.x))
+                        a.pos = r.atoms.front().pos;
+                }
+
+    // A residue is refined where the dictionary describes it and every one of its atoms.
+    std::set<std::string> fixed_names;
+    for (const gemmi::Topo::ChainInfo &ci : topo->chain_infos)
+        for (const gemmi::Topo::ResInfo &ri : ci.res_infos) {
+            const gemmi::Residue &res = *ri.res;
+            bool known = ri.orig_chemcomp != nullptr && InEmbeddedMonomerLibrary(res.name);
+            for (const gemmi::Atom &a : res.atoms)
+                known = known && ri.get_final_chemcomp(a.altloc).has_atom(a.name);
+            if (known)
+                out.restrained_residues++;
+            else {
+                out.fixed_residues++;
+                fixed_names.insert(res.name);
+            }
+            for (const gemmi::Atom &a : res.atoms) {
+                const auto it = index.find(&a);
+                if (it == index.end())
+                    continue;
+                const int i = it->second;
+                out.refinable[i] = known && a.occ > 0 && !a.is_hydrogen();
+                out.vdw_radius[i] = VdwRadius(monlib, res.name, a);
+                out.hbond[i] = res.is_water() || CanHydrogenBond(monlib, res.name, a);
+                out.metal[i] = IsMetal(a.element);
+                out.altloc[i] = a.altloc;
+                out.element[i] = a.element.elem;
+            }
+        }
+    out.fixed_names.assign(fixed_names.begin(), fixed_names.end());
+
+    auto idx = [&](const gemmi::Atom *a) { return index.at(a); };
+    auto has_h = [](std::initializer_list<const gemmi::Atom *> atoms) {
+        for (const gemmi::Atom *a : atoms)
+            if (a->is_hydrogen())
+                return true;
+        return false;
+    };
+    auto any_refinable = [&](std::initializer_list<int> atoms) {
+        for (int a : atoms)
+            if (out.refinable[a])
+                return true;
+        return false;
+    };
+    std::vector<std::set<int>> excluded(n);
+    std::vector<std::vector<int>> bonded(n);
+    for (size_t i = 0; i < n; i++)
+        excluded[i].insert(static_cast<int>(i));
+
+    for (const gemmi::Topo::Bond &b : topo->bonds) {
+        if (b.asu == gemmi::Asu::Different || has_h({b.atoms[0], b.atoms[1]}))
+            continue;
+        const int i = idx(b.atoms[0]), j = idx(b.atoms[1]);
+        excluded[i].insert(j);
+        excluded[j].insert(i);
+        bonded[i].push_back(j);
+        bonded[j].push_back(i);
+        if (!any_refinable({i, j}) || !(b.restr->esd > 0))
+            continue;
+        RestraintRecord r;
+        r.kind = static_cast<int>(RestraintKind::Bond);
+        r.atom[0] = i;
+        r.atom[1] = j;
+        r.ideal = static_cast<float>(b.restr->value);
+        r.sigma = static_cast<float>(b.restr->esd);
+        if (out.metal[i] || out.metal[j])
+            out.metal_bonds.Add(r, 2);   // a metal's coordination, kept apart from the covalent bonds
+        else {
+            out.geometry.Add(r, 2);
+            out.bonds++;
+        }
+        RestraintRecord rb;
+        rb.kind = static_cast<int>(RestraintKind::BSimilarity);
+        rb.atom[0] = i;
+        rb.atom[1] = j;
+        const bool main = IsMainChain(*b.atoms[0]) && IsMainChain(*b.atoms[1]);
+        rb.sigma = main ? B_KAPPA_MAIN_BOND : B_KAPPA_SIDE_BOND;
+        out.adp.Add(rb, 2);
+    }
+    for (const gemmi::Topo::Angle &an : topo->angles) {
+        if (has_h({an.atoms[0], an.atoms[1], an.atoms[2]}))
+            continue;
+        const int i = idx(an.atoms[0]), j = idx(an.atoms[1]), k = idx(an.atoms[2]);
+        excluded[i].insert(k);
+        excluded[k].insert(i);
+        if (!any_refinable({i, j, k}) || !(an.restr->esd > 0))
+            continue;
+        RestraintRecord r;
+        r.kind = static_cast<int>(RestraintKind::Angle);
+        r.atom[0] = i;
+        r.atom[1] = j;
+        r.atom[2] = k;
+        r.ideal = static_cast<float>(an.restr->value);
+        r.sigma = static_cast<float>(an.restr->esd);
+        out.geometry.Add(r, 3);
+        out.angles++;
+        RestraintRecord rb;
+        rb.kind = static_cast<int>(RestraintKind::BSimilarity);
+        rb.atom[0] = i;
+        rb.atom[1] = k;
+        const bool main = IsMainChain(*an.atoms[0]) && IsMainChain(*an.atoms[2]);
+        rb.sigma = main ? B_KAPPA_MAIN_ANGLE : B_KAPPA_SIDE_ANGLE;
+        out.adp.Add(rb, 2);
+    }
+    for (const gemmi::Topo::Torsion &t : topo->torsions) {
+        const std::string &label = t.restr->label;
+        if (has_h({t.atoms[0], t.atoms[1], t.atoms[2], t.atoms[3]}))
+            continue;
+        if (!(t.restr->esd > 0) || label.rfind("phi", 0) == 0 || label.rfind("psi", 0) == 0 ||
+            label.rfind("C2e", 0) == 0 || label.rfind("C3e", 0) == 0)
+            continue;
+        const int a = idx(t.atoms[0]), b = idx(t.atoms[1]), c = idx(t.atoms[2]), d = idx(t.atoms[3]);
+        if (!any_refinable({a, b, c, d}))
+            continue;
+        RestraintRecord r;
+        r.kind = static_cast<int>(RestraintKind::Torsion);
+        r.atom[0] = a;
+        r.atom[1] = b;
+        r.atom[2] = c;
+        r.atom[3] = d;
+        r.ideal = static_cast<float>(t.restr->value);
+        r.sigma = static_cast<float>(t.restr->esd);
+        r.period = t.restr->period;
+        out.geometry.Add(r, 4);
+        out.torsions++;
+    }
+    for (const gemmi::Topo::Chirality &ch : topo->chirs) {
+        if (ch.restr->sign == gemmi::ChiralityType::Both || has_h({ch.atoms[0], ch.atoms[1], ch.atoms[2], ch.atoms[3]}))
+            continue;
+        const int c = idx(ch.atoms[0]), a1 = idx(ch.atoms[1]), a2 = idx(ch.atoms[2]), a3 = idx(ch.atoms[3]);
+        if (!any_refinable({c, a1, a2, a3}))
+            continue;
+        const double volume = topo->ideal_chiral_abs_volume(ch);
+        RestraintRecord r;
+        r.kind = static_cast<int>(RestraintKind::Chiral);
+        r.atom[0] = c;
+        r.atom[1] = a1;
+        r.atom[2] = a2;
+        r.atom[3] = a3;
+        r.ideal = static_cast<float>(ch.restr->sign == gemmi::ChiralityType::Negative ? -volume : volume);
+        r.sigma = CHIRAL_SIGMA;
+        out.geometry.Add(r, 4);
+        out.chirals++;
+    }
+    for (const gemmi::Topo::Plane &p_all : topo->planes) {
+        gemmi::Topo::Plane p = p_all;
+        std::erase_if(p.atoms, [](const gemmi::Atom *a) { return a->is_hydrogen(); });
+        if (p.atoms.size() < 4 || !(p.restr->esd > 0))
+            continue;
+        bool any = false;
+        for (const gemmi::Atom *a : p.atoms)
+            any = any || out.refinable[idx(a)];
+        if (!any)
+            continue;
+        RestraintRecord r;
+        r.kind = static_cast<int>(RestraintKind::Plane);
+        r.atom[0] = static_cast<int>(out.geometry.plane_atoms.size());
+        r.atom[1] = static_cast<int>(p.atoms.size());
+        r.sigma = static_cast<float>(p.restr->esd);
+        for (const gemmi::Atom *a : p.atoms)
+            out.geometry.plane_atoms.push_back(idx(a));
+        out.geometry.Add(r, r.atom[1]);
+        out.planes++;
+    }
+    // and those three bonds away, whose distance the torsions and planes govern
+    std::vector<std::set<int>> within3 = excluded;
+    for (size_t i = 0; i < n; i++)
+        for (int j : excluded[i])
+            for (int k : bonded[j])
+                within3[i].insert(k);
+    out.excluded.resize(n);
+    for (size_t i = 0; i < n; i++)
+        out.excluded[i].assign(within3[i].begin(), within3[i].end());
+    out.geometry.Finalize(n);
+    out.metal_bonds.Finalize(n);
+    out.adp.Finalize(n);
+    return out;
+}
+
+namespace {
+
+// The pairs of atoms of `model`, symmetry mates and lattice translates included, closer than `reach` and not excluded, where at least one of
+// the two is refinable, neither is a hydrogen and the two are not alternative conformations of each other: `make`
+// turns each into a record (the image of j as x -> rot x + tran, Cartesian, and the distance), or says to leave it out.
+// The search runs on `nthreads` threads; the list is in atom order whatever their number.
+RestraintSet Contacts(const RefinementTopology &topo, gemmi::Model &model, const gemmi::UnitCell &cell_in,
+                      const gemmi::SpaceGroup &sg, double reach, size_t nthreads,
+                      const std::function<bool(int i, int j, double d, RestraintRecord &r)> &make) {
+    gemmi::UnitCell cell = cell_in;
+    cell.set_cell_images_from_spacegroup(&sg);
+    gemmi::NeighborSearch ns(model, cell, std::max(reach, 5.0));
+    ns.populate(false);
+
+    std::vector<std::vector<int>> first(model.chains.size());
+    std::vector<gemmi::Position> pos;
+    for (size_t c = 0; c < model.chains.size(); c++)
+        for (const gemmi::Residue &r : model.chains[c].residues) {
+            first[c].push_back(static_cast<int>(pos.size()));
+            for (const gemmi::Atom &a : r.atoms)
+                pos.push_back(a.pos);
+        }
+
+    // The atoms in blocks searched on the threads, each block's pairs listed in atom order; the blocks are
+    // joined in order below, so the list is the same for any number of threads.
+    constexpr int BLOCKS = 64;
+    std::vector<std::vector<RestraintRecord>> found(BLOCKS);
+    ParallelFor(BLOCKS, nthreads, [&](int block) {
+        const size_t lo = pos.size() * block / BLOCKS, hi = pos.size() * (block + 1) / BLOCKS;
+        for (size_t i = lo; i < hi; i++) {
+            if (topo.rider_parent[i] >= 0 || topo.element[i] == gemmi::El::H)
+                continue;
+            const gemmi::Fractional fi = cell.fractionalize(pos[i]);
+            ns.for_each(pos[i], '\0', reach, [&](gemmi::NeighborSearch::Mark &m, double) {
+                const int j = first[m.chain_idx][m.residue_idx] + m.atom_idx;
+                if (topo.rider_parent[j] >= 0 || topo.element[j] == gemmi::El::H)
+                    return;
+                if (!topo.refinable[i] && !topo.refinable[j])
+                    return;
+                if (topo.altloc[i] && topo.altloc[j] && topo.altloc[i] != topo.altloc[j])
+                    return;
+                // The image of j nearest to i, as a Cartesian x -> R x + t.
+                const gemmi::FTransform ft = ns.get_image_transformation(m.image_idx);
+                const gemmi::Fractional fj = ft.apply(cell.fractionalize(pos[j]));
+                const gemmi::Vec3 shift(std::round(fi.x - fj.x), std::round(fi.y - fj.y), std::round(fi.z - fj.z));
+                const bool same_copy = m.image_idx == 0 && shift.x == 0 && shift.y == 0 && shift.z == 0;
+                // Within the copy itself: each pair once, the excluded ones left out. With any other copy
+                // (a symmetry mate or a lattice translate): the pair is met again from j, so it is kept from
+                // the lower atom only.
+                if (same_copy && (static_cast<int>(i) >= j ||
+                                  std::binary_search(topo.excluded[i].begin(), topo.excluded[i].end(), j)))
+                    return;
+                if (!same_copy && static_cast<int>(i) > j)
+                    return;
+                // An atom against its own image x -> T x is met again through T^-1, at the same distance:
+                // the one of the two images that comes first in fractional coordinates is kept.
+                if (static_cast<int>(i) == j) {
+                    gemmi::Transform t = ft;
+                    t.vec += shift;
+                    const gemmi::Vec3 there = t.apply(fi), back = t.inverse().apply(fi);
+                    for (int a = 0; a < 3; a++) {
+                        if (back.at(a) < there.at(a) - 1e-6)
+                            return;
+                        if (back.at(a) > there.at(a) + 1e-6)
+                            break;
+                    }
+                }
+                const gemmi::Mat33 rot = cell.orth.mat.multiply(ft.mat).multiply(cell.frac.mat);
+                const gemmi::Vec3 tran = cell.orth.mat.multiply(ft.vec + shift);
+                const gemmi::Position image(rot.multiply(pos[j]) + tran);
+                RestraintRecord r;
+                r.atom[0] = static_cast<int>(i);
+                r.atom[1] = j;
+                for (int a = 0; a < 3; a++) {
+                    for (int b = 0; b < 3; b++)
+                        r.rot[3 * a + b] = static_cast<float>(rot[a][b]);
+                    r.tran[a] = static_cast<float>(tran.at(a));
+                }
+                if (make(static_cast<int>(i), j, pos[i].dist(image), r))
+                    found[block].push_back(r);
+            });
+        }
+    });
+    RestraintSet out;
+    for (const std::vector<RestraintRecord> &records : found)
+        for (const RestraintRecord &r : records)
+            out.Add(r, 2);
+    out.Finalize(pos.size());
+    return out;
+}
+
+}  // namespace
+
+RestraintSet BuildRepulsions(const RefinementTopology &topo, gemmi::Model &model, const gemmi::UnitCell &cell,
+                             const gemmi::SpaceGroup &sg, double margin, size_t nthreads) {
+    float max_radius = 0;
+    for (float r : topo.vdw_radius)
+        max_radius = std::max(max_radius, r);
+    return Contacts(topo, model, cell, sg, 2 * max_radius + margin, nthreads,
+                    [&](int i, int j, double d, RestraintRecord &r) {
+                        float d0 = topo.vdw_radius[i] + topo.vdw_radius[j];
+                        if (topo.metal[i] || topo.metal[j]) {
+                            const gemmi::El other = topo.element[topo.metal[i] ? j : i];
+                            if (other == gemmi::El::N || other == gemmi::El::O || other == gemmi::El::S)
+                                d0 = METAL_CONTACT;
+                        } else if (topo.hbond[i] && topo.hbond[j])
+                            d0 = HBOND_CONTACT;
+                        if (!(d < d0 + margin))
+                            return false;
+                        r.kind = static_cast<int>(RestraintKind::Repulsion);
+                        r.ideal = d0;
+                        r.sigma = REPULSION_SIGMA;
+                        return true;
+                    });
+}
+
+RestraintSet BuildBContacts(const RefinementTopology &topo, gemmi::Model &model, const gemmi::UnitCell &cell,
+                            const gemmi::SpaceGroup &sg, size_t nthreads) {
+    return Contacts(topo, model, cell, sg, B_CONTACT_DISTANCE, nthreads, [&](int i, int j, double d, RestraintRecord &r) {
+        if (i == j || !(d < B_CONTACT_DISTANCE))
+            return false;
+        r.kind = static_cast<int>(RestraintKind::BSimilarity);
+        r.sigma = B_KAPPA_CONTACT;
+        return true;
+    });
+}
+
+void PlaceRidingHydrogens(RefinementTopology &topo) {
+    gemmi::place_hydrogens_on_all_atoms(*topo.topo);
+}
+
+GeometryStatistics MeasureGeometry(const RestraintSet &geometry, const RestraintSet &repulsions,
+                                   const std::vector<std::array<double, 4>> &xyzb, const RestraintSet *metal_bonds) {
+    GeometryStatistics s;
+    if (metal_bonds != nullptr) {
+        double sm = 0, zm = 0;
+        for (const RestraintRecord &r : metal_bonds->records) {
+            const double d = RestraintValue(*metal_bonds, r, xyzb) - r.ideal;
+            sm += d * d;
+            zm += d * d / (double(r.sigma) * r.sigma);
+            s.metal_bonds++;
+        }
+        s.rmsd_metal = s.metal_bonds > 0 ? std::sqrt(sm / s.metal_bonds) : 0;
+        s.rmsz_metal = s.metal_bonds > 0 ? std::sqrt(zm / s.metal_bonds) : 0;
+    }
+    double sb = 0, sa = 0, sc = 0, zb = 0, za = 0;
+    int nc = 0;
+    for (const RestraintRecord &r : geometry.records) {
+        const RestraintKind kind = static_cast<RestraintKind>(r.kind);
+        if (kind == RestraintKind::Bond) {
+            const double d = RestraintValue(geometry, r, xyzb) - r.ideal;
+            sb += d * d;
+            zb += d * d / (double(r.sigma) * r.sigma);
+            s.bonds++;
+        } else if (kind == RestraintKind::Angle) {
+            const double d = RestraintValue(geometry, r, xyzb) - r.ideal;
+            sa += d * d;
+            za += d * d / (double(r.sigma) * r.sigma);
+            s.angles++;
+        } else if (kind == RestraintKind::Chiral) {
+            const double d = RestraintValue(geometry, r, xyzb) - r.ideal;
+            sc += d * d;
+            nc++;
+        }
+    }
+    for (const RestraintRecord &r : repulsions.records)
+        if (RestraintValue(repulsions, r, xyzb) < r.ideal - 0.4)
+            s.clashes++;
+    s.rmsd_bonds = s.bonds > 0 ? std::sqrt(sb / s.bonds) : 0;
+    s.rmsd_angles = s.angles > 0 ? std::sqrt(sa / s.angles) : 0;
+    s.rmsd_chirals = nc > 0 ? std::sqrt(sc / nc) : 0;
+    s.rmsz_bonds = s.bonds > 0 ? std::sqrt(zb / s.bonds) : 0;
+    s.rmsz_angles = s.angles > 0 ? std::sqrt(za / s.angles) : 0;
+    return s;
+}
diff --git a/image_analysis/structure_refinement/RefinementRestraints.h b/image_analysis/structure_refinement/RefinementRestraints.h
new file mode 100644
index 000000000..335a511bc
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementRestraints.h
@@ -0,0 +1,124 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <array>
+#include <cmath>
+#include <string>
+#include <vector>
+
+#include <memory>
+
+#include "gemmi/model.hpp"
+#include "gemmi/monlib.hpp"
+#include "gemmi/topo.hpp"
+#include "gemmi/unitcell.hpp"
+
+#include "RefinementMath.h"   // RestraintRecord
+
+// The geometry side of restrained refinement (Refinement.h): what the dictionary says each refinable atom's
+// surroundings should look like, as flat lists of restraints the CPU and the GPU evaluate alike
+// (RefinementMath.h). Atoms are numbered in model order, as ModelPositions() lists them.
+
+// A list of restraints and how their gradients reach the atoms: each restraint writes one gradient slot per
+// atom it involves, and atom a sums the slots slot_index[slot_start[a] ... slot_start[a + 1]) in that order -
+// a gather, so that a GPU, summing in the same order, needs no atomics and gives the same bits every run.
+struct RestraintSet {
+    std::vector<RestraintRecord> records;
+    std::vector<int> plane_atoms;
+    int n_slots = 0;
+    std::vector<int> slot_start;   // n_atoms + 1
+    std::vector<int> slot_index;
+
+    void Add(RestraintRecord r, int n_atoms_of_r);
+    void Append(const RestraintSet &other);   // other's records after these; Finalize() again afterwards
+    void Finalize(size_t n_atoms);
+    // Which atom each slot belongs to (Finalize() works it out); -1 for none.
+    std::vector<int> slot_atom;
+};
+
+// The value of one restraint's own quantity (a distance, an angle, a volume ...) at `xyzb`, for statistics.
+double RestraintValue(const RestraintSet &set, const RestraintRecord &r, const std::vector<std::array<double, 4>> &xyzb);
+
+// The sum of E over the set at `xyzb` (x, y, z, B per atom) and, with `grad`, dE/d(x, y, z, B) per atom (added
+// to it). On the CPU, in double.
+double EvaluateRestraints(const RestraintSet &set, const std::vector<std::array<double, 4>> &xyzb,
+                          std::vector<std::array<double, 4>> *grad);
+
+// The diagonal of the Hessian of the set's B similarity restraints with respect to each atom's B, at `xyzb`.
+std::vector<double> BRestraintCurvature(const RestraintSet &set, const std::vector<std::array<double, 4>> &xyzb);
+
+// What refinement knows of a model's chemistry.
+struct RefinementTopology {
+    RestraintSet geometry;   // bonds, angles, torsions, chiral volumes, planes
+    RestraintSet metal_bonds;   // the bonds of metals (ions, a heme's iron) to their donors, apart from the rest
+    RestraintSet adp;        // B of bonded and angle-related atoms alike
+    std::vector<char> refinable;           // per atom: its residue is described by the dictionary
+    // Per atom: the atoms the repulsion leaves out - itself and those up to three bonds away (sorted).
+    std::vector<std::vector<int>> excluded;
+    std::vector<float> vdw_radius;         // A
+    std::vector<char> hbond;               // donor, acceptor or both (water included)
+    std::vector<char> metal;               // a metal atom: an ion, or a metal within a ligand (a heme's iron)
+    std::vector<char> altloc;
+    std::vector<gemmi::El> element;
+    // Per atom: the heavy atom a hydrogen rides on, -1 for every other atom.
+    std::vector<int> rider_parent;
+    // The topology itself and the dictionary it points into, for placing the hydrogens again.
+    std::shared_ptr<gemmi::MonLib> monlib;
+    std::shared_ptr<gemmi::Topo> topo;
+    int restrained_residues = 0;
+    int fixed_residues = 0;
+    std::vector<std::string> fixed_names;  // the residue names held fixed, each once
+    int bonds = 0, angles = 0, torsions = 0, chirals = 0, planes = 0;
+    int metal_links = 0;                   // metal-donor bonds made from the model's LINK records (AddMetalLinks)
+};
+
+// The topology of the first model of `st` (hydrogens already removed) from the embedded monomer library
+// (MonomerLibrary.h), through gemmi's prepare_topology(): links between residues (peptide, cis-peptide,
+// nucleic-acid backbone, disulfides, the model's LINK records the library describes) and their
+// modifications included; the LINK records of metals (ions, a heme's iron) the library has no link for are
+// restrained at the library's metal-site distances (RefinementRestraints.cpp, AddMetalLinks). A residue the library
+// does not describe, or with an atom it does not know, is held fixed: it stays in the structure factors and the
+// bulk-solvent mask, and it is restrained against.
+// Torsions: those with an esd, except the main-chain phi/psi and the sugar puckers given as alternatives.
+// With `hydrogens`, the dictionary's hydrogens are added to the residues it describes (waters excepted) and
+// placed; they ride on their parent atoms and take part in no restraint.
+RefinementTopology BuildRefinementTopology(gemmi::Structure &st, bool hydrogens = false);
+
+// The riding hydrogens placed again on their parents as they are now (gemmi's place_hydrogens_on_all_atoms).
+void PlaceRidingHydrogens(RefinementTopology &topo);
+
+// The repulsions of the model as it is now: every pair of atoms, symmetry mates included, closer than its
+// contact distance plus `margin` and not excluded, where at least one of the two is refinable and the two are
+// not alternative conformations of each other. Contact distances: van der Waals radii summed, 2.6 A where
+// both can hydrogen-bond, 1.9 A between a metal and N, O or S. `model` is not changed (gemmi's NeighborSearch
+// takes it non-const); the search runs on `nthreads` threads.
+RestraintSet BuildRepulsions(const RefinementTopology &topo, gemmi::Model &model, const gemmi::UnitCell &cell,
+                             const gemmi::SpaceGroup &sg, double margin, size_t nthreads = 1);
+
+// The B similarity of the atoms in contact (closer than 4 A, symmetry mates included) that no bond or angle relates,
+// waters among them, under the same conditions as BuildRepulsions().
+RestraintSet BuildBContacts(const RefinementTopology &topo, gemmi::Model &model, const gemmi::UnitCell &cell,
+                            const gemmi::SpaceGroup &sg, size_t nthreads = 1);
+
+// The usual summary of a model's geometry.
+struct GeometryStatistics {
+    double rmsd_bonds = 0, rmsd_angles = 0, rmsd_chirals = 0;
+    double rmsz_bonds = 0, rmsz_angles = 0;   // rms of (deviation / the dictionary's sigma)
+    int bonds = 0, angles = 0;
+    int clashes = 0;     // repulsions overlapping by more than 0.4 A
+    // The metal-donor bonds, apart: their sigma is the spread of real sites (0.04-0.1 A), so they sit further
+    // from ideal than covalent bonds do and are not what the bond rmsd's bound is about.
+    double rmsd_metal = 0, rmsz_metal = 0;
+    int metal_bonds = 0;
+    // Bonds and metal bonds together, as one rmsd (what REFMAC lists as its bond distances).
+    double RmsdAllBonds() const {
+        const int n = bonds + metal_bonds;
+        return n > 0 ? std::sqrt((rmsd_bonds * rmsd_bonds * bonds + rmsd_metal * rmsd_metal * metal_bonds) / n) : 0;
+    }
+};
+// `metal_bonds`: where given, its bonds are measured too (rmsd_metal), apart from `geometry`'s.
+GeometryStatistics MeasureGeometry(const RestraintSet &geometry, const RestraintSet &repulsions,
+                                   const std::vector<std::array<double, 4>> &xyzb,
+                                   const RestraintSet *metal_bonds = nullptr);
diff --git a/image_analysis/structure_refinement/RefinementXray.cpp b/image_analysis/structure_refinement/RefinementXray.cpp
new file mode 100644
index 000000000..faba0a11d
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementXray.cpp
@@ -0,0 +1,531 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "RefinementXray.h"
+
+#include <algorithm>
+#include <cmath>
+#include <map>
+#include <mutex>
+
+#include <fftw3.h>
+
+#include "gemmi/dencalc.hpp"
+#include "gemmi/it92.hpp"
+#include "gemmi/math.hpp"
+
+#include "../../common/Logger.h"
+#include "../../common/ParallelFor.h"
+#include "ModelFFT.h"
+#include "ModelGrid.h"
+#include "RefinementMath.h"
+
+namespace {
+
+using Table = gemmi::IT92<float>;
+
+// The free reflections a likelihood bin is fitted on, at least.
+constexpr size_t FREE_PER_BIN = 100;
+constexpr size_t MAX_BINS = 30;
+
+// The density calculator the refinement grids atoms with: DensityCalculator's settings for the grid of
+// RigidBodyZoneGrid(), and the given blur.
+gemmi::DensityCalculator<Table, float> Calculator(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg,
+                                                  double d_min, double blur) {
+    gemmi::DensityCalculator<Table, float> dc;
+    dc.d_min = d_min;
+    dc.rate = 1.5;   // RigidBodyRefine.cpp's GRID_RATE, which RigidBodyZoneGrid sizes the grid with
+    dc.grid.unit_cell = cell;
+    dc.grid.spacegroup = &sg;
+    dc.blur = blur;
+    dc.cutoff = REFINEMENT_DENSITY_CUTOFF;
+    return dc;
+}
+
+// The likelihood's variance of reflection i: epsilon beta, plus the measurement error of each of the structure
+// factor's components that the observed amplitude measures - sigma^2 twice for an acentric reflection, once for a
+// centric one (with_sigma = false leaves it out).
+double Variance(const RefinementReflections &refl, size_t i, double beta, bool with_sigma) {
+    const double s2 = with_sigma ? double(refl.sigma[i]) * refl.sigma[i] : 0.0;
+    return refl.epsilon[i] * beta + (refl.centric[i] ? s2 : 2.0 * s2);
+}
+
+// The first and second derivatives of one row's -ln L (refine_math::AmplitudeNegLogLikelihood) in D and in the
+// variance, at D and var.
+struct RowDerivatives {
+    double d, dd, v, vv;
+};
+
+RowDerivatives LikelihoodDerivatives(double fo, double fc, double d, double var, bool centric) {
+    const double q = fo * fo + d * d * fc * fc;
+    if (!centric) {
+        // x = 2 D Fo Fc / var, m = I1(x) / I0(x) = d ln I0 / dx, m' = 1 - m / x - m^2
+        const double a = 2.0 * fo * fc / var, x = a * d;
+        double log_i0, m;
+        refine_math::BesselI0I1(x, log_i0, m);
+        const double m1 = x > 0 ? 1.0 - m / x - m * m : 0.5;
+        return {2.0 * d * fc * fc / var - a * m,
+                2.0 * fc * fc / var - a * a * m1,
+                1.0 / var - q / (var * var) + m * x / var,
+                (-1.0 + 2.0 * q / var - x * (m1 * x + 2.0 * m)) / (var * var)};
+    }
+    // x = D Fo Fc / var, t = tanh x = d ln cosh / dx
+    const double a = fo * fc / var, x = a * d;
+    const double t = std::tanh(x), t1 = 1.0 - t * t;
+    return {d * fc * fc / var - a * t,
+            fc * fc / var - a * a * t1,
+            0.5 / var - q / (2.0 * var * var) + t * x / var,
+            (-0.5 + q / var - x * (t1 * x + 2.0 * t)) / (var * var)};
+}
+
+// The minimum of a function over [lo, hi] from x, given its first and second derivative (derivatives(x, g, h)):
+// Newton's method on the first derivative, kept inside the interval where that changes sign and bisecting it
+// wherever a step would leave it or the curvature is not positive. A minimum on a bound is the bound.
+template <typename F>
+double NewtonMinimum(F derivatives, double x, double lo, double hi) {
+    x = std::clamp(x, lo, hi);
+    for (int iteration = 0; iteration < 200; iteration++) {
+        double g = 0, h = 0;
+        derivatives(x, g, h);
+        if (g < 0)
+            lo = x;
+        else
+            hi = x;
+        double next = h > 0 ? x - g / h : lo - 1.0;
+        if (!(next > lo && next < hi))
+            next = 0.5 * (lo + hi);
+        const bool converged = std::fabs(next - x) < 1e-10 || hi - lo < 1e-10;
+        x = next;
+        if (converged)
+            break;
+    }
+    return x;
+}
+
+class RefinementEngineCPU : public RefinementEngine {
+public:
+    RefinementEngineCPU(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min,
+                            const RefinementReflections &refl, size_t nthreads)
+        : cell_(cell), sg_(sg), d_min_(d_min), refl_(refl), nthreads_(nthreads),
+          grid_(RigidBodyZoneGrid(cell, sg, d_min)), composition_(grid_, d_min, refl.hkl),
+          orbit_leaders_(OrbitLeaders(grid_, nthreads)) {}
+
+    void SetBlur(double blur) override { blur_ = blur; }
+    void SetRowModel(const XrayRowModel &rows) override { rows_ = rows; }
+    bool OnGPU() const override { return false; }
+
+    void Fcalc(const gemmi::Model &model, std::vector<std::complex<float>> &f) override {
+        std::vector<std::complex<double>> fd;
+        Compose(model, fd);
+        f.assign(fd.begin(), fd.end());
+    }
+
+    void Fmask(const gemmi::Model &model, std::vector<std::complex<float>> &f) override {
+        gemmi::Grid<float> mask = grid_;
+        PutMaskOnGrid(mask, model, orbit_leaders_, nthreads_);
+        const gemmi::FPhiGrid<float> fm = MapToFPhi(mask);
+        f.clear();
+        for (const gemmi::Miller &h : refl_.hkl)
+            f.push_back(fm.get_value_by_hkl(h));
+    }
+
+    double Evaluate(const gemmi::Model &model, std::vector<std::array<double, 4>> *grad) override {
+        std::vector<std::complex<double>> f;
+        Compose(model, f);
+        const size_t n = f.size();
+        // The target and, per reflection, dT/dF of the atoms' structure factor (dT/dRe F + i dT/dIm F).
+        std::vector<std::complex<double>> dt_df(n, 0.0);
+        double sum = 0;
+        for (size_t m = 0; m < n; m++) {
+            if (refl_.free[m])
+                continue;
+            const double k = rows_.k_total[m];
+            const std::complex<double> fm = k * (f[m] + std::complex<double>(rows_.fmask[m]));
+            const double fc = std::abs(fm);
+            double dfc = 0;
+            sum += refine_math::AmplitudeNegLogLikelihood<double>(refl_.fo[m], fc, rows_.d[m], rows_.var[m],
+                                                                 refl_.centric[m], dfc);
+            if (fc > 0)
+                dt_df[m] = k * dfc * fm / fc;
+        }
+        if (grad == nullptr)
+            return sum;
+
+        // The FFT method's map, dT/drho(x) = (V/N) Re sum_m sum_ops conj(dT/dF_m) scale_m exp(2 pi i h.t)
+        // exp(2 pi i (hR).x), as the inverse real transform of a half-l coefficient grid: a term A at index k
+        // goes in as A/2 at k, or as conj(A)/2 at -k where k is in the half not stored; on the planes l = 0 and
+        // l = nw/2, which hold both, as both.
+        const int nu = grid_.nu, nv = grid_.nv, nw = grid_.nw, nwh = nw / 2 + 1;
+        const size_t ncomplex = static_cast<size_t>(nu) * nv * nwh;
+        std::complex<float> *in = reinterpret_cast<std::complex<float> *>(fftwf_alloc_complex(ncomplex));
+        float *out = fftwf_alloc_real(static_cast<size_t>(nu) * nv * nw);
+        std::fill(in, in + ncomplex, std::complex<float>(0, 0));
+        const std::vector<SymmetryComposition::Term> &terms = composition_.Terms();
+        const size_t ops = composition_.Ops();
+        auto add = [&](int ku, int kv, int kw, std::complex<double> value) {
+            in[gemmi::modulo(ku, nu) + static_cast<size_t>(nu) * (gemmi::modulo(kv, nv) + static_cast<size_t>(nv) * kw)] +=
+                std::complex<float>(value);
+        };
+        for (size_t m = 0; m < n; m++) {
+            if (dt_df[m] == 0.0)
+                continue;
+            const double scale = composition_.Centring() * std::exp(blur_ * 0.25 * composition_.InvD2()[m]);
+            const std::complex<double> c = std::conj(dt_df[m]) * scale;
+            for (size_t o = 0; o < ops; o++) {
+                const SymmetryComposition::Term &t = terms[m * ops + o];
+                const std::complex<double> a = 0.5 * c * t.phase;
+                const gemmi::Miller &k = t.k;
+                if (k[2] > 0 && 2 * k[2] != nw)
+                    add(k[0], k[1], k[2], a);
+                else if (k[2] < 0 && -2 * k[2] != nw)
+                    add(-k[0], -k[1], -k[2], std::conj(a));
+                else {
+                    const int l = k[2] < 0 ? -k[2] : k[2];
+                    add(k[0], k[1], l, a);
+                    add(-k[0], -k[1], l, std::conj(a));
+                }
+            }
+        }
+        MapFromFPhiExecute(nu, nv, nw, in, out);
+        gemmi::Grid<float> map = grid_;
+        const float norm = static_cast<float>(cell_.volume / static_cast<double>(map.point_count()));
+        for (size_t i = 0; i < map.data.size(); i++)
+            map.data[i] = out[i] * norm;
+        fftwf_free(in);
+        fftwf_free(out);
+        AtomGradientsFromMap(map, model, blur_, nthreads_, *grad);
+        return sum;
+    }
+
+private:
+    void Compose(const gemmi::Model &model, std::vector<std::complex<double>> &f) const {
+        gemmi::DensityCalculator<Table, float> dc = Calculator(cell_, sg_, d_min_, blur_);
+        PutModelDensityOnGrid(dc, model, {}, nthreads_);   // one copy: the symmetry is composed below
+        composition_.Compose(MapToFPhi(dc.grid), blur_, f, nullptr, nthreads_);
+    }
+
+    gemmi::UnitCell cell_;
+    const gemmi::SpaceGroup &sg_;
+    double d_min_;
+    const RefinementReflections &refl_;
+    size_t nthreads_;
+    gemmi::Grid<float> grid_;
+    SymmetryComposition composition_;
+    std::vector<size_t> orbit_leaders_;
+    double blur_ = 0;
+    XrayRowModel rows_;
+};
+
+}  // namespace
+
+RefinementReflections PrepareRefinementReflections(const std::vector<MergedReflection> &merged,
+                                                   const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg,
+                                                   double d_min) {
+    const gemmi::GroupOps gops = sg.operations();
+    const gemmi::ReciprocalAsu asu(&sg);
+    // ASU, last one wins where a reflection is listed twice (both hands of an anomalous merge)
+    std::map<gemmi::Miller, const MergedReflection *> by_hkl;
+    for (const MergedReflection &r : merged) {
+        if (!std::isfinite(r.F) || r.F < 0)
+            continue;
+        gemmi::Miller h{{r.h, r.k, r.l}};
+        if (!asu.is_in(h))
+            h = asu.to_asu(h, gops).first;
+        by_hkl[h] = &r;
+    }
+    std::vector<gemmi::Miller> hkl;
+    for (const auto &[h, r] : by_hkl)
+        hkl.push_back(h);
+    const SymmetryComposition composition(RigidBodyZoneGrid(cell, sg, d_min), d_min, hkl);
+    RefinementReflections out;
+    for (size_t i = 0; i < hkl.size(); i++) {
+        if (composition.Row()[i] < 0)
+            continue;
+        const MergedReflection &r = *by_hkl[hkl[i]];
+        out.hkl.push_back(hkl[i]);
+        out.fo.push_back(r.F);
+        out.sigma.push_back(std::isfinite(r.sigmaF) ? r.sigmaF : 0.0f);
+        out.free.push_back(r.rfree_flag);
+        out.centric.push_back(gops.is_reflection_centric(hkl[i]));
+        out.epsilon.push_back(static_cast<float>(gops.epsilon_factor(hkl[i])));
+        out.inv_d2.push_back(cell.calculate_1_d2(hkl[i]));
+    }
+    return out;
+}
+
+BulkSolventMask::BulkSolventMask(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min,
+                                 size_t nthreads)
+    : grid_(MaskGrid(cell, sg, d_min)), nthreads_(nthreads),
+      spacing_(std::max(std::min(d_min / 3.0, MASK_SPACING_MAX), std::cbrt(cell.volume / MASK_POINTS_MAX))) {}
+
+gemmi::Grid<float> BulkSolventMask::MaskGrid(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min) {
+    gemmi::Grid<float> grid;
+    grid.unit_cell = cell;
+    grid.spacegroup = &sg;
+    const double spacing = std::max(std::min(d_min / 3.0, MASK_SPACING_MAX), std::cbrt(cell.volume / MASK_POINTS_MAX));
+    // set_size_from_spacing()'s size, without allocating the values
+    const std::array<int, 3> n = gemmi::good_grid_size({{cell.a / spacing, cell.b / spacing, cell.c / spacing}},
+                                                       gemmi::GridSizeRounding::Up, &sg);
+    grid.nu = n[0];
+    grid.nv = n[1];
+    grid.nw = n[2];
+    grid.calculate_spacing();
+    grid.axis_order = gemmi::AxisOrder::XYZ;
+    return grid;
+}
+
+void BulkSolventMask::Fmask(const gemmi::Model &model, const std::vector<gemmi::Miller> &hkl,
+                            std::vector<std::complex<float>> &f) const {
+    if (orbit_leaders_.empty())   // at the first mask: a GPU engine's refinement never draws one here
+        orbit_leaders_ = OrbitLeaders(grid_, nthreads_);
+    gemmi::Grid<float> mask = grid_;
+    mask.data.resize(mask.point_count());
+    PutMaskOnGrid(mask, model, orbit_leaders_, nthreads_);
+    const gemmi::FPhiGrid<float> fm = MapToFPhi(mask);
+    f.clear();
+    for (const gemmi::Miller &h : hkl)
+        f.push_back(fm.get_value_by_hkl(h));
+}
+
+void EstimateLikelihoodParameters(const RefinementReflections &refl, const std::vector<std::complex<float>> &fmodel,
+                                  XrayRowModel &rows, size_t nthreads) {
+    const size_t n = refl.Size();
+    std::vector<double> fc(n);
+    for (size_t i = 0; i < n; i++)
+        fc[i] = std::abs(fmodel[i]);
+    std::vector<size_t> free, work;
+    for (size_t i = 0; i < n; i++)
+        if (fc[i] > 0)
+            (refl.free[i] ? free : work).push_back(i);
+    // Too few free reflections to bin: the working set, which says the model is better than it is, but
+    // still gives the likelihood a scale.
+    if (free.size() < FREE_PER_BIN)
+        free.insert(free.end(), work.begin(), work.end());
+    std::sort(free.begin(), free.end(), [&](size_t a, size_t b) { return refl.inv_d2[a] < refl.inv_d2[b]; });
+    const size_t bins = std::clamp<size_t>(free.size() / FREE_PER_BIN, 1, MAX_BINS);
+    // the working reflections of each bin: those from its first free reflection's 1/d^2 to the next bin's
+    std::vector<double> lower(bins);
+    for (size_t b = 0; b < bins; b++)
+        lower[b] = refl.inv_d2[free[b * free.size() / bins]];
+    std::vector<std::vector<size_t>> work_in_bin(bins);
+    for (size_t i : work) {
+        const size_t b = std::upper_bound(lower.begin(), lower.end(), refl.inv_d2[i]) - lower.begin();
+        work_in_bin[b > 0 ? b - 1 : 0].push_back(i);
+    }
+
+    std::vector<double> centre(bins), bin_d(bins), bin_beta(bins);
+    const bool warm = rows.bin_d.size() == bins;
+    // each bin is fitted on its own
+    ParallelFor(static_cast<int>(bins), nthreads, [&](int b) {
+        const std::vector<size_t> idx(free.begin() + b * free.size() / bins, free.begin() + (b + 1) * free.size() / bins);
+        double s2 = 0, sfo = 0, sfc2 = 0, sfofc = 0;
+        for (size_t i : idx) {
+            s2 += refl.inv_d2[i];
+            sfo += double(refl.fo[i]) * refl.fo[i] / refl.epsilon[i];
+            sfc2 += fc[i] * fc[i] / refl.epsilon[i];
+            sfofc += refl.fo[i] * fc[i] / refl.epsilon[i];
+        }
+        centre[b] = s2 / static_cast<double>(idx.size());
+        double d = sfc2 > 0 ? std::max(sfofc / sfc2, 0.05) : 1.0;
+        double beta = std::max((sfo - d * d * sfc2) / static_cast<double>(idx.size()), 1e-3 * sfo / idx.size());
+        // beta: the spread of the free amplitudes about D Fc, measurement error included, by maximum likelihood
+        // (alternating one-dimensional minimisations over ln D and ln beta)
+        for (int round = 0; round < 4; round++) {
+            const double ld = NewtonMinimum([&](double x, double &g, double &h) {
+                const double dx = std::exp(x);
+                for (size_t i : idx) {
+                    const RowDerivatives r = LikelihoodDerivatives(refl.fo[i], fc[i], dx, refl.epsilon[i] * beta,
+                                                                   refl.centric[i]);
+                    g += dx * r.d;
+                    h += dx * dx * r.dd + dx * r.d;
+                }
+            }, std::log(d), std::log(d) - 2.0, std::log(std::min(d * 7.4, 3.0)));
+            d = std::exp(ld);
+            const double lb = NewtonMinimum([&](double x, double &g, double &h) {
+                for (size_t i : idx) {
+                    const double var = refl.epsilon[i] * std::exp(x);
+                    const RowDerivatives r = LikelihoodDerivatives(refl.fo[i], fc[i], d, var, refl.centric[i]);
+                    g += var * r.v;
+                    h += var * var * r.vv + var * r.v;
+                }
+            }, std::log(beta), std::log(beta) - 3.0, std::log(beta) + 3.0);
+            beta = std::exp(lb);
+        }
+        // D: by maximum likelihood on the working reflections, with the measurement error added to that beta, from
+        // where the last fit found it. Where the error is a large part of the spread, the variance counts it twice
+        // and D falls towards 0 - the high-resolution D and figure of merit REFMAC 5.8 reports.
+        // Following Murshudov et al. (2011) Acta Cryst. D67, 355-367 (D from the working set, the variance from the free)
+        if (!work_in_bin[b].empty()) {
+            std::vector<double> var;
+            for (size_t i : work_in_bin[b])
+                var.push_back(Variance(refl, i, beta, true));
+            d = NewtonMinimum([&](double x, double &g, double &h) {
+                for (size_t k = 0; k < var.size(); k++) {
+                    const size_t i = work_in_bin[b][k];
+                    const RowDerivatives r = LikelihoodDerivatives(refl.fo[i], fc[i], x, var[k], refl.centric[i]);
+                    g += r.d;
+                    h += r.dd;
+                }
+            }, warm ? rows.bin_d[b] : d, 0.0, 3.0);
+        }
+        bin_d[b] = d;
+        bin_beta[b] = beta;
+    });
+    rows.bin_d = bin_d;
+    rows.d.resize(n);
+    rows.var.resize(n);
+    for (size_t i = 0; i < n; i++) {
+        // linear in 1/d^2 between the bins' centres, flat beyond the outermost
+        const double s = refl.inv_d2[i];
+        double d = bin_d[0], beta = bin_beta[0];
+        if (s >= centre[bins - 1]) {
+            d = bin_d[bins - 1];
+            beta = bin_beta[bins - 1];
+        } else if (s > centre[0]) {
+            const size_t b = std::upper_bound(centre.begin(), centre.end(), s) - centre.begin();
+            const double t = (s - centre[b - 1]) / (centre[b] - centre[b - 1]);
+            d = bin_d[b - 1] + t * (bin_d[b] - bin_d[b - 1]);
+            beta = bin_beta[b - 1] + t * (bin_beta[b] - bin_beta[b - 1]);
+        }
+        rows.d[i] = static_cast<float>(d);
+        rows.var[i] = static_cast<float>(Variance(refl, i, beta, true));
+    }
+}
+
+RFactors ComputeRFactors(const RefinementReflections &refl, const std::vector<std::complex<float>> &fmodel) {
+    double nw = 0, dw = 0, nf = 0, df = 0;
+    RFactors r;
+    for (size_t i = 0; i < refl.Size(); i++) {
+        const double diff = std::fabs(refl.fo[i] - std::abs(fmodel[i]));
+        if (refl.free[i]) {
+            nf += diff;
+            df += refl.fo[i];
+            r.n_free++;
+        } else {
+            nw += diff;
+            dw += refl.fo[i];
+            r.n_work++;
+        }
+    }
+    r.r_work = dw > 0 ? nw / dw : 1;
+    r.r_free = df > 0 ? nf / df : 1;
+    return r;
+}
+
+std::vector<std::array<double, 4>> ModelXyzB(const gemmi::Model &model) {
+    std::vector<std::array<double, 4>> out;
+    for (const gemmi::Chain &ch : model.chains)
+        for (const gemmi::Residue &r : ch.residues)
+            for (const gemmi::Atom &a : r.atoms)
+                out.push_back({a.pos.x, a.pos.y, a.pos.z, a.b_iso});
+    return out;
+}
+
+namespace {
+std::mutex stage_mutex;
+std::map<std::string, std::pair<double, int>> stage_times;
+}  // namespace
+
+RefinementStage::RefinementStage(const char *name)
+    : name_(name), start_(std::chrono::steady_clock::now()), nvtx_(NvtxRangeStart(name)) {}
+
+RefinementStage::~RefinementStage() {
+    NvtxRangeEnd(nvtx_);
+    const double seconds = std::chrono::duration<double>(std::chrono::steady_clock::now() - start_).count();
+    std::lock_guard lock(stage_mutex);
+    std::pair<double, int> &t = stage_times[name_];
+    t.first += seconds;
+    t.second++;
+}
+
+void RefinementStage::Log(Logger &logger) {
+    std::lock_guard lock(stage_mutex);
+    for (const auto &[name, t] : stage_times)
+        logger.Debug("TIMING refine.{} {:.3f} {}", name, t.first, t.second);
+    stage_times.clear();
+}
+
+double RefinementBlur(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min, double b_floor) {
+    // set_refmac_compatible_blur(): u_to_b / 1.1 * spacing^2 - b_min, not below 0, the spacing the one asked for
+    const gemmi::DensityCalculator<Table, float> dc = Calculator(cell, sg, d_min, 0);
+    const double spacing = dc.requested_grid_spacing();
+    return std::max(0.0, gemmi::u_to_b() / 1.1 * spacing * spacing - b_floor);
+}
+
+std::unique_ptr<RefinementEngine> MakeRefinementEngineCPU(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg,
+                                                          double d_min, const RefinementReflections &refl,
+                                                          size_t nthreads) {
+    return std::make_unique<RefinementEngineCPU>(cell, sg, d_min, refl, nthreads);
+}
+
+void AtomGradientsFromMap(const gemmi::Grid<float> &map, const gemmi::Model &model, double blur, size_t nthreads,
+                          std::vector<std::array<double, 4>> &grad) {
+    const gemmi::DensityCalculator<Table, float> dc = Calculator(map.unit_cell, *map.spacegroup, 1.0, blur);
+    std::vector<const gemmi::Atom *> atoms;
+    for (const gemmi::Chain &ch : model.chains)
+        for (const gemmi::Residue &r : ch.residues)
+            for (const gemmi::Atom &a : r.atoms)
+                atoms.push_back(&a);
+    grad.assign(atoms.size(), {0, 0, 0, 0});
+    const int nu = map.nu, nv = map.nv, nw = map.nw;
+    // As ModelGrid.cpp walks a density box: the orthogonalization over the grid size in single precision.
+    const gemmi::UpperTriangularMat33 &om = map.orth_n;
+    const float m00 = static_cast<float>(om.a11), m01 = static_cast<float>(om.a12), m02 = static_cast<float>(om.a13),
+                m11 = static_cast<float>(om.a22), m12 = static_cast<float>(om.a23), m22 = static_cast<float>(om.a33);
+    constexpr double FOUR_PI2 = 4 * refine_math::PI * refine_math::PI;
+    ParallelChunks(static_cast<int>(atoms.size()), nthreads, [&](int lo, int hi) {
+        for (int i = lo; i < hi; i++) {
+            const gemmi::Atom &atom = *atoms[i];
+            const float b = static_cast<float>(atom.b_iso + blur);
+            const auto precal = Table::get(atom.element, atom.charge, atom.serial).precalculate_density_iso(b, 0.0f);
+            const double radius = dc.estimate_radius(precal, b);
+            const float max_r2 = static_cast<float>(radius * radius);
+            const gemmi::Fractional fpos = map.unit_cell.fractionalize(atom.pos);
+            const double n3[3] = {fpos.x * nu, fpos.y * nv, fpos.z * nw};
+            float nctr[3];
+            int c[3], d[3];
+            for (int k = 0; k < 3; k++) {
+                nctr[k] = static_cast<float>(n3[k]);
+                c[k] = gemmi::iround(n3[k]);
+            }
+            d[0] = std::min(static_cast<int>(std::ceil(radius / map.spacing[0])), nu - 1);
+            d[1] = std::min(static_cast<int>(std::ceil(radius / map.spacing[1])), nv - 1);
+            d[2] = std::min(static_cast<int>(std::ceil(radius / map.spacing[2])), nw - 1);
+            double gx = 0, gy = 0, gz = 0, gb = 0;
+            for (int w = c[2] - d[2]; w <= c[2] + d[2]; w++) {
+                const float fz = nctr[2] - static_cast<float>(w);
+                const float z = m22 * fz;
+                const int w_ = gemmi::modulo(w, nw);
+                for (int v = c[1] - d[1]; v <= c[1] + d[1]; v++) {
+                    const float fy = nctr[1] - static_cast<float>(v);
+                    const float y = m11 * fy + m12 * fz;
+                    const float yz = y * y + z * z;
+                    if (yz > max_r2)
+                        continue;
+                    const float x_yz = m01 * fy + m02 * fz;
+                    const size_t row = static_cast<size_t>(nu) * (gemmi::modulo(v, nv) + static_cast<size_t>(nv) * w_);
+                    for (int u = c[0] - d[0]; u <= c[0] + d[0]; u++) {
+                        const float x = m00 * (nctr[0] - static_cast<float>(u)) + x_yz;
+                        const float r2 = yz + x * x;
+                        if (r2 > max_r2)
+                            continue;
+                        const double value = map.data[row + gemmi::modulo(u, nu)];
+                        double dr2 = 0, db = 0;
+                        for (size_t q = 0; q < std::size(precal.a); q++) {
+                            const double e = precal.a[q] * gemmi::unsafe_expapprox(std::max(precal.b[q] * r2, -88.f));
+                            dr2 += e * precal.b[q];
+                            db += e * precal.b[q] * (1.5 + precal.b[q] * r2);
+                        }
+                        gx += value * dr2 * x;
+                        gy += value * dr2 * y;
+                        gz += value * dr2 * z;
+                        gb += value * db;
+                    }
+                }
+            }
+            // rho = occ sum_q a_q exp(b_q r^2): d rho / d(centre) = occ 2 (sum a_q b_q e_q) (centre - point), and
+            // with b_q = -4 pi^2 / (B_q + B + blur), d rho / dB = occ sum a_q e_q b_q (1.5 + b_q r^2) / (4 pi^2).
+            grad[i] = {2.0 * atom.occ * gx, 2.0 * atom.occ * gy, 2.0 * atom.occ * gz, atom.occ * gb / FOUR_PI2};
+        }
+    });
+}
diff --git a/image_analysis/structure_refinement/RefinementXray.h b/image_analysis/structure_refinement/RefinementXray.h
new file mode 100644
index 000000000..d7062afbf
--- /dev/null
+++ b/image_analysis/structure_refinement/RefinementXray.h
@@ -0,0 +1,184 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <array>
+#include <chrono>
+#include <cstdint>
+#include <complex>
+#include <memory>
+#include <optional>
+#include <vector>
+
+#include "gemmi/grid.hpp"
+#include "gemmi/model.hpp"
+#include "gemmi/symmetry.hpp"
+#include "gemmi/unitcell.hpp"
+
+#include "../../common/Reflection.h"   // MergedReflection
+#include "RefinementRestraints.h"     // RestraintSet
+#include "RigidBodyRefine.h"           // SymmetryComposition
+
+class Logger;
+
+// The X-ray side of restrained refinement (Refinement.h): the observed amplitudes, the model's structure
+// factors and the maximum-likelihood target that compares them, with its gradient with respect to every
+// atom's position and B.
+
+// The reflections a refinement fits and scores: the observed amplitudes, in the group's reciprocal ASU, that
+// the refinement grid composes (SymmetryComposition) - every observed one in practice.
+struct RefinementReflections {
+    std::vector<gemmi::Miller> hkl;
+    std::vector<float> fo, sigma;
+    std::vector<char> free, centric;
+    std::vector<float> epsilon;
+    std::vector<double> inv_d2;
+    size_t Size() const { return hkl.size(); }
+};
+
+// The French-Wilson amplitudes of `merged` (NaN dropped) into the ASU of `sg`, those the grid of
+// RigidBodyZoneGrid(cell, sg, d_min) composes.
+RefinementReflections PrepareRefinementReflections(const std::vector<MergedReflection> &merged,
+                                                   const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg,
+                                                   double d_min);
+
+// What turns the atoms' structure factors F into the model the target compares with the data, per reflection:
+//   F_model = k_total (F + fmask),
+// with k_total the overall scale and anisotropic B and fmask the bulk solvent already scaled by k_sol
+// exp(-b_sol s^2/4); and the two parameters of the likelihood, D and the variance. Fixed for one macro-cycle.
+struct XrayRowModel {
+    std::vector<float> k_total;
+    std::vector<std::complex<float>> fmask;
+    std::vector<float> d, var;
+    // D per likelihood bin, where EstimateLikelihoodParameters() found it - the next fit's start (empty: none)
+    std::vector<double> bin_d;
+};
+
+// The flat bulk-solvent model's mask (SolventMasker with the Refmac radii, PutMaskOnGrid) and its structure factors
+// at the reflections, on a grid of its own rather than the atoms' density grid: the mask's edge is set by the
+// probe and shrink radii (1.0 and 0.8 A), which a grid at d_min / 3 cannot resolve at low resolution - at 3 A
+// its 1 A step leaves no grid point within the shrink radius and the shrink is skipped. The step is therefore
+// d_min / 3 or MASK_SPACING_MAX, whichever is finer - where the mask grid stays within MASK_POINTS_MAX points; a
+// cell too large for that gets the spacing that fills it. The R-factors of low-resolution models settle at a
+// step of 0.4 A (within 0.001 of 0.3 A) and move by up to 0.005 between 0.4 and 0.8 A.
+// The flat solvent model of Fokine & Urzhumtsev (2002) Acta Cryst. D58, 1387-1392
+// The probe-and-shrink mask of Jiang & Brunger (1994) J. Mol. Biol. 243, 100-115
+class BulkSolventMask {
+public:
+    static constexpr double MASK_SPACING_MAX = 0.4;   // A
+    static constexpr double MASK_POINTS_MAX = 1 << 26;
+    BulkSolventMask(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min, size_t nthreads);
+    // The mask's grid (sizes and spacing set, values not allocated) - also the GPU engine's (RefinementGPU.cpp).
+    static gemmi::Grid<float> MaskGrid(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min);
+    // Fmask (unscaled) of `model` at `hkl`.
+    void Fmask(const gemmi::Model &model, const std::vector<gemmi::Miller> &hkl,
+               std::vector<std::complex<float>> &f) const;
+    double Spacing() const { return spacing_; }
+
+private:
+    gemmi::Grid<float> grid_;
+    mutable std::vector<size_t> orbit_leaders_;   // made at the first Fmask()
+    size_t nthreads_;
+    double spacing_;
+};
+
+// The ML parameters per reflection, in resolution bins of the free set interpolated between the bins' centres:
+// beta fitted by maximum likelihood to the free reflections as the whole spread of Fo about D Fc, D then fitted to
+// the working reflections with the variance epsilon beta + 2 sigma^2 (acentric; + sigma^2 centric), which is also
+// the variance of a reflection in the target. `fmodel` is k_total (F + fmask), without D.
+// Following Lunin & Skovoroda (1995) Acta Cryst. A51, 880-887, and Murshudov et al. (2011) Acta Cryst. D67, 355-367
+void EstimateLikelihoodParameters(const RefinementReflections &refl, const std::vector<std::complex<float>> &fmodel,
+                                  XrayRowModel &rows, size_t nthreads = 1);
+
+// R-work and R-free of k_total (F + fmask) against the observations.
+struct RFactors {
+    double r_work = 1, r_free = 1;
+    int n_work = 0, n_free = 0;
+};
+RFactors ComputeRFactors(const RefinementReflections &refl, const std::vector<std::complex<float>> &fmodel);
+
+// x, y, z and B of every atom of `model`, in model order.
+std::vector<std::array<double, 4>> ModelXyzB(const gemmi::Model &model);
+
+// What evaluates the targets for a set of atom positions and B: the CPU below, or a GPU (RefinementGPU.h). The
+// atoms are the model's, all of them, in model order; the grid and the reflections are fixed when the engine is
+// made, the row model each macro-cycle, the blur where SetBlur is called.
+class RefinementEngine {
+public:
+    virtual ~RefinementEngine() = default;
+    // The blur the atoms are gridded with (DensityCalculator's), and the matching unblur of their transform.
+    // Every atom's B must stay above what the blur was chosen for (RefinementBlur) while it is in use.
+    virtual void SetBlur(double blur) = 0;
+    virtual void SetRowModel(const XrayRowModel &rows) = 0;
+    // F of the atoms at the reflections.
+    virtual void Fcalc(const gemmi::Model &model, std::vector<std::complex<float>> &f) = 0;
+    // The bulk-solvent mask's structure factors at the reflections (unscaled).
+    virtual void Fmask(const gemmi::Model &model, std::vector<std::complex<float>> &f) = 0;
+    // The sum of -ln L over the working reflections and, with `grad`, its derivatives with respect to every
+    // atom's x, y, z (Cartesian, A) and B (A^2), in model order.
+    virtual double Evaluate(const gemmi::Model &model, std::vector<std::array<double, 4>> *grad) = 0;
+    virtual bool OnGPU() const = 0;
+
+    // Restraint set `which` (0: the geometry and the repulsions, 1: the B similarity) and its sum of E at xyzb
+    // (x, y, z, B per atom) with, given `grad`, dE/d(x, y, z, B) per atom. On the CPU unless the engine has its own.
+    virtual void SetRestraints(int which, const RestraintSet &set) { restraints_[which] = set; }
+    virtual double EvaluateRestraints(int which, const std::vector<std::array<double, 4>> &xyzb,
+                                      std::vector<std::array<double, 4>> *grad) {
+        if (grad != nullptr)
+            grad->assign(xyzb.size(), {0, 0, 0, 0});
+        return ::EvaluateRestraints(restraints_[which], xyzb, grad);
+    }
+    // Evaluate() and EvaluateRestraints(which) at the atoms of `model` as they are, in one go: returns the X-ray
+    // target, and the restraints' sum in `restraints`.
+    virtual double EvaluateWithRestraints(const gemmi::Model &model, int which, std::vector<std::array<double, 4>> *grad,
+                                          std::vector<std::array<double, 4>> *restraint_grad, double &restraints) {
+        const double xray = Evaluate(model, grad);
+        restraints = EvaluateRestraints(which, ModelXyzB(model), restraint_grad);
+        return xray;
+    }
+
+private:
+    RestraintSet restraints_[2];
+};
+
+// The time a refinement spends in one stage, summed over every call (and over threads) until Log(): the scope of
+// an instance is one call, and an NVTX range of the stage's name.
+class RefinementStage {
+public:
+    explicit RefinementStage(const char *name);
+    ~RefinementStage();
+    RefinementStage(const RefinementStage &) = delete;
+    RefinementStage &operator=(const RefinementStage &) = delete;
+    // "TIMING refine.<stage> <seconds> <calls>" per stage at debug level, then the sums start again.
+    static void Log(Logger &logger);
+
+private:
+    const char *name_;
+    std::chrono::steady_clock::time_point start_;
+    uint64_t nvtx_;
+};
+
+// The density an atom is gridded out to, in e/A^3 of its blurred density (DensityCalculator::cutoff, 1e-5 by
+// default): the radius of every atom, and with it the gather and the gradient, follow from it.
+constexpr float REFINEMENT_DENSITY_CUTOFF = 1e-4f;
+
+// The blur for a model whose smallest B may go as low as b_floor: DensityCalculator's
+// set_refmac_compatible_blur() for that B, on the refinement grid of d_min.
+double RefinementBlur(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min, double b_floor);
+
+// The CPU engine: the density of one copy of the atoms on the grid of RigidBodyZoneGrid(cell, sg, d_min)
+// (PutModelDensityOnGrid), its transform and the crystal's symmetry composed in reciprocal space
+// (SymmetryComposition). The gradient by the FFT method: the derivative of the target with respect to each
+// structure factor, taken back to real space by one inverse transform, is a map; each atom's derivatives are
+// that map summed against the derivatives of its own density.
+// Following Agarwal (1978) Acta Cryst. A34, 791-809
+std::unique_ptr<RefinementEngine> MakeRefinementEngineCPU(const gemmi::UnitCell &cell,
+                                                          const gemmi::SpaceGroup &sg, double d_min,
+                                                          const RefinementReflections &refl, size_t nthreads);
+
+// The derivative map of the X-ray target on a grid (the FFT method's map), summed against each atom's density
+// derivatives: dT/d(x, y, z, B) per atom. `map` is u fastest on the grid of RigidBodyZoneGrid(), the atoms
+// gridded with `blur`. Exposed for the tests.
+void AtomGradientsFromMap(const gemmi::Grid<float> &map, const gemmi::Model &model, double blur, size_t nthreads,
+                          std::vector<std::array<double, 4>> &grad);
diff --git a/image_analysis/structure_refinement/monomers/1MA.cif b/image_analysis/structure_refinement/monomers/1MA.cif
new file mode 100644
index 000000000..256d8c361
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/1MA.cif
@@ -0,0 +1,288 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+1MA     1MA      "6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE"     RNA     38     24     .     
+#
+data_comp_1MA
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+1MA     P       P       P       0       46.199      22.985      33.948      
+1MA     OP1     O       O       0       45.612      23.494      35.251      
+1MA     OP2     O       OP      -1      45.300      23.247      32.755      
+1MA     OP3     O       OP      -1      47.626      23.448      33.724      
+1MA     "O5'"   O       O2      0       46.275      21.379      34.098      
+1MA     "C5'"   C       CH2     0       46.795      20.601      32.990      
+1MA     "C4'"   C       CH1     0       46.838      19.142      33.374      
+1MA     "O4'"   O       O2      0       47.700      18.984      34.533      
+1MA     "C3'"   C       CH1     0       45.487      18.504      33.742      
+1MA     "O3'"   O       OH1     0       45.334      17.241      33.106      
+1MA     "C2'"   C       CH1     0       45.552      18.382      35.269      
+1MA     "O2'"   O       OH1     0       44.831      17.281      35.781      
+1MA     "C1'"   C       CH1     0       47.059      18.182      35.494      
+1MA     N9      N       NR5     0       47.526      18.600      36.823      
+1MA     C8      C       CR15    0       47.503      19.881      37.308      
+1MA     N7      N       NRD5    0       47.981      19.974      38.529      
+1MA     C5      C       CR56    0       48.339      18.679      38.866      
+1MA     C6      C       CR6     0       48.912      18.172      40.064      
+1MA     N6      N       NH1     0       49.200      18.794      41.137      
+1MA     N1      N       NR6     0       49.184      16.766      39.984      
+1MA     CM1     C       CH3     0       49.814      16.095      41.139      
+1MA     C2      C       CR16    0       48.871      16.031      38.868      
+1MA     N3      N       NRD6    0       48.283      16.491      37.799      
+1MA     C4      C       CR56    0       48.059      17.831      37.814      
+1MA     "H5'"   H       H       0       47.706      20.911      32.761      
+1MA     "H5''"  H       H       0       46.216      20.718      32.197      
+1MA     "H4'"   H       H       0       47.231      18.646      32.624      
+1MA     "H3'"   H       H       0       44.746      19.109      33.479      
+1MA     "HO3'"  H       H       0       44.509      17.042      33.090      
+1MA     "H2'"   H       H       0       45.240      19.223      35.696      
+1MA     "HO2'"  H       H       0       44.907      17.268      36.626      
+1MA     "H1'"   H       H       0       47.295      17.228      35.362      
+1MA     H8      H       H       0       47.164      20.641      36.793      
+1MA     HN61    H       H       0       50.024      19.033      41.188      
+1MA     HM11    H       H       0       49.949      15.154      40.947      
+1MA     HM12    H       H       0       49.240      16.184      41.916      
+1MA     HM13    H       H       0       50.672      16.510      41.324      
+1MA     H2      H       H       0       49.096      15.129      38.869      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+1MA           P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+1MA           P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+1MA           P         OP3      SINGLE       n     1.517  0.0192     1.517  0.0192
+1MA           P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+1MA       "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+1MA       "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+1MA       "C4'"       "O4'"      SINGLE       n     1.451  0.0100     1.451  0.0100
+1MA       "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+1MA       "O4'"       "C1'"      SINGLE       n     1.408  0.0100     1.408  0.0100
+1MA       "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+1MA       "C3'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+1MA       "C2'"       "O2'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+1MA       "C2'"       "C1'"      SINGLE       n     1.539  0.0100     1.539  0.0100
+1MA       "C1'"          N9      SINGLE       n     1.468  0.0100     1.468  0.0100
+1MA          N9          C8      SINGLE       y     1.369  0.0100     1.369  0.0100
+1MA          N9          C4      SINGLE       y     1.364  0.0100     1.364  0.0100
+1MA          C8          N7      DOUBLE       y     1.313  0.0100     1.313  0.0100
+1MA          N7          C5      SINGLE       y     1.384  0.0100     1.384  0.0100
+1MA          C5          C6      SINGLE       n     1.410  0.0200     1.410  0.0200
+1MA          C5          C4      DOUBLE       y     1.379  0.0109     1.379  0.0109
+1MA          C6          N6      DOUBLE       n     1.272  0.0100     1.272  0.0100
+1MA          C6          N1      SINGLE       n     1.406  0.0200     1.406  0.0200
+1MA          N1         CM1      SINGLE       n     1.471  0.0118     1.471  0.0118
+1MA          N1          C2      SINGLE       n     1.366  0.0100     1.366  0.0100
+1MA          C2          N3      DOUBLE       n     1.299  0.0100     1.299  0.0100
+1MA          N3          C4      SINGLE       n     1.355  0.0100     1.355  0.0100
+1MA       "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+1MA       "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+1MA       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+1MA       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+1MA       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+1MA       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.994  0.0200
+1MA       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+1MA       "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+1MA          C8          H8      SINGLE       n     1.082  0.0130     0.979  0.0200
+1MA          N6        HN61      SINGLE       n     1.016  0.0100     0.860  0.0100
+1MA         CM1        HM11      SINGLE       n     1.089  0.0100     0.970  0.0158
+1MA         CM1        HM12      SINGLE       n     1.089  0.0100     0.970  0.0158
+1MA         CM1        HM13      SINGLE       n     1.089  0.0100     0.970  0.0158
+1MA          C2          H2      SINGLE       n     1.082  0.0130     0.930  0.0100
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+1MA         OP1           P         OP2     112.864    1.69
+1MA         OP1           P         OP3     112.864    1.69
+1MA         OP1           P       "O5'"     105.808    2.07
+1MA         OP2           P         OP3     112.864    1.69
+1MA         OP2           P       "O5'"     105.808    2.07
+1MA         OP3           P       "O5'"     105.808    2.07
+1MA           P       "O5'"       "C5'"     118.783    1.50
+1MA       "O5'"       "C5'"       "C4'"     109.342    1.50
+1MA       "O5'"       "C5'"       "H5'"     109.845    1.50
+1MA       "O5'"       "C5'"      "H5''"     109.845    1.50
+1MA       "C4'"       "C5'"       "H5'"     109.624    1.50
+1MA       "C4'"       "C5'"      "H5''"     109.624    1.50
+1MA       "H5'"       "C5'"      "H5''"     108.472    1.50
+1MA       "C5'"       "C4'"       "O4'"     109.123    1.50
+1MA       "C5'"       "C4'"       "C3'"     116.008    1.52
+1MA       "C5'"       "C4'"       "H4'"     108.268    1.50
+1MA       "O4'"       "C4'"       "C3'"     105.388    1.50
+1MA       "O4'"       "C4'"       "H4'"     108.947    1.50
+1MA       "C3'"       "C4'"       "H4'"     109.363    1.86
+1MA       "C4'"       "O4'"       "C1'"     109.426    1.50
+1MA       "C4'"       "C3'"       "O3'"     111.281    2.46
+1MA       "C4'"       "C3'"       "C2'"     102.602    1.50
+1MA       "C4'"       "C3'"       "H3'"     110.452    2.54
+1MA       "O3'"       "C3'"       "C2'"     111.581    2.83
+1MA       "O3'"       "C3'"       "H3'"     110.380    1.67
+1MA       "C2'"       "C3'"       "H3'"     110.504    1.75
+1MA       "C3'"       "O3'"      "HO3'"     108.744    3.00
+1MA       "C3'"       "C2'"       "O2'"     112.782    2.45
+1MA       "C3'"       "C2'"       "C1'"     101.779    1.50
+1MA       "C3'"       "C2'"       "H2'"     110.596    1.51
+1MA       "O2'"       "C2'"       "C1'"     110.620    3.00
+1MA       "O2'"       "C2'"       "H2'"     110.448    1.97
+1MA       "C1'"       "C2'"       "H2'"     110.803    1.50
+1MA       "C2'"       "O2'"      "HO2'"     109.103    2.13
+1MA       "O4'"       "C1'"       "C2'"     106.588    1.50
+1MA       "O4'"       "C1'"          N9     107.830    1.50
+1MA       "O4'"       "C1'"       "H1'"     110.469    1.59
+1MA       "C2'"       "C1'"          N9     113.810    1.50
+1MA       "C2'"       "C1'"       "H1'"     109.847    1.50
+1MA          N9       "C1'"       "H1'"     108.233    1.86
+1MA       "C1'"          N9          C8     125.615    2.25
+1MA       "C1'"          N9          C4     127.393    3.00
+1MA          C8          N9          C4     106.992    1.50
+1MA          N9          C8          N7     112.621    1.50
+1MA          N9          C8          H8     123.218    1.50
+1MA          N7          C8          H8     124.162    1.50
+1MA          C8          N7          C5     103.718    1.50
+1MA          N7          C5          C6     129.894    1.50
+1MA          N7          C5          C4     109.368    1.50
+1MA          C6          C5          C4     120.738    1.50
+1MA          C5          C6          N6     129.510    1.50
+1MA          C5          C6          N1     112.223    1.50
+1MA          N6          C6          N1     118.267    1.50
+1MA          C6          N6        HN61     113.739    3.00
+1MA          C6          N1         CM1     118.703    1.50
+1MA          C6          N1          C2     122.333    1.50
+1MA         CM1          N1          C2     118.965    1.66
+1MA          N1         CM1        HM11     109.481    1.50
+1MA          N1         CM1        HM12     109.481    1.50
+1MA          N1         CM1        HM13     109.481    1.50
+1MA        HM11         CM1        HM12     109.428    1.50
+1MA        HM11         CM1        HM13     109.428    1.50
+1MA        HM12         CM1        HM13     109.428    1.50
+1MA          N1          C2          N3     125.328    1.50
+1MA          N1          C2          H2     117.343    1.50
+1MA          N3          C2          H2     117.329    1.50
+1MA          C2          N3          C4     113.724    1.50
+1MA          N9          C4          C5     107.302    1.96
+1MA          N9          C4          N3     127.043    1.50
+1MA          C5          C4          N3     125.654    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+1MA     C2e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+1MA     C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+1MA     C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+1MA     C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+1MA     C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+1MA     C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+1MA     C3e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+1MA     C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+1MA     C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+1MA     C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+1MA     C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+1MA     C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+1MA     alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+1MA     beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+1MA     epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+1MA     gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+1MA     sp3_sp3_52      "C3'"     "C2'"     "O2'"     "HO2'"    180.000       10.00     3     
+1MA       const_sp2_sp2_2          N7          C8          N9       "C1'"     180.000     5.0     2
+1MA              const_14          C5          C4          N9       "C1'"     180.000    10.0     2
+1MA       const_sp2_sp2_5          N9          C8          N7          C5       0.000     5.0     2
+1MA       const_sp2_sp2_8          C6          C5          N7          C8     180.000     5.0     2
+1MA             sp2_sp2_4          N7          C5          C6          N6       0.000     5.0     2
+1MA       const_sp2_sp2_9          N9          C4          C5          N7       0.000     5.0     2
+1MA            sp2_sp2_17          C5          C6          N6        HN61     180.000     5.0     2
+1MA             sp2_sp2_8          N6          C6          N1         CM1       0.000     5.0     2
+1MA             sp2_sp3_7          C6          N1         CM1        HM11     150.000    10.0     6
+1MA            sp2_sp2_10          N3          C2          N1         CM1     180.000     5.0     2
+1MA            sp2_sp2_13          N1          C2          N3          C4       0.000     5.0     2
+1MA            sp2_sp2_16          N9          C4          N3          C2     180.000     5.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+1MA    chir_1    P    "O5'"    OP2    OP3    both
+1MA    chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+1MA    chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+1MA    chir_4    "C2'"    "O2'"    "C1'"    "C3'"    negative
+1MA    chir_5    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+1MA    plan-1       "C1'"   0.020
+1MA    plan-1          C4   0.020
+1MA    plan-1          C5   0.020
+1MA    plan-1          C6   0.020
+1MA    plan-1          C8   0.020
+1MA    plan-1          H8   0.020
+1MA    plan-1          N3   0.020
+1MA    plan-1          N7   0.020
+1MA    plan-1          N9   0.020
+1MA    plan-2          C5   0.020
+1MA    plan-2          C6   0.020
+1MA    plan-2          N1   0.020
+1MA    plan-2          N6   0.020
+1MA    plan-3          C2   0.020
+1MA    plan-3          C6   0.020
+1MA    plan-3         CM1   0.020
+1MA    plan-3          N1   0.020
+1MA    plan-4          C2   0.020
+1MA    plan-4          H2   0.020
+1MA    plan-4          N1   0.020
+1MA    plan-4          N3   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+1MA           SMILES              ACDLabs 12.01                                                                                                                     P(=O)(O)(O)OCC1OC(C(C1O)O)n2cnc3\C(=N)N(C)C=Nc23
+1MA            InChI                InChI  1.03 InChI=1S/C11H16N5O7P/c1-15-3-14-10-6(9(15)12)13-4-16(10)11-8(18)7(17)5(23-11)2-22-24(19,20)21/h3-5,7-8,11-12,17-18H,2H2,1H3,(H2,19,20,21)/b12-9-/t5-,7-,8-,11-/m1/s1
+1MA         InChIKey                InChI  1.03                                                                                                                                          BKBYKEWNXKDACS-JOLDIKRXSA-N
+1MA SMILES_CANONICAL               CACTVS 3.385                                                                                                      CN1C=Nc2n(cnc2C1=N)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
+1MA           SMILES               CACTVS 3.385                                                                                                            CN1C=Nc2n(cnc2C1=N)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
+1MA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6                                                                                            "[H]/N=C\1/c2c(n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=CN1C"
+1MA           SMILES "OpenEye OEToolkits" 1.7.6                                                                                                                        CN1C=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C1=N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+1MA acedrg               243         "dictionary generator"                  
+1MA acedrg_database      11          "data source"                           
+1MA rdkit                2017.03.2   "Chemoinformatics tool"
+1MA refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/1PE.cif b/image_analysis/structure_refinement/monomers/1PE.cif
new file mode 100644
index 000000000..426368f17
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/1PE.cif
@@ -0,0 +1,228 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+1PE     1PE      "PENTAETHYLENE GLYCOL"     NON-POLYMER     38     16     .     
+#
+data_comp_1PE
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+1PE     OH2     O       OH1     0       21.840      38.426      32.717      
+1PE     C12     C       CH2     0       21.457      39.572      31.984      
+1PE     C22     C       CH2     0       22.615      40.477      31.702      
+1PE     OH3     O       O2      0       22.207      41.540      30.844      
+1PE     C13     C       CH2     0       21.271      43.721      30.536      
+1PE     C23     C       CH2     0       21.666      42.667      31.529      
+1PE     OH4     O       O2      0       22.390      44.073      29.724      
+1PE     C14     C       CH2     0       24.698      44.588      30.044      
+1PE     C24     C       CH2     0       23.288      45.017      30.307      
+1PE     OH5     O       O2      0       24.933      43.322      30.652      
+1PE     C15     C       CH2     0       26.417      41.501      31.086      
+1PE     C25     C       CH2     0       26.288      42.896      30.557      
+1PE     OH6     O       O2      0       26.057      41.474      32.464      
+1PE     C16     C       CH2     0       25.748      40.226      34.478      
+1PE     C26     C       CH2     0       26.168      40.178      33.042      
+1PE     OH7     O       OH1     0       26.621      41.011      35.266      
+1PE     HO2     H       H       0       21.179      37.901      32.781      
+1PE     H121    H       H       0       20.778      40.064      32.492      
+1PE     H122    H       H       0       21.055      39.289      31.136      
+1PE     H221    H       H       0       23.332      39.966      31.269      
+1PE     H222    H       H       0       22.967      40.837      32.546      
+1PE     H131    H       H       0       20.932      44.514      31.009      
+1PE     H132    H       H       0       20.549      43.378      29.966      
+1PE     H231    H       H       0       22.333      43.031      32.150      
+1PE     H232    H       H       0       20.880      42.393      32.049      
+1PE     H141    H       H       0       25.320      45.254      30.410      
+1PE     H142    H       H       0       24.850      44.524      29.076      
+1PE     H241    H       H       0       23.142      45.083      31.276      
+1PE     H242    H       H       0       23.134      45.903      29.913      
+1PE     H151    H       H       0       27.342      41.191      30.979      
+1PE     H152    H       H       0       25.829      40.900      30.579      
+1PE     H251    H       H       0       26.862      43.501      31.075      
+1PE     H252    H       H       0       26.581      42.922      29.619      
+1PE     H161    H       H       0       25.725      39.315      34.837      
+1PE     H162    H       H       0       24.843      40.599      34.536      
+1PE     H261    H       H       0       27.097      39.867      32.979      
+1PE     H262    H       H       0       25.598      39.547      32.551      
+1PE     HO7     H       H       0       26.588      41.816      35.006      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+1PE         OH2         C12      SINGLE       n     1.414  0.0200     1.414  0.0200
+1PE         C12         C22      SINGLE       n     1.496  0.0200     1.496  0.0200
+1PE         C22         OH3      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         OH3         C23      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         C13         C23      SINGLE       n     1.496  0.0200     1.496  0.0200
+1PE         C13         OH4      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         OH4         C24      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         C14         C24      SINGLE       n     1.496  0.0200     1.496  0.0200
+1PE         C14         OH5      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         OH5         C25      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         C15         C25      SINGLE       n     1.496  0.0200     1.496  0.0200
+1PE         C15         OH6      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         OH6         C26      SINGLE       n     1.423  0.0106     1.423  0.0106
+1PE         C16         C26      SINGLE       n     1.496  0.0200     1.496  0.0200
+1PE         C16         OH7      SINGLE       n     1.414  0.0200     1.414  0.0200
+1PE         OH2         HO2      SINGLE       n     0.970  0.0120     0.846  0.0200
+1PE         C12        H121      SINGLE       n     1.089  0.0100     0.980  0.0144
+1PE         C12        H122      SINGLE       n     1.089  0.0100     0.980  0.0144
+1PE         C22        H221      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C22        H222      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C13        H131      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C13        H132      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C23        H231      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C23        H232      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C14        H141      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C14        H142      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C24        H241      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C24        H242      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C15        H151      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C15        H152      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C25        H251      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C25        H252      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C16        H161      SINGLE       n     1.089  0.0100     0.980  0.0144
+1PE         C16        H162      SINGLE       n     1.089  0.0100     0.980  0.0144
+1PE         C26        H261      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         C26        H262      SINGLE       n     1.089  0.0100     0.982  0.0175
+1PE         OH7         HO7      SINGLE       n     0.970  0.0120     0.846  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+1PE         C12         OH2         HO2     109.347    1.86
+1PE         OH2         C12         C22     112.284    1.56
+1PE         OH2         C12        H121     109.012    1.50
+1PE         OH2         C12        H122     109.012    1.50
+1PE         C22         C12        H121     109.198    1.50
+1PE         C22         C12        H122     109.198    1.50
+1PE        H121         C12        H122     108.093    1.50
+1PE         C12         C22         OH3     109.904    1.68
+1PE         C12         C22        H221     109.795    1.50
+1PE         C12         C22        H222     109.795    1.50
+1PE         OH3         C22        H221     109.691    1.50
+1PE         OH3         C22        H222     109.691    1.50
+1PE        H221         C22        H222     108.274    1.50
+1PE         C22         OH3         C23     112.795    1.50
+1PE         C23         C13         OH4     109.613    1.74
+1PE         C23         C13        H131     109.729    1.50
+1PE         C23         C13        H132     109.729    1.50
+1PE         OH4         C13        H131     109.691    1.50
+1PE         OH4         C13        H132     109.691    1.50
+1PE        H131         C13        H132     108.274    1.50
+1PE         OH3         C23         C13     109.613    1.74
+1PE         OH3         C23        H231     109.691    1.50
+1PE         OH3         C23        H232     109.691    1.50
+1PE         C13         C23        H231     109.729    1.50
+1PE         C13         C23        H232     109.729    1.50
+1PE        H231         C23        H232     108.274    1.50
+1PE         C13         OH4         C24     112.795    1.50
+1PE         C24         C14         OH5     109.613    1.74
+1PE         C24         C14        H141     109.729    1.50
+1PE         C24         C14        H142     109.729    1.50
+1PE         OH5         C14        H141     109.691    1.50
+1PE         OH5         C14        H142     109.691    1.50
+1PE        H141         C14        H142     108.274    1.50
+1PE         OH4         C24         C14     109.613    1.74
+1PE         OH4         C24        H241     109.691    1.50
+1PE         OH4         C24        H242     109.691    1.50
+1PE         C14         C24        H241     109.729    1.50
+1PE         C14         C24        H242     109.729    1.50
+1PE        H241         C24        H242     108.274    1.50
+1PE         C14         OH5         C25     112.795    1.50
+1PE         C25         C15         OH6     109.613    1.74
+1PE         C25         C15        H151     109.729    1.50
+1PE         C25         C15        H152     109.729    1.50
+1PE         OH6         C15        H151     109.691    1.50
+1PE         OH6         C15        H152     109.691    1.50
+1PE        H151         C15        H152     108.274    1.50
+1PE         OH5         C25         C15     109.613    1.74
+1PE         OH5         C25        H251     109.691    1.50
+1PE         OH5         C25        H252     109.691    1.50
+1PE         C15         C25        H251     109.729    1.50
+1PE         C15         C25        H252     109.729    1.50
+1PE        H251         C25        H252     108.274    1.50
+1PE         C15         OH6         C26     112.795    1.50
+1PE         C26         C16         OH7     112.284    1.56
+1PE         C26         C16        H161     109.198    1.50
+1PE         C26         C16        H162     109.198    1.50
+1PE         OH7         C16        H161     109.012    1.50
+1PE         OH7         C16        H162     109.012    1.50
+1PE        H161         C16        H162     108.093    1.50
+1PE         OH6         C26         C16     109.904    1.68
+1PE         OH6         C26        H261     109.691    1.50
+1PE         OH6         C26        H262     109.691    1.50
+1PE         C16         C26        H261     109.795    1.50
+1PE         C16         C26        H262     109.795    1.50
+1PE        H261         C26        H262     108.274    1.50
+1PE         C16         OH7         HO7     109.347    1.86
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+1PE             sp3_sp3_1         C22         C12         OH2         HO2     180.000    10.0     3
+1PE            sp3_sp3_49         OH6         C15         C25         OH5     180.000    10.0     3
+1PE            sp3_sp3_58         C25         C15         OH6         C26     180.000    10.0     3
+1PE            sp3_sp3_61         C16         C26         OH6         C15     180.000    10.0     3
+1PE            sp3_sp3_64         OH7         C16         C26         OH6     180.000    10.0     3
+1PE            sp3_sp3_73         C26         C16         OH7         HO7     180.000    10.0     3
+1PE             sp3_sp3_4         OH2         C12         C22         OH3     180.000    10.0     3
+1PE            sp3_sp3_13         C12         C22         OH3         C23     180.000    10.0     3
+1PE            sp3_sp3_16         C13         C23         OH3         C22     180.000    10.0     3
+1PE            sp3_sp3_19         OH4         C13         C23         OH3     180.000    10.0     3
+1PE            sp3_sp3_28         C23         C13         OH4         C24     180.000    10.0     3
+1PE            sp3_sp3_31         C14         C24         OH4         C13     180.000    10.0     3
+1PE            sp3_sp3_34         OH5         C14         C24         OH4     180.000    10.0     3
+1PE            sp3_sp3_43         C24         C14         OH5         C25     180.000    10.0     3
+1PE            sp3_sp3_46         C15         C25         OH5         C14     180.000    10.0     3
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+1PE           SMILES              ACDLabs 10.04                                                       O(CCO)CCOCCOCCOCCO
+1PE SMILES_CANONICAL               CACTVS 3.341                                                         OCCOCCOCCOCCOCCO
+1PE           SMILES               CACTVS 3.341                                                         OCCOCCOCCOCCOCCO
+1PE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                       C(COCCOCCOCCOCCO)O
+1PE           SMILES "OpenEye OEToolkits" 1.5.0                                                       C(COCCOCCOCCOCCO)O
+1PE            InChI                InChI  1.03 InChI=1S/C10H22O6/c11-1-3-13-5-7-15-9-10-16-8-6-14-4-2-12/h11-12H,1-10H2
+1PE         InChIKey                InChI  1.03                                              JLFNLZLINWHATN-UHFFFAOYSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+1PE acedrg               243         "dictionary generator"                  
+1PE acedrg_database      11          "data source"                           
+1PE rdkit                2017.03.2   "Chemoinformatics tool"
+1PE refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/2MG.cif b/image_analysis/structure_refinement/monomers/2MG.cif
new file mode 100644
index 000000000..4603d5a4c
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/2MG.cif
@@ -0,0 +1,294 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+2MG 2MG "2N-METHYLGUANOSINE-5'-MONOPHOSPHATE" RNA 39 25 .
+
+data_comp_2MG
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+2MG P      P P    0  33.727 6.946  21.647
+2MG OP1    O O    0  33.329 6.945  23.111
+2MG OP2    O OP   -1 32.927 7.934  20.820
+2MG OP3    O OP   -1 35.224 7.082  21.443
+2MG "O5'"  O O2   0  33.337 5.484  21.085
+2MG "C5'"  C CH2  0  31.942 5.086  21.079
+2MG "C4'"  C CH1  0  31.822 3.646  20.642
+2MG "O4'"  O O2   0  32.464 3.473  19.354
+2MG "C3'"  C CH1  0  32.490 2.602  21.543
+2MG "O3'"  O OH1  0  31.638 2.231  22.620
+2MG "C2'"  C CH1  0  32.737 1.450  20.564
+2MG "O2'"  O OH1  0  31.625 0.591  20.413
+2MG "C1'"  C CH1  0  33.058 2.195  19.266
+2MG N9     N NR5  0  34.492 2.337  19.018
+2MG C8     C CR15 0  35.255 3.479  19.051
+2MG N7     N NRD5 0  36.521 3.268  18.782
+2MG C5     C CR56 0  36.603 1.900  18.557
+2MG C6     C CR6  0  37.720 1.084  18.223
+2MG O6     O O    0  38.896 1.435  18.058
+2MG N1     N NR16 0  37.361 -0.264 18.084
+2MG C2     C CR6  0  36.088 -0.759 18.253
+2MG N2     N NH1  0  35.917 -2.084 18.070
+2MG CM2    C CH3  0  34.985 -2.901 18.830
+2MG N3     N NRD6 0  35.044 0.005  18.552
+2MG C4     C CR56 0  35.359 1.317  18.698
+2MG "H5'"  H H    0  31.432 5.664  20.459
+2MG "H5''" H H    0  31.561 5.189  21.986
+2MG "H4'"  H H    0  30.869 3.432  20.553
+2MG "H3'"  H H    0  33.352 2.945  21.893
+2MG "HO3'" H H    0  32.005 1.601  23.055
+2MG "H2'"  H H    0  33.522 0.917  20.859
+2MG "HO2'" H H    0  30.963 1.025  20.105
+2MG "H1'"  H H    0  32.654 1.702  18.516
+2MG H8     H H    0  34.907 4.331  19.245
+2MG HN1    H H    0  38.016 -0.841 17.874
+2MG HN2    H H    0  36.394 -2.476 17.453
+2MG HM21   H H    0  34.406 -2.341 19.371
+2MG HM22   H H    0  35.480 -3.500 19.410
+2MG HM23   H H    0  34.443 -3.423 18.218
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+2MG P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+2MG P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+2MG P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+2MG P     "O5'"  SINGLE n 1.614 0.0178 1.614 0.0178
+2MG "O5'" "C5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+2MG "C5'" "C4'"  SINGLE n 1.509 0.0100 1.509 0.0100
+2MG "C4'" "O4'"  SINGLE n 1.451 0.0100 1.451 0.0100
+2MG "C4'" "C3'"  SINGLE n 1.535 0.0100 1.535 0.0100
+2MG "O4'" "C1'"  SINGLE n 1.409 0.0100 1.409 0.0100
+2MG "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+2MG "C3'" "C2'"  SINGLE n 1.531 0.0100 1.531 0.0100
+2MG "C2'" "O2'"  SINGLE n 1.411 0.0100 1.411 0.0100
+2MG "C2'" "C1'"  SINGLE n 1.525 0.0100 1.525 0.0100
+2MG "C1'" N9     SINGLE n 1.458 0.0100 1.458 0.0100
+2MG N9    C8     SINGLE y 1.372 0.0100 1.372 0.0100
+2MG N9    C4     SINGLE y 1.375 0.0100 1.375 0.0100
+2MG C8    N7     DOUBLE y 1.312 0.0100 1.312 0.0100
+2MG N7    C5     SINGLE y 1.390 0.0100 1.390 0.0100
+2MG C5    C6     SINGLE y 1.417 0.0103 1.417 0.0103
+2MG C5    C4     DOUBLE y 1.377 0.0100 1.377 0.0100
+2MG C6    O6     DOUBLE n 1.239 0.0100 1.239 0.0100
+2MG C6    N1     SINGLE y 1.396 0.0107 1.396 0.0107
+2MG N1    C2     SINGLE y 1.372 0.0100 1.372 0.0100
+2MG C2    N2     SINGLE n 1.342 0.0119 1.342 0.0119
+2MG C2    N3     DOUBLE y 1.324 0.0127 1.324 0.0127
+2MG N2    CM2    SINGLE n 1.450 0.0100 1.450 0.0100
+2MG N3    C4     SINGLE y 1.355 0.0100 1.355 0.0100
+2MG "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+2MG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+2MG "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+2MG "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+2MG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+2MG "C2'" "H2'"  SINGLE n 1.089 0.0100 0.994 0.0200
+2MG "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+2MG "C1'" "H1'"  SINGLE n 1.089 0.0100 0.984 0.0200
+2MG C8    H8     SINGLE n 1.082 0.0130 0.942 0.0170
+2MG N1    HN1    SINGLE n 1.016 0.0100 0.897 0.0200
+2MG N2    HN2    SINGLE n 1.016 0.0100 0.873 0.0200
+2MG CM2   HM21   SINGLE n 1.089 0.0100 0.970 0.0159
+2MG CM2   HM22   SINGLE n 1.089 0.0100 0.970 0.0159
+2MG CM2   HM23   SINGLE n 1.089 0.0100 0.970 0.0159
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+2MG OP1   P     OP2    112.864 1.69
+2MG OP1   P     OP3    112.864 1.69
+2MG OP1   P     "O5'"  105.808 2.07
+2MG OP2   P     OP3    112.864 1.69
+2MG OP2   P     "O5'"  105.808 2.07
+2MG OP3   P     "O5'"  105.808 2.07
+2MG P     "O5'" "C5'"  118.783 1.50
+2MG "O5'" "C5'" "C4'"  109.342 1.50
+2MG "O5'" "C5'" "H5'"  109.845 1.50
+2MG "O5'" "C5'" "H5''" 109.845 1.50
+2MG "C4'" "C5'" "H5'"  109.624 1.50
+2MG "C4'" "C5'" "H5''" 109.624 1.50
+2MG "H5'" "C5'" "H5''" 108.472 1.50
+2MG "C5'" "C4'" "O4'"  109.123 1.50
+2MG "C5'" "C4'" "C3'"  116.008 1.52
+2MG "C5'" "C4'" "H4'"  108.268 1.50
+2MG "O4'" "C4'" "C3'"  105.388 1.50
+2MG "O4'" "C4'" "H4'"  108.947 1.50
+2MG "C3'" "C4'" "H4'"  109.363 1.86
+2MG "C4'" "O4'" "C1'"  109.903 1.50
+2MG "C4'" "C3'" "O3'"  111.281 2.46
+2MG "C4'" "C3'" "C2'"  102.602 1.50
+2MG "C4'" "C3'" "H3'"  110.452 2.54
+2MG "O3'" "C3'" "C2'"  111.581 2.83
+2MG "O3'" "C3'" "H3'"  110.380 1.67
+2MG "C2'" "C3'" "H3'"  110.504 1.75
+2MG "C3'" "O3'" "HO3'" 108.744 3.00
+2MG "C3'" "C2'" "O2'"  112.782 2.45
+2MG "C3'" "C2'" "C1'"  101.239 1.50
+2MG "C3'" "C2'" "H2'"  110.596 1.51
+2MG "O2'" "C2'" "C1'"  111.715 2.69
+2MG "O2'" "C2'" "H2'"  110.448 1.97
+2MG "C1'" "C2'" "H2'"  110.636 1.70
+2MG "C2'" "O2'" "HO2'" 109.103 2.13
+2MG "O4'" "C1'" "C2'"  106.047 1.50
+2MG "O4'" "C1'" N9     108.477 1.50
+2MG "O4'" "C1'" "H1'"  109.807 1.50
+2MG "C2'" "C1'" N9     113.824 1.50
+2MG "C2'" "C1'" "H1'"  109.015 1.50
+2MG N9    "C1'" "H1'"  109.561 1.50
+2MG "C1'" N9    C8     126.829 1.91
+2MG "C1'" N9    C4     127.440 1.80
+2MG C8    N9    C4     105.731 1.50
+2MG N9    C8    N7     113.507 1.50
+2MG N9    C8    H8     123.187 1.50
+2MG N7    C8    H8     123.307 1.50
+2MG C8    N7    C5     104.778 1.50
+2MG N7    C5    C6     130.614 1.50
+2MG N7    C5    C4     110.574 1.50
+2MG C6    C5    C4     118.812 1.50
+2MG C5    C6    O6     128.536 1.50
+2MG C5    C6    N1     110.783 1.50
+2MG O6    C6    N1     120.681 1.50
+2MG C6    N1    C2     124.695 1.50
+2MG C6    N1    HN1    117.267 2.44
+2MG C2    N1    HN1    118.037 1.50
+2MG N1    C2    N2     116.538 1.50
+2MG N1    C2    N3     124.501 1.50
+2MG N2    C2    N3     118.961 1.50
+2MG C2    N2    CM2    121.703 2.30
+2MG C2    N2    HN2    119.049 1.68
+2MG CM2   N2    HN2    119.248 1.66
+2MG N2    CM2   HM21   109.503 1.50
+2MG N2    CM2   HM22   109.503 1.50
+2MG N2    CM2   HM23   109.503 1.50
+2MG HM21  CM2   HM22   109.396 1.50
+2MG HM21  CM2   HM23   109.396 1.50
+2MG HM22  CM2   HM23   109.396 1.50
+2MG C2    N3    C4     113.582 1.50
+2MG N9    C4    C5     105.411 1.50
+2MG N9    C4    N3     126.963 1.50
+2MG C5    C4    N3     127.627 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+2MG C2e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+2MG C2e-nyu0        "C4'" "O4'" "C1'" "C2'"  340.700 6.300  1
+2MG C2e-nyu1        "O4'" "C1'" "C2'" "C3'"  32.800  4.900  1
+2MG C2e-nyu2        "C1'" "C2'" "C3'" "C4'"  326.9   3.600  1
+2MG C2e-nyu3        "C2'" "C3'" "C4'" "O4'"  22.600  4.500  1
+2MG C2e-nyu4        "C3'" "C4'" "O4'" "C1'"  357.700 6.100  1
+2MG C3e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+2MG C3e-nyu0        "C4'" "O4'" "C1'" "C2'"  2.8     6.100  1
+2MG C3e-nyu1        "O4'" "C1'" "C2'" "C3'"  335.00  4.900  1
+2MG C3e-nyu2        "C1'" "C2'" "C3'" "C4'"  35.9    2.800  1
+2MG C3e-nyu3        "C2'" "C3'" "C4'" "O4'"  324.700 3.100  1
+2MG C3e-nyu4        "C3'" "C4'" "O4'" "C1'"  20.500  5.100  1
+2MG alpha           "C5'" "O5'" P     OP3    -60.000 10.00  3
+2MG beta            P     "O5'" "C5'" "C4'"  180.000 10.00  3
+2MG epsi            "C4'" "C3'" "O3'" "HO3'" 180.000 10.00  3
+2MG gamma           "O5'" "C5'" "C4'" "C3'"  180.000 10.00  3
+2MG sp3_sp3_52      "C3'" "C2'" "O2'" "HO2'" 180.000 10.00  3
+2MG const_18        N7    C8    N9    "C1'"  180.000 10.0   2
+2MG const_30        C5    C4    N9    "C1'"  180.000 10.0   2
+2MG const_21        N9    C8    N7    C5     0.000   10.0   2
+2MG const_24        C6    C5    N7    C8     180.000 10.0   2
+2MG const_sp2_sp2_4 N7    C5    C6    O6     0.000   5.0    2
+2MG const_25        N9    C4    C5    N7     0.000   10.0   2
+2MG const_sp2_sp2_7 O6    C6    N1    C2     180.000 5.0    2
+2MG const_11        N2    C2    N1    C6     180.000 10.0   2
+2MG sp2_sp2_1       N1    C2    N2    CM2    180.000 5.0    2
+2MG const_14        N2    C2    N3    C4     180.000 10.0   2
+2MG sp2_sp3_7       C2    N2    CM2   HM21   0.000   10.0   6
+2MG const_16        N9    C4    N3    C2     180.000 10.0   2
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+2MG chir_1 P     "O5'" OP2   OP3   both
+2MG chir_2 "C4'" "O4'" "C3'" "C5'" negative
+2MG chir_3 "C3'" "O3'" "C4'" "C2'" positive
+2MG chir_4 "C2'" "O2'" "C1'" "C3'" negative
+2MG chir_5 "C1'" "O4'" N9    "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+2MG plan-1 "C1'" 0.020
+2MG plan-1 C2    0.020
+2MG plan-1 C4    0.020
+2MG plan-1 C5    0.020
+2MG plan-1 C6    0.020
+2MG plan-1 C8    0.020
+2MG plan-1 H8    0.020
+2MG plan-1 HN1   0.020
+2MG plan-1 N1    0.020
+2MG plan-1 N2    0.020
+2MG plan-1 N3    0.020
+2MG plan-1 N7    0.020
+2MG plan-1 N9    0.020
+2MG plan-1 O6    0.020
+2MG plan-2 C2    0.020
+2MG plan-2 CM2   0.020
+2MG plan-2 HN2   0.020
+2MG plan-2 N2    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+2MG SMILES           ACDLabs              10.04 O=C1c2ncn(c2N=C(NC)N1)C3OC(C(O)C3O)COP(=O)(O)O
+2MG SMILES_CANONICAL CACTVS               3.341 CNC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
+2MG SMILES           CACTVS               3.341 CNC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
+2MG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CNC1=Nc2c(ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)C(=O)N1
+2MG SMILES           "OpenEye OEToolkits" 1.5.0 CNC1=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C(=O)N1
+2MG InChI            InChI                1.03  InChI=1S/C11H16N5O8P/c1-12-11-14-8-5(9(19)15-11)13-3-16(8)10-7(18)6(17)4(24-10)2-23-25(20,21)22/h3-4,6-7,10,17-18H,2H2,1H3,(H2,20,21,22)(H2,12,14,15,19)/t4-,6-,7-,10-/m1/s1
+2MG InChIKey         InChI                1.03  ZSKBUUXHFBEFIJ-KQYNXXCUSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+2MG acedrg          243       "dictionary generator"
+2MG acedrg_database 11        "data source"
+2MG rdkit           2017.03.2 "Chemoinformatics tool"
+2MG refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/5MC.cif b/image_analysis/structure_refinement/monomers/5MC.cif
new file mode 100644
index 000000000..1358828fc
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/5MC.cif
@@ -0,0 +1,268 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+5MC     5MC      "5-METHYLCYTIDINE-5'-MONOPHOSPHATE"     RNA     36     22     .     
+#
+data_comp_5MC
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+5MC     P       P       P       0       50.440      -8.664      9.985       
+5MC     OP1     O       O       0       48.933      -8.494      10.029      
+5MC     OP2     O       OP      -1      51.110      -8.329      11.305      
+5MC     OP3     O       OP      -1      50.865      -10.012     9.434       
+5MC     "O5'"   O       O2      0       50.976      -7.568      8.928       
+5MC     "C5'"   C       CH2     0       52.398      -7.502      8.649       
+5MC     "C4'"   C       CH1     0       52.685      -6.336      7.734       
+5MC     "O4'"   O       O2      0       51.869      -6.428      6.541       
+5MC     "C3'"   C       CH1     0       52.360      -4.941      8.282       
+5MC     "O3'"   O       OH1     0       53.402      -4.481      9.135       
+5MC     "C2'"   C       CH1     0       52.217      -4.110      6.997       
+5MC     "O2'"   O       OH1     0       53.434      -3.537      6.561       
+5MC     "C1'"   C       CH1     0       51.731      -5.144      5.969       
+5MC     N1      N       NR6     0       50.307      -4.941      5.576       
+5MC     C2      C       CR6     0       49.973      -4.500      4.284       
+5MC     O2      O       O       0       50.870      -4.281      3.453       
+5MC     N3      N       NRD6    0       48.663      -4.323      3.969       
+5MC     C4      C       CR6     0       47.697      -4.561      4.872       
+5MC     N4      N       NH2     0       46.429      -4.359      4.472       
+5MC     C5      C       CR6     0       48.009      -5.004      6.186       
+5MC     C6      C       CR16    0       49.309      -5.173      6.486       
+5MC     CM5     C       CH3     0       46.922      -5.266      7.189       
+5MC     "H5'"   H       H       0       52.694      -8.342      8.219       
+5MC     "H5''"  H       H       0       52.900      -7.390      9.494       
+5MC     "H4'"   H       H       0       53.630      -6.373      7.473       
+5MC     "H3'"   H       H       0       51.499      -4.954      8.773       
+5MC     "HO3'"  H       H       0       53.276      -3.658      9.306       
+5MC     "H2'"   H       H       0       51.542      -3.413      7.124       
+5MC     "HO2'"  H       H       0       54.035      -4.136      6.511       
+5MC     "H1'"   H       H       0       52.305      -5.099      5.170       
+5MC     HN41    H       H       0       46.115      -4.796      3.779       
+5MC     HN42    H       H       0       45.920      -3.791      4.905       
+5MC     H6      H       H       0       49.548      -5.468      7.358       
+5MC     HM51    H       H       0       47.279      -5.777      7.934       
+5MC     HM52    H       H       0       46.206      -5.770      6.770       
+5MC     HM53    H       H       0       46.572      -4.422      7.518       
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+5MC           P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+5MC           P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+5MC           P         OP3      SINGLE       n     1.517  0.0192     1.517  0.0192
+5MC           P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+5MC       "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+5MC       "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+5MC       "C4'"       "O4'"      SINGLE       n     1.451  0.0111     1.451  0.0111
+5MC       "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+5MC       "O4'"       "C1'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+5MC       "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+5MC       "C3'"       "C2'"      SINGLE       n     1.533  0.0109     1.533  0.0109
+5MC       "C2'"       "O2'"      SINGLE       n     1.412  0.0100     1.412  0.0100
+5MC       "C2'"       "C1'"      SINGLE       n     1.532  0.0100     1.532  0.0100
+5MC       "C1'"          N1      SINGLE       n     1.485  0.0100     1.485  0.0100
+5MC          N1          C2      SINGLE       y     1.395  0.0100     1.395  0.0100
+5MC          N1          C6      SINGLE       y     1.364  0.0100     1.364  0.0100
+5MC          C2          O2      DOUBLE       n     1.241  0.0100     1.241  0.0100
+5MC          C2          N3      SINGLE       y     1.353  0.0117     1.353  0.0117
+5MC          N3          C4      DOUBLE       y     1.341  0.0100     1.341  0.0100
+5MC          C4          N4      SINGLE       n     1.343  0.0151     1.343  0.0151
+5MC          C4          C5      SINGLE       y     1.416  0.0131     1.416  0.0131
+5MC          C5          C6      DOUBLE       y     1.342  0.0102     1.342  0.0102
+5MC          C5         CM5      SINGLE       n     1.501  0.0100     1.501  0.0100
+5MC       "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+5MC       "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+5MC       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+5MC       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+5MC       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+5MC       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.978  0.0200
+5MC       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+5MC       "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.985  0.0100
+5MC          N4        HN41      SINGLE       n     1.016  0.0100     0.877  0.0200
+5MC          N4        HN42      SINGLE       n     1.016  0.0100     0.877  0.0200
+5MC          C6          H6      SINGLE       n     1.082  0.0130     0.951  0.0200
+5MC         CM5        HM51      SINGLE       n     1.089  0.0100     0.971  0.0135
+5MC         CM5        HM52      SINGLE       n     1.089  0.0100     0.971  0.0135
+5MC         CM5        HM53      SINGLE       n     1.089  0.0100     0.971  0.0135
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+5MC         OP1           P         OP2     112.864    1.69
+5MC         OP1           P         OP3     112.864    1.69
+5MC         OP1           P       "O5'"     105.808    2.07
+5MC         OP2           P         OP3     112.864    1.69
+5MC         OP2           P       "O5'"     105.808    2.07
+5MC         OP3           P       "O5'"     105.808    2.07
+5MC           P       "O5'"       "C5'"     118.783    1.50
+5MC       "O5'"       "C5'"       "C4'"     109.342    1.50
+5MC       "O5'"       "C5'"       "H5'"     109.845    1.50
+5MC       "O5'"       "C5'"      "H5''"     109.845    1.50
+5MC       "C4'"       "C5'"       "H5'"     109.624    1.50
+5MC       "C4'"       "C5'"      "H5''"     109.624    1.50
+5MC       "H5'"       "C5'"      "H5''"     108.472    1.50
+5MC       "C5'"       "C4'"       "O4'"     109.615    1.50
+5MC       "C5'"       "C4'"       "C3'"     116.008    1.52
+5MC       "C5'"       "C4'"       "H4'"     108.268    1.50
+5MC       "O4'"       "C4'"       "C3'"     104.439    1.50
+5MC       "O4'"       "C4'"       "H4'"     108.698    1.50
+5MC       "C3'"       "C4'"       "H4'"     109.363    1.86
+5MC       "C4'"       "O4'"       "C1'"     109.578    1.50
+5MC       "C4'"       "C3'"       "O3'"     111.281    2.46
+5MC       "C4'"       "C3'"       "C2'"     102.071    1.50
+5MC       "C4'"       "C3'"       "H3'"     110.452    2.54
+5MC       "O3'"       "C3'"       "C2'"     111.993    3.00
+5MC       "O3'"       "C3'"       "H3'"     110.380    1.67
+5MC       "C2'"       "C3'"       "H3'"     110.108    1.66
+5MC       "C3'"       "O3'"      "HO3'"     108.744    3.00
+5MC       "C3'"       "C2'"       "O2'"     112.861    2.52
+5MC       "C3'"       "C2'"       "C1'"     101.269    1.50
+5MC       "C3'"       "C2'"       "H2'"     110.799    1.82
+5MC       "O2'"       "C2'"       "C1'"     109.476    3.00
+5MC       "O2'"       "C2'"       "H2'"     111.022    1.77
+5MC       "C1'"       "C2'"       "H2'"     110.760    1.63
+5MC       "C2'"       "O2'"      "HO2'"     109.449    1.85
+5MC       "O4'"       "C1'"       "C2'"     106.825    1.50
+5MC       "O4'"       "C1'"          N1     108.667    1.50
+5MC       "O4'"       "C1'"       "H1'"     109.327    1.50
+5MC       "C2'"       "C1'"          N1     112.859    1.50
+5MC       "C2'"       "C1'"       "H1'"     109.776    1.83
+5MC          N1       "C1'"       "H1'"     109.166    1.50
+5MC       "C1'"          N1          C2     118.572    2.26
+5MC       "C1'"          N1          C6     121.186    1.50
+5MC          C2          N1          C6     120.242    1.50
+5MC          N1          C2          O2     118.953    1.50
+5MC          N1          C2          N3     118.440    1.50
+5MC          O2          C2          N3     122.606    1.50
+5MC          C2          N3          C4     119.913    1.50
+5MC          N3          C4          N4     117.013    1.55
+5MC          N3          C4          C5     121.550    1.50
+5MC          N4          C4          C5     121.437    1.50
+5MC          C4          N4        HN41     119.860    1.50
+5MC          C4          N4        HN42     119.860    1.50
+5MC        HN41          N4        HN42     120.280    1.85
+5MC          C4          C5          C6     117.857    1.50
+5MC          C4          C5         CM5     120.410    1.50
+5MC          C6          C5         CM5     121.734    1.50
+5MC          N1          C6          C5     121.998    1.50
+5MC          N1          C6          H6     118.660    1.56
+5MC          C5          C6          H6     119.342    1.50
+5MC          C5         CM5        HM51     109.580    1.50
+5MC          C5         CM5        HM52     109.580    1.50
+5MC          C5         CM5        HM53     109.580    1.50
+5MC        HM51         CM5        HM52     109.348    1.50
+5MC        HM51         CM5        HM53     109.348    1.50
+5MC        HM52         CM5        HM53     109.348    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+5MC     C2e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+5MC     C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+5MC     C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+5MC     C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+5MC     C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+5MC     C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+5MC     C3e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+5MC     C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+5MC     C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+5MC     C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+5MC     C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+5MC     C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+5MC     alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+5MC     beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+5MC     epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+5MC     gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+5MC     sp3_sp3_52      "C3'"     "C2'"     "O2'"     "HO2'"    180.000       10.00     3     
+5MC       const_sp2_sp2_4          O2          C2          N1       "C1'"       0.000     5.0     2
+5MC              const_18          C5          C6          N1       "C1'"     180.000    10.0     2
+5MC       const_sp2_sp2_6          O2          C2          N3          C4     180.000     5.0     2
+5MC       const_sp2_sp2_8          N4          C4          N3          C2     180.000     5.0     2
+5MC             sp2_sp2_3          N3          C4          N4        HN41       0.000     5.0     2
+5MC              const_12          N4          C4          C5         CM5       0.000    10.0     2
+5MC              const_15         CM5          C5          C6          N1     180.000    10.0     2
+5MC             sp2_sp3_7          C4          C5         CM5        HM51     150.000    10.0     6
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+5MC    chir_1    P    "O5'"    OP2    OP3    both
+5MC    chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+5MC    chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+5MC    chir_4    "C2'"    "O2'"    "C1'"    "C3'"    negative
+5MC    chir_5    "C1'"    "O4'"    N1    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+5MC    plan-1       "C1'"   0.020
+5MC    plan-1          C2   0.020
+5MC    plan-1          C4   0.020
+5MC    plan-1          C5   0.020
+5MC    plan-1          C6   0.020
+5MC    plan-1         CM5   0.020
+5MC    plan-1          H6   0.020
+5MC    plan-1          N1   0.020
+5MC    plan-1          N3   0.020
+5MC    plan-1          N4   0.020
+5MC    plan-1          O2   0.020
+5MC    plan-2          C4   0.020
+5MC    plan-2        HN41   0.020
+5MC    plan-2        HN42   0.020
+5MC    plan-2          N4   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+5MC           SMILES              ACDLabs 10.04                                                                                                               O=C1N=C(N)C(=CN1C2OC(C(O)C2O)COP(=O)(O)O)C
+5MC SMILES_CANONICAL               CACTVS 3.341                                                                                           CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N=C1N
+5MC           SMILES               CACTVS 3.341                                                                                                 CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N=C1N
+5MC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                           CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
+5MC           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                             CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
+5MC            InChI                InChI  1.03 InChI=1S/C10H16N3O8P/c1-4-2-13(10(16)12-8(4)11)9-7(15)6(14)5(21-9)3-20-22(17,18)19/h2,5-7,9,14-15H,3H2,1H3,(H2,11,12,16)(H2,17,18,19)/t5-,6-,7-,9-/m1/s1
+5MC         InChIKey                InChI  1.03                                                                                                                              NJQONZSFUKNYOY-JXOAFFINSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+5MC acedrg               243         "dictionary generator"                  
+5MC acedrg_database      11          "data source"                           
+5MC rdkit                2017.03.2   "Chemoinformatics tool"
+5MC refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/5MU.cif b/image_analysis/structure_refinement/monomers/5MU.cif
new file mode 100644
index 000000000..cec03d0f6
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/5MU.cif
@@ -0,0 +1,266 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+5MU 5MU "5-METHYLURIDINE 5'-MONOPHOSPHATE" RNA 35 22 .
+
+data_comp_5MU
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+5MU N1     N NR6  0  45.964 22.742 42.610
+5MU C2     C CR6  0  46.310 21.509 42.078
+5MU N3     N NR16 0  45.881 21.292 40.788
+5MU C4     C CR6  0  45.162 22.161 39.983
+5MU C5     C CR6  0  44.836 23.436 40.589
+5MU C5M    C CH3  0  44.058 24.436 39.786
+5MU C6     C CR16 0  45.249 23.665 41.851
+5MU O2     O O    0  46.944 20.657 42.690
+5MU O4     O O    0  44.849 21.819 38.838
+5MU "C1'"  C CH1  0  46.396 23.062 43.999
+5MU "C2'"  C CH1  0  47.646 23.950 44.041
+5MU "O2'"  O OH1  0  48.573 23.414 44.962
+5MU "C3'"  C CH1  0  47.081 25.308 44.482
+5MU "C4'"  C CH1  0  45.911 24.881 45.376
+5MU "O3'"  O OH1  0  48.020 26.094 45.207
+5MU "O4'"  O O2   0  45.356 23.744 44.672
+5MU "C5'"  C CH2  0  44.839 25.915 45.625
+5MU "O5'"  O O2   0  44.216 26.287 44.368
+5MU P      P P    0  43.153 27.501 44.357
+5MU OP1    O O    0  42.658 27.605 42.927
+5MU OP2    O OP   -1 43.921 28.730 44.805
+5MU OP3    O OP   -1 42.060 27.102 45.331
+5MU HN3    H H    0  46.097 20.497 40.440
+5MU H71    H H    0  43.917 25.242 40.310
+5MU H72    H H    0  43.197 24.059 39.541
+5MU H73    H H    0  44.550 24.660 38.980
+5MU H6     H H    0  45.037 24.501 42.250
+5MU "H1'"  H H    0  46.577 22.230 44.486
+5MU "H2'"  H H    0  48.047 24.022 43.151
+5MU "HO2'" H H    0  49.240 23.936 45.028
+5MU "H3'"  H H    0  46.752 25.810 43.693
+5MU "H4'"  H H    0  46.255 24.578 46.244
+5MU "HO3'" H H    0  47.644 26.816 45.448
+5MU "H5'"  H H    0  45.241 26.713 46.049
+5MU "H5''" H H    0  44.158 25.544 46.239
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+5MU N1    C2     SINGLE y 1.376 0.0100 1.376 0.0100
+5MU N1    C6     SINGLE y 1.386 0.0100 1.386 0.0100
+5MU N1    "C1'"  SINGLE n 1.476 0.0133 1.476 0.0133
+5MU C2    N3     SINGLE y 1.373 0.0100 1.373 0.0100
+5MU C2    O2     DOUBLE n 1.224 0.0111 1.224 0.0111
+5MU N3    C4     SINGLE y 1.383 0.0100 1.383 0.0100
+5MU C4    C5     SINGLE y 1.446 0.0100 1.446 0.0100
+5MU C4    O4     DOUBLE n 1.234 0.0141 1.234 0.0141
+5MU C5    C5M    SINGLE n 1.500 0.0100 1.500 0.0100
+5MU C5    C6     DOUBLE y 1.343 0.0112 1.343 0.0112
+5MU "C1'" "C2'"  SINGLE n 1.529 0.0100 1.529 0.0100
+5MU "C1'" "O4'"  SINGLE n 1.412 0.0100 1.412 0.0100
+5MU "C2'" "O2'"  SINGLE n 1.412 0.0100 1.412 0.0100
+5MU "C2'" "C3'"  SINGLE n 1.533 0.0109 1.533 0.0109
+5MU "C3'" "C4'"  SINGLE n 1.535 0.0100 1.535 0.0100
+5MU "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+5MU "C4'" "O4'"  SINGLE n 1.451 0.0111 1.451 0.0111
+5MU "C4'" "C5'"  SINGLE n 1.509 0.0100 1.509 0.0100
+5MU "C5'" "O5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+5MU "O5'" P      SINGLE n 1.614 0.0178 1.614 0.0178
+5MU P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+5MU P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+5MU P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+5MU N3    HN3    SINGLE n 1.016 0.0100 0.893 0.0200
+5MU C5M   H71    SINGLE n 1.089 0.0100 0.971 0.0135
+5MU C5M   H72    SINGLE n 1.089 0.0100 0.971 0.0135
+5MU C5M   H73    SINGLE n 1.089 0.0100 0.971 0.0135
+5MU C6    H6     SINGLE n 1.082 0.0130 0.951 0.0200
+5MU "C1'" "H1'"  SINGLE n 1.089 0.0100 0.981 0.0118
+5MU "C2'" "H2'"  SINGLE n 1.089 0.0100 0.978 0.0200
+5MU "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+5MU "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+5MU "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+5MU "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+5MU "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+5MU "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+5MU C2    N1    C6     121.243 1.50
+5MU C2    N1    "C1'"  117.446 1.50
+5MU C6    N1    "C1'"  121.311 1.50
+5MU N1    C2    N3     114.786 1.50
+5MU N1    C2    O2     122.872 1.50
+5MU N3    C2    O2     122.342 1.50
+5MU C2    N3    C4     127.106 1.50
+5MU C2    N3    HN3    115.584 1.79
+5MU C4    N3    HN3    117.311 1.81
+5MU N3    C4    C5     115.265 1.50
+5MU N3    C4    O4     119.787 1.50
+5MU C5    C4    O4     124.948 1.50
+5MU C4    C5    C5M    118.650 1.50
+5MU C4    C5    C6     118.305 1.50
+5MU C5M   C5    C6     123.045 1.50
+5MU C5    C5M   H71    109.652 1.50
+5MU C5    C5M   H72    109.652 1.50
+5MU C5    C5M   H73    109.652 1.50
+5MU H71   C5M   H72    109.348 1.50
+5MU H71   C5M   H73    109.348 1.50
+5MU H72   C5M   H73    109.348 1.50
+5MU N1    C6    C5     123.296 1.50
+5MU N1    C6    H6     117.926 1.56
+5MU C5    C6    H6     118.779 1.68
+5MU N1    "C1'" "C2'"  112.859 1.50
+5MU N1    "C1'" "O4'"  108.667 1.50
+5MU N1    "C1'" "H1'"  109.166 1.50
+5MU "C2'" "C1'" "O4'"  106.825 1.50
+5MU "C2'" "C1'" "H1'"  109.776 1.83
+5MU "O4'" "C1'" "H1'"  109.327 1.50
+5MU "C1'" "C2'" "O2'"  109.476 3.00
+5MU "C1'" "C2'" "C3'"  101.269 1.50
+5MU "C1'" "C2'" "H2'"  110.760 1.63
+5MU "O2'" "C2'" "C3'"  112.861 2.52
+5MU "O2'" "C2'" "H2'"  111.022 1.77
+5MU "C3'" "C2'" "H2'"  110.799 1.82
+5MU "C2'" "O2'" "HO2'" 109.449 1.85
+5MU "C2'" "C3'" "C4'"  102.071 1.50
+5MU "C2'" "C3'" "O3'"  111.993 3.00
+5MU "C2'" "C3'" "H3'"  110.108 1.66
+5MU "C4'" "C3'" "O3'"  111.281 2.46
+5MU "C4'" "C3'" "H3'"  110.452 2.54
+5MU "O3'" "C3'" "H3'"  110.380 1.67
+5MU "C3'" "C4'" "O4'"  104.439 1.50
+5MU "C3'" "C4'" "C5'"  116.008 1.52
+5MU "C3'" "C4'" "H4'"  109.363 1.86
+5MU "O4'" "C4'" "C5'"  109.615 1.50
+5MU "O4'" "C4'" "H4'"  108.698 1.50
+5MU "C5'" "C4'" "H4'"  108.268 1.50
+5MU "C3'" "O3'" "HO3'" 108.744 3.00
+5MU "C1'" "O4'" "C4'"  109.578 1.50
+5MU "C4'" "C5'" "O5'"  109.342 1.50
+5MU "C4'" "C5'" "H5'"  109.624 1.50
+5MU "C4'" "C5'" "H5''" 109.624 1.50
+5MU "O5'" "C5'" "H5'"  109.845 1.50
+5MU "O5'" "C5'" "H5''" 109.845 1.50
+5MU "H5'" "C5'" "H5''" 108.472 1.50
+5MU "C5'" "O5'" P      118.783 1.50
+5MU "O5'" P     OP1    105.808 2.07
+5MU "O5'" P     OP2    105.808 2.07
+5MU "O5'" P     OP3    105.808 2.07
+5MU OP1   P     OP2    112.864 1.69
+5MU OP1   P     OP3    112.864 1.69
+5MU OP2   P     OP3    112.864 1.69
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+5MU C2e-chi         "O4'" "C1'" N1    C2     210.000 10.000 6
+5MU C2e-nyu0        "C4'" "O4'" "C1'" "C2"   340.700 6.300  1
+5MU C2e-nyu1        "O4'" "C1'" "C2'" "C3'"  32.800  4.900  1
+5MU C2e-nyu2        "C1'" "C2'" "C3'" "C4'"  326.9   3.600  1
+5MU C2e-nyu3        "C2'" "C3'" "C4'" "O4'"  22.600  4.500  1
+5MU C2e-nyu4        "C3'" "C4'" "O4'" "C1'"  357.700 6.100  1
+5MU C3e-chi         "O4'" "C1'" N1    C2     210.000 10.000 6
+5MU C3e-nyu0        "C4'" "O4'" "C1'" "C2'"  2.8     6.100  1
+5MU C3e-nyu1        "O4'" "C1'" "C2'" "C3'"  335.00  4.900  1
+5MU C3e-nyu2        "C1'" "C2'" "C3'" "C4'"  35.9    2.800  1
+5MU C3e-nyu3        "C2'" "C3'" "C4'" "O4'"  324.700 3.100  1
+5MU C3e-nyu4        "C3'" "C4'" "O4'" "C1'"  20.500  5.100  1
+5MU alpha           "C5'" "O5'" P     OP3    -60.000 10.00  3
+5MU beta            P     "O5'" "C5'" "C4'"  180.000 10.00  3
+5MU epsi            "C4'" "C3'" "O3'" "HO3'" 180.000 10.00  3
+5MU gamma           "O5'" "C5'" "C4'" "C3'"  180.000 10.00  3
+5MU const_sp2_sp2_3 O2    C2    N1    C6     180.000 5.0    2
+5MU const_21        C5    C6    N1    C2     0.000   10.0   2
+5MU sp3_sp3_34      "C1'" "C2'" "O2'" "HO2'" 180.000 10.0   3
+5MU const_sp2_sp2_7 O2    C2    N3    C4     180.000 5.0    2
+5MU const_11        O4    C4    N3    C2     180.000 10.0   2
+5MU const_16        O4    C4    C5    C5M    0.000   10.0   2
+5MU sp2_sp3_7       C4    C5    C5M   H71    150.000 10.0   6
+5MU const_19        C5M   C5    C6    N1     180.000 10.0   2
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+5MU chir_1 "C1'" "O4'" N1    "C2'" negative
+5MU chir_2 "C2'" "O2'" "C1'" "C3'" negative
+5MU chir_3 "C3'" "O3'" "C4'" "C2'" positive
+5MU chir_4 "C4'" "O4'" "C3'" "C5'" negative
+5MU chir_5 P     "O5'" OP2   OP3   both
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+5MU plan-1 "C1'" 0.020
+5MU plan-1 C2    0.020
+5MU plan-1 C4    0.020
+5MU plan-1 C5    0.020
+5MU plan-1 C5M   0.020
+5MU plan-1 C6    0.020
+5MU plan-1 H6    0.020
+5MU plan-1 HN3   0.020
+5MU plan-1 N1    0.020
+5MU plan-1 N3    0.020
+5MU plan-1 O2    0.020
+5MU plan-1 O4    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+5MU SMILES           ACDLabs              10.04 O=C1NC(=O)N(C=C1C)C2OC(C(O)C2O)COP(=O)(O)O
+5MU SMILES_CANONICAL CACTVS               3.341 CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)NC1=O
+5MU SMILES           CACTVS               3.341 CC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)NC1=O
+5MU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
+5MU SMILES           "OpenEye OEToolkits" 1.5.0 CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
+5MU InChI            InChI                1.03  InChI=1S/C10H15N2O9P/c1-4-2-12(10(16)11-8(4)15)9-7(14)6(13)5(21-9)3-20-22(17,18)19/h2,5-7,9,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/t5-,6-,7-,9-/m1/s1
+5MU InChIKey         InChI                1.03  IGWHDMPTQKSDTL-JXOAFFINSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+5MU acedrg          243       "dictionary generator"
+5MU acedrg_database 11        "data source"
+5MU rdkit           2017.03.2 "Chemoinformatics tool"
+5MU refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/7MG.cif b/image_analysis/structure_refinement/monomers/7MG.cif
new file mode 100644
index 000000000..17dafc8c9
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/7MG.cif
@@ -0,0 +1,308 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+7MG 7MG "7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE" RNA 41 25 .
+
+data_comp_7MG
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+7MG P      P P    0  36.755 11.551 18.304
+7MG OP1    O O    0  37.842 12.410 17.686
+7MG OP2    O OP   -1 35.360 12.088 18.045
+7MG OP3    O OP   -1 36.894 10.081 17.952
+7MG "O5'"  O O2   0  36.974 11.645 19.900
+7MG "C5'"  C CH2  0  36.067 10.924 20.772
+7MG "C4'"  C CH1  0  36.506 11.088 22.207
+7MG "O4'"  O O2   0  37.856 10.573 22.349
+7MG "C3'"  C CH1  0  36.546 12.531 22.736
+7MG "O3'"  O OH1  0  35.933 12.618 24.017
+7MG "C2'"  C CH1  0  38.028 12.882 22.708
+7MG "O2'"  O OH1  0  38.387 13.794 23.729
+7MG "C1'"  C CH1  0  38.659 11.524 23.021
+7MG N9     N NR5  0  40.065 11.364 22.595
+7MG C8     C CH2  0  40.895 12.383 21.944
+7MG N7     N NR5  0  42.179 11.711 21.783
+7MG C5     C CR56 0  42.096 10.393 22.267
+7MG C6     C CR6  0  43.053 9.354  22.315
+7MG O6     O O    0  44.218 9.367  21.927
+7MG N1     N NR16 0  42.512 8.199  22.893
+7MG C2     C CR6  0  41.228 8.062  23.362
+7MG N2     N NH2  0  40.894 6.876  23.884
+7MG N3     N NRD6 0  40.334 9.040  23.317
+7MG C4     C CR56 0  40.795 10.194 22.764
+7MG CM7    C CH3  0  43.334 12.377 21.203
+7MG "H5'"  H H    0  36.065 9.964  20.533
+7MG "H5''" H H    0  35.148 11.275 20.664
+7MG "H4'"  H H    0  35.901 10.557 22.768
+7MG "H3'"  H H    0  36.091 13.140 22.099
+7MG "HO3'" H H    0  36.051 13.402 24.323
+7MG "H2'"  H H    0  38.278 13.222 21.823
+7MG "HO2'" H H    0  39.220 13.942 23.778
+7MG "H1'"  H H    0  38.572 11.340 23.987
+7MG H81    H H    0  40.524 12.630 21.083
+7MG H82    H H    0  40.988 13.166 22.507
+7MG HN1    H H    0  43.041 7.506  22.961
+7MG HN21   H H    0  40.414 6.841  24.617
+7MG HN22   H H    0  41.156 6.137  23.490
+7MG HM71   H H    0  44.116 11.808 21.264
+7MG HM72   H H    0  43.505 13.205 21.682
+7MG HM73   H H    0  43.157 12.579 20.269
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+7MG P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+7MG P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+7MG P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+7MG P     "O5'"  SINGLE n 1.614 0.0178 1.614 0.0178
+7MG "O5'" "C5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+7MG "C5'" "C4'"  SINGLE n 1.509 0.0100 1.509 0.0100
+7MG "C4'" "O4'"  SINGLE n 1.450 0.0100 1.450 0.0100
+7MG "C4'" "C3'"  SINGLE n 1.535 0.0100 1.535 0.0100
+7MG "O4'" "C1'"  SINGLE n 1.416 0.0117 1.416 0.0117
+7MG "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+7MG "C3'" "C2'"  SINGLE n 1.517 0.0200 1.517 0.0200
+7MG "C2'" "O2'"  SINGLE n 1.412 0.0200 1.412 0.0200
+7MG "C2'" "C1'"  SINGLE n 1.529 0.0100 1.529 0.0100
+7MG "C1'" N9     SINGLE n 1.466 0.0175 1.466 0.0175
+7MG N9    C8     SINGLE n 1.461 0.0141 1.461 0.0141
+7MG N9    C4     SINGLE n 1.376 0.0200 1.376 0.0200
+7MG C8    N7     SINGLE n 1.461 0.0141 1.461 0.0141
+7MG N7    C5     SINGLE n 1.405 0.0200 1.405 0.0200
+7MG N7    CM7    SINGLE n 1.453 0.0100 1.453 0.0100
+7MG C5    C6     SINGLE y 1.393 0.0169 1.393 0.0169
+7MG C5    C4     DOUBLE y 1.389 0.0200 1.389 0.0200
+7MG C6    O6     DOUBLE n 1.228 0.0131 1.228 0.0131
+7MG C6    N1     SINGLE y 1.394 0.0121 1.394 0.0121
+7MG N1    C2     SINGLE y 1.371 0.0108 1.371 0.0108
+7MG C2    N2     SINGLE n 1.337 0.0113 1.337 0.0113
+7MG C2    N3     DOUBLE y 1.323 0.0117 1.323 0.0117
+7MG N3    C4     SINGLE y 1.348 0.0185 1.348 0.0185
+7MG "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+7MG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+7MG "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+7MG "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+7MG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+7MG "C2'" "H2'"  SINGLE n 1.089 0.0100 0.981 0.0200
+7MG "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+7MG "C1'" "H1'"  SINGLE n 1.089 0.0100 0.987 0.0200
+7MG C8    H81    SINGLE n 1.089 0.0100 0.970 0.0140
+7MG C8    H82    SINGLE n 1.089 0.0100 0.970 0.0140
+7MG N1    HN1    SINGLE n 1.016 0.0100 0.873 0.0200
+7MG N2    HN21   SINGLE n 1.016 0.0100 0.877 0.0200
+7MG N2    HN22   SINGLE n 1.016 0.0100 0.877 0.0200
+7MG CM7   HM71   SINGLE n 1.089 0.0100 0.972 0.0143
+7MG CM7   HM72   SINGLE n 1.089 0.0100 0.972 0.0143
+7MG CM7   HM73   SINGLE n 1.089 0.0100 0.972 0.0143
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+7MG OP1   P     OP2    112.864 1.69
+7MG OP1   P     OP3    112.864 1.69
+7MG OP1   P     "O5'"  105.808 2.07
+7MG OP2   P     OP3    112.864 1.69
+7MG OP2   P     "O5'"  105.808 2.07
+7MG OP3   P     "O5'"  105.808 2.07
+7MG P     "O5'" "C5'"  118.783 1.50
+7MG "O5'" "C5'" "C4'"  109.342 1.50
+7MG "O5'" "C5'" "H5'"  109.845 1.50
+7MG "O5'" "C5'" "H5''" 109.845 1.50
+7MG "C4'" "C5'" "H5'"  109.624 1.50
+7MG "C4'" "C5'" "H5''" 109.624 1.50
+7MG "H5'" "C5'" "H5''" 108.472 1.50
+7MG "C5'" "C4'" "O4'"  109.123 1.50
+7MG "C5'" "C4'" "C3'"  116.008 1.52
+7MG "C5'" "C4'" "H4'"  108.268 1.50
+7MG "O4'" "C4'" "C3'"  104.641 1.82
+7MG "O4'" "C4'" "H4'"  110.466 2.90
+7MG "C3'" "C4'" "H4'"  109.363 1.86
+7MG "C4'" "O4'" "C1'"  109.585 1.50
+7MG "C4'" "C3'" "O3'"  111.281 2.46
+7MG "C4'" "C3'" "C2'"  101.879 2.07
+7MG "C4'" "C3'" "H3'"  110.452 2.54
+7MG "O3'" "C3'" "C2'"  114.431 3.00
+7MG "O3'" "C3'" "H3'"  110.380 1.67
+7MG "C2'" "C3'" "H3'"  107.880 2.97
+7MG "C3'" "O3'" "HO3'" 108.744 3.00
+7MG "C3'" "C2'" "O2'"  112.637 3.00
+7MG "C3'" "C2'" "C1'"  101.599 1.50
+7MG "C3'" "C2'" "H2'"  111.559 3.00
+7MG "O2'" "C2'" "C1'"  107.625 3.00
+7MG "O2'" "C2'" "H2'"  111.144 3.00
+7MG "C1'" "C2'" "H2'"  111.470 3.00
+7MG "C2'" "O2'" "HO2'" 112.841 3.00
+7MG "O4'" "C1'" "C2'"  106.883 1.50
+7MG "O4'" "C1'" N9     109.703 1.83
+7MG "O4'" "C1'" "H1'"  108.522 3.00
+7MG "C2'" "C1'" N9     113.039 1.91
+7MG "C2'" "C1'" "H1'"  111.147 3.00
+7MG N9    "C1'" "H1'"  110.672 1.50
+7MG "C1'" N9    C8     124.243 2.92
+7MG "C1'" N9    C4     126.514 3.00
+7MG C8    N9    C4     109.243 1.81
+7MG N9    C8    N7     102.166 2.68
+7MG N9    C8    H81    111.296 1.50
+7MG N9    C8    H82    111.296 1.50
+7MG N7    C8    H81    111.296 1.50
+7MG N7    C8    H82    111.296 1.50
+7MG H81   C8    H82    111.548 2.37
+7MG C8    N7    C5     111.115 1.81
+7MG C8    N7    CM7    122.962 1.87
+7MG C5    N7    CM7    125.923 1.74
+7MG N7    C5    C6     130.345 1.50
+7MG N7    C5    C4     109.346 2.06
+7MG C6    C5    C4     120.309 1.50
+7MG C5    C6    O6     128.640 1.50
+7MG C5    C6    N1     110.185 1.50
+7MG O6    C6    N1     121.175 1.50
+7MG C6    N1    C2     125.932 1.50
+7MG C6    N1    HN1    116.880 1.50
+7MG C2    N1    HN1    117.188 1.50
+7MG N1    C2    N2     116.451 1.50
+7MG N1    C2    N3     123.751 1.50
+7MG N2    C2    N3     119.799 1.50
+7MG C2    N2    HN21   119.815 1.50
+7MG C2    N2    HN22   119.815 1.50
+7MG HN21  N2    HN22   120.371 1.96
+7MG C2    N3    C4     114.279 1.50
+7MG N9    C4    C5     107.842 2.06
+7MG N9    C4    N3     126.614 1.94
+7MG C5    C4    N3     125.545 1.50
+7MG N7    CM7   HM71   109.783 1.50
+7MG N7    CM7   HM72   109.783 1.50
+7MG N7    CM7   HM73   109.783 1.50
+7MG HM71  CM7   HM72   109.459 1.50
+7MG HM71  CM7   HM73   109.459 1.50
+7MG HM72  CM7   HM73   109.459 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+7MG C2e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+7MG C2e-nyu0        "C4'" "O4'" "C1'" "C2'"  340.700 6.300  1
+7MG C2e-nyu1        "O4'" "C1'" "C2'" "C3'"  32.800  4.900  1
+7MG C2e-nyu2        "C1'" "C2'" "C3'" "C4'"  326.9   3.600  1
+7MG C2e-nyu3        "C2'" "C3'" "C4'" "O4'"  22.600  4.500  1
+7MG C2e-nyu4        "C3'" "C4'" "O4'" "C1'"  357.700 6.100  1
+7MG C3e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+7MG C3e-nyu0        "C4'" "O4'" "C1'" "C2'"  2.8     6.100  1
+7MG C3e-nyu1        "O4'" "C1'" "C2'" "C3'"  335.00  4.900  1
+7MG C3e-nyu2        "C1'" "C2'" "C3'" "C4'"  35.9    2.800  1
+7MG C3e-nyu3        "C2'" "C3'" "C4'" "O4'"  324.700 3.100  1
+7MG C3e-nyu4        "C3'" "C4'" "O4'" "C1'"  20.500  5.100  1
+7MG alpha           "C5'" "O5'" P     OP3    -60.000 10.00  3
+7MG beta            P     "O5'" "C5'" "C4'"  180.000 10.00  3
+7MG epsi            "C4'" "C3'" "O3'" "HO3'" 180.000 10.00  3
+7MG gamma           "O5'" "C5'" "C4'" "C3'"  180.000 10.00  3
+7MG sp3_sp3_52      "C3'" "C2'" "O2'" "HO2'" 180.000 10.00  3
+7MG sp2_sp3_4       "C1'" N9    C8    N7     180.000 10.0   6
+7MG sp2_sp2_6       C5    C4    N9    "C1'"  180.000 5.0    2
+7MG sp2_sp3_10      CM7   N7    C8    N9     180.000 10.0   6
+7MG sp2_sp2_4       C6    C5    N7    CM7    0.000   5.0    2
+7MG sp2_sp3_19      C8    N7    CM7   HM71   150.000 10.0   6
+7MG const_sp2_sp2_4 N7    C5    C6    O6     0.000   5.0    2
+7MG const_17        N9    C4    C5    N7     0.000   10.0   2
+7MG const_sp2_sp2_7 O6    C6    N1    C2     180.000 5.0    2
+7MG const_11        N2    C2    N1    C6     180.000 10.0   2
+7MG sp2_sp2_9       N1    C2    N2    HN21   180.000 5.0    2
+7MG const_14        N2    C2    N3    C4     180.000 10.0   2
+7MG const_16        N9    C4    N3    C2     180.000 10.0   2
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+7MG chir_1 P     "O5'" OP2   OP3   both
+7MG chir_2 "C4'" "O4'" "C3'" "C5'" negative
+7MG chir_3 "C3'" "O3'" "C4'" "C2'" positive
+7MG chir_4 "C2'" "O2'" "C1'" "C3'" negative
+7MG chir_5 "C1'" "O4'" N9    "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+7MG plan-1 C2    0.020
+7MG plan-1 C4    0.020
+7MG plan-1 C5    0.020
+7MG plan-1 C6    0.020
+7MG plan-1 HN1   0.020
+7MG plan-1 N1    0.020
+7MG plan-1 N2    0.020
+7MG plan-1 N3    0.020
+7MG plan-1 N7    0.020
+7MG plan-1 N9    0.020
+7MG plan-1 O6    0.020
+7MG plan-2 "C1'" 0.020
+7MG plan-2 C4    0.020
+7MG plan-2 C8    0.020
+7MG plan-2 N9    0.020
+7MG plan-3 C5    0.020
+7MG plan-3 C8    0.020
+7MG plan-3 CM7   0.020
+7MG plan-3 N7    0.020
+7MG plan-4 C2    0.020
+7MG plan-4 HN21  0.020
+7MG plan-4 HN22  0.020
+7MG plan-4 N2    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+7MG SMILES           ACDLabs              10.04 O=C1C=2N(CN(C=2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O)C
+7MG SMILES_CANONICAL CACTVS               3.341 CN1CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C3=C1C(=O)NC(=N3)N
+7MG SMILES           CACTVS               3.341 CN1CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C3=C1C(=O)NC(=N3)N
+7MG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CN1CN(C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O
+7MG SMILES           "OpenEye OEToolkits" 1.5.0 CN1CN(C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)O)O)O
+7MG InChI            InChI                1.03  InChI=1S/C11H18N5O8P/c1-15-3-16(8-5(15)9(19)14-11(12)13-8)10-7(18)6(17)4(24-10)2-23-25(20,21)22/h4,6-7,10,17-18H,2-3H2,1H3,(H2,20,21,22)(H3,12,13,14,19)/t4-,6-,7-,10-/m1/s1
+7MG InChIKey         InChI                1.03  ZMWJGXGSWZFZPJ-KQYNXXCUSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+7MG acedrg          243       "dictionary generator"
+7MG acedrg_database 11        "data source"
+7MG rdkit           2017.03.2 "Chemoinformatics tool"
+7MG refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/A.cif b/image_analysis/structure_refinement/monomers/A.cif
new file mode 100644
index 000000000..613cc0cea
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/A.cif
@@ -0,0 +1,271 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+A     A       "ADENOSINE-5'-MONOPHOSPHATE"     RNA     35     23     .     
+#
+data_comp_A
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+A       OP3     O       OP      -1      22.184      9.416       -6.467      
+A       P       P       P       0       23.061      10.073      -7.517      
+A       OP1     O       O       0       22.426      10.079      -8.894      
+A       OP2     O       OP      -1      24.478      9.532       -7.523      
+A       "O5'"   O       O2      0       23.184      11.622      -7.081      
+A       "C5'"   C       CH2     0       23.997      12.510      -7.889      
+A       "C4'"   C       CH1     0       23.959      13.900      -7.302      
+A       "O4'"   O       O2      0       24.489      13.865      -5.952      
+A       "C3'"   C       CH1     0       24.795      14.957      -8.033      
+A       "O3'"   O       OH1     0       24.040      15.590      -9.060      
+A       "C2'"   C       CH1     0       25.162      15.917      -6.899      
+A       "O2'"   O       OH1     0       24.142      16.849      -6.609      
+A       "C1'"   C       CH1     0       25.367      14.950      -5.735      
+A       N9      N       NR5     0       26.737      14.457      -5.612      
+A       C8      C       CR15    0       27.206      13.184      -5.839      
+A       N7      N       NRD5    0       28.493      13.056      -5.636      
+A       C5      C       CR56    0       28.908      14.321      -5.248      
+A       C6      C       CR6     0       30.172      14.840      -4.890      
+A       N6      N       NH2     0       31.287      14.114      -4.866      
+A       N1      N       NRD6    0       30.240      16.155      -4.553      
+A       C2      C       CR16    0       29.111      16.881      -4.579      
+A       N3      N       NRD6    0       27.874      16.499      -4.898      
+A       C4      C       CR56    0       27.833      15.193      -5.227      
+A       "H5'"   H       H       0       23.653      12.531      -8.815      
+A       "H5''"  H       H       0       24.931      12.185      -7.909      
+A       "H4'"   H       H       0       23.023      14.194      -7.269      
+A       "H3'"   H       H       0       25.613      14.544      -8.414      
+A       "HO3'"  H       H       0       24.512      16.204      -9.407      
+A       "H2'"   H       H       0       26.008      16.394      -7.110      
+A       "HO2'"  H       H       0       24.469      17.486      -6.152      
+A       "H1'"   H       H       0       25.116      15.407      -4.901      
+A       H8      H       H       0       26.656      12.471      -6.115      
+A       H61     H       H       0       31.972      14.381      -4.386      
+A       H62     H       H       0       31.333      13.371      -5.331      
+A       H2      H       H       0       29.207      17.789      -4.337      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+A       OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+A         P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+A         P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+A         P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+A     "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+A     "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+A     "C4'"       "O4'"      SINGLE       n     1.451  0.0100     1.451  0.0100
+A     "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+A     "O4'"       "C1'"      SINGLE       n     1.409  0.0100     1.409  0.0100
+A     "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+A     "C3'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+A     "C2'"       "O2'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+A     "C2'"       "C1'"      SINGLE       n     1.525  0.0100     1.525  0.0100
+A     "C1'"          N9      SINGLE       n     1.458  0.0100     1.458  0.0100
+A        N9          C8      SINGLE       y     1.372  0.0100     1.372  0.0100
+A        N9          C4      SINGLE       y     1.374  0.0101     1.374  0.0101
+A        C8          N7      DOUBLE       y     1.310  0.0100     1.310  0.0100
+A        N7          C5      SINGLE       y     1.388  0.0100     1.388  0.0100
+A        C5          C6      SINGLE       y     1.408  0.0100     1.408  0.0100
+A        C5          C4      DOUBLE       y     1.381  0.0100     1.381  0.0100
+A        C6          N6      SINGLE       n     1.330  0.0100     1.330  0.0100
+A        C6          N1      DOUBLE       y     1.354  0.0100     1.354  0.0100
+A        N1          C2      SINGLE       y     1.339  0.0100     1.339  0.0100
+A        C2          N3      DOUBLE       y     1.330  0.0100     1.330  0.0100
+A        N3          C4      SINGLE       y     1.343  0.0100     1.343  0.0100
+A     "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+A     "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+A     "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+A     "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+A     "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+A     "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.994  0.0200
+A     "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+A     "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.984  0.0200
+A        C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+A        N6         H61      SINGLE       n     1.016  0.0100     0.877  0.0200
+A        N6         H62      SINGLE       n     1.016  0.0100     0.877  0.0200
+A        C2          H2      SINGLE       n     1.082  0.0130     0.945  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+A       OP3           P         OP1     112.864    1.69
+A       OP3           P         OP2     112.864    1.69
+A       OP3           P       "O5'"     105.808    2.07
+A       OP1           P         OP2     112.864    1.69
+A       OP1           P       "O5'"     105.808    2.07
+A       OP2           P       "O5'"     105.808    2.07
+A         P       "O5'"       "C5'"     118.783    1.50
+A     "O5'"       "C5'"       "C4'"     109.342    1.50
+A     "O5'"       "C5'"       "H5'"     109.845    1.50
+A     "O5'"       "C5'"      "H5''"     109.845    1.50
+A     "C4'"       "C5'"       "H5'"     109.624    1.50
+A     "C4'"       "C5'"      "H5''"     109.624    1.50
+A     "H5'"       "C5'"      "H5''"     108.472    1.50
+A     "C5'"       "C4'"       "O4'"     109.123    1.50
+A     "C5'"       "C4'"       "C3'"     116.008    1.52
+A     "C5'"       "C4'"       "H4'"     108.268    1.50
+A     "O4'"       "C4'"       "C3'"     105.388    1.50
+A     "O4'"       "C4'"       "H4'"     108.947    1.50
+A     "C3'"       "C4'"       "H4'"     109.363    1.86
+A     "C4'"       "O4'"       "C1'"     109.903    1.50
+A     "C4'"       "C3'"       "O3'"     111.281    2.46
+A     "C4'"       "C3'"       "C2'"     102.602    1.50
+A     "C4'"       "C3'"       "H3'"     110.452    2.54
+A     "O3'"       "C3'"       "C2'"     111.581    2.83
+A     "O3'"       "C3'"       "H3'"     110.380    1.67
+A     "C2'"       "C3'"       "H3'"     110.504    1.75
+A     "C3'"       "O3'"      "HO3'"     108.744    3.00
+A     "C3'"       "C2'"       "O2'"     112.782    2.45
+A     "C3'"       "C2'"       "C1'"     101.239    1.50
+A     "C3'"       "C2'"       "H2'"     110.596    1.51
+A     "O2'"       "C2'"       "C1'"     111.715    2.69
+A     "O2'"       "C2'"       "H2'"     110.448    1.97
+A     "C1'"       "C2'"       "H2'"     110.636    1.70
+A     "C2'"       "O2'"      "HO2'"     109.103    2.13
+A     "O4'"       "C1'"       "C2'"     106.047    1.50
+A     "O4'"       "C1'"          N9     108.477    1.50
+A     "O4'"       "C1'"       "H1'"     109.807    1.50
+A     "C2'"       "C1'"          N9     113.824    1.50
+A     "C2'"       "C1'"       "H1'"     109.015    1.50
+A        N9       "C1'"       "H1'"     109.561    1.50
+A     "C1'"          N9          C8     126.848    1.91
+A     "C1'"          N9          C4     127.459    1.80
+A        C8          N9          C4     105.693    1.50
+A        N9          C8          N7     113.469    1.50
+A        N9          C8          H8     123.206    1.50
+A        N7          C8          H8     123.326    1.50
+A        C8          N7          C5     104.739    1.50
+A        N7          C5          C6     132.250    1.50
+A        N7          C5          C4     110.483    1.50
+A        C6          C5          C4     117.267    1.50
+A        C5          C6          N6     123.792    1.50
+A        C5          C6          N1     117.409    1.50
+A        N6          C6          N1     118.799    1.50
+A        C6          N6         H61     119.723    1.50
+A        C6          N6         H62     119.723    1.50
+A       H61          N6         H62     120.554    1.88
+A        C6          N1          C2     118.521    1.50
+A        N1          C2          N3     129.332    1.50
+A        N1          C2          H2     115.313    1.50
+A        N3          C2          H2     115.355    1.50
+A        C2          N3          C4     110.982    1.50
+A        N9          C4          C5     105.616    1.50
+A        N9          C4          N3     127.895    1.50
+A        C5          C4          N3     126.489    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+A       C2e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+A       C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+A       C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+A       C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+A       C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+A       C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+A       C3e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+A       C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+A       C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+A       C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+A       C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+A       C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+A       alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+A       beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+A       epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+A       gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+A       sp3_sp3_52      "C3'"     "C2'"     "O2'"     "HO2'"    180.000       10.00     3     
+A              const_14          N7          C8          N9       "C1'"     180.000    10.0     2
+A              const_26          C5          C4          N9       "C1'"     180.000    10.0     2
+A              const_17          N9          C8          N7          C5       0.000    10.0     2
+A              const_20          C6          C5          N7          C8     180.000    10.0     2
+A       const_sp2_sp2_4          N7          C5          C6          N6       0.000     5.0     2
+A              const_21          N9          C4          C5          N7       0.000    10.0     2
+A             sp2_sp2_1          C5          C6          N6         H61     180.000     5.0     2
+A       const_sp2_sp2_6          N6          C6          N1          C2     180.000     5.0     2
+A       const_sp2_sp2_7          N3          C2          N1          C6       0.000     5.0     2
+A       const_sp2_sp2_9          N1          C2          N3          C4       0.000     5.0     2
+A              const_12          N9          C4          N3          C2     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+A  chir_1    P    "O5'"    OP3    OP2    both
+A  chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+A  chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+A  chir_4    "C2'"    "O2'"    "C1'"    "C3'"    negative
+A  chir_5    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+A  plan-1       "C1'"   0.020
+A  plan-1          C2   0.020
+A  plan-1          C4   0.020
+A  plan-1          C5   0.020
+A  plan-1          C6   0.020
+A  plan-1          C8   0.020
+A  plan-1          H2   0.020
+A  plan-1          H8   0.020
+A  plan-1          N1   0.020
+A  plan-1          N3   0.020
+A  plan-1          N6   0.020
+A  plan-1          N7   0.020
+A  plan-1          N9   0.020
+A  plan-2          C6   0.020
+A  plan-2         H61   0.020
+A  plan-2         H62   0.020
+A  plan-2          N6   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+A           SMILES              ACDLabs 10.04                                                                                                                       O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
+A SMILES_CANONICAL               CACTVS 3.341                                                                                                   Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
+A           SMILES               CACTVS 3.341                                                                                                         Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
+A SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                               c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
+A           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
+A            InChI                InChI  1.03 InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+A         InChIKey                InChI  1.03                                                                                                                                    UDMBCSSLTHHNCD-KQYNXXCUSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+A   acedrg               243         "dictionary generator"                  
+A   acedrg_database      11          "data source"                           
+A   rdkit                2017.03.2   "Chemoinformatics tool"
+A   refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/ACT.cif b/image_analysis/structure_refinement/monomers/ACT.cif
new file mode 100644
index 000000000..c46c46947
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ACT.cif
@@ -0,0 +1,104 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ACT     ACT      "ACETATE ION"     NON-POLYMER     7     4     .     
+#
+data_comp_ACT
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ACT     C       C       C       0       50.652      -7.080      41.537      
+ACT     O       O       O       0       50.915      -7.323      42.732      
+ACT     OXT     O       OC      -1      51.516      -6.945      40.648      
+ACT     CH3     C       CH3     0       49.181      -6.939      41.139      
+ACT     H1      H       H       0       49.117      -6.760      40.187      
+ACT     H2      H       H       0       48.780      -6.205      41.632      
+ACT     H3      H       H       0       48.708      -7.761      41.345      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ACT           C           O      DOUBLE       n     1.247  0.0187     1.247  0.0187
+ACT           C         OXT      SINGLE       n     1.247  0.0187     1.247  0.0187
+ACT           C         CH3      SINGLE       n     1.530  0.0200     1.530  0.0200
+ACT         CH3          H1      SINGLE       n     1.089  0.0100     0.971  0.0140
+ACT         CH3          H2      SINGLE       n     1.089  0.0100     0.971  0.0140
+ACT         CH3          H3      SINGLE       n     1.089  0.0100     0.971  0.0140
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ACT           O           C         OXT     123.884    1.50
+ACT           O           C         CH3     118.052    1.94
+ACT         OXT           C         CH3     118.052    1.94
+ACT           C         CH3          H1     109.670    1.50
+ACT           C         CH3          H2     109.670    1.50
+ACT           C         CH3          H3     109.670    1.50
+ACT          H1         CH3          H2     109.424    1.50
+ACT          H1         CH3          H3     109.424    1.50
+ACT          H2         CH3          H3     109.424    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ACT             sp2_sp3_1           O           C         CH3          H1       0.000    10.0     6
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ACT    plan-1           C   0.020
+ACT    plan-1         CH3   0.020
+ACT    plan-1           O   0.020
+ACT    plan-1         OXT   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ACT           SMILES              ACDLabs 10.04                              "[O-]C(=O)C"
+ACT SMILES_CANONICAL               CACTVS 3.341                                CC([O-])=O
+ACT           SMILES               CACTVS 3.341                                CC([O-])=O
+ACT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                CC(=O)[O-]
+ACT           SMILES "OpenEye OEToolkits" 1.5.0                                CC(=O)[O-]
+ACT            InChI                InChI  1.03 InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
+ACT         InChIKey                InChI  1.03               QTBSBXVTEAMEQO-UHFFFAOYSA-M
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ACT acedrg               243         "dictionary generator"                  
+ACT acedrg_database      11          "data source"                           
+ACT rdkit                2017.03.2   "Chemoinformatics tool"
+ACT refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/ADP.cif b/image_analysis/structure_refinement/monomers/ADP.cif
new file mode 100644
index 000000000..8dd58c16f
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ADP.cif
@@ -0,0 +1,283 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ADP     ADP      "ADENOSINE-5'-DIPHOSPHATE"     NON-POLYMER     39     27     .     
+#
+data_comp_ADP
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ADP     PB      P       P       0       46.212      2.934       41.132      
+ADP     O1B     O       O       0       47.352      3.648       41.816      
+ADP     O2B     O       OP      -1      46.188      3.167       39.642      
+ADP     O3B     O       OP      -1      46.138      1.471       41.495      
+ADP     PA      P       P       0       43.308      3.312       41.426      
+ADP     O1A     O       O       0       42.947      3.885       40.095      
+ADP     O2A     O       OP      -1      43.043      1.862       41.663      
+ADP     O3A     O       O2      0       44.860      3.603       41.708      
+ADP     "O5'"   O       O2      0       42.611      4.176       42.585      
+ADP     "C5'"   C       CH2     0       42.803      5.614       42.612      
+ADP     "C4'"   C       CH1     0       41.916      6.217       43.675      
+ADP     "O4'"   O       O2      0       42.237      5.618       44.957      
+ADP     "C3'"   C       CH1     0       42.060      7.727       43.896      
+ADP     "O3'"   O       OH1     0       40.836      8.295       44.347      
+ADP     "C2'"   C       CH1     0       43.161      7.787       44.958      
+ADP     "O2'"   O       OH1     0       43.139      8.979       45.714      
+ADP     "C1'"   C       CH1     0       42.808      6.577       45.819      
+ADP     N9      N       NR5     0       43.956      5.966       46.481      
+ADP     C8      C       CR15    0       45.032      5.373       45.867      
+ADP     N7      N       NRD5    0       45.919      4.902       46.707      
+ADP     C5      C       CR56    0       45.398      5.197       47.958      
+ADP     C6      C       CR6     0       45.872      4.953       49.266      
+ADP     N6      N       NH2     0       47.020      4.334       49.530      
+ADP     N1      N       NRD6    0       45.104      5.379       50.303      
+ADP     C2      C       CR16    0       43.948      6.003       50.029      
+ADP     N3      N       NRD6    0       43.405      6.285       48.844      
+ADP     C4      C       CR56    0       44.184      5.853       47.833      
+ADP     "H5'1"  H       H       0       42.575      6.001       41.731      
+ADP     "H5'2"  H       H       0       43.749      5.824       42.811      
+ADP     "H4'"   H       H       0       40.984      6.008       43.451      
+ADP     "H3'"   H       H       0       42.359      8.172       43.061      
+ADP     "HO3'"  H       H       0       40.903      9.141       44.325      
+ADP     "H2'"   H       H       0       44.053      7.669       44.537      
+ADP     "HO2'"  H       H       0       43.755      8.950       46.297      
+ADP     "H1'"   H       H       0       42.146      6.850       46.493      
+ADP     H8      H       H       0       45.124      5.315       44.932      
+ADP     HN61    H       H       0       47.233      4.142       50.360      
+ADP     HN62    H       H       0       47.561      4.119       48.873      
+ADP     H2      H       H       0       43.448      6.281       50.782      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ADP          PB         O1B      DOUBLE       n     1.509  0.0200     1.509  0.0200
+ADP          PB         O2B      SINGLE       n     1.509  0.0200     1.509  0.0200
+ADP          PB         O3B      SINGLE       n     1.509  0.0200     1.509  0.0200
+ADP          PB         O3A      SINGLE       n     1.614  0.0178     1.614  0.0178
+ADP          PA         O1A      DOUBLE       n     1.493  0.0122     1.493  0.0122
+ADP          PA         O2A      SINGLE       n     1.493  0.0122     1.493  0.0122
+ADP          PA         O3A      SINGLE       n     1.604  0.0133     1.604  0.0133
+ADP          PA       "O5'"      SINGLE       n     1.604  0.0133     1.604  0.0133
+ADP       "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+ADP       "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+ADP       "C4'"       "O4'"      SINGLE       n     1.451  0.0100     1.451  0.0100
+ADP       "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+ADP       "O4'"       "C1'"      SINGLE       n     1.409  0.0100     1.409  0.0100
+ADP       "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+ADP       "C3'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+ADP       "C2'"       "O2'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+ADP       "C2'"       "C1'"      SINGLE       n     1.525  0.0100     1.525  0.0100
+ADP       "C1'"          N9      SINGLE       n     1.458  0.0100     1.458  0.0100
+ADP          N9          C8      SINGLE       y     1.372  0.0100     1.372  0.0100
+ADP          N9          C4      SINGLE       y     1.374  0.0101     1.374  0.0101
+ADP          C8          N7      DOUBLE       y     1.310  0.0100     1.310  0.0100
+ADP          N7          C5      SINGLE       y     1.388  0.0100     1.388  0.0100
+ADP          C5          C6      SINGLE       y     1.408  0.0100     1.408  0.0100
+ADP          C5          C4      DOUBLE       y     1.381  0.0100     1.381  0.0100
+ADP          C6          N6      SINGLE       n     1.330  0.0100     1.330  0.0100
+ADP          C6          N1      DOUBLE       y     1.354  0.0100     1.354  0.0100
+ADP          N1          C2      SINGLE       y     1.339  0.0100     1.339  0.0100
+ADP          C2          N3      DOUBLE       y     1.330  0.0100     1.330  0.0100
+ADP          N3          C4      SINGLE       y     1.343  0.0100     1.343  0.0100
+ADP       "C5'"      "H5'1"      SINGLE       n     1.089  0.0100     0.989  0.0200
+ADP       "C5'"      "H5'2"      SINGLE       n     1.089  0.0100     0.989  0.0200
+ADP       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+ADP       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+ADP       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+ADP       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.994  0.0200
+ADP       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+ADP       "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.984  0.0200
+ADP          C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+ADP          N6        HN61      SINGLE       n     1.016  0.0100     0.877  0.0200
+ADP          N6        HN62      SINGLE       n     1.016  0.0100     0.877  0.0200
+ADP          C2          H2      SINGLE       n     1.082  0.0130     0.945  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ADP         O1B          PB         O2B     112.716    1.50
+ADP         O1B          PB         O3B     112.716    1.50
+ADP         O1B          PB         O3A     105.965    2.38
+ADP         O2B          PB         O3B     112.716    1.50
+ADP         O2B          PB         O3A     105.965    2.38
+ADP         O3B          PB         O3A     105.965    2.38
+ADP         O1A          PA         O2A     118.411    2.35
+ADP         O1A          PA         O3A     108.816    2.14
+ADP         O1A          PA       "O5'"     109.410    1.50
+ADP         O2A          PA         O3A     108.816    2.14
+ADP         O2A          PA       "O5'"     109.410    1.50
+ADP         O3A          PA       "O5'"     101.065    1.97
+ADP          PB         O3A          PA     132.584    3.00
+ADP          PA       "O5'"       "C5'"     118.553    2.41
+ADP       "O5'"       "C5'"       "C4'"     109.342    1.50
+ADP       "O5'"       "C5'"      "H5'1"     109.845    1.50
+ADP       "O5'"       "C5'"      "H5'2"     109.845    1.50
+ADP       "C4'"       "C5'"      "H5'1"     109.624    1.50
+ADP       "C4'"       "C5'"      "H5'2"     109.624    1.50
+ADP      "H5'1"       "C5'"      "H5'2"     108.472    1.50
+ADP       "C5'"       "C4'"       "O4'"     109.123    1.50
+ADP       "C5'"       "C4'"       "C3'"     116.008    1.52
+ADP       "C5'"       "C4'"       "H4'"     108.268    1.50
+ADP       "O4'"       "C4'"       "C3'"     105.388    1.50
+ADP       "O4'"       "C4'"       "H4'"     108.947    1.50
+ADP       "C3'"       "C4'"       "H4'"     109.363    1.86
+ADP       "C4'"       "O4'"       "C1'"     109.903    1.50
+ADP       "C4'"       "C3'"       "O3'"     111.281    2.46
+ADP       "C4'"       "C3'"       "C2'"     102.602    1.50
+ADP       "C4'"       "C3'"       "H3'"     110.452    2.54
+ADP       "O3'"       "C3'"       "C2'"     111.581    2.83
+ADP       "O3'"       "C3'"       "H3'"     110.380    1.67
+ADP       "C2'"       "C3'"       "H3'"     110.504    1.75
+ADP       "C3'"       "O3'"      "HO3'"     108.744    3.00
+ADP       "C3'"       "C2'"       "O2'"     112.782    2.45
+ADP       "C3'"       "C2'"       "C1'"     101.239    1.50
+ADP       "C3'"       "C2'"       "H2'"     110.596    1.51
+ADP       "O2'"       "C2'"       "C1'"     111.715    2.69
+ADP       "O2'"       "C2'"       "H2'"     110.448    1.97
+ADP       "C1'"       "C2'"       "H2'"     110.636    1.70
+ADP       "C2'"       "O2'"      "HO2'"     109.103    2.13
+ADP       "O4'"       "C1'"       "C2'"     106.047    1.50
+ADP       "O4'"       "C1'"          N9     108.477    1.50
+ADP       "O4'"       "C1'"       "H1'"     109.807    1.50
+ADP       "C2'"       "C1'"          N9     113.824    1.50
+ADP       "C2'"       "C1'"       "H1'"     109.015    1.50
+ADP          N9       "C1'"       "H1'"     109.561    1.50
+ADP       "C1'"          N9          C8     126.848    1.91
+ADP       "C1'"          N9          C4     127.459    1.80
+ADP          C8          N9          C4     105.693    1.50
+ADP          N9          C8          N7     113.469    1.50
+ADP          N9          C8          H8     123.206    1.50
+ADP          N7          C8          H8     123.326    1.50
+ADP          C8          N7          C5     104.739    1.50
+ADP          N7          C5          C6     132.250    1.50
+ADP          N7          C5          C4     110.483    1.50
+ADP          C6          C5          C4     117.267    1.50
+ADP          C5          C6          N6     123.792    1.50
+ADP          C5          C6          N1     117.409    1.50
+ADP          N6          C6          N1     118.799    1.50
+ADP          C6          N6        HN61     119.723    1.50
+ADP          C6          N6        HN62     119.723    1.50
+ADP        HN61          N6        HN62     120.554    1.88
+ADP          C6          N1          C2     118.521    1.50
+ADP          N1          C2          N3     129.332    1.50
+ADP          N1          C2          H2     115.313    1.50
+ADP          N3          C2          H2     115.355    1.50
+ADP          C2          N3          C4     110.982    1.50
+ADP          N9          C4          C5     105.616    1.50
+ADP          N9          C4          N3     127.895    1.50
+ADP          C5          C4          N3     126.489    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ADP            sp3_sp3_27          PA         O3A          PB         O1B      60.000    10.0     3
+ADP             sp3_sp3_2       "C5'"       "C4'"       "O4'"       "C1'"     -60.000    10.0     3
+ADP            sp3_sp3_50       "O3'"       "C3'"       "C4'"       "C5'"     180.000    10.0     3
+ADP             sp3_sp3_4       "C2'"       "C1'"       "O4'"       "C4'"     -60.000    10.0     3
+ADP            sp3_sp3_55       "C4'"       "C3'"       "O3'"      "HO3'"     180.000    10.0     3
+ADP            sp3_sp3_20       "O2'"       "C2'"       "C3'"       "O3'"     -60.000    10.0     3
+ADP            sp3_sp3_58       "C3'"       "C2'"       "O2'"      "HO2'"     180.000    10.0     3
+ADP             sp3_sp3_8       "O4'"       "C1'"       "C2'"       "O2'"     180.000    10.0     3
+ADP             sp2_sp3_1          C8          N9       "C1'"       "O4'"     150.000    10.0     6
+ADP              const_14          N7          C8          N9       "C1'"     180.000    10.0     2
+ADP              const_26          C5          C4          N9       "C1'"     180.000    10.0     2
+ADP              const_17          N9          C8          N7          C5       0.000    10.0     2
+ADP              const_20          C6          C5          N7          C8     180.000    10.0     2
+ADP       const_sp2_sp2_4          N7          C5          C6          N6       0.000     5.0     2
+ADP              const_21          N9          C4          C5          N7       0.000    10.0     2
+ADP             sp2_sp2_1          C5          C6          N6        HN61     180.000     5.0     2
+ADP       const_sp2_sp2_6          N6          C6          N1          C2     180.000     5.0     2
+ADP       const_sp2_sp2_7          N3          C2          N1          C6       0.000     5.0     2
+ADP       const_sp2_sp2_9          N1          C2          N3          C4       0.000     5.0     2
+ADP              const_12          N9          C4          N3          C2     180.000    10.0     2
+ADP            sp3_sp3_30          PB         O3A          PA         O1A      60.000    10.0     3
+ADP            sp3_sp3_33       "C5'"       "O5'"          PA         O1A      60.000    10.0     3
+ADP            sp3_sp3_34       "C4'"       "C5'"       "O5'"          PA     180.000    10.0     3
+ADP            sp3_sp3_37       "O4'"       "C4'"       "C5'"       "O5'"     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ADP    chir_1    PB    O3A    O2B    O3B    both
+ADP    chir_2    PA    O3A    "O5'"    O2A    both
+ADP    chir_3    "C4'"    "O4'"    "C3'"    "C5'"    negative
+ADP    chir_4    "C3'"    "O3'"    "C4'"    "C2'"    positive
+ADP    chir_5    "C2'"    "O2'"    "C1'"    "C3'"    negative
+ADP    chir_6    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ADP    plan-1       "C1'"   0.020
+ADP    plan-1          C2   0.020
+ADP    plan-1          C4   0.020
+ADP    plan-1          C5   0.020
+ADP    plan-1          C6   0.020
+ADP    plan-1          C8   0.020
+ADP    plan-1          H2   0.020
+ADP    plan-1          H8   0.020
+ADP    plan-1          N1   0.020
+ADP    plan-1          N3   0.020
+ADP    plan-1          N6   0.020
+ADP    plan-1          N7   0.020
+ADP    plan-1          N9   0.020
+ADP    plan-2          C6   0.020
+ADP    plan-2        HN61   0.020
+ADP    plan-2        HN62   0.020
+ADP    plan-2          N6   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ADP           SMILES              ACDLabs 10.04                                                                                                                                     O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
+ADP SMILES_CANONICAL               CACTVS 3.341                                                                                                             Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
+ADP           SMILES               CACTVS 3.341                                                                                                                     Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
+ADP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                                          c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
+ADP           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                               c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
+ADP            InChI                InChI  1.03 InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+ADP         InChIKey                InChI  1.03                                                                                                                                                           XTWYTFMLZFPYCI-KQYNXXCUSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ADP acedrg               243         "dictionary generator"                  
+ADP acedrg_database      11          "data source"                           
+ADP rdkit                2017.03.2   "Chemoinformatics tool"
+ADP refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/ALA.cif b/image_analysis/structure_refinement/monomers/ALA.cif
new file mode 100644
index 000000000..be45c4253
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ALA.cif
@@ -0,0 +1,182 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ALA ALA ALANINE peptide 13 6 .
+
+data_comp_ALA
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ALA N N NT3 1 2.474 26.375 12.879
+ALA CA C CH1 0 1.190 26.935 13.368
+ALA C C C 0 1.429 28.314 13.990
+ALA O O O 0 2.253 28.383 14.929
+ALA CB C CH3 0 0.557 25.983 14.359
+ALA OXT O OC -1 0.782 29.274 13.516
+ALA H H H 0 3.050 26.285 13.567
+ALA H2 H H 0 2.832 26.925 12.260
+ALA H3 H H 0 2.330 25.565 12.507
+ALA HA H H 0 0.581 27.046 12.587
+ALA HB3 H H 0 -0.324 26.308 14.608
+ALA HB2 H H 0 1.113 25.921 15.155
+ALA HB1 H H 0 0.472 25.102 13.958
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ALA N n/a CA START
+ALA H N . .
+ALA H2 N . .
+ALA H3 N . .
+ALA CA N C .
+ALA HA CA . .
+ALA CB CA HB3 .
+ALA HB1 CB . .
+ALA HB2 CB . .
+ALA HB3 CB . .
+ALA C CA . END
+ALA O C . .
+ALA OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+ALA N N(CCCH)(H)3
+ALA CA C(CH3)(NH3)(COO)(H)
+ALA C C(CCHN)(O)2
+ALA O O(CCO)
+ALA CB C(CCHN)(H)3
+ALA OXT O(CCO)
+ALA H H(NCHH)
+ALA H2 H(NCHH)
+ALA H3 H(NCHH)
+ALA HA H(CCCN)
+ALA HB3 H(CCHH)
+ALA HB2 H(CCHH)
+ALA HB1 H(CCHH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ALA N CA SINGLE n 1.483 0.0100 1.483 0.0100
+ALA CA C SINGLE n 1.531 0.0100 1.531 0.0100
+ALA CA CB SINGLE n 1.513 0.0158 1.513 0.0158
+ALA C O DOUBLE n 1.251 0.0183 1.251 0.0183
+ALA C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+ALA N H SINGLE n 1.018 0.0520 0.902 0.0102
+ALA N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+ALA N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+ALA CA HA SINGLE n 1.092 0.0100 0.997 0.0200
+ALA CB HB3 SINGLE n 1.092 0.0100 0.972 0.0148
+ALA CB HB2 SINGLE n 1.092 0.0100 0.972 0.0148
+ALA CB HB1 SINGLE n 1.092 0.0100 0.972 0.0148
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ALA CA N H 109.611 2.03
+ALA CA N H2 109.611 2.03
+ALA CA N H3 109.611 2.03
+ALA H N H2 109.032 3.00
+ALA H N H3 109.032 3.00
+ALA H2 N H3 109.032 3.00
+ALA N CA C 109.720 1.50
+ALA N CA CB 109.927 1.50
+ALA N CA HA 108.247 1.50
+ALA C CA CB 111.515 1.50
+ALA C CA HA 108.267 1.50
+ALA CB CA HA 109.172 1.57
+ALA CA C O 117.191 2.33
+ALA CA C OXT 117.191 2.33
+ALA O C OXT 125.618 1.50
+ALA CA CB HB3 109.742 1.50
+ALA CA CB HB2 109.742 1.50
+ALA CA CB HB1 109.742 1.50
+ALA HB3 CB HB2 109.365 1.60
+ALA HB3 CB HB1 109.365 1.60
+ALA HB2 CB HB1 109.365 1.60
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ALA hh1 N CA CB HB3 180.000 10.0 3
+ALA sp3_sp3_1 C CA N H 180.000 10.0 3
+ALA sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ALA chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ALA plan-1 C 0.020
+ALA plan-1 CA 0.020
+ALA plan-1 O 0.020
+ALA plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ALA SMILES ACDLabs 10.04 O=C(O)C(N)C
+ALA SMILES_CANONICAL CACTVS 3.341 C[C@H](N)C(O)=O
+ALA SMILES CACTVS 3.341 C[CH](N)C(O)=O
+ALA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H](C(=O)O)N
+ALA SMILES "OpenEye OEToolkits" 1.5.0 CC(C(=O)O)N
+ALA InChI InChI 1.03 InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1
+ALA InChIKey InChI 1.03 QNAYBMKLOCPYGJ-REOHCLBHSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ALA acedrg 278 "dictionary generator"
+ALA acedrg_database 12 "data source"
+ALA rdkit 2019.09.1 "Chemoinformatics tool"
+ALA refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/AMP.cif b/image_analysis/structure_refinement/monomers/AMP.cif
new file mode 100644
index 000000000..af979b28b
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/AMP.cif
@@ -0,0 +1,279 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+AMP AMP "ADENOSINE MONOPHOSPHATE" NON-POLYMER 35 23 .
+
+data_comp_AMP
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+AMP P      P P    0  7.785  40.217 19.087
+AMP O1P    O O    0  7.126  41.546 19.404
+AMP O2P    O OP   -1 6.783  39.104 18.848
+AMP O3P    O OP   -1 8.858  39.838 20.091
+AMP "O5'"  O O2   0  8.550  40.429 17.682
+AMP "C5'"  C CH2  0  9.613  41.413 17.608
+AMP "C4'"  C CH1  0  10.179 41.441 16.209
+AMP "O4'"  O O2   0  10.693 40.125 15.878
+AMP "C3'"  C CH1  0  9.188  41.799 15.089
+AMP "O3'"  O OH1  0  9.786  42.675 14.141
+AMP "C2'"  C CH1  0  8.844  40.434 14.483
+AMP "O2'"  O OH1  0  8.453  40.504 13.128
+AMP "C1'"  C CH1  0  10.173 39.703 14.640
+AMP N9     N NR5  0  10.056 38.248 14.658
+AMP C8     C CR15 0  9.355  37.497 15.568
+AMP N7     N NRD5 0  9.424  36.209 15.347
+AMP C5     C CR56 0  10.226 36.096 14.221
+AMP C6     C CR6  0  10.678 34.979 13.484
+AMP N6     N NH2  0  10.371 33.721 13.791
+AMP N1     N NRD6 0  11.469 35.215 12.406
+AMP C2     C CR16 0  11.775 36.486 12.102
+AMP N3     N NRD6 0  11.408 37.609 12.720
+AMP C4     C CR56 0  10.625 37.349 13.785
+AMP "H5'1" H H    0  10.329 41.183 18.250
+AMP "H5'2" H H    0  9.260  42.307 17.841
+AMP "H4'"  H H    0  10.923 42.081 16.196
+AMP "H3'"  H H    0  8.376  42.217 15.476
+AMP "HO3'" H H    0  9.174  43.023 13.667
+AMP "H2'"  H H    0  8.135  39.989 15.017
+AMP "HO2'" H H    0  8.294  39.721 12.844
+AMP "H1'"  H H    0  10.777 39.979 13.915
+AMP H8     H H    0  8.867  37.874 16.281
+AMP HN61   H H    0  10.832 33.060 13.441
+AMP HN62   H H    0  9.709  33.556 14.343
+AMP H2     H H    0  12.327 36.601 11.344
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+AMP P     O1P    DOUBLE n 1.517 0.0192 1.517 0.0192
+AMP P     O2P    SINGLE n 1.517 0.0192 1.517 0.0192
+AMP P     O3P    SINGLE n 1.517 0.0192 1.517 0.0192
+AMP P     "O5'"  SINGLE n 1.614 0.0178 1.614 0.0178
+AMP "O5'" "C5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+AMP "C5'" "C4'"  SINGLE n 1.509 0.0100 1.509 0.0100
+AMP "C4'" "O4'"  SINGLE n 1.451 0.0100 1.451 0.0100
+AMP "C4'" "C3'"  SINGLE n 1.535 0.0100 1.535 0.0100
+AMP "O4'" "C1'"  SINGLE n 1.409 0.0100 1.409 0.0100
+AMP "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+AMP "C3'" "C2'"  SINGLE n 1.531 0.0100 1.531 0.0100
+AMP "C2'" "O2'"  SINGLE n 1.411 0.0100 1.411 0.0100
+AMP "C2'" "C1'"  SINGLE n 1.525 0.0100 1.525 0.0100
+AMP "C1'" N9     SINGLE n 1.458 0.0100 1.458 0.0100
+AMP N9    C8     SINGLE y 1.372 0.0100 1.372 0.0100
+AMP N9    C4     SINGLE y 1.374 0.0101 1.374 0.0101
+AMP C8    N7     DOUBLE y 1.310 0.0100 1.310 0.0100
+AMP N7    C5     SINGLE y 1.388 0.0100 1.388 0.0100
+AMP C5    C6     SINGLE y 1.408 0.0100 1.408 0.0100
+AMP C5    C4     DOUBLE y 1.381 0.0100 1.381 0.0100
+AMP C6    N6     SINGLE n 1.330 0.0100 1.330 0.0100
+AMP C6    N1     DOUBLE y 1.354 0.0100 1.354 0.0100
+AMP N1    C2     SINGLE y 1.339 0.0100 1.339 0.0100
+AMP C2    N3     DOUBLE y 1.330 0.0100 1.330 0.0100
+AMP N3    C4     SINGLE y 1.343 0.0100 1.343 0.0100
+AMP "C5'" "H5'1" SINGLE n 1.089 0.0100 0.989 0.0200
+AMP "C5'" "H5'2" SINGLE n 1.089 0.0100 0.989 0.0200
+AMP "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+AMP "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+AMP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+AMP "C2'" "H2'"  SINGLE n 1.089 0.0100 0.994 0.0200
+AMP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+AMP "C1'" "H1'"  SINGLE n 1.089 0.0100 0.984 0.0200
+AMP C8    H8     SINGLE n 1.082 0.0130 0.942 0.0170
+AMP N6    HN61   SINGLE n 1.016 0.0100 0.877 0.0200
+AMP N6    HN62   SINGLE n 1.016 0.0100 0.877 0.0200
+AMP C2    H2     SINGLE n 1.082 0.0130 0.945 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+AMP O1P    P     O2P    112.864 1.69
+AMP O1P    P     O3P    112.864 1.69
+AMP O1P    P     "O5'"  105.808 2.07
+AMP O2P    P     O3P    112.864 1.69
+AMP O2P    P     "O5'"  105.808 2.07
+AMP O3P    P     "O5'"  105.808 2.07
+AMP P      "O5'" "C5'"  118.783 1.50
+AMP "O5'"  "C5'" "C4'"  109.342 1.50
+AMP "O5'"  "C5'" "H5'1" 109.845 1.50
+AMP "O5'"  "C5'" "H5'2" 109.845 1.50
+AMP "C4'"  "C5'" "H5'1" 109.624 1.50
+AMP "C4'"  "C5'" "H5'2" 109.624 1.50
+AMP "H5'1" "C5'" "H5'2" 108.472 1.50
+AMP "C5'"  "C4'" "O4'"  109.123 1.50
+AMP "C5'"  "C4'" "C3'"  116.008 1.52
+AMP "C5'"  "C4'" "H4'"  108.268 1.50
+AMP "O4'"  "C4'" "C3'"  105.388 1.50
+AMP "O4'"  "C4'" "H4'"  108.947 1.50
+AMP "C3'"  "C4'" "H4'"  109.363 1.86
+AMP "C4'"  "O4'" "C1'"  109.903 1.50
+AMP "C4'"  "C3'" "O3'"  111.281 2.46
+AMP "C4'"  "C3'" "C2'"  102.602 1.50
+AMP "C4'"  "C3'" "H3'"  110.452 2.54
+AMP "O3'"  "C3'" "C2'"  111.581 2.83
+AMP "O3'"  "C3'" "H3'"  110.380 1.67
+AMP "C2'"  "C3'" "H3'"  110.504 1.75
+AMP "C3'"  "O3'" "HO3'" 108.744 3.00
+AMP "C3'"  "C2'" "O2'"  112.782 2.45
+AMP "C3'"  "C2'" "C1'"  101.239 1.50
+AMP "C3'"  "C2'" "H2'"  110.596 1.51
+AMP "O2'"  "C2'" "C1'"  111.715 2.69
+AMP "O2'"  "C2'" "H2'"  110.448 1.97
+AMP "C1'"  "C2'" "H2'"  110.636 1.70
+AMP "C2'"  "O2'" "HO2'" 109.103 2.13
+AMP "O4'"  "C1'" "C2'"  106.047 1.50
+AMP "O4'"  "C1'" N9     108.477 1.50
+AMP "O4'"  "C1'" "H1'"  109.807 1.50
+AMP "C2'"  "C1'" N9     113.824 1.50
+AMP "C2'"  "C1'" "H1'"  109.015 1.50
+AMP N9     "C1'" "H1'"  109.561 1.50
+AMP "C1'"  N9    C8     126.848 1.91
+AMP "C1'"  N9    C4     127.459 1.80
+AMP C8     N9    C4     105.693 1.50
+AMP N9     C8    N7     113.469 1.50
+AMP N9     C8    H8     123.206 1.50
+AMP N7     C8    H8     123.326 1.50
+AMP C8     N7    C5     104.739 1.50
+AMP N7     C5    C6     132.250 1.50
+AMP N7     C5    C4     110.483 1.50
+AMP C6     C5    C4     117.267 1.50
+AMP C5     C6    N6     123.792 1.50
+AMP C5     C6    N1     117.409 1.50
+AMP N6     C6    N1     118.799 1.50
+AMP C6     N6    HN61   119.723 1.50
+AMP C6     N6    HN62   119.723 1.50
+AMP HN61   N6    HN62   120.554 1.88
+AMP C6     N1    C2     118.521 1.50
+AMP N1     C2    N3     129.332 1.50
+AMP N1     C2    H2     115.313 1.50
+AMP N3     C2    H2     115.355 1.50
+AMP C2     N3    C4     110.982 1.50
+AMP N9     C4    C5     105.616 1.50
+AMP N9     C4    N3     127.895 1.50
+AMP C5     C4    N3     126.489 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+AMP sp3_sp3_27      "C5'" "O5'" P     O1P    60.000  10.0 3
+AMP sp3_sp3_52      "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
+AMP sp3_sp3_8       "O4'" "C1'" "C2'" "O2'"  180.000 10.0 3
+AMP sp2_sp3_1       C8    N9    "C1'" "O4'"  150.000 10.0 6
+AMP const_14        N7    C8    N9    "C1'"  180.000 10.0 2
+AMP const_26        C5    C4    N9    "C1'"  180.000 10.0 2
+AMP const_17        N9    C8    N7    C5     0.000   10.0 2
+AMP const_20        C6    C5    N7    C8     180.000 10.0 2
+AMP const_sp2_sp2_4 N7    C5    C6    N6     0.000   5.0  2
+AMP const_21        N9    C4    C5    N7     0.000   10.0 2
+AMP sp2_sp2_1       C5    C6    N6    HN61   180.000 5.0  2
+AMP const_sp2_sp2_6 N6    C6    N1    C2     180.000 5.0  2
+AMP const_sp2_sp2_7 N3    C2    N1    C6     0.000   5.0  2
+AMP const_sp2_sp2_9 N1    C2    N3    C4     0.000   5.0  2
+AMP const_12        N9    C4    N3    C2     180.000 10.0 2
+AMP sp3_sp3_28      "C4'" "C5'" "O5'" P      180.000 10.0 3
+AMP sp3_sp3_31      "O4'" "C4'" "C5'" "O5'"  180.000 10.0 3
+AMP sp3_sp3_2       "C5'" "C4'" "O4'" "C1'"  -60.000 10.0 3
+AMP sp3_sp3_44      "O3'" "C3'" "C4'" "C5'"  180.000 10.0 3
+AMP sp3_sp3_4       "C2'" "C1'" "O4'" "C4'"  -60.000 10.0 3
+AMP sp3_sp3_20      "O2'" "C2'" "C3'" "O3'"  -60.000 10.0 3
+AMP sp3_sp3_49      "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+AMP chir_1 P     "O5'" O2P   O3P   both
+AMP chir_2 "C4'" "O4'" "C3'" "C5'" negative
+AMP chir_3 "C3'" "O3'" "C4'" "C2'" positive
+AMP chir_4 "C2'" "O2'" "C1'" "C3'" negative
+AMP chir_5 "C1'" "O4'" N9    "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+AMP plan-1 "C1'" 0.020
+AMP plan-1 C2    0.020
+AMP plan-1 C4    0.020
+AMP plan-1 C5    0.020
+AMP plan-1 C6    0.020
+AMP plan-1 C8    0.020
+AMP plan-1 H2    0.020
+AMP plan-1 H8    0.020
+AMP plan-1 N1    0.020
+AMP plan-1 N3    0.020
+AMP plan-1 N6    0.020
+AMP plan-1 N7    0.020
+AMP plan-1 N9    0.020
+AMP plan-2 C6    0.020
+AMP plan-2 HN61  0.020
+AMP plan-2 HN62  0.020
+AMP plan-2 N6    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+AMP SMILES           ACDLabs              12.01 O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
+AMP InChI            InChI                1.03  InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+AMP InChIKey         InChI                1.03  UDMBCSSLTHHNCD-KQYNXXCUSA-N
+AMP SMILES_CANONICAL CACTVS               3.370 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
+AMP SMILES           CACTVS               3.370 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
+AMP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
+AMP SMILES           "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+AMP acedrg          243       "dictionary generator"
+AMP acedrg_database 11        "data source"
+AMP rdkit           2017.03.2 "Chemoinformatics tool"
+AMP refmac5         5.8.0238  "optimization tool"
+
+loop_
+_chem_comp_alias.comp_id
+_chem_comp_alias.group
+_chem_comp_alias.atom_id
+_chem_comp_alias.atom_id_standard
+AMP DNA/RNA O2P OP2
+AMP DNA/RNA O1P OP1
+AMP DNA/RNA O3P OP3
diff --git a/image_analysis/structure_refinement/monomers/ARG.cif b/image_analysis/structure_refinement/monomers/ARG.cif
new file mode 100644
index 000000000..f92a52e96
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ARG.cif
@@ -0,0 +1,284 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ARG ARG ARGININE peptide 27 12 .
+
+data_comp_ARG
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ARG N N NT3 1 70.130 14.992 90.045
+ARG CA C CH1 0 70.443 14.368 91.360
+ARG C C C 0 71.906 13.892 91.367
+ARG O O O 0 72.245 13.075 90.483
+ARG CB C CH2 0 69.504 13.191 91.652
+ARG CG C CH2 0 68.033 13.562 91.785
+ARG CD C CH2 0 67.166 12.373 92.178
+ARG NE N NC1 0 67.123 11.321 91.154
+ARG CZ C C 0 66.488 10.157 91.270
+ARG NH1 N NC2 0 65.818 9.861 92.371
+ARG NH2 N NC2 1 66.525 9.285 90.278
+ARG OXT O OC -1 72.653 14.357 92.256
+ARG H H H 0 70.064 14.355 89.409
+ARG H2 H H 0 70.776 15.575 89.808
+ARG H3 H H 0 69.349 15.441 90.092
+ARG HA H H 0 70.328 15.054 92.065
+ARG HB3 H H 0 69.794 12.761 92.485
+ARG HB2 H H 0 69.597 12.533 90.931
+ARG HG3 H H 0 67.712 13.922 90.930
+ARG HG2 H H 0 67.938 14.265 92.464
+ARG HD3 H H 0 66.255 12.690 92.348
+ARG HD2 H H 0 67.510 11.993 93.012
+ARG HE H H 0 67.542 11.468 90.404
+ARG HH11 H H 0 66.247 9.797 93.142
+ARG HH12 H H 0 64.945 9.729 92.332
+ARG HH21 H H 0 66.438 9.566 89.444
+ARG HH22 H H 0 66.637 8.426 90.452
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ARG N n/a CA START
+ARG H N . .
+ARG H2 N . .
+ARG H3 N . .
+ARG CA N C .
+ARG HA CA . .
+ARG CB CA CG .
+ARG HB3 CB . .
+ARG HB2 CB . .
+ARG CG CB CD .
+ARG HG3 CG . .
+ARG HG2 CG . .
+ARG CD CG NE .
+ARG HD3 CD . .
+ARG HD2 CD . .
+ARG NE CD CZ .
+ARG HE NE . .
+ARG CZ NE NH2 .
+ARG NH1 CZ HH12 .
+ARG HH11 NH1 . .
+ARG HH12 NH1 . .
+ARG NH2 CZ HH22 .
+ARG HH21 NH2 . .
+ARG HH22 NH2 . .
+ARG C CA . END
+ARG O C . .
+ARG OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+ARG N N(CCCH)(H)3
+ARG CA C(CCHH)(NH3)(COO)(H)
+ARG C C(CCHN)(O)2
+ARG O O(CCO)
+ARG CB C(CCHH)(CCHN)(H)2
+ARG CG C(CCHH)(CHHN)(H)2
+ARG CD C(CCHH)(NCH)(H)2
+ARG NE N(CCHH)(CNN)(H)
+ARG CZ C(NCH)(NHH)2
+ARG NH1 N(CNN)(H)2
+ARG NH2 N(CNN)(H)2
+ARG OXT O(CCO)
+ARG H H(NCHH)
+ARG H2 H(NCHH)
+ARG H3 H(NCHH)
+ARG HA H(CCCN)
+ARG HB3 H(CCCH)
+ARG HB2 H(CCCH)
+ARG HG3 H(CCCH)
+ARG HG2 H(CCCH)
+ARG HD3 H(CCHN)
+ARG HD2 H(CCHN)
+ARG HE H(NCC)
+ARG HH11 H(NCH)
+ARG HH12 H(NCH)
+ARG HH21 H(NCH)
+ARG HH22 H(NCH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ARG N CA SINGLE n 1.487 0.0100 1.487 0.0100
+ARG CA C SINGLE n 1.538 0.0113 1.538 0.0113
+ARG CA CB SINGLE n 1.533 0.0100 1.533 0.0100
+ARG C O DOUBLE n 1.251 0.0183 1.251 0.0183
+ARG C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+ARG CB CG SINGLE n 1.522 0.0100 1.522 0.0100
+ARG CG CD SINGLE n 1.521 0.0200 1.521 0.0200
+ARG CD NE SINGLE n 1.467 0.0100 1.467 0.0100
+ARG NE CZ SINGLE n 1.327 0.0153 1.327 0.0153
+ARG CZ NH1 SINGLE n 1.321 0.0134 1.321 0.0134
+ARG CZ NH2 DOUBLE n 1.321 0.0134 1.321 0.0134
+ARG N H SINGLE n 1.018 0.0520 0.902 0.0102
+ARG N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+ARG N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+ARG CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+ARG CB HB3 SINGLE n 1.092 0.0100 0.981 0.0141
+ARG CB HB2 SINGLE n 1.092 0.0100 0.981 0.0141
+ARG CG HG3 SINGLE n 1.092 0.0100 0.982 0.0161
+ARG CG HG2 SINGLE n 1.092 0.0100 0.982 0.0161
+ARG CD HD3 SINGLE n 1.092 0.0100 0.979 0.0175
+ARG CD HD2 SINGLE n 1.092 0.0100 0.979 0.0175
+ARG NE HE SINGLE n 1.013 0.0120 0.871 0.0200
+ARG NH1 HH11 SINGLE n 1.013 0.0120 0.884 0.0200
+ARG NH1 HH12 SINGLE n 1.013 0.0120 0.884 0.0200
+ARG NH2 HH21 SINGLE n 1.013 0.0120 0.884 0.0200
+ARG NH2 HH22 SINGLE n 1.013 0.0120 0.884 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ARG CA N H 109.990 3.00
+ARG CA N H2 109.990 3.00
+ARG CA N H3 109.990 3.00
+ARG H N H2 109.032 3.00
+ARG H N H3 109.032 3.00
+ARG H2 N H3 109.032 3.00
+ARG N CA C 109.258 1.50
+ARG N CA CB 110.440 2.46
+ARG N CA HA 108.387 1.58
+ARG C CA CB 111.059 3.00
+ARG C CA HA 108.774 1.79
+ARG CB CA HA 109.080 2.33
+ARG CA C O 117.148 1.60
+ARG CA C OXT 117.148 1.60
+ARG O C OXT 125.704 1.50
+ARG CA CB CG 114.160 3.00
+ARG CA CB HB3 108.677 1.74
+ARG CA CB HB2 108.677 1.74
+ARG CG CB HB3 108.721 1.50
+ARG CG CB HB2 108.721 1.50
+ARG HB3 CB HB2 107.655 1.50
+ARG CB CG CD 112.025 3.00
+ARG CB CG HG3 109.216 1.64
+ARG CB CG HG2 109.216 1.64
+ARG CD CG HG3 108.991 1.50
+ARG CD CG HG2 108.991 1.50
+ARG HG3 CG HG2 107.958 2.23
+ARG CG CD NE 112.275 3.00
+ARG CG CD HD3 109.172 2.35
+ARG CG CD HD2 109.172 2.35
+ARG NE CD HD3 109.193 1.50
+ARG NE CD HD2 109.193 1.50
+ARG HD3 CD HD2 107.932 1.94
+ARG CD NE CZ 124.614 2.32
+ARG CD NE HE 117.935 2.37
+ARG CZ NE HE 117.451 2.77
+ARG NE CZ NH1 120.032 1.90
+ARG NE CZ NH2 120.032 1.90
+ARG NH1 CZ NH2 119.937 1.95
+ARG CZ NH1 HH11 119.775 3.00
+ARG CZ NH1 HH12 119.775 3.00
+ARG HH11 NH1 HH12 120.450 3.00
+ARG CZ NH2 HH21 119.775 3.00
+ARG CZ NH2 HH22 119.775 3.00
+ARG HH21 NH2 HH22 120.450 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ARG chi1 N CA CB CG -60.000 10.0 3
+ARG chi2 CA CB CG CD 180.000 10.0 3
+ARG chi3 CB CG CD NE 60.000 10.0 3
+ARG chi4 CG CD NE CZ 180.000 10.0 6
+ARG chi5 CD NE CZ NH2 0.000 5.0 2
+ARG hh1 NE CZ NH1 HH12 0.000 5.0 2
+ARG hh2 NE CZ NH2 HH22 0.000 5.0 2
+ARG sp3_sp3_1 C CA N H 180.000 10.0 3
+ARG sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ARG chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ARG plan-1 C 0.020
+ARG plan-1 CA 0.020
+ARG plan-1 O 0.020
+ARG plan-1 OXT 0.020
+ARG plan-2 CD 0.020
+ARG plan-2 CZ 0.020
+ARG plan-2 HE 0.020
+ARG plan-2 NE 0.020
+ARG plan-3 CZ 0.020
+ARG plan-3 NE 0.020
+ARG plan-3 NH1 0.020
+ARG plan-3 NH2 0.020
+ARG plan-4 CZ 0.020
+ARG plan-4 HH11 0.020
+ARG plan-4 HH12 0.020
+ARG plan-4 NH1 0.020
+ARG plan-5 CZ 0.020
+ARG plan-5 HH21 0.020
+ARG plan-5 HH22 0.020
+ARG plan-5 NH2 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ARG SMILES ACDLabs 10.04 O=C(O)C(N)CCCN\C(=[NH2+])N
+ARG SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCCNC(N)=[NH2+])C(O)=O
+ARG SMILES CACTVS 3.341 N[CH](CCCNC(N)=[NH2+])C(O)=O
+ARG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
+ARG SMILES "OpenEye OEToolkits" 1.5.0 C(CC(C(=O)O)N)CNC(=[NH2+])N
+ARG InChI InChI 1.03 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
+ARG InChIKey InChI 1.03 ODKSFYDXXFIFQN-BYPYZUCNSA-O
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ARG acedrg 278 "dictionary generator"
+ARG acedrg_database 12 "data source"
+ARG rdkit 2019.09.1 "Chemoinformatics tool"
+ARG refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/ASN.cif b/image_analysis/structure_refinement/monomers/ASN.cif
new file mode 100644
index 000000000..50e7df06f
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ASN.cif
@@ -0,0 +1,214 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ASN ASN ASPARAGINE peptide 17 9 .
+
+data_comp_ASN
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ASN N N NT3 1 14.911 16.808 19.868
+ASN CA C CH1 0 15.816 17.894 20.345
+ASN C C C 0 15.155 18.638 21.512
+ASN O O O 0 15.771 18.659 22.602
+ASN CB C CH2 0 16.178 18.868 19.226
+ASN CG C C 0 16.898 18.214 18.068
+ASN OD1 O O 0 17.108 16.995 18.059
+ASN ND2 N NH2 0 17.282 19.004 17.075
+ASN OXT O OC -1 14.046 19.172 21.292
+ASN H H H 0 14.283 17.146 19.316
+ASN H2 H H 0 14.499 16.402 20.561
+ASN H3 H H 0 15.385 16.183 19.422
+ASN HA H H 0 16.651 17.482 20.665
+ASN HB3 H H 0 16.746 19.574 19.593
+ASN HB2 H H 0 15.359 19.286 18.893
+ASN HD21 H H 0 16.894 19.794 16.957
+ASN HD22 H H 0 17.928 18.741 16.527
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ASN N n/a CA START
+ASN H N . .
+ASN H2 N . .
+ASN H3 N . .
+ASN CA N C .
+ASN HA CA . .
+ASN CB CA CG .
+ASN HB3 CB . .
+ASN HB2 CB . .
+ASN CG CB ND2 .
+ASN OD1 CG . .
+ASN ND2 CG HD22 .
+ASN HD21 ND2 . .
+ASN HD22 ND2 . .
+ASN C CA . END
+ASN O C . .
+ASN OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+ASN N N(CCCH)(H)3
+ASN CA C(CCHH)(NH3)(COO)(H)
+ASN C C(CCHN)(O)2
+ASN O O(CCO)
+ASN CB C(CCHN)(CNO)(H)2
+ASN CG C(CCHH)(NHH)(O)
+ASN OD1 O(CCN)
+ASN ND2 N(CCO)(H)2
+ASN OXT O(CCO)
+ASN H H(NCHH)
+ASN H2 H(NCHH)
+ASN H3 H(NCHH)
+ASN HA H(CCCN)
+ASN HB3 H(CCCH)
+ASN HB2 H(CCCH)
+ASN HD21 H(NCH)
+ASN HD22 H(NCH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ASN N CA SINGLE n 1.490 0.0100 1.490 0.0100
+ASN CA C SINGLE n 1.533 0.0100 1.533 0.0100
+ASN CA CB SINGLE n 1.525 0.0100 1.525 0.0100
+ASN C O DOUBLE n 1.251 0.0183 1.251 0.0183
+ASN C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+ASN CB CG SINGLE n 1.510 0.0100 1.510 0.0100
+ASN CG OD1 DOUBLE n 1.236 0.0100 1.236 0.0100
+ASN CG ND2 SINGLE n 1.325 0.0100 1.325 0.0100
+ASN N H SINGLE n 1.018 0.0520 0.902 0.0102
+ASN N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+ASN N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+ASN CA HA SINGLE n 1.092 0.0100 0.984 0.0200
+ASN CB HB3 SINGLE n 1.092 0.0100 0.978 0.0143
+ASN CB HB2 SINGLE n 1.092 0.0100 0.978 0.0143
+ASN ND2 HD21 SINGLE n 1.013 0.0120 0.887 0.0200
+ASN ND2 HD22 SINGLE n 1.013 0.0120 0.887 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ASN CA N H 109.990 3.00
+ASN CA N H2 109.990 3.00
+ASN CA N H3 109.990 3.00
+ASN H N H2 109.032 3.00
+ASN H N H3 109.032 3.00
+ASN H2 N H3 109.032 3.00
+ASN N CA C 109.258 1.50
+ASN N CA CB 111.558 1.50
+ASN N CA HA 108.387 1.58
+ASN C CA CB 111.904 3.00
+ASN C CA HA 108.774 1.79
+ASN CB CA HA 107.748 1.50
+ASN CA C O 117.148 1.60
+ASN CA C OXT 117.148 1.60
+ASN O C OXT 125.704 1.50
+ASN CA CB CG 112.193 1.50
+ASN CA CB HB3 109.177 1.50
+ASN CA CB HB2 109.177 1.50
+ASN CG CB HB3 109.132 1.50
+ASN CG CB HB2 109.132 1.50
+ASN HB3 CB HB2 108.039 1.50
+ASN CB CG OD1 120.239 1.50
+ASN CB CG ND2 117.180 1.62
+ASN OD1 CG ND2 122.581 1.50
+ASN CG ND2 HD21 119.917 2.87
+ASN CG ND2 HD22 119.917 2.87
+ASN HD21 ND2 HD22 120.165 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ASN chi1 N CA CB CG -60.000 10.0 3
+ASN chi2 CA CB CG ND2 180.000 10.0 6
+ASN hh1 CB CG ND2 HD22 180.000 5.0 2
+ASN sp3_sp3_1 C CA N H 180.000 10.0 3
+ASN sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ASN chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ASN plan-1 C 0.020
+ASN plan-1 CA 0.020
+ASN plan-1 O 0.020
+ASN plan-1 OXT 0.020
+ASN plan-2 CB 0.020
+ASN plan-2 CG 0.020
+ASN plan-2 ND2 0.020
+ASN plan-2 OD1 0.020
+ASN plan-3 CG 0.020
+ASN plan-3 HD21 0.020
+ASN plan-3 HD22 0.020
+ASN plan-3 ND2 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ASN SMILES ACDLabs 12.01 O=C(N)CC(N)C(=O)O
+ASN InChI InChI 1.03 InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m0/s1
+ASN InChIKey InChI 1.03 DCXYFEDJOCDNAF-REOHCLBHSA-N
+ASN SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC(N)=O)C(O)=O
+ASN SMILES CACTVS 3.370 N[CH](CC(N)=O)C(O)=O
+ASN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 C([C@@H](C(=O)O)N)C(=O)N
+ASN SMILES "OpenEye OEToolkits" 1.7.2 C(C(C(=O)O)N)C(=O)N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ASN acedrg 278 "dictionary generator"
+ASN acedrg_database 12 "data source"
+ASN rdkit 2019.09.1 "Chemoinformatics tool"
+ASN refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/ASP.cif b/image_analysis/structure_refinement/monomers/ASP.cif
new file mode 100644
index 000000000..08958a6f6
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ASP.cif
@@ -0,0 +1,198 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ASP ASP "ASPARTIC        ACID" peptide 15 9 .
+
+data_comp_ASP
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ASP N N NT3 1 33.542 17.835 39.145
+ASP CA C CH1 0 34.991 17.614 38.867
+ASP C C C 0 35.178 17.161 37.413
+ASP O O O 0 36.268 17.442 36.867
+ASP CB C CH2 0 35.617 16.650 39.866
+ASP CG C C 0 34.932 15.299 40.037
+ASP OD1 O O 0 35.515 14.435 40.725
+ASP OD2 O OC -1 33.817 15.122 39.501
+ASP OXT O OC -1 34.232 16.542 36.875
+ASP H H H 0 33.408 17.940 40.031
+ASP H2 H H 0 33.045 17.139 38.857
+ASP H3 H H 0 33.263 18.581 38.722
+ASP HA H H 0 35.453 18.476 38.978
+ASP HB3 H H 0 35.641 17.087 40.742
+ASP HB2 H H 0 36.543 16.483 39.592
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ASP N n/a CA START
+ASP H N . .
+ASP H2 N . .
+ASP H3 N . .
+ASP CA N C .
+ASP HA CA . .
+ASP CB CA CG .
+ASP HB3 CB . .
+ASP HB2 CB . .
+ASP CG CB OD2 .
+ASP OD1 CG . .
+ASP OD2 CG . .
+ASP C CA . END
+ASP O C . .
+ASP OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+ASP N N(CCCH)(H)3
+ASP CA C(CCHH)(NH3)(COO)(H)
+ASP C C(CCHN)(O)2
+ASP O O(CCO)
+ASP CB C(CCHN)(COO)(H)2
+ASP CG C(CCHH)(O)2
+ASP OD1 O(CCO)
+ASP OD2 O(CCO)
+ASP OXT O(CCO)
+ASP H H(NCHH)
+ASP H2 H(NCHH)
+ASP H3 H(NCHH)
+ASP HA H(CCCN)
+ASP HB3 H(CCCH)
+ASP HB2 H(CCCH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ASP N CA SINGLE n 1.490 0.0100 1.490 0.0100
+ASP CA C SINGLE n 1.533 0.0100 1.533 0.0100
+ASP CA CB SINGLE n 1.521 0.0100 1.521 0.0100
+ASP C O DOUBLE n 1.251 0.0183 1.251 0.0183
+ASP C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+ASP CB CG SINGLE n 1.522 0.0100 1.522 0.0100
+ASP CG OD1 DOUBLE n 1.249 0.0161 1.249 0.0161
+ASP CG OD2 SINGLE n 1.249 0.0161 1.249 0.0161
+ASP N H SINGLE n 1.018 0.0520 0.902 0.0102
+ASP N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+ASP N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+ASP CA HA SINGLE n 1.092 0.0100 0.984 0.0200
+ASP CB HB3 SINGLE n 1.092 0.0100 0.980 0.0165
+ASP CB HB2 SINGLE n 1.092 0.0100 0.980 0.0165
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ASP CA N H 109.990 3.00
+ASP CA N H2 109.990 3.00
+ASP CA N H3 109.990 3.00
+ASP H N H2 109.032 3.00
+ASP H N H3 109.032 3.00
+ASP H2 N H3 109.032 3.00
+ASP N CA C 109.258 1.50
+ASP N CA CB 111.400 1.50
+ASP N CA HA 108.387 1.58
+ASP C CA CB 112.421 3.00
+ASP C CA HA 108.774 1.79
+ASP CB CA HA 108.472 2.65
+ASP CA C O 117.148 1.60
+ASP CA C OXT 117.148 1.60
+ASP O C OXT 125.704 1.50
+ASP CA CB CG 115.436 1.50
+ASP CA CB HB3 108.799 3.00
+ASP CA CB HB2 108.799 3.00
+ASP CG CB HB3 108.242 2.79
+ASP CG CB HB2 108.242 2.79
+ASP HB3 CB HB2 107.976 2.66
+ASP CB CG OD1 117.985 1.50
+ASP CB CG OD2 117.985 1.50
+ASP OD1 CG OD2 124.031 1.82
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ASP chi1 N CA CB CG -60.000 10.0 3
+ASP chi2 CA CB CG OD1 180.000 10.0 6
+ASP sp3_sp3_1 C CA N H 180.000 10.0 3
+ASP sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ASP chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ASP plan-1 C 0.020
+ASP plan-1 CA 0.020
+ASP plan-1 O 0.020
+ASP plan-1 OXT 0.020
+ASP plan-2 CB 0.020
+ASP plan-2 CG 0.020
+ASP plan-2 OD1 0.020
+ASP plan-2 OD2 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ASP SMILES ACDLabs 12.01 O=C(O)CC(N)C(=O)O
+ASP SMILES_CANONICAL CACTVS 3.370 N[C@@H](CC(O)=O)C(O)=O
+ASP SMILES CACTVS 3.370 N[CH](CC(O)=O)C(O)=O
+ASP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C([C@@H](C(=O)O)N)C(=O)O
+ASP SMILES "OpenEye OEToolkits" 1.7.0 C(C(C(=O)O)N)C(=O)O
+ASP InChI InChI 1.03 InChI=1S/C4H7NO4/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H,6,7)(H,8,9)/t2-/m0/s1
+ASP InChIKey InChI 1.03 CKLJMWTZIZZHCS-REOHCLBHSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ASP acedrg 278 "dictionary generator"
+ASP acedrg_database 12 "data source"
+ASP rdkit 2019.09.1 "Chemoinformatics tool"
+ASP refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/ATP.cif b/image_analysis/structure_refinement/monomers/ATP.cif
new file mode 100644
index 000000000..d59d901cc
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ATP.cif
@@ -0,0 +1,301 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ATP     ATP      "ADENOSINE-5'-TRIPHOSPHATE"     NON-POLYMER     43     31     .     
+#
+data_comp_ATP
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ATP     PG      P       P       0       44.662      45.077      58.117      
+ATP     O1G     O       O       0       43.261      45.625      58.004      
+ATP     O2G     O       OP      -1      45.679      45.923      57.392      
+ATP     O3G     O       OP      -1      45.059      44.781      59.542      
+ATP     PB      P       P       0       44.268      43.226      55.860      
+ATP     O1B     O       O       0       44.078      41.746      55.818      
+ATP     O2B     O       OP      -1      43.182      44.124      55.365      
+ATP     O3B     O       O2      0       44.645      43.653      57.356      
+ATP     PA      P       P       0       46.020      43.596      53.536      
+ATP     O1A     O       O       0       47.423      44.087      53.400      
+ATP     O2A     O       OP      -1      44.948      44.301      52.771      
+ATP     O3A     O       O2      0       45.624      43.591      55.090      
+ATP     "O5'"   O       O2      0       45.968      42.029      53.199      
+ATP     "C5'"   C       CH2     0       46.946      41.148      53.808      
+ATP     "C4'"   C       CH1     0       46.681      39.728      53.369      
+ATP     "O4'"   O       O2      0       46.924      39.620      51.943      
+ATP     "C3'"   C       CH1     0       47.567      38.650      54.004      
+ATP     "O3'"   O       OH1     0       46.881      37.406      54.075      
+ATP     "C2'"   C       CH1     0       48.756      38.611      53.041      
+ATP     "O2'"   O       OH1     0       49.451      37.383      53.067      
+ATP     "C1'"   C       CH1     0       48.066      38.829      51.697      
+ATP     N9      N       NT      0       48.916      39.514      50.718      
+ATP     C8      C       CR15    0       48.960      40.860      50.413      
+ATP     N7      N       NRD5    0       49.847      41.139      49.485      
+ATP     C5      C       CR56    0       50.421      39.915      49.166      
+ATP     C6      C       CR6     0       51.429      39.540      48.250      
+ATP     N6      N       NH2     0       52.063      40.400      47.457      
+ATP     N1      N       NRD6    0       51.760      38.223      48.186      
+ATP     C2      C       CR16    0       51.117      37.359      48.990      
+ATP     N3      N       NRD6    0       50.158      37.599      49.885      
+ATP     C4      C       CR56    0       49.852      38.909      49.924      
+ATP     "H5'1"  H       H       0       46.885      41.207      54.794      
+ATP     "H5'2"  H       H       0       47.858      41.415      53.533      
+ATP     "H4'"   H       H       0       45.738      39.523      53.548      
+ATP     "H3'"   H       H       0       47.862      38.933      54.908      
+ATP     "HO3'"  H       H       0       47.400      36.827      54.416      
+ATP     "H2'"   H       H       0       49.382      39.360      53.233      
+ATP     "HO2'"  H       H       0       50.094      37.416      52.513      
+ATP     "H1'"   H       H       0       47.793      37.957      51.333      
+ATP     H8      H       H       0       48.417      41.517      50.815      
+ATP     HN61    H       H       0       52.825      40.173      47.086      
+ATP     HN62    H       H       0       51.716      41.193      47.308      
+ATP     H2      H       H       0       51.382      36.456      48.909      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ATP          PG         O1G      DOUBLE       n     1.509  0.0200     1.509  0.0200
+ATP          PG         O2G      SINGLE       n     1.509  0.0200     1.509  0.0200
+ATP          PG         O3G      SINGLE       n     1.509  0.0200     1.509  0.0200
+ATP          PG         O3B      SINGLE       n     1.614  0.0178     1.614  0.0178
+ATP          PB         O1B      DOUBLE       n     1.493  0.0157     1.493  0.0157
+ATP          PB         O2B      SINGLE       n     1.493  0.0157     1.493  0.0157
+ATP          PB         O3B      SINGLE       n     1.601  0.0114     1.601  0.0114
+ATP          PB         O3A      SINGLE       n     1.601  0.0114     1.601  0.0114
+ATP          PA         O1A      DOUBLE       n     1.493  0.0122     1.493  0.0122
+ATP          PA         O2A      SINGLE       n     1.493  0.0122     1.493  0.0122
+ATP          PA         O3A      SINGLE       n     1.604  0.0133     1.604  0.0133
+ATP          PA       "O5'"      SINGLE       n     1.604  0.0133     1.604  0.0133
+ATP       "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+ATP       "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+ATP       "C4'"       "O4'"      SINGLE       n     1.451  0.0100     1.451  0.0100
+ATP       "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+ATP       "O4'"       "C1'"      SINGLE       n     1.409  0.0100     1.409  0.0100
+ATP       "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+ATP       "C3'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+ATP       "C2'"       "O2'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+ATP       "C2'"       "C1'"      SINGLE       n     1.525  0.0100     1.525  0.0100
+ATP       "C1'"          N9      SINGLE       n     1.458  0.0200     1.458  0.0200
+ATP          N9          C8      SINGLE       y     1.372  0.0200     1.372  0.0200
+ATP          N9          C4      SINGLE       y     1.372  0.0100     1.372  0.0100
+ATP          C8          N7      DOUBLE       y     1.310  0.0100     1.310  0.0100
+ATP          N7          C5      SINGLE       y     1.388  0.0100     1.388  0.0100
+ATP          C5          C6      SINGLE       y     1.408  0.0100     1.408  0.0100
+ATP          C5          C4      DOUBLE       y     1.381  0.0100     1.381  0.0100
+ATP          C6          N6      SINGLE       n     1.330  0.0100     1.330  0.0100
+ATP          C6          N1      DOUBLE       y     1.354  0.0100     1.354  0.0100
+ATP          N1          C2      SINGLE       y     1.339  0.0100     1.339  0.0100
+ATP          C2          N3      DOUBLE       y     1.330  0.0100     1.330  0.0100
+ATP          N3          C4      SINGLE       y     1.343  0.0100     1.343  0.0100
+ATP       "C5'"      "H5'1"      SINGLE       n     1.089  0.0100     0.989  0.0200
+ATP       "C5'"      "H5'2"      SINGLE       n     1.089  0.0100     0.989  0.0200
+ATP       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+ATP       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+ATP       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+ATP       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.994  0.0200
+ATP       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+ATP       "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.984  0.0200
+ATP          C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+ATP          N6        HN61      SINGLE       n     1.016  0.0100     0.877  0.0200
+ATP          N6        HN62      SINGLE       n     1.016  0.0100     0.877  0.0200
+ATP          C2          H2      SINGLE       n     1.082  0.0130     0.945  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ATP         O1G          PG         O2G     112.716    1.50
+ATP         O1G          PG         O3G     112.716    1.50
+ATP         O1G          PG         O3B     105.965    2.38
+ATP         O2G          PG         O3G     112.716    1.50
+ATP         O2G          PG         O3B     105.965    2.38
+ATP         O3G          PG         O3B     105.965    2.38
+ATP         O1B          PB         O2B     119.630    1.50
+ATP         O1B          PB         O3B     108.678    2.29
+ATP         O1B          PB         O3A     108.678    2.29
+ATP         O2B          PB         O3B     108.678    2.29
+ATP         O2B          PB         O3A     108.678    2.29
+ATP         O3B          PB         O3A     100.890    2.10
+ATP          PG         O3B          PB     132.584    3.00
+ATP         O1A          PA         O2A     118.411    2.35
+ATP         O1A          PA         O3A     108.816    2.14
+ATP         O1A          PA       "O5'"     109.410    1.50
+ATP         O2A          PA         O3A     108.816    2.14
+ATP         O2A          PA       "O5'"     109.410    1.50
+ATP         O3A          PA       "O5'"     101.065    1.97
+ATP          PB         O3A          PA     132.542    3.00
+ATP          PA       "O5'"       "C5'"     118.553    2.41
+ATP       "O5'"       "C5'"       "C4'"     109.342    1.50
+ATP       "O5'"       "C5'"      "H5'1"     109.845    1.50
+ATP       "O5'"       "C5'"      "H5'2"     109.845    1.50
+ATP       "C4'"       "C5'"      "H5'1"     109.624    1.50
+ATP       "C4'"       "C5'"      "H5'2"     109.624    1.50
+ATP      "H5'1"       "C5'"      "H5'2"     108.472    1.50
+ATP       "C5'"       "C4'"       "O4'"     109.123    1.50
+ATP       "C5'"       "C4'"       "C3'"     116.008    1.52
+ATP       "C5'"       "C4'"       "H4'"     108.268    1.50
+ATP       "O4'"       "C4'"       "C3'"     105.388    1.50
+ATP       "O4'"       "C4'"       "H4'"     108.947    1.50
+ATP       "C3'"       "C4'"       "H4'"     109.363    1.86
+ATP       "C4'"       "O4'"       "C1'"     109.903    1.50
+ATP       "C4'"       "C3'"       "O3'"     111.281    2.46
+ATP       "C4'"       "C3'"       "C2'"     102.602    1.50
+ATP       "C4'"       "C3'"       "H3'"     110.452    2.54
+ATP       "O3'"       "C3'"       "C2'"     111.581    2.83
+ATP       "O3'"       "C3'"       "H3'"     110.380    1.67
+ATP       "C2'"       "C3'"       "H3'"     110.504    1.75
+ATP       "C3'"       "O3'"      "HO3'"     108.744    3.00
+ATP       "C3'"       "C2'"       "O2'"     112.782    2.45
+ATP       "C3'"       "C2'"       "C1'"     101.239    1.50
+ATP       "C3'"       "C2'"       "H2'"     110.596    1.51
+ATP       "O2'"       "C2'"       "C1'"     111.715    2.69
+ATP       "O2'"       "C2'"       "H2'"     110.448    1.97
+ATP       "C1'"       "C2'"       "H2'"     110.636    1.70
+ATP       "C2'"       "O2'"      "HO2'"     109.103    2.13
+ATP       "O4'"       "C1'"       "C2'"     106.047    1.50
+ATP       "O4'"       "C1'"          N9     108.167    1.51
+ATP       "O4'"       "C1'"       "H1'"     109.807    1.50
+ATP       "C2'"       "C1'"          N9     113.752    2.20
+ATP       "C2'"       "C1'"       "H1'"     109.015    1.50
+ATP          N9       "C1'"       "H1'"     109.246    1.50
+ATP       "C1'"          N9          C8     126.078    2.46
+ATP       "C1'"          N9          C4     125.158    1.54
+ATP          C8          N9          C4     107.594    1.50
+ATP          N9          C8          N7     112.130    1.94
+ATP          N9          C8          H8     124.701    2.19
+ATP          N7          C8          H8     123.170    1.50
+ATP          C8          N7          C5     103.927    1.50
+ATP          N7          C5          C6     132.145    1.50
+ATP          N7          C5          C4     110.588    1.50
+ATP          C6          C5          C4     117.267    1.50
+ATP          C5          C6          N6     123.792    1.50
+ATP          C5          C6          N1     117.409    1.50
+ATP          N6          C6          N1     118.799    1.50
+ATP          C6          N6        HN61     119.723    1.50
+ATP          C6          N6        HN62     119.723    1.50
+ATP        HN61          N6        HN62     120.554    1.88
+ATP          C6          N1          C2     118.521    1.50
+ATP          N1          C2          N3     129.332    1.50
+ATP          N1          C2          H2     115.313    1.50
+ATP          N3          C2          H2     115.355    1.50
+ATP          C2          N3          C4     110.982    1.50
+ATP          N9          C4          C5     107.666    1.69
+ATP          N9          C4          N3     125.845    1.50
+ATP          C5          C4          N3     126.489    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ATP            sp3_sp3_27          PB         O3B          PG         O1G      60.000    10.0     3
+ATP            sp3_sp3_40       "C4'"       "C5'"       "O5'"          PA     180.000    10.0     3
+ATP            sp3_sp3_43       "O4'"       "C4'"       "C5'"       "O5'"     180.000    10.0     3
+ATP             sp3_sp3_2       "C5'"       "C4'"       "O4'"       "C1'"     -60.000    10.0     3
+ATP            sp3_sp3_56       "O3'"       "C3'"       "C4'"       "C5'"     180.000    10.0     3
+ATP             sp3_sp3_4       "C2'"       "C1'"       "O4'"       "C4'"     -60.000    10.0     3
+ATP            sp3_sp3_61       "C4'"       "C3'"       "O3'"      "HO3'"     180.000    10.0     3
+ATP            sp3_sp3_20       "O2'"       "C2'"       "C3'"       "O3'"     -60.000    10.0     3
+ATP            sp3_sp3_64       "C3'"       "C2'"       "O2'"      "HO2'"     180.000    10.0     3
+ATP             sp3_sp3_8       "O4'"       "C1'"       "C2'"       "O2'"     180.000    10.0     3
+ATP             sp2_sp3_1          C8          N9       "C1'"       "O4'"     150.000    10.0     6
+ATP              const_14          N7          C8          N9       "C1'"     180.000    10.0     2
+ATP              const_26          C5          C4          N9       "C1'"     180.000    10.0     2
+ATP              const_17          N9          C8          N7          C5       0.000    10.0     2
+ATP              const_20          C6          C5          N7          C8     180.000    10.0     2
+ATP       const_sp2_sp2_4          N7          C5          C6          N6       0.000     5.0     2
+ATP              const_21          N9          C4          C5          N7       0.000    10.0     2
+ATP             sp2_sp2_1          C5          C6          N6        HN61     180.000     5.0     2
+ATP       const_sp2_sp2_6          N6          C6          N1          C2     180.000     5.0     2
+ATP       const_sp2_sp2_7          N3          C2          N1          C6       0.000     5.0     2
+ATP       const_sp2_sp2_9          N1          C2          N3          C4       0.000     5.0     2
+ATP              const_12          N9          C4          N3          C2     180.000    10.0     2
+ATP            sp3_sp3_33          PA         O3A          PB         O1B      60.000    10.0     3
+ATP            sp3_sp3_30          PG         O3B          PB         O1B      60.000    10.0     3
+ATP            sp3_sp3_36          PB         O3A          PA         O1A      60.000    10.0     3
+ATP            sp3_sp3_39       "C5'"       "O5'"          PA         O1A      60.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ATP    chir_1    PG    O3B    O2G    O3G    both
+ATP    chir_2    PB    O3A    O3B    O2B    both
+ATP    chir_3    PA    O3A    "O5'"    O2A    both
+ATP    chir_4    "C4'"    "O4'"    "C3'"    "C5'"    negative
+ATP    chir_5    "C3'"    "O3'"    "C4'"    "C2'"    positive
+ATP    chir_6    "C2'"    "O2'"    "C1'"    "C3'"    negative
+ATP    chir_7    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ATP    plan-1       "C1'"   0.020
+ATP    plan-1          C2   0.020
+ATP    plan-1          C4   0.020
+ATP    plan-1          C5   0.020
+ATP    plan-1          C6   0.020
+ATP    plan-1          C8   0.020
+ATP    plan-1          H2   0.020
+ATP    plan-1          H8   0.020
+ATP    plan-1          N1   0.020
+ATP    plan-1          N3   0.020
+ATP    plan-1          N6   0.020
+ATP    plan-1          N7   0.020
+ATP    plan-1          N9   0.020
+ATP    plan-2          C6   0.020
+ATP    plan-2        HN61   0.020
+ATP    plan-2        HN62   0.020
+ATP    plan-2          N6   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ATP           SMILES              ACDLabs 10.04                                                                                                                                                 O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
+ATP SMILES_CANONICAL               CACTVS 3.341                                                                                                                      Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
+ATP           SMILES               CACTVS 3.341                                                                                                                               Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
+ATP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                                                  c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
+ATP           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                                           c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
+ATP            InChI                InChI  1.03 InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
+ATP         InChIKey                InChI  1.03                                                                                                                                                                                ZKHQWZAMYRWXGA-KQYNXXCUSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ATP acedrg               243         "dictionary generator"                  
+ATP acedrg_database      11          "data source"                           
+ATP rdkit                2017.03.2   "Chemoinformatics tool"
+ATP refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/BR.cif b/image_analysis/structure_refinement/monomers/BR.cif
new file mode 100644
index 000000000..64698cd70
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/BR.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+BR BR 'BROMIDE ION                         ' NON-POLYMER 1 1 .
+
+data_comp_BR
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+BR BR BR BR -1.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+BR BR n/a . END
diff --git a/image_analysis/structure_refinement/monomers/C.cif b/image_analysis/structure_refinement/monomers/C.cif
new file mode 100644
index 000000000..0d0c89011
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/C.cif
@@ -0,0 +1,255 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+C     C       "CYTIDINE-5'-MONOPHOSPHATE"     RNA     33     21     .     
+#
+data_comp_C
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+C       OP3     O       OP      -1      26.264      21.286      -11.211     
+C       P       P       P       0       27.065      20.768      -12.391     
+C       OP1     O       O       0       26.731      21.481      -13.688     
+C       OP2     O       OP      -1      27.015      19.258      -12.520     
+C       "O5'"   O       O2      0       28.604      21.132      -12.071     
+C       "C5'"   C       CH2     0       28.962      22.520      -11.845     
+C       "C4'"   C       CH1     0       30.463      22.648      -11.735     
+C       "O4'"   O       O2      0       30.967      21.749      -10.719     
+C       "C3'"   C       CH1     0       31.273      22.268      -12.980     
+C       "O3'"   O       OH1     0       31.285      23.333      -13.923     
+C       "C2'"   C       CH1     0       32.660      21.973      -12.387     
+C       "O2'"   O       OH1     0       33.494      23.113      -12.311     
+C       "C1'"   C       CH1     0       32.329      21.476      -10.970     
+C       N1      N       NR6     0       32.565      20.011      -10.805     
+C       C2      C       CR6     0       33.589      19.539      -9.963      
+C       O2      O       O       0       34.302      20.347      -9.344      
+C       N3      N       NRD6    0       33.778      18.197      -9.840      
+C       C4      C       CR6     0       33.005      17.329      -10.512     
+C       N4      N       NH2     0       33.237      16.032      -10.352     
+C       C5      C       CR16    0       31.965      17.787      -11.373     
+C       C6      C       CR16    0       31.786      19.115      -11.490     
+C       "H5'"   H       H       0       28.541      22.842      -11.010     
+C       "H5''"  H       H       0       28.636      23.077      -12.594     
+C       "H4'"   H       H       0       30.676      23.570      -11.475     
+C       "H3'"   H       H       0       30.904      21.447      -13.396     
+C       "HO3'"  H       H       0       31.819      23.134      -14.553     
+C       "H2'"   H       H       0       33.101      21.267      -12.901     
+C       "HO2'"  H       H       0       33.087      23.744      -11.913     
+C       "H1'"   H       H       0       32.871      21.976      -10.317     
+C       H41     H       H       0       33.920      15.764      -9.869      
+C       H42     H       H       0       32.707      15.443      -10.731     
+C       H5      H       H       0       31.420      17.183      -11.847     
+C       H6      H       H       0       31.112      19.446      -12.046     
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+C       OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+C         P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+C         P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+C         P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+C     "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+C     "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+C     "C4'"       "O4'"      SINGLE       n     1.451  0.0111     1.451  0.0111
+C     "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+C     "O4'"       "C1'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+C     "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+C     "C3'"       "C2'"      SINGLE       n     1.533  0.0109     1.533  0.0109
+C     "C2'"       "O2'"      SINGLE       n     1.412  0.0100     1.412  0.0100
+C     "C2'"       "C1'"      SINGLE       n     1.532  0.0100     1.532  0.0100
+C     "C1'"          N1      SINGLE       n     1.487  0.0100     1.487  0.0100
+C        N1          C2      SINGLE       y     1.397  0.0100     1.397  0.0100
+C        N1          C6      SINGLE       y     1.364  0.0108     1.364  0.0108
+C        C2          O2      DOUBLE       n     1.241  0.0100     1.241  0.0100
+C        C2          N3      SINGLE       y     1.355  0.0119     1.355  0.0119
+C        N3          C4      DOUBLE       y     1.339  0.0110     1.339  0.0110
+C        C4          N4      SINGLE       n     1.325  0.0109     1.325  0.0109
+C        C4          C5      SINGLE       y     1.422  0.0123     1.422  0.0123
+C        C5          C6      DOUBLE       y     1.342  0.0100     1.342  0.0100
+C     "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+C     "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+C     "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+C     "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+C     "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+C     "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.978  0.0200
+C     "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+C     "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.985  0.0100
+C        N4         H41      SINGLE       n     1.016  0.0100     0.877  0.0200
+C        N4         H42      SINGLE       n     1.016  0.0100     0.877  0.0200
+C        C5          H5      SINGLE       n     1.082  0.0130     0.941  0.0174
+C        C6          H6      SINGLE       n     1.082  0.0130     0.935  0.0143
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+C       OP3           P         OP1     112.864    1.69
+C       OP3           P         OP2     112.864    1.69
+C       OP3           P       "O5'"     105.808    2.07
+C       OP1           P         OP2     112.864    1.69
+C       OP1           P       "O5'"     105.808    2.07
+C       OP2           P       "O5'"     105.808    2.07
+C         P       "O5'"       "C5'"     118.783    1.50
+C     "O5'"       "C5'"       "C4'"     109.342    1.50
+C     "O5'"       "C5'"       "H5'"     109.845    1.50
+C     "O5'"       "C5'"      "H5''"     109.845    1.50
+C     "C4'"       "C5'"       "H5'"     109.624    1.50
+C     "C4'"       "C5'"      "H5''"     109.624    1.50
+C     "H5'"       "C5'"      "H5''"     108.472    1.50
+C     "C5'"       "C4'"       "O4'"     109.615    1.50
+C     "C5'"       "C4'"       "C3'"     116.008    1.52
+C     "C5'"       "C4'"       "H4'"     108.268    1.50
+C     "O4'"       "C4'"       "C3'"     104.439    1.50
+C     "O4'"       "C4'"       "H4'"     108.698    1.50
+C     "C3'"       "C4'"       "H4'"     109.363    1.86
+C     "C4'"       "O4'"       "C1'"     109.578    1.50
+C     "C4'"       "C3'"       "O3'"     111.281    2.46
+C     "C4'"       "C3'"       "C2'"     102.071    1.50
+C     "C4'"       "C3'"       "H3'"     110.452    2.54
+C     "O3'"       "C3'"       "C2'"     111.993    3.00
+C     "O3'"       "C3'"       "H3'"     110.380    1.67
+C     "C2'"       "C3'"       "H3'"     110.108    1.66
+C     "C3'"       "O3'"      "HO3'"     108.744    3.00
+C     "C3'"       "C2'"       "O2'"     112.861    2.52
+C     "C3'"       "C2'"       "C1'"     101.269    1.50
+C     "C3'"       "C2'"       "H2'"     110.799    1.82
+C     "O2'"       "C2'"       "C1'"     109.476    3.00
+C     "O2'"       "C2'"       "H2'"     111.022    1.77
+C     "C1'"       "C2'"       "H2'"     110.760    1.63
+C     "C2'"       "O2'"      "HO2'"     109.449    1.85
+C     "O4'"       "C1'"       "C2'"     106.825    1.50
+C     "O4'"       "C1'"          N1     108.667    1.50
+C     "O4'"       "C1'"       "H1'"     109.327    1.50
+C     "C2'"       "C1'"          N1     112.859    1.50
+C     "C2'"       "C1'"       "H1'"     109.776    1.83
+C        N1       "C1'"       "H1'"     109.166    1.50
+C     "C1'"          N1          C2     118.189    2.26
+C     "C1'"          N1          C6     121.301    1.52
+C        C2          N1          C6     120.510    1.50
+C        N1          C2          O2     118.710    1.50
+C        N1          C2          N3     118.927    1.50
+C        O2          C2          N3     122.370    1.50
+C        C2          N3          C4     120.266    1.50
+C        N3          C4          N4     117.855    1.50
+C        N3          C4          C5     121.269    1.50
+C        N4          C4          C5     120.876    1.50
+C        C4          N4         H41     119.818    1.59
+C        C4          N4         H42     119.818    1.59
+C       H41          N4         H42     120.363    1.85
+C        C4          C5          C6     117.808    1.50
+C        C4          C5          H5     121.350    1.50
+C        C6          C5          H5     120.848    1.50
+C        N1          C6          C5     121.215    1.50
+C        N1          C6          H6     118.510    1.50
+C        C5          C6          H6     120.275    1.75
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+C       C2e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+C       C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+C       C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+C       C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+C       C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+C       C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+C       C3e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+C       C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+C       C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+C       C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+C       C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+C       C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+C       alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+C       beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+C       epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+C       gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+C       sp3_sp3_52      "C3'"     "C2'"     "O2'"     "HO2'"    180.000       10.00     3     
+C       const_sp2_sp2_4          O2          C2          N1       "C1'"       0.000     5.0     2
+C              const_18          C5          C6          N1       "C1'"     180.000    10.0     2
+C       const_sp2_sp2_6          O2          C2          N3          C4     180.000     5.0     2
+C       const_sp2_sp2_8          N4          C4          N3          C2     180.000     5.0     2
+C             sp2_sp2_3          N3          C4          N4         H41       0.000     5.0     2
+C              const_11          N4          C4          C5          C6     180.000    10.0     2
+C              const_13          C4          C5          C6          N1       0.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+C  chir_1    P    "O5'"    OP3    OP2    both
+C  chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+C  chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+C  chir_4    "C2'"    "O2'"    "C1'"    "C3'"    negative
+C  chir_5    "C1'"    "O4'"    N1    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+C  plan-1       "C1'"   0.020
+C  plan-1          C2   0.020
+C  plan-1          C4   0.020
+C  plan-1          C5   0.020
+C  plan-1          C6   0.020
+C  plan-1          H5   0.020
+C  plan-1          H6   0.020
+C  plan-1          N1   0.020
+C  plan-1          N3   0.020
+C  plan-1          N4   0.020
+C  plan-1          O2   0.020
+C  plan-2          C4   0.020
+C  plan-2         H41   0.020
+C  plan-2         H42   0.020
+C  plan-2          N4   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+C           SMILES              ACDLabs 10.04                                                                                                            O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
+C SMILES_CANONICAL               CACTVS 3.341                                                                                      NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
+C           SMILES               CACTVS 3.341                                                                                            NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
+C SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                      C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
+C           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                        C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
+C            InChI                InChI  1.03 InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
+C         InChIKey                InChI  1.03                                                                                                                        IERHLVCPSMICTF-XVFCMESISA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+C   acedrg               243         "dictionary generator"                  
+C   acedrg_database      11          "data source"                           
+C   rdkit                2017.03.2   "Chemoinformatics tool"
+C   refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/CA.cif b/image_analysis/structure_refinement/monomers/CA.cif
new file mode 100644
index 000000000..d1cacc170
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/CA.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+CA CA 'CALCIUM ION                         ' NON-POLYMER 1 1 .
+
+data_comp_CA
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+CA CA CA CA 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+CA CA n/a . END
diff --git a/image_analysis/structure_refinement/monomers/CD.cif b/image_analysis/structure_refinement/monomers/CD.cif
new file mode 100644
index 000000000..fbdd3d2de
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/CD.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+CD CD 'CADMIUM ION                         ' NON-POLYMER 1 1 .
+
+data_comp_CD
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+CD CD CD CD 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+CD CD n/a . END
diff --git a/image_analysis/structure_refinement/monomers/CL.cif b/image_analysis/structure_refinement/monomers/CL.cif
new file mode 100644
index 000000000..0d614ea71
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/CL.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+CL CL 'CHLORIDE ION                        ' NON-POLYMER 1 1 .
+
+data_comp_CL
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+CL CL CL CL -1.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+CL CL n/a . END
diff --git a/image_analysis/structure_refinement/monomers/CO.cif b/image_analysis/structure_refinement/monomers/CO.cif
new file mode 100644
index 000000000..6942e5689
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/CO.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+CO CO 'COBALT (II) ION                     ' NON-POLYMER 1 1 .
+
+data_comp_CO
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+CO CO CO CO 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+CO CO n/a . END
diff --git a/image_analysis/structure_refinement/monomers/COPYING b/image_analysis/structure_refinement/monomers/COPYING
new file mode 100644
index 000000000..3f7b8b1e5
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/COPYING
@@ -0,0 +1,166 @@
+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions. 
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version. 
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
+
diff --git a/image_analysis/structure_refinement/monomers/CU.cif b/image_analysis/structure_refinement/monomers/CU.cif
new file mode 100644
index 000000000..138b89fac
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/CU.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+CU CU 'COPPER (II) ION                     ' NON-POLYMER 1 1 .
+
+data_comp_CU
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+CU CU CU CU 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+CU CU n/a . END
diff --git a/image_analysis/structure_refinement/monomers/CYS.cif b/image_analysis/structure_refinement/monomers/CYS.cif
new file mode 100644
index 000000000..190d34acf
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/CYS.cif
@@ -0,0 +1,188 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+CYS CYS CYSTEINE peptide 14 7 .
+
+data_comp_CYS
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+CYS N N NT3 1 22.713 13.517 37.695
+CYS CA C CH1 0 22.373 13.685 39.137
+CYS C C C 0 22.022 15.153 39.440
+CYS O O O 0 22.838 16.024 39.065
+CYS CB C CH2 0 23.514 13.225 40.038
+CYS SG S SH1 0 25.070 14.106 39.742
+CYS OXT O OC -1 20.945 15.370 40.038
+CYS H H H 0 23.605 13.433 37.588
+CYS H2 H H 0 22.430 14.227 37.214
+CYS H3 H H 0 22.308 12.777 37.375
+CYS HA H H 0 21.577 13.127 39.328
+CYS HB3 H H 0 23.668 12.265 39.898
+CYS HB2 H H 0 23.255 13.357 40.977
+CYS HG H HSH1 0 25.737 13.537 40.579
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+CYS N n/a CA START
+CYS H N . .
+CYS H2 N . .
+CYS H3 N . .
+CYS CA N C .
+CYS HA CA . .
+CYS CB CA SG .
+CYS HB3 CB . .
+CYS HB2 CB . .
+CYS SG CB . .
+CYS HG SG . .
+CYS C CA . END
+CYS O C . .
+CYS OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+CYS N N(CCCH)(H)3
+CYS CA C(CHHS)(NH3)(COO)(H)
+CYS C C(CCHN)(O)2
+CYS O O(CCO)
+CYS CB C(CCHN)(SH)(H)2
+CYS SG S(CCHH)(H)
+CYS OXT O(CCO)
+CYS H H(NCHH)
+CYS H2 H(NCHH)
+CYS H3 H(NCHH)
+CYS HA H(CCCN)
+CYS HB3 H(CCHS)
+CYS HB2 H(CCHS)
+CYS HG H(SC)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+CYS N CA SINGLE n 1.487 0.0100 1.487 0.0100
+CYS CA C SINGLE n 1.538 0.0113 1.538 0.0113
+CYS CA CB SINGLE n 1.524 0.0100 1.524 0.0100
+CYS C O DOUBLE n 1.251 0.0183 1.251 0.0183
+CYS C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+CYS CB SG SINGLE n 1.812 0.0101 1.812 0.0101
+CYS N H SINGLE n 1.018 0.0520 0.902 0.0102
+CYS N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+CYS N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+CYS CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+CYS CB HB3 SINGLE n 1.092 0.0100 0.983 0.0131
+CYS CB HB2 SINGLE n 1.092 0.0100 0.983 0.0131
+CYS SG HG SINGLE n 1.338 0.0100 1.212 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+CYS CA N H 109.684 2.12
+CYS CA N H2 109.684 2.12
+CYS CA N H3 109.684 2.12
+CYS H N H2 109.032 3.00
+CYS H N H3 109.032 3.00
+CYS H2 N H3 109.032 3.00
+CYS N CA C 109.504 1.50
+CYS N CA CB 110.927 1.50
+CYS N CA HA 107.886 1.50
+CYS C CA CB 110.126 3.00
+CYS C CA HA 108.362 1.50
+CYS CB CA HA 108.525 2.42
+CYS CA C O 117.126 1.50
+CYS CA C OXT 117.126 1.50
+CYS O C OXT 125.747 1.50
+CYS CA CB SG 113.492 1.50
+CYS CA CB HB3 109.109 1.50
+CYS CA CB HB2 109.109 1.50
+CYS SG CB HB3 108.513 1.50
+CYS SG CB HB2 108.513 1.50
+CYS HB3 CB HB2 107.963 1.50
+CYS CB SG HG 97.543 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+CYS chi1 N CA CB SG -60.000 10.0 3
+CYS chi2 CA CB SG HG 180.000 10.0 3
+CYS sp3_sp3_1 C CA N H 180.000 10.0 3
+CYS sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+CYS chir_1 CA N CB C negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+CYS plan-1 C 0.020
+CYS plan-1 CA 0.020
+CYS plan-1 O 0.020
+CYS plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+CYS SMILES ACDLabs 10.04 O=C(O)C(N)CS
+CYS SMILES_CANONICAL CACTVS 3.341 N[C@@H](CS)C(O)=O
+CYS SMILES CACTVS 3.341 N[CH](CS)C(O)=O
+CYS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)S
+CYS SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)S
+CYS InChI InChI 1.03 InChI=1S/C3H7NO2S/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
+CYS InChIKey InChI 1.03 XUJNEKJLAYXESH-REOHCLBHSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+CYS acedrg 278 "dictionary generator"
+CYS acedrg_database 12 "data source"
+CYS rdkit 2019.09.1 "Chemoinformatics tool"
+CYS refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/DA.cif b/image_analysis/structure_refinement/monomers/DA.cif
new file mode 100644
index 000000000..268788579
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/DA.cif
@@ -0,0 +1,266 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+DA    DA        "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE"     DNA     34     22     .     
+#
+data_comp_DA
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+DA      OP3     O       OP      -1      -6.497      8.522       9.951       
+DA      P       P       P       0       -5.346      9.062       9.122       
+DA      OP1     O       O       0       -4.898      10.441      9.565       
+DA      OP2     O       OP      -1      -5.605      8.977       7.630       
+DA      "O5'"   O       O2      0       -4.097      8.080       9.408       
+DA      "C5'"   C       CH2     0       -3.640      7.912       10.774      
+DA      "C4'"   C       CH1     0       -2.470      6.958       10.801      
+DA      "O4'"   O       O2      0       -2.888      5.686       10.260      
+DA      "C3'"   C       CH1     0       -1.251      7.408       9.993       
+DA      "O3'"   O       OH1     0       -0.049      7.159       10.716      
+DA      "C2'"   C       CH2     0       -1.324      6.542       8.739       
+DA      "C1'"   C       CH1     0       -1.962      5.267       9.263       
+DA      N9      N       NR5     0       -2.687      4.489       8.258       
+DA      C8      C       CR15    0       -3.753      4.911       7.501       
+DA      N7      N       NRD5    0       -4.206      3.997       6.680       
+DA      C5      C       CR56    0       -3.393      2.896       6.907       
+DA      C6      C       CR6     0       -3.368      1.602       6.342       
+DA      N6      N       NH2     0       -4.214      1.192       5.400       
+DA      N1      N       NRD6    0       -2.423      0.736       6.793       
+DA      C2      C       CR16    0       -1.573      1.156       7.744       
+DA      N3      N       NRD6    0       -1.504      2.345       8.344       
+DA      C4      C       CR56    0       -2.450      3.184       7.880       
+DA      "H5'"   H       H       0       -4.373      7.554       11.332      
+DA      "H5''"  H       H       0       -3.363      8.786       11.145      
+DA      "H4'"   H       H       0       -2.203      6.829       11.743      
+DA      "H3'"   H       H       0       -1.322      8.365       9.759       
+DA      "HO3'"  H       H       0       0.583       7.601       10.361      
+DA      "H2'"   H       H       0       -0.433      6.369       8.376       
+DA      "H2''"  H       H       0       -1.875      6.962       8.051       
+DA      "H1'"   H       H       0       -1.264      4.700       9.685       
+DA      H8      H       H       0       -4.120      5.776       7.565       
+DA      H61     H       H       0       -4.304      0.334       5.236       
+DA      H62     H       H       0       -4.679      1.782       4.946       
+DA      H2      H       H       0       -0.933      0.520       8.026       
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+DA        OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+DA          P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+DA          P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+DA          P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+DA      "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+DA      "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+DA      "C4'"       "O4'"      SINGLE       n     1.442  0.0100     1.442  0.0100
+DA      "C4'"       "C3'"      SINGLE       n     1.526  0.0115     1.526  0.0115
+DA      "O4'"       "C1'"      SINGLE       n     1.425  0.0100     1.425  0.0100
+DA      "C3'"       "O3'"      SINGLE       n     1.424  0.0100     1.424  0.0100
+DA      "C3'"       "C2'"      SINGLE       n     1.526  0.0101     1.526  0.0101
+DA      "C2'"       "C1'"      SINGLE       n     1.521  0.0118     1.521  0.0118
+DA      "C1'"          N9      SINGLE       n     1.462  0.0111     1.462  0.0111
+DA         N9          C8      SINGLE       y     1.373  0.0100     1.373  0.0100
+DA         N9          C4      SINGLE       y     1.377  0.0100     1.377  0.0100
+DA         C8          N7      DOUBLE       y     1.310  0.0100     1.310  0.0100
+DA         N7          C5      SINGLE       y     1.388  0.0100     1.388  0.0100
+DA         C5          C6      SINGLE       y     1.408  0.0100     1.408  0.0100
+DA         C5          C4      DOUBLE       y     1.381  0.0100     1.381  0.0100
+DA         C6          N6      SINGLE       n     1.330  0.0100     1.330  0.0100
+DA         C6          N1      DOUBLE       y     1.354  0.0100     1.354  0.0100
+DA         N1          C2      SINGLE       y     1.339  0.0100     1.339  0.0100
+DA         C2          N3      DOUBLE       y     1.330  0.0100     1.330  0.0100
+DA         N3          C4      SINGLE       y     1.343  0.0100     1.343  0.0100
+DA      "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DA      "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DA      "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.987  0.0170
+DA      "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.988  0.0189
+DA      "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+DA      "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.977  0.0113
+DA      "C2'"      "H2''"      SINGLE       n     1.089  0.0100     0.977  0.0113
+DA      "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.993  0.0101
+DA         C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+DA         N6         H61      SINGLE       n     1.016  0.0100     0.877  0.0200
+DA         N6         H62      SINGLE       n     1.016  0.0100     0.877  0.0200
+DA         C2          H2      SINGLE       n     1.082  0.0130     0.945  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+DA        OP3           P         OP1     112.864    1.69
+DA        OP3           P         OP2     112.864    1.69
+DA        OP3           P       "O5'"     105.808    2.07
+DA        OP1           P         OP2     112.864    1.69
+DA        OP1           P       "O5'"     105.808    2.07
+DA        OP2           P       "O5'"     105.808    2.07
+DA          P       "O5'"       "C5'"     118.783    1.50
+DA      "O5'"       "C5'"       "C4'"     109.342    1.50
+DA      "O5'"       "C5'"       "H5'"     109.845    1.50
+DA      "O5'"       "C5'"      "H5''"     109.845    1.50
+DA      "C4'"       "C5'"       "H5'"     109.624    1.50
+DA      "C4'"       "C5'"      "H5''"     109.624    1.50
+DA      "H5'"       "C5'"      "H5''"     108.472    1.50
+DA      "C5'"       "C4'"       "O4'"     109.123    1.50
+DA      "C5'"       "C4'"       "C3'"     114.866    1.63
+DA      "C5'"       "C4'"       "H4'"     108.268    1.50
+DA      "O4'"       "C4'"       "C3'"     105.506    1.50
+DA      "O4'"       "C4'"       "H4'"     108.947    1.50
+DA      "C3'"       "C4'"       "H4'"     109.069    1.50
+DA      "C4'"       "O4'"       "C1'"     108.795    1.50
+DA      "C4'"       "C3'"       "O3'"     110.527    2.37
+DA      "C4'"       "C3'"       "C2'"     102.433    1.50
+DA      "C4'"       "C3'"       "H3'"     110.775    1.50
+DA      "O3'"       "C3'"       "C2'"     111.424    1.96
+DA      "O3'"       "C3'"       "H3'"     110.713    1.50
+DA      "C2'"       "C3'"       "H3'"     110.846    1.50
+DA      "C3'"       "O3'"      "HO3'"     109.026    2.38
+DA      "C3'"       "C2'"       "C1'"     102.663    1.50
+DA      "C3'"       "C2'"       "H2'"     111.194    1.50
+DA      "C3'"       "C2'"      "H2''"     111.194    1.50
+DA      "C1'"       "C2'"       "H2'"     111.213    1.50
+DA      "C1'"       "C2'"      "H2''"     111.213    1.50
+DA      "H2'"       "C2'"      "H2''"     109.148    1.50
+DA      "O4'"       "C1'"       "C2'"     106.035    1.50
+DA      "O4'"       "C1'"          N9     108.236    1.50
+DA      "O4'"       "C1'"       "H1'"     109.059    1.50
+DA      "C2'"       "C1'"          N9     114.190    1.67
+DA      "C2'"       "C1'"       "H1'"     109.272    1.50
+DA         N9       "C1'"       "H1'"     109.282    1.50
+DA      "C1'"          N9          C8     127.636    2.81
+DA      "C1'"          N9          C4     126.671    2.93
+DA         C8          N9          C4     105.693    1.50
+DA         N9          C8          N7     113.469    1.50
+DA         N9          C8          H8     123.206    1.50
+DA         N7          C8          H8     123.326    1.50
+DA         C8          N7          C5     104.739    1.50
+DA         N7          C5          C6     132.250    1.50
+DA         N7          C5          C4     110.483    1.50
+DA         C6          C5          C4     117.267    1.50
+DA         C5          C6          N6     123.792    1.50
+DA         C5          C6          N1     117.409    1.50
+DA         N6          C6          N1     118.799    1.50
+DA         C6          N6         H61     119.723    1.50
+DA         C6          N6         H62     119.723    1.50
+DA        H61          N6         H62     120.554    1.88
+DA         C6          N1          C2     118.521    1.50
+DA         N1          C2          N3     129.332    1.50
+DA         N1          C2          H2     115.313    1.50
+DA         N3          C2          H2     115.355    1.50
+DA         C2          N3          C4     110.982    1.50
+DA         N9          C4          C5     105.616    1.50
+DA         N9          C4          N3     127.895    1.50
+DA         C5          C4          N3     126.489    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+DA      C2e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+DA      C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+DA      C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+DA      C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+DA      C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+DA      C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+DA      C3e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+DA      C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+DA      C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+DA      C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+DA      C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+DA      C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+DA      alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+DA      beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+DA      epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+DA      gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+DA              const_14          N7          C8          N9       "C1'"     180.000    10.0     2
+DA              const_26          C5          C4          N9       "C1'"     180.000    10.0     2
+DA              const_17          N9          C8          N7          C5       0.000    10.0     2
+DA              const_20          C6          C5          N7          C8     180.000    10.0     2
+DA       const_sp2_sp2_4          N7          C5          C6          N6       0.000     5.0     2
+DA              const_21          N9          C4          C5          N7       0.000    10.0     2
+DA             sp2_sp2_1          C5          C6          N6         H61     180.000     5.0     2
+DA       const_sp2_sp2_6          N6          C6          N1          C2     180.000     5.0     2
+DA       const_sp2_sp2_7          N3          C2          N1          C6       0.000     5.0     2
+DA       const_sp2_sp2_9          N1          C2          N3          C4       0.000     5.0     2
+DA              const_12          N9          C4          N3          C2     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+DA   chir_1    P    "O5'"    OP3    OP2    both
+DA   chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+DA   chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+DA   chir_4    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+DA   plan-1       "C1'"   0.020
+DA   plan-1          C2   0.020
+DA   plan-1          C4   0.020
+DA   plan-1          C5   0.020
+DA   plan-1          C6   0.020
+DA   plan-1          C8   0.020
+DA   plan-1          H2   0.020
+DA   plan-1          H8   0.020
+DA   plan-1          N1   0.020
+DA   plan-1          N3   0.020
+DA   plan-1          N6   0.020
+DA   plan-1          N7   0.020
+DA   plan-1          N9   0.020
+DA   plan-2          C6   0.020
+DA   plan-2         H61   0.020
+DA   plan-2         H62   0.020
+DA   plan-2          N6   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+DA           SMILES              ACDLabs 10.04                                                                                                          O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
+DA SMILES_CANONICAL               CACTVS 3.341                                                                                         Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
+DA           SMILES               CACTVS 3.341                                                                                             Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
+DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                       c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N
+DA           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                    c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)O)O)N
+DA            InChI                InChI  1.03 InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
+DA         InChIKey                InChI  1.03                                                                                                                    KHWCHTKSEGGWEX-RRKCRQDMSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+DA  acedrg               243         "dictionary generator"                  
+DA  acedrg_database      11          "data source"                           
+DA  rdkit                2017.03.2   "Chemoinformatics tool"
+DA  refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/DC.cif b/image_analysis/structure_refinement/monomers/DC.cif
new file mode 100644
index 000000000..f0373996c
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/DC.cif
@@ -0,0 +1,250 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+DC    DC        "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"     DNA     32     20     .     
+#
+data_comp_DC
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+DC      OP3     O       OP      -1      4.759       -6.216      1.740       
+DC      P       P       P       0       5.427       -6.783      0.501       
+DC      OP1     O       O       0       5.450       -8.300      0.487       
+DC      OP2     O       OP      -1      6.788       -6.171      0.232       
+DC      "O5'"   O       O2      0       4.494       -6.346      -0.742      
+DC      "C5'"   C       CH2     0       3.097       -6.734      -0.736      
+DC      "C4'"   C       CH1     0       2.438       -6.261      -2.009      
+DC      "O4'"   O       O2      0       2.537       -4.821      -2.097      
+DC      "C3'"   C       CH1     0       3.044       -6.825      -3.297      
+DC      "O3'"   O       OH1     0       2.035       -7.363      -4.147      
+DC      "C2'"   C       CH2     0       3.705       -5.618      -3.951      
+DC      "C1'"   C       CH1     0       2.890       -4.454      -3.414      
+DC      N1      N       NR6     0       3.622       -3.158      -3.358      
+DC      C2      C       CR6     0       3.233       -2.087      -4.185      
+DC      O2      O       O       0       2.273       -2.221      -4.961      
+DC      N3      N       NRD6    0       3.923       -0.917      -4.114      
+DC      C4      C       CR6     0       4.961       -0.779      -3.274      
+DC      N4      N       NH2     0       5.596       0.387       -3.250      
+DC      C5      C       CR16    0       5.371       -1.854      -2.432      
+DC      C6      C       CR16    0       4.683       -3.007      -2.507      
+DC      "H5'"   H       H       0       2.640       -6.331      0.044       
+DC      "H5''"  H       H       0       3.022       -7.718      -0.669      
+DC      "H4'"   H       H       0       1.482       -6.507      -1.967      
+DC      "H3'"   H       H       0       3.719       -7.516      -3.087      
+DC      "HO3'"  H       H       0       1.460       -6.765      -4.330      
+DC      "H2'"   H       H       0       3.647       -5.668      -4.930      
+DC      "H2''"  H       H       0       4.648       -5.546      -3.691      
+DC      "H1'"   H       H       0       2.063       -4.358      -3.951      
+DC      H41     H       H       0       5.385       1.014       -3.827      
+DC      H42     H       H       0       6.226       0.528       -2.656      
+DC      H5      H       H       0       6.097       -1.763      -1.841      
+DC      H6      H       H       0       4.929       -3.731      -1.969      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+DC        OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+DC          P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+DC          P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+DC          P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+DC      "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+DC      "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+DC      "C4'"       "O4'"      SINGLE       n     1.445  0.0100     1.445  0.0100
+DC      "C4'"       "C3'"      SINGLE       n     1.526  0.0115     1.526  0.0115
+DC      "O4'"       "C1'"      SINGLE       n     1.413  0.0100     1.413  0.0100
+DC      "C3'"       "O3'"      SINGLE       n     1.424  0.0100     1.424  0.0100
+DC      "C3'"       "C2'"      SINGLE       n     1.522  0.0100     1.522  0.0100
+DC      "C2'"       "C1'"      SINGLE       n     1.520  0.0100     1.520  0.0100
+DC      "C1'"          N1      SINGLE       n     1.480  0.0115     1.480  0.0115
+DC         N1          C2      SINGLE       y     1.397  0.0100     1.397  0.0100
+DC         N1          C6      SINGLE       y     1.360  0.0118     1.360  0.0118
+DC         C2          O2      DOUBLE       n     1.241  0.0100     1.241  0.0100
+DC         C2          N3      SINGLE       y     1.355  0.0119     1.355  0.0119
+DC         N3          C4      DOUBLE       y     1.339  0.0110     1.339  0.0110
+DC         C4          N4      SINGLE       n     1.325  0.0109     1.325  0.0109
+DC         C4          C5      SINGLE       y     1.422  0.0123     1.422  0.0123
+DC         C5          C6      DOUBLE       y     1.342  0.0100     1.342  0.0100
+DC      "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DC      "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DC      "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.987  0.0170
+DC      "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.988  0.0189
+DC      "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+DC      "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.982  0.0200
+DC      "C2'"      "H2''"      SINGLE       n     1.089  0.0100     0.982  0.0200
+DC      "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.991  0.0103
+DC         N4         H41      SINGLE       n     1.016  0.0100     0.877  0.0200
+DC         N4         H42      SINGLE       n     1.016  0.0100     0.877  0.0200
+DC         C5          H5      SINGLE       n     1.082  0.0130     0.941  0.0174
+DC         C6          H6      SINGLE       n     1.082  0.0130     0.935  0.0143
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+DC        OP3           P         OP1     112.864    1.69
+DC        OP3           P         OP2     112.864    1.69
+DC        OP3           P       "O5'"     105.808    2.07
+DC        OP1           P         OP2     112.864    1.69
+DC        OP1           P       "O5'"     105.808    2.07
+DC        OP2           P       "O5'"     105.808    2.07
+DC          P       "O5'"       "C5'"     118.783    1.50
+DC      "O5'"       "C5'"       "C4'"     109.342    1.50
+DC      "O5'"       "C5'"       "H5'"     109.845    1.50
+DC      "O5'"       "C5'"      "H5''"     109.845    1.50
+DC      "C4'"       "C5'"       "H5'"     109.624    1.50
+DC      "C4'"       "C5'"      "H5''"     109.624    1.50
+DC      "H5'"       "C5'"      "H5''"     108.472    1.50
+DC      "C5'"       "C4'"       "O4'"     109.615    1.50
+DC      "C5'"       "C4'"       "C3'"     114.866    1.63
+DC      "C5'"       "C4'"       "H4'"     108.268    1.50
+DC      "O4'"       "C4'"       "C3'"     105.770    1.50
+DC      "O4'"       "C4'"       "H4'"     108.698    1.50
+DC      "C3'"       "C4'"       "H4'"     109.069    1.50
+DC      "C4'"       "O4'"       "C1'"     109.692    1.50
+DC      "C4'"       "C3'"       "O3'"     110.527    2.37
+DC      "C4'"       "C3'"       "C2'"     102.800    1.50
+DC      "C4'"       "C3'"       "H3'"     110.775    1.50
+DC      "O3'"       "C3'"       "C2'"     110.636    2.59
+DC      "O3'"       "C3'"       "H3'"     110.713    1.50
+DC      "C2'"       "C3'"       "H3'"     110.862    1.50
+DC      "C3'"       "O3'"      "HO3'"     109.026    2.38
+DC      "C3'"       "C2'"       "C1'"     102.834    1.50
+DC      "C3'"       "C2'"       "H2'"     111.310    1.50
+DC      "C3'"       "C2'"      "H2''"     111.310    1.50
+DC      "C1'"       "C2'"       "H2'"     111.187    1.50
+DC      "C1'"       "C2'"      "H2''"     111.187    1.50
+DC      "H2'"       "C2'"      "H2''"     108.952    1.50
+DC      "O4'"       "C1'"       "C2'"     106.308    1.50
+DC      "O4'"       "C1'"          N1     107.584    1.50
+DC      "O4'"       "C1'"       "H1'"     109.550    1.50
+DC      "C2'"       "C1'"          N1     114.268    1.50
+DC      "C2'"       "C1'"       "H1'"     109.741    1.50
+DC         N1       "C1'"       "H1'"     109.342    1.50
+DC      "C1'"          N1          C2     118.777    1.50
+DC      "C1'"          N1          C6     120.713    1.50
+DC         C2          N1          C6     120.510    1.50
+DC         N1          C2          O2     118.710    1.50
+DC         N1          C2          N3     118.927    1.50
+DC         O2          C2          N3     122.370    1.50
+DC         C2          N3          C4     120.266    1.50
+DC         N3          C4          N4     117.855    1.50
+DC         N3          C4          C5     121.269    1.50
+DC         N4          C4          C5     120.876    1.50
+DC         C4          N4         H41     119.818    1.59
+DC         C4          N4         H42     119.818    1.59
+DC        H41          N4         H42     120.363    1.85
+DC         C4          C5          C6     117.808    1.50
+DC         C4          C5          H5     121.350    1.50
+DC         C6          C5          H5     120.848    1.50
+DC         N1          C6          C5     121.215    1.50
+DC         N1          C6          H6     118.510    1.50
+DC         C5          C6          H6     120.275    1.75
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+DC      C2e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+DC      C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+DC      C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+DC      C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+DC      C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+DC      C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+DC      C3e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+DC      C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+DC      C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+DC      C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+DC      C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+DC      C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+DC      alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+DC      beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+DC      epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+DC      gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+DC       const_sp2_sp2_4          O2          C2          N1       "C1'"       0.000     5.0     2
+DC              const_18          C5          C6          N1       "C1'"     180.000    10.0     2
+DC       const_sp2_sp2_6          O2          C2          N3          C4     180.000     5.0     2
+DC       const_sp2_sp2_8          N4          C4          N3          C2     180.000     5.0     2
+DC             sp2_sp2_3          N3          C4          N4         H41       0.000     5.0     2
+DC              const_11          N4          C4          C5          C6     180.000    10.0     2
+DC              const_13          C4          C5          C6          N1       0.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+DC   chir_1    P    "O5'"    OP3    OP2    both
+DC   chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+DC   chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+DC   chir_4    "C1'"    "O4'"    N1    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+DC   plan-1       "C1'"   0.020
+DC   plan-1          C2   0.020
+DC   plan-1          C4   0.020
+DC   plan-1          C5   0.020
+DC   plan-1          C6   0.020
+DC   plan-1          H5   0.020
+DC   plan-1          H6   0.020
+DC   plan-1          N1   0.020
+DC   plan-1          N3   0.020
+DC   plan-1          N4   0.020
+DC   plan-1          O2   0.020
+DC   plan-2          C4   0.020
+DC   plan-2         H41   0.020
+DC   plan-2         H42   0.020
+DC   plan-2          N4   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+DC           SMILES              ACDLabs 10.04                                                                                                      O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O
+DC SMILES_CANONICAL               CACTVS 3.341                                                                                     NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
+DC           SMILES               CACTVS 3.341                                                                                         NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
+DC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                         C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
+DC           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                      C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
+DC            InChI                InChI  1.03 InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
+DC         InChIKey                InChI  1.03                                                                                                                 NCMVOABPESMRCP-SHYZEUOFSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+DC  acedrg               243         "dictionary generator"                  
+DC  acedrg_database      11          "data source"                           
+DC  rdkit                2017.03.2   "Chemoinformatics tool"
+DC  refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/DG.cif b/image_analysis/structure_refinement/monomers/DG.cif
new file mode 100644
index 000000000..1073727b3
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/DG.cif
@@ -0,0 +1,271 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+DG    DG        "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE"     DNA     35     23     .     
+#
+data_comp_DG
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+DG      OP3     O       OP      -1      0.424       -8.734      -9.816      
+DG      P       P       P       0       0.296       -8.811      -11.326     
+DG      OP1     O       O       0       -0.898      -9.631      -11.775     
+DG      OP2     O       OP      -1      1.587       -9.229      -12.005     
+DG      "O5'"   O       O2      0       0.007       -7.303      -11.822     
+DG      "C5'"   C       CH2     0       -1.170      -6.617      -11.324     
+DG      "C4'"   C       CH1     0       -1.206      -5.213      -11.876     
+DG      "O4'"   O       O2      0       -0.018      -4.512      -11.450     
+DG      "C3'"   C       CH1     0       -1.259      -5.123      -13.404     
+DG      "O3'"   O       OH1     0       -2.248      -4.188      -13.827     
+DG      "C2'"   C       CH2     0       0.144       -4.654      -13.783     
+DG      "C1'"   C       CH1     0       0.565       -3.849      -12.566     
+DG      N9      N       NR5     0       2.012       -3.775      -12.354     
+DG      C8      C       CR15    0       2.857       -4.830      -12.111     
+DG      N7      N       NRD5    0       4.108       -4.471      -11.958     
+DG      C5      C       CR56    0       4.088       -3.091      -12.106     
+DG      C6      C       CR6     0       5.150       -2.149      -12.042     
+DG      O6      O       O       0       6.352       -2.369      -11.834     
+DG      N1      N       NR16    0       4.698       -0.841      -12.249     
+DG      C2      C       CR6     0       3.388       -0.485      -12.487     
+DG      N2      N       NH2     0       3.138       0.820       -12.662     
+DG      N3      N       NRD6    0       2.387       -1.368      -12.548     
+DG      C4      C       CR56    0       2.803       -2.647      -12.350     
+DG      "H5'"   H       H       0       -1.147      -6.585      -10.336     
+DG      "H5''"  H       H       0       -1.985      -7.104      -11.602     
+DG      "H4'"   H       H       0       -1.996      -4.756      -11.498     
+DG      "H3'"   H       H       0       -1.441      -6.012      -13.795     
+DG      "HO3'"  H       H       0       -2.096      -3.427      -13.481     
+DG      "H2'"   H       H       0       0.125       -4.097      -14.586     
+DG      "H2''"  H       H       0       0.741       -5.412      -13.932     
+DG      "H1'"   H       H       0       0.190       -2.932      -12.632     
+DG      H8      H       H       0       2.565       -5.725      -12.063     
+DG      H1      H       H       0       5.314       -0.188      -12.222     
+DG      H21     H       H       0       2.584       1.078       -13.291     
+DG      H22     H       H       0       3.528       1.412       -12.146     
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+DG        OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+DG          P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+DG          P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+DG          P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+DG      "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+DG      "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+DG      "C4'"       "O4'"      SINGLE       n     1.442  0.0100     1.442  0.0100
+DG      "C4'"       "C3'"      SINGLE       n     1.526  0.0115     1.526  0.0115
+DG      "O4'"       "C1'"      SINGLE       n     1.425  0.0100     1.425  0.0100
+DG      "C3'"       "O3'"      SINGLE       n     1.424  0.0100     1.424  0.0100
+DG      "C3'"       "C2'"      SINGLE       n     1.526  0.0101     1.526  0.0101
+DG      "C2'"       "C1'"      SINGLE       n     1.521  0.0118     1.521  0.0118
+DG      "C1'"          N9      SINGLE       n     1.462  0.0111     1.462  0.0111
+DG         N9          C8      SINGLE       y     1.373  0.0100     1.373  0.0100
+DG         N9          C4      SINGLE       y     1.375  0.0100     1.375  0.0100
+DG         C8          N7      DOUBLE       y     1.312  0.0100     1.312  0.0100
+DG         N7          C5      SINGLE       y     1.390  0.0100     1.390  0.0100
+DG         C5          C6      SINGLE       y     1.417  0.0103     1.417  0.0103
+DG         C5          C4      DOUBLE       y     1.377  0.0100     1.377  0.0100
+DG         C6          O6      DOUBLE       n     1.239  0.0100     1.239  0.0100
+DG         C6          N1      SINGLE       y     1.396  0.0107     1.396  0.0107
+DG         N1          C2      SINGLE       y     1.374  0.0100     1.374  0.0100
+DG         C2          N2      SINGLE       n     1.340  0.0101     1.340  0.0101
+DG         C2          N3      DOUBLE       y     1.333  0.0104     1.333  0.0104
+DG         N3          C4      SINGLE       y     1.355  0.0100     1.355  0.0100
+DG      "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DG      "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DG      "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.987  0.0170
+DG      "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.988  0.0189
+DG      "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+DG      "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.977  0.0113
+DG      "C2'"      "H2''"      SINGLE       n     1.089  0.0100     0.977  0.0113
+DG      "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.993  0.0101
+DG         C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+DG         N1          H1      SINGLE       n     1.016  0.0100     0.897  0.0200
+DG         N2         H21      SINGLE       n     1.016  0.0100     0.877  0.0200
+DG         N2         H22      SINGLE       n     1.016  0.0100     0.877  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+DG        OP3           P         OP1     112.864    1.69
+DG        OP3           P         OP2     112.864    1.69
+DG        OP3           P       "O5'"     105.808    2.07
+DG        OP1           P         OP2     112.864    1.69
+DG        OP1           P       "O5'"     105.808    2.07
+DG        OP2           P       "O5'"     105.808    2.07
+DG          P       "O5'"       "C5'"     118.783    1.50
+DG      "O5'"       "C5'"       "C4'"     109.342    1.50
+DG      "O5'"       "C5'"       "H5'"     109.845    1.50
+DG      "O5'"       "C5'"      "H5''"     109.845    1.50
+DG      "C4'"       "C5'"       "H5'"     109.624    1.50
+DG      "C4'"       "C5'"      "H5''"     109.624    1.50
+DG      "H5'"       "C5'"      "H5''"     108.472    1.50
+DG      "C5'"       "C4'"       "O4'"     109.123    1.50
+DG      "C5'"       "C4'"       "C3'"     114.866    1.63
+DG      "C5'"       "C4'"       "H4'"     108.268    1.50
+DG      "O4'"       "C4'"       "C3'"     105.506    1.50
+DG      "O4'"       "C4'"       "H4'"     108.947    1.50
+DG      "C3'"       "C4'"       "H4'"     109.069    1.50
+DG      "C4'"       "O4'"       "C1'"     108.795    1.50
+DG      "C4'"       "C3'"       "O3'"     110.527    2.37
+DG      "C4'"       "C3'"       "C2'"     102.433    1.50
+DG      "C4'"       "C3'"       "H3'"     110.775    1.50
+DG      "O3'"       "C3'"       "C2'"     111.424    1.96
+DG      "O3'"       "C3'"       "H3'"     110.713    1.50
+DG      "C2'"       "C3'"       "H3'"     110.846    1.50
+DG      "C3'"       "O3'"      "HO3'"     109.026    2.38
+DG      "C3'"       "C2'"       "C1'"     102.663    1.50
+DG      "C3'"       "C2'"       "H2'"     111.194    1.50
+DG      "C3'"       "C2'"      "H2''"     111.194    1.50
+DG      "C1'"       "C2'"       "H2'"     111.213    1.50
+DG      "C1'"       "C2'"      "H2''"     111.213    1.50
+DG      "H2'"       "C2'"      "H2''"     109.148    1.50
+DG      "O4'"       "C1'"       "C2'"     106.035    1.50
+DG      "O4'"       "C1'"          N9     108.236    1.50
+DG      "O4'"       "C1'"       "H1'"     109.059    1.50
+DG      "C2'"       "C1'"          N9     114.190    1.67
+DG      "C2'"       "C1'"       "H1'"     109.272    1.50
+DG         N9       "C1'"       "H1'"     109.282    1.50
+DG      "C1'"          N9          C8     127.617    2.81
+DG      "C1'"          N9          C4     126.652    2.93
+DG         C8          N9          C4     105.731    1.50
+DG         N9          C8          N7     113.507    1.50
+DG         N9          C8          H8     123.187    1.50
+DG         N7          C8          H8     123.307    1.50
+DG         C8          N7          C5     104.778    1.50
+DG         N7          C5          C6     130.030    1.50
+DG         N7          C5          C4     110.574    1.50
+DG         C6          C5          C4     119.397    1.50
+DG         C5          C6          O6     128.244    1.50
+DG         C5          C6          N1     111.367    1.50
+DG         O6          C6          N1     120.389    1.50
+DG         C6          N1          C2     125.351    1.50
+DG         C6          N1          H1     116.978    2.44
+DG         C2          N1          H1     117.677    2.71
+DG         N1          C2          N2     116.576    1.50
+DG         N1          C2          N3     123.602    1.50
+DG         N2          C2          N3     119.821    1.50
+DG         C2          N2         H21     119.868    1.50
+DG         C2          N2         H22     119.868    1.50
+DG        H21          N2         H22     120.263    1.96
+DG         C2          N3          C4     112.066    1.50
+DG         N9          C4          C5     105.411    1.50
+DG         N9          C4          N3     126.378    1.50
+DG         C5          C4          N3     128.211    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+DG      C2e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+DG      C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+DG      C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+DG      C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+DG      C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+DG      C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+DG      C3e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+DG      C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+DG      C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+DG      C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+DG      C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+DG      C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+DG      alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+DG      beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+DG      epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+DG      gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+DG              const_18          N7          C8          N9       "C1'"     180.000    10.0     2
+DG              const_30          C5          C4          N9       "C1'"     180.000    10.0     2
+DG              const_21          N9          C8          N7          C5       0.000    10.0     2
+DG              const_24          C6          C5          N7          C8     180.000    10.0     2
+DG       const_sp2_sp2_4          N7          C5          C6          O6       0.000     5.0     2
+DG              const_25          N9          C4          C5          N7       0.000    10.0     2
+DG       const_sp2_sp2_7          O6          C6          N1          C2     180.000     5.0     2
+DG              const_11          N2          C2          N1          C6     180.000    10.0     2
+DG             sp2_sp2_1          N1          C2          N2         H21     180.000     5.0     2
+DG              const_14          N2          C2          N3          C4     180.000    10.0     2
+DG              const_16          N9          C4          N3          C2     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+DG   chir_1    P    "O5'"    OP3    OP2    both
+DG   chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+DG   chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+DG   chir_4    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+DG   plan-1       "C1'"   0.020
+DG   plan-1          C2   0.020
+DG   plan-1          C4   0.020
+DG   plan-1          C5   0.020
+DG   plan-1          C6   0.020
+DG   plan-1          C8   0.020
+DG   plan-1          H1   0.020
+DG   plan-1          H8   0.020
+DG   plan-1          N1   0.020
+DG   plan-1          N2   0.020
+DG   plan-1          N3   0.020
+DG   plan-1          N7   0.020
+DG   plan-1          N9   0.020
+DG   plan-1          O6   0.020
+DG   plan-2          C2   0.020
+DG   plan-2         H21   0.020
+DG   plan-2         H22   0.020
+DG   plan-2          N2   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+DG           SMILES              ACDLabs 10.04                                                                                                          O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3)COP(=O)(O)O
+DG SMILES_CANONICAL               CACTVS 3.341                                                                                           NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
+DG           SMILES               CACTVS 3.341                                                                                               NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
+DG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                             c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N
+DG           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                          c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N
+DG            InChI                InChI  1.03 InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
+DG         InChIKey                InChI  1.03                                                                                                                           LTFMZDNNPPEQNG-KVQBGUIXSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+DG  acedrg               243         "dictionary generator"                  
+DG  acedrg_database      11          "data source"                           
+DG  rdkit                2017.03.2   "Chemoinformatics tool"
+DG  refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/DMS.cif b/image_analysis/structure_refinement/monomers/DMS.cif
new file mode 100644
index 000000000..209672234
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/DMS.cif
@@ -0,0 +1,117 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+DMS     DMS      "DIMETHYL SULFOXIDE"     NON-POLYMER     10     4     .     
+#
+data_comp_DMS
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+DMS     S       S       S3      0       63.218      46.394      -11.587     
+DMS     O       O       O       0       63.732      46.133      -12.975     
+DMS     C1      C       CH3     0       64.619      46.928      -10.638     
+DMS     C2      C       CH3     0       63.010      44.801      -10.834     
+DMS     H11     H       H       0       64.347      47.082      -9.723      
+DMS     H12     H       H       0       64.967      47.748      -11.014     
+DMS     H13     H       H       0       65.302      46.245      -10.662     
+DMS     H21     H       H       0       63.858      44.337      -10.825     
+DMS     H22     H       H       0       62.366      44.288      -11.340     
+DMS     H23     H       H       0       62.693      44.913      -9.927      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+DMS           S           O      DOUBLE       n     1.503  0.0200     1.503  0.0200
+DMS           S          C1      SINGLE       n     1.774  0.0176     1.774  0.0176
+DMS           S          C2      SINGLE       n     1.774  0.0176     1.774  0.0176
+DMS          C1         H11      SINGLE       n     1.089  0.0100     0.967  0.0136
+DMS          C1         H12      SINGLE       n     1.089  0.0100     0.967  0.0136
+DMS          C1         H13      SINGLE       n     1.089  0.0100     0.967  0.0136
+DMS          C2         H21      SINGLE       n     1.089  0.0100     0.967  0.0136
+DMS          C2         H22      SINGLE       n     1.089  0.0100     0.967  0.0136
+DMS          C2         H23      SINGLE       n     1.089  0.0100     0.967  0.0136
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+DMS           O           S          C1     106.047    1.50
+DMS           O           S          C2     106.047    1.50
+DMS          C1           S          C2      97.789    1.50
+DMS           S          C1         H11     109.408    1.50
+DMS           S          C1         H12     109.408    1.50
+DMS           S          C1         H13     109.408    1.50
+DMS         H11          C1         H12     109.545    1.50
+DMS         H11          C1         H13     109.545    1.50
+DMS         H12          C1         H13     109.545    1.50
+DMS           S          C2         H21     109.408    1.50
+DMS           S          C2         H22     109.408    1.50
+DMS           S          C2         H23     109.408    1.50
+DMS         H21          C2         H22     109.545    1.50
+DMS         H21          C2         H23     109.545    1.50
+DMS         H22          C2         H23     109.545    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+DMS             sp3_sp3_1         H11          C1           S           O     180.000    10.0     3
+DMS             sp3_sp3_8         H21          C2           S           O     -60.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+DMS    chir_1    S    O    C1    C2    both
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+DMS           SMILES              ACDLabs 10.04               sulfinyldimethane
+DMS SMILES_CANONICAL               CACTVS 3.341                       C[S](C)=O
+DMS           SMILES               CACTVS 3.341                       C[S](C)=O
+DMS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                         CS(=O)C
+DMS           SMILES "OpenEye OEToolkits" 1.5.0                         CS(=O)C
+DMS            InChI                InChI  1.03 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
+DMS         InChIKey                InChI  1.03     IAZDPXIOMUYVGZ-UHFFFAOYSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+DMS acedrg               243         "dictionary generator"                  
+DMS acedrg_database      11          "data source"                           
+DMS rdkit                2017.03.2   "Chemoinformatics tool"
+DMS refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/DT.cif b/image_analysis/structure_refinement/monomers/DT.cif
new file mode 100644
index 000000000..affc26c5a
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/DT.cif
@@ -0,0 +1,256 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+DT    DT        "THYMIDINE-5'-MONOPHOSPHATE"     DNA     34     21     .     
+#
+data_comp_DT
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+DT      OP3     O       OP      -1      -9.033      1.811       3.710       
+DT      P       P       P       0       -8.813      3.246       4.151       
+DT      OP1     O       O       0       -9.790      3.689       5.223       
+DT      OP2     O       OP      -1      -8.738      4.214       2.986       
+DT      "O5'"   O       O2      0       -7.356      3.277       4.843       
+DT      "C5'"   C       CH2     0       -7.098      2.397       5.967       
+DT      "C4'"   C       CH1     0       -5.688      2.610       6.462       
+DT      "O4'"   O       O2      0       -4.754      2.345       5.391       
+DT      "C3'"   C       CH1     0       -5.391      4.024       6.970       
+DT      "O3'"   O       OH1     0       -4.766      3.989       8.251       
+DT      "C2'"   C       CH2     0       -4.437      4.599       5.930       
+DT      "C1'"   C       CH1     0       -3.760      3.359       5.367       
+DT      N1      N       NR6     0       -3.270      3.502       3.966       
+DT      C2      C       CR6     0       -1.905      3.474       3.713       
+DT      O2      O       O       0       -1.053      3.332       4.583       
+DT      N3      N       NR16    0       -1.559      3.618       2.388       
+DT      C4      C       CR6     0       -2.414      3.786       1.310       
+DT      O4      O       O       0       -1.948      3.903       0.172       
+DT      C5      C       CR6     0       -3.824      3.809       1.640       
+DT      C7      C       CH3     0       -4.824      3.988       0.535       
+DT      C6      C       CR16    0       -4.178      3.669       2.932       
+DT      "H5'"   H       H       0       -7.213      1.455       5.689       
+DT      "H5''"  H       H       0       -7.738      2.588       6.696       
+DT      "H4'"   H       H       0       -5.520      1.964       7.190       
+DT      "H3'"   H       H       0       -6.221      4.559       7.010       
+DT      "HO3'"  H       H       0       -4.051      3.531       8.213       
+DT      "H2'"   H       H       0       -3.782      5.203       6.342       
+DT      "H2''"  H       H       0       -4.926      5.088       5.233       
+DT      "H1'"   H       H       0       -3.014      3.092       5.967       
+DT      H3      H       H       0       -0.682      3.600       2.215       
+DT      H71     H       H       0       -5.705      3.724       0.845       
+DT      H72     H       H       0       -4.574      3.437       -0.224      
+DT      H73     H       H       0       -4.846      4.920       0.263       
+DT      H6      H       H       0       -5.103      3.686       3.152       
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+DT        OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+DT          P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+DT          P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+DT          P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+DT      "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+DT      "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+DT      "C4'"       "O4'"      SINGLE       n     1.445  0.0100     1.445  0.0100
+DT      "C4'"       "C3'"      SINGLE       n     1.526  0.0115     1.526  0.0115
+DT      "O4'"       "C1'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+DT      "C3'"       "O3'"      SINGLE       n     1.424  0.0100     1.424  0.0100
+DT      "C3'"       "C2'"      SINGLE       n     1.522  0.0100     1.522  0.0100
+DT      "C2'"       "C1'"      SINGLE       n     1.523  0.0130     1.523  0.0130
+DT      "C1'"          N1      SINGLE       n     1.477  0.0139     1.477  0.0139
+DT         N1          C2      SINGLE       y     1.379  0.0100     1.379  0.0100
+DT         N1          C6      SINGLE       y     1.380  0.0107     1.380  0.0107
+DT         C2          O2      DOUBLE       n     1.224  0.0111     1.224  0.0111
+DT         C2          N3      SINGLE       y     1.373  0.0100     1.373  0.0100
+DT         N3          C4      SINGLE       y     1.383  0.0100     1.383  0.0100
+DT         C4          O4      DOUBLE       n     1.234  0.0141     1.234  0.0141
+DT         C4          C5      SINGLE       y     1.446  0.0100     1.446  0.0100
+DT         C5          C7      SINGLE       n     1.500  0.0100     1.500  0.0100
+DT         C5          C6      DOUBLE       y     1.343  0.0112     1.343  0.0112
+DT      "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DT      "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+DT      "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.987  0.0170
+DT      "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.988  0.0189
+DT      "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+DT      "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.982  0.0200
+DT      "C2'"      "H2''"      SINGLE       n     1.089  0.0100     0.982  0.0200
+DT      "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.996  0.0200
+DT         N3          H3      SINGLE       n     1.016  0.0100     0.893  0.0200
+DT         C7         H71      SINGLE       n     1.089  0.0100     0.971  0.0135
+DT         C7         H72      SINGLE       n     1.089  0.0100     0.971  0.0135
+DT         C7         H73      SINGLE       n     1.089  0.0100     0.971  0.0135
+DT         C6          H6      SINGLE       n     1.082  0.0130     0.951  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+DT        OP3           P         OP1     112.864    1.69
+DT        OP3           P         OP2     112.864    1.69
+DT        OP3           P       "O5'"     105.808    2.07
+DT        OP1           P         OP2     112.864    1.69
+DT        OP1           P       "O5'"     105.808    2.07
+DT        OP2           P       "O5'"     105.808    2.07
+DT          P       "O5'"       "C5'"     118.783    1.50
+DT      "O5'"       "C5'"       "C4'"     109.342    1.50
+DT      "O5'"       "C5'"       "H5'"     109.845    1.50
+DT      "O5'"       "C5'"      "H5''"     109.845    1.50
+DT      "C4'"       "C5'"       "H5'"     109.624    1.50
+DT      "C4'"       "C5'"      "H5''"     109.624    1.50
+DT      "H5'"       "C5'"      "H5''"     108.472    1.50
+DT      "C5'"       "C4'"       "O4'"     109.615    1.50
+DT      "C5'"       "C4'"       "C3'"     114.866    1.63
+DT      "C5'"       "C4'"       "H4'"     108.268    1.50
+DT      "O4'"       "C4'"       "C3'"     105.770    1.50
+DT      "O4'"       "C4'"       "H4'"     108.698    1.50
+DT      "C3'"       "C4'"       "H4'"     109.069    1.50
+DT      "C4'"       "O4'"       "C1'"     109.692    1.50
+DT      "C4'"       "C3'"       "O3'"     110.527    2.37
+DT      "C4'"       "C3'"       "C2'"     102.800    1.50
+DT      "C4'"       "C3'"       "H3'"     110.775    1.50
+DT      "O3'"       "C3'"       "C2'"     110.636    2.59
+DT      "O3'"       "C3'"       "H3'"     110.713    1.50
+DT      "C2'"       "C3'"       "H3'"     110.862    1.50
+DT      "C3'"       "O3'"      "HO3'"     109.026    2.38
+DT      "C3'"       "C2'"       "C1'"     102.834    1.50
+DT      "C3'"       "C2'"       "H2'"     111.310    1.50
+DT      "C3'"       "C2'"      "H2''"     111.310    1.50
+DT      "C1'"       "C2'"       "H2'"     111.187    1.50
+DT      "C1'"       "C2'"      "H2''"     111.187    1.50
+DT      "H2'"       "C2'"      "H2''"     108.952    1.50
+DT      "O4'"       "C1'"       "C2'"     106.308    1.50
+DT      "O4'"       "C1'"          N1     107.584    1.50
+DT      "O4'"       "C1'"       "H1'"     109.550    1.50
+DT      "C2'"       "C1'"          N1     114.268    1.50
+DT      "C2'"       "C1'"       "H1'"     109.741    1.50
+DT         N1       "C1'"       "H1'"     109.342    1.50
+DT      "C1'"          N1          C2     118.265    1.50
+DT      "C1'"          N1          C6     120.492    1.50
+DT         C2          N1          C6     121.243    1.50
+DT         N1          C2          O2     122.872    1.50
+DT         N1          C2          N3     114.786    1.50
+DT         O2          C2          N3     122.342    1.50
+DT         C2          N3          C4     127.106    1.50
+DT         C2          N3          H3     115.584    1.79
+DT         C4          N3          H3     117.311    1.81
+DT         N3          C4          O4     119.787    1.50
+DT         N3          C4          C5     115.265    1.50
+DT         O4          C4          C5     124.948    1.50
+DT         C4          C5          C7     118.650    1.50
+DT         C4          C5          C6     118.305    1.50
+DT         C7          C5          C6     123.045    1.50
+DT         C5          C7         H71     109.652    1.50
+DT         C5          C7         H72     109.652    1.50
+DT         C5          C7         H73     109.652    1.50
+DT        H71          C7         H72     109.348    1.50
+DT        H71          C7         H73     109.348    1.50
+DT        H72          C7         H73     109.348    1.50
+DT         N1          C6          C5     123.296    1.50
+DT         N1          C6          H6     117.926    1.56
+DT         C5          C6          H6     118.779    1.68
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+DT      C2e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+DT      C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+DT      C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+DT      C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+DT      C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+DT      C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+DT      C3e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+DT      C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+DT      C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+DT      C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+DT      C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+DT      C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+DT      alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+DT      beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+DT      epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+DT      gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+DT       const_sp2_sp2_4          O2          C2          N1       "C1'"       0.000     5.0     2
+DT              const_22          C5          C6          N1       "C1'"     180.000    10.0     2
+DT       const_sp2_sp2_7          O2          C2          N3          C4     180.000     5.0     2
+DT              const_11          O4          C4          N3          C2     180.000    10.0     2
+DT              const_16          O4          C4          C5          C7       0.000    10.0     2
+DT             sp2_sp3_7          C4          C5          C7         H71     150.000    10.0     6
+DT              const_19          C7          C5          C6          N1     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+DT   chir_1    P    "O5'"    OP3    OP2    both
+DT   chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+DT   chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+DT   chir_4    "C1'"    "O4'"    N1    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+DT   plan-1       "C1'"   0.020
+DT   plan-1          C2   0.020
+DT   plan-1          C4   0.020
+DT   plan-1          C5   0.020
+DT   plan-1          C6   0.020
+DT   plan-1          C7   0.020
+DT   plan-1          H3   0.020
+DT   plan-1          H6   0.020
+DT   plan-1          N1   0.020
+DT   plan-1          N3   0.020
+DT   plan-1          O2   0.020
+DT   plan-1          O4   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+DT           SMILES              ACDLabs 10.04                                                                                                      O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
+DT SMILES_CANONICAL               CACTVS 3.341                                                                                       CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
+DT           SMILES               CACTVS 3.341                                                                                           CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
+DT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                         CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
+DT           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                      CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
+DT            InChI                InChI  1.03 InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
+DT         InChIKey                InChI  1.03                                                                                                                    GYOZYWVXFNDGLU-XLPZGREQSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+DT  acedrg               243         "dictionary generator"                  
+DT  acedrg_database      11          "data source"                           
+DT  rdkit                2017.03.2   "Chemoinformatics tool"
+DT  refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/EDO.cif b/image_analysis/structure_refinement/monomers/EDO.cif
new file mode 100644
index 000000000..9d74e7fbe
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/EDO.cif
@@ -0,0 +1,108 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+EDO     EDO      1,2-ETHANEDIOL     NON-POLYMER     10     4     .     
+#
+data_comp_EDO
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+EDO     C1      C       CH2     0       5.160       28.149      5.379       
+EDO     O1      O       OH1     0       6.106       28.471      4.378       
+EDO     C2      C       CH2     0       3.762       28.430      4.968       
+EDO     O2      O       OH1     0       3.416       27.839      3.730       
+EDO     H11     H       H       0       5.362       28.666      6.186       
+EDO     H12     H       H       0       5.240       27.198      5.599       
+EDO     HO1     H       H       0       6.871       28.201      4.619       
+EDO     H21     H       H       0       3.642       29.401      4.901       
+EDO     H22     H       H       0       3.156       28.097      5.661       
+EDO     HO2     H       H       0       3.485       26.998      3.790       
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+EDO          C1          O1      SINGLE       n     1.414  0.0200     1.414  0.0200
+EDO          C1          C2      SINGLE       n     1.483  0.0200     1.483  0.0200
+EDO          C2          O2      SINGLE       n     1.414  0.0200     1.414  0.0200
+EDO          C1         H11      SINGLE       n     1.089  0.0100     0.980  0.0144
+EDO          C1         H12      SINGLE       n     1.089  0.0100     0.980  0.0144
+EDO          O1         HO1      SINGLE       n     0.970  0.0120     0.846  0.0200
+EDO          C2         H21      SINGLE       n     1.089  0.0100     0.980  0.0144
+EDO          C2         H22      SINGLE       n     1.089  0.0100     0.980  0.0144
+EDO          O2         HO2      SINGLE       n     0.970  0.0120     0.846  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+EDO          O1          C1          C2     113.236    3.00
+EDO          O1          C1         H11     109.012    1.50
+EDO          O1          C1         H12     109.012    1.50
+EDO          C2          C1         H11     108.881    1.50
+EDO          C2          C1         H12     108.881    1.50
+EDO         H11          C1         H12     108.093    1.50
+EDO          C1          O1         HO1     109.347    1.86
+EDO          C1          C2          O2     113.236    3.00
+EDO          C1          C2         H21     108.881    1.50
+EDO          C1          C2         H22     108.881    1.50
+EDO          O2          C2         H21     109.012    1.50
+EDO          O2          C2         H22     109.012    1.50
+EDO         H21          C2         H22     108.093    1.50
+EDO          C2          O2         HO2     109.347    1.86
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+EDO             sp3_sp3_1          C2          C1          O1         HO1     180.000    10.0     3
+EDO             sp3_sp3_4          O1          C1          C2          O2     180.000    10.0     3
+EDO            sp3_sp3_13          C1          C2          O2         HO2     180.000    10.0     3
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+EDO           SMILES              ACDLabs 10.04                                 OCCO
+EDO SMILES_CANONICAL               CACTVS 3.341                                 OCCO
+EDO           SMILES               CACTVS 3.341                                 OCCO
+EDO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                               C(CO)O
+EDO           SMILES "OpenEye OEToolkits" 1.5.0                               C(CO)O
+EDO            InChI                InChI  1.03 InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
+EDO         InChIKey                InChI  1.03          LYCAIKOWRPUZTN-UHFFFAOYSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+EDO acedrg               243         "dictionary generator"                  
+EDO acedrg_database      11          "data source"                           
+EDO rdkit                2017.03.2   "Chemoinformatics tool"
+EDO refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/FAD.cif b/image_analysis/structure_refinement/monomers/FAD.cif
new file mode 100644
index 000000000..9952352d8
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/FAD.cif
@@ -0,0 +1,619 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+FAD     FAD      "FLAVIN-ADENINE DINUCLEOTIDE"     NON-POLYMER     84     53     .     
+#
+data_comp_FAD
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+FAD     PA      P       P       0       20.714      1.770       23.791      
+FAD     O1A     O       O       0       19.737      0.994       22.985      
+FAD     O2A     O       OP      -1      20.556      3.244       23.868      
+FAD     O5B     O       O2      0       20.784      1.154       25.265      
+FAD     C5B     C       CH2     0       21.508      1.920       26.259      
+FAD     C4B     C       CH1     0       21.685      1.088       27.506      
+FAD     O4B     O       O2      0       22.496      1.819       28.451      
+FAD     C3B     C       CH1     0       20.398      0.757       28.265      
+FAD     O3B     O       OH1     0       20.556      -0.451      28.999      
+FAD     C2B     C       CH1     0       20.243      1.982       29.172      
+FAD     O2B     O       OH1     0       19.475      1.727       30.330      
+FAD     C1B     C       CH1     0       21.699      2.264       29.545      
+FAD     N9A     N       NR5     0       21.959      3.685       29.781      
+FAD     C8A     C       CR15    0       22.300      4.646       28.862      
+FAD     N7A     N       NRD5    0       22.466      5.839       29.380      
+FAD     C5A     C       CR56    0       22.214      5.654       30.732      
+FAD     C6A     C       CR6     0       22.225      6.545       31.827      
+FAD     N6A     N       NH2     0       22.509      7.843       31.720      
+FAD     N1A     N       NRD6    0       21.925      6.038       33.053      
+FAD     C2A     C       CR16    0       21.639      4.731       33.155      
+FAD     N3A     N       NRD6    0       21.600      3.805       32.197      
+FAD     C4A     C       CR56    0       21.899      4.330       30.993      
+FAD     N1      N       NRD6    0       21.477      -2.068      14.310      
+FAD     C2      C       CR6     0       21.990      -3.170      13.678      
+FAD     O2      O       O       0       23.119      -3.600      13.933      
+FAD     N3      N       NR16    0       21.215      -3.824      12.720      
+FAD     C4      C       CR6     0       19.939      -3.467      12.324      
+FAD     O4      O       O       0       19.331      -4.099      11.476      
+FAD     C4X     C       CR66    0       19.428      -2.318      12.997      
+FAD     N5      N       NRD6    0       18.223      -1.922      12.672      
+FAD     C5X     C       CR66    0       17.708      -0.822      13.305      
+FAD     C6      C       CR16    0       16.407      -0.419      12.939      
+FAD     C7      C       CR6     0       15.794      0.671       13.514      
+FAD     C7M     C       CH3     0       14.398      1.039       13.068      
+FAD     C8      C       CR6     0       16.505      1.416       14.514      
+FAD     C8M     C       CH3     0       15.889      2.619       15.180      
+FAD     C9      C       CR16    0       17.784      1.024       14.876      
+FAD     C9A     C       CR66    0       18.422      -0.094      14.291      
+FAD     N10     N       NR6     0       19.717      -0.536      14.620      
+FAD     C10     C       CR66    0       20.261      -1.663      13.986      
+FAD     "C1'"   C       CH2     0       20.546      0.156       15.638      
+FAD     "C2'"   C       CH1     0       20.455      -0.488      17.014      
+FAD     "O2'"   O       OH1     0       19.095      -0.421      17.451      
+FAD     "C3'"   C       CH1     0       21.373      0.159       18.058      
+FAD     "O3'"   O       OH1     0       22.723      0.097       17.602      
+FAD     "C4'"   C       CH1     0       21.301      -0.479      19.449      
+FAD     "O4'"   O       OH1     0       19.957      -0.463      19.936      
+FAD     "C5'"   C       CH2     0       22.167      0.224       20.481      
+FAD     "O5'"   O       O2      0       22.110      -0.483      21.743      
+FAD     P       P       P       0       22.951      0.052       22.986      
+FAD     O1P     O       O       0       22.742      -0.871      24.130      
+FAD     O2P     O       OP      -1      24.340      0.346       22.551      
+FAD     O3P     O       O2      0       22.191      1.429       23.280      
+FAD     H51A    H       H       0       21.005      2.745       26.481      
+FAD     H52A    H       H       0       22.397      2.180       25.905      
+FAD     H4B     H       H       0       22.151      0.249       27.259      
+FAD     H3B     H       H       0       19.629      0.687       27.645      
+FAD     HO3A    H       H       0       19.777      -0.616      29.334      
+FAD     H2B     H       H       0       19.868      2.745       28.663      
+FAD     HO2A    H       H       0       19.501      2.350       30.867      
+FAD     H1B     H       H       0       21.939      1.734       30.378      
+FAD     H8A     H       H       0       22.407      4.462       27.944      
+FAD     H61A    H       H       0       22.502      8.360       32.433      
+FAD     H62A    H       H       0       22.705      8.186       30.933      
+FAD     H2A     H       H       0       21.438      4.425       34.027      
+FAD     HN3     H       H       0       21.567      -4.529      12.329      
+FAD     H6      H       H       0       15.940      -0.918      12.276      
+FAD     HM71    H       H       0       14.059      1.787       13.584      
+FAD     HM72    H       H       0       13.809      0.276       13.191      
+FAD     HM73    H       H       0       14.414      1.282       12.127      
+FAD     HM81    H       H       0       16.515      3.008       15.814      
+FAD     HM82    H       H       0       15.082      2.352       15.651      
+FAD     HM83    H       H       0       15.664      3.283       14.507      
+FAD     H9      H       H       0       18.238      1.530       15.543      
+FAD     "H1'1"  H       H       0       20.293      1.095       15.702      
+FAD     "H1'2"  H       H       0       21.480      0.169       15.345      
+FAD     "H2'"   H       H       0       20.705      -1.452      16.929      
+FAD     "HO2'"  H       H       0       19.029      -0.034      18.222      
+FAD     "H3'"   H       H       0       21.118      1.116       18.145      
+FAD     "HO3'"  H       H       0       23.179      -0.185      18.222      
+FAD     "H4'"   H       H       0       21.600      -1.422      19.381      
+FAD     "HO4'"  H       H       0       19.930      -0.056      20.740      
+FAD     "H5'1"  H       H       0       21.854      1.142       20.606      
+FAD     "H5'2"  H       H       0       23.095      0.252       20.176      
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+FAD        PA    P(OC)(OP)(O)2
+FAD       O1A    O(PO3)
+FAD       O2A    O(PO3)
+FAD       O5B    O(CC[5]HH)(PO3)
+FAD       C5B    C(C[5]C[5]O[5]H)(OP)(H)2
+FAD       C4B    C[5](C[5]C[5]HO)(O[5]C[5])(CHHO)(H){1|N<3>,1|O<2>,2|H<1>}
+FAD       O4B    O[5](C[5]N[5a]C[5]H)(C[5]C[5]CH){2|C<3>,2|H<1>,2|O<2>}
+FAD       C3B    C[5](C[5]C[5]HO)(C[5]O[5]CH)(OH)(H){1|H<1>,1|N<3>}
+FAD       O3B    O(C[5]C[5]2H)(H)
+FAD       C2B    C[5](C[5]N[5a]O[5]H)(C[5]C[5]HO)(OH)(H){1|C<4>,1|H<1>,2|C<3>}
+FAD       O2B    O(C[5]C[5]2H)(H)
+FAD       C1B    C[5](N[5a]C[5a,6a]C[5a])(C[5]C[5]HO)(O[5]C[5])(H){1|C<3>,1|C<4>,1|O<2>,2|N<2>,3|H<1>}
+FAD       N9A    N[5a](C[5a,6a]C[5a,6a]N[6a])(C[5]C[5]O[5]H)(C[5a]N[5a]H){1|H<1>,1|O<2>,2|C<3>,2|C<4>}
+FAD       C8A    C[5a](N[5a]C[5a,6a]C[5])(N[5a]C[5a,6a])(H){1|C<3>,1|C<4>,1|H<1>,1|N<2>,1|O<2>}
+FAD       N7A    N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H){1|C<4>,1|N<3>,2|N<2>}
+FAD       C5A    C[5a,6a](C[5a,6a]N[5a]N[6a])(C[6a]N[6a]N)(N[5a]C[5a]){1|C<3>,1|C<4>,1|H<1>}
+FAD       C6A    C[6a](C[5a,6a]C[5a,6a]N[5a])(N[6a]C[6a])(NHH){1|C<3>,1|H<1>,1|N<2>,1|N<3>}
+FAD       N6A    N(C[6a]C[5a,6a]N[6a])(H)2
+FAD       N1A    N[6a](C[6a]C[5a,6a]N)(C[6a]N[6a]H){1|C<3>,1|N<2>}
+FAD       C2A    C[6a](N[6a]C[5a,6a])(N[6a]C[6a])(H){1|C<3>,2|N<3>}
+FAD       N3A    N[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]N[6a]H){1|C<4>,1|N<2>,2|C<3>}
+FAD       C4A    C[5a,6a](C[5a,6a]C[6a]N[5a])(N[5a]C[5a]C[5])(N[6a]C[6a]){1|C<4>,1|N<2>,1|N<3>,1|O<2>,3|H<1>}
+FAD        N1    N[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]N[6a]O){1|C<4>,1|H<1>,1|N<2>,2|C<3>}
+FAD        C2    C[6a](N[6a]C[6a,6a])(N[6a]C[6a]H)(O){1|C<3>,1|N<3>,1|O<1>}
+FAD        O2    O(C[6a]N[6a]2)
+FAD        N3    N[6a](C[6a]C[6a,6a]O)(C[6a]N[6a]O)(H){1|C<3>,1|N<2>}
+FAD        C4    C[6a](C[6a,6a]C[6a,6a]N[6a])(N[6a]C[6a]H)(O){1|C<3>,1|N<2>,1|N<3>,1|O<1>}
+FAD        O4    O(C[6a]C[6a,6a]N[6a])
+FAD       C4X    C[6a,6a](C[6a,6a]N[6a]2)(N[6a]C[6a,6a])(C[6a]N[6a]O){1|C<4>,1|H<1>,3|C<3>}
+FAD        N5    N[6a](C[6a,6a]C[6a,6a]C[6a])2{1|H<1>,1|N<2>,1|O<1>,2|C<3>,2|N<3>}
+FAD       C5X    C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a])(C[6a]C[6a]H){1|H<1>,2|C<4>,3|C<3>}
+FAD        C6    C[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]C[6a]C)(H){1|C<4>,1|N<3>,2|C<3>}
+FAD        C7    C[6a](C[6a]C[6a,6a]H)(C[6a]C[6a]C)(CH3){1|C<3>,1|H<1>,1|N<2>}
+FAD       C7M    C(C[6a]C[6a]2)(H)3
+FAD        C8    C[6a](C[6a]C[6a,6a]H)(C[6a]C[6a]C)(CH3){1|C<3>,1|H<1>,1|N<3>}
+FAD       C8M    C(C[6a]C[6a]2)(H)3
+FAD        C9    C[6a](C[6a,6a]C[6a,6a]N[6a])(C[6a]C[6a]C)(H){1|N<2>,2|C<3>,2|C<4>}
+FAD       C9A    C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a]C)(C[6a]C[6a]H){1|C<4>,1|H<1>,1|N<2>,2|C<3>}
+FAD       N10    N[6a](C[6a,6a]C[6a,6a]C[6a])(C[6a,6a]C[6a,6a]N[6a])(CCHH){1|H<1>,1|N<2>,4|C<3>}
+FAD       C10    C[6a,6a](C[6a,6a]C[6a]N[6a])(N[6a]C[6a,6a]C)(N[6a]C[6a]){1|N<3>,2|C<3>,2|O<1>}
+FAD     "C1'"    C(N[6a]C[6a,6a]2)(CCHO)(H)2
+FAD     "C2'"    C(CN[6a]HH)(CCHO)(OH)(H)
+FAD     "O2'"    O(CCCH)(H)
+FAD     "C3'"    C(CCHO)2(OH)(H)
+FAD     "O3'"    O(CCCH)(H)
+FAD     "C4'"    C(CCHO)(CHHO)(OH)(H)
+FAD     "O4'"    O(CCCH)(H)
+FAD     "C5'"    C(CCHO)(OP)(H)2
+FAD     "O5'"    O(CCHH)(PO3)
+FAD         P    P(OC)(OP)(O)2
+FAD       O1P    O(PO3)
+FAD       O2P    O(PO3)
+FAD       O3P    O(PO3)2
+FAD      H51A    H(CC[5]HO)
+FAD      H52A    H(CC[5]HO)
+FAD       H4B    H(C[5]C[5]O[5]C)
+FAD       H3B    H(C[5]C[5]2O)
+FAD      HO3A    H(OC[5])
+FAD       H2B    H(C[5]C[5]2O)
+FAD      HO2A    H(OC[5])
+FAD       H1B    H(C[5]N[5a]C[5]O[5])
+FAD       H8A    H(C[5a]N[5a]2)
+FAD      H61A    H(NC[6a]H)
+FAD      H62A    H(NC[6a]H)
+FAD       H2A    H(C[6a]N[6a]2)
+FAD       HN3    H(N[6a]C[6a]2)
+FAD        H6    H(C[6a]C[6a,6a]C[6a])
+FAD      HM71    H(CC[6a]HH)
+FAD      HM72    H(CC[6a]HH)
+FAD      HM73    H(CC[6a]HH)
+FAD      HM81    H(CC[6a]HH)
+FAD      HM82    H(CC[6a]HH)
+FAD      HM83    H(CC[6a]HH)
+FAD        H9    H(C[6a]C[6a,6a]C[6a])
+FAD    "H1'1"    H(CN[6a]CH)
+FAD    "H1'2"    H(CN[6a]CH)
+FAD     "H2'"    H(CCCO)
+FAD    "HO2'"    H(OC)
+FAD     "H3'"    H(CCCO)
+FAD    "HO3'"    H(OC)
+FAD     "H4'"    H(CCCO)
+FAD    "HO4'"    H(OC)
+FAD    "H5'1"    H(CCHO)
+FAD    "H5'2"    H(CCHO)
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+FAD          PA         O1A      DOUBLE       n     1.485  0.0100     1.485  0.0100
+FAD          PA         O2A      SINGLE       n     1.485  0.0100     1.485  0.0100
+FAD          PA         O5B      SINGLE       n     1.598  0.0100     1.598  0.0100
+FAD          PA         O3P      SINGLE       n     1.600  0.0185     1.600  0.0185
+FAD         O5B         C5B      SINGLE       n     1.445  0.0200     1.445  0.0200
+FAD         C5B         C4B      SINGLE       n     1.509  0.0100     1.509  0.0100
+FAD         C4B         O4B      SINGLE       n     1.444  0.0100     1.444  0.0100
+FAD         C4B         C3B      SINGLE       n     1.532  0.0100     1.532  0.0100
+FAD         O4B         C1B      SINGLE       n     1.423  0.0100     1.423  0.0100
+FAD         C3B         O3B      SINGLE       n     1.422  0.0100     1.422  0.0100
+FAD         C3B         C2B      SINGLE       n     1.532  0.0103     1.532  0.0103
+FAD         C2B         O2B      SINGLE       n     1.412  0.0100     1.412  0.0100
+FAD         C2B         C1B      SINGLE       n     1.528  0.0100     1.528  0.0100
+FAD         C1B         N9A      SINGLE       n     1.462  0.0102     1.462  0.0102
+FAD         N9A         C8A      SINGLE       y     1.371  0.0100     1.371  0.0100
+FAD         N9A         C4A      SINGLE       y     1.374  0.0101     1.374  0.0101
+FAD         C8A         N7A      DOUBLE       y     1.311  0.0100     1.311  0.0100
+FAD         N7A         C5A      SINGLE       y     1.388  0.0100     1.388  0.0100
+FAD         C5A         C6A      SINGLE       y     1.407  0.0100     1.407  0.0100
+FAD         C5A         C4A      DOUBLE       y     1.382  0.0100     1.382  0.0100
+FAD         C6A         N6A      SINGLE       n     1.332  0.0107     1.332  0.0107
+FAD         C6A         N1A      DOUBLE       y     1.355  0.0106     1.355  0.0106
+FAD         N1A         C2A      SINGLE       y     1.338  0.0100     1.338  0.0100
+FAD         C2A         N3A      DOUBLE       y     1.329  0.0100     1.329  0.0100
+FAD         N3A         C4A      SINGLE       y     1.344  0.0100     1.344  0.0100
+FAD          N1          C2      SINGLE       y     1.369  0.0100     1.369  0.0100
+FAD          N1         C10      DOUBLE       y     1.317  0.0100     1.317  0.0100
+FAD          C2          O2      DOUBLE       n     1.235  0.0100     1.235  0.0100
+FAD          C2          N3      SINGLE       y     1.393  0.0104     1.393  0.0104
+FAD          N3          C4      SINGLE       y     1.377  0.0130     1.377  0.0130
+FAD          C4          O4      DOUBLE       n     1.218  0.0100     1.218  0.0100
+FAD          C4         C4X      SINGLE       y     1.398  0.0190     1.398  0.0190
+FAD         C4X          N5      DOUBLE       y     1.308  0.0122     1.308  0.0122
+FAD         C4X         C10      SINGLE       y     1.443  0.0100     1.443  0.0100
+FAD          N5         C5X      SINGLE       y     1.368  0.0100     1.368  0.0100
+FAD         C5X          C6      SINGLE       y     1.409  0.0100     1.409  0.0100
+FAD         C5X         C9A      DOUBLE       y     1.410  0.0100     1.410  0.0100
+FAD          C6          C7      DOUBLE       y     1.376  0.0100     1.376  0.0100
+FAD          C7         C7M      SINGLE       n     1.507  0.0100     1.507  0.0100
+FAD          C7          C8      SINGLE       y     1.417  0.0165     1.417  0.0165
+FAD          C8         C8M      SINGLE       n     1.504  0.0100     1.504  0.0100
+FAD          C8          C9      DOUBLE       y     1.379  0.0100     1.379  0.0100
+FAD          C9         C9A      SINGLE       y     1.403  0.0100     1.403  0.0100
+FAD         C9A         N10      SINGLE       y     1.392  0.0100     1.392  0.0100
+FAD         N10         C10      SINGLE       y     1.385  0.0119     1.385  0.0119
+FAD         N10       "C1'"      SINGLE       n     1.475  0.0100     1.475  0.0100
+FAD       "C1'"       "C2'"      SINGLE       n     1.518  0.0148     1.518  0.0148
+FAD       "C2'"       "O2'"      SINGLE       n     1.429  0.0132     1.429  0.0132
+FAD       "C2'"       "C3'"      SINGLE       n     1.529  0.0130     1.529  0.0130
+FAD       "C3'"       "O3'"      SINGLE       n     1.426  0.0100     1.426  0.0100
+FAD       "C3'"       "C4'"      SINGLE       n     1.528  0.0126     1.528  0.0126
+FAD       "C4'"       "O4'"      SINGLE       n     1.429  0.0111     1.429  0.0111
+FAD       "C4'"       "C5'"      SINGLE       n     1.518  0.0135     1.518  0.0135
+FAD       "C5'"       "O5'"      SINGLE       n     1.445  0.0200     1.445  0.0200
+FAD       "O5'"           P      SINGLE       n     1.592  0.0137     1.592  0.0137
+FAD           P         O1P      DOUBLE       n     1.485  0.0100     1.485  0.0100
+FAD           P         O2P      SINGLE       n     1.485  0.0100     1.485  0.0100
+FAD           P         O3P      SINGLE       n     1.600  0.0185     1.600  0.0185
+FAD         C5B        H51A      SINGLE       n     1.089  0.0100     0.991  0.0200
+FAD         C5B        H52A      SINGLE       n     1.089  0.0100     0.991  0.0200
+FAD         C4B         H4B      SINGLE       n     1.089  0.0100     0.990  0.0200
+FAD         C3B         H3B      SINGLE       n     1.089  0.0100     0.991  0.0200
+FAD         O3B        HO3A      SINGLE       n     0.970  0.0120     0.839  0.0200
+FAD         C2B         H2B      SINGLE       n     1.089  0.0100     0.991  0.0200
+FAD         O2B        HO2A      SINGLE       n     0.970  0.0120     0.839  0.0200
+FAD         C1B         H1B      SINGLE       n     1.089  0.0100     1.016  0.0200
+FAD         C8A         H8A      SINGLE       n     1.082  0.0130     0.942  0.0168
+FAD         N6A        H61A      SINGLE       n     1.016  0.0100     0.880  0.0200
+FAD         N6A        H62A      SINGLE       n     1.016  0.0100     0.880  0.0200
+FAD         C2A         H2A      SINGLE       n     1.082  0.0130     0.946  0.0200
+FAD          N3         HN3      SINGLE       n     1.016  0.0100     0.880  0.0100
+FAD          C6          H6      SINGLE       n     1.082  0.0130     0.952  0.0100
+FAD         C7M        HM71      SINGLE       n     1.089  0.0100     0.972  0.0144
+FAD         C7M        HM72      SINGLE       n     1.089  0.0100     0.972  0.0144
+FAD         C7M        HM73      SINGLE       n     1.089  0.0100     0.972  0.0144
+FAD         C8M        HM81      SINGLE       n     1.089  0.0100     0.972  0.0144
+FAD         C8M        HM82      SINGLE       n     1.089  0.0100     0.972  0.0144
+FAD         C8M        HM83      SINGLE       n     1.089  0.0100     0.972  0.0144
+FAD          C9          H9      SINGLE       n     1.082  0.0130     0.954  0.0100
+FAD       "C1'"      "H1'1"      SINGLE       n     1.089  0.0100     0.980  0.0162
+FAD       "C1'"      "H1'2"      SINGLE       n     1.089  0.0100     0.980  0.0162
+FAD       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     1.000  0.0200
+FAD       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.864  0.0200
+FAD       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.994  0.0118
+FAD       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.864  0.0200
+FAD       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.991  0.0117
+FAD       "O4'"      "HO4'"      SINGLE       n     0.970  0.0120     0.864  0.0200
+FAD       "C5'"      "H5'1"      SINGLE       n     1.089  0.0100     0.978  0.0200
+FAD       "C5'"      "H5'2"      SINGLE       n     1.089  0.0100     0.978  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+FAD         O1A          PA         O2A     118.805    3.00
+FAD         O1A          PA         O5B     109.340    2.31
+FAD         O1A          PA         O3P     109.053    3.00
+FAD         O2A          PA         O5B     109.340    2.31
+FAD         O2A          PA         O3P     109.053    3.00
+FAD         O5B          PA         O3P     100.137    3.00
+FAD          PA         O5B         C5B     116.362    1.50
+FAD         O5B         C5B         C4B     109.454    1.61
+FAD         O5B         C5B        H51A     109.882    1.50
+FAD         O5B         C5B        H52A     109.882    1.50
+FAD         C4B         C5B        H51A     109.589    1.50
+FAD         C4B         C5B        H52A     109.589    1.50
+FAD        H51A         C5B        H52A     108.471    1.50
+FAD         C5B         C4B         O4B     109.154    1.50
+FAD         C5B         C4B         C3B     115.288    1.50
+FAD         C5B         C4B         H4B     108.351    1.59
+FAD         O4B         C4B         C3B     105.318    1.50
+FAD         O4B         C4B         H4B     109.120    1.50
+FAD         C3B         C4B         H4B     109.322    2.54
+FAD         C4B         O4B         C1B     109.502    2.85
+FAD         C4B         C3B         O3B     110.713    3.00
+FAD         C4B         C3B         C2B     102.593    1.50
+FAD         C4B         C3B         H3B     110.577    3.00
+FAD         O3B         C3B         C2B     111.671    3.00
+FAD         O3B         C3B         H3B     110.541    2.08
+FAD         C2B         C3B         H3B     110.454    1.85
+FAD         C3B         O3B        HO3A     109.389    3.00
+FAD         C3B         C2B         O2B     112.677    3.00
+FAD         C3B         C2B         C1B     101.406    1.50
+FAD         C3B         C2B         H2B     110.788    1.91
+FAD         O2B         C2B         C1B     110.814    3.00
+FAD         O2B         C2B         H2B     110.904    1.50
+FAD         C1B         C2B         H2B     110.342    1.91
+FAD         C2B         O2B        HO2A     109.217    3.00
+FAD         O4B         C1B         C2B     106.114    1.65
+FAD         O4B         C1B         N9A     108.577    1.50
+FAD         O4B         C1B         H1B     109.833    2.53
+FAD         C2B         C1B         N9A     113.380    2.77
+FAD         C2B         C1B         H1B     109.222    1.50
+FAD         N9A         C1B         H1B     109.411    1.50
+FAD         C1B         N9A         C8A     127.072    3.00
+FAD         C1B         N9A         C4A     126.969    2.94
+FAD         C8A         N9A         C4A     105.958    1.50
+FAD         N9A         C8A         N7A     113.692    1.50
+FAD         N9A         C8A         H8A     122.949    1.50
+FAD         N7A         C8A         H8A     123.359    1.50
+FAD         C8A         N7A         C5A     103.906    1.50
+FAD         N7A         C5A         C6A     131.998    1.50
+FAD         N7A         C5A         C4A     110.646    1.50
+FAD         C6A         C5A         C4A     117.356    1.50
+FAD         C5A         C6A         N6A     123.773    1.50
+FAD         C5A         C6A         N1A     117.375    1.50
+FAD         N6A         C6A         N1A     118.852    1.50
+FAD         C6A         N6A        H61A     119.818    3.00
+FAD         C6A         N6A        H62A     119.818    3.00
+FAD        H61A         N6A        H62A     120.363    3.00
+FAD         C6A         N1A         C2A     118.603    1.50
+FAD         N1A         C2A         N3A     129.210    1.50
+FAD         N1A         C2A         H2A     115.363    1.50
+FAD         N3A         C2A         H2A     115.427    1.50
+FAD         C2A         N3A         C4A     111.101    1.50
+FAD         N9A         C4A         C5A     105.797    1.50
+FAD         N9A         C4A         N3A     127.848    1.50
+FAD         C5A         C4A         N3A     126.355    1.50
+FAD          C2          N1         C10     118.461    1.50
+FAD          N1          C2          O2     121.468    1.50
+FAD          N1          C2          N3     119.897    1.50
+FAD          O2          C2          N3     118.636    1.50
+FAD          C2          N3          C4     126.347    1.50
+FAD          C2          N3         HN3     117.238    1.50
+FAD          C4          N3         HN3     116.415    2.90
+FAD          N3          C4          O4     122.539    1.50
+FAD          N3          C4         C4X     112.794    1.50
+FAD          O4          C4         C4X     124.668    1.50
+FAD          C4         C4X          N5     117.421    1.50
+FAD          C4         C4X         C10     117.741    1.50
+FAD          N5         C4X         C10     124.838    1.50
+FAD         C4X          N5         C5X     117.454    1.50
+FAD          N5         C5X          C6     118.145    1.50
+FAD          N5         C5X         C9A     122.298    1.50
+FAD          C6         C5X         C9A     119.556    1.50
+FAD         C5X          C6          C7     121.774    1.50
+FAD         C5X          C6          H6     118.910    1.63
+FAD          C7          C6          H6     119.325    1.50
+FAD          C6          C7         C7M     119.966    1.50
+FAD          C6          C7          C8     119.488    1.50
+FAD         C7M          C7          C8     120.546    1.50
+FAD          C7         C7M        HM71     109.566    1.50
+FAD          C7         C7M        HM72     109.566    1.50
+FAD          C7         C7M        HM73     109.566    1.50
+FAD        HM71         C7M        HM72     109.334    1.91
+FAD        HM71         C7M        HM73     109.334    1.91
+FAD        HM72         C7M        HM73     109.334    1.91
+FAD          C7          C8         C8M     120.546    1.50
+FAD          C7          C8          C9     119.488    1.50
+FAD         C8M          C8          C9     119.966    1.50
+FAD          C8         C8M        HM81     109.566    1.50
+FAD          C8         C8M        HM82     109.566    1.50
+FAD          C8         C8M        HM83     109.566    1.50
+FAD        HM81         C8M        HM82     109.334    1.91
+FAD        HM81         C8M        HM83     109.334    1.91
+FAD        HM82         C8M        HM83     109.334    1.91
+FAD          C8          C9         C9A     120.779    1.50
+FAD          C8          C9          H9     119.551    1.50
+FAD         C9A          C9          H9     119.670    1.50
+FAD         C5X         C9A          C9     118.907    1.50
+FAD         C5X         C9A         N10     118.199    1.50
+FAD          C9         C9A         N10     122.894    1.50
+FAD         C9A         N10         C10     120.671    1.50
+FAD         C9A         N10       "C1'"     120.592    1.50
+FAD         C10         N10       "C1'"     118.737    1.50
+FAD          N1         C10         C4X     124.761    1.50
+FAD          N1         C10         N10     118.699    1.50
+FAD         C4X         C10         N10     116.541    1.50
+FAD         N10       "C1'"       "C2'"     112.123    2.65
+FAD         N10       "C1'"      "H1'1"     108.981    1.50
+FAD         N10       "C1'"      "H1'2"     108.981    1.50
+FAD       "C2'"       "C1'"      "H1'1"     109.180    1.50
+FAD       "C2'"       "C1'"      "H1'2"     109.180    1.50
+FAD      "H1'1"       "C1'"      "H1'2"     107.924    2.79
+FAD       "C1'"       "C2'"       "O2'"     109.718    2.99
+FAD       "C1'"       "C2'"       "C3'"     111.239    3.00
+FAD       "C1'"       "C2'"       "H2'"     108.435    1.50
+FAD       "O2'"       "C2'"       "C3'"     109.426    3.00
+FAD       "O2'"       "C2'"       "H2'"     108.176    3.00
+FAD       "C3'"       "C2'"       "H2'"     108.439    2.58
+FAD       "C2'"       "O2'"      "HO2'"     109.126    3.00
+FAD       "C2'"       "C3'"       "O3'"     109.426    3.00
+FAD       "C2'"       "C3'"       "C4'"     113.599    3.00
+FAD       "C2'"       "C3'"       "H3'"     108.439    2.58
+FAD       "O3'"       "C3'"       "C4'"     109.190    2.87
+FAD       "O3'"       "C3'"       "H3'"     108.315    1.83
+FAD       "C4'"       "C3'"       "H3'"     108.171    1.50
+FAD       "C3'"       "O3'"      "HO3'"     108.910    3.00
+FAD       "C3'"       "C4'"       "O4'"     109.920    2.94
+FAD       "C3'"       "C4'"       "C5'"     112.050    2.78
+FAD       "C3'"       "C4'"       "H4'"     108.859    1.50
+FAD       "O4'"       "C4'"       "C5'"     109.162    3.00
+FAD       "O4'"       "C4'"       "H4'"     108.709    1.50
+FAD       "C5'"       "C4'"       "H4'"     108.615    1.79
+FAD       "C4'"       "O4'"      "HO4'"     109.757    3.00
+FAD       "C4'"       "C5'"       "O5'"     109.303    3.00
+FAD       "C4'"       "C5'"      "H5'1"     109.594    1.50
+FAD       "C4'"       "C5'"      "H5'2"     109.594    1.50
+FAD       "O5'"       "C5'"      "H5'1"     108.621    3.00
+FAD       "O5'"       "C5'"      "H5'2"     108.621    3.00
+FAD      "H5'1"       "C5'"      "H5'2"     108.315    1.66
+FAD       "C5'"       "O5'"           P     119.008    2.40
+FAD       "O5'"           P         O1P     108.662    3.00
+FAD       "O5'"           P         O2P     108.662    3.00
+FAD       "O5'"           P         O3P     100.260    3.00
+FAD         O1P           P         O2P     118.805    3.00
+FAD         O1P           P         O3P     109.053    3.00
+FAD         O2P           P         O3P     109.053    3.00
+FAD          PA         O3P           P     133.108    3.00
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+FAD            sp3_sp3_27         C5B         O5B          PA         O1A      60.000    10.0     3
+FAD            sp3_sp3_30           P         O3P          PA         O1A      60.000    10.0     3
+FAD             sp2_sp3_1         C8A         N9A         C1B         O4B     150.000    10.0     6
+FAD              const_48         N7A         C8A         N9A         C1B     180.000     0.0     2
+FAD              const_80         C5A         C4A         N9A         C1B     180.000     0.0     2
+FAD              const_51         N9A         C8A         N7A         C5A       0.000     0.0     2
+FAD              const_54         C6A         C5A         N7A         C8A     180.000     0.0     2
+FAD              const_38         N7A         C5A         C6A         N6A       0.000     0.0     2
+FAD              const_55         N9A         C4A         C5A         N7A       0.000     0.0     2
+FAD            sp2_sp2_83         C5A         C6A         N6A        H61A     180.000      20     2
+FAD              const_40         N6A         C6A         N1A         C2A     180.000     0.0     2
+FAD              const_41         N3A         C2A         N1A         C6A       0.000     0.0     2
+FAD              const_43         N1A         C2A         N3A         C4A       0.000     0.0     2
+FAD              const_46         N9A         C4A         N3A         C2A     180.000     0.0     2
+FAD       const_sp2_sp2_2          O2          C2          N1         C10     180.000     0.0     2
+FAD              const_87         C4X         C10          N1          C2       0.000     0.0     2
+FAD       const_sp2_sp2_5          O2          C2          N3          C4     180.000     0.0     2
+FAD       const_sp2_sp2_9          O4          C4          N3          C2     180.000     0.0     2
+FAD              const_14          O4          C4         C4X          N5       0.000     0.0     2
+FAD              const_20          C4         C4X          N5         C5X     180.000     0.0     2
+FAD              const_15          N1         C10         C4X          C4       0.000     0.0     2
+FAD              const_22          C6         C5X          N5         C4X     180.000     0.0     2
+FAD              const_61          N5         C5X          C6          C7     180.000     0.0     2
+FAD              const_24          N5         C5X         C9A          C9     180.000     0.0     2
+FAD              const_64         C5X          C6          C7         C7M     180.000     0.0     2
+FAD             sp2_sp3_7          C6          C7         C7M        HM71     150.000    10.0     6
+FAD              const_70         C7M          C7          C8         C8M       0.000     0.0     2
+FAD            sp2_sp3_13          C7          C8         C8M        HM81     150.000    10.0     6
+FAD              const_73         C8M          C8          C9         C9A     180.000     0.0     2
+FAD              const_75          C8          C9         C9A         C5X       0.000     0.0     2
+FAD              const_28         C5X         C9A         N10       "C1'"     180.000     0.0     2
+FAD              const_34          N1         C10         N10       "C1'"       0.000     0.0     2
+FAD            sp2_sp3_20         C9A         N10       "C1'"       "C2'"     -90.000    10.0     6
+FAD            sp3_sp3_31         C4B         C5B         O5B          PA     180.000    10.0     3
+FAD            sp3_sp3_58         N10       "C1'"       "C2'"       "O2'"     180.000    10.0     3
+FAD            sp3_sp3_67       "C1'"       "C2'"       "O2'"      "HO2'"     180.000    10.0     3
+FAD            sp3_sp3_70       "C1'"       "C2'"       "C3'"       "O3'"     180.000    10.0     3
+FAD            sp3_sp3_79       "C2'"       "C3'"       "O3'"      "HO3'"     180.000    10.0     3
+FAD            sp3_sp3_82       "C2'"       "C3'"       "C4'"       "O4'"     180.000    10.0     3
+FAD            sp3_sp3_91       "C3'"       "C4'"       "O4'"      "HO4'"     180.000    10.0     3
+FAD            sp3_sp3_94       "C3'"       "C4'"       "C5'"       "O5'"     180.000    10.0     3
+FAD           sp3_sp3_103       "C4'"       "C5'"       "O5'"           P     180.000    10.0     3
+FAD           sp3_sp3_108       "C5'"       "O5'"           P         O1P      60.000    10.0     3
+FAD           sp3_sp3_110          PA         O3P           P       "O5'"     -60.000    10.0     3
+FAD            sp3_sp3_34         O4B         C4B         C5B         O5B     180.000    10.0     3
+FAD             sp3_sp3_2         C5B         C4B         O4B         C1B     -60.000    10.0     3
+FAD            sp3_sp3_47         O3B         C3B         C4B         C5B     180.000    10.0     3
+FAD             sp3_sp3_4         C2B         C1B         O4B         C4B     -60.000    10.0     3
+FAD            sp3_sp3_52         C4B         C3B         O3B        HO3A     180.000    10.0     3
+FAD            sp3_sp3_20         O2B         C2B         C3B         O3B     -60.000    10.0     3
+FAD            sp3_sp3_55         C3B         C2B         O2B        HO2A     180.000    10.0     3
+FAD             sp3_sp3_8         O4B         C1B         C2B         O2B     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+FAD    chir_1    PA    O3P    O5B    O2A    both
+FAD    chir_2    C4B    O4B    C3B    C5B    negative
+FAD    chir_3    C3B    O3B    C4B    C2B    positive
+FAD    chir_4    C2B    O2B    C1B    C3B    negative
+FAD    chir_5    C1B    O4B    N9A    C2B    negative
+FAD    chir_6    "C2'"    "O2'"    "C3'"    "C1'"    positive
+FAD    chir_7    "C3'"    "O3'"    "C4'"    "C2'"    positive
+FAD    chir_8    "C4'"    "O4'"    "C3'"    "C5'"    negative
+FAD    chir_9    P    O3P    "O5'"    O2P    both
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+FAD    plan-1         C1B   0.020
+FAD    plan-1         C4A   0.020
+FAD    plan-1         C5A   0.020
+FAD    plan-1         C6A   0.020
+FAD    plan-1         C8A   0.020
+FAD    plan-1         H8A   0.020
+FAD    plan-1         N3A   0.020
+FAD    plan-1         N7A   0.020
+FAD    plan-1         N9A   0.020
+FAD    plan-2         C2A   0.020
+FAD    plan-2         C4A   0.020
+FAD    plan-2         C5A   0.020
+FAD    plan-2         C6A   0.020
+FAD    plan-2         H2A   0.020
+FAD    plan-2         N1A   0.020
+FAD    plan-2         N3A   0.020
+FAD    plan-2         N6A   0.020
+FAD    plan-2         N7A   0.020
+FAD    plan-2         N9A   0.020
+FAD    plan-3         C10   0.020
+FAD    plan-3          C2   0.020
+FAD    plan-3          C4   0.020
+FAD    plan-3         C4X   0.020
+FAD    plan-3         HN3   0.020
+FAD    plan-3          N1   0.020
+FAD    plan-3         N10   0.020
+FAD    plan-3          N3   0.020
+FAD    plan-3          N5   0.020
+FAD    plan-3          O2   0.020
+FAD    plan-3          O4   0.020
+FAD    plan-4       "C1'"   0.020
+FAD    plan-4         C10   0.020
+FAD    plan-4          C4   0.020
+FAD    plan-4         C4X   0.020
+FAD    plan-4         C5X   0.020
+FAD    plan-4          C6   0.020
+FAD    plan-4          C9   0.020
+FAD    plan-4         C9A   0.020
+FAD    plan-4          N1   0.020
+FAD    plan-4         N10   0.020
+FAD    plan-4          N5   0.020
+FAD    plan-5         C5X   0.020
+FAD    plan-5          C6   0.020
+FAD    plan-5          C7   0.020
+FAD    plan-5         C7M   0.020
+FAD    plan-5          C8   0.020
+FAD    plan-5         C8M   0.020
+FAD    plan-5          C9   0.020
+FAD    plan-5         C9A   0.020
+FAD    plan-5          H6   0.020
+FAD    plan-5          H9   0.020
+FAD    plan-5         N10   0.020
+FAD    plan-5          N5   0.020
+FAD    plan-6         C6A   0.020
+FAD    plan-6        H61A   0.020
+FAD    plan-6        H62A   0.020
+FAD    plan-6         N6A   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+FAD  SMILES            ACDLabs               10.04  "O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C"
+FAD  SMILES_CANONICAL  CACTVS                3.341  "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C"
+FAD  SMILES            CACTVS                3.341  "Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C"
+FAD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O"
+FAD  SMILES            "OpenEye OEToolkits"  1.5.0  "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O"
+FAD  InChI             InChI                 1.03   "InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1"
+FAD  InChIKey          InChI                 1.03   VWWQXMAJTJZDQX-UYBVJOGSSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+FAD acedrg               275         "dictionary generator"                  
+FAD acedrg_database      12          "data source"                           
+FAD rdkit                2019.09.1   "Chemoinformatics tool"
+FAD refmac5              5.8.0405    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/FE.cif b/image_analysis/structure_refinement/monomers/FE.cif
new file mode 100644
index 000000000..eabe098cd
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/FE.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+FE FE 'FE (III) ION                        ' NON-POLYMER 1 1 .
+
+data_comp_FE
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+FE FE FE FE 3.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+FE FE n/a . END
diff --git a/image_analysis/structure_refinement/monomers/FE2.cif b/image_analysis/structure_refinement/monomers/FE2.cif
new file mode 100644
index 000000000..fb5535321
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/FE2.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+FE2 FE2 'FE (II) ION                         ' NON-POLYMER 1 1 .
+
+data_comp_FE2
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+FE2 FE FE FE 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+FE2 FE n/a . END
diff --git a/image_analysis/structure_refinement/monomers/FMN.cif b/image_analysis/structure_refinement/monomers/FMN.cif
new file mode 100644
index 000000000..220ed4327
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/FMN.cif
@@ -0,0 +1,337 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+FMN     FMN      "FLAVIN MONONUCLEOTIDE"     NON-POLYMER     50     31     .     
+#
+data_comp_FMN
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+FMN     N1      N       NRD6    0       33.067      6.557       14.888      
+FMN     C2      C       CR6     0       32.180      5.530       15.005      
+FMN     O2      O       O       0       32.567      4.383       15.250      
+FMN     N3      N       NR6     0       30.830      5.721       14.860      
+FMN     C4      C       CR6     0       30.302      6.963       14.585      
+FMN     O4      O       O       0       29.090      7.087       14.463      
+FMN     C4A     C       CR66    0       31.209      8.062       14.453      
+FMN     N5      N       NRD6    0       30.723      9.250       14.191      
+FMN     C5A     C       CR66    0       31.604      10.293      14.068      
+FMN     C6      C       CR16    0       31.061      11.563      13.788      
+FMN     C7      C       CR6     0       31.851      12.681      13.648      
+FMN     C7M     C       CH3     0       31.199      14.009      13.347      
+FMN     C8      C       CR6     0       33.272      12.544      13.787      
+FMN     C8M     C       CH3     0       34.190      13.733      13.641      
+FMN     C9      C       CR16    0       33.814      11.292      14.063      
+FMN     C9A     C       CR66    0       33.007      10.140      14.210      
+FMN     N10     N       NR6     0       33.500      8.849       14.490      
+FMN     C10     C       CR66    0       32.615      7.770       14.622      
+FMN     "C1'"   C       CH2     0       34.953      8.600       14.655      
+FMN     "C2'"   C       CH1     0       35.393      8.656       16.119      
+FMN     "O2'"   O       OH1     0       34.975      9.887       16.712      
+FMN     "C3'"   C       CH1     0       36.908      8.505       16.320      
+FMN     "O3'"   O       OH1     0       37.577      9.611       15.699      
+FMN     "C4'"   C       CH1     0       37.505      7.182       15.823      
+FMN     "O4'"   O       OH1     0       36.840      6.086       16.455      
+FMN     "C5'"   C       CH2     0       38.990      7.063       16.085      
+FMN     "O5'"   O       O2      0       39.268      7.119       17.512      
+FMN     P       P       P       0       40.802      7.026       18.006      
+FMN     O1P     O       O       0       40.755      7.133       19.519      
+FMN     O2P     O       OP      -1      41.519      8.194       17.355      
+FMN     O3P     O       OP      -1      41.310      5.680       17.526      
+FMN     HN3     H       H       0       30.294      5.027       14.946      
+FMN     H6      H       H       0       30.115      11.646      13.696      
+FMN     HM71    H       H       0       31.765      14.737      13.647      
+FMN     HM72    H       H       0       30.346      14.059      13.808      
+FMN     HM73    H       H       0       31.051      14.088      12.391      
+FMN     HM81    H       H       0       35.116      13.445      13.677      
+FMN     HM82    H       H       0       34.022      14.362      14.361      
+FMN     HM83    H       H       0       34.023      14.169      12.789      
+FMN     H9      H       H       0       34.761      11.223      14.156      
+FMN     "H1'1"  H       H       0       35.460      9.245       14.138      
+FMN     "H1'2"  H       H       0       35.168      7.720       14.292      
+FMN     "H2'"   H       H       0       34.941      7.923       16.609      
+FMN     "HO2'"  H       H       0       35.387      10.537      16.354      
+FMN     "H3'"   H       H       0       37.078      8.565       17.295      
+FMN     "HO3'"  H       H       0       37.689      9.467       14.871      
+FMN     "H4'"   H       H       0       37.357      7.113       14.833      
+FMN     "HO4'"  H       H       0       36.918      6.118       17.299      
+FMN     "H5'1"  H       H       0       39.467      7.788       15.630      
+FMN     "H5'2"  H       H       0       39.317      6.211       15.727      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+FMN          N1          C2      SINGLE       y     1.349  0.0188     1.349  0.0188
+FMN          N1         C10      DOUBLE       y     1.316  0.0100     1.316  0.0100
+FMN          C2          O2      DOUBLE       n     1.233  0.0164     1.233  0.0164
+FMN          C2          N3      SINGLE       y     1.354  0.0200     1.354  0.0200
+FMN          N3          C4      SINGLE       y     1.372  0.0117     1.372  0.0117
+FMN          C4          O4      DOUBLE       n     1.223  0.0119     1.223  0.0119
+FMN          C4         C4A      SINGLE       y     1.412  0.0200     1.412  0.0200
+FMN         C4A          N5      DOUBLE       y     1.309  0.0135     1.309  0.0135
+FMN         C4A         C10      SINGLE       y     1.442  0.0100     1.442  0.0100
+FMN          N5         C5A      SINGLE       y     1.369  0.0100     1.369  0.0100
+FMN         C5A          C6      SINGLE       y     1.407  0.0100     1.407  0.0100
+FMN         C5A         C9A      DOUBLE       y     1.409  0.0100     1.409  0.0100
+FMN          C6          C7      DOUBLE       y     1.375  0.0100     1.375  0.0100
+FMN          C7         C7M      SINGLE       n     1.507  0.0100     1.507  0.0100
+FMN          C7          C8      SINGLE       y     1.415  0.0183     1.415  0.0183
+FMN          C8         C8M      SINGLE       n     1.507  0.0100     1.507  0.0100
+FMN          C8          C9      DOUBLE       y     1.378  0.0152     1.378  0.0152
+FMN          C9         C9A      SINGLE       y     1.404  0.0100     1.404  0.0100
+FMN         C9A         N10      SINGLE       y     1.393  0.0100     1.393  0.0100
+FMN         N10         C10      SINGLE       y     1.383  0.0127     1.383  0.0127
+FMN         N10       "C1'"      SINGLE       n     1.474  0.0100     1.474  0.0100
+FMN       "C1'"       "C2'"      SINGLE       n     1.517  0.0189     1.517  0.0189
+FMN       "C2'"       "O2'"      SINGLE       n     1.424  0.0199     1.424  0.0199
+FMN       "C2'"       "C3'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+FMN       "C3'"       "O3'"      SINGLE       n     1.424  0.0199     1.424  0.0199
+FMN       "C3'"       "C4'"      SINGLE       n     1.530  0.0100     1.530  0.0100
+FMN       "C4'"       "O4'"      SINGLE       n     1.429  0.0100     1.429  0.0100
+FMN       "C4'"       "C5'"      SINGLE       n     1.511  0.0100     1.511  0.0100
+FMN       "C5'"       "O5'"      SINGLE       n     1.454  0.0165     1.454  0.0165
+FMN       "O5'"           P      SINGLE       n     1.614  0.0178     1.614  0.0178
+FMN           P         O1P      DOUBLE       n     1.517  0.0192     1.517  0.0192
+FMN           P         O2P      SINGLE       n     1.517  0.0192     1.517  0.0192
+FMN           P         O3P      SINGLE       n     1.517  0.0192     1.517  0.0192
+FMN          N3         HN3      SINGLE       n     1.016  0.0100     0.880  0.0200
+FMN          C6          H6      SINGLE       n     1.082  0.0130     0.954  0.0100
+FMN         C7M        HM71      SINGLE       n     1.089  0.0100     0.971  0.0135
+FMN         C7M        HM72      SINGLE       n     1.089  0.0100     0.971  0.0135
+FMN         C7M        HM73      SINGLE       n     1.089  0.0100     0.971  0.0135
+FMN         C8M        HM81      SINGLE       n     1.089  0.0100     0.971  0.0135
+FMN         C8M        HM82      SINGLE       n     1.089  0.0100     0.971  0.0135
+FMN         C8M        HM83      SINGLE       n     1.089  0.0100     0.971  0.0135
+FMN          C9          H9      SINGLE       n     1.082  0.0130     0.956  0.0118
+FMN       "C1'"      "H1'1"      SINGLE       n     1.089  0.0100     0.978  0.0200
+FMN       "C1'"      "H1'2"      SINGLE       n     1.089  0.0100     0.978  0.0200
+FMN       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.992  0.0184
+FMN       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.848  0.0200
+FMN       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0184
+FMN       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.848  0.0200
+FMN       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     1.004  0.0200
+FMN       "O4'"      "HO4'"      SINGLE       n     0.970  0.0120     0.848  0.0200
+FMN       "C5'"      "H5'1"      SINGLE       n     1.089  0.0100     0.980  0.0146
+FMN       "C5'"      "H5'2"      SINGLE       n     1.089  0.0100     0.980  0.0146
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+FMN          C2          N1         C10     118.131    1.50
+FMN          N1          C2          O2     121.177    1.50
+FMN          N1          C2          N3     121.483    2.18
+FMN          O2          C2          N3     117.340    1.50
+FMN          C2          N3          C4     121.560    1.50
+FMN          C2          N3         HN3     118.500    2.31
+FMN          C4          N3         HN3     119.939    1.50
+FMN          N3          C4          O4     119.688    1.50
+FMN          N3          C4         C4A     118.005    1.65
+FMN          O4          C4         C4A     122.306    1.50
+FMN          C4         C4A          N5     118.186    1.50
+FMN          C4         C4A         C10     116.947    1.50
+FMN          N5         C4A         C10     124.867    1.50
+FMN         C4A          N5         C5A     117.421    1.50
+FMN          N5         C5A          C6     118.199    1.50
+FMN          N5         C5A         C9A     122.273    1.50
+FMN          C6         C5A         C9A     119.529    1.50
+FMN         C5A          C6          C7     121.879    1.50
+FMN         C5A          C6          H6     118.690    1.50
+FMN          C7          C6          H6     119.431    1.50
+FMN          C6          C7         C7M     120.045    1.50
+FMN          C6          C7          C8     119.399    1.50
+FMN         C7M          C7          C8     120.556    1.50
+FMN          C7         C7M        HM71     109.535    1.50
+FMN          C7         C7M        HM72     109.535    1.50
+FMN          C7         C7M        HM73     109.535    1.50
+FMN        HM71         C7M        HM72     109.348    1.50
+FMN        HM71         C7M        HM73     109.348    1.50
+FMN        HM72         C7M        HM73     109.348    1.50
+FMN          C7          C8         C8M     120.556    1.50
+FMN          C7          C8          C9     119.399    1.50
+FMN         C8M          C8          C9     120.045    1.50
+FMN          C8         C8M        HM81     109.535    1.50
+FMN          C8         C8M        HM82     109.535    1.50
+FMN          C8         C8M        HM83     109.535    1.50
+FMN        HM81         C8M        HM82     109.348    1.50
+FMN        HM81         C8M        HM83     109.348    1.50
+FMN        HM82         C8M        HM83     109.348    1.50
+FMN          C8          C9         C9A     120.818    1.51
+FMN          C8          C9          H9     119.507    1.50
+FMN         C9A          C9          H9     119.676    1.64
+FMN         C5A         C9A          C9     118.977    1.50
+FMN         C5A         C9A         N10     118.178    1.50
+FMN          C9         C9A         N10     122.846    1.50
+FMN         C9A         N10         C10     120.732    1.50
+FMN         C9A         N10       "C1'"     119.696    1.50
+FMN         C10         N10       "C1'"     119.572    1.50
+FMN          N1         C10         C4A     123.873    1.50
+FMN          N1         C10         N10     119.597    1.50
+FMN         C4A         C10         N10     116.530    1.50
+FMN         N10       "C1'"       "C2'"     112.079    1.50
+FMN         N10       "C1'"      "H1'1"     108.897    1.50
+FMN         N10       "C1'"      "H1'2"     108.897    1.50
+FMN       "C2'"       "C1'"      "H1'1"     109.291    1.50
+FMN       "C2'"       "C1'"      "H1'2"     109.291    1.50
+FMN      "H1'1"       "C1'"      "H1'2"     107.893    1.50
+FMN       "C1'"       "C2'"       "O2'"     109.698    2.33
+FMN       "C1'"       "C2'"       "C3'"     110.999    2.33
+FMN       "C1'"       "C2'"       "H2'"     108.757    1.75
+FMN       "O2'"       "C2'"       "C3'"     109.320    2.01
+FMN       "O2'"       "C2'"       "H2'"     108.183    1.96
+FMN       "C3'"       "C2'"       "H2'"     108.450    1.83
+FMN       "C2'"       "O2'"      "HO2'"     109.265    3.00
+FMN       "C2'"       "C3'"       "O3'"     109.320    2.01
+FMN       "C2'"       "C3'"       "C4'"     113.695    2.13
+FMN       "C2'"       "C3'"       "H3'"     108.450    1.83
+FMN       "O3'"       "C3'"       "C4'"     109.164    1.97
+FMN       "O3'"       "C3'"       "H3'"     108.243    1.50
+FMN       "C4'"       "C3'"       "H3'"     108.336    1.50
+FMN       "C3'"       "O3'"      "HO3'"     108.564    3.00
+FMN       "C3'"       "C4'"       "O4'"     109.549    1.85
+FMN       "C3'"       "C4'"       "C5'"     112.503    1.50
+FMN       "C3'"       "C4'"       "H4'"     108.777    1.50
+FMN       "O4'"       "C4'"       "C5'"     109.314    1.96
+FMN       "O4'"       "C4'"       "H4'"     108.591    1.50
+FMN       "C5'"       "C4'"       "H4'"     108.656    1.50
+FMN       "C4'"       "O4'"      "HO4'"     111.202    3.00
+FMN       "C4'"       "C5'"       "O5'"     109.438    2.56
+FMN       "C4'"       "C5'"      "H5'1"     109.582    1.50
+FMN       "C4'"       "C5'"      "H5'2"     109.582    1.50
+FMN       "O5'"       "C5'"      "H5'1"     109.393    1.91
+FMN       "O5'"       "C5'"      "H5'2"     109.393    1.91
+FMN      "H5'1"       "C5'"      "H5'2"     108.319    1.50
+FMN       "C5'"       "O5'"           P     118.671    1.50
+FMN       "O5'"           P         O1P     105.795    2.09
+FMN       "O5'"           P         O2P     105.795    2.09
+FMN       "O5'"           P         O3P     105.795    2.09
+FMN         O1P           P         O2P     112.864    1.69
+FMN         O1P           P         O3P     112.864    1.69
+FMN         O2P           P         O3P     112.864    1.69
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+FMN       const_sp2_sp2_2          O2          C2          N1         C10     180.000     5.0     2
+FMN              const_55         C4A         C10          N1          C2       0.000    10.0     2
+FMN             sp2_sp3_1          C6          C7         C7M        HM71     150.000    10.0     6
+FMN              const_46         C7M          C7          C8         C8M       0.000    10.0     2
+FMN             sp2_sp3_7          C7          C8         C8M        HM81     150.000    10.0     6
+FMN              const_49         C8M          C8          C9         C9A     180.000    10.0     2
+FMN              const_51          C8          C9         C9A         C5A       0.000    10.0     2
+FMN              const_28         C5A         C9A         N10       "C1'"     180.000    10.0     2
+FMN              const_34          N1         C10         N10       "C1'"       0.000    10.0     2
+FMN            sp2_sp3_14         C9A         N10       "C1'"       "C2'"     -90.000    10.0     6
+FMN             sp3_sp3_1         N10       "C1'"       "C2'"       "O2'"     180.000    10.0     3
+FMN            sp3_sp3_10       "C1'"       "C2'"       "O2'"      "HO2'"     180.000    10.0     3
+FMN            sp3_sp3_13       "C1'"       "C2'"       "C3'"       "O3'"     180.000    10.0     3
+FMN       const_sp2_sp2_5          O2          C2          N3          C4     180.000     5.0     2
+FMN            sp3_sp3_22       "C2'"       "C3'"       "O3'"      "HO3'"     180.000    10.0     3
+FMN            sp3_sp3_25       "C2'"       "C3'"       "C4'"       "O4'"     180.000    10.0     3
+FMN            sp3_sp3_34       "C3'"       "C4'"       "O4'"      "HO4'"     180.000    10.0     3
+FMN            sp3_sp3_37       "C3'"       "C4'"       "C5'"       "O5'"     180.000    10.0     3
+FMN            sp3_sp3_46       "C4'"       "C5'"       "O5'"           P     180.000    10.0     3
+FMN            sp3_sp3_51       "C5'"       "O5'"           P         O1P      60.000    10.0     3
+FMN       const_sp2_sp2_9          O4          C4          N3          C2     180.000     5.0     2
+FMN              const_14          O4          C4         C4A          N5       0.000    10.0     2
+FMN              const_15          N1         C10         C4A          C4       0.000    10.0     2
+FMN              const_20          C4         C4A          N5         C5A     180.000    10.0     2
+FMN              const_22          C6         C5A          N5         C4A     180.000    10.0     2
+FMN              const_24          N5         C5A         C9A          C9     180.000    10.0     2
+FMN              const_37          N5         C5A          C6          C7     180.000    10.0     2
+FMN              const_40         C5A          C6          C7         C7M     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+FMN    chir_1    "C2'"    "O2'"    "C3'"    "C1'"    positive
+FMN    chir_2    "C3'"    "O3'"    "C4'"    "C2'"    positive
+FMN    chir_3    "C4'"    "O4'"    "C3'"    "C5'"    negative
+FMN    chir_4    P    "O5'"    O2P    O3P    both
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+FMN    plan-1       "C1'"   0.020
+FMN    plan-1         C10   0.020
+FMN    plan-1          C2   0.020
+FMN    plan-1          C4   0.020
+FMN    plan-1         C4A   0.020
+FMN    plan-1         C5A   0.020
+FMN    plan-1          C6   0.020
+FMN    plan-1          C9   0.020
+FMN    plan-1         C9A   0.020
+FMN    plan-1         HN3   0.020
+FMN    plan-1          N1   0.020
+FMN    plan-1         N10   0.020
+FMN    plan-1          N3   0.020
+FMN    plan-1          N5   0.020
+FMN    plan-1          O2   0.020
+FMN    plan-1          O4   0.020
+FMN    plan-2         C5A   0.020
+FMN    plan-2          C6   0.020
+FMN    plan-2          C7   0.020
+FMN    plan-2         C7M   0.020
+FMN    plan-2          C8   0.020
+FMN    plan-2         C8M   0.020
+FMN    plan-2          C9   0.020
+FMN    plan-2         C9A   0.020
+FMN    plan-2          H6   0.020
+FMN    plan-2          H9   0.020
+FMN    plan-2         N10   0.020
+FMN    plan-2          N5   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+FMN           SMILES              ACDLabs 12.01                                                                                                                                N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
+FMN            InChI                InChI  1.03 InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
+FMN         InChIKey                InChI  1.03                                                                                                                                                                    FVTCRASFADXXNN-SCRDCRAPSA-N
+FMN SMILES_CANONICAL               CACTVS 3.385                                                                                                                       Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
+FMN           SMILES               CACTVS 3.385                                                                                                                          Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
+FMN SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6                                                                                                                    Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
+FMN           SMILES "OpenEye OEToolkits" 1.7.6                                                                                                                                   Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+FMN acedrg               243         "dictionary generator"                  
+FMN acedrg_database      11          "data source"                           
+FMN rdkit                2017.03.2   "Chemoinformatics tool"
+FMN refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/G.cif b/image_analysis/structure_refinement/monomers/G.cif
new file mode 100644
index 000000000..a948bdc2c
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/G.cif
@@ -0,0 +1,276 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+G     G       "GUANOSINE-5'-MONOPHOSPHATE"     RNA     36     24     .     
+#
+data_comp_G
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+G       OP3     O       OP      -1      34.040      3.415       -1.077      
+G       P       P       P       0       34.210      4.003       0.312       
+G       OP1     O       O       0       34.487      5.494       0.290       
+G       OP2     O       OP      -1      35.203      3.231       1.161       
+G       "O5'"   O       O2      0       32.781      3.831       1.041       
+G       "C5'"   C       CH2     0       32.260      2.493       1.252       
+G       "C4'"   C       CH1     0       30.851      2.571       1.788       
+G       "O4'"   O       O2      0       30.831      3.382       2.990       
+G       "C3'"   C       CH1     0       29.808      3.223       0.875       
+G       "O3'"   O       OH1     0       29.289      2.285       -0.060      
+G       "C2'"   C       CH1     0       28.754      3.698       1.881       
+G       "O2'"   O       OH1     0       27.799      2.707       2.202       
+G       "C1'"   C       CH1     0       29.604      4.073       3.097       
+G       N9      N       NR5     0       29.861      5.508       3.212       
+G       C8      C       CR15    0       31.057      6.172       3.071       
+G       N7      N       NRD5    0       30.958      7.468       3.239       
+G       C5      C       CR56    0       29.612      7.676       3.509       
+G       C6      C       CR6     0       28.906      8.880       3.777       
+G       O6      O       O       0       29.357      10.033      3.827       
+G       N1      N       NR16    0       27.544      8.645       3.999       
+G       C2      C       CR6     0       26.939      7.407       3.968       
+G       N2      N       NH2     0       25.620      7.371       4.205       
+G       N3      N       NRD6    0       27.601      6.273       3.716       
+G       C4      C       CR56    0       28.926      6.478       3.499       
+G       "H5'"   H       H       0       32.833      2.008       1.895       
+G       "H5''"  H       H       0       32.261      1.995       0.397       
+G       "H4'"   H       H       0       30.559      1.662       2.015       
+G       "H3'"   H       H       0       30.200      3.999       0.398       
+G       "HO3'"  H       H       0       28.659      2.653       -0.495      
+G       "H2'"   H       H       0       28.286      4.500       1.527       
+G       "HO2'"  H       H       0       28.188      2.026       2.527       
+G       "H1'"   H       H       0       29.136      3.771       3.909       
+G       H8      H       H       0       31.870      5.740       2.872       
+G       H1      H       H       0       27.031      9.361       4.176       
+G       H21     H       H       0       25.105      6.850       3.723       
+G       H22     H       H       0       25.277      7.868       4.840       
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+G       OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+G         P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+G         P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+G         P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+G     "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+G     "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+G     "C4'"       "O4'"      SINGLE       n     1.451  0.0100     1.451  0.0100
+G     "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+G     "O4'"       "C1'"      SINGLE       n     1.409  0.0100     1.409  0.0100
+G     "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+G     "C3'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+G     "C2'"       "O2'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+G     "C2'"       "C1'"      SINGLE       n     1.525  0.0100     1.525  0.0100
+G     "C1'"          N9      SINGLE       n     1.458  0.0100     1.458  0.0100
+G        N9          C8      SINGLE       y     1.372  0.0100     1.372  0.0100
+G        N9          C4      SINGLE       y     1.375  0.0100     1.375  0.0100
+G        C8          N7      DOUBLE       y     1.312  0.0100     1.312  0.0100
+G        N7          C5      SINGLE       y     1.390  0.0100     1.390  0.0100
+G        C5          C6      SINGLE       y     1.417  0.0103     1.417  0.0103
+G        C5          C4      DOUBLE       y     1.377  0.0100     1.377  0.0100
+G        C6          O6      DOUBLE       n     1.239  0.0100     1.239  0.0100
+G        C6          N1      SINGLE       y     1.396  0.0107     1.396  0.0107
+G        N1          C2      SINGLE       y     1.374  0.0100     1.374  0.0100
+G        C2          N2      SINGLE       n     1.340  0.0101     1.340  0.0101
+G        C2          N3      DOUBLE       y     1.333  0.0104     1.333  0.0104
+G        N3          C4      SINGLE       y     1.355  0.0100     1.355  0.0100
+G     "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+G     "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+G     "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+G     "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+G     "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+G     "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.994  0.0200
+G     "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+G     "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.984  0.0200
+G        C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+G        N1          H1      SINGLE       n     1.016  0.0100     0.897  0.0200
+G        N2         H21      SINGLE       n     1.016  0.0100     0.877  0.0200
+G        N2         H22      SINGLE       n     1.016  0.0100     0.877  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+G       OP3           P         OP1     112.864    1.69
+G       OP3           P         OP2     112.864    1.69
+G       OP3           P       "O5'"     105.808    2.07
+G       OP1           P         OP2     112.864    1.69
+G       OP1           P       "O5'"     105.808    2.07
+G       OP2           P       "O5'"     105.808    2.07
+G         P       "O5'"       "C5'"     118.783    1.50
+G     "O5'"       "C5'"       "C4'"     109.342    1.50
+G     "O5'"       "C5'"       "H5'"     109.845    1.50
+G     "O5'"       "C5'"      "H5''"     109.845    1.50
+G     "C4'"       "C5'"       "H5'"     109.624    1.50
+G     "C4'"       "C5'"      "H5''"     109.624    1.50
+G     "H5'"       "C5'"      "H5''"     108.472    1.50
+G     "C5'"       "C4'"       "O4'"     109.123    1.50
+G     "C5'"       "C4'"       "C3'"     116.008    1.52
+G     "C5'"       "C4'"       "H4'"     108.268    1.50
+G     "O4'"       "C4'"       "C3'"     105.388    1.50
+G     "O4'"       "C4'"       "H4'"     108.947    1.50
+G     "C3'"       "C4'"       "H4'"     109.363    1.86
+G     "C4'"       "O4'"       "C1'"     109.903    1.50
+G     "C4'"       "C3'"       "O3'"     111.281    2.46
+G     "C4'"       "C3'"       "C2'"     102.602    1.50
+G     "C4'"       "C3'"       "H3'"     110.452    2.54
+G     "O3'"       "C3'"       "C2'"     111.581    2.83
+G     "O3'"       "C3'"       "H3'"     110.380    1.67
+G     "C2'"       "C3'"       "H3'"     110.504    1.75
+G     "C3'"       "O3'"      "HO3'"     108.744    3.00
+G     "C3'"       "C2'"       "O2'"     112.782    2.45
+G     "C3'"       "C2'"       "C1'"     101.239    1.50
+G     "C3'"       "C2'"       "H2'"     110.596    1.51
+G     "O2'"       "C2'"       "C1'"     111.715    2.69
+G     "O2'"       "C2'"       "H2'"     110.448    1.97
+G     "C1'"       "C2'"       "H2'"     110.636    1.70
+G     "C2'"       "O2'"      "HO2'"     109.103    2.13
+G     "O4'"       "C1'"       "C2'"     106.047    1.50
+G     "O4'"       "C1'"          N9     108.477    1.50
+G     "O4'"       "C1'"       "H1'"     109.807    1.50
+G     "C2'"       "C1'"          N9     113.824    1.50
+G     "C2'"       "C1'"       "H1'"     109.015    1.50
+G        N9       "C1'"       "H1'"     109.561    1.50
+G     "C1'"          N9          C8     126.829    1.91
+G     "C1'"          N9          C4     127.440    1.80
+G        C8          N9          C4     105.731    1.50
+G        N9          C8          N7     113.507    1.50
+G        N9          C8          H8     123.187    1.50
+G        N7          C8          H8     123.307    1.50
+G        C8          N7          C5     104.778    1.50
+G        N7          C5          C6     130.030    1.50
+G        N7          C5          C4     110.574    1.50
+G        C6          C5          C4     119.397    1.50
+G        C5          C6          O6     128.244    1.50
+G        C5          C6          N1     111.367    1.50
+G        O6          C6          N1     120.389    1.50
+G        C6          N1          C2     125.351    1.50
+G        C6          N1          H1     116.978    2.44
+G        C2          N1          H1     117.677    2.71
+G        N1          C2          N2     116.576    1.50
+G        N1          C2          N3     123.602    1.50
+G        N2          C2          N3     119.821    1.50
+G        C2          N2         H21     119.868    1.50
+G        C2          N2         H22     119.868    1.50
+G       H21          N2         H22     120.263    1.96
+G        C2          N3          C4     112.066    1.50
+G        N9          C4          C5     105.411    1.50
+G        N9          C4          N3     126.378    1.50
+G        C5          C4          N3     128.211    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+G       C2e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+G       C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+G       C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+G       C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+G       C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+G       C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+G       C3e-chi         "O4'"     "C1'"     N9        C4        210.000       10.000    6     
+G       C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+G       C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+G       C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+G       C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+G       C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+G       alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+G       beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+G       epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+G       gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+G       sp3_sp3_52      "C3'"     "C2'"     "O2'"     "HO2'"    180.000       10.00     3     
+G              const_18          N7          C8          N9       "C1'"     180.000    10.0     2
+G              const_30          C5          C4          N9       "C1'"     180.000    10.0     2
+G              const_21          N9          C8          N7          C5       0.000    10.0     2
+G              const_24          C6          C5          N7          C8     180.000    10.0     2
+G       const_sp2_sp2_4          N7          C5          C6          O6       0.000     5.0     2
+G              const_25          N9          C4          C5          N7       0.000    10.0     2
+G       const_sp2_sp2_7          O6          C6          N1          C2     180.000     5.0     2
+G              const_11          N2          C2          N1          C6     180.000    10.0     2
+G             sp2_sp2_1          N1          C2          N2         H21     180.000     5.0     2
+G              const_14          N2          C2          N3          C4     180.000    10.0     2
+G              const_16          N9          C4          N3          C2     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+G  chir_1    P    "O5'"    OP3    OP2    both
+G  chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+G  chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+G  chir_4    "C2'"    "O2'"    "C1'"    "C3'"    negative
+G  chir_5    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+G  plan-1       "C1'"   0.020
+G  plan-1          C2   0.020
+G  plan-1          C4   0.020
+G  plan-1          C5   0.020
+G  plan-1          C6   0.020
+G  plan-1          C8   0.020
+G  plan-1          H1   0.020
+G  plan-1          H8   0.020
+G  plan-1          N1   0.020
+G  plan-1          N2   0.020
+G  plan-1          N3   0.020
+G  plan-1          N7   0.020
+G  plan-1          N9   0.020
+G  plan-1          O6   0.020
+G  plan-2          C2   0.020
+G  plan-2         H21   0.020
+G  plan-2         H22   0.020
+G  plan-2          N2   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+G           SMILES              ACDLabs 10.04                                                                                                                      O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)COP(=O)(O)O
+G SMILES_CANONICAL               CACTVS 3.341                                                                                                  NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
+G           SMILES               CACTVS 3.341                                                                                                        NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
+G SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                                  c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
+G           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                    c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N
+G            InChI                InChI  1.03 InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
+G         InChIKey                InChI  1.03                                                                                                                                        RQFCJASXJCIDSX-UUOKFMHZSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+G   acedrg               243         "dictionary generator"                  
+G   acedrg_database      11          "data source"                           
+G   rdkit                2017.03.2   "Chemoinformatics tool"
+G   refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/GDP.cif b/image_analysis/structure_refinement/monomers/GDP.cif
new file mode 100644
index 000000000..833d710c0
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/GDP.cif
@@ -0,0 +1,299 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+GDP GDP "GUANOSINE-5'-DIPHOSPHATE" NON-POLYMER 40 28 .
+
+data_comp_GDP
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+GDP PB P P 0 13.504 16.639 28.649
+GDP O1B O O 0 13.923 17.830 29.476
+GDP O2B O OP -1 14.420 15.453 28.828
+GDP O3B O OP -1 12.049 16.284 28.833
+GDP O3A O O2 0 13.659 17.092 27.107
+GDP PA P P 0 12.620 17.691 26.043
+GDP O1A O O 0 11.548 16.681 25.800
+GDP O2A O OP -1 12.214 19.058 26.485
+GDP "O5'" O O2 0 13.547 17.806 24.737
+GDP "C5'" C CH2 0 14.774 18.580 24.803
+GDP "C4'" C CH1 0 15.248 18.905 23.407
+GDP "O4'" O O2 0 15.427 17.678 22.656
+GDP "C3'" C CH1 0 14.302 19.747 22.544
+GDP "O3'" O OH1 0 14.480 21.136 22.797
+GDP "C2'" C CH1 0 14.722 19.349 21.125
+GDP "O2'" O OH1 0 15.810 20.102 20.630
+GDP "C1'" C CH1 0 15.090 17.873 21.298
+GDP N9 N NR5 0 14.017 16.952 20.924
+GDP C8 C CR15 0 13.290 16.120 21.742
+GDP N7 N NRD5 0 12.395 15.408 21.100
+GDP C5 C CR56 0 12.541 15.792 19.774
+GDP C6 C CR6 0 11.843 15.360 18.614
+GDP O6 O O 0 10.930 14.526 18.539
+GDP N1 N NR6 0 12.305 16.006 17.460
+GDP C2 C CR6 0 13.311 16.946 17.429
+GDP N2 N NH2 0 13.623 17.460 16.231
+GDP N3 N NRD6 0 13.969 17.354 18.519
+GDP C4 C CR56 0 13.538 16.739 19.651
+GDP "H5'" H H 0 15.470 18.062 25.277
+GDP "H5''" H H 0 14.616 19.420 25.301
+GDP "H4'" H H 0 16.113 19.362 23.477
+GDP "H3'" H H 0 13.359 19.490 22.706
+GDP "HO3'" H H 0 14.000 21.576 22.253
+GDP "H2'" H H 0 13.951 19.442 20.505
+GDP "HO2'" H H 0 16.487 19.998 21.132
+GDP "H1'" H H 0 15.878 17.683 20.741
+GDP H8 H H 0 13.418 16.065 22.673
+GDP HN1 H H 0 11.910 15.784 16.684
+GDP HN21 H H 0 13.778 18.320 16.152
+GDP HN22 H H 0 13.671 16.936 15.530
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+GDP PB O1B DOUBLE n 1.509 0.0200 1.509 0.0200
+GDP PB O2B SINGLE n 1.509 0.0200 1.509 0.0200
+GDP PB O3B SINGLE n 1.509 0.0200 1.509 0.0200
+GDP PB O3A SINGLE n 1.614 0.0178 1.614 0.0178
+GDP O3A PA SINGLE n 1.604 0.0133 1.604 0.0133
+GDP PA O1A DOUBLE n 1.493 0.0122 1.493 0.0122
+GDP PA O2A SINGLE n 1.493 0.0122 1.493 0.0122
+GDP PA "O5'" SINGLE n 1.604 0.0133 1.604 0.0133
+GDP "O5'" "C5'" SINGLE n 1.450 0.0166 1.450 0.0166
+GDP "C5'" "C4'" SINGLE n 1.509 0.0100 1.509 0.0100
+GDP "C4'" "O4'" SINGLE n 1.451 0.0100 1.451 0.0100
+GDP "C4'" "C3'" SINGLE n 1.535 0.0100 1.535 0.0100
+GDP "O4'" "C1'" SINGLE n 1.409 0.0100 1.409 0.0100
+GDP "C3'" "O3'" SINGLE n 1.422 0.0100 1.422 0.0100
+GDP "C3'" "C2'" SINGLE n 1.531 0.0100 1.531 0.0100
+GDP "C2'" "O2'" SINGLE n 1.411 0.0100 1.411 0.0100
+GDP "C2'" "C1'" SINGLE n 1.525 0.0100 1.525 0.0100
+GDP "C1'" N9 SINGLE n 1.458 0.0100 1.458 0.0100
+GDP N9 C8 SINGLE y 1.372 0.0100 1.372 0.0100
+GDP N9 C4 SINGLE y 1.375 0.0100 1.375 0.0100
+GDP C8 N7 DOUBLE y 1.312 0.0100 1.312 0.0100
+GDP N7 C5 SINGLE y 1.390 0.0100 1.390 0.0100
+GDP C5 C6 SINGLE y 1.417 0.0103 1.417 0.0103
+GDP C5 C4 DOUBLE y 1.377 0.0100 1.377 0.0100
+GDP C6 O6 DOUBLE n 1.239 0.0100 1.239 0.0100
+GDP C6 N1 SINGLE y 1.396 0.0107 1.396 0.0107
+GDP N1 C2 SINGLE y 1.374 0.0100 1.374 0.0100
+GDP C2 N2 SINGLE n 1.340 0.0101 1.340 0.0101
+GDP C2 N3 DOUBLE y 1.333 0.0104 1.333 0.0104
+GDP N3 C4 SINGLE y 1.355 0.0100 1.355 0.0100
+GDP "C5'" "H5'" SINGLE n 1.089 0.0100 0.989 0.0200
+GDP "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+GDP "C4'" "H4'" SINGLE n 1.089 0.0100 0.981 0.0200
+GDP "C3'" "H3'" SINGLE n 1.089 0.0100 0.992 0.0200
+GDP "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+GDP "C2'" "H2'" SINGLE n 1.089 0.0100 0.994 0.0200
+GDP "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+GDP "C1'" "H1'" SINGLE n 1.089 0.0100 0.984 0.0200
+GDP C8 H8 SINGLE n 1.082 0.0130 0.942 0.0170
+GDP N1 HN1 SINGLE n 1.016 0.0100 0.897 0.0200
+GDP N2 HN21 SINGLE n 1.016 0.0100 0.877 0.0200
+GDP N2 HN22 SINGLE n 1.016 0.0100 0.877 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+GDP O1B PB O2B 112.716 1.50
+GDP O1B PB O3B 112.716 1.50
+GDP O1B PB O3A 105.965 2.38
+GDP O2B PB O3B 112.716 1.50
+GDP O2B PB O3A 105.965 2.38
+GDP O3B PB O3A 105.965 2.38
+GDP PB O3A PA 132.584 3.00
+GDP O3A PA O1A 108.816 2.14
+GDP O3A PA O2A 108.816 2.14
+GDP O3A PA "O5'" 101.065 1.97
+GDP O1A PA O2A 118.411 2.35
+GDP O1A PA "O5'" 109.410 1.50
+GDP O2A PA "O5'" 109.410 1.50
+GDP PA "O5'" "C5'" 118.553 2.41
+GDP "O5'" "C5'" "C4'" 109.342 1.50
+GDP "O5'" "C5'" "H5'" 109.845 1.50
+GDP "O5'" "C5'" "H5''" 109.845 1.50
+GDP "C4'" "C5'" "H5'" 109.624 1.50
+GDP "C4'" "C5'" "H5''" 109.624 1.50
+GDP "H5'" "C5'" "H5''" 108.472 1.50
+GDP "C5'" "C4'" "O4'" 109.123 1.50
+GDP "C5'" "C4'" "C3'" 116.008 1.52
+GDP "C5'" "C4'" "H4'" 108.268 1.50
+GDP "O4'" "C4'" "C3'" 105.388 1.50
+GDP "O4'" "C4'" "H4'" 108.947 1.50
+GDP "C3'" "C4'" "H4'" 109.363 1.86
+GDP "C4'" "O4'" "C1'" 109.903 1.50
+GDP "C4'" "C3'" "O3'" 111.281 2.46
+GDP "C4'" "C3'" "C2'" 102.602 1.50
+GDP "C4'" "C3'" "H3'" 110.452 2.54
+GDP "O3'" "C3'" "C2'" 111.581 2.83
+GDP "O3'" "C3'" "H3'" 110.380 1.67
+GDP "C2'" "C3'" "H3'" 110.504 1.75
+GDP "C3'" "O3'" "HO3'" 108.744 3.00
+GDP "C3'" "C2'" "O2'" 112.782 2.45
+GDP "C3'" "C2'" "C1'" 101.239 1.50
+GDP "C3'" "C2'" "H2'" 110.596 1.51
+GDP "O2'" "C2'" "C1'" 111.715 2.69
+GDP "O2'" "C2'" "H2'" 110.448 1.97
+GDP "C1'" "C2'" "H2'" 110.636 1.70
+GDP "C2'" "O2'" "HO2'" 109.103 2.13
+GDP "O4'" "C1'" "C2'" 106.047 1.50
+GDP "O4'" "C1'" N9 108.477 1.50
+GDP "O4'" "C1'" "H1'" 109.807 1.50
+GDP "C2'" "C1'" N9 113.824 1.50
+GDP "C2'" "C1'" "H1'" 109.015 1.50
+GDP N9 "C1'" "H1'" 109.561 1.50
+GDP "C1'" N9 C8 126.829 1.91
+GDP "C1'" N9 C4 127.440 1.80
+GDP C8 N9 C4 105.731 1.50
+GDP N9 C8 N7 113.507 1.50
+GDP N9 C8 H8 123.187 1.50
+GDP N7 C8 H8 123.307 1.50
+GDP C8 N7 C5 104.778 1.50
+GDP N7 C5 C6 130.030 1.50
+GDP N7 C5 C4 110.574 1.50
+GDP C6 C5 C4 119.397 1.50
+GDP C5 C6 O6 128.244 1.50
+GDP C5 C6 N1 111.367 1.50
+GDP O6 C6 N1 120.389 1.50
+GDP C6 N1 C2 125.351 1.50
+GDP C6 N1 HN1 116.978 2.44
+GDP C2 N1 HN1 117.677 2.71
+GDP N1 C2 N2 116.576 1.50
+GDP N1 C2 N3 123.602 1.50
+GDP N2 C2 N3 119.821 1.50
+GDP C2 N2 HN21 119.868 1.50
+GDP C2 N2 HN22 119.868 1.50
+GDP HN21 N2 HN22 120.263 1.96
+GDP C2 N3 C4 112.066 1.50
+GDP N9 C4 C5 105.411 1.50
+GDP N9 C4 N3 126.378 1.50
+GDP C5 C4 N3 128.211 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+GDP C2e-chi "O4'" "C1'" N9 C4 210.000 10.000 6
+GDP C2e-nyu0 "C4'" "O4'" "C1'" "C2'" 340.700 6.300 1
+GDP C2e-nyu1 "O4'" "C1'" "C2'" "C3'" 32.800 4.900 1
+GDP C2e-nyu2 "C1'" "C2'" "C3'" "C4'" 326.9 3.600 1
+GDP C2e-nyu3 "C2'" "C3'" "C4'" "O4'" 22.600 4.500 1
+GDP C2e-nyu4 "C3'" "C4'" "O4'" "C1'" 357.700 6.100 1
+GDP C3e-chi "O4'" "C1'" N9 C4 210.000 10.000 6
+GDP C3e-nyu0 "C4'" "O4'" "C1'" "C2'" 2.8 6.100 1
+GDP C3e-nyu1 "O4'" "C1'" "C2'" "C3'" 335.00 4.900 1
+GDP C3e-nyu2 "C1'" "C2'" "C3'" "C4'" 35.9 2.800 1
+GDP C3e-nyu3 "C2'" "C3'" "C4'" "O4'" 324.700 3.100 1
+GDP C3e-nyu4 "C3'" "C4'" "O4'" "C1'" 20.500 5.100 1
+GDP epsi "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
+GDP gamma "O5'" "C5'" "C4'" "C3'" 180.000 10.00 3
+GDP sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00 3
+GDP sp3_sp3_27 PA O3A PB O1B 60.000 10.0 3
+GDP const_18 N7 C8 N9 "C1'" 180.000 10.0 2
+GDP const_30 C5 C4 N9 "C1'" 180.000 10.0 2
+GDP const_21 N9 C8 N7 C5 0.000 10.0 2
+GDP const_24 C6 C5 N7 C8 180.000 10.0 2
+GDP const_sp2_sp2_4 N7 C5 C6 O6 0.000 5.0 2
+GDP const_25 N9 C4 C5 N7 0.000 10.0 2
+GDP const_sp2_sp2_7 O6 C6 N1 C2 180.000 5.0 2
+GDP const_11 N2 C2 N1 C6 180.000 10.0 2
+GDP sp2_sp2_1 N1 C2 N2 HN21 180.000 5.0 2
+GDP const_14 N2 C2 N3 C4 180.000 10.0 2
+GDP const_16 N9 C4 N3 C2 180.000 10.0 2
+GDP sp3_sp3_30 PB O3A PA O1A 60.000 10.0 3
+GDP sp3_sp3_31 "C5'" "O5'" PA O3A 180.000 10.0 3
+GDP sp3_sp3_34 "C4'" "C5'" "O5'" PA 180.000 10.0 3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+GDP chir_1 PB O3A O2B O3B both
+GDP chir_2 PA O3A "O5'" O2A both
+GDP chir_3 "C4'" "O4'" "C3'" "C5'" negative
+GDP chir_4 "C3'" "O3'" "C4'" "C2'" positive
+GDP chir_5 "C2'" "O2'" "C1'" "C3'" negative
+GDP chir_6 "C1'" "O4'" N9 "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+GDP plan-1 "C1'" 0.020
+GDP plan-1 C2 0.020
+GDP plan-1 C4 0.020
+GDP plan-1 C5 0.020
+GDP plan-1 C6 0.020
+GDP plan-1 C8 0.020
+GDP plan-1 H8 0.020
+GDP plan-1 HN1 0.020
+GDP plan-1 N1 0.020
+GDP plan-1 N2 0.020
+GDP plan-1 N3 0.020
+GDP plan-1 N7 0.020
+GDP plan-1 N9 0.020
+GDP plan-1 O6 0.020
+GDP plan-2 C2 0.020
+GDP plan-2 HN21 0.020
+GDP plan-2 HN22 0.020
+GDP plan-2 N2 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+GDP SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
+GDP InChI InChI 1.03 InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
+GDP InChIKey InChI 1.03 QGWNDRXFNXRZMB-UUOKFMHZSA-N
+GDP SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
+GDP SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
+GDP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
+GDP SMILES "OpenEye OEToolkits" 1.7.6 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+GDP acedrg 243 "dictionary generator"
+GDP acedrg_database 11 "data source"
+GDP rdkit 2017.03.2 "Chemoinformatics tool"
+GDP refmac5 5.8.0238 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/GLN.cif b/image_analysis/structure_refinement/monomers/GLN.cif
new file mode 100644
index 000000000..ab85e9d2d
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/GLN.cif
@@ -0,0 +1,233 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+GLN GLN GLUTAMINE peptide 20 10 .
+
+data_comp_GLN
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+GLN N N NT3 1 -13.189 34.859 120.921
+GLN CA C CH1 0 -12.155 35.335 119.962
+GLN C C C 0 -10.823 35.547 120.705
+GLN O O O 0 -9.774 35.259 120.087
+GLN CB C CH2 0 -12.610 36.599 119.226
+GLN CG C CH2 0 -12.991 37.771 120.127
+GLN CD C C 0 -13.453 38.985 119.351
+GLN OE1 O O 0 -14.437 38.935 118.605
+GLN NE2 N NH2 0 -12.747 40.094 119.519
+GLN OXT O OC -1 -10.882 35.991 121.873
+GLN H H H 0 -14.005 34.886 120.536
+GLN H2 H H 0 -13.202 35.368 121.666
+GLN H3 H H 0 -13.012 34.007 121.158
+GLN HA H H 0 -12.019 34.624 119.285
+GLN HB3 H H 0 -13.381 36.370 118.666
+GLN HB2 H H 0 -11.887 36.885 118.629
+GLN HG3 H H 0 -12.221 38.023 120.680
+GLN HG2 H H 0 -13.713 37.495 120.731
+GLN HE21 H H 0 -11.862 40.066 119.472
+GLN HE22 H H 0 -13.160 40.862 119.679
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+GLN N n/a CA START
+GLN H N . .
+GLN H2 N . .
+GLN H3 N . .
+GLN CA N C .
+GLN HA CA . .
+GLN CB CA CG .
+GLN HB3 CB . .
+GLN HB2 CB . .
+GLN CG CB CD .
+GLN HG3 CG . .
+GLN HG2 CG . .
+GLN CD CG NE2 .
+GLN OE1 CD . .
+GLN NE2 CD HE22 .
+GLN HE21 NE2 . .
+GLN HE22 NE2 . .
+GLN C CA . END
+GLN O C . .
+GLN OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+GLN N N(CCCH)(H)3
+GLN CA C(CCHH)(NH3)(COO)(H)
+GLN C C(CCHN)(O)2
+GLN O O(CCO)
+GLN CB C(CCHH)(CCHN)(H)2
+GLN CG C(CCHH)(CNO)(H)2
+GLN CD C(CCHH)(NHH)(O)
+GLN OE1 O(CCN)
+GLN NE2 N(CCO)(H)2
+GLN OXT O(CCO)
+GLN H H(NCHH)
+GLN H2 H(NCHH)
+GLN H3 H(NCHH)
+GLN HA H(CCCN)
+GLN HB3 H(CCCH)
+GLN HB2 H(CCCH)
+GLN HG3 H(CCCH)
+GLN HG2 H(CCCH)
+GLN HE21 H(NCH)
+GLN HE22 H(NCH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+GLN N CA SINGLE n 1.487 0.0100 1.487 0.0100
+GLN CA C SINGLE n 1.538 0.0113 1.538 0.0113
+GLN CA CB SINGLE n 1.529 0.0100 1.529 0.0100
+GLN C O DOUBLE n 1.251 0.0183 1.251 0.0183
+GLN C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+GLN CB CG SINGLE n 1.525 0.0100 1.525 0.0100
+GLN CG CD SINGLE n 1.513 0.0100 1.513 0.0100
+GLN CD OE1 DOUBLE n 1.236 0.0100 1.236 0.0100
+GLN CD NE2 SINGLE n 1.325 0.0100 1.325 0.0100
+GLN N H SINGLE n 1.018 0.0520 0.902 0.0102
+GLN N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+GLN N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+GLN CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+GLN CB HB3 SINGLE n 1.092 0.0100 0.980 0.0168
+GLN CB HB2 SINGLE n 1.092 0.0100 0.980 0.0168
+GLN CG HG3 SINGLE n 1.092 0.0100 0.981 0.0172
+GLN CG HG2 SINGLE n 1.092 0.0100 0.981 0.0172
+GLN NE2 HE21 SINGLE n 1.013 0.0120 0.887 0.0200
+GLN NE2 HE22 SINGLE n 1.013 0.0120 0.887 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+GLN CA N H 109.990 3.00
+GLN CA N H2 109.990 3.00
+GLN CA N H3 109.990 3.00
+GLN H N H2 109.032 3.00
+GLN H N H3 109.032 3.00
+GLN H2 N H3 109.032 3.00
+GLN N CA C 109.258 1.50
+GLN N CA CB 110.440 2.46
+GLN N CA HA 108.387 1.58
+GLN C CA CB 111.059 3.00
+GLN C CA HA 108.774 1.79
+GLN CB CA HA 109.080 2.33
+GLN CA C O 117.148 1.60
+GLN CA C OXT 117.148 1.60
+GLN O C OXT 125.704 1.50
+GLN CA CB CG 113.998 1.50
+GLN CA CB HB3 108.677 1.74
+GLN CA CB HB2 108.677 1.74
+GLN CG CB HB3 108.907 1.50
+GLN CG CB HB2 108.907 1.50
+GLN HB3 CB HB2 107.655 1.50
+GLN CB CG CD 113.265 1.50
+GLN CB CG HG3 109.355 1.50
+GLN CB CG HG2 109.355 1.50
+GLN CD CG HG3 108.958 1.89
+GLN CD CG HG2 108.958 1.89
+GLN HG3 CG HG2 107.827 1.56
+GLN CG CD OE1 121.487 1.50
+GLN CG CD NE2 116.074 1.76
+GLN OE1 CD NE2 122.439 1.50
+GLN CD NE2 HE21 119.917 2.87
+GLN CD NE2 HE22 119.917 2.87
+GLN HE21 NE2 HE22 120.165 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+GLN chi1 N CA CB CG -60.000 10.0 3
+GLN chi2 CA CB CG CD 180.000 10.0 3
+GLN chi3 CB CG CD NE2 180.000 10.0 6
+GLN hh1 CG CD NE2 HE22 180.000 5.0 2
+GLN sp3_sp3_1 C CA N H 180.000 10.0 3
+GLN sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+GLN chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+GLN plan-1 C 0.020
+GLN plan-1 CA 0.020
+GLN plan-1 O 0.020
+GLN plan-1 OXT 0.020
+GLN plan-2 CD 0.020
+GLN plan-2 CG 0.020
+GLN plan-2 NE2 0.020
+GLN plan-2 OE1 0.020
+GLN plan-3 CD 0.020
+GLN plan-3 HE21 0.020
+GLN plan-3 HE22 0.020
+GLN plan-3 NE2 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+GLN SMILES ACDLabs 10.04 O=C(N)CCC(N)C(=O)O
+GLN SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCC(N)=O)C(O)=O
+GLN SMILES CACTVS 3.341 N[CH](CCC(N)=O)C(O)=O
+GLN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CC(=O)N)[C@@H](C(=O)O)N
+GLN SMILES "OpenEye OEToolkits" 1.5.0 C(CC(=O)N)C(C(=O)O)N
+GLN InChI InChI 1.03 InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1
+GLN InChIKey InChI 1.03 ZDXPYRJPNDTMRX-VKHMYHEASA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+GLN acedrg 278 "dictionary generator"
+GLN acedrg_database 12 "data source"
+GLN rdkit 2019.09.1 "Chemoinformatics tool"
+GLN refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/GLU.cif b/image_analysis/structure_refinement/monomers/GLU.cif
new file mode 100644
index 000000000..1eefa693b
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/GLU.cif
@@ -0,0 +1,217 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+GLU GLU "GLUTAMIC        ACID" peptide 18 10 .
+
+data_comp_GLU
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+GLU N N NT3 1 88.319 -7.751 -10.089
+GLU CA C CH1 0 87.677 -7.162 -11.296
+GLU C C C 0 88.359 -5.826 -11.640
+GLU O O O 0 88.389 -4.954 -10.744
+GLU CB C CH2 0 86.177 -6.950 -11.080
+GLU CG C CH2 0 85.390 -8.247 -10.908
+GLU CD C C 0 83.891 -8.048 -10.773
+GLU OE1 O O 0 83.281 -7.495 -11.711
+GLU OE2 O OC -1 83.334 -8.447 -9.728
+GLU OXT O OC -1 88.836 -5.708 -12.790
+GLU H H H 0 88.066 -7.298 -9.352
+GLU H2 H H 0 89.218 -7.717 -10.158
+GLU H3 H H 0 88.077 -8.615 -9.999
+GLU HA H H 0 87.806 -7.788 -12.054
+GLU HB3 H H 0 85.814 -6.460 -11.847
+GLU HB2 H H 0 86.049 -6.394 -10.284
+GLU HG3 H H 0 85.714 -8.714 -10.110
+GLU HG2 H H 0 85.559 -8.827 -11.681
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+GLU N n/a CA START
+GLU H N . .
+GLU H2 N . .
+GLU H3 N . .
+GLU CA N C .
+GLU HA CA . .
+GLU CB CA CG .
+GLU HB3 CB . .
+GLU HB2 CB . .
+GLU CG CB CD .
+GLU HG3 CG . .
+GLU HG2 CG . .
+GLU CD CG OE2 .
+GLU OE1 CD . .
+GLU OE2 CD . .
+GLU C CA . END
+GLU O C . .
+GLU OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+GLU N N(CCCH)(H)3
+GLU CA C(CCHH)(NH3)(COO)(H)
+GLU C C(CCHN)(O)2
+GLU O O(CCO)
+GLU CB C(CCHH)(CCHN)(H)2
+GLU CG C(CCHH)(COO)(H)2
+GLU CD C(CCHH)(O)2
+GLU OE1 O(CCO)
+GLU OE2 O(CCO)
+GLU OXT O(CCO)
+GLU H H(NCHH)
+GLU H2 H(NCHH)
+GLU H3 H(NCHH)
+GLU HA H(CCCN)
+GLU HB3 H(CCCH)
+GLU HB2 H(CCCH)
+GLU HG3 H(CCCH)
+GLU HG2 H(CCCH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+GLU N CA SINGLE n 1.487 0.0100 1.487 0.0100
+GLU CA C SINGLE n 1.538 0.0113 1.538 0.0113
+GLU CA CB SINGLE n 1.529 0.0100 1.529 0.0100
+GLU C O DOUBLE n 1.251 0.0183 1.251 0.0183
+GLU C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+GLU CB CG SINGLE n 1.526 0.0100 1.526 0.0100
+GLU CG CD SINGLE n 1.518 0.0135 1.518 0.0135
+GLU CD OE1 DOUBLE n 1.249 0.0161 1.249 0.0161
+GLU CD OE2 SINGLE n 1.249 0.0161 1.249 0.0161
+GLU N H SINGLE n 1.018 0.0520 0.902 0.0102
+GLU N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+GLU N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+GLU CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+GLU CB HB3 SINGLE n 1.092 0.0100 0.980 0.0168
+GLU CB HB2 SINGLE n 1.092 0.0100 0.980 0.0168
+GLU CG HG3 SINGLE n 1.092 0.0100 0.981 0.0172
+GLU CG HG2 SINGLE n 1.092 0.0100 0.981 0.0172
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+GLU CA N H 109.990 3.00
+GLU CA N H2 109.990 3.00
+GLU CA N H3 109.990 3.00
+GLU H N H2 109.032 3.00
+GLU H N H3 109.032 3.00
+GLU H2 N H3 109.032 3.00
+GLU N CA C 109.258 1.50
+GLU N CA CB 110.440 2.46
+GLU N CA HA 108.387 1.58
+GLU C CA CB 111.059 3.00
+GLU C CA HA 108.774 1.79
+GLU CB CA HA 109.080 2.33
+GLU CA C O 117.148 1.60
+GLU CA C OXT 117.148 1.60
+GLU O C OXT 125.704 1.50
+GLU CA CB CG 113.294 1.61
+GLU CA CB HB3 108.677 1.74
+GLU CA CB HB2 108.677 1.74
+GLU CG CB HB3 108.696 2.80
+GLU CG CB HB2 108.696 2.80
+GLU HB3 CB HB2 107.655 1.50
+GLU CB CG CD 114.140 3.00
+GLU CB CG HG3 108.968 1.50
+GLU CB CG HG2 108.968 1.50
+GLU CD CG HG3 108.472 1.50
+GLU CD CG HG2 108.472 1.50
+GLU HG3 CG HG2 107.541 1.92
+GLU CG CD OE1 118.251 3.00
+GLU CG CD OE2 118.251 3.00
+GLU OE1 CD OE2 123.498 1.82
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+GLU chi1 N CA CB CG -60.000 10.0 3
+GLU chi2 CA CB CG CD 180.000 10.0 3
+GLU chi3 CB CG CD OE1 180.000 10.0 6
+GLU sp3_sp3_1 C CA N H 180.000 10.0 3
+GLU sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+GLU chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+GLU plan-1 C 0.020
+GLU plan-1 CA 0.020
+GLU plan-1 O 0.020
+GLU plan-1 OXT 0.020
+GLU plan-2 CD 0.020
+GLU plan-2 CG 0.020
+GLU plan-2 OE1 0.020
+GLU plan-2 OE2 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+GLU SMILES ACDLabs 12.01 O=C(O)C(N)CCC(=O)O
+GLU SMILES_CANONICAL CACTVS 3.370 N[C@@H](CCC(O)=O)C(O)=O
+GLU SMILES CACTVS 3.370 N[CH](CCC(O)=O)C(O)=O
+GLU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)[C@@H](C(=O)O)N
+GLU SMILES "OpenEye OEToolkits" 1.7.0 C(CC(=O)O)C(C(=O)O)N
+GLU InChI InChI 1.03 InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1
+GLU InChIKey InChI 1.03 WHUUTDBJXJRKMK-VKHMYHEASA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+GLU acedrg 278 "dictionary generator"
+GLU acedrg_database 12 "data source"
+GLU rdkit 2019.09.1 "Chemoinformatics tool"
+GLU refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/GLY.cif b/image_analysis/structure_refinement/monomers/GLY.cif
new file mode 100644
index 000000000..1eab291b6
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/GLY.cif
@@ -0,0 +1,153 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+GLY GLY GLYCINE peptide 10 5 .
+
+data_comp_GLY
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+GLY N N NT3 1 25.320 35.545 47.014
+GLY CA C CH2 0 25.532 37.001 46.897
+GLY C C C 0 26.039 37.376 45.517
+GLY O O O 0 27.114 36.860 45.146
+GLY OXT O OC -1 25.343 38.172 44.853
+GLY H H H 0 26.098 35.105 46.869
+GLY H2 H H 0 24.710 35.270 46.405
+GLY H3 H H 0 25.019 35.342 47.843
+GLY HA3 H H 0 26.185 37.288 47.578
+GLY HA2 H H 0 24.682 37.467 47.075
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+GLY N n/a CA START
+GLY H N . .
+GLY H2 N . .
+GLY H3 N . .
+GLY CA N C .
+GLY HA3 CA . .
+GLY HA2 CA . .
+GLY C CA . END
+GLY O C . .
+GLY OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+GLY N N(CCHH)(H)3
+GLY CA C(NH3)(COO)(H)2
+GLY C C(CHHN)(O)2
+GLY O O(CCO)
+GLY OXT O(CCO)
+GLY H H(NCHH)
+GLY H2 H(NCHH)
+GLY H3 H(NCHH)
+GLY HA3 H(CCHN)
+GLY HA2 H(CCHN)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+GLY N CA SINGLE n 1.476 0.0106 1.476 0.0106
+GLY CA C SINGLE n 1.517 0.0121 1.517 0.0121
+GLY C O DOUBLE n 1.249 0.0161 1.249 0.0161
+GLY C OXT SINGLE n 1.249 0.0161 1.249 0.0161
+GLY N H SINGLE n 1.018 0.0520 0.905 0.0200
+GLY N H2 SINGLE n 1.018 0.0520 0.905 0.0200
+GLY N H3 SINGLE n 1.018 0.0520 0.905 0.0200
+GLY CA HA3 SINGLE n 1.092 0.0100 0.986 0.0200
+GLY CA HA2 SINGLE n 1.092 0.0100 0.986 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+GLY CA N H 110.151 2.94
+GLY CA N H2 110.151 2.94
+GLY CA N H3 110.151 2.94
+GLY H N H2 109.089 3.00
+GLY H N H3 109.089 3.00
+GLY H2 N H3 109.089 3.00
+GLY N CA C 111.292 1.50
+GLY N CA HA3 109.172 1.50
+GLY N CA HA2 109.172 1.50
+GLY C CA HA3 109.620 1.50
+GLY C CA HA2 109.620 1.50
+GLY HA3 CA HA2 108.054 1.50
+GLY CA C O 117.080 1.50
+GLY CA C OXT 117.080 1.50
+GLY O C OXT 125.839 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+GLY sp3_sp3_1 C CA N H 180.000 10.0 3
+GLY sp2_sp3_1 O C CA HA3 0.000 10.0 6
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+GLY plan-1 C 0.020
+GLY plan-1 CA 0.020
+GLY plan-1 O 0.020
+GLY plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+GLY SMILES ACDLabs 10.04 O=C(O)CN
+GLY SMILES_CANONICAL CACTVS 3.341 NCC(O)=O
+GLY SMILES CACTVS 3.341 NCC(O)=O
+GLY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C(=O)O)N
+GLY SMILES "OpenEye OEToolkits" 1.5.0 C(C(=O)O)N
+GLY InChI InChI 1.03 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
+GLY InChIKey InChI 1.03 DHMQDGOQFOQNFH-UHFFFAOYSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+GLY acedrg 278 "dictionary generator"
+GLY acedrg_database 12 "data source"
+GLY rdkit 2019.09.1 "Chemoinformatics tool"
+GLY refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/GMP.cif b/image_analysis/structure_refinement/monomers/GMP.cif
new file mode 100644
index 000000000..8c4b2aa55
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/GMP.cif
@@ -0,0 +1,256 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+GMP     GMP      GUANOSINE     NON-POLYMER     33     20     .     
+#
+data_comp_GMP
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+GMP     "O5'"   O       OH1     0       31.023      62.348      13.095      
+GMP     "C5'"   C       CH2     0       30.880      60.990      13.491      
+GMP     "C4'"   C       CH1     0       32.039      60.141      13.016      
+GMP     "O4'"   O       O2      0       32.223      60.322      11.591      
+GMP     "C3'"   C       CH1     0       33.402      60.499      13.617      
+GMP     "O3'"   O       OH1     0       33.583      59.871      14.880      
+GMP     "C2'"   C       CH1     0       34.373      59.978      12.551      
+GMP     "O2'"   O       OH1     0       34.741      58.628      12.744      
+GMP     "C1'"   C       CH1     0       33.583      60.160      11.252      
+GMP     N9      N       NR5     0       33.999      61.321      10.471      
+GMP     C8      C       CR15    0       33.932      62.634      10.866      
+GMP     N7      N       NRD5    0       34.376      63.473      9.962       
+GMP     C5      C       CR56    0       34.763      62.661      8.903       
+GMP     C6      C       CR6     0       35.321      63.006      7.643       
+GMP     O6      O       O       0       35.589      64.136      7.210       
+GMP     N1      N       NR6     0       35.569      61.874      6.857       
+GMP     C2      C       CR6     0       35.310      60.575      7.237       
+GMP     N2      N       NH2     0       35.612      59.614      6.354       
+GMP     N3      N       NRD6    0       34.785      60.248      8.422       
+GMP     C4      C       CR56    0       34.537      61.332      9.203       
+GMP     "HO5'"  H       H       0       30.412      62.808      13.461      
+GMP     "H5'1"  H       H       0       30.045      60.632      13.121      
+GMP     "H5'2"  H       H       0       30.824      60.943      14.469      
+GMP     "H4'"   H       H       0       31.840      59.197      13.196      
+GMP     "H3'"   H       H       0       33.489      61.482      13.709      
+GMP     "HO3'"  H       H       0       34.374      60.022      15.150      
+GMP     "H2'"   H       H       0       35.192      60.542      12.533      
+GMP     "HO2'"  H       H       0       34.046      58.141      12.763      
+GMP     "H1'"   H       H       0       33.686      59.348      10.707      
+GMP     H8      H       H       0       33.598      62.904      11.704      
+GMP     HN1     H       H       0       35.923      62.012      6.043       
+GMP     HN21    H       H       0       35.993      58.873      6.627       
+GMP     HN22    H       H       0       35.427      59.728      5.504       
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+GMP       "O5'"       "C5'"      SINGLE       n     1.421  0.0131     1.421  0.0131
+GMP       "C5'"       "C4'"      SINGLE       n     1.511  0.0177     1.511  0.0177
+GMP       "C4'"       "O4'"      SINGLE       n     1.451  0.0100     1.451  0.0100
+GMP       "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+GMP       "O4'"       "C1'"      SINGLE       n     1.409  0.0100     1.409  0.0100
+GMP       "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+GMP       "C3'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+GMP       "C2'"       "O2'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+GMP       "C2'"       "C1'"      SINGLE       n     1.525  0.0100     1.525  0.0100
+GMP       "C1'"          N9      SINGLE       n     1.458  0.0100     1.458  0.0100
+GMP          N9          C8      SINGLE       y     1.372  0.0100     1.372  0.0100
+GMP          N9          C4      SINGLE       y     1.375  0.0100     1.375  0.0100
+GMP          C8          N7      DOUBLE       y     1.312  0.0100     1.312  0.0100
+GMP          N7          C5      SINGLE       y     1.390  0.0100     1.390  0.0100
+GMP          C5          C6      SINGLE       y     1.417  0.0103     1.417  0.0103
+GMP          C5          C4      DOUBLE       y     1.377  0.0100     1.377  0.0100
+GMP          C6          O6      DOUBLE       n     1.239  0.0100     1.239  0.0100
+GMP          C6          N1      SINGLE       y     1.396  0.0107     1.396  0.0107
+GMP          N1          C2      SINGLE       y     1.374  0.0100     1.374  0.0100
+GMP          C2          N2      SINGLE       n     1.340  0.0101     1.340  0.0101
+GMP          C2          N3      DOUBLE       y     1.333  0.0104     1.333  0.0104
+GMP          N3          C4      SINGLE       y     1.355  0.0100     1.355  0.0100
+GMP       "O5'"      "HO5'"      SINGLE       n     0.970  0.0120     0.848  0.0200
+GMP       "C5'"      "H5'1"      SINGLE       n     1.089  0.0100     0.981  0.0200
+GMP       "C5'"      "H5'2"      SINGLE       n     1.089  0.0100     0.981  0.0200
+GMP       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+GMP       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+GMP       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+GMP       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.994  0.0200
+GMP       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+GMP       "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.984  0.0200
+GMP          C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0170
+GMP          N1         HN1      SINGLE       n     1.016  0.0100     0.897  0.0200
+GMP          N2        HN21      SINGLE       n     1.016  0.0100     0.877  0.0200
+GMP          N2        HN22      SINGLE       n     1.016  0.0100     0.877  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+GMP       "C5'"       "O5'"      "HO5'"     109.007    3.00
+GMP       "O5'"       "C5'"       "C4'"     111.279    1.98
+GMP       "O5'"       "C5'"      "H5'1"     109.280    1.50
+GMP       "O5'"       "C5'"      "H5'2"     109.280    1.50
+GMP       "C4'"       "C5'"      "H5'1"     109.326    2.00
+GMP       "C4'"       "C5'"      "H5'2"     109.326    2.00
+GMP      "H5'1"       "C5'"      "H5'2"     108.248    2.26
+GMP       "C5'"       "C4'"       "O4'"     109.170    1.50
+GMP       "C5'"       "C4'"       "C3'"     114.598    1.97
+GMP       "C5'"       "C4'"       "H4'"     109.037    1.87
+GMP       "O4'"       "C4'"       "C3'"     105.388    1.50
+GMP       "O4'"       "C4'"       "H4'"     108.947    1.50
+GMP       "C3'"       "C4'"       "H4'"     109.363    1.86
+GMP       "C4'"       "O4'"       "C1'"     109.903    1.50
+GMP       "C4'"       "C3'"       "O3'"     111.281    2.46
+GMP       "C4'"       "C3'"       "C2'"     102.602    1.50
+GMP       "C4'"       "C3'"       "H3'"     110.452    2.54
+GMP       "O3'"       "C3'"       "C2'"     111.581    2.83
+GMP       "O3'"       "C3'"       "H3'"     110.380    1.67
+GMP       "C2'"       "C3'"       "H3'"     110.504    1.75
+GMP       "C3'"       "O3'"      "HO3'"     108.744    3.00
+GMP       "C3'"       "C2'"       "O2'"     112.782    2.45
+GMP       "C3'"       "C2'"       "C1'"     101.239    1.50
+GMP       "C3'"       "C2'"       "H2'"     110.596    1.51
+GMP       "O2'"       "C2'"       "C1'"     111.715    2.69
+GMP       "O2'"       "C2'"       "H2'"     110.448    1.97
+GMP       "C1'"       "C2'"       "H2'"     110.636    1.70
+GMP       "C2'"       "O2'"      "HO2'"     109.103    2.13
+GMP       "O4'"       "C1'"       "C2'"     106.047    1.50
+GMP       "O4'"       "C1'"          N9     108.477    1.50
+GMP       "O4'"       "C1'"       "H1'"     109.807    1.50
+GMP       "C2'"       "C1'"          N9     113.824    1.50
+GMP       "C2'"       "C1'"       "H1'"     109.015    1.50
+GMP          N9       "C1'"       "H1'"     109.561    1.50
+GMP       "C1'"          N9          C8     126.829    1.91
+GMP       "C1'"          N9          C4     127.440    1.80
+GMP          C8          N9          C4     105.731    1.50
+GMP          N9          C8          N7     113.507    1.50
+GMP          N9          C8          H8     123.187    1.50
+GMP          N7          C8          H8     123.307    1.50
+GMP          C8          N7          C5     104.778    1.50
+GMP          N7          C5          C6     130.030    1.50
+GMP          N7          C5          C4     110.574    1.50
+GMP          C6          C5          C4     119.397    1.50
+GMP          C5          C6          O6     128.244    1.50
+GMP          C5          C6          N1     111.367    1.50
+GMP          O6          C6          N1     120.389    1.50
+GMP          C6          N1          C2     125.351    1.50
+GMP          C6          N1         HN1     116.978    2.44
+GMP          C2          N1         HN1     117.677    2.71
+GMP          N1          C2          N2     116.576    1.50
+GMP          N1          C2          N3     123.602    1.50
+GMP          N2          C2          N3     119.821    1.50
+GMP          C2          N2        HN21     119.868    1.50
+GMP          C2          N2        HN22     119.868    1.50
+GMP        HN21          N2        HN22     120.263    1.96
+GMP          C2          N3          C4     112.066    1.50
+GMP          N9          C4          C5     105.411    1.50
+GMP          N9          C4          N3     126.378    1.50
+GMP          C5          C4          N3     128.211    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+GMP            sp3_sp3_25       "C4'"       "C5'"       "O5'"      "HO5'"     180.000    10.0     3
+GMP              const_21          N9          C8          N7          C5       0.000    10.0     2
+GMP              const_24          C6          C5          N7          C8     180.000    10.0     2
+GMP       const_sp2_sp2_4          N7          C5          C6          O6       0.000     5.0     2
+GMP              const_25          N9          C4          C5          N7       0.000    10.0     2
+GMP       const_sp2_sp2_7          O6          C6          N1          C2     180.000     5.0     2
+GMP              const_11          N2          C2          N1          C6     180.000    10.0     2
+GMP             sp2_sp2_1          N1          C2          N2        HN21     180.000     5.0     2
+GMP              const_14          N2          C2          N3          C4     180.000    10.0     2
+GMP              const_16          N9          C4          N3          C2     180.000    10.0     2
+GMP            sp3_sp3_28       "O4'"       "C4'"       "C5'"       "O5'"     180.000    10.0     3
+GMP             sp3_sp3_2       "C5'"       "C4'"       "O4'"       "C1'"     -60.000    10.0     3
+GMP            sp3_sp3_41       "O3'"       "C3'"       "C4'"       "C5'"     180.000    10.0     3
+GMP             sp3_sp3_4       "C2'"       "C1'"       "O4'"       "C4'"     -60.000    10.0     3
+GMP            sp3_sp3_46       "C4'"       "C3'"       "O3'"      "HO3'"     180.000    10.0     3
+GMP            sp3_sp3_20       "O2'"       "C2'"       "C3'"       "O3'"     -60.000    10.0     3
+GMP            sp3_sp3_49       "C3'"       "C2'"       "O2'"      "HO2'"     180.000    10.0     3
+GMP             sp3_sp3_8       "O4'"       "C1'"       "C2'"       "O2'"     180.000    10.0     3
+GMP             sp2_sp3_1          C8          N9       "C1'"       "O4'"     150.000    10.0     6
+GMP              const_18          N7          C8          N9       "C1'"     180.000    10.0     2
+GMP              const_30          C5          C4          N9       "C1'"     180.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+GMP    chir_1    "C4'"    "O4'"    "C3'"    "C5'"    negative
+GMP    chir_2    "C3'"    "O3'"    "C4'"    "C2'"    positive
+GMP    chir_3    "C2'"    "O2'"    "C1'"    "C3'"    negative
+GMP    chir_4    "C1'"    "O4'"    N9    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+GMP    plan-1       "C1'"   0.020
+GMP    plan-1          C2   0.020
+GMP    plan-1          C4   0.020
+GMP    plan-1          C5   0.020
+GMP    plan-1          C6   0.020
+GMP    plan-1          C8   0.020
+GMP    plan-1          H8   0.020
+GMP    plan-1         HN1   0.020
+GMP    plan-1          N1   0.020
+GMP    plan-1          N2   0.020
+GMP    plan-1          N3   0.020
+GMP    plan-1          N7   0.020
+GMP    plan-1          N9   0.020
+GMP    plan-1          O6   0.020
+GMP    plan-2          C2   0.020
+GMP    plan-2        HN21   0.020
+GMP    plan-2        HN22   0.020
+GMP    plan-2          N2   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+GMP           SMILES              ACDLabs 10.04                                                                                                     O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3O)CO
+GMP            InChI                InChI  1.03 InChI=1S/C10H13N5O5/c11-10-13-7-4(8(19)14-10)12-2-15(7)9-6(18)5(17)3(1-16)20-9/h2-3,5-6,9,16-18H,1H2,(H3,11,13,14,19)/t3-,5-,6-,9-/m1/s1
+GMP         InChIKey                InChI  1.03                                                                                                              NYHBQMYGNKIUIF-UUOKFMHZSA-N
+GMP SMILES_CANONICAL               CACTVS 3.385                                                                                   NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
+GMP           SMILES               CACTVS 3.385                                                                                         NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O
+GMP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5                                                                                 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=C(NC2=O)N
+GMP           SMILES "OpenEye OEToolkits" 1.7.5                                                                                                   c1nc2c(n1C3C(C(C(O3)CO)O)O)N=C(NC2=O)N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+GMP acedrg               243         "dictionary generator"                  
+GMP acedrg_database      11          "data source"                           
+GMP rdkit                2017.03.2   "Chemoinformatics tool"
+GMP refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/GOL.cif b/image_analysis/structure_refinement/monomers/GOL.cif
new file mode 100644
index 000000000..f4a3e10af
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/GOL.cif
@@ -0,0 +1,134 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+GOL     GOL      GLYCEROL     NON-POLYMER     14     6     .     
+#
+data_comp_GOL
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+GOL     C1      C       CH2     0       29.630      3.832       30.945      
+GOL     O1      O       OH1     0       28.425      3.137       31.257      
+GOL     C2      C       CH1     0       30.401      3.142       29.840      
+GOL     O2      O       OH1     0       31.484      3.970       29.416      
+GOL     C3      C       CH2     0       30.919      1.777       30.241      
+GOL     O3      O       OH1     0       31.679      1.174       29.197      
+GOL     H11     H       H       0       30.196      3.882       31.753      
+GOL     H12     H       H       0       29.411      4.753       30.662      
+GOL     HO1     H       H       0       28.030      3.557       31.876      
+GOL     H2      H       H       0       29.790      3.020       29.074      
+GOL     HO2     H       H       0       32.019      4.078       30.068      
+GOL     H31     H       H       0       30.155      1.193       30.467      
+GOL     H32     H       H       0       31.486      1.869       31.045      
+GOL     HO3     H       H       0       31.160      1.020       28.546      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+GOL          C1          O1      SINGLE       n     1.425  0.0100     1.425  0.0100
+GOL          C1          C2      SINGLE       n     1.514  0.0105     1.514  0.0105
+GOL          C2          O2      SINGLE       n     1.427  0.0100     1.427  0.0100
+GOL          C2          C3      SINGLE       n     1.514  0.0105     1.514  0.0105
+GOL          C3          O3      SINGLE       n     1.425  0.0100     1.425  0.0100
+GOL          C1         H11      SINGLE       n     1.089  0.0100     0.988  0.0200
+GOL          C1         H12      SINGLE       n     1.089  0.0100     0.988  0.0200
+GOL          O1         HO1      SINGLE       n     0.970  0.0120     0.846  0.0200
+GOL          C2          H2      SINGLE       n     1.089  0.0100     0.987  0.0186
+GOL          O2         HO2      SINGLE       n     0.970  0.0120     0.848  0.0200
+GOL          C3         H31      SINGLE       n     1.089  0.0100     0.988  0.0200
+GOL          C3         H32      SINGLE       n     1.089  0.0100     0.988  0.0200
+GOL          O3         HO3      SINGLE       n     0.970  0.0120     0.846  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+GOL          O1          C1          C2     111.586    1.51
+GOL          O1          C1         H11     109.268    1.50
+GOL          O1          C1         H12     109.268    1.50
+GOL          C2          C1         H11     109.193    1.50
+GOL          C2          C1         H12     109.193    1.50
+GOL         H11          C1         H12     108.313    1.50
+GOL          C1          O1         HO1     108.280    3.00
+GOL          C1          C2          O2     110.247    1.72
+GOL          C1          C2          C3     113.504    1.50
+GOL          C1          C2          H2     108.441    1.50
+GOL          O2          C2          C3     110.247    1.72
+GOL          O2          C2          H2     108.721    1.50
+GOL          C3          C2          H2     108.441    1.50
+GOL          C2          O2         HO2     107.936    3.00
+GOL          C2          C3          O3     111.586    1.51
+GOL          C2          C3         H31     109.193    1.50
+GOL          C2          C3         H32     109.193    1.50
+GOL          O3          C3         H31     109.268    1.50
+GOL          O3          C3         H32     109.268    1.50
+GOL         H31          C3         H32     108.313    1.50
+GOL          C3          O3         HO3     108.280    3.00
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+GOL             sp3_sp3_1          C2          C1          O1         HO1     180.000    10.0     3
+GOL             sp3_sp3_4          O1          C1          C2          O2     180.000    10.0     3
+GOL            sp3_sp3_14          C1          C2          O2         HO2      60.000    10.0     3
+GOL            sp3_sp3_16          C1          C2          C3          O3     180.000    10.0     3
+GOL            sp3_sp3_25          C2          C3          O3         HO3     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+GOL    chir_1    C2    O2    C1    C3    both
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+GOL           SMILES              ACDLabs 12.01                                 OCC(O)CO
+GOL SMILES_CANONICAL               CACTVS 3.370                                 OCC(O)CO
+GOL           SMILES               CACTVS 3.370                                 OCC(O)CO
+GOL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0                               C(C(CO)O)O
+GOL           SMILES "OpenEye OEToolkits" 1.7.0                               C(C(CO)O)O
+GOL            InChI                InChI  1.03 InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
+GOL         InChIKey                InChI  1.03              PEDCQBHIVMGVHV-UHFFFAOYSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+GOL acedrg               243         "dictionary generator"                  
+GOL acedrg_database      11          "data source"                           
+GOL rdkit                2017.03.2   "Chemoinformatics tool"
+GOL refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/GTP.cif b/image_analysis/structure_refinement/monomers/GTP.cif
new file mode 100644
index 000000000..53fdeff81
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/GTP.cif
@@ -0,0 +1,312 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+GTP     GTP      "GUANOSINE-5'-TRIPHOSPHATE"     NON-POLYMER     44     32     .     
+#
+data_comp_GTP
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+GTP     PG      P       P       0       4.560       31.688      21.477      
+GTP     O1G     O       O       0       4.404       32.256      22.874      
+GTP     O2G     O       OP      -1      4.031       32.621      20.405      
+GTP     O3G     O       OP      -1      4.007       30.282      21.352      
+GTP     O3B     O       O2      0       6.154       31.567      21.217      
+GTP     PB      P       P       0       7.014       30.840      20.078      
+GTP     O1B     O       O       0       7.367       29.484      20.548      
+GTP     O2B     O       OP      -1      6.320       31.011      18.784      
+GTP     O3A     O       O2      0       8.339       31.740      20.070      
+GTP     PA      P       P       0       8.640       33.246      19.616      
+GTP     O1A     O       O       0       8.465       33.336      18.144      
+GTP     O2A     O       OP      -1      7.853       34.171      20.471      
+GTP     "O5'"   O       O2      0       10.195      33.377      19.964      
+GTP     "C5'"   C       CH2     0       10.583      33.182      21.348      
+GTP     "C4'"   C       CH1     0       12.036      33.553      21.524      
+GTP     "O4'"   O       O2      0       12.846      32.727      20.657      
+GTP     "C3'"   C       CH1     0       12.389      35.007      21.180      
+GTP     "O3'"   O       OH1     0       13.296      35.538      22.138      
+GTP     "C2'"   C       CH1     0       13.016      34.892      19.786      
+GTP     "O2'"   O       OH1     0       13.937      35.921      19.490      
+GTP     "C1'"   C       CH1     0       13.732      33.549      19.908      
+GTP     N9      N       NR5     0       14.014      32.895      18.629      
+GTP     C8      C       CR15    0       13.089      32.464      17.714      
+GTP     N7      N       NRD5    0       13.617      31.910      16.650      
+GTP     C5      C       CR56    0       14.986      31.978      16.880      
+GTP     C6      C       CR6     0       16.070      31.533      16.074      
+GTP     O6      O       O       0       16.021      30.976      14.968      
+GTP     N1      N       NR16    0       17.307      31.793      16.676      
+GTP     C2      C       CR6     0       17.480      32.406      17.902      
+GTP     N2      N       NH2     0       18.744      32.578      18.332      
+GTP     N3      N       NRD6    0       16.461      32.825      18.660      
+GTP     C4      C       CR56    0       15.250      32.581      18.093      
+GTP     "H5'"   H       H       0       10.452      32.234      21.605      
+GTP     "H5''"  H       H       0       10.026      33.747      21.941      
+GTP     "H4'"   H       H       0       12.287      33.371      22.464      
+GTP     "H3'"   H       H       0       11.567      35.560      21.142      
+GTP     "HO3'"  H       H       0       14.015      35.710      21.778      
+GTP     "H2'"   H       H       0       12.311      34.844      19.092      
+GTP     "HO2'"  H       H       0       14.731      35.591      19.468      
+GTP     "H1'"   H       H       0       14.596      33.678      20.425      
+GTP     H8      H       H       0       12.160      32.561      17.840      
+GTP     HN1     H       H       0       18.034      31.538      16.221      
+GTP     HN21    H       H       0       18.891      32.964      19.107      
+GTP     HN22    H       H       0       19.424      32.310      17.847      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+GTP          PG         O1G      DOUBLE       n     1.516  0.0200     1.516  0.0200
+GTP          PG         O2G      SINGLE       n     1.516  0.0200     1.516  0.0200
+GTP          PG         O3G      SINGLE       n     1.516  0.0200     1.516  0.0200
+GTP          PG         O3B      SINGLE       n     1.620  0.0143     1.620  0.0143
+GTP         O3B          PB      SINGLE       n     1.601  0.0108     1.601  0.0108
+GTP          PB         O1B      DOUBLE       n     1.478  0.0100     1.478  0.0100
+GTP          PB         O2B      SINGLE       n     1.478  0.0100     1.478  0.0100
+GTP          PB         O3A      SINGLE       n     1.602  0.0126     1.602  0.0126
+GTP         O3A          PA      SINGLE       n     1.600  0.0185     1.600  0.0185
+GTP          PA         O1A      DOUBLE       n     1.485  0.0100     1.485  0.0100
+GTP          PA         O2A      SINGLE       n     1.485  0.0100     1.485  0.0100
+GTP          PA       "O5'"      SINGLE       n     1.598  0.0100     1.598  0.0100
+GTP       "O5'"       "C5'"      SINGLE       n     1.445  0.0200     1.445  0.0200
+GTP       "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+GTP       "C4'"       "O4'"      SINGLE       n     1.444  0.0100     1.444  0.0100
+GTP       "C4'"       "C3'"      SINGLE       n     1.532  0.0100     1.532  0.0100
+GTP       "O4'"       "C1'"      SINGLE       n     1.423  0.0100     1.423  0.0100
+GTP       "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+GTP       "C3'"       "C2'"      SINGLE       n     1.532  0.0103     1.532  0.0103
+GTP       "C2'"       "O2'"      SINGLE       n     1.412  0.0100     1.412  0.0100
+GTP       "C2'"       "C1'"      SINGLE       n     1.528  0.0100     1.528  0.0100
+GTP       "C1'"          N9      SINGLE       n     1.462  0.0102     1.462  0.0102
+GTP          N9          C8      SINGLE       y     1.371  0.0100     1.371  0.0100
+GTP          N9          C4      SINGLE       y     1.383  0.0114     1.383  0.0114
+GTP          C8          N7      DOUBLE       y     1.311  0.0104     1.311  0.0104
+GTP          N7          C5      SINGLE       y     1.390  0.0100     1.390  0.0100
+GTP          C5          C6      SINGLE       y     1.418  0.0111     1.418  0.0111
+GTP          C5          C4      DOUBLE       y     1.377  0.0100     1.377  0.0100
+GTP          C6          O6      DOUBLE       n     1.240  0.0104     1.240  0.0104
+GTP          C6          N1      SINGLE       y     1.394  0.0120     1.394  0.0120
+GTP          N1          C2      SINGLE       y     1.374  0.0124     1.374  0.0124
+GTP          C2          N2      SINGLE       n     1.341  0.0143     1.341  0.0143
+GTP          C2          N3      DOUBLE       y     1.331  0.0119     1.331  0.0119
+GTP          N3          C4      SINGLE       y     1.355  0.0100     1.355  0.0100
+GTP       "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.991  0.0200
+GTP       "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.991  0.0200
+GTP       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.990  0.0200
+GTP       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.991  0.0200
+GTP       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.839  0.0200
+GTP       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.991  0.0200
+GTP       "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.839  0.0200
+GTP       "C1'"       "H1'"      SINGLE       n     1.089  0.0100     1.016  0.0200
+GTP          C8          H8      SINGLE       n     1.082  0.0130     0.942  0.0168
+GTP          N1         HN1      SINGLE       n     1.016  0.0100     0.894  0.0200
+GTP          N2        HN21      SINGLE       n     1.016  0.0100     0.877  0.0200
+GTP          N2        HN22      SINGLE       n     1.016  0.0100     0.877  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+GTP         O1G          PG         O2G     112.609    3.00
+GTP         O1G          PG         O3G     112.609    3.00
+GTP         O1G          PG         O3B     106.004    3.00
+GTP         O2G          PG         O3G     112.609    3.00
+GTP         O2G          PG         O3B     106.004    3.00
+GTP         O3G          PG         O3B     106.004    3.00
+GTP          PG         O3B          PB     132.613    3.00
+GTP         O3B          PB         O1B     108.634    3.00
+GTP         O3B          PB         O2B     108.634    3.00
+GTP         O3B          PB         O3A     100.990    3.00
+GTP         O1B          PB         O2B     119.776    1.50
+GTP         O1B          PB         O3A     108.634    3.00
+GTP         O2B          PB         O3A     108.634    3.00
+GTP          PB         O3A          PA     133.108    3.00
+GTP         O3A          PA         O1A     109.053    3.00
+GTP         O3A          PA         O2A     109.053    3.00
+GTP         O3A          PA       "O5'"     100.137    3.00
+GTP         O1A          PA         O2A     118.805    3.00
+GTP         O1A          PA       "O5'"     109.340    2.31
+GTP         O2A          PA       "O5'"     109.340    2.31
+GTP          PA       "O5'"       "C5'"     116.362    1.50
+GTP       "O5'"       "C5'"       "C4'"     109.454    1.61
+GTP       "O5'"       "C5'"       "H5'"     109.882    1.50
+GTP       "O5'"       "C5'"      "H5''"     109.882    1.50
+GTP       "C4'"       "C5'"       "H5'"     109.589    1.50
+GTP       "C4'"       "C5'"      "H5''"     109.589    1.50
+GTP       "H5'"       "C5'"      "H5''"     108.471    1.50
+GTP       "C5'"       "C4'"       "O4'"     109.154    1.50
+GTP       "C5'"       "C4'"       "C3'"     115.288    1.50
+GTP       "C5'"       "C4'"       "H4'"     108.351    1.59
+GTP       "O4'"       "C4'"       "C3'"     105.318    1.50
+GTP       "O4'"       "C4'"       "H4'"     109.120    1.50
+GTP       "C3'"       "C4'"       "H4'"     109.322    2.54
+GTP       "C4'"       "O4'"       "C1'"     109.502    2.85
+GTP       "C4'"       "C3'"       "O3'"     110.713    3.00
+GTP       "C4'"       "C3'"       "C2'"     102.593    1.50
+GTP       "C4'"       "C3'"       "H3'"     110.577    3.00
+GTP       "O3'"       "C3'"       "C2'"     111.671    3.00
+GTP       "O3'"       "C3'"       "H3'"     110.541    2.08
+GTP       "C2'"       "C3'"       "H3'"     110.454    1.85
+GTP       "C3'"       "O3'"      "HO3'"     109.389    3.00
+GTP       "C3'"       "C2'"       "O2'"     112.677    3.00
+GTP       "C3'"       "C2'"       "C1'"     101.406    1.50
+GTP       "C3'"       "C2'"       "H2'"     110.788    1.91
+GTP       "O2'"       "C2'"       "C1'"     110.814    3.00
+GTP       "O2'"       "C2'"       "H2'"     110.904    1.50
+GTP       "C1'"       "C2'"       "H2'"     110.342    1.91
+GTP       "C2'"       "O2'"      "HO2'"     109.217    3.00
+GTP       "O4'"       "C1'"       "C2'"     106.114    1.65
+GTP       "O4'"       "C1'"          N9     108.577    1.50
+GTP       "O4'"       "C1'"       "H1'"     109.833    2.53
+GTP       "C2'"       "C1'"          N9     113.380    2.77
+GTP       "C2'"       "C1'"       "H1'"     109.222    1.50
+GTP          N9       "C1'"       "H1'"     109.411    1.50
+GTP       "C1'"          N9          C8     127.058    3.00
+GTP       "C1'"          N9          C4     126.955    2.94
+GTP          C8          N9          C4     105.987    1.50
+GTP          N9          C8          N7     113.721    1.50
+GTP          N9          C8          H8     122.935    1.50
+GTP          N7          C8          H8     123.345    1.50
+GTP          C8          N7          C5     103.926    1.50
+GTP          N7          C5          C6     129.926    1.50
+GTP          N7          C5          C4     110.770    1.50
+GTP          C6          C5          C4     119.304    1.50
+GTP          C5          C6          O6     128.237    1.50
+GTP          C5          C6          N1     111.514    1.50
+GTP          O6          C6          N1     120.248    1.50
+GTP          C6          N1          C2     125.452    1.50
+GTP          C6          N1         HN1     117.160    2.45
+GTP          C2          N1         HN1     117.387    2.97
+GTP          N1          C2          N2     116.657    1.50
+GTP          N1          C2          N3     123.538    1.50
+GTP          N2          C2          N3     119.805    1.50
+GTP          C2          N2        HN21     119.712    3.00
+GTP          C2          N2        HN22     119.712    3.00
+GTP        HN21          N2        HN22     120.576    3.00
+GTP          C2          N3          C4     111.926    1.50
+GTP          N9          C4          C5     105.596    1.50
+GTP          N9          C4          N3     126.138    1.50
+GTP          C5          C4          N3     128.265    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+GTP            sp3_sp3_27          PB         O3B          PG         O1G      60.000    10.0     3
+GTP            sp3_sp3_40       "C4'"       "C5'"       "O5'"          PA     180.000    10.0     3
+GTP            sp3_sp3_43       "O4'"       "C4'"       "C5'"       "O5'"     180.000    10.0     3
+GTP             sp3_sp3_2       "C5'"       "C4'"       "O4'"       "C1'"     -60.000    10.0     3
+GTP            sp3_sp3_56       "O3'"       "C3'"       "C4'"       "C5'"     180.000    10.0     3
+GTP             sp3_sp3_4       "C2'"       "C1'"       "O4'"       "C4'"     -60.000    10.0     3
+GTP            sp3_sp3_61       "C4'"       "C3'"       "O3'"      "HO3'"     180.000    10.0     3
+GTP            sp3_sp3_20       "O2'"       "C2'"       "C3'"       "O3'"     -60.000    10.0     3
+GTP            sp3_sp3_64       "C3'"       "C2'"       "O2'"      "HO2'"     180.000    10.0     3
+GTP             sp3_sp3_8       "O4'"       "C1'"       "C2'"       "O2'"     180.000    10.0     3
+GTP             sp2_sp3_1          C8          N9       "C1'"       "O4'"     150.000    10.0     6
+GTP              const_18          N7          C8          N9       "C1'"     180.000     0.0     2
+GTP              const_30          C5          C4          N9       "C1'"     180.000     0.0     2
+GTP              const_21          N9          C8          N7          C5       0.000     0.0     2
+GTP              const_24          C6          C5          N7          C8     180.000     0.0     2
+GTP       const_sp2_sp2_4          N7          C5          C6          O6       0.000     0.0     2
+GTP              const_25          N9          C4          C5          N7       0.000     0.0     2
+GTP       const_sp2_sp2_7          O6          C6          N1          C2     180.000     0.0     2
+GTP              const_11          N2          C2          N1          C6     180.000     0.0     2
+GTP            sp2_sp2_33          N1          C2          N2        HN21     180.000     5.0     2
+GTP              const_14          N2          C2          N3          C4     180.000     0.0     2
+GTP              const_16          N9          C4          N3          C2     180.000     0.0     2
+GTP            sp3_sp3_30          PG         O3B          PB         O1B      60.000    10.0     3
+GTP            sp3_sp3_32          PA         O3A          PB         O3B     -60.000    10.0     3
+GTP            sp3_sp3_36          PB         O3A          PA         O1A      60.000    10.0     3
+GTP            sp3_sp3_37       "C5'"       "O5'"          PA         O3A     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+GTP    chir_1    PB    O3A    O3B    O2B    both
+GTP    chir_2    PA    O3A    "O5'"    O2A    both
+GTP    chir_3    "C4'"    "O4'"    "C3'"    "C5'"    negative
+GTP    chir_4    "C3'"    "O3'"    "C4'"    "C2'"    positive
+GTP    chir_5    "C2'"    "O2'"    "C1'"    "C3'"    negative
+GTP    chir_6    "C1'"    "O4'"    N9    "C2'"    negative
+GTP    chir_7    PG    O3B    O2G    O3G    both
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+GTP    plan-1       "C1'"   0.020
+GTP    plan-1          C4   0.020
+GTP    plan-1          C5   0.020
+GTP    plan-1          C6   0.020
+GTP    plan-1          C8   0.020
+GTP    plan-1          H8   0.020
+GTP    plan-1          N3   0.020
+GTP    plan-1          N7   0.020
+GTP    plan-1          N9   0.020
+GTP    plan-2          C2   0.020
+GTP    plan-2          C4   0.020
+GTP    plan-2          C5   0.020
+GTP    plan-2          C6   0.020
+GTP    plan-2         HN1   0.020
+GTP    plan-2          N1   0.020
+GTP    plan-2          N2   0.020
+GTP    plan-2          N3   0.020
+GTP    plan-2          N7   0.020
+GTP    plan-2          N9   0.020
+GTP    plan-2          O6   0.020
+GTP    plan-3          C2   0.020
+GTP    plan-3        HN21   0.020
+GTP    plan-3        HN22   0.020
+GTP    plan-3          N2   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+GTP  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O"
+GTP  InChI             InChI                 1.03   "InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1"
+GTP  InChIKey          InChI                 1.03   XKMLYUALXHKNFT-UUOKFMHZSA-N
+GTP  SMILES_CANONICAL  CACTVS                3.370  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O"
+GTP  SMILES            CACTVS                3.370  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O"
+GTP  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N"
+GTP  SMILES            "OpenEye OEToolkits"  1.7.6  "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N"
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+GTP acedrg               271         "dictionary generator"                  
+GTP acedrg_database      12          "data source"                           
+GTP rdkit                2019.09.1   "Chemoinformatics tool"
+GTP refmac5              5.8.0405    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/H2U.cif b/image_analysis/structure_refinement/monomers/H2U.cif
new file mode 100644
index 000000000..4e8fff729
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/H2U.cif
@@ -0,0 +1,267 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+H2U H2U "5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE" RNA 34 21 .
+
+data_comp_H2U
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+H2U P      P P    0  50.726 5.590 34.203
+H2U OP1    O O    0  49.785 6.717 34.586
+H2U OP2    O OP   -1 50.408 4.289 34.915
+H2U OP3    O OP   -1 50.864 5.422 32.702
+H2U "O5'"  O O2   0  52.185 6.036 34.731
+H2U "C5'"  C CH2  0  52.783 7.247 34.201
+H2U "C4'"  C CH1  0  54.080 7.529 34.920
+H2U "O4'"  O O2   0  53.820 7.636 36.343
+H2U "C3'"  C CH1  0  55.180 6.469 34.768
+H2U "O3'"  O OH1  0  56.455 7.077 34.600
+H2U "C1'"  C CH1  0  54.676 6.785 37.073
+H2U "C2'"  C CH1  0  55.056 5.687 36.077
+H2U "O2'"  O OH1  0  56.271 5.034 36.427
+H2U N1     N NR6  0  53.958 6.335 38.328
+H2U C2     C CR6  0  53.665 7.317 39.260
+H2U O2     O O    0  54.100 8.459 39.144
+H2U N3     N NR16 0  52.842 7.004 40.287
+H2U C4     C CR6  0  52.614 5.723 40.737
+H2U O4     O O    0  51.852 5.514 41.665
+H2U C5     C CH2  0  53.341 4.623 40.030
+H2U C6     C CH2  0  53.582 4.925 38.551
+H2U "H5'"  H H    0  52.163 8.008 34.324
+H2U "H5''" H H    0  52.957 7.139 33.234
+H2U "H4'"  H H    0  54.420 8.393 34.602
+H2U "H3'"  H H    0  54.979 5.876 33.998
+H2U "HO3'" H H    0  57.050 6.470 34.603
+H2U "H1'"  H H    0  55.490 7.284 37.333
+H2U "H2'"  H H    0  54.331 5.025 35.984
+H2U "HO2'" H H    0  56.337 4.943 37.269
+H2U HN3    H H    0  52.424 7.661 40.692
+H2U H51    H H    0  52.822 3.807 40.107
+H2U H52    H H    0  54.195 4.483 40.469
+H2U H61    H H    0  54.297 4.331 38.228
+H2U H62    H H    0  52.764 4.720 38.043
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+H2U P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+H2U P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+H2U P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+H2U P     "O5'"  SINGLE n 1.614 0.0178 1.614 0.0178
+H2U "O5'" "C5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+H2U "C5'" "C4'"  SINGLE n 1.509 0.0100 1.509 0.0100
+H2U "C4'" "O4'"  SINGLE n 1.449 0.0100 1.449 0.0100
+H2U "C4'" "C3'"  SINGLE n 1.535 0.0100 1.535 0.0100
+H2U "O4'" "C1'"  SINGLE n 1.409 0.0106 1.409 0.0106
+H2U "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+H2U "C3'" "C2'"  SINGLE n 1.530 0.0134 1.530 0.0134
+H2U "C1'" "C2'"  SINGLE n 1.527 0.0119 1.527 0.0119
+H2U "C1'" N1     SINGLE n 1.489 0.0155 1.489 0.0155
+H2U "C2'" "O2'"  SINGLE n 1.420 0.0122 1.420 0.0122
+H2U N1    C2     SINGLE n 1.343 0.0200 1.343 0.0200
+H2U N1    C6     SINGLE n 1.467 0.0100 1.467 0.0100
+H2U C2    O2     DOUBLE n 1.226 0.0110 1.226 0.0110
+H2U C2    N3     SINGLE n 1.343 0.0163 1.343 0.0163
+H2U N3    C4     SINGLE n 1.377 0.0101 1.377 0.0101
+H2U C4    O4     DOUBLE n 1.218 0.0100 1.218 0.0100
+H2U C4    C5     SINGLE n 1.497 0.0100 1.497 0.0100
+H2U C5    C6     SINGLE n 1.525 0.0128 1.525 0.0128
+H2U "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+H2U "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+H2U "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+H2U "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+H2U "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+H2U "C1'" "H1'"  SINGLE n 1.089 0.0100 0.989 0.0200
+H2U "C2'" "H2'"  SINGLE n 1.089 0.0100 0.988 0.0200
+H2U "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+H2U N3    HN3    SINGLE n 1.016 0.0100 0.876 0.0200
+H2U C5    H51    SINGLE n 1.089 0.0100 0.970 0.0100
+H2U C5    H52    SINGLE n 1.089 0.0100 0.970 0.0100
+H2U C6    H61    SINGLE n 1.089 0.0100 0.985 0.0100
+H2U C6    H62    SINGLE n 1.089 0.0100 0.985 0.0100
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+H2U OP1   P     OP2    112.864 1.69
+H2U OP1   P     OP3    112.864 1.69
+H2U OP1   P     "O5'"  105.808 2.07
+H2U OP2   P     OP3    112.864 1.69
+H2U OP2   P     "O5'"  105.808 2.07
+H2U OP3   P     "O5'"  105.808 2.07
+H2U P     "O5'" "C5'"  118.783 1.50
+H2U "O5'" "C5'" "C4'"  109.342 1.50
+H2U "O5'" "C5'" "H5'"  109.845 1.50
+H2U "O5'" "C5'" "H5''" 109.845 1.50
+H2U "C4'" "C5'" "H5'"  109.624 1.50
+H2U "C4'" "C5'" "H5''" 109.624 1.50
+H2U "H5'" "C5'" "H5''" 108.472 1.50
+H2U "C5'" "C4'" "O4'"  109.123 1.50
+H2U "C5'" "C4'" "C3'"  116.008 1.52
+H2U "C5'" "C4'" "H4'"  108.268 1.50
+H2U "O4'" "C4'" "C3'"  105.508 1.50
+H2U "O4'" "C4'" "H4'"  108.642 1.50
+H2U "C3'" "C4'" "H4'"  109.363 1.86
+H2U "C4'" "O4'" "C1'"  109.926 1.50
+H2U "C4'" "C3'" "O3'"  111.281 2.46
+H2U "C4'" "C3'" "C2'"  102.352 1.50
+H2U "C4'" "C3'" "H3'"  110.452 2.54
+H2U "O3'" "C3'" "C2'"  112.463 2.73
+H2U "O3'" "C3'" "H3'"  110.380 1.67
+H2U "C2'" "C3'" "H3'"  110.255 2.04
+H2U "C3'" "O3'" "HO3'" 108.744 3.00
+H2U "O4'" "C1'" "C2'"  106.204 2.50
+H2U "O4'" "C1'" N1     108.858 1.71
+H2U "O4'" "C1'" "H1'"  109.395 1.50
+H2U "C2'" "C1'" N1     112.110 1.66
+H2U "C2'" "C1'" "H1'"  109.914 1.68
+H2U N1    "C1'" "H1'"  108.795 2.24
+H2U "C3'" "C2'" "C1'"  104.443 2.26
+H2U "C3'" "C2'" "O2'"  112.463 2.73
+H2U "C3'" "C2'" "H2'"  110.255 2.04
+H2U "C1'" "C2'" "O2'"  111.164 2.38
+H2U "C1'" "C2'" "H2'"  110.518 1.74
+H2U "O2'" "C2'" "H2'"  110.259 1.63
+H2U "C2'" "O2'" "HO2'" 109.104 3.00
+H2U "C1'" N1    C2     118.428 3.00
+H2U "C1'" N1    C6     119.226 3.00
+H2U C2    N1    C6     122.347 2.69
+H2U N1    C2    O2     121.078 1.61
+H2U N1    C2    N3     117.002 2.84
+H2U O2    C2    N3     121.921 1.50
+H2U C2    N3    C4     123.512 2.15
+H2U C2    N3    HN3    118.376 1.92
+H2U C4    N3    HN3    118.112 1.50
+H2U N3    C4    O4     120.553 1.50
+H2U N3    C4    C5     116.998 1.50
+H2U O4    C4    C5     122.450 1.72
+H2U C4    C5    C6     112.021 2.38
+H2U C4    C5    H51    108.560 1.50
+H2U C4    C5    H52    108.560 1.50
+H2U C6    C5    H51    108.959 1.50
+H2U C6    C5    H52    108.959 1.50
+H2U H51   C5    H52    108.118 1.50
+H2U N1    C6    C5     110.160 1.50
+H2U N1    C6    H61    109.581 1.50
+H2U N1    C6    H62    109.581 1.50
+H2U C5    C6    H61    109.272 1.50
+H2U C5    C6    H62    109.272 1.50
+H2U H61   C6    H62    108.112 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+H2U C2e-chi    "O4'" "C1'" N1    C2     210.000 10.000 6
+H2U C2e-nyu0   "C4'" "O4'" "C1'" "C2'"  340.700 6.300  1
+H2U C2e-nyu1   "O4'" "C1'" "C2'" "C3'"  32.800  4.900  1
+H2U C2e-nyu2   "C1'" "C2'" "C3'" "C4'"  326.9   3.600  1
+H2U C2e-nyu3   "C2'" "C3'" "C4'" "O4'"  22.600  4.500  1
+H2U C2e-nyu4   "C3'" "C4'" "O4'" "C1'"  357.700 6.100  1
+H2U C3e-chi    "O4'" "C1'" N1    C2     210.000 10.000 6
+H2U C3e-nyu0   "C4'" "O4'" "C1'" "C2'"  2.8     6.100  1
+H2U C3e-nyu1   "O4'" "C1'" "C2'" "C3'"  335.00  4.900  1
+H2U C3e-nyu2   "C1'" "C2'" "C3'" "C4'"  35.9    2.800  1
+H2U C3e-nyu3   "C2'" "C3'" "C4'" "O4'"  324.700 3.100  1
+H2U C3e-nyu4   "C3'" "C4'" "O4'" "C1'"  20.500  5.100  1
+H2U alpha      "C5'" "O5'" P     OP3    -60.000 10.00  3
+H2U beta       P     "O5'" "C5'" "C4'"  180.000 10.00  3
+H2U epsi       "C4'" "C3'" "O3'" "HO3'" 180.000 10.00  3
+H2U gamma      "O5'" "C5'" "C4'" "C3'"  180.000 10.00  3
+H2U sp3_sp3_52 "C3'" "C2'" "O2'" "HO2'" 180.000 10.00  3
+H2U sp2_sp2_4  O2    C2    N1    "C1'"  0.000   5.0    2
+H2U sp2_sp3_16 "C1'" N1    C6    C5     180.000 10.0   6
+H2U sp2_sp2_7  O2    C2    N3    C4     180.000 5.0    2
+H2U sp2_sp2_11 O4    C4    N3    C2     180.000 5.0    2
+H2U sp2_sp3_4  O4    C4    C5    C6     180.000 10.0   6
+H2U sp3_sp3_25 C4    C5    C6    N1     60.000  10.0   3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+H2U chir_1 P     "O5'" OP2   OP3   both
+H2U chir_2 "C4'" "O4'" "C3'" "C5'" negative
+H2U chir_3 "C3'" "O3'" "C4'" "C2'" positive
+H2U chir_4 "C1'" "O4'" N1    "C2'" negative
+H2U chir_5 "C2'" "O2'" "C1'" "C3'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+H2U plan-1 "C1'" 0.020
+H2U plan-1 C2    0.020
+H2U plan-1 C6    0.020
+H2U plan-1 N1    0.020
+H2U plan-2 C2    0.020
+H2U plan-2 N1    0.020
+H2U plan-2 N3    0.020
+H2U plan-2 O2    0.020
+H2U plan-3 C2    0.020
+H2U plan-3 C4    0.020
+H2U plan-3 HN3   0.020
+H2U plan-3 N3    0.020
+H2U plan-4 C4    0.020
+H2U plan-4 C5    0.020
+H2U plan-4 N3    0.020
+H2U plan-4 O4    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+H2U SMILES           ACDLabs              10.04 O=C1N(CCC(=O)N1)C2OC(C(O)C2O)COP(=O)(O)O
+H2U SMILES_CANONICAL CACTVS               3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
+H2U SMILES           CACTVS               3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2CCC(=O)NC2=O
+H2U SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
+H2U SMILES           "OpenEye OEToolkits" 1.5.0 C1CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
+H2U InChI            InChI                1.03  InChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
+H2U InChIKey         InChI                1.03  NBWDKGJHOHJBRJ-XVFCMESISA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+H2U acedrg          243       "dictionary generator"
+H2U acedrg_database 11        "data source"
+H2U rdkit           2017.03.2 "Chemoinformatics tool"
+H2U refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/HEC.cif b/image_analysis/structure_refinement/monomers/HEC.cif
new file mode 100644
index 000000000..95ec1620f
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/HEC.cif
@@ -0,0 +1,689 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+HEC HEC "HEME C" NON-POLYMER 74 42 .
+
+data_comp_HEC
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.alt_atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+HEC FE   FE   FE FE   2.00 -0.636 0.011  0.178
+HEC CHA  CHA  C  C1   0    2.705  0.563  -0.191
+HEC CHB  CHB  C  C1   0    -1.246 3.264  -0.651
+HEC CHC  CHC  C  C1   0    -3.983 -0.606 0.238
+HEC CHD  CHD  C  C1   0    -0.013 -3.313 0.643
+HEC NA   NA   N  NRD5 -1   0.536  1.644  -0.354
+HEC C1A  C1A  C  CR5  0    1.894  1.679  -0.418
+HEC C2A  C2A  C  CR5  0    2.308  2.957  -0.744
+HEC C3A  C3A  C  CR5  0    1.186  3.724  -0.874
+HEC C4A  C4A  C  CR5  0    0.106  2.908  -0.630
+HEC CMA  CMA  C  CH3  0    1.153  5.194  -1.212
+HEC CAA  CAA  C  CH2  0    3.737  3.412  -0.906
+HEC CBA  CBA  C  CH2  0    4.414  3.848  0.391
+HEC CGA  CGA  C  C    0    4.256  5.326  0.738
+HEC O1A  O1A  O  O    0    5.052  6.137  0.220
+HEC O2A  O2A  O  OC   -1   3.339  5.649  1.522
+HEC NB   NB   N  NRD5 0    -2.344 1.145  -0.176
+HEC C1B  C1B  C  CR5  0    -2.390 2.485  -0.453
+HEC C2B  C2B  C  CR5  0    -3.695 2.917  -0.499
+HEC C3B  C3B  C  CR5  0    -4.521 1.785  -0.231
+HEC C4B  C4B  C  CR5  0    -3.632 0.716  -0.043
+HEC CMB  CMB  C  CH3  0    -4.205 4.311  -0.764
+HEC CAB  CAB  C  CH1  -1   -5.944 1.794  -0.181
+HEC CBB  CBB  C  CH3  0    -6.457 1.964  1.230
+HEC NC   NC   N  NRD5 -1   -1.812 -1.692 0.391
+HEC C1C  C1C  C  CR5  0    -3.180 -1.736 0.415
+HEC C2C  C2C  C  CR5  0    -3.614 -3.025 0.618
+HEC C3C  C3C  C  CR5  0    -2.443 -3.843 0.743
+HEC C4C  C4C  C  CR5  0    -1.365 -2.963 0.597
+HEC CMC  CMC  C  CH3  0    -5.039 -3.509 0.709
+HEC CAC  CAC  C  CH1  -1   -2.369 -5.248 0.970
+HEC CBC  CBC  C  CH3  0    -2.389 -6.034 -0.319
+HEC ND   ND   N  NRD5 0    1.066  -1.186 0.196
+HEC C1D  C1D  C  CR5  0    1.125  -2.521 0.464
+HEC C2D  C2D  C  CR5  0    2.438  -2.923 0.528
+HEC C3D  C3D  C  CR5  0    3.211  -1.822 0.301
+HEC C4D  C4D  C  CR5  0    2.353  -0.759 0.089
+HEC CMD  CMD  C  CH3  0    2.947  -4.314 0.810
+HEC CAD  CAD  C  CH2  0    4.718  -1.775 0.271
+HEC CBD  CBD  C  CH2  0    5.319  -1.958 -1.119
+HEC CGD  CGD  C  C    0    6.842  -1.867 -1.168
+HEC O1D  O1D  O  O    0    7.354  -0.784 -1.521
+HEC O2D  O2D  O  OC   -1   7.499  -2.881 -0.852
+HEC HHA  HHA  H  H    0    3.635  0.731  -0.226
+HEC HHB  HHB  H  H    0    -1.412 4.181  -0.802
+HEC HHC  HHC  H  H    0    -4.913 -0.752 0.339
+HEC HHD  HHD  H  H    0    0.158  -4.224 0.834
+HEC HMA1 HMA1 H  H    0    0.311  5.421  -1.635
+HEC HMA2 HMA2 H  H    0    1.871  5.414  -1.827
+HEC HMA3 HMA3 H  H    0    1.255  5.717  -0.400
+HEC HAA1 HAA1 H  H    0    3.782  4.153  -1.549
+HEC HAA2 HAA2 H  H    0    4.266  2.686  -1.303
+HEC HBA1 HBA1 H  H    0    5.376  3.645  0.328
+HEC HBA2 HBA2 H  H    0    4.050  3.313  1.134
+HEC HMB1 HMB1 H  H    0    -5.042 4.275  -1.254
+HEC HMB2 HMB2 H  H    0    -3.561 4.806  -1.294
+HEC HMB3 HMB3 H  H    0    -4.346 4.770  0.080
+HEC HAB  HAB  H  H    0    -6.300 1.007  -0.566
+HEC HBB1 HBB1 H  H    0    -7.428 1.953  1.202
+HEC HBB2 HBB2 H  H    0    -6.133 2.815  1.569
+HEC HBB3 HBB3 H  H    0    -6.120 1.229  1.767
+HEC HMC1 HMC1 H  H    0    -5.098 -4.434 0.423
+HEC HMC2 HMC2 H  H    0    -5.609 -2.971 0.136
+HEC HMC3 HMC3 H  H    0    -5.349 -3.437 1.627
+HEC HAC  HAC  H  H    0    -3.040 -5.552 1.562
+HEC HBC1 HBC1 H  H    0    -2.345 -6.978 -0.098
+HEC HBC2 HBC2 H  H    0    -1.619 -5.768 -0.848
+HEC HBC3 HBC3 H  H    0    -3.215 -5.828 -0.786
+HEC HMD1 HMD1 H  H    0    3.793  -4.460 0.359
+HEC HMD2 HMD2 H  H    0    2.311  -4.973 0.490
+HEC HMD3 HMD3 H  H    0    3.070  -4.427 1.767
+HEC HAD1 HAD1 H  H    0    5.084  -2.466 0.865
+HEC HAD2 HAD2 H  H    0    5.025  -0.915 0.634
+HEC HBD1 HBD1 H  H    0    4.945  -1.271 -1.719
+HEC HBD2 HBD2 H  H    0    5.046  -2.837 -1.469
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+HEC O2D  n/a CGD  START
+HEC CGD  O2D CBD  .
+HEC O1D  CGD .    .
+HEC CBD  CGD CAD  .
+HEC HBD1 CBD .    .
+HEC HBD2 CBD .    .
+HEC CAD  CBD C3D  .
+HEC HAD1 CAD .    .
+HEC HAD2 CAD .    .
+HEC C3D  CAD C4D  .
+HEC C2D  C3D C1D  .
+HEC CMD  C2D HMD1 .
+HEC HMD3 CMD .    .
+HEC HMD2 CMD .    .
+HEC HMD1 CMD .    .
+HEC C1D  C2D CHD  .
+HEC CHD  C1D HHD  .
+HEC HHD  CHD .    .
+HEC C4D  C3D ND   .
+HEC CHA  C4D HHA  .
+HEC HHA  CHA .    .
+HEC ND   C4D FE   .
+HEC FE   ND  NA   .
+HEC NB   FE  C4B  .
+HEC C4B  NB  C3B  .
+HEC C3B  C4B C2B  .
+HEC CAB  C3B CBB  .
+HEC HAB  CAB .    .
+HEC CBB  CAB HBB1 .
+HEC HBB3 CBB .    .
+HEC HBB2 CBB .    .
+HEC HBB1 CBB .    .
+HEC C2B  C3B C1B  .
+HEC CMB  C2B HMB1 .
+HEC HMB3 CMB .    .
+HEC HMB2 CMB .    .
+HEC HMB1 CMB .    .
+HEC C1B  C2B CHB  .
+HEC CHB  C1B HHB  .
+HEC HHB  CHB .    .
+HEC NC   FE  C4C  .
+HEC C4C  NC  C3C  .
+HEC C3C  C4C C2C  .
+HEC CAC  C3C CBC  .
+HEC HAC  CAC .    .
+HEC CBC  CAC HBC1 .
+HEC HBC3 CBC .    .
+HEC HBC2 CBC .    .
+HEC HBC1 CBC .    .
+HEC C2C  C3C C1C  .
+HEC CMC  C2C HMC1 .
+HEC HMC3 CMC .    .
+HEC HMC2 CMC .    .
+HEC HMC1 CMC .    .
+HEC C1C  C2C CHC  .
+HEC CHC  C1C HHC  .
+HEC HHC  CHC .    .
+HEC NA   FE  C4A  .
+HEC C4A  NA  C3A  .
+HEC C3A  C4A C2A  .
+HEC CMA  C3A HMA1 .
+HEC HMA3 CMA .    .
+HEC HMA2 CMA .    .
+HEC HMA1 CMA .    .
+HEC C2A  C3A CAA  .
+HEC C1A  C2A .    .
+HEC CAA  C2A CBA  .
+HEC HAA1 CAA .    .
+HEC HAA2 CAA .    .
+HEC CBA  CAA CGA  .
+HEC HBA1 CBA .    .
+HEC HBA2 CBA .    .
+HEC CGA  CBA O2A  .
+HEC O1A  CGA .    .
+HEC O2A  CGA .    END
+HEC CHA  C1A .    ADD
+HEC CHB  C4A .    ADD
+HEC CHC  C4B .    ADD
+HEC CHD  C4C .    ADD
+HEC NA   C1A .    ADD
+HEC NB   C1B .    ADD
+HEC NC   C1C .    ADD
+HEC ND   C1D .    ADD
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+HEC CHA  C(C[5a]C[5a]N[5a])2(H)
+HEC CHB  C(C[5a]C[5a]N[5a])2(H)
+HEC CHC  C(C[5a]C[5a]N[5a])2(H)
+HEC CHD  C(C[5a]C[5a]N[5a])2(H)
+HEC NA   N[5a](C[5a]C[5a]C)2{2|C<4>}
+HEC C1A  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEC C2A  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>}
+HEC C3A  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEC C4A  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEC CMA  C(C[5a]C[5a]2)(H)3
+HEC CAA  C(C[5a]C[5a]2)(CCHH)(H)2
+HEC CBA  C(CC[5a]HH)(COO)(H)2
+HEC CGA  C(CCHH)(O)2
+HEC O1A  O(CCO)
+HEC O2A  O(CCO)
+HEC NB   N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>}
+HEC C1B  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>}
+HEC C2B  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEC C3B  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>}
+HEC C4B  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEC CMB  C(C[5a]C[5a]2)(H)3
+HEC CAB  C(C[5a]C[5a]2)(CH3)(H)
+HEC CBB  C(CC[5a]H)(H)3
+HEC NC   N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>}
+HEC C1C  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>}
+HEC C2C  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEC C3C  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>}
+HEC C4C  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEC CMC  C(C[5a]C[5a]2)(H)3
+HEC CAC  C(C[5a]C[5a]2)(CH3)(H)
+HEC CBC  C(CC[5a]H)(H)3
+HEC ND   N[5a](C[5a]C[5a]C)2{2|C<4>}
+HEC C1D  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEC C2D  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEC C3D  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>}
+HEC C4D  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEC CMD  C(C[5a]C[5a]2)(H)3
+HEC CAD  C(C[5a]C[5a]2)(CCHH)(H)2
+HEC CBD  C(CC[5a]HH)(COO)(H)2
+HEC CGD  C(CCHH)(O)2
+HEC O1D  O(CCO)
+HEC O2D  O(CCO)
+HEC HHA  H(CC[5a]2)
+HEC HHB  H(CC[5a]2)
+HEC HHC  H(CC[5a]2)
+HEC HHD  H(CC[5a]2)
+HEC HMA1 H(CC[5a]HH)
+HEC HMA2 H(CC[5a]HH)
+HEC HMA3 H(CC[5a]HH)
+HEC HAA1 H(CC[5a]CH)
+HEC HAA2 H(CC[5a]CH)
+HEC HBA1 H(CCCH)
+HEC HBA2 H(CCCH)
+HEC HMB1 H(CC[5a]HH)
+HEC HMB2 H(CC[5a]HH)
+HEC HMB3 H(CC[5a]HH)
+HEC HAB  H(CC[5a]C)
+HEC HBB1 H(CCHH)
+HEC HBB2 H(CCHH)
+HEC HBB3 H(CCHH)
+HEC HMC1 H(CC[5a]HH)
+HEC HMC2 H(CC[5a]HH)
+HEC HMC3 H(CC[5a]HH)
+HEC HAC  H(CC[5a]C)
+HEC HBC1 H(CCHH)
+HEC HBC2 H(CCHH)
+HEC HBC3 H(CCHH)
+HEC HMD1 H(CC[5a]HH)
+HEC HMD2 H(CC[5a]HH)
+HEC HMD3 H(CC[5a]HH)
+HEC HAD1 H(CC[5a]CH)
+HEC HAD2 H(CC[5a]CH)
+HEC HBD1 H(CCCH)
+HEC HBD2 H(CCCH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+HEC FE  NA   SINGLE n 1.9   0.06   1.9   0.06
+HEC FE  NB   SINGLE n 1.9   0.06   1.9   0.06
+HEC FE  NC   SINGLE n 1.9   0.06   1.9   0.06
+HEC FE  ND   SINGLE n 1.9   0.06   1.9   0.06
+HEC CHA C1A  DOUBLE n 1.393 0.0200 1.393 0.0200
+HEC CHA C4D  SINGLE n 1.393 0.0200 1.393 0.0200
+HEC CHB C4A  DOUBLE n 1.393 0.0200 1.393 0.0200
+HEC CHB C1B  SINGLE n 1.393 0.0200 1.393 0.0200
+HEC CHC C4B  DOUBLE n 1.393 0.0200 1.393 0.0200
+HEC CHC C1C  SINGLE n 1.393 0.0200 1.393 0.0200
+HEC CHD C4C  SINGLE n 1.393 0.0200 1.393 0.0200
+HEC CHD C1D  DOUBLE n 1.393 0.0200 1.393 0.0200
+HEC NA  C1A  SINGLE y 1.350 0.0200 1.350 0.0200
+HEC NA  C4A  SINGLE y 1.350 0.0200 1.350 0.0200
+HEC C1A C2A  SINGLE y 1.374 0.0147 1.374 0.0147
+HEC C2A C3A  DOUBLE y 1.361 0.0149 1.361 0.0149
+HEC C2A CAA  SINGLE n 1.502 0.0100 1.502 0.0100
+HEC C3A C4A  SINGLE y 1.361 0.0165 1.361 0.0165
+HEC C3A CMA  SINGLE n 1.501 0.0106 1.501 0.0106
+HEC CAA CBA  SINGLE n 1.526 0.0100 1.526 0.0100
+HEC CBA CGA  SINGLE n 1.526 0.0100 1.526 0.0100
+HEC CGA O1A  DOUBLE n 1.249 0.0161 1.249 0.0161
+HEC CGA O2A  SINGLE n 1.249 0.0161 1.249 0.0161
+HEC NB  C1B  DOUBLE y 1.350 0.0200 1.350 0.0200
+HEC NB  C4B  SINGLE y 1.350 0.0200 1.350 0.0200
+HEC C1B C2B  SINGLE y 1.361 0.0165 1.361 0.0165
+HEC C2B C3B  DOUBLE y 1.436 0.0200 1.436 0.0200
+HEC C2B CMB  SINGLE n 1.501 0.0106 1.501 0.0106
+HEC C3B C4B  SINGLE y 1.393 0.0200 1.393 0.0200
+HEC C3B CAB  SINGLE n 1.407 0.0200 1.407 0.0200
+HEC CAB CBB  SINGLE n 1.506 0.0200 1.506 0.0200
+HEC NC  C1C  SINGLE y 1.350 0.0200 1.350 0.0200
+HEC NC  C4C  SINGLE y 1.350 0.0200 1.350 0.0200
+HEC C1C C2C  DOUBLE y 1.361 0.0165 1.361 0.0165
+HEC C2C C3C  SINGLE y 1.436 0.0200 1.436 0.0200
+HEC C2C CMC  SINGLE n 1.501 0.0106 1.501 0.0106
+HEC C3C C4C  DOUBLE y 1.393 0.0200 1.393 0.0200
+HEC C3C CAC  SINGLE n 1.407 0.0200 1.407 0.0200
+HEC CAC CBC  SINGLE n 1.506 0.0200 1.506 0.0200
+HEC ND  C1D  SINGLE y 1.350 0.0200 1.350 0.0200
+HEC ND  C4D  DOUBLE y 1.350 0.0200 1.350 0.0200
+HEC C1D C2D  SINGLE y 1.361 0.0165 1.361 0.0165
+HEC C2D C3D  DOUBLE y 1.361 0.0149 1.361 0.0149
+HEC C2D CMD  SINGLE n 1.501 0.0106 1.501 0.0106
+HEC C3D C4D  SINGLE y 1.374 0.0147 1.374 0.0147
+HEC C3D CAD  SINGLE n 1.502 0.0100 1.502 0.0100
+HEC CAD CBD  SINGLE n 1.526 0.0100 1.526 0.0100
+HEC CBD CGD  SINGLE n 1.526 0.0100 1.526 0.0100
+HEC CGD O1D  DOUBLE n 1.249 0.0161 1.249 0.0161
+HEC CGD O2D  SINGLE n 1.249 0.0161 1.249 0.0161
+HEC CHA HHA  SINGLE n 1.085 0.0150 0.948 0.0107
+HEC CHB HHB  SINGLE n 1.085 0.0150 0.948 0.0107
+HEC CHC HHC  SINGLE n 1.085 0.0150 0.948 0.0107
+HEC CHD HHD  SINGLE n 1.085 0.0150 0.948 0.0107
+HEC CMA HMA1 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMA HMA2 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMA HMA3 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CAA HAA1 SINGLE n 1.092 0.0100 0.983 0.0149
+HEC CAA HAA2 SINGLE n 1.092 0.0100 0.983 0.0149
+HEC CBA HBA1 SINGLE n 1.092 0.0100 0.985 0.0125
+HEC CBA HBA2 SINGLE n 1.092 0.0100 0.985 0.0125
+HEC CMB HMB1 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMB HMB2 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMB HMB3 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CAB HAB  SINGLE n 1.092 0.0100 0.945 0.0129
+HEC CBB HBB1 SINGLE n 1.092 0.0100 0.971 0.0160
+HEC CBB HBB2 SINGLE n 1.092 0.0100 0.971 0.0160
+HEC CBB HBB3 SINGLE n 1.092 0.0100 0.971 0.0160
+HEC CMC HMC1 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMC HMC2 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMC HMC3 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CAC HAC  SINGLE n 1.092 0.0100 0.945 0.0129
+HEC CBC HBC1 SINGLE n 1.092 0.0100 0.971 0.0160
+HEC CBC HBC2 SINGLE n 1.092 0.0100 0.971 0.0160
+HEC CBC HBC3 SINGLE n 1.092 0.0100 0.971 0.0160
+HEC CMD HMD1 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMD HMD2 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CMD HMD3 SINGLE n 1.092 0.0100 0.971 0.0135
+HEC CAD HAD1 SINGLE n 1.092 0.0100 0.983 0.0149
+HEC CAD HAD2 SINGLE n 1.092 0.0100 0.983 0.0149
+HEC CBD HBD1 SINGLE n 1.092 0.0100 0.985 0.0125
+HEC CBD HBD2 SINGLE n 1.092 0.0100 0.985 0.0125
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+HEC FE   NA  C1A  127.3755 5.0
+HEC FE   NA  C4A  127.3755 5.0
+HEC FE   NB  C1B  127.1020 5.0
+HEC FE   NB  C4B  127.1020 5.0
+HEC FE   NC  C1C  127.1020 5.0
+HEC FE   NC  C4C  127.1020 5.0
+HEC FE   ND  C1D  127.3755 5.0
+HEC FE   ND  C4D  127.3755 5.0
+HEC C1A  CHA C4D  124.237  3.00
+HEC C1A  CHA HHA  117.882  3.00
+HEC C4D  CHA HHA  117.882  3.00
+HEC C4A  CHB C1B  124.237  3.00
+HEC C4A  CHB HHB  117.882  3.00
+HEC C1B  CHB HHB  117.882  3.00
+HEC C4B  CHC C1C  124.237  3.00
+HEC C4B  CHC HHC  117.882  3.00
+HEC C1C  CHC HHC  117.882  3.00
+HEC C4C  CHD C1D  124.237  3.00
+HEC C4C  CHD HHD  117.882  3.00
+HEC C1D  CHD HHD  117.882  3.00
+HEC C1A  NA  C4A  105.249  3.00
+HEC CHA  C1A NA   122.751  3.00
+HEC CHA  C1A C2A  128.506  3.00
+HEC NA   C1A C2A  108.743  1.50
+HEC C1A  C2A C3A  108.632  3.00
+HEC C1A  C2A CAA  125.377  3.00
+HEC C3A  C2A CAA  125.990  1.50
+HEC C2A  C3A C4A  108.632  3.00
+HEC C2A  C3A CMA  124.744  3.00
+HEC C4A  C3A CMA  126.624  1.50
+HEC CHB  C4A NA   122.751  3.00
+HEC CHB  C4A C3A  128.506  3.00
+HEC NA   C4A C3A  108.743  1.50
+HEC C3A  CMA HMA1 109.572  1.50
+HEC C3A  CMA HMA2 109.572  1.50
+HEC C3A  CMA HMA3 109.572  1.50
+HEC HMA1 CMA HMA2 109.322  1.87
+HEC HMA1 CMA HMA3 109.322  1.87
+HEC HMA2 CMA HMA3 109.322  1.87
+HEC C2A  CAA CBA  113.932  3.00
+HEC C2A  CAA HAA1 109.001  1.50
+HEC C2A  CAA HAA2 109.001  1.50
+HEC CBA  CAA HAA1 108.631  1.50
+HEC CBA  CAA HAA2 108.631  1.50
+HEC HAA1 CAA HAA2 107.419  2.31
+HEC CAA  CBA CGA  114.716  3.00
+HEC CAA  CBA HBA1 108.790  1.50
+HEC CAA  CBA HBA2 108.790  1.50
+HEC CGA  CBA HBA1 108.586  1.50
+HEC CGA  CBA HBA2 108.586  1.50
+HEC HBA1 CBA HBA2 107.505  1.50
+HEC CBA  CGA O1A  117.968  3.00
+HEC CBA  CGA O2A  117.968  3.00
+HEC O1A  CGA O2A  124.063  1.82
+HEC C1B  NB  C4B  105.796  3.00
+HEC CHB  C1B NB   122.477  3.00
+HEC CHB  C1B C2B  128.232  3.00
+HEC NB   C1B C2B  109.291  1.50
+HEC C1B  C2B C3B  108.186  3.00
+HEC C1B  C2B CMB  126.778  1.50
+HEC C3B  C2B CMB  125.036  3.00
+HEC C2B  C3B C4B  107.432  3.00
+HEC C2B  C3B CAB  126.284  3.00
+HEC C4B  C3B CAB  126.284  3.00
+HEC CHC  C4B NB   121.757  3.00
+HEC CHC  C4B C3B  128.949  3.00
+HEC NB   C4B C3B  109.294  2.29
+HEC C2B  CMB HMB1 109.572  1.50
+HEC C2B  CMB HMB2 109.572  1.50
+HEC C2B  CMB HMB3 109.572  1.50
+HEC HMB1 CMB HMB2 109.322  1.87
+HEC HMB1 CMB HMB3 109.322  1.87
+HEC HMB2 CMB HMB3 109.322  1.87
+HEC C3B  CAB CBB  109.471  3.00
+HEC C3B  CAB HAB  109.471  3.00
+HEC CBB  CAB HAB  109.471  3.00
+HEC CAB  CBB HBB1 109.211  1.50
+HEC CAB  CBB HBB2 109.211  1.50
+HEC CAB  CBB HBB3 109.211  1.50
+HEC HBB1 CBB HBB2 111.860  1.50
+HEC HBB1 CBB HBB3 111.860  1.50
+HEC HBB2 CBB HBB3 111.860  1.50
+HEC C1C  NC  C4C  105.796  3.00
+HEC CHC  C1C NC   122.477  3.00
+HEC CHC  C1C C2C  128.232  3.00
+HEC NC   C1C C2C  109.291  1.50
+HEC C1C  C2C C3C  108.186  3.00
+HEC C1C  C2C CMC  126.778  1.50
+HEC C3C  C2C CMC  125.036  3.00
+HEC C2C  C3C C4C  107.432  3.00
+HEC C2C  C3C CAC  126.284  3.00
+HEC C4C  C3C CAC  126.284  3.00
+HEC CHD  C4C NC   121.757  3.00
+HEC CHD  C4C C3C  128.949  3.00
+HEC NC   C4C C3C  109.294  2.29
+HEC C2C  CMC HMC1 109.572  1.50
+HEC C2C  CMC HMC2 109.572  1.50
+HEC C2C  CMC HMC3 109.572  1.50
+HEC HMC1 CMC HMC2 109.322  1.87
+HEC HMC1 CMC HMC3 109.322  1.87
+HEC HMC2 CMC HMC3 109.322  1.87
+HEC C3C  CAC CBC  109.471  3.00
+HEC C3C  CAC HAC  109.471  3.00
+HEC CBC  CAC HAC  109.471  3.00
+HEC CAC  CBC HBC1 109.211  1.50
+HEC CAC  CBC HBC2 109.211  1.50
+HEC CAC  CBC HBC3 109.211  1.50
+HEC HBC1 CBC HBC2 111.860  1.50
+HEC HBC1 CBC HBC3 111.860  1.50
+HEC HBC2 CBC HBC3 111.860  1.50
+HEC C1D  ND  C4D  105.249  3.00
+HEC CHD  C1D ND   122.751  3.00
+HEC CHD  C1D C2D  128.506  3.00
+HEC ND   C1D C2D  108.743  1.50
+HEC C1D  C2D C3D  108.632  3.00
+HEC C1D  C2D CMD  126.624  1.50
+HEC C3D  C2D CMD  124.744  3.00
+HEC C2D  C3D C4D  108.632  3.00
+HEC C2D  C3D CAD  125.990  1.50
+HEC C4D  C3D CAD  125.377  3.00
+HEC CHA  C4D ND   122.751  3.00
+HEC CHA  C4D C3D  128.506  3.00
+HEC ND   C4D C3D  108.743  1.50
+HEC C2D  CMD HMD1 109.572  1.50
+HEC C2D  CMD HMD2 109.572  1.50
+HEC C2D  CMD HMD3 109.572  1.50
+HEC HMD1 CMD HMD2 109.322  1.87
+HEC HMD1 CMD HMD3 109.322  1.87
+HEC HMD2 CMD HMD3 109.322  1.87
+HEC C3D  CAD CBD  113.932  3.00
+HEC C3D  CAD HAD1 109.001  1.50
+HEC C3D  CAD HAD2 109.001  1.50
+HEC CBD  CAD HAD1 108.631  1.50
+HEC CBD  CAD HAD2 108.631  1.50
+HEC HAD1 CAD HAD2 107.419  2.31
+HEC CAD  CBD CGD  114.716  3.00
+HEC CAD  CBD HBD1 108.790  1.50
+HEC CAD  CBD HBD2 108.790  1.50
+HEC CGD  CBD HBD1 108.586  1.50
+HEC CGD  CBD HBD2 108.586  1.50
+HEC HBD1 CBD HBD2 107.505  1.50
+HEC CBD  CGD O1D  117.968  3.00
+HEC CBD  CGD O2D  117.968  3.00
+HEC O1D  CGD O2D  124.063  1.82
+HEC NA   FE  NB   87.8     5.52
+HEC NA   FE  NC   157.26   7.8
+HEC NA   FE  ND   87.8     5.52
+HEC NB   FE  NC   87.8     5.52
+HEC NB   FE  ND   157.26   7.8
+HEC NC   FE  ND   87.8     5.52
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+HEC sp2_sp2_1  ND  C4D CHA C1A  0.000   5.0  2
+HEC sp2_sp2_2  NA  C1A CHA C4D  0.000   5.0  2
+HEC sp3_sp3_1  C2A CAA CBA CGA  180.000 10.0 3
+HEC sp2_sp3_1  O1A CGA CBA CAA  120.000 20.0 6
+HEC const_0    CHB C1B NB  C4B  180.000 0.0  1
+HEC const_1    CHC C4B NB  C1B  180.000 0.0  1
+HEC const_2    CHB C1B C2B CMB  0.000   0.0  1
+HEC const_3    CMB C2B C3B CAB  0.000   0.0  1
+HEC sp2_sp3_2  C1B C2B CMB HMB1 150.000 20.0 6
+HEC const_4    CAB C3B C4B CHC  0.000   0.0  1
+HEC sp2_sp3_3  C2B C3B CAB CBB  -90.000 20.0 6
+HEC sp2_sp2_3  NB  C1B CHB C4A  0.000   5.0  2
+HEC sp2_sp2_4  NA  C4A CHB C1B  0.000   5.0  2
+HEC sp3_sp3_2  C3B CAB CBB HBB1 180.000 10.0 3
+HEC const_5    CHC C1C NC  C4C  180.000 0.0  1
+HEC const_6    CHD C4C NC  C1C  180.000 0.0  1
+HEC const_7    CHC C1C C2C CMC  0.000   0.0  1
+HEC const_8    CMC C2C C3C CAC  0.000   0.0  1
+HEC sp2_sp3_4  C1C C2C CMC HMC1 150.000 20.0 6
+HEC const_9    CAC C3C C4C CHD  0.000   0.0  1
+HEC sp2_sp3_5  C2C C3C CAC CBC  -90.000 20.0 6
+HEC sp3_sp3_3  C3C CAC CBC HBC1 180.000 10.0 3
+HEC sp2_sp2_5  NB  C4B CHC C1C  0.000   5.0  2
+HEC sp2_sp2_6  NC  C1C CHC C4B  0.000   5.0  2
+HEC const_10   CHD C1D ND  C4D  180.000 0.0  1
+HEC const_11   CHA C4D ND  C1D  180.000 0.0  1
+HEC const_12   CHD C1D C2D CMD  0.000   0.0  1
+HEC const_13   CMD C2D C3D CAD  0.000   0.0  1
+HEC sp2_sp3_6  C1D C2D CMD HMD1 150.000 20.0 6
+HEC const_14   CAD C3D C4D CHA  0.000   0.0  1
+HEC sp2_sp3_7  C2D C3D CAD CBD  -90.000 20.0 6
+HEC sp3_sp3_4  C3D CAD CBD CGD  180.000 10.0 3
+HEC sp2_sp3_8  O1D CGD CBD CAD  120.000 20.0 6
+HEC sp2_sp2_7  NC  C4C CHD C1D  0.000   5.0  2
+HEC sp2_sp2_8  ND  C1D CHD C4C  0.000   5.0  2
+HEC const_15   CHA C1A NA  C4A  180.000 0.0  1
+HEC const_16   CHB C4A NA  C1A  180.000 0.0  1
+HEC const_17   CHA C1A C2A CAA  0.000   0.0  1
+HEC sp2_sp3_9  C1A C2A CAA CBA  -90.000 20.0 6
+HEC const_18   CAA C2A C3A CMA  0.000   0.0  1
+HEC const_19   CMA C3A C4A CHB  0.000   0.0  1
+HEC sp2_sp3_10 C2A C3A CMA HMA1 150.000 20.0 6
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+HEC plan-11 FE  0.060
+HEC plan-11 NA  0.060
+HEC plan-11 C1A 0.060
+HEC plan-11 C4A 0.060
+HEC plan-12 FE  0.060
+HEC plan-12 NB  0.060
+HEC plan-12 C1B 0.060
+HEC plan-12 C4B 0.060
+HEC plan-13 FE  0.060
+HEC plan-13 NC  0.060
+HEC plan-13 C1C 0.060
+HEC plan-13 C4C 0.060
+HEC plan-14 FE  0.060
+HEC plan-14 ND  0.060
+HEC plan-14 C1D 0.060
+HEC plan-14 C4D 0.060
+HEC plan-1  C1B 0.020
+HEC plan-1  C2B 0.020
+HEC plan-1  C3B 0.020
+HEC plan-1  C4B 0.020
+HEC plan-1  CAB 0.020
+HEC plan-1  CHB 0.020
+HEC plan-1  CHC 0.020
+HEC plan-1  CMB 0.020
+HEC plan-1  NB  0.020
+HEC plan-2  C1C 0.020
+HEC plan-2  C2C 0.020
+HEC plan-2  C3C 0.020
+HEC plan-2  C4C 0.020
+HEC plan-2  CAC 0.020
+HEC plan-2  CHC 0.020
+HEC plan-2  CHD 0.020
+HEC plan-2  CMC 0.020
+HEC plan-2  NC  0.020
+HEC plan-3  C1D 0.020
+HEC plan-3  C2D 0.020
+HEC plan-3  C3D 0.020
+HEC plan-3  C4D 0.020
+HEC plan-3  CAD 0.020
+HEC plan-3  CHA 0.020
+HEC plan-3  CHD 0.020
+HEC plan-3  CMD 0.020
+HEC plan-3  ND  0.020
+HEC plan-4  C1A 0.020
+HEC plan-4  C2A 0.020
+HEC plan-4  C3A 0.020
+HEC plan-4  C4A 0.020
+HEC plan-4  CAA 0.020
+HEC plan-4  CHA 0.020
+HEC plan-4  CHB 0.020
+HEC plan-4  CMA 0.020
+HEC plan-4  NA  0.020
+HEC plan-5  C1A 0.020
+HEC plan-5  C4D 0.020
+HEC plan-5  CHA 0.020
+HEC plan-5  HHA 0.020
+HEC plan-6  C1B 0.020
+HEC plan-6  C4A 0.020
+HEC plan-6  CHB 0.020
+HEC plan-6  HHB 0.020
+HEC plan-7  C1C 0.020
+HEC plan-7  C4B 0.020
+HEC plan-7  CHC 0.020
+HEC plan-7  HHC 0.020
+HEC plan-8  C1D 0.020
+HEC plan-8  C4C 0.020
+HEC plan-8  CHD 0.020
+HEC plan-8  HHD 0.020
+HEC plan-9  CBA 0.020
+HEC plan-9  CGA 0.020
+HEC plan-9  O1A 0.020
+HEC plan-9  O2A 0.020
+HEC plan-10 CBD 0.020
+HEC plan-10 CGD 0.020
+HEC plan-10 O1D 0.020
+HEC plan-10 O2D 0.020
+
+loop_
+_chem_comp_ring_atom.comp_id
+_chem_comp_ring_atom.ring_serial_number
+_chem_comp_ring_atom.atom_id
+_chem_comp_ring_atom.is_aromatic_ring
+HEC ring-1 NB  YES
+HEC ring-1 C1B YES
+HEC ring-1 C2B YES
+HEC ring-1 C3B YES
+HEC ring-1 C4B YES
+HEC ring-2 NC  YES
+HEC ring-2 C1C YES
+HEC ring-2 C2C YES
+HEC ring-2 C3C YES
+HEC ring-2 C4C YES
+HEC ring-3 ND  YES
+HEC ring-3 C1D YES
+HEC ring-3 C2D YES
+HEC ring-3 C3D YES
+HEC ring-3 C4D YES
+HEC ring-4 NA  YES
+HEC ring-4 C1A YES
+HEC ring-4 C2A YES
+HEC ring-4 C3A YES
+HEC ring-4 C4A YES
+
+loop_
+_acedrg_chem_comp_descriptor.comp_id
+_acedrg_chem_comp_descriptor.program_name
+_acedrg_chem_comp_descriptor.program_version
+_acedrg_chem_comp_descriptor.type
+HEC acedrg            314       'dictionary generator'
+HEC 'acedrg_database' 12        'data source'
+HEC rdkit             2023.03.3 'Chemoinformatics tool'
+HEC servalcat         0.4.99    'optimization tool'
+HEC metalCoord        0.1.77    'metal coordination analysis'
diff --git a/image_analysis/structure_refinement/monomers/HEM.cif b/image_analysis/structure_refinement/monomers/HEM.cif
new file mode 100644
index 000000000..a0dfd75e5
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/HEM.cif
@@ -0,0 +1,691 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+HEM HEM "PROTOPORPHYRIN IX CONTAINING FE" NON-POLYMER 72 42 .
+
+data_comp_HEM
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.alt_atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+HEM FE   FE   FE FE   2.00 2.113  -20.686 36.710
+HEM CHA  CHA  C  C1   0    2.720  -19.528 39.866
+HEM CHB  CHB  C  C1   0    3.392  -17.792 35.417
+HEM CHC  CHC  C  C1   0    1.647  -21.910 33.552
+HEM CHD  CHD  C  C1   0    0.970  -23.635 38.034
+HEM C1A  C1A  C  CR5  0    3.084  -18.642 38.839
+HEM C2A  C2A  C  CR5  0    3.624  -17.376 38.970
+HEM C3A  C3A  C  CR5  0    3.821  -16.888 37.707
+HEM C4A  C4A  C  CR5  0    3.395  -17.851 36.822
+HEM CMA  CMA  C  CH3  0    4.397  -15.536 37.368
+HEM CAA  CAA  C  CH2  0    3.948  -16.673 40.264
+HEM CBA  CBA  C  CH2  0    5.335  -16.990 40.817
+HEM CGA  CGA  C  C    0    5.753  -16.132 42.008
+HEM O1A  O1A  O  O    0    6.478  -15.139 41.789
+HEM O2A  O2A  O  OC   -1   5.350  -16.467 43.141
+HEM C1B  C1B  C  CR5  0    3.012  -18.742 34.450
+HEM C2B  C2B  C  CR5  0    3.088  -18.615 33.063
+HEM C3B  C3B  C  CR5  0    2.602  -19.823 32.491
+HEM C4B  C4B  C  CR5  0    2.223  -20.612 33.577
+HEM CMB  CMB  C  CH3  0    3.637  -17.437 32.305
+HEM CAB  CAB  C  C1   0    2.444  -20.228 31.062
+HEM CBB  CBB  C  C2   0    2.468  -19.589 29.912
+HEM C1C  C1C  C  CR5  0    1.305  -22.806 34.583
+HEM C2C  C2C  C  CR5  0    0.791  -24.096 34.439
+HEM C3C  C3C  C  CR5  0    0.605  -24.635 35.742
+HEM C4C  C4C  C  CR5  0    0.990  -23.616 36.614
+HEM CMC  CMC  C  CH3  0    0.531  -24.813 33.142
+HEM CAC  CAC  C  C1   0    0.071  -25.962 36.177
+HEM CBC  CBC  C  C2   0    -0.577 -26.940 35.580
+HEM C1D  C1D  C  CR5  0    1.386  -22.691 38.991
+HEM C2D  C2D  C  CR5  0    1.361  -22.807 40.363
+HEM C3D  C3D  C  CR5  0    1.858  -21.643 40.882
+HEM C4D  C4D  C  CR5  0    2.180  -20.824 39.815
+HEM CMD  CMD  C  CH3  0    0.875  -23.984 41.171
+HEM CAD  CAD  C  CH2  0    2.015  -21.306 42.343
+HEM CBD  CBD  C  CH2  0    0.815  -20.581 42.946
+HEM CGD  CGD  C  C    0    0.988  -20.172 44.406
+HEM O1D  O1D  O  O    0    1.599  -19.110 44.648
+HEM O2D  O2D  O  OC   -1   0.509  -20.920 45.284
+HEM NA   NA   N  NRD5 -1   2.940  -18.925 37.520
+HEM NB   NB   N  NRD5 1    2.476  -19.944 34.769
+HEM NC   NC   N  NRD5 -1   1.417  -22.504 35.897
+HEM ND   ND   N  NRD5 1    1.887  -21.472 38.658
+HEM HHA  HHA  H  H    0    2.859  -19.193 40.740
+HEM HHB  HHB  H  H    0    3.670  -16.961 35.061
+HEM HHC  HHC  H  H    0    1.422  -22.211 32.685
+HEM HHD  HHD  H  H    0    0.585  -24.416 38.400
+HEM HMA  HMA  H  H    0    4.826  -15.566 36.499
+HEM HMAA HMAA H  H    0    5.058  -15.279 38.029
+HEM HMAB HMAB H  H    0    3.686  -14.875 37.351
+HEM HAA  HAA  H  H    0    3.279  -16.915 40.942
+HEM HAAA HAAA H  H    0    3.873  -15.702 40.143
+HEM HBA  HBA  H  H    0    5.997  -16.872 40.097
+HEM HBAA HBAA H  H    0    5.359  -17.937 41.089
+HEM HMB  HMB  H  H    0    4.047  -17.740 31.479
+HEM HMBA HMBA H  H    0    4.310  -16.982 32.835
+HEM HMBB HMBB H  H    0    2.918  -16.818 32.099
+HEM HAB  HAB  H  H    0    2.329  -21.154 30.922
+HEM HBB  HBB  H  H    0    2.384  -20.072 29.107
+HEM HBBA HBBA H  H    0    2.536  -18.650 29.889
+HEM HMC  HMC  H  H    0    0.678  -25.764 33.258
+HEM HMCA HMCA H  H    0    1.133  -24.489 32.454
+HEM HMCB HMCB H  H    0    -0.387 -24.660 32.864
+HEM HAC  HAC  H  H    0    0.253  -26.188 37.076
+HEM HBC  HBC  H  H    0    -0.782 -27.725 36.060
+HEM HBCA HBCA H  H    0    -0.864 -26.848 34.688
+HEM HMD  HMD  H  H    0    1.479  -24.149 41.913
+HEM HMDA HMDA H  H    0    0.841  -24.780 40.620
+HEM HMDB HMDB H  H    0    -0.013 -23.796 41.516
+HEM HAD  HAD  H  H    0    2.812  -20.745 42.464
+HEM HADA HADA H  H    0    2.181  -22.124 42.860
+HEM HBD  HBD  H  H    0    0.025  -21.165 42.876
+HEM HBDA HBDA H  H    0    0.633  -19.773 42.413
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+HEM O2D  n/a CGD START
+HEM CGD  O2D CBD .
+HEM O1D  CGD .   .
+HEM CBD  CGD CAD .
+HEM HBD  CBD .   .
+HEM HBDA CBD .   .
+HEM CAD  CBD C3D .
+HEM HAD  CAD .   .
+HEM HADA CAD .   .
+HEM C3D  CAD C4D .
+HEM C2D  C3D CMD .
+HEM CMD  C2D HMD .
+HEM HMDB CMD .   .
+HEM HMDA CMD .   .
+HEM HMD  CMD .   .
+HEM C4D  C3D ND  .
+HEM CHA  C4D HHA .
+HEM HHA  CHA .   .
+HEM ND   C4D FE  .
+HEM C1D  ND  CHD .
+HEM CHD  C1D HHD .
+HEM HHD  CHD .   .
+HEM FE   ND  NA  .
+HEM NB   FE  C1B .
+HEM C4B  NB  C3B .
+HEM C3B  C4B C2B .
+HEM CAB  C3B CBB .
+HEM HAB  CAB .   .
+HEM CBB  CAB HBB .
+HEM HBBA CBB .   .
+HEM HBB  CBB .   .
+HEM C2B  C3B CMB .
+HEM CMB  C2B HMB .
+HEM HMBB CMB .   .
+HEM HMBA CMB .   .
+HEM HMB  CMB .   .
+HEM C1B  NB  CHB .
+HEM CHB  C1B HHB .
+HEM HHB  CHB .   .
+HEM NC   FE  C1C .
+HEM C4C  NC  C3C .
+HEM C3C  C4C C2C .
+HEM CAC  C3C CBC .
+HEM HAC  CAC .   .
+HEM CBC  CAC HBC .
+HEM HBCA CBC .   .
+HEM HBC  CBC .   .
+HEM C2C  C3C CMC .
+HEM CMC  C2C HMC .
+HEM HMCB CMC .   .
+HEM HMCA CMC .   .
+HEM HMC  CMC .   .
+HEM C1C  NC  CHC .
+HEM CHC  C1C HHC .
+HEM HHC  CHC .   .
+HEM NA   FE  C4A .
+HEM C1A  NA  .   .
+HEM C4A  NA  C3A .
+HEM C3A  C4A C2A .
+HEM CMA  C3A HMA .
+HEM HMAB CMA .   .
+HEM HMAA CMA .   .
+HEM HMA  CMA .   .
+HEM C2A  C3A CAA .
+HEM CAA  C2A CBA .
+HEM HAA  CAA .   .
+HEM HAAA CAA .   .
+HEM CBA  CAA CGA .
+HEM HBA  CBA .   .
+HEM HBAA CBA .   .
+HEM CGA  CBA O2A .
+HEM O1A  CGA .   .
+HEM O2A  CGA .   END
+HEM CHA  C1A .   ADD
+HEM CHB  C4A .   ADD
+HEM CHC  C4B .   ADD
+HEM CHD  C4C .   ADD
+HEM C1A  C2A .   ADD
+HEM C1B  C2B .   ADD
+HEM C1C  C2C .   ADD
+HEM C1D  C2D .   ADD
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+HEM CHA  C(C[5a]C[5a]N[5a])2(H)
+HEM CHB  C(C[5a]C[5a]N[5a])2(H)
+HEM CHC  C(C[5a]C[5a]N[5a])2(H)
+HEM CHD  C(C[5a]C[5a]N[5a])2(H)
+HEM C1A  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEM C2A  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>}
+HEM C3A  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEM C4A  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEM CMA  C(C[5a]C[5a]2)(H)3
+HEM CAA  C(C[5a]C[5a]2)(CCHH)(H)2
+HEM CBA  C(CC[5a]HH)(COO)(H)2
+HEM CGA  C(CCHH)(O)2
+HEM O1A  O(CCO)
+HEM O2A  O(CCO)
+HEM C1B  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>}
+HEM C2B  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEM C3B  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>}
+HEM C4B  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEM CMB  C(C[5a]C[5a]2)(H)3
+HEM CAB  C(C[5a]C[5a]2)(CHH)(H)
+HEM CBB  C(CC[5a]H)(H)2
+HEM C1C  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){2|C<3>}
+HEM C2C  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEM C3C  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCH){1|C<3>}
+HEM C4C  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEM CMC  C(C[5a]C[5a]2)(H)3
+HEM CAC  C(C[5a]C[5a]2)(CHH)(H)
+HEM CBC  C(CC[5a]H)(H)2
+HEM C1D  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEM C2D  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CH3){1|C<3>}
+HEM C3D  C[5a](C[5a]C[5a]C)(C[5a]N[5a]C)(CCHH){1|C<3>}
+HEM C4D  C[5a](C[5a]C[5a]C)(N[5a]C[5a])(CC[5a]H){1|C<3>,1|C<4>}
+HEM CMD  C(C[5a]C[5a]2)(H)3
+HEM CAD  C(C[5a]C[5a]2)(CCHH)(H)2
+HEM CBD  C(CC[5a]HH)(COO)(H)2
+HEM CGD  C(CCHH)(O)2
+HEM O1D  O(CCO)
+HEM O2D  O(CCO)
+HEM NA   N[5a](C[5a]C[5a]C)2{2|C<4>}
+HEM NB   N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>}
+HEM NC   N[5a](C[5a]C[5a]C)2{1|C<3>,1|C<4>}
+HEM ND   N[5a](C[5a]C[5a]C)2{2|C<4>}
+HEM HHA  H(CC[5a]2)
+HEM HHB  H(CC[5a]2)
+HEM HHC  H(CC[5a]2)
+HEM HHD  H(CC[5a]2)
+HEM HMA  H(CC[5a]HH)
+HEM HMAA H(CC[5a]HH)
+HEM HMAB H(CC[5a]HH)
+HEM HAA  H(CC[5a]CH)
+HEM HAAA H(CC[5a]CH)
+HEM HBA  H(CCCH)
+HEM HBAA H(CCCH)
+HEM HMB  H(CC[5a]HH)
+HEM HMBA H(CC[5a]HH)
+HEM HMBB H(CC[5a]HH)
+HEM HAB  H(CC[5a]C)
+HEM HBB  H(CCH)
+HEM HBBA H(CCH)
+HEM HMC  H(CC[5a]HH)
+HEM HMCA H(CC[5a]HH)
+HEM HMCB H(CC[5a]HH)
+HEM HAC  H(CC[5a]C)
+HEM HBC  H(CCH)
+HEM HBCA H(CCH)
+HEM HMD  H(CC[5a]HH)
+HEM HMDA H(CC[5a]HH)
+HEM HMDB H(CC[5a]HH)
+HEM HAD  H(CC[5a]CH)
+HEM HADA H(CC[5a]CH)
+HEM HBD  H(CCCH)
+HEM HBDA H(CCCH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+HEM FE  NA   SINGLE n 2.04  0.09   2.04  0.09
+HEM FE  NB   SINGLE n 2.04  0.09   2.04  0.09
+HEM FE  NC   SINGLE n 2.04  0.09   2.04  0.09
+HEM FE  ND   SINGLE n 2.04  0.09   2.04  0.09
+HEM CHA C1A  DOUBLE n 1.393 0.0200 1.393 0.0200
+HEM CHA C4D  SINGLE n 1.393 0.0200 1.393 0.0200
+HEM CHB C4A  DOUBLE n 1.393 0.0200 1.393 0.0200
+HEM CHB C1B  SINGLE n 1.393 0.0200 1.393 0.0200
+HEM CHC C4B  DOUBLE n 1.407 0.0200 1.407 0.0200
+HEM CHC C1C  SINGLE n 1.393 0.0200 1.393 0.0200
+HEM CHD C4C  SINGLE n 1.407 0.0200 1.407 0.0200
+HEM CHD C1D  DOUBLE n 1.393 0.0200 1.393 0.0200
+HEM C1A C2A  SINGLE y 1.374 0.0147 1.374 0.0147
+HEM C1A NA   SINGLE y 1.350 0.0200 1.350 0.0200
+HEM C2A C3A  DOUBLE y 1.361 0.0149 1.361 0.0149
+HEM C2A CAA  SINGLE n 1.502 0.0100 1.502 0.0100
+HEM C3A C4A  SINGLE y 1.361 0.0165 1.361 0.0165
+HEM C3A CMA  SINGLE n 1.501 0.0106 1.501 0.0106
+HEM C4A NA   SINGLE y 1.350 0.0200 1.350 0.0200
+HEM CAA CBA  SINGLE n 1.526 0.0100 1.526 0.0100
+HEM CBA CGA  SINGLE n 1.526 0.0100 1.526 0.0100
+HEM CGA O1A  DOUBLE n 1.249 0.0161 1.249 0.0161
+HEM CGA O2A  SINGLE n 1.249 0.0161 1.249 0.0161
+HEM C1B C2B  SINGLE y 1.379 0.0175 1.379 0.0175
+HEM C1B NB   DOUBLE y 1.350 0.0200 1.350 0.0200
+HEM C2B C3B  DOUBLE y 1.401 0.0200 1.401 0.0200
+HEM C2B CMB  SINGLE n 1.500 0.0100 1.500 0.0100
+HEM C3B C4B  SINGLE y 1.388 0.0111 1.388 0.0111
+HEM C3B CAB  SINGLE n 1.456 0.0200 1.456 0.0200
+HEM C4B NB   SINGLE y 1.388 0.0142 1.388 0.0142
+HEM CAB CBB  DOUBLE n 1.306 0.0200 1.306 0.0200
+HEM C1C C2C  DOUBLE y 1.379 0.0175 1.379 0.0175
+HEM C1C NC   SINGLE y 1.350 0.0200 1.350 0.0200
+HEM C2C C3C  SINGLE y 1.401 0.0200 1.401 0.0200
+HEM C2C CMC  SINGLE n 1.500 0.0100 1.500 0.0100
+HEM C3C C4C  DOUBLE y 1.388 0.0111 1.388 0.0111
+HEM C3C CAC  SINGLE n 1.456 0.0200 1.456 0.0200
+HEM C4C NC   SINGLE y 1.388 0.0142 1.388 0.0142
+HEM CAC CBC  DOUBLE n 1.306 0.0200 1.306 0.0200
+HEM C1D C2D  SINGLE y 1.361 0.0165 1.361 0.0165
+HEM C1D ND   SINGLE y 1.350 0.0200 1.350 0.0200
+HEM C2D C3D  DOUBLE y 1.361 0.0149 1.361 0.0149
+HEM C2D CMD  SINGLE n 1.501 0.0106 1.501 0.0106
+HEM C3D C4D  SINGLE y 1.374 0.0147 1.374 0.0147
+HEM C3D CAD  SINGLE n 1.502 0.0100 1.502 0.0100
+HEM C4D ND   DOUBLE y 1.350 0.0200 1.350 0.0200
+HEM CAD CBD  SINGLE n 1.526 0.0100 1.526 0.0100
+HEM CBD CGD  SINGLE n 1.526 0.0100 1.526 0.0100
+HEM CGD O1D  DOUBLE n 1.249 0.0161 1.249 0.0161
+HEM CGD O2D  SINGLE n 1.249 0.0161 1.249 0.0161
+HEM CHA HHA  SINGLE n 1.085 0.0150 0.948 0.0107
+HEM CHB HHB  SINGLE n 1.085 0.0150 0.948 0.0107
+HEM CHC HHC  SINGLE n 1.085 0.0150 0.948 0.0107
+HEM CHD HHD  SINGLE n 1.085 0.0150 0.948 0.0107
+HEM CMA HMA  SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMA HMAA SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMA HMAB SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CAA HAA  SINGLE n 1.092 0.0100 0.983 0.0149
+HEM CAA HAAA SINGLE n 1.092 0.0100 0.983 0.0149
+HEM CBA HBA  SINGLE n 1.092 0.0100 0.985 0.0125
+HEM CBA HBAA SINGLE n 1.092 0.0100 0.985 0.0125
+HEM CMB HMB  SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMB HMBA SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMB HMBB SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CAB HAB  SINGLE n 1.085 0.0150 0.945 0.0100
+HEM CBB HBB  SINGLE n 1.085 0.0150 0.943 0.0100
+HEM CBB HBBA SINGLE n 1.085 0.0150 0.943 0.0100
+HEM CMC HMC  SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMC HMCA SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMC HMCB SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CAC HAC  SINGLE n 1.085 0.0150 0.945 0.0100
+HEM CBC HBC  SINGLE n 1.085 0.0150 0.943 0.0100
+HEM CBC HBCA SINGLE n 1.085 0.0150 0.943 0.0100
+HEM CMD HMD  SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMD HMDA SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CMD HMDB SINGLE n 1.092 0.0100 0.971 0.0135
+HEM CAD HAD  SINGLE n 1.092 0.0100 0.983 0.0149
+HEM CAD HADA SINGLE n 1.092 0.0100 0.983 0.0149
+HEM CBD HBD  SINGLE n 1.092 0.0100 0.985 0.0125
+HEM CBD HBDA SINGLE n 1.092 0.0100 0.985 0.0125
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+HEM FE   NA  C1A  127.3755 5.0
+HEM FE   NA  C4A  127.3755 5.0
+HEM FE   NB  C1B  127.1020 5.0
+HEM FE   NB  C4B  127.1020 5.0
+HEM FE   NC  C1C  127.1020 5.0
+HEM FE   NC  C4C  127.1020 5.0
+HEM FE   ND  C1D  127.3755 5.0
+HEM FE   ND  C4D  127.3755 5.0
+HEM C1A  CHA C4D  124.237  3.00
+HEM C1A  CHA HHA  117.882  3.00
+HEM C4D  CHA HHA  117.882  3.00
+HEM C4A  CHB C1B  124.237  3.00
+HEM C4A  CHB HHB  117.882  3.00
+HEM C1B  CHB HHB  117.882  3.00
+HEM C4B  CHC C1C  124.237  3.00
+HEM C4B  CHC HHC  117.882  3.00
+HEM C1C  CHC HHC  117.882  3.00
+HEM C4C  CHD C1D  124.237  3.00
+HEM C4C  CHD HHD  117.882  3.00
+HEM C1D  CHD HHD  117.882  3.00
+HEM CHA  C1A C2A  128.506  3.00
+HEM CHA  C1A NA   122.751  3.00
+HEM C2A  C1A NA   108.743  1.50
+HEM C1A  C2A C3A  108.632  3.00
+HEM C1A  C2A CAA  125.377  3.00
+HEM C3A  C2A CAA  125.990  1.50
+HEM C2A  C3A C4A  108.632  3.00
+HEM C2A  C3A CMA  124.744  3.00
+HEM C4A  C3A CMA  126.624  1.50
+HEM CHB  C4A C3A  128.506  3.00
+HEM CHB  C4A NA   122.751  3.00
+HEM C3A  C4A NA   108.743  1.50
+HEM C3A  CMA HMA  109.572  1.50
+HEM C3A  CMA HMAA 109.572  1.50
+HEM C3A  CMA HMAB 109.572  1.50
+HEM HMA  CMA HMAA 109.322  1.87
+HEM HMA  CMA HMAB 109.322  1.87
+HEM HMAA CMA HMAB 109.322  1.87
+HEM C2A  CAA CBA  113.932  3.00
+HEM C2A  CAA HAA  109.001  1.50
+HEM C2A  CAA HAAA 109.001  1.50
+HEM CBA  CAA HAA  108.631  1.50
+HEM CBA  CAA HAAA 108.631  1.50
+HEM HAA  CAA HAAA 107.419  2.31
+HEM CAA  CBA CGA  114.716  3.00
+HEM CAA  CBA HBA  108.790  1.50
+HEM CAA  CBA HBAA 108.790  1.50
+HEM CGA  CBA HBA  108.586  1.50
+HEM CGA  CBA HBAA 108.586  1.50
+HEM HBA  CBA HBAA 107.505  1.50
+HEM CBA  CGA O1A  117.968  3.00
+HEM CBA  CGA O2A  117.968  3.00
+HEM O1A  CGA O2A  124.063  1.82
+HEM CHB  C1B C2B  128.232  3.00
+HEM CHB  C1B NB   122.477  3.00
+HEM C2B  C1B NB   109.291  1.50
+HEM C1B  C2B C3B  108.186  3.00
+HEM C1B  C2B CMB  126.778  1.50
+HEM C3B  C2B CMB  125.036  3.00
+HEM C2B  C3B C4B  107.432  3.00
+HEM C2B  C3B CAB  125.770  3.00
+HEM C4B  C3B CAB  126.798  3.00
+HEM CHC  C4B C3B  128.949  3.00
+HEM CHC  C4B NB   121.757  3.00
+HEM C3B  C4B NB   109.294  2.29
+HEM C2B  CMB HMB  109.572  1.50
+HEM C2B  CMB HMBA 109.572  1.50
+HEM C2B  CMB HMBB 109.572  1.50
+HEM HMB  CMB HMBA 109.322  1.87
+HEM HMB  CMB HMBB 109.322  1.87
+HEM HMBA CMB HMBB 109.322  1.87
+HEM C3B  CAB CBB  127.109  3.00
+HEM C3B  CAB HAB  116.019  1.61
+HEM CBB  CAB HAB  116.872  2.59
+HEM CAB  CBB HBB  119.970  1.50
+HEM CAB  CBB HBBA 119.970  1.50
+HEM HBB  CBB HBBA 120.061  1.50
+HEM CHC  C1C C2C  128.232  3.00
+HEM CHC  C1C NC   122.477  3.00
+HEM C2C  C1C NC   109.291  1.50
+HEM C1C  C2C C3C  108.186  3.00
+HEM C1C  C2C CMC  126.778  1.50
+HEM C3C  C2C CMC  125.036  3.00
+HEM C2C  C3C C4C  107.432  3.00
+HEM C2C  C3C CAC  125.770  3.00
+HEM C4C  C3C CAC  126.798  3.00
+HEM CHD  C4C C3C  128.949  3.00
+HEM CHD  C4C NC   121.757  3.00
+HEM C3C  C4C NC   109.294  2.29
+HEM C2C  CMC HMC  109.572  1.50
+HEM C2C  CMC HMCA 109.572  1.50
+HEM C2C  CMC HMCB 109.572  1.50
+HEM HMC  CMC HMCA 109.322  1.87
+HEM HMC  CMC HMCB 109.322  1.87
+HEM HMCA CMC HMCB 109.322  1.87
+HEM C3C  CAC CBC  127.109  3.00
+HEM C3C  CAC HAC  116.019  1.61
+HEM CBC  CAC HAC  116.872  2.59
+HEM CAC  CBC HBC  119.970  1.50
+HEM CAC  CBC HBCA 119.970  1.50
+HEM HBC  CBC HBCA 120.061  1.50
+HEM CHD  C1D C2D  128.506  3.00
+HEM CHD  C1D ND   122.751  3.00
+HEM C2D  C1D ND   108.743  1.50
+HEM C1D  C2D C3D  108.632  3.00
+HEM C1D  C2D CMD  126.624  1.50
+HEM C3D  C2D CMD  124.744  3.00
+HEM C2D  C3D C4D  108.632  3.00
+HEM C2D  C3D CAD  125.990  1.50
+HEM C4D  C3D CAD  125.377  3.00
+HEM CHA  C4D C3D  128.506  3.00
+HEM CHA  C4D ND   122.751  3.00
+HEM C3D  C4D ND   108.743  1.50
+HEM C2D  CMD HMD  109.572  1.50
+HEM C2D  CMD HMDA 109.572  1.50
+HEM C2D  CMD HMDB 109.572  1.50
+HEM HMD  CMD HMDA 109.322  1.87
+HEM HMD  CMD HMDB 109.322  1.87
+HEM HMDA CMD HMDB 109.322  1.87
+HEM C3D  CAD CBD  113.932  3.00
+HEM C3D  CAD HAD  109.001  1.50
+HEM C3D  CAD HADA 109.001  1.50
+HEM CBD  CAD HAD  108.631  1.50
+HEM CBD  CAD HADA 108.631  1.50
+HEM HAD  CAD HADA 107.419  2.31
+HEM CAD  CBD CGD  114.716  3.00
+HEM CAD  CBD HBD  108.790  1.50
+HEM CAD  CBD HBDA 108.790  1.50
+HEM CGD  CBD HBD  108.586  1.50
+HEM CGD  CBD HBDA 108.586  1.50
+HEM HBD  CBD HBDA 107.505  1.50
+HEM CBD  CGD O1D  117.968  3.00
+HEM CBD  CGD O2D  117.968  3.00
+HEM O1D  CGD O2D  124.063  1.82
+HEM C1A  NA  C4A  105.249  3.00
+HEM C1B  NB  C4B  105.796  3.00
+HEM C1C  NC  C4C  105.796  3.00
+HEM C1D  ND  C4D  105.249  3.00
+HEM NA   FE  ND   89.77    6.92
+HEM NA   FE  NB   89.77    6.92
+HEM NA   FE  NC   172.48   12.51
+HEM ND   FE  NB   172.48   12.51
+HEM ND   FE  NC   89.77    6.92
+HEM NB   FE  NC   89.77    6.92
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+HEM sp2_sp2_1  C3D C4D CHA C1A 180.000 5.0  2
+HEM sp2_sp2_2  C2A C1A CHA C4D 180.000 5.0  2
+HEM sp2_sp3_1  O1A CGA CBA CAA 120.000 20.0 6
+HEM const_0    CHB C1B C2B CMB 0.000   0.0  1
+HEM const_1    CHB C1B NB  C4B 180.000 0.0  1
+HEM const_2    CMB C2B C3B CAB 0.000   0.0  1
+HEM sp2_sp3_2  C1B C2B CMB HMB 150.000 20.0 6
+HEM const_3    CAB C3B C4B CHC 0.000   0.0  1
+HEM sp2_sp2_3  C2B C3B CAB CBB 180.000 5.0  2
+HEM const_4    CHC C4B NB  C1B 180.000 0.0  1
+HEM sp2_sp2_4  C3B CAB CBB HBB 180.000 5.0  2
+HEM sp2_sp2_5  C2B C1B CHB C4A 180.000 5.0  2
+HEM sp2_sp2_6  C3A C4A CHB C1B 180.000 5.0  2
+HEM const_5    CHC C1C C2C CMC 0.000   0.0  1
+HEM const_6    CHC C1C NC  C4C 180.000 0.0  1
+HEM const_7    CMC C2C C3C CAC 0.000   0.0  1
+HEM sp2_sp3_3  C1C C2C CMC HMC 150.000 20.0 6
+HEM const_8    CAC C3C C4C CHD 0.000   0.0  1
+HEM sp2_sp2_7  C2C C3C CAC CBC 180.000 5.0  2
+HEM const_9    CHD C4C NC  C1C 180.000 0.0  1
+HEM sp2_sp2_8  C3C CAC CBC HBC 180.000 5.0  2
+HEM const_10   CHD C1D C2D CMD 0.000   0.0  1
+HEM const_11   CHD C1D ND  C4D 180.000 0.0  1
+HEM const_12   CMD C2D C3D CAD 0.000   0.0  1
+HEM sp2_sp3_4  C1D C2D CMD HMD 150.000 20.0 6
+HEM sp2_sp2_9  C3B C4B CHC C1C 180.000 5.0  2
+HEM sp2_sp2_10 C2C C1C CHC C4B 180.000 5.0  2
+HEM const_13   CAD C3D C4D CHA 0.000   0.0  1
+HEM sp2_sp3_5  C2D C3D CAD CBD -90.000 20.0 6
+HEM const_14   CHA C4D ND  C1D 180.000 0.0  1
+HEM sp3_sp3_1  C3D CAD CBD CGD 180.000 10.0 3
+HEM sp2_sp3_6  O1D CGD CBD CAD 120.000 20.0 6
+HEM sp2_sp2_11 C3C C4C CHD C1D 180.000 5.0  2
+HEM sp2_sp2_12 C2D C1D CHD C4C 180.000 5.0  2
+HEM const_15   CHA C1A NA  C4A 180.000 0.0  1
+HEM const_16   CHA C1A C2A CAA 0.000   0.0  1
+HEM const_17   CAA C2A C3A CMA 0.000   0.0  1
+HEM sp2_sp3_7  C1A C2A CAA CBA -90.000 20.0 6
+HEM const_18   CMA C3A C4A CHB 0.000   0.0  1
+HEM sp2_sp3_8  C2A C3A CMA HMA 150.000 20.0 6
+HEM const_19   CHB C4A NA  C1A 180.000 0.0  1
+HEM sp3_sp3_2  C2A CAA CBA CGA 180.000 10.0 3
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+HEM plan-15 FE   0.060
+HEM plan-15 NA   0.060
+HEM plan-15 C1A  0.060
+HEM plan-15 C4A  0.060
+HEM plan-16 FE   0.060
+HEM plan-16 NB   0.060
+HEM plan-16 C1B  0.060
+HEM plan-16 C4B  0.060
+HEM plan-17 FE   0.060
+HEM plan-17 NC   0.060
+HEM plan-17 C1C  0.060
+HEM plan-17 C4C  0.060
+HEM plan-18 FE   0.060
+HEM plan-18 ND   0.060
+HEM plan-18 C1D  0.060
+HEM plan-18 C4D  0.060
+HEM plan-1  C1B  0.020
+HEM plan-1  C2B  0.020
+HEM plan-1  C3B  0.020
+HEM plan-1  C4B  0.020
+HEM plan-1  CAB  0.020
+HEM plan-1  CHB  0.020
+HEM plan-1  CHC  0.020
+HEM plan-1  CMB  0.020
+HEM plan-1  NB   0.020
+HEM plan-2  C1C  0.020
+HEM plan-2  C2C  0.020
+HEM plan-2  C3C  0.020
+HEM plan-2  C4C  0.020
+HEM plan-2  CAC  0.020
+HEM plan-2  CHC  0.020
+HEM plan-2  CHD  0.020
+HEM plan-2  CMC  0.020
+HEM plan-2  NC   0.020
+HEM plan-3  C1D  0.020
+HEM plan-3  C2D  0.020
+HEM plan-3  C3D  0.020
+HEM plan-3  C4D  0.020
+HEM plan-3  CAD  0.020
+HEM plan-3  CHA  0.020
+HEM plan-3  CHD  0.020
+HEM plan-3  CMD  0.020
+HEM plan-3  ND   0.020
+HEM plan-4  C1A  0.020
+HEM plan-4  C2A  0.020
+HEM plan-4  C3A  0.020
+HEM plan-4  C4A  0.020
+HEM plan-4  CAA  0.020
+HEM plan-4  CHA  0.020
+HEM plan-4  CHB  0.020
+HEM plan-4  CMA  0.020
+HEM plan-4  NA   0.020
+HEM plan-5  C1A  0.020
+HEM plan-5  C4D  0.020
+HEM plan-5  CHA  0.020
+HEM plan-5  HHA  0.020
+HEM plan-6  C1B  0.020
+HEM plan-6  C4A  0.020
+HEM plan-6  CHB  0.020
+HEM plan-6  HHB  0.020
+HEM plan-7  C1C  0.020
+HEM plan-7  C4B  0.020
+HEM plan-7  CHC  0.020
+HEM plan-7  HHC  0.020
+HEM plan-8  C1D  0.020
+HEM plan-8  C4C  0.020
+HEM plan-8  CHD  0.020
+HEM plan-8  HHD  0.020
+HEM plan-9  CBA  0.020
+HEM plan-9  CGA  0.020
+HEM plan-9  O1A  0.020
+HEM plan-9  O2A  0.020
+HEM plan-10 C3B  0.020
+HEM plan-10 CAB  0.020
+HEM plan-10 CBB  0.020
+HEM plan-10 HAB  0.020
+HEM plan-11 CAB  0.020
+HEM plan-11 CBB  0.020
+HEM plan-11 HBB  0.020
+HEM plan-11 HBBA 0.020
+HEM plan-12 C3C  0.020
+HEM plan-12 CAC  0.020
+HEM plan-12 CBC  0.020
+HEM plan-12 HAC  0.020
+HEM plan-13 CAC  0.020
+HEM plan-13 CBC  0.020
+HEM plan-13 HBC  0.020
+HEM plan-13 HBCA 0.020
+HEM plan-14 CBD  0.020
+HEM plan-14 CGD  0.020
+HEM plan-14 O1D  0.020
+HEM plan-14 O2D  0.020
+
+loop_
+_chem_comp_ring_atom.comp_id
+_chem_comp_ring_atom.ring_serial_number
+_chem_comp_ring_atom.atom_id
+_chem_comp_ring_atom.is_aromatic_ring
+HEM ring-1 C1B YES
+HEM ring-1 C2B YES
+HEM ring-1 C3B YES
+HEM ring-1 C4B YES
+HEM ring-1 NB  YES
+HEM ring-2 C1C YES
+HEM ring-2 C2C YES
+HEM ring-2 C3C YES
+HEM ring-2 C4C YES
+HEM ring-2 NC  YES
+HEM ring-3 C1D YES
+HEM ring-3 C2D YES
+HEM ring-3 C3D YES
+HEM ring-3 C4D YES
+HEM ring-3 ND  YES
+HEM ring-4 C1A YES
+HEM ring-4 C2A YES
+HEM ring-4 C3A YES
+HEM ring-4 C4A YES
+HEM ring-4 NA  YES
+
+loop_
+_acedrg_chem_comp_descriptor.comp_id
+_acedrg_chem_comp_descriptor.program_name
+_acedrg_chem_comp_descriptor.program_version
+_acedrg_chem_comp_descriptor.type
+HEM acedrg            311       'dictionary generator'
+HEM 'acedrg_database' 12        'data source'
+HEM rdkit             2019.09.1 'Chemoinformatics tool'
+HEM servalcat         0.4.93    'optimization tool'
+HEM metalCoord        0.1.63    'metal coordination analysis'
diff --git a/image_analysis/structure_refinement/monomers/HIS.cif b/image_analysis/structure_refinement/monomers/HIS.cif
new file mode 100644
index 000000000..9aa774d8a
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/HIS.cif
@@ -0,0 +1,247 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+HIS HIS HISTIDINE peptide 21 11 .
+
+data_comp_HIS
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+HIS N N NT3 1 33.660 42.779 -4.734
+HIS CA C CH1 0 33.418 41.805 -5.835
+HIS C C C 0 33.362 42.558 -7.170
+HIS O O O 0 32.473 43.428 -7.296
+HIS CB C CH2 0 32.141 40.999 -5.566
+HIS CG C CR5 0 31.907 39.881 -6.528
+HIS ND1 N NR15 1 32.388 38.605 -6.324
+HIS CD2 C CR15 0 31.249 39.846 -7.694
+HIS CE1 C CR15 0 32.025 37.834 -7.339
+HIS NE2 N NR15 0 31.332 38.567 -8.183
+HIS OXT O OC -1 34.210 42.245 -8.036
+HIS H H H 0 32.989 43.381 -4.702
+HIS H2 H H 0 34.439 43.213 -4.870
+HIS H3 H H 0 33.701 42.345 -3.944
+HIS HA H H 0 34.186 41.182 -5.863
+HIS HB3 H H 0 31.373 41.610 -5.597
+HIS HB2 H H 0 32.189 40.630 -4.657
+HIS HD1 H H 0 32.878 38.369 -5.655
+HIS HD2 H H 0 30.808 40.561 -8.109
+HIS HE1 H H 0 32.229 36.920 -7.437
+HIS HE2 H H 0 30.960 38.279 -8.940
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+HIS N n/a CA START
+HIS H N . .
+HIS H2 N . .
+HIS H3 N . .
+HIS CA N C .
+HIS HA CA . .
+HIS CB CA CG .
+HIS HB3 CB . .
+HIS HB2 CB . .
+HIS CG CB ND1 .
+HIS ND1 CG CE1 .
+HIS HD1 ND1 . .
+HIS CE1 ND1 NE2 .
+HIS HE1 CE1 . .
+HIS NE2 CE1 CD2 .
+HIS HE2 NE2 . .
+HIS CD2 NE2 HD2 .
+HIS HD2 CD2 . .
+HIS C CA . END
+HIS O C . .
+HIS OXT C . .
+HIS CD2 CG . ADD
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+HIS N N(CCCH)(H)3
+HIS CA C(CC[5]HH)(NH3)(COO)(H)
+HIS C C(CCHN)(O)2
+HIS O O(CCO)
+HIS CB C(C[5]C[5]N[5])(CCHN)(H)2
+HIS CG C[5](C[5]N[5]H)(N[5]C[5]H)(CCHH){2|H<1>}
+HIS ND1 N[5](C[5]C[5]C)(C[5]N[5]H)(H){2|H<1>}
+HIS CD2 C[5](C[5]N[5]C)(N[5]C[5]H)(H){2|H<1>}
+HIS CE1 C[5](N[5]C[5]H)2(H){1|C<4>,1|H<1>}
+HIS NE2 N[5](C[5]C[5]H)(C[5]N[5]H)(H){1|C<4>,1|H<1>}
+HIS OXT O(CCO)
+HIS H H(NCHH)
+HIS H2 H(NCHH)
+HIS H3 H(NCHH)
+HIS HA H(CCCN)
+HIS HB3 H(CC[5]CH)
+HIS HB2 H(CC[5]CH)
+HIS HD1 H(N[5]C[5]2)
+HIS HD2 H(C[5]C[5]N[5])
+HIS HE1 H(C[5]N[5]2)
+HIS HE2 H(N[5]C[5]2)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+HIS N CA SINGLE n 1.489 0.0100 1.489 0.0100
+HIS CA C SINGLE n 1.533 0.0100 1.533 0.0100
+HIS CA CB SINGLE n 1.533 0.0104 1.533 0.0104
+HIS C O DOUBLE n 1.251 0.0183 1.251 0.0183
+HIS C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+HIS CB CG SINGLE n 1.493 0.0146 1.493 0.0146
+HIS CG ND1 SINGLE y 1.378 0.0100 1.378 0.0100
+HIS CG CD2 DOUBLE y 1.338 0.0174 1.338 0.0174
+HIS ND1 CE1 DOUBLE y 1.326 0.0133 1.326 0.0133
+HIS CD2 NE2 SINGLE y 1.371 0.0154 1.371 0.0154
+HIS CE1 NE2 SINGLE y 1.316 0.0157 1.316 0.0157
+HIS N H SINGLE n 1.018 0.0520 0.902 0.0102
+HIS N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+HIS N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+HIS CA HA SINGLE n 1.092 0.0100 0.989 0.0200
+HIS CB HB3 SINGLE n 1.092 0.0100 0.982 0.0176
+HIS CB HB2 SINGLE n 1.092 0.0100 0.982 0.0176
+HIS ND1 HD1 SINGLE n 1.013 0.0120 0.881 0.0200
+HIS CD2 HD2 SINGLE n 1.085 0.0150 0.937 0.0104
+HIS CE1 HE1 SINGLE n 1.085 0.0150 0.942 0.0200
+HIS NE2 HE2 SINGLE n 1.013 0.0120 0.877 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+HIS CA N H 109.992 2.14
+HIS CA N H2 109.992 2.14
+HIS CA N H3 109.992 2.14
+HIS H N H2 109.032 3.00
+HIS H N H3 109.032 3.00
+HIS H2 N H3 109.032 3.00
+HIS N CA C 109.292 1.55
+HIS N CA CB 110.573 1.50
+HIS N CA HA 108.019 2.27
+HIS C CA CB 111.874 3.00
+HIS C CA HA 108.290 1.50
+HIS CB CA HA 108.890 2.34
+HIS CA C O 117.058 3.00
+HIS CA C OXT 117.058 3.00
+HIS O C OXT 125.883 1.50
+HIS CA CB CG 113.931 1.83
+HIS CA CB HB3 108.697 1.50
+HIS CA CB HB2 108.697 1.50
+HIS CG CB HB3 108.948 1.50
+HIS CG CB HB2 108.948 1.50
+HIS HB3 CB HB2 107.846 2.68
+HIS CB CG ND1 122.940 3.00
+HIS CB CG CD2 131.173 3.00
+HIS ND1 CG CD2 105.887 1.50
+HIS CG ND1 CE1 109.313 1.50
+HIS CG ND1 HD1 125.337 2.60
+HIS CE1 ND1 HD1 125.350 3.00
+HIS CG CD2 NE2 107.589 1.50
+HIS CG CD2 HD2 126.688 3.00
+HIS NE2 CD2 HD2 125.723 3.00
+HIS ND1 CE1 NE2 108.287 1.50
+HIS ND1 CE1 HE1 125.729 2.42
+HIS NE2 CE1 HE1 125.984 1.51
+HIS CD2 NE2 CE1 108.930 1.50
+HIS CD2 NE2 HE2 125.575 3.00
+HIS CE1 NE2 HE2 125.489 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+HIS chi1 N CA CB CG -60.000 10.0 3
+HIS chi2 CA CB CG CD2 90.000 10.0 6
+HIS sp3_sp3_1 C CA N H 180.000 10.0 3
+HIS const_17 NE2 CD2 CG ND1 0.000 0.0 1
+HIS const_13 CG CD2 NE2 CE1 0.000 0.0 1
+HIS const_sp2_sp2_5 NE2 CE1 ND1 CG 0.000 0.0 1
+HIS const_sp2_sp2_9 ND1 CE1 NE2 CD2 0.000 0.0 1
+HIS const_sp2_sp2_1 CD2 CG ND1 CE1 0.000 0.0 1
+HIS sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+HIS chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+HIS plan-1 CB 0.020
+HIS plan-1 CD2 0.020
+HIS plan-1 CE1 0.020
+HIS plan-1 CG 0.020
+HIS plan-1 HD1 0.020
+HIS plan-1 HD2 0.020
+HIS plan-1 HE1 0.020
+HIS plan-1 HE2 0.020
+HIS plan-1 ND1 0.020
+HIS plan-1 NE2 0.020
+HIS plan-2 C 0.020
+HIS plan-2 CA 0.020
+HIS plan-2 O 0.020
+HIS plan-2 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+HIS SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1cnc[nH+]1"
+HIS SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1c[nH]c[nH+]1)C(O)=O"
+HIS SMILES CACTVS 3.341 "N[CH](Cc1c[nH]c[nH+]1)C(O)=O"
+HIS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1c([nH+]c[nH]1)C[C@@H](C(=O)O)N"
+HIS SMILES "OpenEye OEToolkits" 1.5.0 "c1c([nH+]c[nH]1)CC(C(=O)O)N"
+HIS InChI InChI 1.03 "InChI=1S/C6H9N3O2/c7-5(6(10)11)1-4-2-8-3-9-4/h2-3,5H,1,7H2,(H,8,9)(H,10,11)/p+1/t5-/m0/s1"
+HIS InChIKey InChI 1.03 HNDVDQJCIGZPNO-YFKPBYRVSA-O
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+HIS acedrg 278 "dictionary generator"
+HIS acedrg_database 12 "data source"
+HIS rdkit 2019.09.1 "Chemoinformatics tool"
+HIS refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/HOH.cif b/image_analysis/structure_refinement/monomers/HOH.cif
new file mode 100644
index 000000000..9b16b4d26
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/HOH.cif
@@ -0,0 +1,79 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+HOH HOH WATER NON-POLYMER 3 1 .
+
+data_comp_HOH
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.alt_atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+HOH O  O  O OH2 0 -23.107 18.382 -21.639
+HOH H1 H1 H H   0 -22.244 18.382 -21.639
+HOH H2 H2 H H   0 -23.365 19.206 -21.639
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+HOH O  O(H)2
+HOH H1 H(OH)
+HOH H2 H(OH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+HOH O H1 SINGLE n 0.972 0.0180 0.863 0.0200
+HOH O H2 SINGLE n 0.972 0.0180 0.863 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+HOH H1 O H2 107.391 3.00
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+HOH SMILES           ACDLabs              10.04 O
+HOH SMILES_CANONICAL CACTVS               3.341 O
+HOH SMILES           CACTVS               3.341 O
+HOH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 O
+HOH SMILES           "OpenEye OEToolkits" 1.5.0 O
+HOH InChI            InChI                1.03  InChI=1S/H2O/h1H2
+HOH InChIKey         InChI                1.03  XLYOFNOQVPJJNP-UHFFFAOYSA-N
+
+loop_
+_acedrg_chem_comp_descriptor.comp_id
+_acedrg_chem_comp_descriptor.program_name
+_acedrg_chem_comp_descriptor.program_version
+_acedrg_chem_comp_descriptor.type
+HOH acedrg          285       "dictionary generator"
+HOH acedrg_database 12        "data source"
+HOH rdkit           2019.09.1 "Chemoinformatics tool"
+HOH servalcat       0.4.57    'optimization tool'
diff --git a/image_analysis/structure_refinement/monomers/ILE.cif b/image_analysis/structure_refinement/monomers/ILE.cif
new file mode 100644
index 000000000..5a1718d9b
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ILE.cif
@@ -0,0 +1,240 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ILE ILE ISOLEUCINE peptide 22 9 .
+
+data_comp_ILE
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ILE N N NT3 1 52.911 76.465 68.493
+ILE CA C CH1 0 53.201 77.811 67.902
+ILE C C C 0 51.886 78.441 67.404
+ILE O O O 0 51.005 77.667 66.962
+ILE CB C CH1 0 54.273 77.728 66.792
+ILE CG1 C CH2 0 54.806 79.117 66.415
+ILE CG2 C CH3 0 53.775 76.967 65.560
+ILE CD1 C CH3 0 55.991 79.094 65.464
+ILE OXT O OC -1 51.789 79.686 67.476
+ILE H H H 0 53.671 75.992 68.596
+ILE H2 H H 0 52.344 75.994 67.973
+ILE H3 H H 0 52.530 76.571 69.304
+ILE HA H H 0 53.554 78.378 68.615
+ILE HB H H 0 55.027 77.224 67.158
+ILE HG12 H H 0 55.071 79.584 67.234
+ILE HG13 H H 0 54.084 79.629 65.999
+ILE HG21 H H 0 53.180 76.249 65.830
+ILE HG22 H H 0 54.534 76.591 65.082
+ILE HG23 H H 0 53.296 77.576 64.972
+ILE HD11 H H 0 56.404 78.209 65.466
+ILE HD12 H H 0 56.648 79.757 65.749
+ILE HD13 H H 0 55.687 79.307 64.562
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ILE N n/a CA START
+ILE H N . .
+ILE H2 N . .
+ILE H3 N . .
+ILE CA N C .
+ILE HA CA . .
+ILE CB CA CG2 .
+ILE HB CB . .
+ILE CG1 CB CD1 .
+ILE HG13 CG1 . .
+ILE HG12 CG1 . .
+ILE CD1 CG1 HD13 .
+ILE HD11 CD1 . .
+ILE HD12 CD1 . .
+ILE HD13 CD1 . .
+ILE CG2 CB HG23 .
+ILE HG21 CG2 . .
+ILE HG22 CG2 . .
+ILE HG23 CG2 . .
+ILE C CA . END
+ILE O C . .
+ILE OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+ILE N N(CCCH)(H)3
+ILE CA C(CCCH)(NH3)(COO)(H)
+ILE C C(CCHN)(O)2
+ILE O O(CCO)
+ILE CB C(CCHH)(CCHN)(CH3)(H)
+ILE CG1 C(CCCH)(CH3)(H)2
+ILE CG2 C(CCCH)(H)3
+ILE CD1 C(CCHH)(H)3
+ILE OXT O(CCO)
+ILE H H(NCHH)
+ILE H2 H(NCHH)
+ILE H3 H(NCHH)
+ILE HA H(CCCN)
+ILE HB H(CC3)
+ILE HG12 H(CCCH)
+ILE HG13 H(CCCH)
+ILE HG21 H(CCHH)
+ILE HG22 H(CCHH)
+ILE HG23 H(CCHH)
+ILE HD11 H(CCHH)
+ILE HD12 H(CCHH)
+ILE HD13 H(CCHH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+ILE N CA SINGLE n 1.495 0.0100 1.495 0.0100
+ILE CA C SINGLE n 1.538 0.0100 1.538 0.0100
+ILE CA CB SINGLE n 1.540 0.0102 1.540 0.0102
+ILE C O DOUBLE n 1.251 0.0183 1.251 0.0183
+ILE C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+ILE CB CG1 SINGLE n 1.529 0.0200 1.529 0.0200
+ILE CB CG2 SINGLE n 1.529 0.0119 1.529 0.0119
+ILE CG1 CD1 SINGLE n 1.518 0.0129 1.518 0.0129
+ILE N H SINGLE n 1.018 0.0520 0.902 0.0102
+ILE N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+ILE N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+ILE CA HA SINGLE n 1.092 0.0100 0.977 0.0200
+ILE CB HB SINGLE n 1.092 0.0100 0.978 0.0189
+ILE CG1 HG12 SINGLE n 1.092 0.0100 0.979 0.0127
+ILE CG1 HG13 SINGLE n 1.092 0.0100 0.979 0.0127
+ILE CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156
+ILE CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156
+ILE CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156
+ILE CD1 HD11 SINGLE n 1.092 0.0100 0.976 0.0140
+ILE CD1 HD12 SINGLE n 1.092 0.0100 0.976 0.0140
+ILE CD1 HD13 SINGLE n 1.092 0.0100 0.976 0.0140
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+ILE CA N H 109.990 2.80
+ILE CA N H2 109.990 2.80
+ILE CA N H3 109.990 2.80
+ILE H N H2 109.032 3.00
+ILE H N H3 109.032 3.00
+ILE H2 N H3 109.032 3.00
+ILE N CA C 108.738 1.50
+ILE N CA CB 110.837 1.50
+ILE N CA HA 108.328 1.50
+ILE C CA CB 111.703 1.50
+ILE C CA HA 108.550 1.50
+ILE CB CA HA 108.373 1.50
+ILE CA C O 117.155 1.50
+ILE CA C OXT 117.155 1.50
+ILE O C OXT 125.690 1.50
+ILE CA CB CG1 111.638 1.50
+ILE CA CB CG2 110.951 1.50
+ILE CA CB HB 107.422 1.50
+ILE CG1 CB CG2 111.728 1.50
+ILE CG1 CB HB 107.389 1.50
+ILE CG2 CB HB 107.597 1.50
+ILE CB CG1 CD1 114.066 1.50
+ILE CB CG1 HG12 108.686 1.50
+ILE CB CG1 HG13 108.686 1.50
+ILE CD1 CG1 HG12 108.722 1.50
+ILE CD1 CG1 HG13 108.722 1.50
+ILE HG12 CG1 HG13 107.774 1.50
+ILE CB CG2 HG21 109.633 1.50
+ILE CB CG2 HG22 109.633 1.50
+ILE CB CG2 HG23 109.633 1.50
+ILE HG21 CG2 HG22 109.390 1.50
+ILE HG21 CG2 HG23 109.390 1.50
+ILE HG22 CG2 HG23 109.390 1.50
+ILE CG1 CD1 HD11 109.644 2.81
+ILE CG1 CD1 HD12 109.644 2.81
+ILE CG1 CD1 HD13 109.644 2.81
+ILE HD11 CD1 HD12 109.381 1.50
+ILE HD11 CD1 HD13 109.381 1.50
+ILE HD12 CD1 HD13 109.381 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+ILE chi1 N CA CB CG2 -60.000 10.0 3
+ILE chi2 CA CB CG1 CD1 180.000 10.0 3
+ILE hh1 CA CB CG2 HG23 -60.000 10.0 3
+ILE hh2 CB CG1 CD1 HD13 60.000 10.0 3
+ILE sp3_sp3_1 C CA N H 180.000 10.0 3
+ILE sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+ILE chir_1 CA N C CB positive
+ILE chir_2 CB CA CG1 CG2 positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+ILE plan-1 C 0.020
+ILE plan-1 CA 0.020
+ILE plan-1 O 0.020
+ILE plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+ILE SMILES ACDLabs 10.04 O=C(O)C(N)C(C)CC
+ILE SMILES_CANONICAL CACTVS 3.341 CC[C@H](C)[C@H](N)C(O)=O
+ILE SMILES CACTVS 3.341 CC[CH](C)[CH](N)C(O)=O
+ILE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC[C@H](C)[C@@H](C(=O)O)N
+ILE SMILES "OpenEye OEToolkits" 1.5.0 CCC(C)C(C(=O)O)N
+ILE InChI InChI 1.03 InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t4-,5-/m0/s1
+ILE InChIKey InChI 1.03 AGPKZVBTJJNPAG-WHFBIAKZSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+ILE acedrg 278 "dictionary generator"
+ILE acedrg_database 12 "data source"
+ILE rdkit 2019.09.1 "Chemoinformatics tool"
+ILE refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/IOD.cif b/image_analysis/structure_refinement/monomers/IOD.cif
new file mode 100644
index 000000000..fe8d1dcfc
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/IOD.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+IOD IOD 'IODIDE ION                          ' NON-POLYMER 1 1 .
+
+data_comp_IOD
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+IOD I I I -1.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+IOD I n/a . END
diff --git a/image_analysis/structure_refinement/monomers/K.cif b/image_analysis/structure_refinement/monomers/K.cif
new file mode 100644
index 000000000..656dfa7f1
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/K.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+K K 'POTASSIUM ION                       ' NON-POLYMER 1 1 .
+
+data_comp_K
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+K K K K 1.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+K K n/a . END
diff --git a/image_analysis/structure_refinement/monomers/LEU.cif b/image_analysis/structure_refinement/monomers/LEU.cif
new file mode 100644
index 000000000..d7a7bc7e4
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/LEU.cif
@@ -0,0 +1,240 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+LEU LEU LEUCINE peptide 22 9 .
+
+data_comp_LEU
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+LEU N N NT3 1 16.397 16.089 52.368
+LEU CA C CH1 0 15.211 16.954 52.118
+LEU C C C 0 13.931 16.126 52.332
+LEU O O O 0 13.023 16.642 53.022
+LEU CB C CH2 0 15.230 17.562 50.712
+LEU CG C CH1 0 16.388 18.503 50.342
+LEU CD1 C CH3 0 16.596 19.599 51.384
+LEU CD2 C CH3 0 17.703 17.774 50.057
+LEU OXT O OC -1 13.888 14.994 51.800
+LEU H H H 0 16.605 15.616 51.628
+LEU H2 H H 0 16.242 15.512 53.045
+LEU H3 H H 0 17.102 16.600 52.600
+LEU HA H H 0 15.218 17.683 52.788
+LEU HB3 H H 0 14.387 18.055 50.587
+LEU HB2 H H 0 15.214 16.822 50.062
+LEU HG H H 0 16.133 18.961 49.500
+LEU HD11 H H 0 15.741 20.011 51.596
+LEU HD12 H H 0 17.200 20.273 51.030
+LEU HD13 H H 0 16.978 19.215 52.192
+LEU HD21 H H 0 17.517 16.879 49.726
+LEU HD22 H H 0 18.230 17.713 50.871
+LEU HD23 H H 0 18.205 18.266 49.386
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+LEU N n/a CA START
+LEU H N . .
+LEU H2 N . .
+LEU H3 N . .
+LEU CA N C .
+LEU HA CA . .
+LEU CB CA CG .
+LEU HB3 CB . .
+LEU HB2 CB . .
+LEU CG CB CD2 .
+LEU HG CG . .
+LEU CD1 CG HD13 .
+LEU HD11 CD1 . .
+LEU HD12 CD1 . .
+LEU HD13 CD1 . .
+LEU CD2 CG HD23 .
+LEU HD21 CD2 . .
+LEU HD22 CD2 . .
+LEU HD23 CD2 . .
+LEU C CA . END
+LEU O C . .
+LEU OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+LEU N N(CCCH)(H)3
+LEU CA C(CCHH)(NH3)(COO)(H)
+LEU C C(CCHN)(O)2
+LEU O O(CCO)
+LEU CB C(CCCH)(CCHN)(H)2
+LEU CG C(CCHH)(CH3)2(H)
+LEU CD1 C(CCCH)(H)3
+LEU CD2 C(CCCH)(H)3
+LEU OXT O(CCO)
+LEU H H(NCHH)
+LEU H2 H(NCHH)
+LEU H3 H(NCHH)
+LEU HA H(CCCN)
+LEU HB3 H(CCCH)
+LEU HB2 H(CCCH)
+LEU HG H(CC3)
+LEU HD11 H(CCHH)
+LEU HD12 H(CCHH)
+LEU HD13 H(CCHH)
+LEU HD21 H(CCHH)
+LEU HD22 H(CCHH)
+LEU HD23 H(CCHH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+LEU N CA SINGLE n 1.487 0.0100 1.487 0.0100
+LEU CA C SINGLE n 1.538 0.0113 1.538 0.0113
+LEU CA CB SINGLE n 1.528 0.0100 1.528 0.0100
+LEU C O DOUBLE n 1.251 0.0183 1.251 0.0183
+LEU C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+LEU CB CG SINGLE n 1.532 0.0100 1.532 0.0100
+LEU CG CD1 SINGLE n 1.519 0.0200 1.519 0.0200
+LEU CG CD2 SINGLE n 1.519 0.0200 1.519 0.0200
+LEU N H SINGLE n 1.018 0.0520 0.902 0.0102
+LEU N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+LEU N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+LEU CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+LEU CB HB3 SINGLE n 1.092 0.0100 0.985 0.0129
+LEU CB HB2 SINGLE n 1.092 0.0100 0.985 0.0129
+LEU CG HG SINGLE n 1.092 0.0100 0.992 0.0164
+LEU CD1 HD11 SINGLE n 1.092 0.0100 0.972 0.0156
+LEU CD1 HD12 SINGLE n 1.092 0.0100 0.972 0.0156
+LEU CD1 HD13 SINGLE n 1.092 0.0100 0.972 0.0156
+LEU CD2 HD21 SINGLE n 1.092 0.0100 0.972 0.0156
+LEU CD2 HD22 SINGLE n 1.092 0.0100 0.972 0.0156
+LEU CD2 HD23 SINGLE n 1.092 0.0100 0.972 0.0156
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+LEU CA N H 109.990 3.00
+LEU CA N H2 109.990 3.00
+LEU CA N H3 109.990 3.00
+LEU H N H2 109.032 3.00
+LEU H N H3 109.032 3.00
+LEU H2 N H3 109.032 3.00
+LEU N CA C 109.258 1.50
+LEU N CA CB 109.859 2.63
+LEU N CA HA 108.387 1.58
+LEU C CA CB 111.627 1.50
+LEU C CA HA 108.774 1.79
+LEU CB CA HA 109.261 1.50
+LEU CA C O 117.148 1.60
+LEU CA C OXT 117.148 1.60
+LEU O C OXT 125.704 1.50
+LEU CA CB CG 115.973 1.50
+LEU CA CB HB3 108.172 1.50
+LEU CA CB HB2 108.172 1.50
+LEU CG CB HB3 108.390 1.50
+LEU CG CB HB2 108.390 1.50
+LEU HB3 CB HB2 107.673 3.00
+LEU CB CG CD1 110.898 3.00
+LEU CB CG CD2 110.898 3.00
+LEU CB CG HG 108.090 1.50
+LEU CD1 CG CD2 110.647 1.82
+LEU CD1 CG HG 107.962 1.81
+LEU CD2 CG HG 107.962 1.81
+LEU CG CD1 HD11 109.527 1.50
+LEU CG CD1 HD12 109.527 1.50
+LEU CG CD1 HD13 109.527 1.50
+LEU HD11 CD1 HD12 109.390 1.50
+LEU HD11 CD1 HD13 109.390 1.50
+LEU HD12 CD1 HD13 109.390 1.50
+LEU CG CD2 HD21 109.527 1.50
+LEU CG CD2 HD22 109.527 1.50
+LEU CG CD2 HD23 109.527 1.50
+LEU HD21 CD2 HD22 109.390 1.50
+LEU HD21 CD2 HD23 109.390 1.50
+LEU HD22 CD2 HD23 109.390 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+LEU chi1 N CA CB CG -60.000 10.0 3
+LEU chi2 CA CB CG CD1 180.000 10.0 3
+LEU hh1 CB CG CD1 HD13 60.000 10.0 3
+LEU hh2 CB CG CD2 HD23 180.000 10.0 3
+LEU sp3_sp3_1 C CA N H 180.000 10.0 3
+LEU sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+LEU chir_1 CA N C CB positive
+LEU chir_2 CG CB CD1 CD2 both
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+LEU plan-1 C 0.020
+LEU plan-1 CA 0.020
+LEU plan-1 O 0.020
+LEU plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+LEU SMILES ACDLabs 10.04 O=C(O)C(N)CC(C)C
+LEU SMILES_CANONICAL CACTVS 3.341 CC(C)C[C@H](N)C(O)=O
+LEU SMILES CACTVS 3.341 CC(C)C[CH](N)C(O)=O
+LEU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)C[C@@H](C(=O)O)N
+LEU SMILES "OpenEye OEToolkits" 1.5.0 CC(C)CC(C(=O)O)N
+LEU InChI InChI 1.03 InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m0/s1
+LEU InChIKey InChI 1.03 ROHFNLRQFUQHCH-YFKPBYRVSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+LEU acedrg 278 "dictionary generator"
+LEU acedrg_database 12 "data source"
+LEU rdkit 2019.09.1 "Chemoinformatics tool"
+LEU refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/LYS.cif b/image_analysis/structure_refinement/monomers/LYS.cif
new file mode 100644
index 000000000..edcceab06
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/LYS.cif
@@ -0,0 +1,258 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+LYS LYS LYSINE peptide 25 10 .
+
+data_comp_LYS
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+LYS N N NT3 1 38.447 40.683 -3.403
+LYS CA C CH1 0 39.289 39.686 -4.119
+LYS C C C 0 38.638 39.335 -5.470
+LYS O O O 0 37.393 39.207 -5.493
+LYS CB C CH2 0 39.527 38.438 -3.257
+LYS CG C CH2 0 38.287 37.697 -2.761
+LYS CD C CH2 0 38.607 36.502 -1.871
+LYS CE C CH2 0 37.387 35.753 -1.425
+LYS NZ N NT3 1 36.499 36.554 -0.576
+LYS OXT O OC -1 39.402 39.203 -6.452
+LYS H H H 0 38.746 40.791 -2.559
+LYS H2 H H 0 37.585 40.417 -3.374
+LYS H3 H H 0 38.489 41.477 -3.829
+LYS HA H H 0 40.169 40.104 -4.300
+LYS HB3 H H 0 40.055 38.704 -2.474
+LYS HB2 H H 0 40.071 37.807 -3.775
+LYS HG3 H H 0 37.773 37.386 -3.537
+LYS HG2 H H 0 37.724 38.326 -2.260
+LYS HD3 H H 0 39.096 36.816 -1.080
+LYS HD2 H H 0 39.195 35.888 -2.363
+LYS HE3 H H 0 37.662 34.961 -0.931
+LYS HE2 H H 0 36.889 35.459 -2.208
+LYS HZ1 H H 0 36.983 37.027 0.027
+LYS HZ2 H H 0 35.931 36.006 -0.132
+LYS HZ3 H H 0 36.017 37.126 -1.086
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+LYS N n/a CA START
+LYS H N . .
+LYS H2 N . .
+LYS H3 N . .
+LYS CA N C .
+LYS HA CA . .
+LYS CB CA CG .
+LYS HB3 CB . .
+LYS HB2 CB . .
+LYS CG CB CD .
+LYS HG3 CG . .
+LYS HG2 CG . .
+LYS CD CG CE .
+LYS HD3 CD . .
+LYS HD2 CD . .
+LYS CE CD NZ .
+LYS HE3 CE . .
+LYS HE2 CE . .
+LYS NZ CE HZ3 .
+LYS HZ1 NZ . .
+LYS HZ2 NZ . .
+LYS HZ3 NZ . .
+LYS C CA . END
+LYS O C . .
+LYS OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+LYS N N(CCCH)(H)3
+LYS CA C(CCHH)(NH3)(COO)(H)
+LYS C C(CCHN)(O)2
+LYS O O(CCO)
+LYS CB C(CCHH)(CCHN)(H)2
+LYS CG C(CCHH)2(H)2
+LYS CD C(CCHH)(CHHN)(H)2
+LYS CE C(CCHH)(NH3)(H)2
+LYS NZ N(CCHH)(H)3
+LYS OXT O(CCO)
+LYS H H(NCHH)
+LYS H2 H(NCHH)
+LYS H3 H(NCHH)
+LYS HA H(CCCN)
+LYS HB3 H(CCCH)
+LYS HB2 H(CCCH)
+LYS HG3 H(CCCH)
+LYS HG2 H(CCCH)
+LYS HD3 H(CCCH)
+LYS HD2 H(CCCH)
+LYS HE3 H(CCHN)
+LYS HE2 H(CCHN)
+LYS HZ1 H(NCHH)
+LYS HZ2 H(NCHH)
+LYS HZ3 H(NCHH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+LYS N CA SINGLE n 1.487 0.0100 1.487 0.0100
+LYS CA C SINGLE n 1.538 0.0113 1.538 0.0113
+LYS CA CB SINGLE n 1.533 0.0100 1.533 0.0100
+LYS C O DOUBLE n 1.251 0.0183 1.251 0.0183
+LYS C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+LYS CB CG SINGLE n 1.523 0.0189 1.523 0.0189
+LYS CG CD SINGLE n 1.524 0.0122 1.524 0.0122
+LYS CD CE SINGLE n 1.496 0.0200 1.496 0.0200
+LYS CE NZ SINGLE n 1.465 0.0130 1.465 0.0130
+LYS N H SINGLE n 1.018 0.0520 0.902 0.0102
+LYS N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+LYS N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+LYS CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+LYS CB HB3 SINGLE n 1.092 0.0100 0.981 0.0141
+LYS CB HB2 SINGLE n 1.092 0.0100 0.981 0.0141
+LYS CG HG3 SINGLE n 1.092 0.0100 0.982 0.0163
+LYS CG HG2 SINGLE n 1.092 0.0100 0.982 0.0163
+LYS CD HD3 SINGLE n 1.092 0.0100 0.982 0.0163
+LYS CD HD2 SINGLE n 1.092 0.0100 0.982 0.0163
+LYS CE HE3 SINGLE n 1.092 0.0100 0.974 0.0147
+LYS CE HE2 SINGLE n 1.092 0.0100 0.974 0.0147
+LYS NZ HZ1 SINGLE n 1.018 0.0520 0.906 0.0200
+LYS NZ HZ2 SINGLE n 1.018 0.0520 0.906 0.0200
+LYS NZ HZ3 SINGLE n 1.018 0.0520 0.906 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+LYS CA N H 109.990 3.00
+LYS CA N H2 109.990 3.00
+LYS CA N H3 109.990 3.00
+LYS H N H2 109.032 3.00
+LYS H N H3 109.032 3.00
+LYS H2 N H3 109.032 3.00
+LYS N CA C 109.258 1.50
+LYS N CA CB 110.440 2.46
+LYS N CA HA 108.387 1.58
+LYS C CA CB 111.059 3.00
+LYS C CA HA 108.774 1.79
+LYS CB CA HA 109.080 2.33
+LYS CA C O 117.148 1.60
+LYS CA C OXT 117.148 1.60
+LYS O C OXT 125.704 1.50
+LYS CA CB CG 115.148 2.35
+LYS CA CB HB3 108.677 1.74
+LYS CA CB HB2 108.677 1.74
+LYS CG CB HB3 108.413 1.50
+LYS CG CB HB2 108.413 1.50
+LYS HB3 CB HB2 107.655 1.50
+LYS CB CG CD 113.403 3.00
+LYS CB CG HG3 108.381 1.50
+LYS CB CG HG2 108.381 1.50
+LYS CD CG HG3 108.819 1.50
+LYS CD CG HG2 108.819 1.50
+LYS HG3 CG HG2 107.566 1.82
+LYS CG CD CE 112.541 3.00
+LYS CG CD HD3 108.993 1.92
+LYS CG CD HD2 108.993 1.92
+LYS CE CD HD3 109.016 1.50
+LYS CE CD HD2 109.016 1.50
+LYS HD3 CD HD2 107.958 2.23
+LYS CD CE NZ 111.716 3.00
+LYS CD CE HE3 109.468 2.65
+LYS CD CE HE2 109.468 2.65
+LYS NZ CE HE3 108.972 2.23
+LYS NZ CE HE2 108.972 2.23
+LYS HE3 CE HE2 108.144 2.57
+LYS CE NZ HZ1 109.659 3.00
+LYS CE NZ HZ2 109.659 3.00
+LYS CE NZ HZ3 109.659 3.00
+LYS HZ1 NZ HZ2 109.089 3.00
+LYS HZ1 NZ HZ3 109.089 3.00
+LYS HZ2 NZ HZ3 109.089 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+LYS chi1 N CA CB CG -60.000 10.0 3
+LYS chi2 CA CB CG CD 180.000 10.0 3
+LYS chi3 CB CG CD CE 180.000 10.0 3
+LYS chi4 CG CD CE NZ 180.000 10.0 3
+LYS hh1 CD CE NZ HZ3 180.000 10.0 3
+LYS sp3_sp3_1 C CA N H 180.000 10.0 3
+LYS sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+LYS chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+LYS plan-1 C 0.020
+LYS plan-1 CA 0.020
+LYS plan-1 O 0.020
+LYS plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+LYS SMILES ACDLabs 10.04 O=C(O)C(N)CCCC[NH3+]
+LYS SMILES_CANONICAL CACTVS 3.341 N[C@@H](CCCC[NH3+])C(O)=O
+LYS SMILES CACTVS 3.341 N[CH](CCCC[NH3+])C(O)=O
+LYS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CC[NH3+])C[C@@H](C(=O)O)N
+LYS SMILES "OpenEye OEToolkits" 1.5.0 C(CC[NH3+])CC(C(=O)O)N
+LYS InChI InChI 1.03 InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
+LYS InChIKey InChI 1.03 KDXKERNSBIXSRK-YFKPBYRVSA-O
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+LYS acedrg 278 "dictionary generator"
+LYS acedrg_database 12 "data source"
+LYS rdkit 2019.09.1 "Chemoinformatics tool"
+LYS refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/M2G.cif b/image_analysis/structure_refinement/monomers/M2G.cif
new file mode 100644
index 000000000..f08ed483a
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/M2G.cif
@@ -0,0 +1,307 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+M2G M2G "N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE" RNA 42 26 .
+
+data_comp_M2G
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+M2G P      P P    0  39.624 -6.580 13.186
+M2G OP1    O O    0  40.880 -5.814 12.816
+M2G OP2    O OP   -1 38.958 -7.232 11.988
+M2G OP3    O OP   -1 39.838 -7.543 14.338
+M2G "O5'"  O O2   0  38.577 -5.476 13.725
+M2G "C5'"  C CH2  0  37.276 -5.917 14.192
+M2G "C4'"  C CH1  0  36.420 -4.719 14.527
+M2G "O4'"  O O2   0  37.113 -3.873 15.478
+M2G "C3'"  C CH1  0  36.075 -3.781 13.366
+M2G "O3'"  O OH1  0  34.949 -4.254 12.637
+M2G "C2'"  C CH1  0  35.793 -2.465 14.098
+M2G "O2'"  O OH1  0  34.465 -2.359 14.571
+M2G "C1'"  C CH1  0  36.802 -2.514 15.248
+M2G N9     N NR5  0  38.030 -1.769 14.978
+M2G C8     C CR15 0  39.306 -2.257 14.820
+M2G N7     N NRD5 0  40.197 -1.323 14.584
+M2G C5     C CR56 0  39.465 -0.144 14.588
+M2G C6     C CR6  0  39.880 1.200  14.389
+M2G O6     O O    0  41.026 1.613  14.162
+M2G N1     N NR16 0  38.812 2.107  14.473
+M2G C2     C CR6  0  37.498 1.761  14.720
+M2G N2     N N    0  36.512 2.761  14.782
+M2G N3     N NRD6 0  37.123 0.497  14.909
+M2G C4     C CR56 0  38.134 -0.404 14.831
+M2G CM1    C CH3  0  35.097 2.452  14.595
+M2G CM2    C CH3  0  36.840 4.157  15.050
+M2G "H5'"  H H    0  37.383 -6.482 14.996
+M2G "H5''" H H    0  36.833 -6.454 13.489
+M2G "H4'"  H H    0  35.589 -5.043 14.937
+M2G "H3'"  H H    0  36.854 -3.676 12.761
+M2G "HO3'" H H    0  34.740 -3.675 12.052
+M2G "H2'"  H H    0  35.987 -1.696 13.500
+M2G "HO2'" H H    0  34.306 -2.977 15.131
+M2G "H1'"  H H    0  36.375 -2.140 16.053
+M2G H8     H H    0  39.523 -3.172 14.874
+M2G HN1    H H    0  39.016 2.969  14.353
+M2G HM11   H H    0  34.999 1.706  13.981
+M2G HM12   H H    0  34.637 3.225  14.228
+M2G HM13   H H    0  34.702 2.219  15.451
+M2G HM21   H H    0  37.546 4.202  15.715
+M2G HM22   H H    0  36.057 4.624  15.385
+M2G HM23   H H    0  37.142 4.581  14.230
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+M2G P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+M2G P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+M2G P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+M2G P     "O5'"  SINGLE n 1.614 0.0178 1.614 0.0178
+M2G "O5'" "C5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+M2G "C5'" "C4'"  SINGLE n 1.509 0.0100 1.509 0.0100
+M2G "C4'" "O4'"  SINGLE n 1.451 0.0100 1.451 0.0100
+M2G "C4'" "C3'"  SINGLE n 1.535 0.0100 1.535 0.0100
+M2G "O4'" "C1'"  SINGLE n 1.409 0.0100 1.409 0.0100
+M2G "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+M2G "C3'" "C2'"  SINGLE n 1.531 0.0100 1.531 0.0100
+M2G "C2'" "O2'"  SINGLE n 1.411 0.0100 1.411 0.0100
+M2G "C2'" "C1'"  SINGLE n 1.525 0.0100 1.525 0.0100
+M2G "C1'" N9     SINGLE n 1.458 0.0100 1.458 0.0100
+M2G N9    C8     SINGLE y 1.372 0.0100 1.372 0.0100
+M2G N9    C4     SINGLE y 1.375 0.0100 1.375 0.0100
+M2G C8    N7     DOUBLE y 1.312 0.0100 1.312 0.0100
+M2G N7    C5     SINGLE y 1.390 0.0100 1.390 0.0100
+M2G C5    C6     SINGLE y 1.417 0.0103 1.417 0.0103
+M2G C5    C4     DOUBLE y 1.377 0.0100 1.377 0.0100
+M2G C6    O6     DOUBLE n 1.239 0.0100 1.239 0.0100
+M2G C6    N1     SINGLE y 1.396 0.0107 1.396 0.0107
+M2G N1    C2     SINGLE y 1.372 0.0100 1.372 0.0100
+M2G C2    N2     SINGLE n 1.370 0.0200 1.370 0.0200
+M2G C2    N3     DOUBLE y 1.324 0.0127 1.324 0.0127
+M2G N2    CM1    SINGLE n 1.453 0.0119 1.453 0.0119
+M2G N2    CM2    SINGLE n 1.453 0.0119 1.453 0.0119
+M2G N3    C4     SINGLE y 1.355 0.0100 1.355 0.0100
+M2G "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+M2G "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+M2G "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+M2G "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+M2G "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+M2G "C2'" "H2'"  SINGLE n 1.089 0.0100 0.994 0.0200
+M2G "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+M2G "C1'" "H1'"  SINGLE n 1.089 0.0100 0.984 0.0200
+M2G C8    H8     SINGLE n 1.082 0.0130 0.942 0.0170
+M2G N1    HN1    SINGLE n 1.016 0.0100 0.897 0.0200
+M2G CM1   HM11   SINGLE n 1.089 0.0100 0.971 0.0181
+M2G CM1   HM12   SINGLE n 1.089 0.0100 0.971 0.0181
+M2G CM1   HM13   SINGLE n 1.089 0.0100 0.971 0.0181
+M2G CM2   HM21   SINGLE n 1.089 0.0100 0.971 0.0181
+M2G CM2   HM22   SINGLE n 1.089 0.0100 0.971 0.0181
+M2G CM2   HM23   SINGLE n 1.089 0.0100 0.971 0.0181
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+M2G OP1   P     OP2    112.864 1.69
+M2G OP1   P     OP3    112.864 1.69
+M2G OP1   P     "O5'"  105.808 2.07
+M2G OP2   P     OP3    112.864 1.69
+M2G OP2   P     "O5'"  105.808 2.07
+M2G OP3   P     "O5'"  105.808 2.07
+M2G P     "O5'" "C5'"  118.783 1.50
+M2G "O5'" "C5'" "C4'"  109.342 1.50
+M2G "O5'" "C5'" "H5'"  109.845 1.50
+M2G "O5'" "C5'" "H5''" 109.845 1.50
+M2G "C4'" "C5'" "H5'"  109.624 1.50
+M2G "C4'" "C5'" "H5''" 109.624 1.50
+M2G "H5'" "C5'" "H5''" 108.472 1.50
+M2G "C5'" "C4'" "O4'"  109.123 1.50
+M2G "C5'" "C4'" "C3'"  116.008 1.52
+M2G "C5'" "C4'" "H4'"  108.268 1.50
+M2G "O4'" "C4'" "C3'"  105.388 1.50
+M2G "O4'" "C4'" "H4'"  108.947 1.50
+M2G "C3'" "C4'" "H4'"  109.363 1.86
+M2G "C4'" "O4'" "C1'"  109.903 1.50
+M2G "C4'" "C3'" "O3'"  111.281 2.46
+M2G "C4'" "C3'" "C2'"  102.602 1.50
+M2G "C4'" "C3'" "H3'"  110.452 2.54
+M2G "O3'" "C3'" "C2'"  111.581 2.83
+M2G "O3'" "C3'" "H3'"  110.380 1.67
+M2G "C2'" "C3'" "H3'"  110.504 1.75
+M2G "C3'" "O3'" "HO3'" 108.744 3.00
+M2G "C3'" "C2'" "O2'"  112.782 2.45
+M2G "C3'" "C2'" "C1'"  101.239 1.50
+M2G "C3'" "C2'" "H2'"  110.596 1.51
+M2G "O2'" "C2'" "C1'"  111.715 2.69
+M2G "O2'" "C2'" "H2'"  110.448 1.97
+M2G "C1'" "C2'" "H2'"  110.636 1.70
+M2G "C2'" "O2'" "HO2'" 109.103 2.13
+M2G "O4'" "C1'" "C2'"  106.047 1.50
+M2G "O4'" "C1'" N9     108.477 1.50
+M2G "O4'" "C1'" "H1'"  109.807 1.50
+M2G "C2'" "C1'" N9     113.824 1.50
+M2G "C2'" "C1'" "H1'"  109.015 1.50
+M2G N9    "C1'" "H1'"  109.561 1.50
+M2G "C1'" N9    C8     126.829 1.91
+M2G "C1'" N9    C4     127.440 1.80
+M2G C8    N9    C4     105.731 1.50
+M2G N9    C8    N7     113.507 1.50
+M2G N9    C8    H8     123.187 1.50
+M2G N7    C8    H8     123.307 1.50
+M2G C8    N7    C5     104.778 1.50
+M2G N7    C5    C6     130.048 1.50
+M2G N7    C5    C4     110.574 1.50
+M2G C6    C5    C4     119.378 1.50
+M2G C5    C6    O6     128.253 1.50
+M2G C5    C6    N1     111.349 1.50
+M2G O6    C6    N1     120.398 1.50
+M2G C6    N1    C2     123.973 1.50
+M2G C6    N1    HN1    117.776 2.44
+M2G C2    N1    HN1    118.251 1.59
+M2G N1    C2    N2     118.650 1.50
+M2G N1    C2    N3     122.959 1.50
+M2G N2    C2    N3     118.391 2.18
+M2G C2    N2    CM1    121.373 2.30
+M2G C2    N2    CM2    121.373 2.30
+M2G CM1   N2    CM2    117.254 1.50
+M2G C2    N3    C4     114.148 1.50
+M2G N9    C4    C5     105.411 1.50
+M2G N9    C4    N3     126.396 1.50
+M2G C5    C4    N3     128.193 1.50
+M2G N2    CM1   HM11   109.468 1.50
+M2G N2    CM1   HM12   109.468 1.50
+M2G N2    CM1   HM13   109.468 1.50
+M2G HM11  CM1   HM12   109.352 1.56
+M2G HM11  CM1   HM13   109.352 1.56
+M2G HM12  CM1   HM13   109.352 1.56
+M2G N2    CM2   HM21   109.468 1.50
+M2G N2    CM2   HM22   109.468 1.50
+M2G N2    CM2   HM23   109.468 1.50
+M2G HM21  CM2   HM22   109.352 1.56
+M2G HM21  CM2   HM23   109.352 1.56
+M2G HM22  CM2   HM23   109.352 1.56
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+M2G C2e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+M2G C2e-nyu0        "C4'" "O4'" "C1'" "C2'"  340.700 6.300  1
+M2G C2e-nyu1        "O4'" "C1'" "C2'" "C3'"  32.800  4.900  1
+M2G C2e-nyu2        "C1'" "C2'" "C3'" "C4'"  326.9   3.600  1
+M2G C2e-nyu3        "C2'" "C3'" "C4'" "O4'"  22.600  4.500  1
+M2G C2e-nyu4        "C3'" "C4'" "O4'" "C1'"  357.700 6.100  1
+M2G C3e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+M2G C3e-nyu0        "C4'" "O4'" "C1'" "C2'"  2.8     6.100  1
+M2G C3e-nyu1        "O4'" "C1'" "C2'" "C3'"  335.00  4.900  1
+M2G C3e-nyu2        "C1'" "C2'" "C3'" "C4'"  35.9    2.800  1
+M2G C3e-nyu3        "C2'" "C3'" "C4'" "O4'"  324.700 3.100  1
+M2G C3e-nyu4        "C3'" "C4'" "O4'" "C1'"  20.500  5.100  1
+M2G alpha           "C5'" "O5'" P     OP3    -60.000 10.00  3
+M2G beta            P     "O5'" "C5'" "C4'"  180.000 10.00  3
+M2G epsi            "C4'" "C3'" "O3'" "HO3'" 180.000 10.00  3
+M2G gamma           "O5'" "C5'" "C4'" "C3'"  180.000 10.00  3
+M2G sp3_sp3_52      "C3'" "C2'" "O2'" "HO2'" 180.000 10.00  3
+M2G const_18        N7    C8    N9    "C1'"  180.000 10.0   2
+M2G const_30        C5    C4    N9    "C1'"  180.000 10.0   2
+M2G const_21        N9    C8    N7    C5     0.000   10.0   2
+M2G const_24        C6    C5    N7    C8     180.000 10.0   2
+M2G const_sp2_sp2_4 N7    C5    C6    O6     0.000   5.0    2
+M2G const_25        N9    C4    C5    N7     0.000   10.0   2
+M2G const_sp2_sp2_7 O6    C6    N1    C2     180.000 5.0    2
+M2G const_11        N2    C2    N1    C6     180.000 10.0   2
+M2G sp2_sp2_1       N1    C2    N2    CM1    180.000 5.0    2
+M2G const_14        N2    C2    N3    C4     180.000 10.0   2
+M2G sp2_sp3_10      CM2   N2    CM1   HM11   180.000 10.0   6
+M2G sp2_sp3_16      CM1   N2    CM2   HM21   180.000 10.0   6
+M2G const_16        N9    C4    N3    C2     180.000 10.0   2
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+M2G chir_1 P     "O5'" OP2   OP3   both
+M2G chir_2 "C4'" "O4'" "C3'" "C5'" negative
+M2G chir_3 "C3'" "O3'" "C4'" "C2'" positive
+M2G chir_4 "C2'" "O2'" "C1'" "C3'" negative
+M2G chir_5 "C1'" "O4'" N9    "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+M2G plan-1 "C1'" 0.020
+M2G plan-1 C2    0.020
+M2G plan-1 C4    0.020
+M2G plan-1 C5    0.020
+M2G plan-1 C6    0.020
+M2G plan-1 C8    0.020
+M2G plan-1 H8    0.020
+M2G plan-1 HN1   0.020
+M2G plan-1 N1    0.020
+M2G plan-1 N2    0.020
+M2G plan-1 N3    0.020
+M2G plan-1 N7    0.020
+M2G plan-1 N9    0.020
+M2G plan-1 O6    0.020
+M2G plan-2 C2    0.020
+M2G plan-2 CM1   0.020
+M2G plan-2 CM2   0.020
+M2G plan-2 N2    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+M2G SMILES           ACDLabs              10.04 O=C1c2ncn(c2N=C(N(C)C)N1)C3OC(C(O)C3O)COP(=O)(O)O
+M2G SMILES_CANONICAL CACTVS               3.341 CN(C)C1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
+M2G SMILES           CACTVS               3.341 CN(C)C1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
+M2G SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CN(C)C1=Nc2c(ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)C(=O)N1
+M2G SMILES           "OpenEye OEToolkits" 1.5.0 CN(C)C1=Nc2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)C(=O)N1
+M2G InChI            InChI                1.03  InChI=1S/C12H18N5O8P/c1-16(2)12-14-9-6(10(20)15-12)13-4-17(9)11-8(19)7(18)5(25-11)3-24-26(21,22)23/h4-5,7-8,11,18-19H,3H2,1-2H3,(H,14,15,20)(H2,21,22,23)/t5-,7-,8-,11-/m1/s1
+M2G InChIKey         InChI                1.03  IWJFVRMOIKWYNZ-IOSLPCCCSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+M2G acedrg          243       "dictionary generator"
+M2G acedrg_database 11        "data source"
+M2G rdkit           2017.03.2 "Chemoinformatics tool"
+M2G refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/MET.cif b/image_analysis/structure_refinement/monomers/MET.cif
new file mode 100644
index 000000000..28a95f5e7
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/MET.cif
@@ -0,0 +1,226 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+MET MET METHIONINE peptide 20 9 .
+
+data_comp_MET
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+MET N N NT3 1 16.235 16.083 52.229
+MET CA C CH1 0 15.074 16.893 51.770
+MET C C C 0 13.874 15.966 51.506
+MET O O O 0 12.749 16.368 51.879
+MET CB C CH2 0 15.401 17.671 50.489
+MET CG C CH2 0 16.529 18.680 50.635
+MET SD S S2 0 18.171 17.933 50.684
+MET CE C CH3 0 18.367 17.396 48.979
+MET OXT O OC -1 14.108 14.877 50.937
+MET H H H 0 16.577 15.615 51.537
+MET H2 H H 0 15.985 15.507 52.876
+MET H3 H H 0 16.877 16.622 52.563
+MET HA H H 0 14.833 17.529 52.491
+MET HB3 H H 0 14.592 18.143 50.197
+MET HB2 H H 0 15.638 17.028 49.787
+MET HG3 H H 0 16.395 19.191 51.458
+MET HG2 H H 0 16.495 19.307 49.886
+MET HE3 H H 0 18.130 18.128 48.379
+MET HE2 H H 0 17.783 16.634 48.809
+MET HE1 H H 0 19.294 17.136 48.825
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+MET N n/a CA START
+MET H N . .
+MET H2 N . .
+MET H3 N . .
+MET CA N C .
+MET HA CA . .
+MET CB CA CG .
+MET HB3 CB . .
+MET HB2 CB . .
+MET CG CB SD .
+MET HG3 CG . .
+MET HG2 CG . .
+MET SD CG CE .
+MET CE SD HE3 .
+MET HE1 CE . .
+MET HE2 CE . .
+MET HE3 CE . .
+MET C CA . END
+MET O C . .
+MET OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+MET N N(CCCH)(H)3
+MET CA C(CCHH)(NH3)(COO)(H)
+MET C C(CCHN)(O)2
+MET O O(CCO)
+MET CB C(CCHN)(CHHS)(H)2
+MET CG C(CCHH)(SC)(H)2
+MET SD S(CCHH)(CH3)
+MET CE C(SC)(H)3
+MET OXT O(CCO)
+MET H H(NCHH)
+MET H2 H(NCHH)
+MET H3 H(NCHH)
+MET HA H(CCCN)
+MET HB3 H(CCCH)
+MET HB2 H(CCCH)
+MET HG3 H(CCHS)
+MET HG2 H(CCHS)
+MET HE3 H(CHHS)
+MET HE2 H(CHHS)
+MET HE1 H(CHHS)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+MET N CA SINGLE n 1.487 0.0100 1.487 0.0100
+MET CA C SINGLE n 1.538 0.0113 1.538 0.0113
+MET CA CB SINGLE n 1.533 0.0100 1.533 0.0100
+MET C O DOUBLE n 1.251 0.0183 1.251 0.0183
+MET C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+MET CB CG SINGLE n 1.517 0.0186 1.517 0.0186
+MET CG SD SINGLE n 1.804 0.0100 1.804 0.0100
+MET SD CE SINGLE n 1.798 0.0100 1.798 0.0100
+MET N H SINGLE n 1.018 0.0520 0.902 0.0102
+MET N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+MET N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+MET CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+MET CB HB3 SINGLE n 1.092 0.0100 0.981 0.0141
+MET CB HB2 SINGLE n 1.092 0.0100 0.981 0.0141
+MET CG HG3 SINGLE n 1.092 0.0100 0.978 0.0200
+MET CG HG2 SINGLE n 1.092 0.0100 0.978 0.0200
+MET CE HE3 SINGLE n 1.092 0.0100 0.975 0.0110
+MET CE HE2 SINGLE n 1.092 0.0100 0.975 0.0110
+MET CE HE1 SINGLE n 1.092 0.0100 0.975 0.0110
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+MET CA N H 109.990 3.00
+MET CA N H2 109.990 3.00
+MET CA N H3 109.990 3.00
+MET H N H2 109.032 3.00
+MET H N H3 109.032 3.00
+MET H2 N H3 109.032 3.00
+MET N CA C 109.258 1.50
+MET N CA CB 110.970 1.50
+MET N CA HA 108.387 1.58
+MET C CA CB 109.608 2.17
+MET C CA HA 108.774 1.79
+MET CB CA HA 109.550 1.56
+MET CA C O 117.148 1.60
+MET CA C OXT 117.148 1.60
+MET O C OXT 125.704 1.50
+MET CA CB CG 113.978 1.60
+MET CA CB HB3 108.606 1.50
+MET CA CB HB2 108.606 1.50
+MET CG CB HB3 108.930 1.50
+MET CG CB HB2 108.930 1.50
+MET HB3 CB HB2 107.726 1.50
+MET CB CG SD 112.846 3.00
+MET CB CG HG3 109.287 1.50
+MET CB CG HG2 109.287 1.50
+MET SD CG HG3 108.733 1.50
+MET SD CG HG2 108.733 1.50
+MET HG3 CG HG2 107.881 1.50
+MET CG SD CE 100.693 3.00
+MET SD CE HE3 109.472 1.50
+MET SD CE HE2 109.472 1.50
+MET SD CE HE1 109.472 1.50
+MET HE3 CE HE2 109.569 2.44
+MET HE3 CE HE1 109.569 2.44
+MET HE2 CE HE1 109.569 2.44
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+MET chi1 N CA CB CG -60.000 10.0 3
+MET chi2 CA CB CG SD 180.000 10.0 3
+MET chi3 CB CG SD CE 180.000 10.0 3
+MET hh1 CG SD CE HE3 60.000 10.0 3
+MET sp3_sp3_1 C CA N H 180.000 10.0 3
+MET sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+MET chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+MET plan-1 C 0.020
+MET plan-1 CA 0.020
+MET plan-1 O 0.020
+MET plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+MET SMILES ACDLabs 10.04 O=C(O)C(N)CCSC
+MET SMILES_CANONICAL CACTVS 3.341 CSCC[C@H](N)C(O)=O
+MET SMILES CACTVS 3.341 CSCC[CH](N)C(O)=O
+MET SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CSCC[C@@H](C(=O)O)N
+MET SMILES "OpenEye OEToolkits" 1.5.0 CSCCC(C(=O)O)N
+MET InChI InChI 1.03 InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
+MET InChIKey InChI 1.03 FFEARJCKVFRZRR-BYPYZUCNSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+MET acedrg 278 "dictionary generator"
+MET acedrg_database 12 "data source"
+MET rdkit 2019.09.1 "Chemoinformatics tool"
+MET refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/MG.cif b/image_analysis/structure_refinement/monomers/MG.cif
new file mode 100644
index 000000000..1b723799b
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/MG.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+MG MG 'MAGNESIUM ION                       ' NON-POLYMER 1 1 .
+
+data_comp_MG
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+MG MG MG MG 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+MG MG n/a . END
diff --git a/image_analysis/structure_refinement/monomers/MN.cif b/image_analysis/structure_refinement/monomers/MN.cif
new file mode 100644
index 000000000..ee5537884
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/MN.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+MN MN 'MANGANESE (II) ION                  ' NON-POLYMER 1 1 .
+
+data_comp_MN
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+MN MN MN MN 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+MN MN n/a . END
diff --git a/image_analysis/structure_refinement/monomers/MPD.cif b/image_analysis/structure_refinement/monomers/MPD.cif
new file mode 100644
index 000000000..bc29cd330
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/MPD.cif
@@ -0,0 +1,170 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+MPD     MPD      (4S)-2-METHYL-2,4-PENTANEDIOL     NON-POLYMER     22     8     .     
+#
+data_comp_MPD
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+MPD     C1      C       CH3     0       -2.742      -3.513      8.489       
+MPD     C2      C       CT      0       -3.104      -4.028      9.879       
+MPD     O2      O       OH1     0       -3.051      -5.468      9.845       
+MPD     CM      C       CH3     0       -4.531      -3.659      10.262      
+MPD     C3      C       CH2     0       -2.100      -3.522      10.924      
+MPD     C4      C       CH1     0       -2.174      -4.161      12.300      
+MPD     O4      O       OH1     0       -1.753      -5.524      12.217      
+MPD     C5      C       CH3     0       -1.373      -3.434      13.348      
+MPD     H11     H       H       0       -2.205      -2.707      8.574       
+MPD     H12     H       H       0       -3.550      -3.311      7.989       
+MPD     H13     H       H       0       -2.231      -4.191      8.014       
+MPD     HO2     H       H       0       -2.246      -5.731      9.774       
+MPD     HM1     H       H       0       -4.554      -2.734      10.562      
+MPD     HM2     H       H       0       -4.831      -4.241      10.980      
+MPD     HM3     H       H       0       -5.116      -3.767      9.494       
+MPD     H31     H       H       0       -2.230      -2.555      11.026      
+MPD     H32     H       H       0       -1.197      -3.662      10.569      
+MPD     H4      H       H       0       -3.118      -4.168      12.600      
+MPD     HO4     H       H       0       -0.938      -5.565      11.984      
+MPD     H51     H       H       0       -0.836      -4.069      13.855      
+MPD     H52     H       H       0       -1.976      -2.969      13.955      
+MPD     H53     H       H       0       -0.783      -2.784      12.924      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+MPD          C1          C2      SINGLE       n     1.520  0.0101     1.520  0.0101
+MPD          C2          O2      SINGLE       n     1.437  0.0141     1.437  0.0141
+MPD          C2          CM      SINGLE       n     1.520  0.0101     1.520  0.0101
+MPD          C2          C3      SINGLE       n     1.531  0.0100     1.531  0.0100
+MPD          C3          C4      SINGLE       n     1.506  0.0200     1.506  0.0200
+MPD          C4          O4      SINGLE       n     1.424  0.0199     1.424  0.0199
+MPD          C4          C5      SINGLE       n     1.501  0.0160     1.501  0.0160
+MPD          C1         H11      SINGLE       n     1.089  0.0100     0.972  0.0148
+MPD          C1         H12      SINGLE       n     1.089  0.0100     0.972  0.0148
+MPD          C1         H13      SINGLE       n     1.089  0.0100     0.972  0.0148
+MPD          O2         HO2      SINGLE       n     0.970  0.0120     0.848  0.0200
+MPD          CM         HM1      SINGLE       n     1.089  0.0100     0.972  0.0148
+MPD          CM         HM2      SINGLE       n     1.089  0.0100     0.972  0.0148
+MPD          CM         HM3      SINGLE       n     1.089  0.0100     0.972  0.0148
+MPD          C3         H31      SINGLE       n     1.089  0.0100     0.981  0.0160
+MPD          C3         H32      SINGLE       n     1.089  0.0100     0.981  0.0160
+MPD          C4          H4      SINGLE       n     1.089  0.0100     0.992  0.0184
+MPD          O4         HO4      SINGLE       n     0.970  0.0120     0.848  0.0200
+MPD          C5         H51      SINGLE       n     1.089  0.0100     0.974  0.0145
+MPD          C5         H52      SINGLE       n     1.089  0.0100     0.974  0.0145
+MPD          C5         H53      SINGLE       n     1.089  0.0100     0.974  0.0145
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+MPD          C2          C1         H11     109.123    1.50
+MPD          C2          C1         H12     109.123    1.50
+MPD          C2          C1         H13     109.123    1.50
+MPD         H11          C1         H12     109.441    1.50
+MPD         H11          C1         H13     109.441    1.50
+MPD         H12          C1         H13     109.441    1.50
+MPD          C1          C2          O2     107.291    2.44
+MPD          C1          C2          CM     110.915    1.50
+MPD          C1          C2          C3     111.119    1.58
+MPD          O2          C2          CM     107.291    2.44
+MPD          O2          C2          C3     107.760    2.12
+MPD          CM          C2          C3     111.119    1.58
+MPD          C2          O2         HO2     109.561    1.92
+MPD          C2          CM         HM1     109.123    1.50
+MPD          C2          CM         HM2     109.123    1.50
+MPD          C2          CM         HM3     109.123    1.50
+MPD         HM1          CM         HM2     109.441    1.50
+MPD         HM1          CM         HM3     109.441    1.50
+MPD         HM2          CM         HM3     109.441    1.50
+MPD          C2          C3          C4     111.094    2.85
+MPD          C2          C3         H31     108.201    1.50
+MPD          C2          C3         H32     108.201    1.50
+MPD          C4          C3         H31     108.468    1.50
+MPD          C4          C3         H32     108.468    1.50
+MPD         H31          C3         H32     107.715    1.50
+MPD          C3          C4          O4     109.024    2.32
+MPD          C3          C4          C5     113.468    3.00
+MPD          C3          C4          H4     108.603    1.50
+MPD          O4          C4          C5     109.534    2.02
+MPD          O4          C4          H4     107.545    2.92
+MPD          C5          C4          H4     108.620    2.54
+MPD          C4          O4         HO4     109.880    2.07
+MPD          C4          C5         H51     109.852    1.50
+MPD          C4          C5         H52     109.852    1.50
+MPD          C4          C5         H53     109.852    1.50
+MPD         H51          C5         H52     109.425    1.50
+MPD         H51          C5         H53     109.425    1.50
+MPD         H52          C5         H53     109.425    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+MPD             sp3_sp3_2         H11          C1          C2          O2     -60.000    10.0     3
+MPD            sp3_sp3_10          C1          C2          O2         HO2     180.000    10.0     3
+MPD            sp3_sp3_19          C1          C2          CM         HM1     -60.000    10.0     3
+MPD            sp3_sp3_25          C1          C2          C3          C4      60.000    10.0     3
+MPD            sp3_sp3_31          C2          C3          C4          O4     180.000    10.0     3
+MPD            sp3_sp3_40          C3          C4          O4         HO4     180.000    10.0     3
+MPD            sp3_sp3_43          C3          C4          C5         H51     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+MPD    chir_1    C2    O2    C3    C1    both
+MPD    chir_2    C4    O4    C3    C5    positive
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+MPD           SMILES              ACDLabs 11.02                                                OC(C)CC(O)(C)C
+MPD SMILES_CANONICAL               CACTVS 3.352                                            C[C@H](O)CC(C)(C)O
+MPD           SMILES               CACTVS 3.352                                             C[CH](O)CC(C)(C)O
+MPD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0                                           C[C@@H](CC(C)(C)O)O
+MPD           SMILES "OpenEye OEToolkits" 1.7.0                                                CC(CC(C)(C)O)O
+MPD            InChI                InChI  1.03 InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
+MPD         InChIKey                InChI  1.03                                   SVTBMSDMJJWYQN-YFKPBYRVSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+MPD acedrg               243         "dictionary generator"                  
+MPD acedrg_database      11          "data source"                           
+MPD rdkit                2017.03.2   "Chemoinformatics tool"
+MPD refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/MSE.cif b/image_analysis/structure_refinement/monomers/MSE.cif
new file mode 100644
index 000000000..d73f9f68b
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/MSE.cif
@@ -0,0 +1,201 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+MSE MSE SELENOMETHIONINE peptide 20 9 .
+
+data_comp_MSE
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+MSE N N NT3 1 10.980 -7.344 20.020
+MSE CA C CH1 0 10.215 -8.538 19.563
+MSE C C C 0 8.775 -8.458 20.089
+MSE O O O 0 8.605 -7.967 21.223
+MSE OXT O OC -1 7.876 -8.895 19.344
+MSE CB C CH2 0 10.896 -9.824 20.043
+MSE CG C CH2 0 12.189 -10.151 19.325
+MSE SE SE SE 0 12.850 -11.935 19.808
+MSE CE C CH3 0 13.628 -11.498 21.557
+MSE H H H 0 11.808 -7.339 19.642
+MSE H2 H H 0 11.069 -7.358 20.927
+MSE H3 H H 0 10.544 -6.581 19.779
+MSE HA H H 0 10.192 -8.533 18.579
+MSE HB2 H H 0 10.295 -10.556 19.923
+MSE HB3 H H 0 11.082 -9.746 20.975
+MSE HG2 H H 0 12.870 -9.483 19.555
+MSE HG3 H H 0 12.044 -10.114 18.355
+MSE HE1 H H 0 14.013 -12.298 21.947
+MSE HE2 H H 0 12.935 -11.153 22.141
+MSE HE3 H H 0 14.320 -10.828 21.443
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+MSE N n/a CA START
+MSE H N . .
+MSE H2 N . .
+MSE H3 N . .
+MSE CA N C .
+MSE HA CA . .
+MSE CB CA CG .
+MSE HB2 CB . .
+MSE HB3 CB . .
+MSE CG CB SE .
+MSE HG2 CG . .
+MSE HG3 CG . .
+MSE SE CG CE .
+MSE CE SE HE1 .
+MSE HE3 CE . .
+MSE HE2 CE . .
+MSE HE1 CE . .
+MSE C CA . END
+MSE O C . .
+MSE OXT C . .
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+MSE N CA SINGLE n 1.488 0.0100 1.488 0.0100
+MSE CA C SINGLE n 1.533 0.0100 1.533 0.0100
+MSE CA CB SINGLE n 1.532 0.0100 1.532 0.0100
+MSE C O DOUBLE n 1.247 0.0187 1.247 0.0187
+MSE C OXT SINGLE n 1.247 0.0187 1.247 0.0187
+MSE CB CG SINGLE n 1.514 0.0200 1.514 0.0200
+MSE CG SE SINGLE n 1.963 0.0200 1.963 0.0200
+MSE SE CE SINGLE n 1.963 0.0200 1.963 0.0200
+MSE N H SINGLE n 1.036 0.0160 0.911 0.0200
+MSE N H2 SINGLE n 1.036 0.0160 0.911 0.0200
+MSE N H3 SINGLE n 1.036 0.0160 0.911 0.0200
+MSE CA HA SINGLE n 1.089 0.0100 0.985 0.0200
+MSE CB HB2 SINGLE n 1.089 0.0100 0.954 0.0200
+MSE CB HB3 SINGLE n 1.089 0.0100 0.954 0.0200
+MSE CG HG2 SINGLE n 1.089 0.0100 0.981 0.0167
+MSE CG HG3 SINGLE n 1.089 0.0100 0.981 0.0167
+MSE CE HE1 SINGLE n 1.089 0.0100 0.970 0.0162
+MSE CE HE2 SINGLE n 1.089 0.0100 0.970 0.0162
+MSE CE HE3 SINGLE n 1.089 0.0100 0.970 0.0162
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+MSE CA N H 110.062 1.93
+MSE CA N H2 110.062 1.93
+MSE CA N H3 110.062 1.93
+MSE H N H2 109.028 2.41
+MSE H N H3 109.028 2.41
+MSE H2 N H3 109.028 2.41
+MSE N CA C 109.241 1.50
+MSE N CA CB 110.245 1.51
+MSE N CA HA 108.487 1.50
+MSE C CA CB 110.728 2.07
+MSE C CA HA 108.824 1.50
+MSE CB CA HA 109.207 1.50
+MSE CA C O 117.124 1.50
+MSE CA C OXT 117.124 1.50
+MSE O C OXT 125.752 1.50
+MSE CA CB CG 113.897 1.50
+MSE CA CB HB2 108.567 1.50
+MSE CA CB HB3 108.567 1.50
+MSE CG CB HB2 108.056 1.50
+MSE CG CB HB3 108.056 1.50
+MSE HB2 CB HB3 107.715 1.50
+MSE CB CG SE 111.593 3.00
+MSE CB CG HG2 109.535 1.63
+MSE CB CG HG3 109.535 1.63
+MSE SE CG HG2 109.134 1.50
+MSE SE CG HG3 109.134 1.50
+MSE HG2 CG HG3 108.011 1.50
+MSE CG SE CE 98.689 1.50
+MSE SE CE HE1 109.134 1.50
+MSE SE CE HE2 109.134 1.50
+MSE SE CE HE3 109.134 1.50
+MSE HE1 CE HE2 109.290 1.50
+MSE HE1 CE HE3 109.290 1.50
+MSE HE2 CE HE3 109.290 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+MSE sp3_sp3_1 C CA N H 180.000 10.0 3
+MSE sp2_sp3_1 O C CA N 0.000 10.0 6
+MSE sp3_sp3_10 N CA CB CG 180.000 10.0 3
+MSE sp3_sp3_19 CA CB CG SE 180.000 10.0 3
+MSE sp3_sp3_28 CB CG SE CE 180.000 10.0 3
+MSE sp3_sp3_31 HE1 CE SE CG 180.000 10.0 3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+MSE chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+MSE plan-1 C 0.020
+MSE plan-1 CA 0.020
+MSE plan-1 O 0.020
+MSE plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+MSE SMILES ACDLabs 10.04 O=C(O)C(N)CC[Se]C
+MSE SMILES_CANONICAL CACTVS 3.341 C[Se]CC[C@H](N)C(O)=O
+MSE SMILES CACTVS 3.341 C[Se]CC[CH](N)C(O)=O
+MSE SMILES_CANONICAL ""OpenEye OEToolkits" 1.5.0 C[Se]CC[C@@H](C(=O)O)N
+MSE SMILES ""OpenEye OEToolkits" 1.5.0 C[Se]CCC(C(=O)O)N
+MSE InChI InChI 1.03 InChI=1S/C5H11NO2Se/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m0/s1
+MSE InChIKey InChI 1.03 RJFAYQIBOAGBLC-BYPYZUCNSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+MSE acedrg 243 ""dictionary generator"
+MSE acedrg_database 11 ""data source"
+MSE rdkit 2017.03.2 ""Chemoinformatics tool"
+MSE refmac5 5.8.0238 ""optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/NA.cif b/image_analysis/structure_refinement/monomers/NA.cif
new file mode 100644
index 000000000..e9d8ecd98
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/NA.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+NA NA 'SODIUM ION                          ' NON-POLYMER 1 1 .
+
+data_comp_NA
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+NA NA NA NA 1.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+NA NA n/a . END
diff --git a/image_analysis/structure_refinement/monomers/NAD.cif b/image_analysis/structure_refinement/monomers/NAD.cif
new file mode 100644
index 000000000..e61090f17
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/NAD.cif
@@ -0,0 +1,447 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+NAD     NAD      NICOTINAMIDE-ADENINE-DINUCLEOTIDE     NON-POLYMER     70     44     .     
+#
+data_comp_NAD
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+NAD     PA      P       P       0       18.626      51.830      -19.907     
+NAD     O1A     O       O       0       18.239      51.977      -21.341     
+NAD     O2A     O       OP      -1      17.725      52.411      -18.868     
+NAD     O5B     O       O2      0       20.113      52.394      -19.696     
+NAD     C5B     C       CH2     0       21.139      52.018      -20.649     
+NAD     C4B     C       CH1     0       22.468      52.578      -20.205     
+NAD     O4B     O       O2      0       23.527      51.931      -20.956     
+NAD     C3B     C       CH1     0       22.679      54.079      -20.440     
+NAD     O3B     O       OH1     0       23.576      54.623      -19.479     
+NAD     C2B     C       CH1     0       23.256      54.094      -21.858     
+NAD     O2B     O       OH1     0       24.009      55.255      -22.137     
+NAD     C1B     C       CH1     0       24.142      52.850      -21.831     
+NAD     N9A     N       NR5     0       24.299      52.206      -23.131     
+NAD     C8A     C       CR15    0       23.301      51.647      -23.891     
+NAD     N7A     N       NRD5    0       23.726      51.133      -25.017     
+NAD     C5A     C       CR56    0       25.095      51.358      -25.002     
+NAD     C6A     C       CR6     0       26.120      51.044      -25.921     
+NAD     N6A     N       NH2     0       25.907      50.413      -27.073     
+NAD     N1A     N       NRD6    0       27.387      51.412      -25.601     
+NAD     C2A     C       CR16    0       27.594      52.049      -24.438     
+NAD     N3A     N       NRD6    0       26.710      52.394      -23.501     
+NAD     C4A     C       CR56    0       25.462      52.019      -23.841     
+NAD     O3      O       O2      0       18.840      50.272      -19.588     
+NAD     PN      P       P       0       18.864      49.438      -18.218     
+NAD     O1N     O       O       0       17.461      49.265      -17.740     
+NAD     O2N     O       OP      -1      19.853      50.066      -17.293     
+NAD     O5D     O       O2      0       19.431      48.023      -18.723     
+NAD     C5D     C       CH2     0       20.701      47.984      -19.424     
+NAD     C4D     C       CH1     0       21.194      46.559      -19.494     
+NAD     O4D     O       O2      0       21.428      46.064      -18.157     
+NAD     C3D     C       CH1     0       20.242      45.551      -20.164     
+NAD     O3D     O       OH1     0       20.944      44.677      -21.042     
+NAD     C2D     C       CH1     0       19.601      44.823      -18.973     
+NAD     O2D     O       OH1     0       19.219      43.486      -19.258     
+NAD     C1D     C       CH1     0       20.764      44.819      -17.978     
+NAD     N1N     N       NR6     1       20.354      44.692      -16.557     
+NAD     C2N     C       CR16    0       19.658      45.714      -15.942     
+NAD     C3N     C       CR6     0       19.271      45.586      -14.608     
+NAD     C7N     C       C       0       18.519      46.700      -13.946     
+NAD     O7N     O       O       0       18.970      47.210      -12.908     
+NAD     N7N     N       NH2     0       17.384      47.110      -14.499     
+NAD     C4N     C       CR16    0       19.587      44.433      -13.901     
+NAD     C5N     C       CR16    0       20.283      43.414      -14.527     
+NAD     C6N     C       CR16    0       20.661      43.549      -15.851     
+NAD     H51A    H       H       0       20.912      52.372      -21.544     
+NAD     H52A    H       H       0       21.197      51.032      -20.708     
+NAD     H4B     H       H       0       22.584      52.377      -19.252     
+NAD     H3B     H       H       0       21.811      54.559      -20.413     
+NAD     HO3A    H       H       0       23.564      55.469      -19.544     
+NAD     H2B     H       H       0       22.529      53.992      -22.526     
+NAD     HO2A    H       H       0       24.306      55.209      -22.931     
+NAD     H1B     H       H       0       25.026      53.099      -21.478     
+NAD     H8A     H       H       0       22.396      51.641      -23.629     
+NAD     H61A    H       H       0       26.528      49.888      -27.403     
+NAD     H62A    H       H       0       25.147      50.524      -27.495     
+NAD     H2A     H       H       0       28.491      52.285      -24.258     
+NAD     H51N    H       H       0       21.366      48.541      -18.948     
+NAD     H52N    H       H       0       20.590      48.342      -20.339     
+NAD     H4D     H       H       0       22.048      46.560      -19.977     
+NAD     H3D     H       H       0       19.542      46.042      -20.668     
+NAD     HO3N    H       H       0       21.584      44.301      -20.630     
+NAD     H2D     H       H       0       18.837      45.341      -18.621     
+NAD     HO2N    H       H       0       18.872      43.138      -18.566     
+NAD     H1D     H       H       0       21.389      44.085      -18.205     
+NAD     H2N     H       H       0       19.441      46.498      -16.419     
+NAD     H71N    H       H       0       16.923      47.775      -14.126     
+NAD     H72N    H       H       0       17.069      46.727      -15.240     
+NAD     H4N     H       H       0       19.329      44.343      -13.000     
+NAD     H5N     H       H       0       20.502      42.627      -14.056     
+NAD     H6N     H       H       0       21.135      42.856      -16.280     
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+NAD          PA         O1A      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NAD          PA         O2A      SINGLE       n     1.493  0.0122     1.493  0.0122
+NAD          PA         O5B      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAD          PA          O3      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAD         O5B         C5B      SINGLE       n     1.450  0.0166     1.450  0.0166
+NAD         C5B         C4B      SINGLE       n     1.509  0.0100     1.509  0.0100
+NAD         C4B         O4B      SINGLE       n     1.451  0.0100     1.451  0.0100
+NAD         C4B         C3B      SINGLE       n     1.535  0.0100     1.535  0.0100
+NAD         O4B         C1B      SINGLE       n     1.409  0.0100     1.409  0.0100
+NAD         C3B         O3B      SINGLE       n     1.422  0.0100     1.422  0.0100
+NAD         C3B         C2B      SINGLE       n     1.531  0.0100     1.531  0.0100
+NAD         C2B         O2B      SINGLE       n     1.411  0.0100     1.411  0.0100
+NAD         C2B         C1B      SINGLE       n     1.525  0.0100     1.525  0.0100
+NAD         C1B         N9A      SINGLE       n     1.458  0.0100     1.458  0.0100
+NAD         N9A         C8A      SINGLE       y     1.372  0.0100     1.372  0.0100
+NAD         N9A         C4A      SINGLE       y     1.374  0.0101     1.374  0.0101
+NAD         C8A         N7A      DOUBLE       y     1.310  0.0100     1.310  0.0100
+NAD         N7A         C5A      SINGLE       y     1.388  0.0100     1.388  0.0100
+NAD         C5A         C6A      SINGLE       y     1.408  0.0100     1.408  0.0100
+NAD         C5A         C4A      DOUBLE       y     1.381  0.0100     1.381  0.0100
+NAD         C6A         N6A      SINGLE       n     1.330  0.0100     1.330  0.0100
+NAD         C6A         N1A      DOUBLE       y     1.354  0.0100     1.354  0.0100
+NAD         N1A         C2A      SINGLE       y     1.339  0.0100     1.339  0.0100
+NAD         C2A         N3A      DOUBLE       y     1.330  0.0100     1.330  0.0100
+NAD         N3A         C4A      SINGLE       y     1.343  0.0100     1.343  0.0100
+NAD          O3          PN      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAD          PN         O1N      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NAD          PN         O2N      SINGLE       n     1.493  0.0122     1.493  0.0122
+NAD          PN         O5D      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAD         O5D         C5D      SINGLE       n     1.450  0.0166     1.450  0.0166
+NAD         C5D         C4D      SINGLE       n     1.509  0.0100     1.509  0.0100
+NAD         C4D         O4D      SINGLE       n     1.443  0.0107     1.443  0.0107
+NAD         C4D         C3D      SINGLE       n     1.535  0.0100     1.535  0.0100
+NAD         O4D         C1D      SINGLE       n     1.425  0.0141     1.425  0.0141
+NAD         C3D         O3D      SINGLE       n     1.422  0.0100     1.422  0.0100
+NAD         C3D         C2D      SINGLE       n     1.533  0.0100     1.533  0.0100
+NAD         C2D         O2D      SINGLE       n     1.419  0.0101     1.419  0.0101
+NAD         C2D         C1D      SINGLE       n     1.533  0.0100     1.533  0.0100
+NAD         C1D         N1N      SINGLE       n     1.477  0.0138     1.477  0.0138
+NAD         N1N         C2N      DOUBLE       y     1.377  0.0105     1.377  0.0105
+NAD         N1N         C6N      SINGLE       y     1.375  0.0105     1.375  0.0105
+NAD         C2N         C3N      SINGLE       y     1.390  0.0105     1.390  0.0105
+NAD         C3N         C7N      SINGLE       n     1.497  0.0100     1.497  0.0100
+NAD         C3N         C4N      DOUBLE       y     1.385  0.0100     1.385  0.0100
+NAD         C7N         O7N      DOUBLE       n     1.241  0.0105     1.241  0.0105
+NAD         C7N         N7N      SINGLE       n     1.326  0.0100     1.326  0.0100
+NAD         C4N         C5N      SINGLE       y     1.380  0.0100     1.380  0.0100
+NAD         C5N         C6N      DOUBLE       y     1.380  0.0128     1.380  0.0128
+NAD         C5B        H51A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAD         C5B        H52A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAD         C4B         H4B      SINGLE       n     1.089  0.0100     0.981  0.0200
+NAD         C3B         H3B      SINGLE       n     1.089  0.0100     0.992  0.0200
+NAD         O3B        HO3A      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAD         C2B         H2B      SINGLE       n     1.089  0.0100     0.994  0.0200
+NAD         O2B        HO2A      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAD         C1B         H1B      SINGLE       n     1.089  0.0100     0.984  0.0200
+NAD         C8A         H8A      SINGLE       n     1.082  0.0130     0.942  0.0170
+NAD         N6A        H61A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NAD         N6A        H62A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NAD         C2A         H2A      SINGLE       n     1.082  0.0130     0.945  0.0200
+NAD         C5D        H51N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAD         C5D        H52N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAD         C4D         H4D      SINGLE       n     1.089  0.0100     0.981  0.0200
+NAD         C3D         H3D      SINGLE       n     1.089  0.0100     0.992  0.0200
+NAD         O3D        HO3N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAD         C2D         H2D      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAD         O2D        HO2N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAD         C1D         H1D      SINGLE       n     1.089  0.0100     0.990  0.0173
+NAD         C2N         H2N      SINGLE       n     1.082  0.0130     0.943  0.0170
+NAD         N7N        H71N      SINGLE       n     1.016  0.0100     0.891  0.0200
+NAD         N7N        H72N      SINGLE       n     1.016  0.0100     0.891  0.0200
+NAD         C4N         H4N      SINGLE       n     1.082  0.0130     0.941  0.0168
+NAD         C5N         H5N      SINGLE       n     1.082  0.0130     0.943  0.0190
+NAD         C6N         H6N      SINGLE       n     1.082  0.0130     0.943  0.0169
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+NAD         O1A          PA         O2A     118.411    2.35
+NAD         O1A          PA         O5B     109.410    1.50
+NAD         O1A          PA          O3     108.816    2.14
+NAD         O2A          PA         O5B     109.410    1.50
+NAD         O2A          PA          O3     108.816    2.14
+NAD         O5B          PA          O3     101.065    1.97
+NAD          PA         O5B         C5B     118.553    2.41
+NAD         O5B         C5B         C4B     109.342    1.50
+NAD         O5B         C5B        H51A     109.845    1.50
+NAD         O5B         C5B        H52A     109.845    1.50
+NAD         C4B         C5B        H51A     109.624    1.50
+NAD         C4B         C5B        H52A     109.624    1.50
+NAD        H51A         C5B        H52A     108.472    1.50
+NAD         C5B         C4B         O4B     109.123    1.50
+NAD         C5B         C4B         C3B     116.008    1.52
+NAD         C5B         C4B         H4B     108.268    1.50
+NAD         O4B         C4B         C3B     105.388    1.50
+NAD         O4B         C4B         H4B     108.947    1.50
+NAD         C3B         C4B         H4B     109.363    1.86
+NAD         C4B         O4B         C1B     109.903    1.50
+NAD         C4B         C3B         O3B     111.281    2.46
+NAD         C4B         C3B         C2B     102.602    1.50
+NAD         C4B         C3B         H3B     110.452    2.54
+NAD         O3B         C3B         C2B     111.581    2.83
+NAD         O3B         C3B         H3B     110.380    1.67
+NAD         C2B         C3B         H3B     110.504    1.75
+NAD         C3B         O3B        HO3A     108.744    3.00
+NAD         C3B         C2B         O2B     112.782    2.45
+NAD         C3B         C2B         C1B     101.239    1.50
+NAD         C3B         C2B         H2B     110.596    1.51
+NAD         O2B         C2B         C1B     111.715    2.69
+NAD         O2B         C2B         H2B     110.448    1.97
+NAD         C1B         C2B         H2B     110.636    1.70
+NAD         C2B         O2B        HO2A     109.103    2.13
+NAD         O4B         C1B         C2B     106.047    1.50
+NAD         O4B         C1B         N9A     108.477    1.50
+NAD         O4B         C1B         H1B     109.807    1.50
+NAD         C2B         C1B         N9A     113.824    1.50
+NAD         C2B         C1B         H1B     109.015    1.50
+NAD         N9A         C1B         H1B     109.561    1.50
+NAD         C1B         N9A         C8A     126.848    1.91
+NAD         C1B         N9A         C4A     127.459    1.80
+NAD         C8A         N9A         C4A     105.693    1.50
+NAD         N9A         C8A         N7A     113.469    1.50
+NAD         N9A         C8A         H8A     123.206    1.50
+NAD         N7A         C8A         H8A     123.326    1.50
+NAD         C8A         N7A         C5A     104.739    1.50
+NAD         N7A         C5A         C6A     132.250    1.50
+NAD         N7A         C5A         C4A     110.483    1.50
+NAD         C6A         C5A         C4A     117.267    1.50
+NAD         C5A         C6A         N6A     123.792    1.50
+NAD         C5A         C6A         N1A     117.409    1.50
+NAD         N6A         C6A         N1A     118.799    1.50
+NAD         C6A         N6A        H61A     119.723    1.50
+NAD         C6A         N6A        H62A     119.723    1.50
+NAD        H61A         N6A        H62A     120.554    1.88
+NAD         C6A         N1A         C2A     118.521    1.50
+NAD         N1A         C2A         N3A     129.332    1.50
+NAD         N1A         C2A         H2A     115.313    1.50
+NAD         N3A         C2A         H2A     115.355    1.50
+NAD         C2A         N3A         C4A     110.982    1.50
+NAD         N9A         C4A         C5A     105.616    1.50
+NAD         N9A         C4A         N3A     127.895    1.50
+NAD         C5A         C4A         N3A     126.489    1.50
+NAD          PA          O3          PN     132.542    3.00
+NAD          O3          PN         O1N     108.816    2.14
+NAD          O3          PN         O2N     108.816    2.14
+NAD          O3          PN         O5D     101.065    1.97
+NAD         O1N          PN         O2N     118.411    2.35
+NAD         O1N          PN         O5D     109.410    1.50
+NAD         O2N          PN         O5D     109.410    1.50
+NAD          PN         O5D         C5D     118.553    2.41
+NAD         O5D         C5D         C4D     109.342    1.50
+NAD         O5D         C5D        H51N     109.845    1.50
+NAD         O5D         C5D        H52N     109.845    1.50
+NAD         C4D         C5D        H51N     109.624    1.50
+NAD         C4D         C5D        H52N     109.624    1.50
+NAD        H51N         C5D        H52N     108.472    1.50
+NAD         C5D         C4D         O4D     109.615    1.50
+NAD         C5D         C4D         C3D     116.008    1.52
+NAD         C5D         C4D         H4D     108.268    1.50
+NAD         O4D         C4D         C3D     104.439    1.50
+NAD         O4D         C4D         H4D     108.698    1.50
+NAD         C3D         C4D         H4D     109.363    1.86
+NAD         C4D         O4D         C1D     109.578    1.50
+NAD         C4D         C3D         O3D     111.281    2.46
+NAD         C4D         C3D         C2D     102.071    1.50
+NAD         C4D         C3D         H3D     110.452    2.54
+NAD         O3D         C3D         C2D     111.993    3.00
+NAD         O3D         C3D         H3D     110.380    1.67
+NAD         C2D         C3D         H3D     110.108    1.66
+NAD         C3D         O3D        HO3N     108.744    3.00
+NAD         C3D         C2D         O2D     112.861    2.52
+NAD         C3D         C2D         C1D     101.269    1.50
+NAD         C3D         C2D         H2D     110.799    1.82
+NAD         O2D         C2D         C1D     109.476    3.00
+NAD         O2D         C2D         H2D     111.022    1.77
+NAD         C1D         C2D         H2D     110.760    1.63
+NAD         C2D         O2D        HO2N     109.449    1.85
+NAD         O4D         C1D         C2D     106.825    1.50
+NAD         O4D         C1D         N1N     108.092    1.50
+NAD         O4D         C1D         H1D     109.327    1.50
+NAD         C2D         C1D         N1N     113.620    1.99
+NAD         C2D         C1D         H1D     109.776    1.83
+NAD         N1N         C1D         H1D     108.901    1.50
+NAD         C1D         N1N         C2N     119.705    1.50
+NAD         C1D         N1N         C6N     119.705    1.50
+NAD         C2N         N1N         C6N     120.590    1.50
+NAD         N1N         C2N         C3N     119.549    3.00
+NAD         N1N         C2N         H2N     120.430    1.53
+NAD         C3N         C2N         H2N     120.021    1.50
+NAD         C2N         C3N         C7N     119.660    2.75
+NAD         C2N         C3N         C4N     119.402    1.64
+NAD         C7N         C3N         C4N     120.938    2.50
+NAD         C3N         C7N         O7N     119.730    1.50
+NAD         C3N         C7N         N7N     118.032    1.50
+NAD         O7N         C7N         N7N     122.238    1.50
+NAD         C7N         N7N        H71N     120.236    2.75
+NAD         C7N         N7N        H72N     120.236    2.75
+NAD        H71N         N7N        H72N     119.529    2.83
+NAD         C3N         C4N         C5N     119.166    1.50
+NAD         C3N         C4N         H4N     120.513    1.50
+NAD         C5N         C4N         H4N     120.320    1.50
+NAD         C4N         C5N         C6N     120.016    1.50
+NAD         C4N         C5N         H5N     120.300    1.50
+NAD         C6N         C5N         H5N     119.683    1.50
+NAD         N1N         C6N         C5N     121.277    1.50
+NAD         N1N         C6N         H6N     118.693    1.53
+NAD         C5N         C6N         H6N     120.031    1.59
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+NAD            sp3_sp3_54          PN          O3          PA         O1A      60.000    10.0     3
+NAD            sp3_sp3_51         C5B         O5B          PA         O1A      60.000    10.0     3
+NAD             sp2_sp3_1         C8A         N9A         C1B         O4B     150.000    10.0     6
+NAD              const_34         N7A         C8A         N9A         C1B     180.000    10.0     2
+NAD              const_46         C5A         C4A         N9A         C1B     180.000    10.0     2
+NAD              const_37         N9A         C8A         N7A         C5A       0.000    10.0     2
+NAD              const_40         C6A         C5A         N7A         C8A     180.000    10.0     2
+NAD       const_sp2_sp2_4         N7A         C5A         C6A         N6A       0.000     5.0     2
+NAD              const_41         N9A         C4A         C5A         N7A       0.000    10.0     2
+NAD             sp2_sp2_1         C5A         C6A         N6A        H61A     180.000     5.0     2
+NAD       const_sp2_sp2_6         N6A         C6A         N1A         C2A     180.000     5.0     2
+NAD       const_sp2_sp2_7         N3A         C2A         N1A         C6A       0.000     5.0     2
+NAD       const_sp2_sp2_9         N1A         C2A         N3A         C4A       0.000     5.0     2
+NAD              const_12         N9A         C4A         N3A         C2A     180.000    10.0     2
+NAD            sp3_sp3_84          PA          O3          PN         O1N      60.000    10.0     3
+NAD            sp3_sp3_85         C5D         O5D          PN          O3     180.000    10.0     3
+NAD            sp3_sp3_88         C4D         C5D         O5D          PN     180.000    10.0     3
+NAD            sp3_sp3_91         O4D         C4D         C5D         O5D     180.000    10.0     3
+NAD            sp3_sp3_26         C5D         C4D         O4D         C1D     -60.000    10.0     3
+NAD           sp3_sp3_104         O3D         C3D         C4D         C5D     180.000    10.0     3
+NAD            sp3_sp3_28         C2D         C1D         O4D         C4D     -60.000    10.0     3
+NAD           sp3_sp3_109         C4D         C3D         O3D        HO3N     180.000    10.0     3
+NAD            sp3_sp3_44         O2D         C2D         C3D         O3D     -60.000    10.0     3
+NAD           sp3_sp3_112         C3D         C2D         O2D        HO2N     180.000    10.0     3
+NAD            sp3_sp3_32         O4D         C1D         C2D         O2D     180.000    10.0     3
+NAD             sp2_sp3_7         C2N         N1N         C1D         O4D     150.000    10.0     6
+NAD              const_14         C3N         C2N         N1N         C1D     180.000    10.0     2
+NAD              const_50         C5N         C6N         N1N         C1D     180.000    10.0     2
+NAD              const_18         N1N         C2N         C3N         C7N     180.000    10.0     2
+NAD             sp2_sp2_6         C2N         C3N         C7N         O7N       0.000     5.0     2
+NAD              const_23         C7N         C3N         C4N         C5N     180.000    10.0     2
+NAD            sp2_sp2_11         O7N         C7N         N7N        H71N       0.000     5.0     2
+NAD            sp3_sp3_55         C4B         C5B         O5B          PA     180.000    10.0     3
+NAD              const_25         C3N         C4N         C5N         C6N       0.000    10.0     2
+NAD              const_29         C4N         C5N         C6N         N1N       0.000    10.0     2
+NAD            sp3_sp3_58         O4B         C4B         C5B         O5B     180.000    10.0     3
+NAD             sp3_sp3_2         C5B         C4B         O4B         C1B     -60.000    10.0     3
+NAD            sp3_sp3_71         O3B         C3B         C4B         C5B     180.000    10.0     3
+NAD             sp3_sp3_4         C2B         C1B         O4B         C4B     -60.000    10.0     3
+NAD            sp3_sp3_76         C4B         C3B         O3B        HO3A     180.000    10.0     3
+NAD            sp3_sp3_20         O2B         C2B         C3B         O3B     -60.000    10.0     3
+NAD            sp3_sp3_79         C3B         C2B         O2B        HO2A     180.000    10.0     3
+NAD             sp3_sp3_8         O4B         C1B         C2B         O2B     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+NAD    chir_1    PA    O3    O5B    O2A    both
+NAD    chir_2    C4B    O4B    C3B    C5B    negative
+NAD    chir_3    C3B    O3B    C4B    C2B    positive
+NAD    chir_4    C2B    O2B    C1B    C3B    negative
+NAD    chir_5    C1B    O4B    N9A    C2B    negative
+NAD    chir_6    PN    O3    O5D    O2N    both
+NAD    chir_7    C4D    O4D    C3D    C5D    negative
+NAD    chir_8    C3D    O3D    C4D    C2D    positive
+NAD    chir_9    C2D    O2D    C1D    C3D    negative
+NAD    chir_10    C1D    O4D    N1N    C2D    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+NAD    plan-1         C1B   0.020
+NAD    plan-1         C2A   0.020
+NAD    plan-1         C4A   0.020
+NAD    plan-1         C5A   0.020
+NAD    plan-1         C6A   0.020
+NAD    plan-1         C8A   0.020
+NAD    plan-1         H2A   0.020
+NAD    plan-1         H8A   0.020
+NAD    plan-1         N1A   0.020
+NAD    plan-1         N3A   0.020
+NAD    plan-1         N6A   0.020
+NAD    plan-1         N7A   0.020
+NAD    plan-1         N9A   0.020
+NAD    plan-2         C1D   0.020
+NAD    plan-2         C2N   0.020
+NAD    plan-2         C3N   0.020
+NAD    plan-2         C4N   0.020
+NAD    plan-2         C5N   0.020
+NAD    plan-2         C6N   0.020
+NAD    plan-2         C7N   0.020
+NAD    plan-2         H2N   0.020
+NAD    plan-2         H4N   0.020
+NAD    plan-2         H5N   0.020
+NAD    plan-2         H6N   0.020
+NAD    plan-2         N1N   0.020
+NAD    plan-3         C6A   0.020
+NAD    plan-3        H61A   0.020
+NAD    plan-3        H62A   0.020
+NAD    plan-3         N6A   0.020
+NAD    plan-4         C3N   0.020
+NAD    plan-4         C7N   0.020
+NAD    plan-4         N7N   0.020
+NAD    plan-4         O7N   0.020
+NAD    plan-5         C7N   0.020
+NAD    plan-5        H71N   0.020
+NAD    plan-5        H72N   0.020
+NAD    plan-5         N7N   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+NAD SMILES_CANONICAL               CACTVS 3.341                                                                                                                                                     NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
+NAD           SMILES               CACTVS 3.341                                                                                                                                                                 NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
+NAD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                                                                             c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
+NAD           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                                                                                         c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
+NAD            InChI                InChI  1.03 InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
+NAD         InChIKey                InChI  1.03                                                                                                                                                                                                                                                       BAWFJGJZGIEFAR-NNYOXOHSSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+NAD acedrg               243         "dictionary generator"                  
+NAD acedrg_database      11          "data source"                           
+NAD rdkit                2017.03.2   "Chemoinformatics tool"
+NAD refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/NAI.cif b/image_analysis/structure_refinement/monomers/NAI.cif
new file mode 100644
index 000000000..5fea12fc9
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/NAI.cif
@@ -0,0 +1,460 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+NAI     NAI      "1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE"     NON-POLYMER     71     44     .     
+#
+data_comp_NAI
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+NAI     PA      P       P       0       32.123      21.120      42.561      
+NAI     O1A     O       O       0       30.870      21.929      42.623      
+NAI     O2A     O       OP      -1      32.361      20.105      43.629      
+NAI     O5B     O       O2      0       33.388      22.102      42.470      
+NAI     C5B     C       CH2     0       33.354      23.194      41.515      
+NAI     C4B     C       CH1     0       34.654      23.958      41.578      
+NAI     O4B     O       O2      0       34.715      24.875      40.456      
+NAI     C3B     C       CH1     0       34.861      24.837      42.817      
+NAI     O3B     O       OH1     0       36.244      24.979      43.116      
+NAI     C2B     C       CH1     0       34.216      26.154      42.376      
+NAI     O2B     O       OH1     0       34.702      27.273      43.085      
+NAI     C1B     C       CH1     0       34.624      26.209      40.905      
+NAI     N9A     N       NR5     0       33.672      26.910      40.050      
+NAI     C8A     C       CR15    0       32.354      26.580      39.853      
+NAI     N7A     N       NRD5    0       31.731      27.382      39.026      
+NAI     C5A     C       CR56    0       32.699      28.299      38.644      
+NAI     C6A     C       CR6     0       32.662      29.411      37.773      
+NAI     N6A     N       NH2     0       31.572      29.792      37.111      
+NAI     N1A     N       NRD6    0       33.809      30.121      37.612      
+NAI     C2A     C       CR16    0       34.903      29.730      38.283      
+NAI     N3A     N       NRD6    0       35.053      28.706      39.124      
+NAI     C4A     C       CR56    0       33.903      28.018      39.267      
+NAI     O3      O       O2      0       32.194      20.391      41.133      
+NAI     PN      P       P       0       33.045      19.141      40.598      
+NAI     O1N     O       OP      -1      32.494      17.894      41.207      
+NAI     O2N     O       O       0       34.496      19.434      40.787      
+NAI     O5D     O       O2      0       32.695      19.167      39.032      
+NAI     C5D     C       CH2     0       32.931      20.381      38.272      
+NAI     C4D     C       CH1     0       32.960      20.056      36.798      
+NAI     O4D     O       O2      0       34.097      19.197      36.527      
+NAI     C3D     C       CH1     0       31.723      19.330      36.245      
+NAI     O3D     O       OH1     0       31.277      19.932      35.035      
+NAI     C2D     C       CH1     0       32.229      17.899      36.048      
+NAI     O2D     O       OH1     0       31.575      17.210      34.992      
+NAI     C1D     C       CH1     0       33.704      18.112      35.723      
+NAI     N1N     N       NR6     0       34.553      16.920      36.041      
+NAI     C2N     C       CR16    0       34.762      16.547      37.347      
+NAI     C3N     C       CR6     0       35.558      15.478      37.694      
+NAI     C7N     C       C       0       35.808      15.235      39.136      
+NAI     O7N     O       O       0       36.965      15.266      39.567      
+NAI     N7N     N       NH2     0       34.772      14.990      39.928      
+NAI     C4N     C       CH2     0       36.124      14.625      36.604      
+NAI     C5N     C       CR16    0       35.864      15.118      35.233      
+NAI     C6N     C       CR16    0       35.119      16.184      35.007      
+NAI     H51A    H       H       0       32.603      23.801      41.726      
+NAI     H52A    H       H       0       33.223      22.838      40.602      
+NAI     H4B     H       H       0       35.393      23.316      41.506      
+NAI     H3B     H       H       0       34.377      24.457      43.595      
+NAI     HO3A    H       H       0       36.323      25.360      43.870      
+NAI     H2B     H       H       0       33.229      26.100      42.466      
+NAI     HO2A    H       H       0       34.323      27.974      42.792      
+NAI     H1B     H       H       0       35.506      26.639      40.838      
+NAI     H8A     H       H       0       31.936      25.850      40.278      
+NAI     H61A    H       H       0       31.623      30.443      36.523      
+NAI     H62A    H       H       0       30.806      29.392      37.264      
+NAI     H2A     H       H       0       35.676      30.255      38.140      
+NAI     H51N    H       H       0       33.794      20.784      38.539      
+NAI     H52N    H       H       0       32.211      21.035      38.453      
+NAI     H4D     H       H       0       33.085      20.897      36.307      
+NAI     H3D     H       H       0       30.994      19.339      36.918      
+NAI     HO3N    H       H       0       30.631      19.477      34.725      
+NAI     H2D     H       H       0       32.129      17.394      36.890      
+NAI     HO2N    H       H       0       31.893      16.425      34.933      
+NAI     H1D     H       H       0       33.809      18.353      34.773      
+NAI     H2N     H       H       0       34.340      17.035      38.031      
+NAI     H71N    H       H       0       34.898      14.848      40.795      
+NAI     H72N    H       H       0       33.947      14.963      39.600      
+NAI     H4N     H       H       0       35.759      13.720      36.687      
+NAI     H42N    H       H       0       37.093      14.548      36.731      
+NAI     H5N     H       H       0       36.247      14.649      34.492      
+NAI     H6N     H       H       0       34.963      16.456      34.120      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+NAI          PA         O1A      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NAI          PA         O2A      SINGLE       n     1.493  0.0122     1.493  0.0122
+NAI          PA         O5B      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAI          PA          O3      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAI         O5B         C5B      SINGLE       n     1.450  0.0166     1.450  0.0166
+NAI         C5B         C4B      SINGLE       n     1.509  0.0100     1.509  0.0100
+NAI         C4B         O4B      SINGLE       n     1.451  0.0100     1.451  0.0100
+NAI         C4B         C3B      SINGLE       n     1.535  0.0100     1.535  0.0100
+NAI         O4B         C1B      SINGLE       n     1.409  0.0100     1.409  0.0100
+NAI         C3B         O3B      SINGLE       n     1.422  0.0100     1.422  0.0100
+NAI         C3B         C2B      SINGLE       n     1.531  0.0100     1.531  0.0100
+NAI         C2B         O2B      SINGLE       n     1.411  0.0100     1.411  0.0100
+NAI         C2B         C1B      SINGLE       n     1.525  0.0100     1.525  0.0100
+NAI         C1B         N9A      SINGLE       n     1.458  0.0100     1.458  0.0100
+NAI         N9A         C8A      SINGLE       y     1.372  0.0100     1.372  0.0100
+NAI         N9A         C4A      SINGLE       y     1.374  0.0101     1.374  0.0101
+NAI         C8A         N7A      DOUBLE       y     1.310  0.0100     1.310  0.0100
+NAI         N7A         C5A      SINGLE       y     1.388  0.0100     1.388  0.0100
+NAI         C5A         C6A      SINGLE       y     1.408  0.0100     1.408  0.0100
+NAI         C5A         C4A      DOUBLE       y     1.381  0.0100     1.381  0.0100
+NAI         C6A         N6A      SINGLE       n     1.330  0.0100     1.330  0.0100
+NAI         C6A         N1A      DOUBLE       y     1.354  0.0100     1.354  0.0100
+NAI         N1A         C2A      SINGLE       y     1.339  0.0100     1.339  0.0100
+NAI         C2A         N3A      DOUBLE       y     1.330  0.0100     1.330  0.0100
+NAI         N3A         C4A      SINGLE       y     1.343  0.0100     1.343  0.0100
+NAI          O3          PN      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAI          PN         O1N      SINGLE       n     1.493  0.0122     1.493  0.0122
+NAI          PN         O2N      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NAI          PN         O5D      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAI         O5D         C5D      SINGLE       n     1.450  0.0166     1.450  0.0166
+NAI         C5D         C4D      SINGLE       n     1.509  0.0100     1.509  0.0100
+NAI         C4D         O4D      SINGLE       n     1.449  0.0100     1.449  0.0100
+NAI         C4D         C3D      SINGLE       n     1.535  0.0100     1.535  0.0100
+NAI         O4D         C1D      SINGLE       n     1.407  0.0132     1.407  0.0132
+NAI         C3D         O3D      SINGLE       n     1.422  0.0100     1.422  0.0100
+NAI         C3D         C2D      SINGLE       n     1.530  0.0134     1.530  0.0134
+NAI         C2D         O2D      SINGLE       n     1.420  0.0122     1.420  0.0122
+NAI         C2D         C1D      SINGLE       n     1.527  0.0119     1.527  0.0119
+NAI         C1D         N1N      SINGLE       n     1.492  0.0124     1.492  0.0124
+NAI         N1N         C2N      SINGLE       n     1.367  0.0104     1.367  0.0104
+NAI         N1N         C6N      SINGLE       n     1.374  0.0156     1.374  0.0156
+NAI         C2N         C3N      DOUBLE       n     1.365  0.0175     1.365  0.0175
+NAI         C3N         C7N      SINGLE       n     1.480  0.0169     1.480  0.0169
+NAI         C3N         C4N      SINGLE       n     1.491  0.0200     1.491  0.0200
+NAI         C7N         O7N      DOUBLE       n     1.235  0.0110     1.235  0.0110
+NAI         C7N         N7N      SINGLE       n     1.325  0.0100     1.325  0.0100
+NAI         C4N         C5N      SINGLE       n     1.477  0.0200     1.477  0.0200
+NAI         C5N         C6N      DOUBLE       n     1.315  0.0139     1.315  0.0139
+NAI         C5B        H51A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAI         C5B        H52A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAI         C4B         H4B      SINGLE       n     1.089  0.0100     0.981  0.0200
+NAI         C3B         H3B      SINGLE       n     1.089  0.0100     0.992  0.0200
+NAI         O3B        HO3A      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAI         C2B         H2B      SINGLE       n     1.089  0.0100     0.994  0.0200
+NAI         O2B        HO2A      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAI         C1B         H1B      SINGLE       n     1.089  0.0100     0.984  0.0200
+NAI         C8A         H8A      SINGLE       n     1.082  0.0130     0.942  0.0170
+NAI         N6A        H61A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NAI         N6A        H62A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NAI         C2A         H2A      SINGLE       n     1.082  0.0130     0.945  0.0200
+NAI         C5D        H51N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAI         C5D        H52N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAI         C4D         H4D      SINGLE       n     1.089  0.0100     0.981  0.0200
+NAI         C3D         H3D      SINGLE       n     1.089  0.0100     0.992  0.0200
+NAI         O3D        HO3N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAI         C2D         H2D      SINGLE       n     1.089  0.0100     0.988  0.0200
+NAI         O2D        HO2N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAI         C1D         H1D      SINGLE       n     1.089  0.0100     0.986  0.0200
+NAI         C2N         H2N      SINGLE       n     1.082  0.0130     0.940  0.0112
+NAI         N7N        H71N      SINGLE       n     1.016  0.0100     0.887  0.0200
+NAI         N7N        H72N      SINGLE       n     1.016  0.0100     0.887  0.0200
+NAI         C4N         H4N      SINGLE       n     1.089  0.0100     0.980  0.0113
+NAI         C4N        H42N      SINGLE       n     1.089  0.0100     0.980  0.0113
+NAI         C5N         H5N      SINGLE       n     1.082  0.0130     0.957  0.0130
+NAI         C6N         H6N      SINGLE       n     1.082  0.0130     0.941  0.0198
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+NAI         O1A          PA         O2A     118.411    2.35
+NAI         O1A          PA         O5B     109.410    1.50
+NAI         O1A          PA          O3     108.816    2.14
+NAI         O2A          PA         O5B     109.410    1.50
+NAI         O2A          PA          O3     108.816    2.14
+NAI         O5B          PA          O3     101.065    1.97
+NAI          PA         O5B         C5B     118.553    2.41
+NAI         O5B         C5B         C4B     109.342    1.50
+NAI         O5B         C5B        H51A     109.845    1.50
+NAI         O5B         C5B        H52A     109.845    1.50
+NAI         C4B         C5B        H51A     109.624    1.50
+NAI         C4B         C5B        H52A     109.624    1.50
+NAI        H51A         C5B        H52A     108.472    1.50
+NAI         C5B         C4B         O4B     109.123    1.50
+NAI         C5B         C4B         C3B     116.008    1.52
+NAI         C5B         C4B         H4B     108.268    1.50
+NAI         O4B         C4B         C3B     105.388    1.50
+NAI         O4B         C4B         H4B     108.947    1.50
+NAI         C3B         C4B         H4B     109.363    1.86
+NAI         C4B         O4B         C1B     109.903    1.50
+NAI         C4B         C3B         O3B     111.281    2.46
+NAI         C4B         C3B         C2B     102.602    1.50
+NAI         C4B         C3B         H3B     110.452    2.54
+NAI         O3B         C3B         C2B     111.581    2.83
+NAI         O3B         C3B         H3B     110.380    1.67
+NAI         C2B         C3B         H3B     110.504    1.75
+NAI         C3B         O3B        HO3A     108.744    3.00
+NAI         C3B         C2B         O2B     112.782    2.45
+NAI         C3B         C2B         C1B     101.239    1.50
+NAI         C3B         C2B         H2B     110.596    1.51
+NAI         O2B         C2B         C1B     111.715    2.69
+NAI         O2B         C2B         H2B     110.448    1.97
+NAI         C1B         C2B         H2B     110.636    1.70
+NAI         C2B         O2B        HO2A     109.103    2.13
+NAI         O4B         C1B         C2B     106.047    1.50
+NAI         O4B         C1B         N9A     108.477    1.50
+NAI         O4B         C1B         H1B     109.807    1.50
+NAI         C2B         C1B         N9A     113.824    1.50
+NAI         C2B         C1B         H1B     109.015    1.50
+NAI         N9A         C1B         H1B     109.561    1.50
+NAI         C1B         N9A         C8A     126.848    1.91
+NAI         C1B         N9A         C4A     127.459    1.80
+NAI         C8A         N9A         C4A     105.693    1.50
+NAI         N9A         C8A         N7A     113.469    1.50
+NAI         N9A         C8A         H8A     123.206    1.50
+NAI         N7A         C8A         H8A     123.326    1.50
+NAI         C8A         N7A         C5A     104.739    1.50
+NAI         N7A         C5A         C6A     132.250    1.50
+NAI         N7A         C5A         C4A     110.483    1.50
+NAI         C6A         C5A         C4A     117.267    1.50
+NAI         C5A         C6A         N6A     123.792    1.50
+NAI         C5A         C6A         N1A     117.409    1.50
+NAI         N6A         C6A         N1A     118.799    1.50
+NAI         C6A         N6A        H61A     119.723    1.50
+NAI         C6A         N6A        H62A     119.723    1.50
+NAI        H61A         N6A        H62A     120.554    1.88
+NAI         C6A         N1A         C2A     118.521    1.50
+NAI         N1A         C2A         N3A     129.332    1.50
+NAI         N1A         C2A         H2A     115.313    1.50
+NAI         N3A         C2A         H2A     115.355    1.50
+NAI         C2A         N3A         C4A     110.982    1.50
+NAI         N9A         C4A         C5A     105.616    1.50
+NAI         N9A         C4A         N3A     127.895    1.50
+NAI         C5A         C4A         N3A     126.489    1.50
+NAI          PA          O3          PN     132.542    3.00
+NAI          O3          PN         O1N     108.816    2.14
+NAI          O3          PN         O2N     108.816    2.14
+NAI          O3          PN         O5D     101.065    1.97
+NAI         O1N          PN         O2N     118.411    2.35
+NAI         O1N          PN         O5D     109.410    1.50
+NAI         O2N          PN         O5D     109.410    1.50
+NAI          PN         O5D         C5D     118.553    2.41
+NAI         O5D         C5D         C4D     109.342    1.50
+NAI         O5D         C5D        H51N     109.845    1.50
+NAI         O5D         C5D        H52N     109.845    1.50
+NAI         C4D         C5D        H51N     109.624    1.50
+NAI         C4D         C5D        H52N     109.624    1.50
+NAI        H51N         C5D        H52N     108.472    1.50
+NAI         C5D         C4D         O4D     109.123    1.50
+NAI         C5D         C4D         C3D     116.008    1.52
+NAI         C5D         C4D         H4D     108.268    1.50
+NAI         O4D         C4D         C3D     105.508    1.50
+NAI         O4D         C4D         H4D     108.642    1.50
+NAI         C3D         C4D         H4D     109.363    1.86
+NAI         C4D         O4D         C1D     109.926    1.50
+NAI         C4D         C3D         O3D     111.281    2.46
+NAI         C4D         C3D         C2D     102.352    1.50
+NAI         C4D         C3D         H3D     110.452    2.54
+NAI         O3D         C3D         C2D     112.463    2.73
+NAI         O3D         C3D         H3D     110.380    1.67
+NAI         C2D         C3D         H3D     110.255    2.04
+NAI         C3D         O3D        HO3N     108.744    3.00
+NAI         C3D         C2D         O2D     112.463    2.73
+NAI         C3D         C2D         C1D     104.443    2.26
+NAI         C3D         C2D         H2D     110.255    2.04
+NAI         O2D         C2D         C1D     111.164    2.38
+NAI         O2D         C2D         H2D     110.259    1.63
+NAI         C1D         C2D         H2D     110.518    1.74
+NAI         C2D         O2D        HO2N     109.104    3.00
+NAI         O4D         C1D         C2D     106.204    2.50
+NAI         O4D         C1D         N1N     108.278    1.50
+NAI         O4D         C1D         H1D     109.395    1.50
+NAI         C2D         C1D         N1N     112.110    1.66
+NAI         C2D         C1D         H1D     109.914    1.68
+NAI         N1N         C1D         H1D     109.209    1.50
+NAI         C1D         N1N         C2N     120.851    1.78
+NAI         C1D         N1N         C6N     120.851    1.78
+NAI         C2N         N1N         C6N     118.299    1.80
+NAI         N1N         C2N         C3N     121.110    1.66
+NAI         N1N         C2N         H2N     119.532    1.52
+NAI         C3N         C2N         H2N     119.358    1.50
+NAI         C2N         C3N         C7N     117.781    1.96
+NAI         C2N         C3N         C4N     118.007    1.50
+NAI         C7N         C3N         C4N     124.211    3.00
+NAI         C3N         C7N         O7N     119.878    1.50
+NAI         C3N         C7N         N7N     118.037    3.00
+NAI         O7N         C7N         N7N     122.085    1.50
+NAI         C7N         N7N        H71N     120.214    2.13
+NAI         C7N         N7N        H72N     120.224    2.13
+NAI        H71N         N7N        H72N     119.583    2.34
+NAI         C3N         C4N         C5N     114.356    2.46
+NAI         C3N         C4N         H4N     108.993    1.50
+NAI         C3N         C4N        H42N     108.993    1.50
+NAI         C5N         C4N         H4N     108.815    3.00
+NAI         C5N         C4N        H42N     108.815    3.00
+NAI         H4N         C4N        H42N     106.630    2.58
+NAI         C4N         C5N         C6N     121.257    2.14
+NAI         C4N         C5N         H5N     119.218    1.70
+NAI         C6N         C5N         H5N     119.525    1.50
+NAI         N1N         C6N         C5N     120.771    1.66
+NAI         N1N         C6N         H6N     119.193    1.52
+NAI         C5N         C6N         H6N     120.036    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+NAI            sp3_sp3_54          PN          O3          PA         O1A      60.000    10.0     3
+NAI            sp3_sp3_51         C5B         O5B          PA         O1A      60.000    10.0     3
+NAI            sp2_sp3_13         C8A         N9A         C1B         O4B     150.000    10.0     6
+NAI              const_14         N7A         C8A         N9A         C1B     180.000    10.0     2
+NAI              const_26         C5A         C4A         N9A         C1B     180.000    10.0     2
+NAI              const_17         N9A         C8A         N7A         C5A       0.000    10.0     2
+NAI              const_20         C6A         C5A         N7A         C8A     180.000    10.0     2
+NAI       const_sp2_sp2_4         N7A         C5A         C6A         N6A       0.000     5.0     2
+NAI              const_21         N9A         C4A         C5A         N7A       0.000    10.0     2
+NAI            sp2_sp2_13         C5A         C6A         N6A        H61A     180.000     5.0     2
+NAI       const_sp2_sp2_6         N6A         C6A         N1A         C2A     180.000     5.0     2
+NAI       const_sp2_sp2_7         N3A         C2A         N1A         C6A       0.000     5.0     2
+NAI       const_sp2_sp2_9         N1A         C2A         N3A         C4A       0.000     5.0     2
+NAI              const_12         N9A         C4A         N3A         C2A     180.000    10.0     2
+NAI            sp3_sp3_82          PA          O3          PN         O1N     180.000    10.0     3
+NAI            sp3_sp3_85         C5D         O5D          PN          O3     180.000    10.0     3
+NAI            sp3_sp3_88         C4D         C5D         O5D          PN     180.000    10.0     3
+NAI            sp3_sp3_91         O4D         C4D         C5D         O5D     180.000    10.0     3
+NAI            sp3_sp3_26         C5D         C4D         O4D         C1D     -60.000    10.0     3
+NAI           sp3_sp3_104         O3D         C3D         C4D         C5D     180.000    10.0     3
+NAI            sp3_sp3_28         C2D         C1D         O4D         C4D     -60.000    10.0     3
+NAI           sp3_sp3_109         C4D         C3D         O3D        HO3N     180.000    10.0     3
+NAI            sp3_sp3_44         O2D         C2D         C3D         O3D     -60.000    10.0     3
+NAI           sp3_sp3_112         C3D         C2D         O2D        HO2N     180.000    10.0     3
+NAI            sp3_sp3_32         O4D         C1D         C2D         O2D     180.000    10.0     3
+NAI            sp2_sp3_19         C2N         N1N         C1D         O4D     150.000    10.0     6
+NAI             sp2_sp2_2         C3N         C2N         N1N         C1D     180.000     5.0     2
+NAI            sp2_sp2_18         C5N         C6N         N1N         C1D     180.000     5.0     2
+NAI             sp2_sp2_6         N1N         C2N         C3N         C7N     180.000     5.0     2
+NAI            sp2_sp2_24         C2N         C3N         C7N         O7N     180.000     5.0     2
+NAI             sp2_sp3_4         C7N         C3N         C4N         C5N     180.000    10.0     6
+NAI            sp2_sp2_27         O7N         C7N         N7N        H71N       0.000     5.0     2
+NAI            sp3_sp3_55         C4B         C5B         O5B          PA     180.000    10.0     3
+NAI             sp2_sp3_7         C6N         C5N         C4N         C3N       0.000    10.0     6
+NAI             sp2_sp2_9         C4N         C5N         C6N         N1N       0.000     5.0     2
+NAI            sp3_sp3_58         O4B         C4B         C5B         O5B     180.000    10.0     3
+NAI             sp3_sp3_2         C5B         C4B         O4B         C1B     -60.000    10.0     3
+NAI            sp3_sp3_71         O3B         C3B         C4B         C5B     180.000    10.0     3
+NAI             sp3_sp3_4         C2B         C1B         O4B         C4B     -60.000    10.0     3
+NAI            sp3_sp3_76         C4B         C3B         O3B        HO3A     180.000    10.0     3
+NAI            sp3_sp3_20         O2B         C2B         C3B         O3B     -60.000    10.0     3
+NAI            sp3_sp3_79         C3B         C2B         O2B        HO2A     180.000    10.0     3
+NAI             sp3_sp3_8         O4B         C1B         C2B         O2B     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+NAI    chir_1    PA    O3    O5B    O2A    both
+NAI    chir_2    C4B    O4B    C3B    C5B    negative
+NAI    chir_3    C3B    O3B    C4B    C2B    positive
+NAI    chir_4    C2B    O2B    C1B    C3B    negative
+NAI    chir_5    C1B    O4B    N9A    C2B    negative
+NAI    chir_6    PN    O3    O5D    O1N    both
+NAI    chir_7    C4D    O4D    C3D    C5D    negative
+NAI    chir_8    C3D    O3D    C4D    C2D    positive
+NAI    chir_9    C2D    O2D    C1D    C3D    negative
+NAI    chir_10    C1D    O4D    N1N    C2D    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+NAI    plan-1         C1B   0.020
+NAI    plan-1         C2A   0.020
+NAI    plan-1         C4A   0.020
+NAI    plan-1         C5A   0.020
+NAI    plan-1         C6A   0.020
+NAI    plan-1         C8A   0.020
+NAI    plan-1         H2A   0.020
+NAI    plan-1         H8A   0.020
+NAI    plan-1         N1A   0.020
+NAI    plan-1         N3A   0.020
+NAI    plan-1         N6A   0.020
+NAI    plan-1         N7A   0.020
+NAI    plan-1         N9A   0.020
+NAI    plan-2         C6A   0.020
+NAI    plan-2        H61A   0.020
+NAI    plan-2        H62A   0.020
+NAI    plan-2         N6A   0.020
+NAI    plan-3         C1D   0.020
+NAI    plan-3         C2N   0.020
+NAI    plan-3         C6N   0.020
+NAI    plan-3         N1N   0.020
+NAI    plan-4         C2N   0.020
+NAI    plan-4         C3N   0.020
+NAI    plan-4         H2N   0.020
+NAI    plan-4         N1N   0.020
+NAI    plan-5         C2N   0.020
+NAI    plan-5         C3N   0.020
+NAI    plan-5         C4N   0.020
+NAI    plan-5         C7N   0.020
+NAI    plan-6         C3N   0.020
+NAI    plan-6         C7N   0.020
+NAI    plan-6         N7N   0.020
+NAI    plan-6         O7N   0.020
+NAI    plan-7         C7N   0.020
+NAI    plan-7        H71N   0.020
+NAI    plan-7        H72N   0.020
+NAI    plan-7         N7N   0.020
+NAI    plan-8         C4N   0.020
+NAI    plan-8         C5N   0.020
+NAI    plan-8         C6N   0.020
+NAI    plan-8         H5N   0.020
+NAI    plan-9         C5N   0.020
+NAI    plan-9         C6N   0.020
+NAI    plan-9         H6N   0.020
+NAI    plan-9         N1N   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+NAI SMILES_CANONICAL               CACTVS 3.341                                                                                                                                                                    NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
+NAI           SMILES               CACTVS 3.341                                                                                                                                                                                  NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
+NAI SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                                                                                           c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
+NAI           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                                                                                                      c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
+NAI            InChI                InChI  1.03 InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
+NAI         InChIKey                InChI  1.03                                                                                                                                                                                                                                                                    BOPGDPNILDQYTO-NNYOXOHSSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+NAI acedrg               243         "dictionary generator"                  
+NAI acedrg_database      11          "data source"                           
+NAI rdkit                2017.03.2   "Chemoinformatics tool"
+NAI refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/NAP.cif b/image_analysis/structure_refinement/monomers/NAP.cif
new file mode 100644
index 000000000..02a6ea31e
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/NAP.cif
@@ -0,0 +1,460 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+NAP     NAP      "NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE"     NON-POLYMER     73     48     .     
+#
+data_comp_NAP
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+NAP     PA      P       P       0       14.707      24.447      12.480      
+NAP     O1A     O       O       0       13.458      23.637      12.602      
+NAP     O2A     O       OP      -1      16.014      23.726      12.475      
+NAP     O5B     O       O2      0       14.609      25.379      11.174      
+NAP     C5B     C       CH2     0       15.409      26.589      11.081      
+NAP     C4B     C       CH1     0       15.737      26.871      9.636       
+NAP     O4B     O       O2      0       16.491      28.107      9.568       
+NAP     C3B     C       CH1     0       16.601      25.819      8.930       
+NAP     O3B     O       OH1     0       15.781      24.855      8.281       
+NAP     C2B     C       CH1     0       17.440      26.644      7.958       
+NAP     O2B     O       O2      0       16.792      26.811      6.691       
+NAP     C1B     C       CH1     0       17.572      27.988      8.672       
+NAP     N9A     N       NR5     0       18.813      28.129      9.426       
+NAP     C8A     C       CR15    0       19.226      27.352      10.480      
+NAP     N7A     N       NRD5    0       20.388      27.707      10.967      
+NAP     C5A     C       CR56    0       20.773      28.787      10.187      
+NAP     C6A     C       CR6     0       21.921      29.609      10.202      
+NAP     N6A     N       NH2     0       22.922      29.462      11.067      
+NAP     N1A     N       NRD6    0       21.993      30.607      9.282       
+NAP     C2A     C       CR16    0       20.979      30.751      8.415       
+NAP     N3A     N       NRD6    0       19.857      30.039      8.308       
+NAP     C4A     C       CR56    0       19.809      29.058      9.231       
+NAP     O3      O       O2      0       14.727      25.535      13.659      
+NAP     PN      P       P       0       15.006      25.433      15.236      
+NAP     O1N     O       O       0       14.417      24.159      15.744      
+NAP     O2N     O       OP      -1      14.583      26.712      15.880      
+NAP     O5D     O       O2      0       16.607      25.326      15.265      
+NAP     C5D     C       CH2     0       17.397      26.371      14.640      
+NAP     C4D     C       CH1     0       18.836      26.241      15.075      
+NAP     O4D     O       O2      0       19.679      27.018      14.196      
+NAP     C3D     C       CH1     0       19.161      26.751      16.486      
+NAP     O3D     O       OH1     0       20.269      26.050      17.038      
+NAP     C2D     C       CH1     0       19.461      28.232      16.227      
+NAP     O2D     O       OH1     0       20.299      28.821      17.209      
+NAP     C1D     C       CH1     0       20.213      28.142      14.894      
+NAP     N1N     N       NR6     1       20.068      29.345      14.038      
+NAP     C2N     C       CR16    0       18.841      29.658      13.486      
+NAP     C3N     C       CR6     0       18.708      30.789      12.681      
+NAP     C7N     C       C       0       17.375      31.126      12.085      
+NAP     O7N     O       O       0       16.914      32.269      12.231      
+NAP     N7N     N       NH2     0       16.721      30.182      11.419      
+NAP     C4N     C       CR16    0       19.808      31.604      12.444      
+NAP     C5N     C       CR16    0       21.032      31.285      13.005      
+NAP     C6N     C       CR16    0       21.155      30.158      13.797      
+NAP     P2B     P       P       0       17.807      26.912      5.431       
+NAP     O1X     O       O       0       18.385      25.523      5.232       
+NAP     O2X     O       OP      -1      16.970      27.355      4.247       
+NAP     O3X     O       OP      -1      18.878      27.929      5.783       
+NAP     H51A    H       H       0       16.247      26.480      11.592      
+NAP     H52A    H       H       0       14.907      27.351      11.463      
+NAP     H4B     H       H       0       14.895      26.984      9.146       
+NAP     H3B     H       H       0       17.191      25.370      9.588       
+NAP     HO3A    H       H       0       16.276      24.329      7.835       
+NAP     H2B     H       H       0       18.322      26.219      7.847       
+NAP     H1B     H       H       0       17.517      28.708      8.003       
+NAP     H8A     H       H       0       18.721      26.635      10.822      
+NAP     H61A    H       H       0       23.626      29.985      11.016      
+NAP     H62A    H       H       0       22.876      28.841      11.686      
+NAP     H2A     H       H       0       21.074      31.456      7.793       
+NAP     H51N    H       H       0       17.050      27.259      14.903      
+NAP     H52N    H       H       0       17.341      26.291      13.658      
+NAP     H4D     H       H       0       19.094      25.297      15.004      
+NAP     H3D     H       H       0       18.368      26.662      17.076      
+NAP     HO3N    H       H       0       20.386      26.311      17.838      
+NAP     H2D     H       H       0       18.621      28.744      16.127      
+NAP     HO2N    H       H       0       20.439      29.635      17.009      
+NAP     H1D     H       H       0       21.174      27.982      15.071      
+NAP     H2N     H       H       0       18.092      29.108      13.647      
+NAP     H71N    H       H       0       17.067      29.367      11.311      
+NAP     H72N    H       H       0       15.919      30.359      11.072      
+NAP     H4N     H       H       0       19.723      32.370      11.903      
+NAP     H5N     H       H       0       21.785      31.830      12.847      
+NAP     H6N     H       H       0       21.988      29.938      14.181      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+NAP          PA         O1A      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NAP          PA         O2A      SINGLE       n     1.493  0.0122     1.493  0.0122
+NAP          PA         O5B      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAP          PA          O3      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAP         O5B         C5B      SINGLE       n     1.450  0.0166     1.450  0.0166
+NAP         C5B         C4B      SINGLE       n     1.509  0.0100     1.509  0.0100
+NAP         C4B         O4B      SINGLE       n     1.451  0.0100     1.451  0.0100
+NAP         C4B         C3B      SINGLE       n     1.535  0.0100     1.535  0.0100
+NAP         O4B         C1B      SINGLE       n     1.409  0.0100     1.409  0.0100
+NAP         C3B         O3B      SINGLE       n     1.422  0.0100     1.422  0.0100
+NAP         C3B         C2B      SINGLE       n     1.523  0.0106     1.523  0.0106
+NAP         C2B         O2B      SINGLE       n     1.425  0.0152     1.425  0.0152
+NAP         C2B         C1B      SINGLE       n     1.524  0.0100     1.524  0.0100
+NAP         O2B         P2B      SINGLE       n     1.614  0.0178     1.614  0.0178
+NAP         C1B         N9A      SINGLE       n     1.458  0.0100     1.458  0.0100
+NAP         N9A         C8A      SINGLE       y     1.372  0.0100     1.372  0.0100
+NAP         N9A         C4A      SINGLE       y     1.374  0.0101     1.374  0.0101
+NAP         C8A         N7A      DOUBLE       y     1.310  0.0100     1.310  0.0100
+NAP         N7A         C5A      SINGLE       y     1.388  0.0100     1.388  0.0100
+NAP         C5A         C6A      SINGLE       y     1.408  0.0100     1.408  0.0100
+NAP         C5A         C4A      DOUBLE       y     1.381  0.0100     1.381  0.0100
+NAP         C6A         N6A      SINGLE       n     1.330  0.0100     1.330  0.0100
+NAP         C6A         N1A      DOUBLE       y     1.354  0.0100     1.354  0.0100
+NAP         N1A         C2A      SINGLE       y     1.339  0.0100     1.339  0.0100
+NAP         C2A         N3A      DOUBLE       y     1.330  0.0100     1.330  0.0100
+NAP         N3A         C4A      SINGLE       y     1.343  0.0100     1.343  0.0100
+NAP          O3          PN      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAP          PN         O1N      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NAP          PN         O2N      SINGLE       n     1.493  0.0122     1.493  0.0122
+NAP          PN         O5D      SINGLE       n     1.604  0.0133     1.604  0.0133
+NAP         O5D         C5D      SINGLE       n     1.450  0.0166     1.450  0.0166
+NAP         C5D         C4D      SINGLE       n     1.509  0.0100     1.509  0.0100
+NAP         C4D         O4D      SINGLE       n     1.443  0.0107     1.443  0.0107
+NAP         C4D         C3D      SINGLE       n     1.535  0.0100     1.535  0.0100
+NAP         O4D         C1D      SINGLE       n     1.425  0.0141     1.425  0.0141
+NAP         C3D         O3D      SINGLE       n     1.422  0.0100     1.422  0.0100
+NAP         C3D         C2D      SINGLE       n     1.533  0.0100     1.533  0.0100
+NAP         C2D         O2D      SINGLE       n     1.419  0.0101     1.419  0.0101
+NAP         C2D         C1D      SINGLE       n     1.533  0.0100     1.533  0.0100
+NAP         C1D         N1N      SINGLE       n     1.477  0.0138     1.477  0.0138
+NAP         N1N         C2N      DOUBLE       y     1.377  0.0105     1.377  0.0105
+NAP         N1N         C6N      SINGLE       y     1.375  0.0105     1.375  0.0105
+NAP         C2N         C3N      SINGLE       y     1.390  0.0105     1.390  0.0105
+NAP         C3N         C7N      SINGLE       n     1.497  0.0100     1.497  0.0100
+NAP         C3N         C4N      DOUBLE       y     1.385  0.0100     1.385  0.0100
+NAP         C7N         O7N      DOUBLE       n     1.241  0.0105     1.241  0.0105
+NAP         C7N         N7N      SINGLE       n     1.326  0.0100     1.326  0.0100
+NAP         C4N         C5N      SINGLE       y     1.380  0.0100     1.380  0.0100
+NAP         C5N         C6N      DOUBLE       y     1.380  0.0128     1.380  0.0128
+NAP         P2B         O1X      DOUBLE       n     1.517  0.0192     1.517  0.0192
+NAP         P2B         O2X      SINGLE       n     1.517  0.0192     1.517  0.0192
+NAP         P2B         O3X      SINGLE       n     1.517  0.0192     1.517  0.0192
+NAP         C5B        H51A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAP         C5B        H52A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAP         C4B         H4B      SINGLE       n     1.089  0.0100     0.981  0.0200
+NAP         C3B         H3B      SINGLE       n     1.089  0.0100     0.992  0.0200
+NAP         O3B        HO3A      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAP         C2B         H2B      SINGLE       n     1.089  0.0100     0.985  0.0119
+NAP         C1B         H1B      SINGLE       n     1.089  0.0100     0.984  0.0200
+NAP         C8A         H8A      SINGLE       n     1.082  0.0130     0.942  0.0170
+NAP         N6A        H61A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NAP         N6A        H62A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NAP         C2A         H2A      SINGLE       n     1.082  0.0130     0.945  0.0200
+NAP         C5D        H51N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAP         C5D        H52N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAP         C4D         H4D      SINGLE       n     1.089  0.0100     0.981  0.0200
+NAP         C3D         H3D      SINGLE       n     1.089  0.0100     0.992  0.0200
+NAP         O3D        HO3N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAP         C2D         H2D      SINGLE       n     1.089  0.0100     0.989  0.0200
+NAP         O2D        HO2N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NAP         C1D         H1D      SINGLE       n     1.089  0.0100     0.990  0.0173
+NAP         C2N         H2N      SINGLE       n     1.082  0.0130     0.943  0.0170
+NAP         N7N        H71N      SINGLE       n     1.016  0.0100     0.891  0.0200
+NAP         N7N        H72N      SINGLE       n     1.016  0.0100     0.891  0.0200
+NAP         C4N         H4N      SINGLE       n     1.082  0.0130     0.941  0.0168
+NAP         C5N         H5N      SINGLE       n     1.082  0.0130     0.943  0.0190
+NAP         C6N         H6N      SINGLE       n     1.082  0.0130     0.943  0.0169
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+NAP         O1A          PA         O2A     118.411    2.35
+NAP         O1A          PA         O5B     109.410    1.50
+NAP         O1A          PA          O3     108.816    2.14
+NAP         O2A          PA         O5B     109.410    1.50
+NAP         O2A          PA          O3     108.816    2.14
+NAP         O5B          PA          O3     101.065    1.97
+NAP          PA         O5B         C5B     118.553    2.41
+NAP         O5B         C5B         C4B     109.342    1.50
+NAP         O5B         C5B        H51A     109.845    1.50
+NAP         O5B         C5B        H52A     109.845    1.50
+NAP         C4B         C5B        H51A     109.624    1.50
+NAP         C4B         C5B        H52A     109.624    1.50
+NAP        H51A         C5B        H52A     108.472    1.50
+NAP         C5B         C4B         O4B     109.123    1.50
+NAP         C5B         C4B         C3B     116.008    1.52
+NAP         C5B         C4B         H4B     108.268    1.50
+NAP         O4B         C4B         C3B     105.388    1.50
+NAP         O4B         C4B         H4B     108.947    1.50
+NAP         C3B         C4B         H4B     109.363    1.86
+NAP         C4B         O4B         C1B     109.903    1.50
+NAP         C4B         C3B         O3B     111.281    2.46
+NAP         C4B         C3B         C2B     102.352    1.50
+NAP         C4B         C3B         H3B     110.452    2.54
+NAP         O3B         C3B         C2B     112.463    2.73
+NAP         O3B         C3B         H3B     110.380    1.67
+NAP         C2B         C3B         H3B     110.255    2.04
+NAP         C3B         O3B        HO3A     108.744    3.00
+NAP         C3B         C2B         O2B     110.766    3.00
+NAP         C3B         C2B         C1B     101.388    1.50
+NAP         C3B         C2B         H2B     110.255    2.04
+NAP         O2B         C2B         C1B     110.738    2.44
+NAP         O2B         C2B         H2B     110.343    1.64
+NAP         C1B         C2B         H2B     111.050    1.62
+NAP         C2B         O2B         P2B     109.471    3.00
+NAP         O4B         C1B         C2B     106.416    1.50
+NAP         O4B         C1B         N9A     108.477    1.50
+NAP         O4B         C1B         H1B     109.807    1.50
+NAP         C2B         C1B         N9A     113.659    1.50
+NAP         C2B         C1B         H1B     109.319    1.50
+NAP         N9A         C1B         H1B     109.561    1.50
+NAP         C1B         N9A         C8A     126.848    1.91
+NAP         C1B         N9A         C4A     127.459    1.80
+NAP         C8A         N9A         C4A     105.693    1.50
+NAP         N9A         C8A         N7A     113.469    1.50
+NAP         N9A         C8A         H8A     123.206    1.50
+NAP         N7A         C8A         H8A     123.326    1.50
+NAP         C8A         N7A         C5A     104.739    1.50
+NAP         N7A         C5A         C6A     132.250    1.50
+NAP         N7A         C5A         C4A     110.483    1.50
+NAP         C6A         C5A         C4A     117.267    1.50
+NAP         C5A         C6A         N6A     123.792    1.50
+NAP         C5A         C6A         N1A     117.409    1.50
+NAP         N6A         C6A         N1A     118.799    1.50
+NAP         C6A         N6A        H61A     119.723    1.50
+NAP         C6A         N6A        H62A     119.723    1.50
+NAP        H61A         N6A        H62A     120.554    1.88
+NAP         C6A         N1A         C2A     118.521    1.50
+NAP         N1A         C2A         N3A     129.332    1.50
+NAP         N1A         C2A         H2A     115.313    1.50
+NAP         N3A         C2A         H2A     115.355    1.50
+NAP         C2A         N3A         C4A     110.982    1.50
+NAP         N9A         C4A         C5A     105.616    1.50
+NAP         N9A         C4A         N3A     127.895    1.50
+NAP         C5A         C4A         N3A     126.489    1.50
+NAP          PA          O3          PN     132.542    3.00
+NAP          O3          PN         O1N     108.816    2.14
+NAP          O3          PN         O2N     108.816    2.14
+NAP          O3          PN         O5D     101.065    1.97
+NAP         O1N          PN         O2N     118.411    2.35
+NAP         O1N          PN         O5D     109.410    1.50
+NAP         O2N          PN         O5D     109.410    1.50
+NAP          PN         O5D         C5D     118.553    2.41
+NAP         O5D         C5D         C4D     109.342    1.50
+NAP         O5D         C5D        H51N     109.845    1.50
+NAP         O5D         C5D        H52N     109.845    1.50
+NAP         C4D         C5D        H51N     109.624    1.50
+NAP         C4D         C5D        H52N     109.624    1.50
+NAP        H51N         C5D        H52N     108.472    1.50
+NAP         C5D         C4D         O4D     109.615    1.50
+NAP         C5D         C4D         C3D     116.008    1.52
+NAP         C5D         C4D         H4D     108.268    1.50
+NAP         O4D         C4D         C3D     104.439    1.50
+NAP         O4D         C4D         H4D     108.698    1.50
+NAP         C3D         C4D         H4D     109.363    1.86
+NAP         C4D         O4D         C1D     109.578    1.50
+NAP         C4D         C3D         O3D     111.281    2.46
+NAP         C4D         C3D         C2D     102.071    1.50
+NAP         C4D         C3D         H3D     110.452    2.54
+NAP         O3D         C3D         C2D     111.993    3.00
+NAP         O3D         C3D         H3D     110.380    1.67
+NAP         C2D         C3D         H3D     110.108    1.66
+NAP         C3D         O3D        HO3N     108.744    3.00
+NAP         C3D         C2D         O2D     112.861    2.52
+NAP         C3D         C2D         C1D     101.269    1.50
+NAP         C3D         C2D         H2D     110.799    1.82
+NAP         O2D         C2D         C1D     109.476    3.00
+NAP         O2D         C2D         H2D     111.022    1.77
+NAP         C1D         C2D         H2D     110.760    1.63
+NAP         C2D         O2D        HO2N     109.449    1.85
+NAP         O4D         C1D         C2D     106.825    1.50
+NAP         O4D         C1D         N1N     108.092    1.50
+NAP         O4D         C1D         H1D     109.327    1.50
+NAP         C2D         C1D         N1N     113.620    1.99
+NAP         C2D         C1D         H1D     109.776    1.83
+NAP         N1N         C1D         H1D     108.901    1.50
+NAP         C1D         N1N         C2N     119.705    1.50
+NAP         C1D         N1N         C6N     119.705    1.50
+NAP         C2N         N1N         C6N     120.590    1.50
+NAP         N1N         C2N         C3N     119.549    3.00
+NAP         N1N         C2N         H2N     120.430    1.53
+NAP         C3N         C2N         H2N     120.021    1.50
+NAP         C2N         C3N         C7N     119.660    2.75
+NAP         C2N         C3N         C4N     119.402    1.64
+NAP         C7N         C3N         C4N     120.938    2.50
+NAP         C3N         C7N         O7N     119.730    1.50
+NAP         C3N         C7N         N7N     118.032    1.50
+NAP         O7N         C7N         N7N     122.238    1.50
+NAP         C7N         N7N        H71N     120.236    2.75
+NAP         C7N         N7N        H72N     120.236    2.75
+NAP        H71N         N7N        H72N     119.529    2.83
+NAP         C3N         C4N         C5N     119.166    1.50
+NAP         C3N         C4N         H4N     120.513    1.50
+NAP         C5N         C4N         H4N     120.320    1.50
+NAP         C4N         C5N         C6N     120.016    1.50
+NAP         C4N         C5N         H5N     120.300    1.50
+NAP         C6N         C5N         H5N     119.683    1.50
+NAP         N1N         C6N         C5N     121.277    1.50
+NAP         N1N         C6N         H6N     118.693    1.53
+NAP         C5N         C6N         H6N     120.031    1.59
+NAP         O2B         P2B         O1X     106.518    3.00
+NAP         O2B         P2B         O2X     106.518    3.00
+NAP         O2B         P2B         O3X     106.518    3.00
+NAP         O1X         P2B         O2X     112.139    1.52
+NAP         O1X         P2B         O3X     112.139    1.52
+NAP         O2X         P2B         O3X     112.139    1.52
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+NAP            sp3_sp3_54          PN          O3          PA         O1A      60.000    10.0     3
+NAP            sp3_sp3_51         C5B         O5B          PA         O1A      60.000    10.0     3
+NAP            sp3_sp3_82         C2B         O2B         P2B         O1X     180.000    10.0     3
+NAP             sp2_sp3_1         C8A         N9A         C1B         O4B     150.000    10.0     6
+NAP              const_34         N7A         C8A         N9A         C1B     180.000    10.0     2
+NAP              const_46         C5A         C4A         N9A         C1B     180.000    10.0     2
+NAP              const_37         N9A         C8A         N7A         C5A       0.000    10.0     2
+NAP              const_40         C6A         C5A         N7A         C8A     180.000    10.0     2
+NAP       const_sp2_sp2_4         N7A         C5A         C6A         N6A       0.000     5.0     2
+NAP              const_41         N9A         C4A         C5A         N7A       0.000    10.0     2
+NAP             sp2_sp2_1         C5A         C6A         N6A        H61A     180.000     5.0     2
+NAP       const_sp2_sp2_6         N6A         C6A         N1A         C2A     180.000     5.0     2
+NAP       const_sp2_sp2_7         N3A         C2A         N1A         C6A       0.000     5.0     2
+NAP       const_sp2_sp2_9         N1A         C2A         N3A         C4A       0.000     5.0     2
+NAP              const_12         N9A         C4A         N3A         C2A     180.000    10.0     2
+NAP            sp3_sp3_87          PA          O3          PN         O1N      60.000    10.0     3
+NAP            sp3_sp3_88         C5D         O5D          PN          O3     180.000    10.0     3
+NAP            sp3_sp3_91         C4D         C5D         O5D          PN     180.000    10.0     3
+NAP            sp3_sp3_94         O4D         C4D         C5D         O5D     180.000    10.0     3
+NAP            sp3_sp3_26         C5D         C4D         O4D         C1D     -60.000    10.0     3
+NAP           sp3_sp3_107         O3D         C3D         C4D         C5D     180.000    10.0     3
+NAP            sp3_sp3_28         C2D         C1D         O4D         C4D     -60.000    10.0     3
+NAP           sp3_sp3_112         C4D         C3D         O3D        HO3N     180.000    10.0     3
+NAP            sp3_sp3_44         O2D         C2D         C3D         O3D     -60.000    10.0     3
+NAP           sp3_sp3_115         C3D         C2D         O2D        HO2N     180.000    10.0     3
+NAP            sp3_sp3_32         O4D         C1D         C2D         O2D     180.000    10.0     3
+NAP             sp2_sp3_7         C2N         N1N         C1D         O4D     150.000    10.0     6
+NAP              const_14         C3N         C2N         N1N         C1D     180.000    10.0     2
+NAP              const_50         C5N         C6N         N1N         C1D     180.000    10.0     2
+NAP              const_18         N1N         C2N         C3N         C7N     180.000    10.0     2
+NAP             sp2_sp2_6         C2N         C3N         C7N         O7N       0.000     5.0     2
+NAP              const_23         C7N         C3N         C4N         C5N     180.000    10.0     2
+NAP            sp2_sp2_11         O7N         C7N         N7N        H71N       0.000     5.0     2
+NAP            sp3_sp3_55         C4B         C5B         O5B          PA     180.000    10.0     3
+NAP              const_25         C3N         C4N         C5N         C6N       0.000    10.0     2
+NAP              const_29         C4N         C5N         C6N         N1N       0.000    10.0     2
+NAP            sp3_sp3_58         O4B         C4B         C5B         O5B     180.000    10.0     3
+NAP             sp3_sp3_2         C5B         C4B         O4B         C1B     -60.000    10.0     3
+NAP            sp3_sp3_71         O3B         C3B         C4B         C5B     180.000    10.0     3
+NAP             sp3_sp3_4         C2B         C1B         O4B         C4B     -60.000    10.0     3
+NAP            sp3_sp3_76         C4B         C3B         O3B        HO3A     180.000    10.0     3
+NAP            sp3_sp3_20         O2B         C2B         C3B         O3B     -60.000    10.0     3
+NAP            sp3_sp3_79         C3B         C2B         O2B         P2B     180.000    10.0     3
+NAP             sp3_sp3_8         O4B         C1B         C2B         O2B     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+NAP    chir_1    PA    O3    O5B    O2A    both
+NAP    chir_2    C4B    O4B    C3B    C5B    negative
+NAP    chir_3    C3B    O3B    C2B    C4B    negative
+NAP    chir_4    C2B    O2B    C1B    C3B    negative
+NAP    chir_5    C1B    O4B    N9A    C2B    negative
+NAP    chir_6    PN    O3    O5D    O2N    both
+NAP    chir_7    C4D    O4D    C3D    C5D    negative
+NAP    chir_8    C3D    O3D    C4D    C2D    positive
+NAP    chir_9    C2D    O2D    C1D    C3D    negative
+NAP    chir_10    C1D    O4D    N1N    C2D    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+NAP    plan-1         C1B   0.020
+NAP    plan-1         C2A   0.020
+NAP    plan-1         C4A   0.020
+NAP    plan-1         C5A   0.020
+NAP    plan-1         C6A   0.020
+NAP    plan-1         C8A   0.020
+NAP    plan-1         H2A   0.020
+NAP    plan-1         H8A   0.020
+NAP    plan-1         N1A   0.020
+NAP    plan-1         N3A   0.020
+NAP    plan-1         N6A   0.020
+NAP    plan-1         N7A   0.020
+NAP    plan-1         N9A   0.020
+NAP    plan-2         C1D   0.020
+NAP    plan-2         C2N   0.020
+NAP    plan-2         C3N   0.020
+NAP    plan-2         C4N   0.020
+NAP    plan-2         C5N   0.020
+NAP    plan-2         C6N   0.020
+NAP    plan-2         C7N   0.020
+NAP    plan-2         H2N   0.020
+NAP    plan-2         H4N   0.020
+NAP    plan-2         H5N   0.020
+NAP    plan-2         H6N   0.020
+NAP    plan-2         N1N   0.020
+NAP    plan-3         C6A   0.020
+NAP    plan-3        H61A   0.020
+NAP    plan-3        H62A   0.020
+NAP    plan-3         N6A   0.020
+NAP    plan-4         C3N   0.020
+NAP    plan-4         C7N   0.020
+NAP    plan-4         N7N   0.020
+NAP    plan-4         O7N   0.020
+NAP    plan-5         C7N   0.020
+NAP    plan-5        H71N   0.020
+NAP    plan-5        H72N   0.020
+NAP    plan-5         N7N   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+NAP SMILES_CANONICAL               CACTVS 3.341                                                                                                                                                              NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
+NAP           SMILES               CACTVS 3.341                                                                                                                                                                           NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
+NAP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                                                                                          c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
+NAP           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                                                                                                     c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
+NAP            InChI                InChI  1.03 InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
+NAP         InChIKey                InChI  1.03                                                                                                                                                                                                                                                                            XJLXINKUBYWONI-NNYOXOHSSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+NAP acedrg               243         "dictionary generator"                  
+NAP acedrg_database      11          "data source"                           
+NAP rdkit                2017.03.2   "Chemoinformatics tool"
+NAP refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/NDP.cif b/image_analysis/structure_refinement/monomers/NDP.cif
new file mode 100644
index 000000000..c3eae3816
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/NDP.cif
@@ -0,0 +1,473 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+NDP     NDP      "NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE"     NON-POLYMER     74     48     .     
+#
+data_comp_NDP
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+NDP     PA      P       P       0       14.746      11.568      81.367      
+NDP     O1A     O       O       0       14.846      12.116      82.752      
+NDP     O2A     O       OP      -1      15.219      10.173      81.123      
+NDP     O5B     O       O2      0       15.480      12.564      80.346      
+NDP     C5B     C       CH2     0       15.269      13.993      80.484      
+NDP     C4B     C       CH1     0       15.682      14.683      79.207      
+NDP     O4B     O       O2      0       15.216      16.056      79.244      
+NDP     C3B     C       CH1     0       17.194      14.748      78.938      
+NDP     O3B     O       OH1     0       17.492      14.414      77.587      
+NDP     C2B     C       CH1     0       17.556      16.184      79.308      
+NDP     O2B     O       O2      0       18.652      16.694      78.540      
+NDP     C1B     C       CH1     0       16.277      16.931      78.947      
+NDP     N9A     N       NR5     0       16.067      18.164      79.699      
+NDP     C8A     C       CR15    0       16.031      18.293      81.065      
+NDP     N7A     N       NRD5    0       15.816      19.519      81.470      
+NDP     C5A     C       CR56    0       15.691      20.250      80.299      
+NDP     C6A     C       CR6     0       15.449      21.620      80.056      
+NDP     N6A     N       NH2     0       15.287      22.522      81.021      
+NDP     N1A     N       NRD6    0       15.382      22.028      78.762      
+NDP     C2A     C       CR16    0       15.546      21.113      77.794      
+NDP     N3A     N       NRD6    0       15.777      19.804      77.905      
+NDP     C4A     C       CR56    0       15.840      19.425      79.196      
+NDP     O3      O       O2      0       13.226      11.692      80.871      
+NDP     PN      P       P       0       12.518      11.379      79.466      
+NDP     O1N     O       O       0       13.514      10.727      78.565      
+NDP     O2N     O       OP      -1      11.231      10.667      79.724      
+NDP     O5D     O       O2      0       12.213      12.863      78.935      
+NDP     C5D     C       CH2     0       11.328      13.716      79.706      
+NDP     C4D     C       CH1     0       11.023      14.974      78.929      
+NDP     O4D     O       O2      0       12.257      15.648      78.585      
+NDP     C3D     C       CH1     0       10.306      14.797      77.585      
+NDP     O3D     O       OH1     0       8.904       14.643      77.770      
+NDP     C2D     C       CH1     0       10.697      16.089      76.857      
+NDP     O2D     O       OH1     0       9.719       17.111      76.999      
+NDP     C1D     C       CH1     0       12.016      16.522      77.506      
+NDP     N1N     N       NR6     0       13.173      16.451      76.558      
+NDP     C2N     C       CR16    0       13.593      15.236      76.075      
+NDP     C3N     C       CR6     0       14.740      15.096      75.322      
+NDP     C7N     C       C       0       15.161      13.734      74.898      
+NDP     O7N     O       O       0       15.511      13.557      73.727      
+NDP     N7N     N       NH2     0       15.161      12.736      75.773      
+NDP     C4N     C       CH2     0       15.493      16.332      74.936      
+NDP     C5N     C       CR16    0       14.940      17.593      75.478      
+NDP     C6N     C       CR16    0       13.806      17.617      76.151      
+NDP     P2B     P       P       0       20.124      16.448      79.172      
+NDP     O1X     O       O       0       20.271      14.965      79.456      
+NDP     O2X     O       OP      -1      20.204      17.281      80.438      
+NDP     O3X     O       OP      -1      21.106      16.923      78.118      
+NDP     H51A    H       H       0       15.806      14.341      81.239      
+NDP     H52A    H       H       0       14.314      14.177      80.667      
+NDP     H4B     H       H       0       15.242      14.224      78.463      
+NDP     H3B     H       H       0       17.664      14.123      79.548      
+NDP     HO3A    H       H       0       17.093      14.951      77.068      
+NDP     H2B     H       H       0       17.743      16.245      80.273      
+NDP     H1B     H       H       0       16.282      17.128      77.984      
+NDP     H8A     H       H       0       16.159      17.569      81.654      
+NDP     H61A    H       H       0       14.828      23.253      80.863      
+NDP     H62A    H       H       0       15.640      22.380      81.812      
+NDP     H2A     H       H       0       15.491      21.442      76.910      
+NDP     H51N    H       H       0       11.757      13.954      80.565      
+NDP     H52N    H       H       0       10.485      13.237      79.901      
+NDP     H4D     H       H       0       10.493      15.568      79.503      
+NDP     H3D     H       H       0       10.672      14.015      77.099      
+NDP     HO3N    H       H       0       8.534       14.576      77.009      
+NDP     H2D     H       H       0       10.834      15.895      75.897      
+NDP     HO2N    H       H       0       9.885       17.733      76.446      
+NDP     H1D     H       H       0       11.933      17.443      77.851      
+NDP     H2N     H       H       0       13.079      14.471      76.264      
+NDP     H71N    H       H       0       14.910      12.863      76.612      
+NDP     H72N    H       H       0       15.415      11.924      75.519      
+NDP     H41N    H       H       0       15.516      16.397      73.959      
+NDP     H42N    H       H       0       16.424      16.244      75.229      
+NDP     H5N     H       H       0       15.417      18.410      75.332      
+NDP     H6N     H       H       0       13.411      18.445      76.360      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+NDP          PA         O1A      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NDP          PA         O2A      SINGLE       n     1.493  0.0122     1.493  0.0122
+NDP          PA         O5B      SINGLE       n     1.604  0.0133     1.604  0.0133
+NDP          PA          O3      SINGLE       n     1.604  0.0133     1.604  0.0133
+NDP         O5B         C5B      SINGLE       n     1.450  0.0166     1.450  0.0166
+NDP         C5B         C4B      SINGLE       n     1.509  0.0100     1.509  0.0100
+NDP         C4B         O4B      SINGLE       n     1.451  0.0100     1.451  0.0100
+NDP         C4B         C3B      SINGLE       n     1.535  0.0100     1.535  0.0100
+NDP         O4B         C1B      SINGLE       n     1.409  0.0100     1.409  0.0100
+NDP         C3B         O3B      SINGLE       n     1.422  0.0100     1.422  0.0100
+NDP         C3B         C2B      SINGLE       n     1.523  0.0106     1.523  0.0106
+NDP         C2B         O2B      SINGLE       n     1.425  0.0152     1.425  0.0152
+NDP         C2B         C1B      SINGLE       n     1.524  0.0100     1.524  0.0100
+NDP         O2B         P2B      SINGLE       n     1.614  0.0178     1.614  0.0178
+NDP         C1B         N9A      SINGLE       n     1.458  0.0100     1.458  0.0100
+NDP         N9A         C8A      SINGLE       y     1.372  0.0100     1.372  0.0100
+NDP         N9A         C4A      SINGLE       y     1.374  0.0101     1.374  0.0101
+NDP         C8A         N7A      DOUBLE       y     1.310  0.0100     1.310  0.0100
+NDP         N7A         C5A      SINGLE       y     1.388  0.0100     1.388  0.0100
+NDP         C5A         C6A      SINGLE       y     1.408  0.0100     1.408  0.0100
+NDP         C5A         C4A      DOUBLE       y     1.381  0.0100     1.381  0.0100
+NDP         C6A         N6A      SINGLE       n     1.330  0.0100     1.330  0.0100
+NDP         C6A         N1A      DOUBLE       y     1.354  0.0100     1.354  0.0100
+NDP         N1A         C2A      SINGLE       y     1.339  0.0100     1.339  0.0100
+NDP         C2A         N3A      DOUBLE       y     1.330  0.0100     1.330  0.0100
+NDP         N3A         C4A      SINGLE       y     1.343  0.0100     1.343  0.0100
+NDP          O3          PN      SINGLE       n     1.604  0.0133     1.604  0.0133
+NDP          PN         O1N      DOUBLE       n     1.493  0.0122     1.493  0.0122
+NDP          PN         O2N      SINGLE       n     1.493  0.0122     1.493  0.0122
+NDP          PN         O5D      SINGLE       n     1.604  0.0133     1.604  0.0133
+NDP         O5D         C5D      SINGLE       n     1.450  0.0166     1.450  0.0166
+NDP         C5D         C4D      SINGLE       n     1.509  0.0100     1.509  0.0100
+NDP         C4D         O4D      SINGLE       n     1.449  0.0100     1.449  0.0100
+NDP         C4D         C3D      SINGLE       n     1.535  0.0100     1.535  0.0100
+NDP         O4D         C1D      SINGLE       n     1.407  0.0132     1.407  0.0132
+NDP         C3D         O3D      SINGLE       n     1.422  0.0100     1.422  0.0100
+NDP         C3D         C2D      SINGLE       n     1.530  0.0134     1.530  0.0134
+NDP         C2D         O2D      SINGLE       n     1.420  0.0122     1.420  0.0122
+NDP         C2D         C1D      SINGLE       n     1.527  0.0119     1.527  0.0119
+NDP         C1D         N1N      SINGLE       n     1.492  0.0124     1.492  0.0124
+NDP         N1N         C2N      SINGLE       n     1.367  0.0104     1.367  0.0104
+NDP         N1N         C6N      SINGLE       n     1.374  0.0156     1.374  0.0156
+NDP         C2N         C3N      DOUBLE       n     1.365  0.0175     1.365  0.0175
+NDP         C3N         C7N      SINGLE       n     1.480  0.0169     1.480  0.0169
+NDP         C3N         C4N      SINGLE       n     1.491  0.0200     1.491  0.0200
+NDP         C7N         O7N      DOUBLE       n     1.235  0.0110     1.235  0.0110
+NDP         C7N         N7N      SINGLE       n     1.325  0.0100     1.325  0.0100
+NDP         C4N         C5N      SINGLE       n     1.477  0.0200     1.477  0.0200
+NDP         C5N         C6N      DOUBLE       n     1.315  0.0139     1.315  0.0139
+NDP         P2B         O1X      DOUBLE       n     1.517  0.0192     1.517  0.0192
+NDP         P2B         O2X      SINGLE       n     1.517  0.0192     1.517  0.0192
+NDP         P2B         O3X      SINGLE       n     1.517  0.0192     1.517  0.0192
+NDP         C5B        H51A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NDP         C5B        H52A      SINGLE       n     1.089  0.0100     0.989  0.0200
+NDP         C4B         H4B      SINGLE       n     1.089  0.0100     0.981  0.0200
+NDP         C3B         H3B      SINGLE       n     1.089  0.0100     0.992  0.0200
+NDP         O3B        HO3A      SINGLE       n     0.970  0.0120     0.849  0.0200
+NDP         C2B         H2B      SINGLE       n     1.089  0.0100     0.985  0.0119
+NDP         C1B         H1B      SINGLE       n     1.089  0.0100     0.984  0.0200
+NDP         C8A         H8A      SINGLE       n     1.082  0.0130     0.942  0.0170
+NDP         N6A        H61A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NDP         N6A        H62A      SINGLE       n     1.016  0.0100     0.877  0.0200
+NDP         C2A         H2A      SINGLE       n     1.082  0.0130     0.945  0.0200
+NDP         C5D        H51N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NDP         C5D        H52N      SINGLE       n     1.089  0.0100     0.989  0.0200
+NDP         C4D         H4D      SINGLE       n     1.089  0.0100     0.981  0.0200
+NDP         C3D         H3D      SINGLE       n     1.089  0.0100     0.992  0.0200
+NDP         O3D        HO3N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NDP         C2D         H2D      SINGLE       n     1.089  0.0100     0.988  0.0200
+NDP         O2D        HO2N      SINGLE       n     0.970  0.0120     0.849  0.0200
+NDP         C1D         H1D      SINGLE       n     1.089  0.0100     0.986  0.0200
+NDP         C2N         H2N      SINGLE       n     1.082  0.0130     0.940  0.0112
+NDP         N7N        H71N      SINGLE       n     1.016  0.0100     0.887  0.0200
+NDP         N7N        H72N      SINGLE       n     1.016  0.0100     0.887  0.0200
+NDP         C4N        H41N      SINGLE       n     1.089  0.0100     0.980  0.0113
+NDP         C4N        H42N      SINGLE       n     1.089  0.0100     0.980  0.0113
+NDP         C5N         H5N      SINGLE       n     1.082  0.0130     0.957  0.0130
+NDP         C6N         H6N      SINGLE       n     1.082  0.0130     0.941  0.0198
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+NDP         O1A          PA         O2A     118.411    2.35
+NDP         O1A          PA         O5B     109.410    1.50
+NDP         O1A          PA          O3     108.816    2.14
+NDP         O2A          PA         O5B     109.410    1.50
+NDP         O2A          PA          O3     108.816    2.14
+NDP         O5B          PA          O3     101.065    1.97
+NDP          PA         O5B         C5B     118.553    2.41
+NDP         O5B         C5B         C4B     109.342    1.50
+NDP         O5B         C5B        H51A     109.845    1.50
+NDP         O5B         C5B        H52A     109.845    1.50
+NDP         C4B         C5B        H51A     109.624    1.50
+NDP         C4B         C5B        H52A     109.624    1.50
+NDP        H51A         C5B        H52A     108.472    1.50
+NDP         C5B         C4B         O4B     109.123    1.50
+NDP         C5B         C4B         C3B     116.008    1.52
+NDP         C5B         C4B         H4B     108.268    1.50
+NDP         O4B         C4B         C3B     105.388    1.50
+NDP         O4B         C4B         H4B     108.947    1.50
+NDP         C3B         C4B         H4B     109.363    1.86
+NDP         C4B         O4B         C1B     109.903    1.50
+NDP         C4B         C3B         O3B     111.281    2.46
+NDP         C4B         C3B         C2B     102.352    1.50
+NDP         C4B         C3B         H3B     110.452    2.54
+NDP         O3B         C3B         C2B     112.463    2.73
+NDP         O3B         C3B         H3B     110.380    1.67
+NDP         C2B         C3B         H3B     110.255    2.04
+NDP         C3B         O3B        HO3A     108.744    3.00
+NDP         C3B         C2B         O2B     110.766    3.00
+NDP         C3B         C2B         C1B     101.388    1.50
+NDP         C3B         C2B         H2B     110.255    2.04
+NDP         O2B         C2B         C1B     110.738    2.44
+NDP         O2B         C2B         H2B     110.343    1.64
+NDP         C1B         C2B         H2B     111.050    1.62
+NDP         C2B         O2B         P2B     109.471    3.00
+NDP         O4B         C1B         C2B     106.416    1.50
+NDP         O4B         C1B         N9A     108.477    1.50
+NDP         O4B         C1B         H1B     109.807    1.50
+NDP         C2B         C1B         N9A     113.659    1.50
+NDP         C2B         C1B         H1B     109.319    1.50
+NDP         N9A         C1B         H1B     109.561    1.50
+NDP         C1B         N9A         C8A     126.848    1.91
+NDP         C1B         N9A         C4A     127.459    1.80
+NDP         C8A         N9A         C4A     105.693    1.50
+NDP         N9A         C8A         N7A     113.469    1.50
+NDP         N9A         C8A         H8A     123.206    1.50
+NDP         N7A         C8A         H8A     123.326    1.50
+NDP         C8A         N7A         C5A     104.739    1.50
+NDP         N7A         C5A         C6A     132.250    1.50
+NDP         N7A         C5A         C4A     110.483    1.50
+NDP         C6A         C5A         C4A     117.267    1.50
+NDP         C5A         C6A         N6A     123.792    1.50
+NDP         C5A         C6A         N1A     117.409    1.50
+NDP         N6A         C6A         N1A     118.799    1.50
+NDP         C6A         N6A        H61A     119.723    1.50
+NDP         C6A         N6A        H62A     119.723    1.50
+NDP        H61A         N6A        H62A     120.554    1.88
+NDP         C6A         N1A         C2A     118.521    1.50
+NDP         N1A         C2A         N3A     129.332    1.50
+NDP         N1A         C2A         H2A     115.313    1.50
+NDP         N3A         C2A         H2A     115.355    1.50
+NDP         C2A         N3A         C4A     110.982    1.50
+NDP         N9A         C4A         C5A     105.616    1.50
+NDP         N9A         C4A         N3A     127.895    1.50
+NDP         C5A         C4A         N3A     126.489    1.50
+NDP          PA          O3          PN     132.542    3.00
+NDP          O3          PN         O1N     108.816    2.14
+NDP          O3          PN         O2N     108.816    2.14
+NDP          O3          PN         O5D     101.065    1.97
+NDP         O1N          PN         O2N     118.411    2.35
+NDP         O1N          PN         O5D     109.410    1.50
+NDP         O2N          PN         O5D     109.410    1.50
+NDP          PN         O5D         C5D     118.553    2.41
+NDP         O5D         C5D         C4D     109.342    1.50
+NDP         O5D         C5D        H51N     109.845    1.50
+NDP         O5D         C5D        H52N     109.845    1.50
+NDP         C4D         C5D        H51N     109.624    1.50
+NDP         C4D         C5D        H52N     109.624    1.50
+NDP        H51N         C5D        H52N     108.472    1.50
+NDP         C5D         C4D         O4D     109.123    1.50
+NDP         C5D         C4D         C3D     116.008    1.52
+NDP         C5D         C4D         H4D     108.268    1.50
+NDP         O4D         C4D         C3D     105.508    1.50
+NDP         O4D         C4D         H4D     108.642    1.50
+NDP         C3D         C4D         H4D     109.363    1.86
+NDP         C4D         O4D         C1D     109.926    1.50
+NDP         C4D         C3D         O3D     111.281    2.46
+NDP         C4D         C3D         C2D     102.352    1.50
+NDP         C4D         C3D         H3D     110.452    2.54
+NDP         O3D         C3D         C2D     112.463    2.73
+NDP         O3D         C3D         H3D     110.380    1.67
+NDP         C2D         C3D         H3D     110.255    2.04
+NDP         C3D         O3D        HO3N     108.744    3.00
+NDP         C3D         C2D         O2D     112.463    2.73
+NDP         C3D         C2D         C1D     104.443    2.26
+NDP         C3D         C2D         H2D     110.255    2.04
+NDP         O2D         C2D         C1D     111.164    2.38
+NDP         O2D         C2D         H2D     110.259    1.63
+NDP         C1D         C2D         H2D     110.518    1.74
+NDP         C2D         O2D        HO2N     109.104    3.00
+NDP         O4D         C1D         C2D     106.204    2.50
+NDP         O4D         C1D         N1N     108.278    1.50
+NDP         O4D         C1D         H1D     109.395    1.50
+NDP         C2D         C1D         N1N     112.110    1.66
+NDP         C2D         C1D         H1D     109.914    1.68
+NDP         N1N         C1D         H1D     109.209    1.50
+NDP         C1D         N1N         C2N     120.851    1.78
+NDP         C1D         N1N         C6N     120.851    1.78
+NDP         C2N         N1N         C6N     118.299    1.80
+NDP         N1N         C2N         C3N     121.110    1.66
+NDP         N1N         C2N         H2N     119.532    1.52
+NDP         C3N         C2N         H2N     119.358    1.50
+NDP         C2N         C3N         C7N     117.781    1.96
+NDP         C2N         C3N         C4N     118.007    1.50
+NDP         C7N         C3N         C4N     124.211    3.00
+NDP         C3N         C7N         O7N     119.878    1.50
+NDP         C3N         C7N         N7N     118.037    3.00
+NDP         O7N         C7N         N7N     122.085    1.50
+NDP         C7N         N7N        H71N     120.214    2.13
+NDP         C7N         N7N        H72N     120.224    2.13
+NDP        H71N         N7N        H72N     119.583    2.34
+NDP         C3N         C4N         C5N     114.356    2.46
+NDP         C3N         C4N        H41N     108.993    1.50
+NDP         C3N         C4N        H42N     108.993    1.50
+NDP         C5N         C4N        H41N     108.815    3.00
+NDP         C5N         C4N        H42N     108.815    3.00
+NDP        H41N         C4N        H42N     106.630    2.58
+NDP         C4N         C5N         C6N     121.257    2.14
+NDP         C4N         C5N         H5N     119.218    1.70
+NDP         C6N         C5N         H5N     119.525    1.50
+NDP         N1N         C6N         C5N     120.771    1.66
+NDP         N1N         C6N         H6N     119.193    1.52
+NDP         C5N         C6N         H6N     120.036    1.50
+NDP         O2B         P2B         O1X     106.518    3.00
+NDP         O2B         P2B         O2X     106.518    3.00
+NDP         O2B         P2B         O3X     106.518    3.00
+NDP         O1X         P2B         O2X     112.139    1.52
+NDP         O1X         P2B         O3X     112.139    1.52
+NDP         O2X         P2B         O3X     112.139    1.52
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+NDP            sp3_sp3_54          PN          O3          PA         O1A      60.000    10.0     3
+NDP            sp3_sp3_51         C5B         O5B          PA         O1A      60.000    10.0     3
+NDP            sp3_sp3_82         C2B         O2B         P2B         O1X     180.000    10.0     3
+NDP            sp2_sp3_13         C8A         N9A         C1B         O4B     150.000    10.0     6
+NDP              const_14         N7A         C8A         N9A         C1B     180.000    10.0     2
+NDP              const_26         C5A         C4A         N9A         C1B     180.000    10.0     2
+NDP              const_17         N9A         C8A         N7A         C5A       0.000    10.0     2
+NDP              const_20         C6A         C5A         N7A         C8A     180.000    10.0     2
+NDP       const_sp2_sp2_4         N7A         C5A         C6A         N6A       0.000     5.0     2
+NDP              const_21         N9A         C4A         C5A         N7A       0.000    10.0     2
+NDP            sp2_sp2_13         C5A         C6A         N6A        H61A     180.000     5.0     2
+NDP       const_sp2_sp2_6         N6A         C6A         N1A         C2A     180.000     5.0     2
+NDP       const_sp2_sp2_7         N3A         C2A         N1A         C6A       0.000     5.0     2
+NDP       const_sp2_sp2_9         N1A         C2A         N3A         C4A       0.000     5.0     2
+NDP              const_12         N9A         C4A         N3A         C2A     180.000    10.0     2
+NDP            sp3_sp3_87          PA          O3          PN         O1N      60.000    10.0     3
+NDP            sp3_sp3_88         C5D         O5D          PN          O3     180.000    10.0     3
+NDP            sp3_sp3_91         C4D         C5D         O5D          PN     180.000    10.0     3
+NDP            sp3_sp3_94         O4D         C4D         C5D         O5D     180.000    10.0     3
+NDP            sp3_sp3_26         C5D         C4D         O4D         C1D     -60.000    10.0     3
+NDP           sp3_sp3_107         O3D         C3D         C4D         C5D     180.000    10.0     3
+NDP            sp3_sp3_28         C2D         C1D         O4D         C4D     -60.000    10.0     3
+NDP           sp3_sp3_112         C4D         C3D         O3D        HO3N     180.000    10.0     3
+NDP            sp3_sp3_44         O2D         C2D         C3D         O3D     -60.000    10.0     3
+NDP           sp3_sp3_115         C3D         C2D         O2D        HO2N     180.000    10.0     3
+NDP            sp3_sp3_32         O4D         C1D         C2D         O2D     180.000    10.0     3
+NDP            sp2_sp3_19         C2N         N1N         C1D         O4D     150.000    10.0     6
+NDP             sp2_sp2_2         C3N         C2N         N1N         C1D     180.000     5.0     2
+NDP            sp2_sp2_18         C5N         C6N         N1N         C1D     180.000     5.0     2
+NDP             sp2_sp2_6         N1N         C2N         C3N         C7N     180.000     5.0     2
+NDP            sp2_sp2_24         C2N         C3N         C7N         O7N     180.000     5.0     2
+NDP             sp2_sp3_4         C7N         C3N         C4N         C5N     180.000    10.0     6
+NDP            sp2_sp2_27         O7N         C7N         N7N        H71N       0.000     5.0     2
+NDP            sp3_sp3_55         C4B         C5B         O5B          PA     180.000    10.0     3
+NDP             sp2_sp3_7         C6N         C5N         C4N         C3N       0.000    10.0     6
+NDP             sp2_sp2_9         C4N         C5N         C6N         N1N       0.000     5.0     2
+NDP            sp3_sp3_58         O4B         C4B         C5B         O5B     180.000    10.0     3
+NDP             sp3_sp3_2         C5B         C4B         O4B         C1B     -60.000    10.0     3
+NDP            sp3_sp3_71         O3B         C3B         C4B         C5B     180.000    10.0     3
+NDP             sp3_sp3_4         C2B         C1B         O4B         C4B     -60.000    10.0     3
+NDP            sp3_sp3_76         C4B         C3B         O3B        HO3A     180.000    10.0     3
+NDP            sp3_sp3_20         O2B         C2B         C3B         O3B     -60.000    10.0     3
+NDP            sp3_sp3_79         C3B         C2B         O2B         P2B     180.000    10.0     3
+NDP             sp3_sp3_8         O4B         C1B         C2B         O2B     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+NDP    chir_1    PA    O3    O5B    O2A    both
+NDP    chir_2    C4B    O4B    C3B    C5B    negative
+NDP    chir_3    C3B    O3B    C2B    C4B    negative
+NDP    chir_4    C2B    O2B    C1B    C3B    negative
+NDP    chir_5    C1B    O4B    N9A    C2B    negative
+NDP    chir_6    PN    O3    O5D    O2N    both
+NDP    chir_7    C4D    O4D    C3D    C5D    negative
+NDP    chir_8    C3D    O3D    C4D    C2D    positive
+NDP    chir_9    C2D    O2D    C1D    C3D    negative
+NDP    chir_10    C1D    O4D    N1N    C2D    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+NDP    plan-1         C1B   0.020
+NDP    plan-1         C2A   0.020
+NDP    plan-1         C4A   0.020
+NDP    plan-1         C5A   0.020
+NDP    plan-1         C6A   0.020
+NDP    plan-1         C8A   0.020
+NDP    plan-1         H2A   0.020
+NDP    plan-1         H8A   0.020
+NDP    plan-1         N1A   0.020
+NDP    plan-1         N3A   0.020
+NDP    plan-1         N6A   0.020
+NDP    plan-1         N7A   0.020
+NDP    plan-1         N9A   0.020
+NDP    plan-2         C6A   0.020
+NDP    plan-2        H61A   0.020
+NDP    plan-2        H62A   0.020
+NDP    plan-2         N6A   0.020
+NDP    plan-3         C1D   0.020
+NDP    plan-3         C2N   0.020
+NDP    plan-3         C6N   0.020
+NDP    plan-3         N1N   0.020
+NDP    plan-4         C2N   0.020
+NDP    plan-4         C3N   0.020
+NDP    plan-4         H2N   0.020
+NDP    plan-4         N1N   0.020
+NDP    plan-5         C2N   0.020
+NDP    plan-5         C3N   0.020
+NDP    plan-5         C4N   0.020
+NDP    plan-5         C7N   0.020
+NDP    plan-6         C3N   0.020
+NDP    plan-6         C7N   0.020
+NDP    plan-6         N7N   0.020
+NDP    plan-6         O7N   0.020
+NDP    plan-7         C7N   0.020
+NDP    plan-7        H71N   0.020
+NDP    plan-7        H72N   0.020
+NDP    plan-7         N7N   0.020
+NDP    plan-8         C4N   0.020
+NDP    plan-8         C5N   0.020
+NDP    plan-8         C6N   0.020
+NDP    plan-8         H5N   0.020
+NDP    plan-9         C5N   0.020
+NDP    plan-9         C6N   0.020
+NDP    plan-9         H6N   0.020
+NDP    plan-9         N1N   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+NDP SMILES_CANONICAL               CACTVS 3.341                                                                                                                                                                                  NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
+NDP           SMILES               CACTVS 3.341                                                                                                                                                                                                NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
+NDP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                                                                                                           c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
+NDP           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                                                                                                                      c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
+NDP            InChI                InChI  1.03 InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
+NDP         InChIKey                InChI  1.03                                                                                                                                                                                                                                                                                             ACFIXJIJDZMPPO-NNYOXOHSSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+NDP acedrg               243         "dictionary generator"                  
+NDP acedrg_database      11          "data source"                           
+NDP rdkit                2017.03.2   "Chemoinformatics tool"
+NDP refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/NI.cif b/image_analysis/structure_refinement/monomers/NI.cif
new file mode 100644
index 000000000..fb5249865
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/NI.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+NI NI 'NICKEL (II) ION                     ' NON-POLYMER 1 1 .
+
+data_comp_NI
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+NI NI NI NI 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+NI NI n/a . END
diff --git a/image_analysis/structure_refinement/monomers/OMC.cif b/image_analysis/structure_refinement/monomers/OMC.cif
new file mode 100644
index 000000000..47bb94cb7
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/OMC.cif
@@ -0,0 +1,268 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+OMC     OMC      "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE"     RNA     36     22     .     
+#
+data_comp_OMC
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+OMC     N1      N       NR6     0       47.593      -6.375      -2.504      
+OMC     C2      C       CR6     0       46.926      -6.660      -1.298      
+OMC     N3      N       NRD6    0       45.724      -6.070      -1.053      
+OMC     C4      C       CR6     0       45.173      -5.232      -1.946      
+OMC     C5      C       CR16    0       45.830      -4.936      -3.175      
+OMC     C6      C       CR16    0       47.017      -5.523      -3.411      
+OMC     O2      O       O       0       47.439      -7.436      -0.475      
+OMC     N4      N       NH2     0       43.999      -4.688      -1.651      
+OMC     "C1'"   C       CH1     0       48.910      -7.010      -2.809      
+OMC     "C2'"   C       CH1     0       48.823      -8.062      -3.926      
+OMC     "O2'"   O       O2      0       49.366      -9.304      -3.486      
+OMC     CM2     C       CH3     0       48.416      -10.158     -2.852      
+OMC     "C3'"   C       CH1     0       49.625      -7.429      -5.073      
+OMC     "C4'"   C       CH1     0       50.603      -6.511      -4.332      
+OMC     "O4'"   O       O2      0       49.817      -6.011      -3.225      
+OMC     "O3'"   O       OH1     0       50.326      -8.382      -5.862      
+OMC     "C5'"   C       CH2     0       51.176      -5.361      -5.125      
+OMC     "O5'"   O       O2      0       50.108      -4.463      -5.525      
+OMC     P       P       P       0       50.445      -3.257      -6.544      
+OMC     OP1     O       O       0       49.150      -2.486      -6.714      
+OMC     OP2     O       OP      -1      50.910      -3.918      -7.829      
+OMC     OP3     O       OP      -1      51.534      -2.441      -5.874      
+OMC     H5      H       H       0       45.449      -4.350      -3.805      
+OMC     H6      H       H       0       47.471      -5.349      -4.209      
+OMC     HN41    H       H       0       43.650      -4.086      -2.185      
+OMC     HN42    H       H       0       43.572      -4.931      -0.922      
+OMC     "H1'"   H       H       0       49.270      -7.434      -1.997      
+OMC     "H2'"   H       H       0       47.883      -8.180      -4.213      
+OMC     HM21    H       H       0       48.873      -10.933     -2.488      
+OMC     HM22    H       H       0       47.756      -10.447     -3.504      
+OMC     HM23    H       H       0       47.974      -9.675      -2.135      
+OMC     "H3'"   H       H       0       49.020      -6.893      -5.647      
+OMC     "H4'"   H       H       0       51.347      -7.043      -3.976      
+OMC     "HO3'"  H       H       0       50.750      -7.973      -6.473      
+OMC     "H5'"   H       H       0       51.639      -5.709      -5.926      
+OMC     "H5''"  H       H       0       51.834      -4.872      -4.571      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+OMC          N1          C2      SINGLE       y     1.397  0.0100     1.397  0.0100
+OMC          N1          C6      SINGLE       y     1.364  0.0108     1.364  0.0108
+OMC          N1       "C1'"      SINGLE       n     1.487  0.0100     1.487  0.0100
+OMC          C2          N3      SINGLE       y     1.355  0.0119     1.355  0.0119
+OMC          C2          O2      DOUBLE       n     1.241  0.0100     1.241  0.0100
+OMC          N3          C4      DOUBLE       y     1.339  0.0110     1.339  0.0110
+OMC          C4          C5      SINGLE       y     1.422  0.0123     1.422  0.0123
+OMC          C4          N4      SINGLE       n     1.325  0.0109     1.325  0.0109
+OMC          C5          C6      DOUBLE       y     1.342  0.0100     1.342  0.0100
+OMC       "C1'"       "C2'"      SINGLE       n     1.531  0.0100     1.531  0.0100
+OMC       "C1'"       "O4'"      SINGLE       n     1.411  0.0100     1.411  0.0100
+OMC       "C2'"       "O2'"      SINGLE       n     1.423  0.0100     1.423  0.0100
+OMC       "C2'"       "C3'"      SINGLE       n     1.530  0.0134     1.530  0.0134
+OMC       "O2'"         CM2      SINGLE       n     1.423  0.0131     1.423  0.0131
+OMC       "C3'"       "C4'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+OMC       "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+OMC       "C4'"       "O4'"      SINGLE       n     1.451  0.0111     1.451  0.0111
+OMC       "C4'"       "C5'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+OMC       "C5'"       "O5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+OMC       "O5'"           P      SINGLE       n     1.614  0.0178     1.614  0.0178
+OMC           P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+OMC           P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+OMC           P         OP3      SINGLE       n     1.517  0.0192     1.517  0.0192
+OMC          C5          H5      SINGLE       n     1.082  0.0130     0.941  0.0174
+OMC          C6          H6      SINGLE       n     1.082  0.0130     0.935  0.0143
+OMC          N4        HN41      SINGLE       n     1.016  0.0100     0.877  0.0200
+OMC          N4        HN42      SINGLE       n     1.016  0.0100     0.877  0.0200
+OMC       "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.985  0.0100
+OMC       "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.988  0.0200
+OMC         CM2        HM21      SINGLE       n     1.089  0.0100     0.971  0.0146
+OMC         CM2        HM22      SINGLE       n     1.089  0.0100     0.971  0.0146
+OMC         CM2        HM23      SINGLE       n     1.089  0.0100     0.971  0.0146
+OMC       "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+OMC       "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+OMC       "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+OMC       "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+OMC       "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+OMC          C2          N1          C6     120.510    1.50
+OMC          C2          N1       "C1'"     118.189    2.26
+OMC          C6          N1       "C1'"     121.301    1.52
+OMC          N1          C2          N3     118.920    1.50
+OMC          N1          C2          O2     118.716    1.50
+OMC          N3          C2          O2     122.370    1.50
+OMC          C2          N3          C4     120.266    1.50
+OMC          N3          C4          C5     121.269    1.50
+OMC          N3          C4          N4     117.855    1.50
+OMC          C5          C4          N4     120.876    1.50
+OMC          C4          C5          C6     117.808    1.50
+OMC          C4          C5          H5     121.350    1.50
+OMC          C6          C5          H5     120.848    1.50
+OMC          N1          C6          C5     121.215    1.50
+OMC          N1          C6          H6     118.510    1.50
+OMC          C5          C6          H6     120.275    1.75
+OMC          C4          N4        HN41     119.818    1.59
+OMC          C4          N4        HN42     119.818    1.59
+OMC        HN41          N4        HN42     120.363    1.85
+OMC          N1       "C1'"       "C2'"     113.620    1.99
+OMC          N1       "C1'"       "O4'"     108.667    1.50
+OMC          N1       "C1'"       "H1'"     109.166    1.50
+OMC       "C2'"       "C1'"       "O4'"     106.391    1.51
+OMC       "C2'"       "C1'"       "H1'"     109.527    1.54
+OMC       "O4'"       "C1'"       "H1'"     109.327    1.50
+OMC       "C1'"       "C2'"       "O2'"     110.738    2.44
+OMC       "C1'"       "C2'"       "C3'"     101.207    1.50
+OMC       "C1'"       "C2'"       "H2'"     110.561    1.96
+OMC       "O2'"       "C2'"       "C3'"     112.623    3.00
+OMC       "O2'"       "C2'"       "H2'"     110.257    1.68
+OMC       "C3'"       "C2'"       "H2'"     110.255    2.04
+OMC       "C2'"       "O2'"         CM2     113.084    1.50
+OMC       "O2'"         CM2        HM21     109.434    1.50
+OMC       "O2'"         CM2        HM22     109.434    1.50
+OMC       "O2'"         CM2        HM23     109.434    1.50
+OMC        HM21         CM2        HM22     109.541    1.50
+OMC        HM21         CM2        HM23     109.541    1.50
+OMC        HM22         CM2        HM23     109.541    1.50
+OMC       "C2'"       "C3'"       "C4'"     102.352    1.50
+OMC       "C2'"       "C3'"       "O3'"     112.463    2.73
+OMC       "C2'"       "C3'"       "H3'"     110.255    2.04
+OMC       "C4'"       "C3'"       "O3'"     111.281    2.46
+OMC       "C4'"       "C3'"       "H3'"     110.452    2.54
+OMC       "O3'"       "C3'"       "H3'"     110.380    1.67
+OMC       "C3'"       "C4'"       "O4'"     104.439    1.50
+OMC       "C3'"       "C4'"       "C5'"     116.008    1.52
+OMC       "C3'"       "C4'"       "H4'"     109.363    1.86
+OMC       "O4'"       "C4'"       "C5'"     109.615    1.50
+OMC       "O4'"       "C4'"       "H4'"     108.698    1.50
+OMC       "C5'"       "C4'"       "H4'"     108.268    1.50
+OMC       "C1'"       "O4'"       "C4'"     109.578    1.50
+OMC       "C3'"       "O3'"      "HO3'"     108.744    3.00
+OMC       "C4'"       "C5'"       "O5'"     109.342    1.50
+OMC       "C4'"       "C5'"       "H5'"     109.624    1.50
+OMC       "C4'"       "C5'"      "H5''"     109.624    1.50
+OMC       "O5'"       "C5'"       "H5'"     109.845    1.50
+OMC       "O5'"       "C5'"      "H5''"     109.845    1.50
+OMC       "H5'"       "C5'"      "H5''"     108.472    1.50
+OMC       "C5'"       "O5'"           P     118.783    1.50
+OMC       "O5'"           P         OP1     105.808    2.07
+OMC       "O5'"           P         OP2     105.808    2.07
+OMC       "O5'"           P         OP3     105.808    2.07
+OMC         OP1           P         OP2     112.864    1.69
+OMC         OP1           P         OP3     112.864    1.69
+OMC         OP2           P         OP3     112.864    1.69
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+OMC     C2e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+OMC     C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2"      340.700       6.300     1     
+OMC     C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+OMC     C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+OMC     C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+OMC     C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+OMC     C3e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+OMC     C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+OMC     C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+OMC     C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+OMC     C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+OMC     C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+OMC     alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+OMC     beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+OMC     epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+OMC     gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+OMC       const_sp2_sp2_3          O2          C2          N1          C6     180.000     5.0     2
+OMC              const_17          C5          C6          N1          C2       0.000    10.0     2
+OMC            sp3_sp3_37        HM21         CM2       "O2'"       "C2'"     180.000    10.0     3
+OMC       const_sp2_sp2_6          O2          C2          N3          C4     180.000     5.0     2
+OMC       const_sp2_sp2_8          N4          C4          N3          C2     180.000     5.0     2
+OMC              const_11          N4          C4          C5          C6     180.000    10.0     2
+OMC             sp2_sp2_3          N3          C4          N4        HN41       0.000     5.0     2
+OMC              const_13          C4          C5          C6          N1       0.000    10.0     2
+OMC            sp3_sp3_34       "C1'"       "C2'"       "O2'"         CM2     180.000    10.0     3
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+OMC    chir_1    "C1'"    "O4'"    N1    "C2'"    negative
+OMC    chir_2    "C2'"    "O2'"    "C1'"    "C3'"    negative
+OMC    chir_3    "C3'"    "O3'"    "C2'"    "C4'"    negative
+OMC    chir_4    "C4'"    "O4'"    "C3'"    "C5'"    negative
+OMC    chir_5    P    "O5'"    OP2    OP3    both
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+OMC    plan-1       "C1'"   0.020
+OMC    plan-1          C2   0.020
+OMC    plan-1          C4   0.020
+OMC    plan-1          C5   0.020
+OMC    plan-1          C6   0.020
+OMC    plan-1          H5   0.020
+OMC    plan-1          H6   0.020
+OMC    plan-1          N1   0.020
+OMC    plan-1          N3   0.020
+OMC    plan-1          N4   0.020
+OMC    plan-1          O2   0.020
+OMC    plan-2          C4   0.020
+OMC    plan-2        HN41   0.020
+OMC    plan-2        HN42   0.020
+OMC    plan-2          N4   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+OMC           SMILES              ACDLabs 10.04                                                                                                                 O=C1N=C(N)C=CN1C2OC(C(O)C2OC)COP(=O)(O)O
+OMC SMILES_CANONICAL               CACTVS 3.341                                                                                             CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N
+OMC           SMILES               CACTVS 3.341                                                                                                   CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N
+OMC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                               CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
+OMC           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                                 COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
+OMC            InChI                InChI  1.03 InChI=1S/C10H16N3O8P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1
+OMC         InChIKey                InChI  1.03                                                                                                                              USRXKJOTSNCJMA-ZOQUXTDFSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+OMC acedrg               243         "dictionary generator"                  
+OMC acedrg_database      11          "data source"                           
+OMC rdkit                2017.03.2   "Chemoinformatics tool"
+OMC refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/OMG.cif b/image_analysis/structure_refinement/monomers/OMG.cif
new file mode 100644
index 000000000..f0bb41e3a
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/OMG.cif
@@ -0,0 +1,294 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+OMG OMG "O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE" RNA 39 25 .
+
+data_comp_OMG
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+OMG P      P P    0  46.680 -11.593 -10.172
+OMG OP1    O O    0  46.840 -10.158 -9.706
+OMG OP2    O OP   -1 47.443 -11.887 -11.449
+OMG OP3    O OP   -1 46.957 -12.602 -9.074
+OMG "O5'"  O O2   0  45.118 -11.766 -10.543
+OMG "C5'"  C CH2  0  44.556 -10.952 -11.605
+OMG "C4'"  C CH1  0  43.054 -11.106 -11.627
+OMG "O4'"  O O2   0  42.713 -12.507 -11.779
+OMG "C3'"  C CH1  0  42.306 -10.664 -10.364
+OMG "O3'"  O OH1  0  42.080 -9.260  -10.371
+OMG "C2'"  C CH1  0  41.018 -11.485 -10.465
+OMG "O2'"  O O2   0  40.048 -10.870 -11.308
+OMG CM2    C CH3  0  38.711 -11.301 -11.064
+OMG "C1'"  C CH1  0  41.518 -12.794 -11.083
+OMG N9     N NR5  0  41.769 -13.832 -10.083
+OMG C8     C CR15 0  42.971 -14.402 -9.735
+OMG N7     N NRD5 0  42.865 -15.317 -8.802
+OMG C5     C CR56 0  41.507 -15.358 -8.517
+OMG C6     C CR6  0  40.790 -16.159 -7.588
+OMG O6     O O    0  41.238 -17.015 -6.813
+OMG N1     N NR16 0  39.417 -15.883 -7.616
+OMG C2     C CR6  0  38.813 -14.955 -8.435
+OMG N2     N NH2  0  37.484 -14.824 -8.326
+OMG N3     N NRD6 0  39.486 -14.200 -9.310
+OMG C4     C CR56 0  40.821 -14.453 -9.301
+OMG "H5'"  H H    0  44.931 -11.234 -12.476
+OMG "H5''" H H    0  44.789 -10.002 -11.458
+OMG "H4'"  H H    0  42.707 -10.610 -12.398
+OMG "H3'"  H H    0  42.809 -10.925 -9.551
+OMG "HO3'" H H    0  41.566 -9.062  -9.725
+OMG "H2'"  H H    0  40.648 -11.625 -9.558
+OMG HM21   H H    0  38.118 -10.894 -11.717
+OMG HM22   H H    0  38.441 -11.032 -10.171
+OMG HM23   H H    0  38.663 -12.267 -11.141
+OMG "H1'"  H H    0  40.844 -13.122 -11.720
+OMG H8     H H    0  43.793 -14.159 -10.125
+OMG HN1    H H    0  38.896 -16.352 -7.054
+OMG HN21   H H    0  37.121 -14.025 -8.337
+OMG HN22   H H    0  36.980 -15.537 -8.245
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+OMG P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+OMG P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+OMG P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+OMG P     "O5'"  SINGLE n 1.614 0.0178 1.614 0.0178
+OMG "O5'" "C5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+OMG "C5'" "C4'"  SINGLE n 1.509 0.0100 1.509 0.0100
+OMG "C4'" "O4'"  SINGLE n 1.451 0.0100 1.451 0.0100
+OMG "C4'" "C3'"  SINGLE n 1.535 0.0100 1.535 0.0100
+OMG "O4'" "C1'"  SINGLE n 1.409 0.0100 1.409 0.0100
+OMG "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+OMG "C3'" "C2'"  SINGLE n 1.530 0.0134 1.530 0.0134
+OMG "C2'" "O2'"  SINGLE n 1.423 0.0100 1.423 0.0100
+OMG "C2'" "C1'"  SINGLE n 1.527 0.0100 1.527 0.0100
+OMG "O2'" CM2    SINGLE n 1.423 0.0131 1.423 0.0131
+OMG "C1'" N9     SINGLE n 1.458 0.0100 1.458 0.0100
+OMG N9    C8     SINGLE y 1.372 0.0100 1.372 0.0100
+OMG N9    C4     SINGLE y 1.375 0.0100 1.375 0.0100
+OMG C8    N7     DOUBLE y 1.312 0.0100 1.312 0.0100
+OMG N7    C5     SINGLE y 1.390 0.0100 1.390 0.0100
+OMG C5    C6     SINGLE y 1.417 0.0103 1.417 0.0103
+OMG C5    C4     DOUBLE y 1.377 0.0100 1.377 0.0100
+OMG C6    O6     DOUBLE n 1.239 0.0100 1.239 0.0100
+OMG C6    N1     SINGLE y 1.396 0.0107 1.396 0.0107
+OMG N1    C2     SINGLE y 1.374 0.0100 1.374 0.0100
+OMG C2    N2     SINGLE n 1.340 0.0101 1.340 0.0101
+OMG C2    N3     DOUBLE y 1.333 0.0104 1.333 0.0104
+OMG N3    C4     SINGLE y 1.355 0.0100 1.355 0.0100
+OMG "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+OMG "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+OMG "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+OMG "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+OMG "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+OMG "C2'" "H2'"  SINGLE n 1.089 0.0100 0.988 0.0200
+OMG CM2   HM21   SINGLE n 1.089 0.0100 0.971 0.0146
+OMG CM2   HM22   SINGLE n 1.089 0.0100 0.971 0.0146
+OMG CM2   HM23   SINGLE n 1.089 0.0100 0.971 0.0146
+OMG "C1'" "H1'"  SINGLE n 1.089 0.0100 0.984 0.0200
+OMG C8    H8     SINGLE n 1.082 0.0130 0.942 0.0170
+OMG N1    HN1    SINGLE n 1.016 0.0100 0.897 0.0200
+OMG N2    HN21   SINGLE n 1.016 0.0100 0.877 0.0200
+OMG N2    HN22   SINGLE n 1.016 0.0100 0.877 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+OMG OP1   P     OP2    112.864 1.69
+OMG OP1   P     OP3    112.864 1.69
+OMG OP1   P     "O5'"  105.808 2.07
+OMG OP2   P     OP3    112.864 1.69
+OMG OP2   P     "O5'"  105.808 2.07
+OMG OP3   P     "O5'"  105.808 2.07
+OMG P     "O5'" "C5'"  118.783 1.50
+OMG "O5'" "C5'" "C4'"  109.342 1.50
+OMG "O5'" "C5'" "H5'"  109.845 1.50
+OMG "O5'" "C5'" "H5''" 109.845 1.50
+OMG "C4'" "C5'" "H5'"  109.624 1.50
+OMG "C4'" "C5'" "H5''" 109.624 1.50
+OMG "H5'" "C5'" "H5''" 108.472 1.50
+OMG "C5'" "C4'" "O4'"  109.123 1.50
+OMG "C5'" "C4'" "C3'"  116.008 1.52
+OMG "C5'" "C4'" "H4'"  108.268 1.50
+OMG "O4'" "C4'" "C3'"  105.388 1.50
+OMG "O4'" "C4'" "H4'"  108.947 1.50
+OMG "C3'" "C4'" "H4'"  109.363 1.86
+OMG "C4'" "O4'" "C1'"  109.903 1.50
+OMG "C4'" "C3'" "O3'"  111.281 2.46
+OMG "C4'" "C3'" "C2'"  102.352 1.50
+OMG "C4'" "C3'" "H3'"  110.452 2.54
+OMG "O3'" "C3'" "C2'"  112.463 2.73
+OMG "O3'" "C3'" "H3'"  110.380 1.67
+OMG "C2'" "C3'" "H3'"  110.255 2.04
+OMG "C3'" "O3'" "HO3'" 108.744 3.00
+OMG "C3'" "C2'" "O2'"  112.623 3.00
+OMG "C3'" "C2'" "C1'"  101.388 1.50
+OMG "C3'" "C2'" "H2'"  110.255 2.04
+OMG "O2'" "C2'" "C1'"  110.738 2.44
+OMG "O2'" "C2'" "H2'"  110.257 1.68
+OMG "C1'" "C2'" "H2'"  111.584 1.94
+OMG "C2'" "O2'" CM2    113.084 1.50
+OMG "O2'" CM2   HM21   109.434 1.50
+OMG "O2'" CM2   HM22   109.434 1.50
+OMG "O2'" CM2   HM23   109.434 1.50
+OMG HM21  CM2   HM22   109.541 1.50
+OMG HM21  CM2   HM23   109.541 1.50
+OMG HM22  CM2   HM23   109.541 1.50
+OMG "O4'" "C1'" "C2'"  106.765 1.50
+OMG "O4'" "C1'" N9     108.477 1.50
+OMG "O4'" "C1'" "H1'"  109.807 1.50
+OMG "C2'" "C1'" N9     112.584 1.50
+OMG "C2'" "C1'" "H1'"  109.263 1.50
+OMG N9    "C1'" "H1'"  109.561 1.50
+OMG "C1'" N9    C8     126.829 1.91
+OMG "C1'" N9    C4     127.440 1.80
+OMG C8    N9    C4     105.731 1.50
+OMG N9    C8    N7     113.507 1.50
+OMG N9    C8    H8     123.187 1.50
+OMG N7    C8    H8     123.307 1.50
+OMG C8    N7    C5     104.778 1.50
+OMG N7    C5    C6     130.030 1.50
+OMG N7    C5    C4     110.574 1.50
+OMG C6    C5    C4     119.397 1.50
+OMG C5    C6    O6     128.244 1.50
+OMG C5    C6    N1     111.367 1.50
+OMG O6    C6    N1     120.389 1.50
+OMG C6    N1    C2     125.351 1.50
+OMG C6    N1    HN1    116.978 2.44
+OMG C2    N1    HN1    117.677 2.71
+OMG N1    C2    N2     116.576 1.50
+OMG N1    C2    N3     123.602 1.50
+OMG N2    C2    N3     119.821 1.50
+OMG C2    N2    HN21   119.868 1.50
+OMG C2    N2    HN22   119.868 1.50
+OMG HN21  N2    HN22   120.263 1.96
+OMG C2    N3    C4     112.066 1.50
+OMG N9    C4    C5     105.411 1.50
+OMG N9    C4    N3     126.378 1.50
+OMG C5    C4    N3     128.211 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+OMG C2e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+OMG C2e-nyu0        "C4'" "O4'" "C1'" "C2'"  340.700 6.300  1
+OMG C2e-nyu1        "O4'" "C1'" "C2'" "C3'"  32.800  4.900  1
+OMG C2e-nyu2        "C1'" "C2'" "C3'" "C4'"  326.9   3.600  1
+OMG C2e-nyu3        "C2'" "C3'" "C4'" "O4'"  22.600  4.500  1
+OMG C2e-nyu4        "C3'" "C4'" "O4'" "C1'"  357.700 6.100  1
+OMG C3e-chi         "O4'" "C1'" N9    C4     210.000 10.000 6
+OMG C3e-nyu0        "C4'" "O4'" "C1'" "C2'"  2.8     6.100  1
+OMG C3e-nyu1        "O4'" "C1'" "C2'" "C3'"  335.00  4.900  1
+OMG C3e-nyu2        "C1'" "C2'" "C3'" "C4'"  35.9    2.800  1
+OMG C3e-nyu3        "C2'" "C3'" "C4'" "O4'"  324.700 3.100  1
+OMG C3e-nyu4        "C3'" "C4'" "O4'" "C1'"  20.500  5.100  1
+OMG alpha           "C5'" "O5'" P     OP3    -60.000 10.00  3
+OMG beta            P     "O5'" "C5'" "C4'"  180.000 10.00  3
+OMG epsi            "C4'" "C3'" "O3'" "HO3'" 180.000 10.00  3
+OMG gamma           "O5'" "C5'" "C4'" "C3'"  180.000 10.00  3
+OMG sp3_sp3_52      "C3'" "C2'" "O2'" CM2    180.000 10.0   3
+OMG sp3_sp3_55      HM21  CM2   "O2'" "C2'"  180.000 10.0   3
+OMG const_18        N7    C8    N9    "C1'"  180.000 10.0   2
+OMG const_30        C5    C4    N9    "C1'"  180.000 10.0   2
+OMG const_21        N9    C8    N7    C5     0.000   10.0   2
+OMG const_24        C6    C5    N7    C8     180.000 10.0   2
+OMG const_sp2_sp2_4 N7    C5    C6    O6     0.000   5.0    2
+OMG const_25        N9    C4    C5    N7     0.000   10.0   2
+OMG const_sp2_sp2_7 O6    C6    N1    C2     180.000 5.0    2
+OMG const_11        N2    C2    N1    C6     180.000 10.0   2
+OMG sp2_sp2_1       N1    C2    N2    HN21   180.000 5.0    2
+OMG const_14        N2    C2    N3    C4     180.000 10.0   2
+OMG const_16        N9    C4    N3    C2     180.000 10.0   2
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+OMG chir_1 P     "O5'" OP2   OP3   both
+OMG chir_2 "C4'" "O4'" "C3'" "C5'" negative
+OMG chir_3 "C3'" "O3'" "C2'" "C4'" negative
+OMG chir_4 "C2'" "O2'" "C1'" "C3'" negative
+OMG chir_5 "C1'" "O4'" N9    "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+OMG plan-1 "C1'" 0.020
+OMG plan-1 C2    0.020
+OMG plan-1 C4    0.020
+OMG plan-1 C5    0.020
+OMG plan-1 C6    0.020
+OMG plan-1 C8    0.020
+OMG plan-1 H8    0.020
+OMG plan-1 HN1   0.020
+OMG plan-1 N1    0.020
+OMG plan-1 N2    0.020
+OMG plan-1 N3    0.020
+OMG plan-1 N7    0.020
+OMG plan-1 N9    0.020
+OMG plan-1 O6    0.020
+OMG plan-2 C2    0.020
+OMG plan-2 HN21  0.020
+OMG plan-2 HN22  0.020
+OMG plan-2 N2    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+OMG SMILES           ACDLabs              10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3OC)COP(=O)(O)O
+OMG SMILES_CANONICAL CACTVS               3.341 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2cnc3C(=O)NC(=Nc23)N
+OMG SMILES           CACTVS               3.341 CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1n2cnc3C(=O)NC(=Nc23)N
+OMG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O
+OMG SMILES           "OpenEye OEToolkits" 1.5.0 COC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O
+OMG InChI            InChI                1.03  InChI=1S/C11H16N5O8P/c1-22-7-6(17)4(2-23-25(19,20)21)24-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,21)(H3,12,14,15,18)/t4-,6-,7-,10-/m1/s1
+OMG InChIKey         InChI                1.03  YPMKZCOIEXUDSS-KQYNXXCUSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+OMG acedrg          243       "dictionary generator"
+OMG acedrg_database 11        "data source"
+OMG rdkit           2017.03.2 "Chemoinformatics tool"
+OMG refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/OMU.cif b/image_analysis/structure_refinement/monomers/OMU.cif
new file mode 100644
index 000000000..4fff76f20
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/OMU.cif
@@ -0,0 +1,266 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+OMU OMU "O2'-METHYLURIDINE 5'-MONOPHOSPHATE" RNA 35 22 .
+
+data_comp_OMU
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+OMU N1     N NR6  0  7.321  3.277  -7.800
+OMU C2     C CR6  0  6.703  4.284  -8.539
+OMU N3     N NR16 0  5.357  4.097  -8.759
+OMU C4     C CR6  0  4.576  3.040  -8.325
+OMU C5     C CR16 0  5.282  2.046  -7.565
+OMU C6     C CR16 0  6.597  2.199  -7.332
+OMU O2     O O    0  7.289  5.268  -8.976
+OMU O4     O O    0  3.377  3.016  -8.605
+OMU "C1'"  C CH1  0  8.775  3.398  -7.507
+OMU "C2'"  C CH1  0  9.066  3.720  -6.033
+OMU "O2'"  O O2   0  9.918  4.857  -5.928
+OMU CM2    C CH3  0  9.221  6.100  -5.894
+OMU "C3'"  C CH1  0  9.716  2.430  -5.513
+OMU "C4'"  C CH1  0  10.361 1.849  -6.776
+OMU "O3'"  O OH1  0  10.695 2.660  -4.506
+OMU "O4'"  O O2   0  9.408  2.172  -7.816
+OMU "C5'"  C CH2  0  10.637 0.365  -6.768
+OMU "O5'"  O O2   0  9.387  -0.365 -6.663
+OMU P      P P    0  9.434  -1.955 -6.390
+OMU OP1    O O    0  10.088 -2.124 -5.032
+OMU OP2    O OP   -1 7.990  -2.420 -6.410
+OMU OP3    O OP   -1 10.258 -2.544 -7.519
+OMU HN3    H H    0  4.952  4.733  -9.234
+OMU H5     H H    0  4.828  1.299  -7.235
+OMU H6     H H    0  7.045  1.542  -6.834
+OMU "H1'"  H H    0  9.170  4.096  -8.070
+OMU "H2'"  H H    0  8.220  3.878  -5.544
+OMU HM21   H H    0  9.861  6.830  -5.932
+OMU HM22   H H    0  8.710  6.162  -5.071
+OMU HM23   H H    0  8.620  6.157  -6.654
+OMU "H3'"  H H    0  9.016  1.816  -5.172
+OMU "H4'"  H H    0  11.202 2.320  -6.961
+OMU "HO3'" H H    0  11.018 1.914  -4.263
+OMU "H5'"  H H    0  11.221 0.141  -6.002
+OMU "H5''" H H    0  11.104 0.110  -7.601
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+OMU N1    C2     SINGLE y 1.383 0.0100 1.383 0.0100
+OMU N1    C6     SINGLE y 1.375 0.0106 1.375 0.0106
+OMU N1    "C1'"  SINGLE n 1.476 0.0133 1.476 0.0133
+OMU C2    N3     SINGLE y 1.372 0.0112 1.372 0.0112
+OMU C2    O2     DOUBLE n 1.224 0.0111 1.224 0.0111
+OMU N3    C4     SINGLE y 1.381 0.0100 1.381 0.0100
+OMU C4    C5     SINGLE y 1.434 0.0100 1.434 0.0100
+OMU C4    O4     DOUBLE n 1.231 0.0100 1.231 0.0100
+OMU C5    C6     DOUBLE y 1.342 0.0100 1.342 0.0100
+OMU "C1'" "C2'"  SINGLE n 1.531 0.0100 1.531 0.0100
+OMU "C1'" "O4'"  SINGLE n 1.412 0.0100 1.412 0.0100
+OMU "C2'" "O2'"  SINGLE n 1.423 0.0100 1.423 0.0100
+OMU "C2'" "C3'"  SINGLE n 1.530 0.0134 1.530 0.0134
+OMU "O2'" CM2    SINGLE n 1.423 0.0131 1.423 0.0131
+OMU "C3'" "C4'"  SINGLE n 1.535 0.0100 1.535 0.0100
+OMU "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+OMU "C4'" "O4'"  SINGLE n 1.451 0.0111 1.451 0.0111
+OMU "C4'" "C5'"  SINGLE n 1.509 0.0100 1.509 0.0100
+OMU "C5'" "O5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+OMU "O5'" P      SINGLE n 1.614 0.0178 1.614 0.0178
+OMU P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+OMU P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+OMU P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+OMU N3    HN3    SINGLE n 1.016 0.0100 0.889 0.0200
+OMU C5    H5     SINGLE n 1.082 0.0130 0.935 0.0100
+OMU C6    H6     SINGLE n 1.082 0.0130 0.938 0.0107
+OMU "C1'" "H1'"  SINGLE n 1.089 0.0100 0.981 0.0118
+OMU "C2'" "H2'"  SINGLE n 1.089 0.0100 0.988 0.0200
+OMU CM2   HM21   SINGLE n 1.089 0.0100 0.971 0.0146
+OMU CM2   HM22   SINGLE n 1.089 0.0100 0.971 0.0146
+OMU CM2   HM23   SINGLE n 1.089 0.0100 0.971 0.0146
+OMU "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+OMU "C4'" "H4'"  SINGLE n 1.089 0.0100 0.981 0.0200
+OMU "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+OMU "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+OMU "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+OMU C2    N1    C6     121.419 1.50
+OMU C2    N1    "C1'"  117.109 1.50
+OMU C6    N1    "C1'"  121.471 1.52
+OMU N1    C2    N3     114.848 1.50
+OMU N1    C2    O2     122.841 1.50
+OMU N3    C2    O2     122.311 1.50
+OMU C2    N3    C4     126.992 1.50
+OMU C2    N3    HN3    115.772 1.79
+OMU C4    N3    HN3    117.236 1.73
+OMU N3    C4    C5     114.659 1.50
+OMU N3    C4    O4     119.401 1.50
+OMU C5    C4    O4     125.940 1.50
+OMU C4    C5    C6     119.525 1.50
+OMU C4    C5    H5     120.151 1.50
+OMU C6    C5    H5     120.325 1.50
+OMU N1    C6    C5     122.557 1.50
+OMU N1    C6    H6     118.477 1.50
+OMU C5    C6    H6     118.966 1.50
+OMU N1    "C1'" "C2'"  113.620 1.99
+OMU N1    "C1'" "O4'"  108.667 1.50
+OMU N1    "C1'" "H1'"  109.166 1.50
+OMU "C2'" "C1'" "O4'"  106.391 1.51
+OMU "C2'" "C1'" "H1'"  109.527 1.54
+OMU "O4'" "C1'" "H1'"  109.327 1.50
+OMU "C1'" "C2'" "O2'"  110.738 2.44
+OMU "C1'" "C2'" "C3'"  101.207 1.50
+OMU "C1'" "C2'" "H2'"  110.561 1.96
+OMU "O2'" "C2'" "C3'"  112.623 3.00
+OMU "O2'" "C2'" "H2'"  110.257 1.68
+OMU "C3'" "C2'" "H2'"  110.255 2.04
+OMU "C2'" "O2'" CM2    113.084 1.50
+OMU "O2'" CM2   HM21   109.434 1.50
+OMU "O2'" CM2   HM22   109.434 1.50
+OMU "O2'" CM2   HM23   109.434 1.50
+OMU HM21  CM2   HM22   109.541 1.50
+OMU HM21  CM2   HM23   109.541 1.50
+OMU HM22  CM2   HM23   109.541 1.50
+OMU "C2'" "C3'" "C4'"  102.352 1.50
+OMU "C2'" "C3'" "O3'"  112.463 2.73
+OMU "C2'" "C3'" "H3'"  110.255 2.04
+OMU "C4'" "C3'" "O3'"  111.281 2.46
+OMU "C4'" "C3'" "H3'"  110.452 2.54
+OMU "O3'" "C3'" "H3'"  110.380 1.67
+OMU "C3'" "C4'" "O4'"  104.439 1.50
+OMU "C3'" "C4'" "C5'"  116.008 1.52
+OMU "C3'" "C4'" "H4'"  109.363 1.86
+OMU "O4'" "C4'" "C5'"  109.615 1.50
+OMU "O4'" "C4'" "H4'"  108.698 1.50
+OMU "C5'" "C4'" "H4'"  108.268 1.50
+OMU "C3'" "O3'" "HO3'" 108.744 3.00
+OMU "C1'" "O4'" "C4'"  109.578 1.50
+OMU "C4'" "C5'" "O5'"  109.342 1.50
+OMU "C4'" "C5'" "H5'"  109.624 1.50
+OMU "C4'" "C5'" "H5''" 109.624 1.50
+OMU "O5'" "C5'" "H5'"  109.845 1.50
+OMU "O5'" "C5'" "H5''" 109.845 1.50
+OMU "H5'" "C5'" "H5''" 108.472 1.50
+OMU "C5'" "O5'" P      118.783 1.50
+OMU "O5'" P     OP1    105.808 2.07
+OMU "O5'" P     OP2    105.808 2.07
+OMU "O5'" P     OP3    105.808 2.07
+OMU OP1   P     OP2    112.864 1.69
+OMU OP1   P     OP3    112.864 1.69
+OMU OP2   P     OP3    112.864 1.69
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+OMU C2e-chi         "O4'" "C1'" N1    C2     210.000 10.000 6
+OMU C2e-nyu0        "C4'" "O4'" "C1'" "C2"   340.700 6.300  1
+OMU C2e-nyu1        "O4'" "C1'" "C2'" "C3'"  32.800  4.900  1
+OMU C2e-nyu2        "C1'" "C2'" "C3'" "C4'"  326.9   3.600  1
+OMU C2e-nyu3        "C2'" "C3'" "C4'" "O4'"  22.600  4.500  1
+OMU C2e-nyu4        "C3'" "C4'" "O4'" "C1'"  357.700 6.100  1
+OMU C3e-chi         "O4'" "C1'" N1    C2     210.000 10.000 6
+OMU C3e-nyu0        "C4'" "O4'" "C1'" "C2'"  2.8     6.100  1
+OMU C3e-nyu1        "O4'" "C1'" "C2'" "C3'"  335.00  4.900  1
+OMU C3e-nyu2        "C1'" "C2'" "C3'" "C4'"  35.9    2.800  1
+OMU C3e-nyu3        "C2'" "C3'" "C4'" "O4'"  324.700 3.100  1
+OMU C3e-nyu4        "C3'" "C4'" "O4'" "C1'"  20.500  5.100  1
+OMU alpha           "C5'" "O5'" P     OP3    -60.000 10.00  3
+OMU beta            P     "O5'" "C5'" "C4'"  180.000 10.00  3
+OMU epsi            "C4'" "C3'" "O3'" "HO3'" 180.000 10.00  3
+OMU gamma           "O5'" "C5'" "C4'" "C3'"  180.000 10.00  3
+OMU const_sp2_sp2_3 O2    C2    N1    C6     180.000 5.0    2
+OMU const_21        C5    C6    N1    C2     0.000   10.0   2
+OMU sp3_sp3_37      HM21  CM2   "O2'" "C2'"  180.000 10.0   3
+OMU const_sp2_sp2_7 O2    C2    N3    C4     180.000 5.0    2
+OMU const_11        O4    C4    N3    C2     180.000 10.0   2
+OMU const_15        O4    C4    C5    C6     180.000 10.0   2
+OMU const_17        C4    C5    C6    N1     0.000   10.0   2
+OMU sp3_sp3_34      "C1'" "C2'" "O2'" CM2    180.000 10.0   3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+OMU chir_1 "C1'" "O4'" N1    "C2'" negative
+OMU chir_2 "C2'" "O2'" "C1'" "C3'" negative
+OMU chir_3 "C3'" "O3'" "C2'" "C4'" negative
+OMU chir_4 "C4'" "O4'" "C3'" "C5'" negative
+OMU chir_5 P     "O5'" OP2   OP3   both
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+OMU plan-1 "C1'" 0.020
+OMU plan-1 C2    0.020
+OMU plan-1 C4    0.020
+OMU plan-1 C5    0.020
+OMU plan-1 C6    0.020
+OMU plan-1 H5    0.020
+OMU plan-1 H6    0.020
+OMU plan-1 HN3   0.020
+OMU plan-1 N1    0.020
+OMU plan-1 N3    0.020
+OMU plan-1 O2    0.020
+OMU plan-1 O4    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+OMU SMILES           ACDLabs              10.04 O=C1NC(=O)N(C=C1)C2OC(C(O)C2OC)COP(=O)(O)O
+OMU SMILES_CANONICAL CACTVS               3.341 CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O
+OMU SMILES           CACTVS               3.341 CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O
+OMU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
+OMU SMILES           "OpenEye OEToolkits" 1.5.0 COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
+OMU InChI            InChI                1.03  InChI=1S/C10H15N2O9P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1
+OMU InChIKey         InChI                1.03  FHMMECZNEPGJSJ-ZOQUXTDFSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+OMU acedrg          243       "dictionary generator"
+OMU acedrg_database 11        "data source"
+OMU rdkit           2017.03.2 "Chemoinformatics tool"
+OMU refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/OXY.cif b/image_analysis/structure_refinement/monomers/OXY.cif
new file mode 100644
index 000000000..2bc6ecfc7
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/OXY.cif
@@ -0,0 +1,57 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+OXY     OXY      "OXYGEN MOLECULE"     NON-POLYMER     2     2     .     
+#
+data_comp_OXY
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+OXY     O1      O       O       0       27.236      26.922      33.744      
+OXY     O2      O       O       0       26.684      27.385      32.771      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+OXY          O1          O2      DOUBLE       n     1.210  0.0200     1.210  0.0200
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+OXY SMILES_CANONICAL               CACTVS 3.341                         O=O
+OXY           SMILES               CACTVS 3.341                         O=O
+OXY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                         O=O
+OXY           SMILES "OpenEye OEToolkits" 1.5.0                         O=O
+OXY            InChI                InChI  1.03            InChI=1S/O2/c1-2
+OXY         InChIKey                InChI  1.03 MYMOFIZGZYHOMD-UHFFFAOYSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+OXY acedrg               243         "dictionary generator"                  
+OXY acedrg_database      11          "data source"                           
+OXY rdkit                2017.03.2   "Chemoinformatics tool"
+OXY refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/PEG.cif b/image_analysis/structure_refinement/monomers/PEG.cif
new file mode 100644
index 000000000..08009cba8
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/PEG.cif
@@ -0,0 +1,138 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+PEG     PEG      DI(HYDROXYETHYL)ETHER     NON-POLYMER     17     7     .     
+#
+data_comp_PEG
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+PEG     C1      C       CH2     0       41.561      37.152      47.063      
+PEG     O1      O       OH1     0       41.065      36.188      46.155      
+PEG     C2      C       CH2     0       42.802      36.690      47.759      
+PEG     O2      O       O2      0       42.505      35.564      48.578      
+PEG     C3      C       CH2     0       43.645      35.062      49.268      
+PEG     C4      C       CH2     0       43.253      33.888      50.109      
+PEG     O4      O       OH1     0       44.370      33.256      50.702      
+PEG     H11     H       H       0       40.870      37.346      47.731      
+PEG     H12     H       H       0       41.754      37.980      46.576      
+PEG     HO1     H       H       0       40.396      36.506      45.747      
+PEG     H21     H       H       0       43.160      37.417      48.314      
+PEG     H22     H       H       0       43.482      36.446      47.095      
+PEG     H31     H       H       0       44.023      35.766      49.839      
+PEG     H32     H       H       0       44.330      34.791      48.620      
+PEG     H41     H       H       0       42.777      33.237      49.552      
+PEG     H42     H       H       0       42.643      34.187      50.815      
+PEG     HO4     H       H       0       44.736      33.789      51.248      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+PEG          C1          O1      SINGLE       n     1.414  0.0200     1.414  0.0200
+PEG          C1          C2      SINGLE       n     1.496  0.0200     1.496  0.0200
+PEG          C2          O2      SINGLE       n     1.423  0.0106     1.423  0.0106
+PEG          O2          C3      SINGLE       n     1.423  0.0106     1.423  0.0106
+PEG          C3          C4      SINGLE       n     1.496  0.0200     1.496  0.0200
+PEG          C4          O4      SINGLE       n     1.414  0.0200     1.414  0.0200
+PEG          C1         H11      SINGLE       n     1.089  0.0100     0.980  0.0144
+PEG          C1         H12      SINGLE       n     1.089  0.0100     0.980  0.0144
+PEG          O1         HO1      SINGLE       n     0.970  0.0120     0.846  0.0200
+PEG          C2         H21      SINGLE       n     1.089  0.0100     0.982  0.0175
+PEG          C2         H22      SINGLE       n     1.089  0.0100     0.982  0.0175
+PEG          C3         H31      SINGLE       n     1.089  0.0100     0.982  0.0175
+PEG          C3         H32      SINGLE       n     1.089  0.0100     0.982  0.0175
+PEG          C4         H41      SINGLE       n     1.089  0.0100     0.980  0.0144
+PEG          C4         H42      SINGLE       n     1.089  0.0100     0.980  0.0144
+PEG          O4         HO4      SINGLE       n     0.970  0.0120     0.846  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+PEG          O1          C1          C2     112.284    1.56
+PEG          O1          C1         H11     109.012    1.50
+PEG          O1          C1         H12     109.012    1.50
+PEG          C2          C1         H11     109.198    1.50
+PEG          C2          C1         H12     109.198    1.50
+PEG         H11          C1         H12     108.093    1.50
+PEG          C1          O1         HO1     109.347    1.86
+PEG          C1          C2          O2     109.904    1.68
+PEG          C1          C2         H21     109.795    1.50
+PEG          C1          C2         H22     109.795    1.50
+PEG          O2          C2         H21     109.691    1.50
+PEG          O2          C2         H22     109.691    1.50
+PEG         H21          C2         H22     108.274    1.50
+PEG          C2          O2          C3     112.795    1.50
+PEG          O2          C3          C4     109.904    1.68
+PEG          O2          C3         H31     109.691    1.50
+PEG          O2          C3         H32     109.691    1.50
+PEG          C4          C3         H31     109.795    1.50
+PEG          C4          C3         H32     109.795    1.50
+PEG         H31          C3         H32     108.274    1.50
+PEG          C3          C4          O4     112.284    1.56
+PEG          C3          C4         H41     109.198    1.50
+PEG          C3          C4         H42     109.198    1.50
+PEG          O4          C4         H41     109.012    1.50
+PEG          O4          C4         H42     109.012    1.50
+PEG         H41          C4         H42     108.093    1.50
+PEG          C4          O4         HO4     109.347    1.86
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+PEG             sp3_sp3_1          C2          C1          O1         HO1     180.000    10.0     3
+PEG             sp3_sp3_4          O1          C1          C2          O2     180.000    10.0     3
+PEG            sp3_sp3_13          C1          C2          O2          C3     180.000    10.0     3
+PEG            sp3_sp3_16          C4          C3          O2          C2     180.000    10.0     3
+PEG            sp3_sp3_19          O2          C3          C4          O4     180.000    10.0     3
+PEG            sp3_sp3_28          C3          C4          O4         HO4     180.000    10.0     3
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+PEG           SMILES              ACDLabs 12.01                                     OCCOCCO
+PEG            InChI                InChI  1.03 InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
+PEG         InChIKey                InChI  1.03                 MTHSVFCYNBDYFN-UHFFFAOYSA-N
+PEG SMILES_CANONICAL               CACTVS 3.370                                     OCCOCCO
+PEG           SMILES               CACTVS 3.370                                     OCCOCCO
+PEG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6                                   C(COCCO)O
+PEG           SMILES "OpenEye OEToolkits" 1.7.6                                   C(COCCO)O
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+PEG acedrg               243         "dictionary generator"                  
+PEG acedrg_database      11          "data source"                           
+PEG rdkit                2017.03.2   "Chemoinformatics tool"
+PEG refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/PG4.cif b/image_analysis/structure_refinement/monomers/PG4.cif
new file mode 100644
index 000000000..77efd2c07
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/PG4.cif
@@ -0,0 +1,198 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+PG4     PG4      "TETRAETHYLENE GLYCOL"     NON-POLYMER     31     13     .     
+#
+data_comp_PG4
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+PG4     O1      O       OH1     0       -3.161      60.725      73.637      
+PG4     C1      C       CH2     0       -2.073      60.164      74.345      
+PG4     C2      C       CH2     0       -1.379      59.093      73.563      
+PG4     O2      O       O2      0       -0.854      59.637      72.355      
+PG4     C3      C       CH2     0       0.478       60.128      72.474      
+PG4     C4      C       CH2     0       0.861       60.848      71.220      
+PG4     O3      O       O2      0       2.240       61.204      71.277      
+PG4     C5      C       CH2     0       2.663       62.051      70.212      
+PG4     C6      C       CH2     0       2.490       63.484      70.609      
+PG4     O4      O       O2      0       2.911       64.332      69.543      
+PG4     C7      C       CH2     0       4.287       64.696      69.603      
+PG4     C8      C       CH2     0       4.670       65.446      68.364      
+PG4     O5      O       OH1     0       3.831       66.560      68.126      
+PG4     HO1     H       H       0       -3.573      61.267      74.139      
+PG4     H11     H       H       0       -2.401      59.786      75.187      
+PG4     H12     H       H       0       -1.432      60.874      74.560      
+PG4     H21     H       H       0       -2.017      58.377      73.349      
+PG4     H22     H       H       0       -0.655      58.704      74.102      
+PG4     H31     H       H       0       1.095       59.379      72.627      
+PG4     H32     H       H       0       0.541       60.741      73.239      
+PG4     H41     H       H       0       0.311       61.656      71.122      
+PG4     H42     H       H       0       0.699       60.270      70.443      
+PG4     H51     H       H       0       2.138       61.866      69.401      
+PG4     H52     H       H       0       3.608       61.877      70.010      
+PG4     H61     H       H       0       3.016       63.670      71.419      
+PG4     H62     H       H       0       1.546       63.659      70.813      
+PG4     H71     H       H       0       4.841       63.889      69.685      
+PG4     H72     H       H       0       4.447       65.258      70.392      
+PG4     H81     H       H       0       4.623       64.841      67.594      
+PG4     H82     H       H       0       5.596       65.757      68.450      
+PG4     HO5     H       H       0       3.919       67.118      68.756      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+PG4          O1          C1      SINGLE       n     1.414  0.0200     1.414  0.0200
+PG4          C1          C2      SINGLE       n     1.496  0.0200     1.496  0.0200
+PG4          C2          O2      SINGLE       n     1.423  0.0106     1.423  0.0106
+PG4          O2          C3      SINGLE       n     1.423  0.0106     1.423  0.0106
+PG4          C3          C4      SINGLE       n     1.496  0.0200     1.496  0.0200
+PG4          C4          O3      SINGLE       n     1.423  0.0106     1.423  0.0106
+PG4          O3          C5      SINGLE       n     1.423  0.0106     1.423  0.0106
+PG4          C5          C6      SINGLE       n     1.496  0.0200     1.496  0.0200
+PG4          C6          O4      SINGLE       n     1.423  0.0106     1.423  0.0106
+PG4          O4          C7      SINGLE       n     1.423  0.0106     1.423  0.0106
+PG4          C7          C8      SINGLE       n     1.496  0.0200     1.496  0.0200
+PG4          C8          O5      SINGLE       n     1.414  0.0200     1.414  0.0200
+PG4          O1         HO1      SINGLE       n     0.970  0.0120     0.846  0.0200
+PG4          C1         H11      SINGLE       n     1.089  0.0100     0.980  0.0144
+PG4          C1         H12      SINGLE       n     1.089  0.0100     0.980  0.0144
+PG4          C2         H21      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C2         H22      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C3         H31      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C3         H32      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C4         H41      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C4         H42      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C5         H51      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C5         H52      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C6         H61      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C6         H62      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C7         H71      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C7         H72      SINGLE       n     1.089  0.0100     0.982  0.0175
+PG4          C8         H81      SINGLE       n     1.089  0.0100     0.980  0.0144
+PG4          C8         H82      SINGLE       n     1.089  0.0100     0.980  0.0144
+PG4          O5         HO5      SINGLE       n     0.970  0.0120     0.846  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+PG4          C1          O1         HO1     109.347    1.86
+PG4          O1          C1          C2     112.284    1.56
+PG4          O1          C1         H11     109.012    1.50
+PG4          O1          C1         H12     109.012    1.50
+PG4          C2          C1         H11     109.198    1.50
+PG4          C2          C1         H12     109.198    1.50
+PG4         H11          C1         H12     108.093    1.50
+PG4          C1          C2          O2     109.904    1.68
+PG4          C1          C2         H21     109.795    1.50
+PG4          C1          C2         H22     109.795    1.50
+PG4          O2          C2         H21     109.691    1.50
+PG4          O2          C2         H22     109.691    1.50
+PG4         H21          C2         H22     108.274    1.50
+PG4          C2          O2          C3     112.795    1.50
+PG4          O2          C3          C4     109.613    1.74
+PG4          O2          C3         H31     109.691    1.50
+PG4          O2          C3         H32     109.691    1.50
+PG4          C4          C3         H31     109.729    1.50
+PG4          C4          C3         H32     109.729    1.50
+PG4         H31          C3         H32     108.274    1.50
+PG4          C3          C4          O3     109.613    1.74
+PG4          C3          C4         H41     109.729    1.50
+PG4          C3          C4         H42     109.729    1.50
+PG4          O3          C4         H41     109.691    1.50
+PG4          O3          C4         H42     109.691    1.50
+PG4         H41          C4         H42     108.274    1.50
+PG4          C4          O3          C5     112.795    1.50
+PG4          O3          C5          C6     109.613    1.74
+PG4          O3          C5         H51     109.691    1.50
+PG4          O3          C5         H52     109.691    1.50
+PG4          C6          C5         H51     109.729    1.50
+PG4          C6          C5         H52     109.729    1.50
+PG4         H51          C5         H52     108.274    1.50
+PG4          C5          C6          O4     109.613    1.74
+PG4          C5          C6         H61     109.729    1.50
+PG4          C5          C6         H62     109.729    1.50
+PG4          O4          C6         H61     109.691    1.50
+PG4          O4          C6         H62     109.691    1.50
+PG4         H61          C6         H62     108.274    1.50
+PG4          C6          O4          C7     112.795    1.50
+PG4          O4          C7          C8     109.904    1.68
+PG4          O4          C7         H71     109.691    1.50
+PG4          O4          C7         H72     109.691    1.50
+PG4          C8          C7         H71     109.795    1.50
+PG4          C8          C7         H72     109.795    1.50
+PG4         H71          C7         H72     108.274    1.50
+PG4          C7          C8          O5     112.284    1.56
+PG4          C7          C8         H81     109.198    1.50
+PG4          C7          C8         H82     109.198    1.50
+PG4          O5          C8         H81     109.012    1.50
+PG4          O5          C8         H82     109.012    1.50
+PG4         H81          C8         H82     108.093    1.50
+PG4          C8          O5         HO5     109.347    1.86
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+PG4             sp3_sp3_1          C2          C1          O1         HO1     180.000    10.0     3
+PG4            sp3_sp3_49          O4          C7          C8          O5     180.000    10.0     3
+PG4            sp3_sp3_58          C7          C8          O5         HO5     180.000    10.0     3
+PG4             sp3_sp3_4          O1          C1          C2          O2     180.000    10.0     3
+PG4            sp3_sp3_13          C1          C2          O2          C3     180.000    10.0     3
+PG4            sp3_sp3_16          C4          C3          O2          C2     180.000    10.0     3
+PG4            sp3_sp3_19          O2          C3          C4          O3     180.000    10.0     3
+PG4            sp3_sp3_28          C3          C4          O3          C5     180.000    10.0     3
+PG4            sp3_sp3_31          C6          C5          O3          C4     180.000    10.0     3
+PG4            sp3_sp3_34          O3          C5          C6          O4     180.000    10.0     3
+PG4            sp3_sp3_43          C5          C6          O4          C7     180.000    10.0     3
+PG4            sp3_sp3_46          C8          C7          O4          C6     180.000    10.0     3
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+PG4           SMILES              ACDLabs 10.04                                                OCCOCCOCCOCCO
+PG4 SMILES_CANONICAL               CACTVS 3.341                                                OCCOCCOCCOCCO
+PG4           SMILES               CACTVS 3.341                                                OCCOCCOCCOCCO
+PG4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                              C(COCCOCCOCCO)O
+PG4           SMILES "OpenEye OEToolkits" 1.5.0                                              C(COCCOCCOCCO)O
+PG4            InChI                InChI  1.03 InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
+PG4         InChIKey                InChI  1.03                                  UWHCKJMYHZGTIT-UHFFFAOYSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+PG4 acedrg               243         "dictionary generator"                  
+PG4 acedrg_database      11          "data source"                           
+PG4 rdkit                2017.03.2   "Chemoinformatics tool"
+PG4 refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/PGE.cif b/image_analysis/structure_refinement/monomers/PGE.cif
new file mode 100644
index 000000000..63666644b
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/PGE.cif
@@ -0,0 +1,168 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+PGE     PGE      "TRIETHYLENE GLYCOL"     NON-POLYMER     24     10     .     
+#
+data_comp_PGE
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+PGE     C1      C       CH2     0       18.715      -18.946     34.930      
+PGE     O1      O       OH1     0       18.098      -20.073     34.339      
+PGE     C2      C       CH2     0       19.228      -19.237     36.305      
+PGE     O2      O       O2      0       18.136      -19.500     37.182      
+PGE     C3      C       CH2     0       18.527      -19.893     38.496      
+PGE     C4      C       CH2     0       18.196      -21.337     38.706      
+PGE     O4      O       OH1     0       19.209      -25.686     36.980      
+PGE     C6      C       CH2     0       19.520      -24.306     36.972      
+PGE     C5      C       CH2     0       18.689      -23.532     37.946      
+PGE     O3      O       O2      0       18.956      -22.140     37.808      
+PGE     H1      H       H       0       18.064      -18.215     34.977      
+PGE     H12     H       H       0       19.459      -18.656     34.363      
+PGE     HO1     H       H       0       17.842      -19.875     33.558      
+PGE     H2      H       H       0       19.741      -18.468     36.636      
+PGE     H22     H       H       0       19.826      -20.016     36.277      
+PGE     H3      H       H       0       18.049      -19.347     39.157      
+PGE     H32     H       H       0       19.492      -19.753     38.624      
+PGE     H4      H       H       0       17.237      -21.483     38.551      
+PGE     H42     H       H       0       18.400      -21.592     39.632      
+PGE     HO4     H       H       0       19.421      -26.016     37.730      
+PGE     H6      H       H       0       19.375      -23.952     36.071      
+PGE     H62     H       H       0       20.468      -24.192     37.195      
+PGE     H5      H       H       0       18.897      -23.819     38.861      
+PGE     H52     H       H       0       17.737      -23.704     37.778      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+PGE          C1          O1      SINGLE       n     1.414  0.0200     1.414  0.0200
+PGE          C1          C2      SINGLE       n     1.496  0.0200     1.496  0.0200
+PGE          C2          O2      SINGLE       n     1.423  0.0106     1.423  0.0106
+PGE          O2          C3      SINGLE       n     1.423  0.0106     1.423  0.0106
+PGE          C3          C4      SINGLE       n     1.496  0.0200     1.496  0.0200
+PGE          C4          O3      SINGLE       n     1.423  0.0106     1.423  0.0106
+PGE          O4          C6      SINGLE       n     1.414  0.0200     1.414  0.0200
+PGE          C6          C5      SINGLE       n     1.496  0.0200     1.496  0.0200
+PGE          C5          O3      SINGLE       n     1.423  0.0106     1.423  0.0106
+PGE          C1          H1      SINGLE       n     1.089  0.0100     0.980  0.0144
+PGE          C1         H12      SINGLE       n     1.089  0.0100     0.980  0.0144
+PGE          O1         HO1      SINGLE       n     0.970  0.0120     0.846  0.0200
+PGE          C2          H2      SINGLE       n     1.089  0.0100     0.982  0.0175
+PGE          C2         H22      SINGLE       n     1.089  0.0100     0.982  0.0175
+PGE          C3          H3      SINGLE       n     1.089  0.0100     0.982  0.0175
+PGE          C3         H32      SINGLE       n     1.089  0.0100     0.982  0.0175
+PGE          C4          H4      SINGLE       n     1.089  0.0100     0.982  0.0175
+PGE          C4         H42      SINGLE       n     1.089  0.0100     0.982  0.0175
+PGE          O4         HO4      SINGLE       n     0.970  0.0120     0.846  0.0200
+PGE          C6          H6      SINGLE       n     1.089  0.0100     0.980  0.0144
+PGE          C6         H62      SINGLE       n     1.089  0.0100     0.980  0.0144
+PGE          C5          H5      SINGLE       n     1.089  0.0100     0.982  0.0175
+PGE          C5         H52      SINGLE       n     1.089  0.0100     0.982  0.0175
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+PGE          O1          C1          C2     112.284    1.56
+PGE          O1          C1          H1     109.012    1.50
+PGE          O1          C1         H12     109.012    1.50
+PGE          C2          C1          H1     109.198    1.50
+PGE          C2          C1         H12     109.198    1.50
+PGE          H1          C1         H12     108.093    1.50
+PGE          C1          O1         HO1     109.347    1.86
+PGE          C1          C2          O2     109.904    1.68
+PGE          C1          C2          H2     109.795    1.50
+PGE          C1          C2         H22     109.795    1.50
+PGE          O2          C2          H2     109.691    1.50
+PGE          O2          C2         H22     109.691    1.50
+PGE          H2          C2         H22     108.274    1.50
+PGE          C2          O2          C3     112.795    1.50
+PGE          O2          C3          C4     109.613    1.74
+PGE          O2          C3          H3     109.691    1.50
+PGE          O2          C3         H32     109.691    1.50
+PGE          C4          C3          H3     109.729    1.50
+PGE          C4          C3         H32     109.729    1.50
+PGE          H3          C3         H32     108.274    1.50
+PGE          C3          C4          O3     109.613    1.74
+PGE          C3          C4          H4     109.729    1.50
+PGE          C3          C4         H42     109.729    1.50
+PGE          O3          C4          H4     109.691    1.50
+PGE          O3          C4         H42     109.691    1.50
+PGE          H4          C4         H42     108.274    1.50
+PGE          C6          O4         HO4     109.347    1.86
+PGE          O4          C6          C5     112.284    1.56
+PGE          O4          C6          H6     109.012    1.50
+PGE          O4          C6         H62     109.012    1.50
+PGE          C5          C6          H6     109.198    1.50
+PGE          C5          C6         H62     109.198    1.50
+PGE          H6          C6         H62     108.093    1.50
+PGE          C6          C5          O3     109.904    1.68
+PGE          C6          C5          H5     109.795    1.50
+PGE          C6          C5         H52     109.795    1.50
+PGE          O3          C5          H5     109.691    1.50
+PGE          O3          C5         H52     109.691    1.50
+PGE          H5          C5         H52     108.274    1.50
+PGE          C4          O3          C5     112.795    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+PGE             sp3_sp3_1          C2          C1          O1         HO1     180.000    10.0     3
+PGE             sp3_sp3_4          O1          C1          C2          O2     180.000    10.0     3
+PGE            sp3_sp3_13          C1          C2          O2          C3     180.000    10.0     3
+PGE            sp3_sp3_16          C4          C3          O2          C2     180.000    10.0     3
+PGE            sp3_sp3_19          O2          C3          C4          O3     180.000    10.0     3
+PGE            sp3_sp3_28          C3          C4          O3          C5     180.000    10.0     3
+PGE            sp3_sp3_31          C5          C6          O4         HO4     180.000    10.0     3
+PGE            sp3_sp3_34          O3          C5          C6          O4     180.000    10.0     3
+PGE            sp3_sp3_43          C6          C5          O3          C4     180.000    10.0     3
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+PGE           SMILES              ACDLabs 10.04                                         OCCOCCOCCO
+PGE SMILES_CANONICAL               CACTVS 3.341                                         OCCOCCOCCO
+PGE           SMILES               CACTVS 3.341                                         OCCOCCOCCO
+PGE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                       C(COCCOCCO)O
+PGE           SMILES "OpenEye OEToolkits" 1.5.0                                       C(COCCOCCO)O
+PGE            InChI                InChI  1.03 InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
+PGE         InChIKey                InChI  1.03                        ZIBGPFATKBEMQZ-UHFFFAOYSA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+PGE acedrg               243         "dictionary generator"                  
+PGE acedrg_database      11          "data source"                           
+PGE rdkit                2017.03.2   "Chemoinformatics tool"
+PGE refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/PHE.cif b/image_analysis/structure_refinement/monomers/PHE.cif
new file mode 100644
index 000000000..57e42ec86
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/PHE.cif
@@ -0,0 +1,261 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+PHE PHE PHENYLALANINE peptide 23 12 .
+
+data_comp_PHE
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+PHE N N NT3 1 3.215 22.308 6.140
+PHE CA C CH1 0 4.240 21.287 5.785
+PHE C C C 0 5.492 21.998 5.258
+PHE O O O 0 5.348 22.751 4.269
+PHE CB C CH2 0 3.652 20.304 4.767
+PHE CG C CR6 0 4.548 19.121 4.423
+PHE CD1 C CR16 0 4.526 17.959 5.195
+PHE CD2 C CR16 0 5.408 19.169 3.325
+PHE CE1 C CR16 0 5.344 16.878 4.879
+PHE CE2 C CR16 0 6.225 18.087 3.012
+PHE CZ C CR16 0 6.192 16.943 3.789
+PHE OXT O OC -1 6.569 21.775 5.853
+PHE H H H 0 2.984 22.781 5.407
+PHE H2 H H 0 3.541 22.872 6.764
+PHE H3 H H 0 2.480 21.902 6.470
+PHE HA H H 0 4.482 20.785 6.608
+PHE HB3 H H 0 3.450 20.797 3.941
+PHE HB2 H H 0 2.802 19.961 5.122
+PHE HD1 H H 0 3.950 17.907 5.941
+PHE HD2 H H 0 5.437 19.946 2.791
+PHE HE1 H H 0 5.320 16.099 5.411
+PHE HE2 H H 0 6.803 18.134 2.267
+PHE HZ H H 0 6.746 16.210 3.575
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+PHE N n/a CA START
+PHE H N . .
+PHE H2 N . .
+PHE H3 N . .
+PHE CA N C .
+PHE HA CA . .
+PHE CB CA CG .
+PHE HB3 CB . .
+PHE HB2 CB . .
+PHE CG CB CD1 .
+PHE CD1 CG CE1 .
+PHE HD1 CD1 . .
+PHE CE1 CD1 CZ .
+PHE HE1 CE1 . .
+PHE CZ CE1 CE2 .
+PHE HZ CZ . .
+PHE CE2 CZ CD2 .
+PHE HE2 CE2 . .
+PHE CD2 CE2 HD2 .
+PHE HD2 CD2 . .
+PHE C CA . END
+PHE O C . .
+PHE OXT C . .
+PHE CD2 CG . ADD
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+PHE N N(CCCH)(H)3
+PHE CA C(CC[6a]HH)(NH3)(COO)(H)
+PHE C C(CCHN)(O)2
+PHE O O(CCO)
+PHE CB C(C[6a]C[6a]2)(CCHN)(H)2
+PHE CG C[6a](C[6a]C[6a]H)2(CCHH){1|C<3>,2|H<1>}
+PHE CD1 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,2|H<1>}
+PHE CD2 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,2|H<1>}
+PHE CE1 C[6a](C[6a]C[6a]H)2(H){1|C<3>,1|C<4>,1|H<1>}
+PHE CE2 C[6a](C[6a]C[6a]H)2(H){1|C<3>,1|C<4>,1|H<1>}
+PHE CZ C[6a](C[6a]C[6a]H)2(H){1|C<3>,2|H<1>}
+PHE OXT O(CCO)
+PHE H H(NCHH)
+PHE H2 H(NCHH)
+PHE H3 H(NCHH)
+PHE HA H(CCCN)
+PHE HB3 H(CC[6a]CH)
+PHE HB2 H(CC[6a]CH)
+PHE HD1 H(C[6a]C[6a]2)
+PHE HD2 H(C[6a]C[6a]2)
+PHE HE1 H(C[6a]C[6a]2)
+PHE HE2 H(C[6a]C[6a]2)
+PHE HZ H(C[6a]C[6a]2)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+PHE N CA SINGLE n 1.489 0.0100 1.489 0.0100
+PHE CA C SINGLE n 1.531 0.0171 1.531 0.0171
+PHE CA CB SINGLE n 1.532 0.0100 1.532 0.0100
+PHE C O DOUBLE n 1.251 0.0183 1.251 0.0183
+PHE C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+PHE CB CG SINGLE n 1.523 0.0100 1.523 0.0100
+PHE CG CD1 DOUBLE y 1.390 0.0116 1.390 0.0116
+PHE CG CD2 SINGLE y 1.390 0.0116 1.390 0.0116
+PHE CD1 CE1 SINGLE y 1.386 0.0131 1.386 0.0131
+PHE CD2 CE2 DOUBLE y 1.386 0.0131 1.386 0.0131
+PHE CE1 CZ DOUBLE y 1.376 0.0151 1.376 0.0151
+PHE CE2 CZ SINGLE y 1.376 0.0151 1.376 0.0151
+PHE N H SINGLE n 1.018 0.0520 0.902 0.0102
+PHE N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+PHE N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+PHE CA HA SINGLE n 1.092 0.0100 0.994 0.0200
+PHE CB HB3 SINGLE n 1.092 0.0100 0.983 0.0163
+PHE CB HB2 SINGLE n 1.092 0.0100 0.983 0.0163
+PHE CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0143
+PHE CD2 HD2 SINGLE n 1.085 0.0150 0.944 0.0143
+PHE CE1 HE1 SINGLE n 1.085 0.0150 0.944 0.0180
+PHE CE2 HE2 SINGLE n 1.085 0.0150 0.944 0.0180
+PHE CZ HZ SINGLE n 1.085 0.0150 0.944 0.0170
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+PHE CA N H 109.791 3.00
+PHE CA N H2 109.791 3.00
+PHE CA N H3 109.791 3.00
+PHE H N H2 109.032 3.00
+PHE H N H3 109.032 3.00
+PHE H2 N H3 109.032 3.00
+PHE N CA C 109.085 1.50
+PHE N CA CB 109.965 3.00
+PHE N CA HA 108.547 1.50
+PHE C CA CB 111.980 3.00
+PHE C CA HA 108.746 1.50
+PHE CB CA HA 108.686 1.50
+PHE CA C O 117.219 3.00
+PHE CA C OXT 117.219 3.00
+PHE O C OXT 125.562 1.50
+PHE CA CB CG 114.693 2.05
+PHE CA CB HB3 108.494 1.50
+PHE CA CB HB2 108.494 1.50
+PHE CG CB HB3 108.859 1.50
+PHE CG CB HB2 108.859 1.50
+PHE HB3 CB HB2 107.843 2.16
+PHE CB CG CD1 120.965 1.50
+PHE CB CG CD2 120.965 1.50
+PHE CD1 CG CD2 118.071 1.50
+PHE CG CD1 CE1 120.673 1.50
+PHE CG CD1 HD1 119.564 1.50
+PHE CE1 CD1 HD1 119.763 1.50
+PHE CG CD2 CE2 120.673 1.50
+PHE CG CD2 HD2 119.564 1.50
+PHE CE2 CD2 HD2 119.763 1.50
+PHE CD1 CE1 CZ 120.297 1.50
+PHE CD1 CE1 HE1 119.796 1.50
+PHE CZ CE1 HE1 119.907 1.50
+PHE CD2 CE2 CZ 120.297 1.50
+PHE CD2 CE2 HE2 119.796 1.50
+PHE CZ CE2 HE2 119.907 1.50
+PHE CE1 CZ CE2 119.995 1.50
+PHE CE1 CZ HZ 120.000 1.50
+PHE CE2 CZ HZ 120.000 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+PHE chi1 N CA CB CG -60.000 10.0 3
+PHE chi2 CA CB CG CD1 90.000 10.0 6
+PHE CONST_1 CB CG CD1 CE1 0.000 0.0 1
+PHE CONST_2 CG CD1 CE1 CZ 0.000 0.0 1
+PHE CONST_3 CZ CE2 CD2 CG 0.000 0.0 1
+PHE CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1
+PHE CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1
+PHE sp3_sp3_1 C CA N H 180.000 10.0 3
+PHE const_21 CE2 CD2 CG CD1 0.000 0.0 1
+PHE sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+PHE chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+PHE plan-1 CB 0.020
+PHE plan-1 CD1 0.020
+PHE plan-1 CD2 0.020
+PHE plan-1 CE1 0.020
+PHE plan-1 CE2 0.020
+PHE plan-1 CG 0.020
+PHE plan-1 CZ 0.020
+PHE plan-1 HD1 0.020
+PHE plan-1 HD2 0.020
+PHE plan-1 HE1 0.020
+PHE plan-1 HE2 0.020
+PHE plan-1 HZ 0.020
+PHE plan-2 C 0.020
+PHE plan-2 CA 0.020
+PHE plan-2 O 0.020
+PHE plan-2 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+PHE SMILES ACDLabs 10.04 O=C(O)C(N)Cc1ccccc1
+PHE SMILES_CANONICAL CACTVS 3.341 N[C@@H](Cc1ccccc1)C(O)=O
+PHE SMILES CACTVS 3.341 N[CH](Cc1ccccc1)C(O)=O
+PHE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)C[C@@H](C(=O)O)N
+PHE SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)CC(C(=O)O)N
+PHE InChI InChI 1.03 InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)/t8-/m0/s1
+PHE InChIKey InChI 1.03 COLNVLDHVKWLRT-QMMMGPOBSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+PHE acedrg 278 "dictionary generator"
+PHE acedrg_database 12 "data source"
+PHE rdkit 2019.09.1 "Chemoinformatics tool"
+PHE refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/PO4.cif b/image_analysis/structure_refinement/monomers/PO4.cif
new file mode 100644
index 000000000..6c80df723
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/PO4.cif
@@ -0,0 +1,86 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+PO4     PO4      "PHOSPHATE ION"     NON-POLYMER     5     5     .     
+#
+data_comp_PO4
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+PO4     P       P       P       0       29.978      23.532      13.276      
+PO4     O1      O       O       0       31.126      22.989      14.118      
+PO4     O2      O       OP      -1      30.372      24.882      12.690      
+PO4     O3      O       OP      -1      29.672      22.557      12.145      
+PO4     O4      O       OP      -1      28.741      23.699      14.151      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+PO4           P          O1      DOUBLE       n     1.524  0.0200     1.524  0.0200
+PO4           P          O2      SINGLE       n     1.524  0.0200     1.524  0.0200
+PO4           P          O3      SINGLE       n     1.524  0.0200     1.524  0.0200
+PO4           P          O4      SINGLE       n     1.524  0.0200     1.524  0.0200
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+PO4          O1           P          O2     109.461    1.50
+PO4          O1           P          O3     109.461    1.50
+PO4          O1           P          O4     109.461    1.50
+PO4          O2           P          O3     109.461    1.50
+PO4          O2           P          O4     109.461    1.50
+PO4          O3           P          O4     109.461    1.50
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+PO4    chir_1    P    O2    O3    O4    both
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+PO4           SMILES              ACDLabs 10.04                       "[O-]P([O-])([O-])=O"
+PO4 SMILES_CANONICAL               CACTVS 3.341                     "[O-][P]([O-])([O-])=O"
+PO4           SMILES               CACTVS 3.341                     "[O-][P]([O-])([O-])=O"
+PO4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                       "[O-]P(=O)([O-])[O-]"
+PO4           SMILES "OpenEye OEToolkits" 1.5.0                       "[O-]P(=O)([O-])[O-]"
+PO4            InChI                InChI  1.03 InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
+PO4         InChIKey                InChI  1.03                 NBIIXXVUZAFLBC-UHFFFAOYSA-K
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+PO4 acedrg               243         "dictionary generator"                  
+PO4 acedrg_database      11          "data source"                           
+PO4 rdkit                2017.03.2   "Chemoinformatics tool"
+PO4 refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/PRO.cif b/image_analysis/structure_refinement/monomers/PRO.cif
new file mode 100644
index 000000000..2330d47a9
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/PRO.cif
@@ -0,0 +1,216 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+PRO PRO PROLINE P-peptide 17 8 .
+
+data_comp_PRO
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.alt_atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+PRO N   N   N NT2 1  39.160 37.649 83.026
+PRO CA  CA  C CH1 0  38.550 38.680 82.125
+PRO C   C   C C   0  37.155 39.077 82.602
+PRO O   O   O O   0  36.450 38.196 83.146
+PRO CB  CB  C CH2 0  38.553 38.007 80.756
+PRO CG  CG  C CH2 0  38.265 36.558 81.098
+PRO CD  CD  C CH2 0  38.934 36.298 82.416
+PRO OXT OXT O OC  -1 36.821 40.268 82.409
+PRO H   H   H H   0  40.054 37.806 83.097
+PRO H2  H2  H H   0  38.800 37.681 83.862
+PRO HA  HA  H H   0  39.125 39.473 82.102
+PRO HB3 HB3 H H   0  39.422 38.100 80.320
+PRO HB2 HB2 H H   0  37.858 38.378 80.178
+PRO HG3 HG3 H H   0  38.625 35.964 80.410
+PRO HG2 HG2 H H   0  37.302 36.406 81.169
+PRO HD3 HD3 H H   0  38.363 35.755 82.994
+PRO HD2 HD2 H H   0  39.785 35.835 82.289
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+PRO N   n/a CA  START
+PRO CA  N   C   .
+PRO HA  CA  .   .
+PRO CB  CA  CG  .
+PRO HB3 CB  .   .
+PRO HB2 CB  .   .
+PRO CG  CB  CD  .
+PRO HG3 CG  .   .
+PRO HG2 CG  .   .
+PRO CD  CG  HD2 .
+PRO HD3 CD  .   .
+PRO HD2 CD  .   .
+PRO C   CA  .   END
+PRO O   C   .   .
+PRO OXT C   .   .
+PRO H   N   .   .
+PRO H2  N   .   .
+PRO CD  N   .   ADD
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+PRO N   N[5](C[5]C[5]CH)(C[5]C[5]HH)(H)2{4|H<1>}
+PRO CA  C[5](C[5]C[5]HH)(N[5]C[5]HH)(COO)(H){4|H<1>}
+PRO C   C(C[5]C[5]N[5]H)(O)2
+PRO O   O(CC[5]O)
+PRO CB  C[5](C[5]C[5]HH)(C[5]N[5]CH)(H)2{4|H<1>}
+PRO CG  C[5](C[5]C[5]HH)(C[5]N[5]HH)(H)2{1|C<3>,3|H<1>}
+PRO CD  C[5](C[5]C[5]HH)(N[5]C[5]HH)(H)2{1|C<3>,3|H<1>}
+PRO OXT O(CC[5]O)
+PRO H   H(N[5]C[5]2H)
+PRO H2  H(N[5]C[5]2H)
+PRO HA  H(C[5]C[5]N[5]C)
+PRO HB3 H(C[5]C[5]2H)
+PRO HB2 H(C[5]C[5]2H)
+PRO HG3 H(C[5]C[5]2H)
+PRO HG2 H(C[5]C[5]2H)
+PRO HD3 H(C[5]C[5]N[5]H)
+PRO HD2 H(C[5]C[5]N[5]H)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.value_order
+_chem_comp_bond.pdbx_aromatic_flag
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+PRO N  CA  SINGLE n 1.496 0.0142 1.496 0.0142
+PRO N  CD  SINGLE n 1.499 0.0135 1.499 0.0135
+PRO CA C   SINGLE n 1.525 0.0103 1.525 0.0103
+PRO CA CB  SINGLE n 1.526 0.0157 1.526 0.0157
+PRO C  O   DOUBLE n 1.252 0.0117 1.252 0.0117
+PRO C  OXT SINGLE n 1.252 0.0117 1.252 0.0117
+PRO CB CG  SINGLE n 1.516 0.0179 1.516 0.0179
+PRO CG CD  SINGLE n 1.497 0.0200 1.497 0.0200
+PRO N  H   SINGLE n 1.018 0.0520 0.910 0.0200
+PRO N  H2  SINGLE n 1.018 0.0520 0.910 0.0200
+PRO CA HA  SINGLE n 1.092 0.0100 0.980 0.0200
+PRO CB HB3 SINGLE n 1.092 0.0100 0.977 0.0145
+PRO CB HB2 SINGLE n 1.092 0.0100 0.977 0.0145
+PRO CG HG3 SINGLE n 1.092 0.0100 0.978 0.0181
+PRO CG HG2 SINGLE n 1.092 0.0100 0.978 0.0181
+PRO CD HD3 SINGLE n 1.092 0.0100 0.977 0.0199
+PRO CD HD2 SINGLE n 1.092 0.0100 0.977 0.0199
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+PRO CA  N  CD  107.978 1.50
+PRO CA  N  H   109.889 3.00
+PRO CA  N  H2  109.889 3.00
+PRO CD  N  H   110.257 3.00
+PRO CD  N  H2  110.257 3.00
+PRO H   N  H2  108.772 3.00
+PRO N   CA C   110.397 1.50
+PRO N   CA CB  103.994 1.50
+PRO N   CA HA  109.579 1.50
+PRO C   CA CB  113.159 3.00
+PRO C   CA HA  109.687 1.50
+PRO CB  CA HA  109.910 1.89
+PRO CA  C  O   116.979 3.00
+PRO CA  C  OXT 116.979 3.00
+PRO O   C  OXT 126.043 1.52
+PRO CA  CB CG  101.701 3.00
+PRO CA  CB HB3 110.865 1.50
+PRO CA  CB HB2 110.865 1.50
+PRO CG  CB HB3 110.891 1.59
+PRO CG  CB HB2 110.891 1.59
+PRO HB3 CB HB2 108.880 2.25
+PRO CB  CG CD  105.541 3.00
+PRO CB  CG HG3 110.897 1.50
+PRO CB  CG HG2 110.897 1.50
+PRO CD  CG HG3 110.621 1.50
+PRO CD  CG HG2 110.621 1.50
+PRO HG3 CG HG2 108.871 1.50
+PRO N   CD CG  104.386 2.30
+PRO N   CD HD3 110.569 1.50
+PRO N   CD HD2 110.569 1.50
+PRO CG  CD HD3 111.131 1.62
+PRO CG  CD HD2 111.131 1.62
+PRO HD3 CD HD2 109.116 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+PRO chi1       N  CA CB CG -60.000 10.0 3
+PRO chi2       CA CB CG CD 180.000 10.0 3
+PRO sp3_sp3_1  CB CA N  CD 60.000  10.0 3
+PRO sp3_sp3_28 N  CD CG CB -60.000 10.0 3
+PRO sp3_sp3_37 CG CD N  CA 180.000 10.0 3
+PRO sp2_sp3_1  O  C  CA N  0.000   10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+PRO chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+PRO plan-1 C   0.020
+PRO plan-1 CA  0.020
+PRO plan-1 O   0.020
+PRO plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+PRO SMILES           ACDLabs              10.04 "O=C(O)C1NCCC1"
+PRO SMILES_CANONICAL CACTVS               3.341 "OC(=O)[C@@H]1CCCN1"
+PRO SMILES           CACTVS               3.341 "OC(=O)[CH]1CCCN1"
+PRO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C[C@H](NC1)C(=O)O"
+PRO SMILES           "OpenEye OEToolkits" 1.5.0 "C1CC(NC1)C(=O)O"
+PRO InChI            InChI                1.03  "InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"
+PRO InChIKey         InChI                1.03  ONIBWKKTOPOVIA-BYPYZUCNSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+PRO acedrg          281       "dictionary generator"
+PRO acedrg_database 12        "data source"
+PRO rdkit           2019.09.1 "Chemoinformatics tool"
+PRO refmac5         5.8.0419  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/PSU.cif b/image_analysis/structure_refinement/monomers/PSU.cif
new file mode 100644
index 000000000..4a2fa8af7
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/PSU.cif
@@ -0,0 +1,250 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+PSU PSU "PSEUDOURIDINE-5'-MONOPHOSPHATE" RNA 32 21 .
+
+data_comp_PSU
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+PSU N1     N NR16 0  46.164 -7.762  4.833
+PSU C2     C CR6  0  46.590 -7.315  3.610
+PSU N3     N NR16 0  47.833 -7.748  3.219
+PSU C4     C CR6  0  48.652 -8.579  3.959
+PSU C5     C CR6  0  48.162 -9.023  5.229
+PSU C6     C CR16 0  46.903 -8.584  5.636
+PSU O2     O O    0  45.910 -6.578  2.906
+PSU O4     O O    0  49.759 -8.895  3.485
+PSU "C1'"  C CH1  0  48.988 -9.928  6.111
+PSU "C2'"  C CH1  0  49.724 -9.224  7.265
+PSU "O2'"  O OH1  0  51.104 -9.536  7.260
+PSU "C3'"  C CH1  0  48.969 -9.682  8.522
+PSU "C4'"  C CH1  0  48.520 -11.085 8.105
+PSU "O3'"  O OH1  0  49.839 -9.721  9.649
+PSU "O4'"  O O2   0  48.167 -10.942 6.712
+PSU "C5'"  C CH2  0  47.359 -11.677 8.866
+PSU "O5'"  O O2   0  46.178 -10.856 8.677
+PSU P      P P    0  44.847 -11.206 9.521
+PSU OP1    O O    0  43.790 -10.223 9.054
+PSU OP2    O OP   -1 45.222 -11.019 10.980
+PSU OP3    O OP   -1 44.507 -12.644 9.180
+PSU HN1    H H    0  45.353 -7.490  5.108
+PSU HN3    H H    0  48.133 -7.472  2.427
+PSU H6     H H    0  46.552 -8.857  6.469
+PSU "H1'"  H H    0  49.672 -10.378 5.553
+PSU "H2'"  H H    0  49.616 -8.252  7.170
+PSU "HO2'" H H    0  51.463 -9.174  7.939
+PSU "H3'"  H H    0  48.194 -9.103  8.707
+PSU "H4'"  H H    0  49.285 -11.706 8.179
+PSU "HO3'" H H    0  49.417 -10.046 10.310
+PSU "H5'"  H H    0  47.583 -11.723 9.829
+PSU "H5''" H H    0  47.184 -12.595 8.543
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+PSU N1    C2     SINGLE y 1.365 0.0100 1.365 0.0100
+PSU N1    C6     SINGLE y 1.355 0.0148 1.355 0.0148
+PSU C2    N3     SINGLE y 1.370 0.0100 1.370 0.0100
+PSU C2    O2     DOUBLE n 1.225 0.0100 1.225 0.0100
+PSU N3    C4     SINGLE y 1.379 0.0122 1.379 0.0122
+PSU C4    C5     SINGLE y 1.418 0.0200 1.418 0.0200
+PSU C4    O4     DOUBLE n 1.242 0.0172 1.242 0.0172
+PSU C5    C6     DOUBLE y 1.389 0.0100 1.389 0.0100
+PSU C5    "C1'"  SINGLE n 1.506 0.0100 1.506 0.0100
+PSU "C1'" "C2'"  SINGLE n 1.532 0.0100 1.532 0.0100
+PSU "C1'" "O4'"  SINGLE n 1.434 0.0100 1.434 0.0100
+PSU "C2'" "O2'"  SINGLE n 1.414 0.0100 1.414 0.0100
+PSU "C2'" "C3'"  SINGLE n 1.533 0.0100 1.533 0.0100
+PSU "C3'" "C4'"  SINGLE n 1.535 0.0100 1.535 0.0100
+PSU "C3'" "O3'"  SINGLE n 1.423 0.0100 1.423 0.0100
+PSU "C4'" "O4'"  SINGLE n 1.448 0.0100 1.448 0.0100
+PSU "C4'" "C5'"  SINGLE n 1.509 0.0100 1.509 0.0100
+PSU "C5'" "O5'"  SINGLE n 1.450 0.0166 1.450 0.0166
+PSU "O5'" P      SINGLE n 1.614 0.0178 1.614 0.0178
+PSU P     OP1    DOUBLE n 1.517 0.0192 1.517 0.0192
+PSU P     OP2    SINGLE n 1.517 0.0192 1.517 0.0192
+PSU P     OP3    SINGLE n 1.517 0.0192 1.517 0.0192
+PSU N1    HN1    SINGLE n 1.016 0.0100 0.898 0.0200
+PSU N3    HN3    SINGLE n 1.016 0.0100 0.889 0.0200
+PSU C6    H6     SINGLE n 1.082 0.0130 0.945 0.0200
+PSU "C1'" "H1'"  SINGLE n 1.089 0.0100 0.991 0.0119
+PSU "C2'" "H2'"  SINGLE n 1.089 0.0100 0.982 0.0200
+PSU "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+PSU "C3'" "H3'"  SINGLE n 1.089 0.0100 0.985 0.0200
+PSU "C4'" "H4'"  SINGLE n 1.089 0.0100 0.988 0.0200
+PSU "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+PSU "C5'" "H5'"  SINGLE n 1.089 0.0100 0.989 0.0200
+PSU "C5'" "H5''" SINGLE n 1.089 0.0100 0.989 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+PSU C2    N1    C6     122.342 1.50
+PSU C2    N1    HN1    117.656 2.18
+PSU C6    N1    HN1    120.002 2.19
+PSU N1    C2    N3     115.268 1.50
+PSU N1    C2    O2     122.598 1.50
+PSU N3    C2    O2     122.134 1.50
+PSU C2    N3    C4     125.337 1.50
+PSU C2    N3    HN3    117.319 2.30
+PSU C4    N3    HN3    117.344 1.50
+PSU N3    C4    C5     118.938 3.00
+PSU N3    C4    O4     117.999 1.50
+PSU C5    C4    O4     123.064 1.50
+PSU C4    C5    C6     119.178 1.66
+PSU C4    C5    "C1'"  120.411 1.56
+PSU C6    C5    "C1'"  120.411 1.56
+PSU N1    C6    C5     118.938 3.00
+PSU N1    C6    H6     120.523 1.97
+PSU C5    C6    H6     120.539 1.50
+PSU C5    "C1'" "C2'"  115.040 1.80
+PSU C5    "C1'" "O4'"  110.287 1.50
+PSU C5    "C1'" "H1'"  108.843 1.50
+PSU "C2'" "C1'" "O4'"  104.658 1.50
+PSU "C2'" "C1'" "H1'"  108.221 2.17
+PSU "O4'" "C1'" "H1'"  109.373 1.78
+PSU "C1'" "C2'" "O2'"  111.625 2.24
+PSU "C1'" "C2'" "C3'"  102.060 1.50
+PSU "C1'" "C2'" "H2'"  108.984 1.81
+PSU "O2'" "C2'" "C3'"  114.225 2.57
+PSU "O2'" "C2'" "H2'"  109.642 2.25
+PSU "C3'" "C2'" "H2'"  109.242 2.24
+PSU "C2'" "O2'" "HO2'" 108.353 3.00
+PSU "C2'" "C3'" "C4'"  101.721 1.50
+PSU "C2'" "C3'" "O3'"  109.895 1.81
+PSU "C2'" "C3'" "H3'"  111.377 1.50
+PSU "C4'" "C3'" "O3'"  111.281 2.46
+PSU "C4'" "C3'" "H3'"  110.452 2.54
+PSU "O3'" "C3'" "H3'"  110.380 1.67
+PSU "C3'" "C4'" "O4'"  106.192 1.50
+PSU "C3'" "C4'" "C5'"  116.008 1.52
+PSU "C3'" "C4'" "H4'"  109.363 1.86
+PSU "O4'" "C4'" "C5'"  109.123 1.50
+PSU "O4'" "C4'" "H4'"  108.995 1.50
+PSU "C5'" "C4'" "H4'"  108.268 1.50
+PSU "C3'" "O3'" "HO3'" 108.744 3.00
+PSU "C1'" "O4'" "C4'"  109.937 1.50
+PSU "C4'" "C5'" "O5'"  109.342 1.50
+PSU "C4'" "C5'" "H5'"  109.624 1.50
+PSU "C4'" "C5'" "H5''" 109.624 1.50
+PSU "O5'" "C5'" "H5'"  109.845 1.50
+PSU "O5'" "C5'" "H5''" 109.845 1.50
+PSU "H5'" "C5'" "H5''" 108.472 1.50
+PSU "C5'" "O5'" P      118.783 1.50
+PSU "O5'" P     OP1    105.808 2.07
+PSU "O5'" P     OP2    105.808 2.07
+PSU "O5'" P     OP3    105.808 2.07
+PSU OP1   P     OP2    112.864 1.69
+PSU OP1   P     OP3    112.864 1.69
+PSU OP2   P     OP3    112.864 1.69
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+PSU C2e-nyu2        "C1'" "C2'" "C3'" "C4'"  326.9   3.600 1
+PSU C2e-nyu3        "C2'" "C3'" "C4'" "O4'"  22.600  4.500 1
+PSU C2e-nyu4        "C3'" "C4'" "O4'" "C1'"  357.700 6.100 1
+PSU C3e-nyu2        "C1'" "C2'" "C3'" "C4'"  35.9    2.800 1
+PSU C3e-nyu3        "C2'" "C3'" "C4'" "O4'"  324.700 3.100 1
+PSU C3e-nyu4        "C3'" "C4'" "O4'" "C1'"  20.500  5.100 1
+PSU alpha           "C5'" "O5'" P     OP3    -60.000 10.00 3
+PSU beta            P     "O5'" "C5'" "C4'"  180.000 10.00 3
+PSU epsi            "C4'" "C3'" "O3'" "HO3'" 180.000 10.00 3
+PSU gamma           "O5'" "C5'" "C4'" "C3'"  180.000 10.00 3
+PSU const_sp2_sp2_3 O2    C2    N1    C6     180.000 5.0   2
+PSU const_21        C5    C6    N1    C2     0.000   10.0  2
+PSU const_sp2_sp2_7 O2    C2    N3    C4     180.000 5.0   2
+PSU const_11        O4    C4    N3    C2     180.000 10.0  2
+PSU const_15        O4    C4    C5    C6     180.000 10.0  2
+PSU const_17        C4    C5    C6    N1     0.000   10.0  2
+PSU sp2_sp3_1       C4    C5    "C1'" "C2'"  150.000 10.0  6
+PSU sp3_sp3_32      C5    "C1'" "O4'" "C4'"  60.000  10.0  3
+PSU sp3_sp3_5       C5    "C1'" "C2'" "O2'"  60.000  10.0  3
+PSU sp3_sp3_34      "C1'" "C2'" "O2'" "HO2'" 180.000 10.0  3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+PSU chir_1 "C1'" "O4'" "C2'" C5    positive
+PSU chir_2 "C2'" "O2'" "C1'" "C3'" negative
+PSU chir_3 "C3'" "O3'" "C4'" "C2'" positive
+PSU chir_4 "C4'" "O4'" "C3'" "C5'" negative
+PSU chir_5 P     "O5'" OP2   OP3   both
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+PSU plan-1 "C1'" 0.020
+PSU plan-1 C2    0.020
+PSU plan-1 C4    0.020
+PSU plan-1 C5    0.020
+PSU plan-1 C6    0.020
+PSU plan-1 H6    0.020
+PSU plan-1 HN1   0.020
+PSU plan-1 HN3   0.020
+PSU plan-1 N1    0.020
+PSU plan-1 N3    0.020
+PSU plan-1 O2    0.020
+PSU plan-1 O4    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+PSU SMILES           ACDLabs              10.04 O=P(OCC2OC(C1=CNC(=O)NC1=O)C(O)C2O)(O)O
+PSU SMILES_CANONICAL CACTVS               3.341 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)C2=CNC(=O)NC2=O
+PSU SMILES           CACTVS               3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)C2=CNC(=O)NC2=O
+PSU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
+PSU SMILES           "OpenEye OEToolkits" 1.5.0 C1=C(C(=O)NC(=O)N1)C2C(C(C(O2)COP(=O)(O)O)O)O
+PSU InChI            InChI                1.03  InChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1
+PSU InChIKey         InChI                1.03  MOBMOJGXNHLLIR-GBNDHIKLSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+PSU acedrg          243       "dictionary generator"
+PSU acedrg_database 11        "data source"
+PSU rdkit           2017.03.2 "Chemoinformatics tool"
+PSU refmac5         5.8.0238  "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/SAH.cif b/image_analysis/structure_refinement/monomers/SAH.cif
new file mode 100644
index 000000000..9f1abc9cb
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/SAH.cif
@@ -0,0 +1,329 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+SAH SAH S-ADENOSYL-L-HOMOCYSTEINE NON-POLYMER 46 26 .
+
+data_comp_SAH
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+SAH N      N NT3  1  -2.642 13.710 24.335
+SAH CA     C CH1  0  -3.261 12.686 25.223
+SAH CB     C CH2  0  -2.531 11.342 25.110
+SAH CG     C CH2  0  -2.701 10.665 23.762
+SAH SD     S S2   0  -1.875 9.057  23.667
+SAH C      C C    0  -3.207 13.172 26.677
+SAH O      O O    0  -4.296 13.351 27.259
+SAH OXT    O OC   -1 -2.078 13.355 27.173
+SAH "C5'"  C CH2  0  -2.426 8.439  22.058
+SAH "C4'"  C CH1  0  -3.830 7.882  22.065
+SAH "O4'"  O O2   0  -4.295 7.751  20.701
+SAH "C3'"  C CH1  0  -3.966 6.491  22.682
+SAH "O3'"  O OH1  0  -5.239 6.333  23.297
+SAH "C2'"  C CH1  0  -3.790 5.584  21.462
+SAH "O2'"  O OH1  0  -4.370 4.309  21.628
+SAH "C1'"  C CH1  0  -4.519 6.393  20.394
+SAH N9     N NR5  0  -4.045 6.148  19.035
+SAH C8     C CR15 0  -2.777 6.375  18.561
+SAH N7     N NRD5 0  -2.628 6.068  17.297
+SAH C5     C CR56 0  -3.878 5.613  16.905
+SAH C6     C CR6  0  -4.372 5.137  15.671
+SAH N6     N NH2  0  -3.632 5.040  14.570
+SAH N1     N NRD6 0  -5.675 4.759  15.617
+SAH C2     C CR16 0  -6.417 4.859  16.731
+SAH N3     N NRD6 0  -6.060 5.290  17.942
+SAH C4     C CR56 0  -4.764 5.658  17.969
+SAH HN1    H H    0  -2.972 14.538 24.529
+SAH HN2    H H    0  -2.828 13.522 23.464
+SAH H3     H H    0  -1.739 13.719 24.450
+SAH HA     H H    0  -4.203 12.573 24.958
+SAH HB1    H H    0  -2.865 10.744 25.808
+SAH HB2    H H    0  -1.578 11.488 25.274
+SAH HG1    H H    0  -2.337 11.245 23.060
+SAH HG2    H H    0  -3.657 10.538 23.583
+SAH "H5'1" H H    0  -1.829 7.752  21.772
+SAH "H5'2" H H    0  -2.386 9.152  21.425
+SAH "H4'"  H H    0  -4.421 8.511  22.548
+SAH "H3'"  H H    0  -3.243 6.329  23.342
+SAH "HO3'" H H    0  -5.240 5.609  23.740
+SAH "H2'"  H H    0  -2.826 5.493  21.237
+SAH "HO2'" H H    0  -4.231 3.847  20.929
+SAH "H1'"  H H    0  -5.481 6.197  20.448
+SAH H8     H H    0  -2.079 6.715  19.096
+SAH HN61   H H    0  -3.998 5.178  13.785
+SAH HN62   H H    0  -2.780 4.840  14.635
+SAH H2     H H    0  -7.317 4.585  16.646
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+SAH N     CA     SINGLE n 1.488 0.0100 1.488 0.0100
+SAH CA    CB     SINGLE n 1.532 0.0100 1.532 0.0100
+SAH CA    C      SINGLE n 1.533 0.0100 1.533 0.0100
+SAH CB    CG     SINGLE n 1.517 0.0200 1.517 0.0200
+SAH CG    SD     SINGLE n 1.810 0.0200 1.810 0.0200
+SAH SD    "C5'"  SINGLE n 1.810 0.0169 1.810 0.0169
+SAH C     O      DOUBLE n 1.247 0.0187 1.247 0.0187
+SAH C     OXT    SINGLE n 1.247 0.0187 1.247 0.0187
+SAH "C5'" "C4'"  SINGLE n 1.510 0.0135 1.510 0.0135
+SAH "C4'" "O4'"  SINGLE n 1.446 0.0100 1.446 0.0100
+SAH "C4'" "C3'"  SINGLE n 1.528 0.0117 1.528 0.0117
+SAH "O4'" "C1'"  SINGLE n 1.409 0.0100 1.409 0.0100
+SAH "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+SAH "C3'" "C2'"  SINGLE n 1.531 0.0100 1.531 0.0100
+SAH "C2'" "O2'"  SINGLE n 1.411 0.0100 1.411 0.0100
+SAH "C2'" "C1'"  SINGLE n 1.525 0.0100 1.525 0.0100
+SAH "C1'" N9     SINGLE n 1.458 0.0100 1.458 0.0100
+SAH N9    C8     SINGLE y 1.372 0.0100 1.372 0.0100
+SAH N9    C4     SINGLE y 1.374 0.0101 1.374 0.0101
+SAH C8    N7     DOUBLE y 1.310 0.0100 1.310 0.0100
+SAH N7    C5     SINGLE y 1.388 0.0100 1.388 0.0100
+SAH C5    C6     SINGLE y 1.408 0.0100 1.408 0.0100
+SAH C5    C4     DOUBLE y 1.381 0.0100 1.381 0.0100
+SAH C6    N6     SINGLE n 1.330 0.0100 1.330 0.0100
+SAH C6    N1     DOUBLE y 1.354 0.0100 1.354 0.0100
+SAH N1    C2     SINGLE y 1.339 0.0100 1.339 0.0100
+SAH C2    N3     DOUBLE y 1.330 0.0100 1.330 0.0100
+SAH N3    C4     SINGLE y 1.343 0.0100 1.343 0.0100
+SAH N     HN1    SINGLE n 1.036 0.0160 0.911 0.0200
+SAH N     HN2    SINGLE n 1.036 0.0160 0.911 0.0200
+SAH N     H3     SINGLE n 1.036 0.0160 0.911 0.0200
+SAH CA    HA     SINGLE n 1.089 0.0100 0.985 0.0200
+SAH CB    HB1    SINGLE n 1.089 0.0100 0.978 0.0200
+SAH CB    HB2    SINGLE n 1.089 0.0100 0.978 0.0200
+SAH CG    HG1    SINGLE n 1.089 0.0100 0.981 0.0122
+SAH CG    HG2    SINGLE n 1.089 0.0100 0.981 0.0122
+SAH "C5'" "H5'1" SINGLE n 1.089 0.0100 0.954 0.0200
+SAH "C5'" "H5'2" SINGLE n 1.089 0.0100 0.954 0.0200
+SAH "C4'" "H4'"  SINGLE n 1.089 0.0100 0.989 0.0197
+SAH "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+SAH "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+SAH "C2'" "H2'"  SINGLE n 1.089 0.0100 0.994 0.0200
+SAH "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+SAH "C1'" "H1'"  SINGLE n 1.089 0.0100 0.984 0.0200
+SAH C8    H8     SINGLE n 1.082 0.0130 0.942 0.0170
+SAH N6    HN61   SINGLE n 1.016 0.0100 0.877 0.0200
+SAH N6    HN62   SINGLE n 1.016 0.0100 0.877 0.0200
+SAH C2    H2     SINGLE n 1.082 0.0130 0.945 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+SAH CA     N     HN1    110.062 1.93
+SAH CA     N     HN2    110.062 1.93
+SAH CA     N     H3     110.062 1.93
+SAH HN1    N     HN2    109.028 2.41
+SAH HN1    N     H3     109.028 2.41
+SAH HN2    N     H3     109.028 2.41
+SAH N      CA    CB     110.906 1.50
+SAH N      CA    C      109.241 1.50
+SAH N      CA    HA     108.487 1.50
+SAH CB     CA    C      109.344 1.50
+SAH CB     CA    HA     109.670 1.50
+SAH C      CA    HA     108.824 1.50
+SAH CA     CB    CG     113.476 1.50
+SAH CA     CB    HB1    108.666 1.50
+SAH CA     CB    HB2    108.666 1.50
+SAH CG     CB    HB1    108.955 1.50
+SAH CG     CB    HB2    108.955 1.50
+SAH HB1    CB    HB2    107.698 1.50
+SAH CB     CG    SD     113.263 2.33
+SAH CB     CG    HG1    109.206 1.50
+SAH CB     CG    HG2    109.206 1.50
+SAH SD     CG    HG1    108.654 1.50
+SAH SD     CG    HG2    108.654 1.50
+SAH HG1    CG    HG2    107.939 1.50
+SAH CG     SD    "C5'"  102.171 1.96
+SAH CA     C     O      117.124 1.50
+SAH CA     C     OXT    117.124 1.50
+SAH O      C     OXT    125.752 1.50
+SAH SD     "C5'" "C4'"  113.180 3.00
+SAH SD     "C5'" "H5'1" 108.574 1.50
+SAH SD     "C5'" "H5'2" 108.574 1.50
+SAH "C4'"  "C5'" "H5'1" 108.376 1.50
+SAH "C4'"  "C5'" "H5'2" 108.376 1.50
+SAH "H5'1" "C5'" "H5'2" 108.127 1.50
+SAH "C5'"  "C4'" "O4'"  109.275 1.50
+SAH "C5'"  "C4'" "C3'"  114.880 1.64
+SAH "C5'"  "C4'" "H4'"  109.000 1.62
+SAH "O4'"  "C4'" "C3'"  105.508 1.50
+SAH "O4'"  "C4'" "H4'"  109.115 1.50
+SAH "C3'"  "C4'" "H4'"  109.143 1.50
+SAH "C4'"  "O4'" "C1'"  109.426 1.50
+SAH "C4'"  "C3'" "O3'"  110.985 2.41
+SAH "C4'"  "C3'" "C2'"  102.352 1.50
+SAH "C4'"  "C3'" "H3'"  110.624 1.81
+SAH "O3'"  "C3'" "C2'"  111.581 2.83
+SAH "O3'"  "C3'" "H3'"  110.380 1.67
+SAH "C2'"  "C3'" "H3'"  110.504 1.75
+SAH "C3'"  "O3'" "HO3'" 108.744 3.00
+SAH "C3'"  "C2'" "O2'"  112.782 2.45
+SAH "C3'"  "C2'" "C1'"  101.239 1.50
+SAH "C3'"  "C2'" "H2'"  110.596 1.51
+SAH "O2'"  "C2'" "C1'"  111.715 2.69
+SAH "O2'"  "C2'" "H2'"  110.448 1.97
+SAH "C1'"  "C2'" "H2'"  110.636 1.70
+SAH "C2'"  "O2'" "HO2'" 109.103 2.13
+SAH "O4'"  "C1'" "C2'"  106.047 1.50
+SAH "O4'"  "C1'" N9     108.477 1.50
+SAH "O4'"  "C1'" "H1'"  109.807 1.50
+SAH "C2'"  "C1'" N9     113.824 1.50
+SAH "C2'"  "C1'" "H1'"  109.015 1.50
+SAH N9     "C1'" "H1'"  109.561 1.50
+SAH "C1'"  N9    C8     126.848 1.91
+SAH "C1'"  N9    C4     127.459 1.80
+SAH C8     N9    C4     105.693 1.50
+SAH N9     C8    N7     113.469 1.50
+SAH N9     C8    H8     123.206 1.50
+SAH N7     C8    H8     123.326 1.50
+SAH C8     N7    C5     104.739 1.50
+SAH N7     C5    C6     132.250 1.50
+SAH N7     C5    C4     110.483 1.50
+SAH C6     C5    C4     117.267 1.50
+SAH C5     C6    N6     123.792 1.50
+SAH C5     C6    N1     117.409 1.50
+SAH N6     C6    N1     118.799 1.50
+SAH C6     N6    HN61   119.723 1.50
+SAH C6     N6    HN62   119.723 1.50
+SAH HN61   N6    HN62   120.554 1.88
+SAH C6     N1    C2     118.521 1.50
+SAH N1     C2    N3     129.332 1.50
+SAH N1     C2    H2     115.313 1.50
+SAH N3     C2    H2     115.355 1.50
+SAH C2     N3    C4     110.982 1.50
+SAH N9     C4    C5     105.616 1.50
+SAH N9     C4    N3     127.895 1.50
+SAH C5     C4    N3     126.489 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+SAH sp3_sp3_25      CB    CA    N     HN1    180.000 10.0 3
+SAH sp3_sp3_4       "C2'" "C1'" "O4'" "C4'"  -60.000 10.0 3
+SAH sp3_sp3_76      "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
+SAH sp3_sp3_20      "O2'" "C2'" "C3'" "O3'"  -60.000 10.0 3
+SAH sp3_sp3_79      "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
+SAH sp3_sp3_8       "O4'" "C1'" "C2'" "O2'"  180.000 10.0 3
+SAH sp2_sp3_7       C8    N9    "C1'" "O4'"  150.000 10.0 6
+SAH const_14        N7    C8    N9    "C1'"  180.000 10.0 2
+SAH const_26        C5    C4    N9    "C1'"  180.000 10.0 2
+SAH const_17        N9    C8    N7    C5     0.000   10.0 2
+SAH const_20        C6    C5    N7    C8     180.000 10.0 2
+SAH const_sp2_sp2_4 N7    C5    C6    N6     0.000   5.0  2
+SAH const_21        N9    C4    C5    N7     0.000   10.0 2
+SAH sp3_sp3_34      N     CA    CB    CG     180.000 10.0 3
+SAH sp2_sp3_1       O     C     CA    N      0.000   10.0 6
+SAH sp2_sp2_1       C5    C6    N6    HN61   180.000 5.0  2
+SAH const_sp2_sp2_6 N6    C6    N1    C2     180.000 5.0  2
+SAH const_sp2_sp2_7 N3    C2    N1    C6     0.000   5.0  2
+SAH const_sp2_sp2_9 N1    C2    N3    C4     0.000   5.0  2
+SAH const_12        N9    C4    N3    C2     180.000 10.0 2
+SAH sp3_sp3_43      CA    CB    CG    SD     180.000 10.0 3
+SAH sp3_sp3_52      CB    CG    SD    "C5'"  180.000 10.0 3
+SAH sp3_sp3_55      "C4'" "C5'" SD    CG     180.000 10.0 3
+SAH sp3_sp3_58      "O4'" "C4'" "C5'" SD     180.000 10.0 3
+SAH sp3_sp3_2       "C5'" "C4'" "O4'" "C1'"  -60.000 10.0 3
+SAH sp3_sp3_71      "O3'" "C3'" "C4'" "C5'"  180.000 10.0 3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+SAH chir_1 CA    N     C     CB    positive
+SAH chir_2 "C4'" "O4'" "C5'" "C3'" positive
+SAH chir_3 "C3'" "O3'" "C4'" "C2'" positive
+SAH chir_4 "C2'" "O2'" "C1'" "C3'" negative
+SAH chir_5 "C1'" "O4'" N9    "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+SAH plan-1 "C1'" 0.020
+SAH plan-1 C2    0.020
+SAH plan-1 C4    0.020
+SAH plan-1 C5    0.020
+SAH plan-1 C6    0.020
+SAH plan-1 C8    0.020
+SAH plan-1 H2    0.020
+SAH plan-1 H8    0.020
+SAH plan-1 N1    0.020
+SAH plan-1 N3    0.020
+SAH plan-1 N6    0.020
+SAH plan-1 N7    0.020
+SAH plan-1 N9    0.020
+SAH plan-2 C     0.020
+SAH plan-2 CA    0.020
+SAH plan-2 O     0.020
+SAH plan-2 OXT   0.020
+SAH plan-3 C6    0.020
+SAH plan-3 HN61  0.020
+SAH plan-3 HN62  0.020
+SAH plan-3 N6    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+SAH SMILES           ACDLabs              10.04 O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
+SAH SMILES_CANONICAL CACTVS               3.341 N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
+SAH SMILES           CACTVS               3.341 N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
+SAH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
+SAH SMILES           "OpenEye OEToolkits" 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
+SAH InChI            InChI                1.03  InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
+SAH InChIKey         InChI                1.03  ZJUKTBDSGOFHSH-WFMPWKQPSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+SAH acedrg          243       "dictionary generator"
+SAH acedrg_database 11        "data source"
+SAH rdkit           2017.03.2 "Chemoinformatics tool"
+SAH refmac5         5.8.0238  "optimization tool"
+
+loop_
+_chem_comp_alias.comp_id
+_chem_comp_alias.group
+_chem_comp_alias.atom_id
+_chem_comp_alias.atom_id_standard
+SAH peptide HN1 H
+SAH peptide HN2 H2
diff --git a/image_analysis/structure_refinement/monomers/SAM.cif b/image_analysis/structure_refinement/monomers/SAM.cif
new file mode 100644
index 000000000..5feded1da
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/SAM.cif
@@ -0,0 +1,347 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+SAM SAM S-ADENOSYLMETHIONINE NON-POLYMER 50 27 .
+
+data_comp_SAM
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+SAM N      N NT3  1  -27.592 29.068 46.677
+SAM CA     C CH1  0  -28.803 28.395 46.134
+SAM C      C C    0  -29.252 27.303 47.112
+SAM O      O O    0  -28.390 26.481 47.482
+SAM OXT    O OC   -1 -30.447 27.315 47.469
+SAM CB     C CH2  0  -28.507 27.780 44.760
+SAM CG     C CH2  0  -29.706 27.205 44.008
+SAM SD     S S3   1  -30.917 28.471 43.547
+SAM CE     C CH3  0  -32.145 27.508 42.679
+SAM "C5'"  C CH2  0  -30.019 29.269 42.194
+SAM "C4'"  C CH1  0  -29.862 30.762 42.411
+SAM "O4'"  O O2   0  -29.159 30.988 43.651
+SAM "C3'"  C CH1  0  -29.042 31.494 41.354
+SAM "O3'"  O OH1  0  -29.880 31.908 40.281
+SAM "C2'"  C CH1  0  -28.448 32.677 42.130
+SAM "O2'"  O OH1  0  -29.235 33.845 42.037
+SAM "C1'"  C CH1  0  -28.400 32.173 43.575
+SAM N9     N NR5  0  -27.055 31.878 44.061
+SAM C8     C CR15 0  -26.399 32.530 45.075
+SAM N7     N NRD5 0  -25.203 32.054 45.314
+SAM C5     C CR56 0  -25.057 31.017 44.404
+SAM C6     C CR6  0  -24.001 30.114 44.153
+SAM N6     N NH2  0  -22.853 30.119 44.825
+SAM N1     N NRD6 0  -24.177 29.196 43.169
+SAM C2     C CR16 0  -25.338 29.196 42.495
+SAM N3     N NRD6 0  -26.395 29.994 42.645
+SAM C4     C CR56 0  -26.195 30.896 43.625
+SAM HN1    H H    0  -27.310 29.714 46.100
+SAM HN2    H H    0  -26.921 28.461 46.790
+SAM H3     H H    0  -27.781 29.453 47.481
+SAM HA     H H    0  -29.519 29.065 46.056
+SAM HB1    H H    0  -27.851 27.065 44.879
+SAM HB2    H H    0  -28.094 28.464 44.200
+SAM HG1    H H    0  -30.155 26.532 44.561
+SAM HG2    H H    0  -29.394 26.764 43.189
+SAM HE1    H H    0  -32.772 28.106 42.242
+SAM HE2    H H    0  -32.619 26.946 43.314
+SAM HE3    H H    0  -31.707 26.952 42.015
+SAM "H5'1" H H    0  -30.506 29.113 41.356
+SAM "H5'2" H H    0  -29.133 28.858 42.111
+SAM "H4'"  H H    0  -30.759 31.175 42.468
+SAM "H3'"  H H    0  -28.320 30.910 41.010
+SAM "HO3'" H H    0  -29.420 32.372 39.739
+SAM "H2'"  H H    0  -27.528 32.871 41.805
+SAM "HO2'" H H    0  -28.800 34.500 42.358
+SAM "H1'"  H H    0  -28.805 32.854 44.158
+SAM H8     H H    0  -26.773 33.252 45.550
+SAM HN61   H H    0  -22.410 29.370 44.938
+SAM HN62   H H    0  -22.544 30.872 45.153
+SAM H2     H H    0  -25.416 28.540 41.820
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+SAM N     CA     SINGLE n 1.488 0.0100 1.488 0.0100
+SAM CA    C      SINGLE n 1.533 0.0100 1.533 0.0100
+SAM CA    CB     SINGLE n 1.532 0.0100 1.532 0.0100
+SAM C     O      DOUBLE n 1.247 0.0187 1.247 0.0187
+SAM C     OXT    SINGLE n 1.247 0.0187 1.247 0.0187
+SAM CB    CG     SINGLE n 1.516 0.0200 1.516 0.0200
+SAM CG    SD     SINGLE n 1.807 0.0171 1.807 0.0171
+SAM SD    CE     SINGLE n 1.786 0.0143 1.786 0.0143
+SAM SD    "C5'"  SINGLE n 1.807 0.0171 1.807 0.0171
+SAM "C5'" "C4'"  SINGLE n 1.516 0.0120 1.516 0.0120
+SAM "C4'" "O4'"  SINGLE n 1.446 0.0100 1.446 0.0100
+SAM "C4'" "C3'"  SINGLE n 1.528 0.0117 1.528 0.0117
+SAM "O4'" "C1'"  SINGLE n 1.409 0.0100 1.409 0.0100
+SAM "C3'" "O3'"  SINGLE n 1.422 0.0100 1.422 0.0100
+SAM "C3'" "C2'"  SINGLE n 1.531 0.0100 1.531 0.0100
+SAM "C2'" "O2'"  SINGLE n 1.411 0.0100 1.411 0.0100
+SAM "C2'" "C1'"  SINGLE n 1.525 0.0100 1.525 0.0100
+SAM "C1'" N9     SINGLE n 1.458 0.0100 1.458 0.0100
+SAM N9    C8     SINGLE y 1.372 0.0100 1.372 0.0100
+SAM N9    C4     SINGLE y 1.374 0.0101 1.374 0.0101
+SAM C8    N7     DOUBLE y 1.310 0.0100 1.310 0.0100
+SAM N7    C5     SINGLE y 1.388 0.0100 1.388 0.0100
+SAM C5    C6     SINGLE y 1.408 0.0100 1.408 0.0100
+SAM C5    C4     DOUBLE y 1.381 0.0100 1.381 0.0100
+SAM C6    N6     SINGLE n 1.330 0.0100 1.330 0.0100
+SAM C6    N1     DOUBLE y 1.354 0.0100 1.354 0.0100
+SAM N1    C2     SINGLE y 1.339 0.0100 1.339 0.0100
+SAM C2    N3     DOUBLE y 1.330 0.0100 1.330 0.0100
+SAM N3    C4     SINGLE y 1.343 0.0100 1.343 0.0100
+SAM N     HN1    SINGLE n 1.036 0.0160 0.911 0.0200
+SAM N     HN2    SINGLE n 1.036 0.0160 0.911 0.0200
+SAM N     H3     SINGLE n 1.036 0.0160 0.911 0.0200
+SAM CA    HA     SINGLE n 1.089 0.0100 0.985 0.0200
+SAM CB    HB1    SINGLE n 1.089 0.0100 0.978 0.0200
+SAM CB    HB2    SINGLE n 1.089 0.0100 0.978 0.0200
+SAM CG    HG1    SINGLE n 1.089 0.0100 0.981 0.0150
+SAM CG    HG2    SINGLE n 1.089 0.0100 0.981 0.0150
+SAM CE    HE1    SINGLE n 1.089 0.0100 0.971 0.0165
+SAM CE    HE2    SINGLE n 1.089 0.0100 0.971 0.0165
+SAM CE    HE3    SINGLE n 1.089 0.0100 0.971 0.0165
+SAM "C5'" "H5'1" SINGLE n 1.089 0.0100 0.981 0.0150
+SAM "C5'" "H5'2" SINGLE n 1.089 0.0100 0.981 0.0150
+SAM "C4'" "H4'"  SINGLE n 1.089 0.0100 0.989 0.0197
+SAM "C3'" "H3'"  SINGLE n 1.089 0.0100 0.992 0.0200
+SAM "O3'" "HO3'" SINGLE n 0.970 0.0120 0.849 0.0200
+SAM "C2'" "H2'"  SINGLE n 1.089 0.0100 0.994 0.0200
+SAM "O2'" "HO2'" SINGLE n 0.970 0.0120 0.849 0.0200
+SAM "C1'" "H1'"  SINGLE n 1.089 0.0100 0.984 0.0200
+SAM C8    H8     SINGLE n 1.082 0.0130 0.942 0.0170
+SAM N6    HN61   SINGLE n 1.016 0.0100 0.877 0.0200
+SAM N6    HN62   SINGLE n 1.016 0.0100 0.877 0.0200
+SAM C2    H2     SINGLE n 1.082 0.0130 0.945 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+SAM CA     N     HN1    110.062 1.93
+SAM CA     N     HN2    110.062 1.93
+SAM CA     N     H3     110.062 1.93
+SAM HN1    N     HN2    109.028 2.41
+SAM HN1    N     H3     109.028 2.41
+SAM HN2    N     H3     109.028 2.41
+SAM N      CA    C      109.241 1.50
+SAM N      CA    CB     110.906 1.50
+SAM N      CA    HA     108.487 1.50
+SAM C      CA    CB     109.344 1.50
+SAM C      CA    HA     108.824 1.50
+SAM CB     CA    HA     109.670 1.50
+SAM CA     C     O      117.124 1.50
+SAM CA     C     OXT    117.124 1.50
+SAM O      C     OXT    125.752 1.50
+SAM CA     CB    CG     113.808 1.88
+SAM CA     CB    HB1    108.666 1.50
+SAM CA     CB    HB2    108.666 1.50
+SAM CG     CB    HB1    108.557 1.50
+SAM CG     CB    HB2    108.557 1.50
+SAM HB1    CB    HB2    107.698 1.50
+SAM CB     CG    SD     108.220 3.00
+SAM CB     CG    HG1    109.481 1.50
+SAM CB     CG    HG2    109.481 1.50
+SAM SD     CG    HG1    108.504 1.57
+SAM SD     CG    HG2    108.504 1.57
+SAM HG1    CG    HG2    108.193 1.50
+SAM CG     SD    CE     102.026 1.83
+SAM CG     SD    "C5'"  98.345  1.79
+SAM CE     SD    "C5'"  102.487 1.89
+SAM SD     CE    HE1    109.268 1.50
+SAM SD     CE    HE2    109.268 1.50
+SAM SD     CE    HE3    109.268 1.50
+SAM HE1    CE    HE2    109.605 1.50
+SAM HE1    CE    HE3    109.605 1.50
+SAM HE2    CE    HE3    109.605 1.50
+SAM SD     "C5'" "C4'"  111.142 2.46
+SAM SD     "C5'" "H5'1" 108.544 1.50
+SAM SD     "C5'" "H5'2" 108.544 1.50
+SAM "C4'"  "C5'" "H5'1" 109.065 1.50
+SAM "C4'"  "C5'" "H5'2" 109.065 1.50
+SAM "H5'1" "C5'" "H5'2" 107.808 1.50
+SAM "C5'"  "C4'" "O4'"  109.393 1.53
+SAM "C5'"  "C4'" "C3'"  115.549 1.59
+SAM "C5'"  "C4'" "H4'"  109.003 1.50
+SAM "O4'"  "C4'" "C3'"  105.508 1.50
+SAM "O4'"  "C4'" "H4'"  109.115 1.50
+SAM "C3'"  "C4'" "H4'"  109.143 1.50
+SAM "C4'"  "O4'" "C1'"  109.426 1.50
+SAM "C4'"  "C3'" "O3'"  110.985 2.41
+SAM "C4'"  "C3'" "C2'"  102.352 1.50
+SAM "C4'"  "C3'" "H3'"  110.624 1.81
+SAM "O3'"  "C3'" "C2'"  111.581 2.83
+SAM "O3'"  "C3'" "H3'"  110.380 1.67
+SAM "C2'"  "C3'" "H3'"  110.504 1.75
+SAM "C3'"  "O3'" "HO3'" 108.744 3.00
+SAM "C3'"  "C2'" "O2'"  112.782 2.45
+SAM "C3'"  "C2'" "C1'"  101.239 1.50
+SAM "C3'"  "C2'" "H2'"  110.596 1.51
+SAM "O2'"  "C2'" "C1'"  111.715 2.69
+SAM "O2'"  "C2'" "H2'"  110.448 1.97
+SAM "C1'"  "C2'" "H2'"  110.636 1.70
+SAM "C2'"  "O2'" "HO2'" 109.103 2.13
+SAM "O4'"  "C1'" "C2'"  106.047 1.50
+SAM "O4'"  "C1'" N9     108.477 1.50
+SAM "O4'"  "C1'" "H1'"  109.807 1.50
+SAM "C2'"  "C1'" N9     113.824 1.50
+SAM "C2'"  "C1'" "H1'"  109.015 1.50
+SAM N9     "C1'" "H1'"  109.561 1.50
+SAM "C1'"  N9    C8     126.848 1.91
+SAM "C1'"  N9    C4     127.459 1.80
+SAM C8     N9    C4     105.693 1.50
+SAM N9     C8    N7     113.469 1.50
+SAM N9     C8    H8     123.206 1.50
+SAM N7     C8    H8     123.326 1.50
+SAM C8     N7    C5     104.739 1.50
+SAM N7     C5    C6     132.250 1.50
+SAM N7     C5    C4     110.483 1.50
+SAM C6     C5    C4     117.267 1.50
+SAM C5     C6    N6     123.792 1.50
+SAM C5     C6    N1     117.409 1.50
+SAM N6     C6    N1     118.799 1.50
+SAM C6     N6    HN61   119.723 1.50
+SAM C6     N6    HN62   119.723 1.50
+SAM HN61   N6    HN62   120.554 1.88
+SAM C6     N1    C2     118.521 1.50
+SAM N1     C2    N3     129.332 1.50
+SAM N1     C2    H2     115.313 1.50
+SAM N3     C2    H2     115.355 1.50
+SAM C2     N3    C4     110.982 1.50
+SAM N9     C4    C5     105.616 1.50
+SAM N9     C4    N3     127.895 1.50
+SAM C5     C4    N3     126.489 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+SAM sp3_sp3_25      C     CA    N     HN1    180.000 10.0 3
+SAM sp3_sp3_2       "C5'" "C4'" "O4'" "C1'"  -60.000 10.0 3
+SAM sp3_sp3_83      "O3'" "C3'" "C4'" "C5'"  180.000 10.0 3
+SAM sp3_sp3_4       "C2'" "C1'" "O4'" "C4'"  -60.000 10.0 3
+SAM sp3_sp3_88      "C4'" "C3'" "O3'" "HO3'" 180.000 10.0 3
+SAM sp3_sp3_20      "O2'" "C2'" "C3'" "O3'"  -60.000 10.0 3
+SAM sp3_sp3_91      "C3'" "C2'" "O2'" "HO2'" 180.000 10.0 3
+SAM sp3_sp3_8       "O4'" "C1'" "C2'" "O2'"  180.000 10.0 3
+SAM sp2_sp3_7       C8    N9    "C1'" "O4'"  150.000 10.0 6
+SAM const_14        N7    C8    N9    "C1'"  180.000 10.0 2
+SAM const_26        C5    C4    N9    "C1'"  180.000 10.0 2
+SAM const_17        N9    C8    N7    C5     0.000   10.0 2
+SAM const_20        C6    C5    N7    C8     180.000 10.0 2
+SAM sp2_sp3_1       O     C     CA    N      0.000   10.0 6
+SAM sp3_sp3_34      N     CA    CB    CG     180.000 10.0 3
+SAM const_sp2_sp2_4 N7    C5    C6    N6     0.000   5.0  2
+SAM const_21        N9    C4    C5    N7     0.000   10.0 2
+SAM sp2_sp2_1       C5    C6    N6    HN61   180.000 5.0  2
+SAM const_sp2_sp2_6 N6    C6    N1    C2     180.000 5.0  2
+SAM const_sp2_sp2_7 N3    C2    N1    C6     0.000   5.0  2
+SAM const_sp2_sp2_9 N1    C2    N3    C4     0.000   5.0  2
+SAM const_12        N9    C4    N3    C2     180.000 10.0 2
+SAM sp3_sp3_43      CA    CB    CG    SD     180.000 10.0 3
+SAM sp3_sp3_52      CB    CG    SD    CE     180.000 10.0 3
+SAM sp3_sp3_58      HE1   CE    SD    CG     180.000 10.0 3
+SAM sp3_sp3_64      "C4'" "C5'" SD    CG     180.000 10.0 3
+SAM sp3_sp3_70      "O4'" "C4'" "C5'" SD     180.000 10.0 3
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+SAM chir_1 CA    N     C     CB    positive
+SAM chir_2 SD    "C5'" CG    CE    positive
+SAM chir_3 "C4'" "O4'" "C5'" "C3'" positive
+SAM chir_4 "C3'" "O3'" "C4'" "C2'" positive
+SAM chir_5 "C2'" "O2'" "C1'" "C3'" negative
+SAM chir_6 "C1'" "O4'" N9    "C2'" negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+SAM plan-1 "C1'" 0.020
+SAM plan-1 C2    0.020
+SAM plan-1 C4    0.020
+SAM plan-1 C5    0.020
+SAM plan-1 C6    0.020
+SAM plan-1 C8    0.020
+SAM plan-1 H2    0.020
+SAM plan-1 H8    0.020
+SAM plan-1 N1    0.020
+SAM plan-1 N3    0.020
+SAM plan-1 N6    0.020
+SAM plan-1 N7    0.020
+SAM plan-1 N9    0.020
+SAM plan-2 C     0.020
+SAM plan-2 CA    0.020
+SAM plan-2 O     0.020
+SAM plan-2 OXT   0.020
+SAM plan-3 C6    0.020
+SAM plan-3 HN61  0.020
+SAM plan-3 HN62  0.020
+SAM plan-3 N6    0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+SAM SMILES           ACDLabs              10.04 "[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O"
+SAM SMILES_CANONICAL CACTVS               3.341 C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
+SAM SMILES           CACTVS               3.341 C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
+SAM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
+SAM SMILES           "OpenEye OEToolkits" 1.5.0 C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
+SAM InChI            InChI                1.03  InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
+SAM InChIKey         InChI                1.03  MEFKEPWMEQBLKI-FCKMPRQPSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+SAM acedrg          243       "dictionary generator"
+SAM acedrg_database 11        "data source"
+SAM rdkit           2017.03.2 "Chemoinformatics tool"
+SAM refmac5         5.8.0238  "optimization tool"
+
+loop_
+_chem_comp_alias.comp_id
+_chem_comp_alias.group
+_chem_comp_alias.atom_id
+_chem_comp_alias.atom_id_standard
+SAM peptide HN1 H
+SAM peptide HN2 H2
diff --git a/image_analysis/structure_refinement/monomers/SER.cif b/image_analysis/structure_refinement/monomers/SER.cif
new file mode 100644
index 000000000..f16baafc7
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/SER.cif
@@ -0,0 +1,188 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+SER SER SERINE peptide 14 7 .
+
+data_comp_SER
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+SER N N NT3 1 88.105 -7.500 -9.831
+SER CA C CH1 0 87.822 -7.221 -11.265
+SER C C C 0 88.475 -5.896 -11.689
+SER O O O 0 88.336 -4.918 -10.921
+SER CB C CH2 0 86.337 -7.203 -11.533
+SER OG O OH1 0 85.742 -8.447 -11.190
+SER OXT O OC -1 89.099 -5.887 -12.773
+SER H H H 0 87.553 -7.016 -9.304
+SER H2 H H 0 88.960 -7.295 -9.626
+SER H3 H H 0 87.971 -8.377 -9.665
+SER HA H H 0 88.226 -7.948 -11.803
+SER HB3 H H 0 86.182 -7.019 -12.479
+SER HB2 H H 0 85.923 -6.490 -11.011
+SER HG H H 0 84.904 -8.380 -11.287
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+SER N n/a CA START
+SER H N . .
+SER H2 N . .
+SER H3 N . .
+SER CA N C .
+SER HA CA . .
+SER CB CA OG .
+SER HB3 CB . .
+SER HB2 CB . .
+SER OG CB HG .
+SER HG OG . .
+SER C CA . END
+SER O C . .
+SER OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+SER N N(CCCH)(H)3
+SER CA C(CHHO)(NH3)(COO)(H)
+SER C C(CCHN)(O)2
+SER O O(CCO)
+SER CB C(CCHN)(OH)(H)2
+SER OG O(CCHH)(H)
+SER OXT O(CCO)
+SER H H(NCHH)
+SER H2 H(NCHH)
+SER H3 H(NCHH)
+SER HA H(CCCN)
+SER HB3 H(CCHO)
+SER HB2 H(CCHO)
+SER HG H(OC)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+SER N CA SINGLE n 1.487 0.0100 1.487 0.0100
+SER CA C SINGLE n 1.536 0.0100 1.536 0.0100
+SER CA CB SINGLE n 1.508 0.0190 1.508 0.0190
+SER C O DOUBLE n 1.251 0.0183 1.251 0.0183
+SER C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+SER CB OG SINGLE n 1.421 0.0108 1.421 0.0108
+SER N H SINGLE n 1.018 0.0520 0.902 0.0102
+SER N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+SER N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+SER CA HA SINGLE n 1.092 0.0100 0.991 0.0200
+SER CB HB3 SINGLE n 1.092 0.0100 0.976 0.0180
+SER CB HB2 SINGLE n 1.092 0.0100 0.976 0.0180
+SER OG HG SINGLE n 0.972 0.0180 0.846 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+SER CA N H 109.696 3.00
+SER CA N H2 109.696 3.00
+SER CA N H3 109.696 3.00
+SER H N H2 109.032 3.00
+SER H N H3 109.032 3.00
+SER H2 N H3 109.032 3.00
+SER N CA C 109.839 1.50
+SER N CA CB 111.152 1.50
+SER N CA HA 108.129 1.50
+SER C CA CB 111.300 1.50
+SER C CA HA 108.235 1.50
+SER CB CA HA 108.445 1.50
+SER CA C O 117.199 1.50
+SER CA C OXT 117.189 1.50
+SER O C OXT 125.593 1.50
+SER CA CB OG 110.934 1.86
+SER CA CB HB3 109.238 1.50
+SER CA CB HB2 109.238 1.50
+SER OG CB HB3 109.353 1.50
+SER OG CB HB2 109.353 1.50
+SER HB3 CB HB2 108.095 1.88
+SER CB OG HG 108.539 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+SER chi1 N CA CB OG -60.000 10.0 3
+SER hh1 CA CB OG HG 180.000 10.0 3
+SER sp3_sp3_1 C CA N H 180.000 10.0 3
+SER sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+SER chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+SER plan-1 C 0.020
+SER plan-1 CA 0.020
+SER plan-1 O 0.020
+SER plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+SER SMILES ACDLabs 10.04 O=C(O)C(N)CO
+SER SMILES_CANONICAL CACTVS 3.341 N[C@@H](CO)C(O)=O
+SER SMILES CACTVS 3.341 N[CH](CO)C(O)=O
+SER SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H](C(=O)O)N)O
+SER SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)O
+SER InChI InChI 1.03 InChI=1S/C3H7NO3/c4-2(1-5)3(6)7/h2,5H,1,4H2,(H,6,7)/t2-/m0/s1
+SER InChIKey InChI 1.03 MTCFGRXMJLQNBG-REOHCLBHSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+SER acedrg 278 "dictionary generator"
+SER acedrg_database 12 "data source"
+SER rdkit 2019.09.1 "Chemoinformatics tool"
+SER refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/SO4.cif b/image_analysis/structure_refinement/monomers/SO4.cif
new file mode 100644
index 000000000..1f560acff
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/SO4.cif
@@ -0,0 +1,86 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+SO4     SO4      "SULFATE ION"     NON-POLYMER     5     5     .     
+#
+data_comp_SO4
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+SO4     S       S       S3      0       16.537      34.975      5.493       
+SO4     O1      O       O       0       17.831      34.952      4.866       
+SO4     O2      O       O       0       16.570      35.855      6.629       
+SO4     O3      O       OS      -1      15.557      35.444      4.551       
+SO4     O4      O       OS      -1      16.190      33.647      5.924       
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+SO4           S          O1      DOUBLE       n     1.438  0.0156     1.438  0.0156
+SO4           S          O2      DOUBLE       n     1.438  0.0156     1.438  0.0156
+SO4           S          O3      SINGLE       n     1.438  0.0156     1.438  0.0156
+SO4           S          O4      SINGLE       n     1.438  0.0156     1.438  0.0156
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+SO4          O1           S          O2     109.467    1.50
+SO4          O1           S          O3     109.467    1.50
+SO4          O1           S          O4     109.467    1.50
+SO4          O2           S          O3     109.467    1.50
+SO4          O2           S          O4     109.467    1.50
+SO4          O3           S          O4     109.467    1.50
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+SO4    chir_1    S    O1    O2    O3    both
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+SO4           SMILES              ACDLabs 10.04                         "[O-]S([O-])(=O)=O"
+SO4 SMILES_CANONICAL               CACTVS 3.341                       "[O-][S]([O-])(=O)=O"
+SO4           SMILES               CACTVS 3.341                       "[O-][S]([O-])(=O)=O"
+SO4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                         "[O-]S(=O)(=O)[O-]"
+SO4           SMILES "OpenEye OEToolkits" 1.5.0                         "[O-]S(=O)(=O)[O-]"
+SO4            InChI                InChI  1.03 InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
+SO4         InChIKey                InChI  1.03                 QAOWNCQODCNURD-UHFFFAOYSA-L
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+SO4 acedrg               243         "dictionary generator"                  
+SO4 acedrg_database      11          "data source"                           
+SO4 rdkit                2017.03.2   "Chemoinformatics tool"
+SO4 refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/THR.cif b/image_analysis/structure_refinement/monomers/THR.cif
new file mode 100644
index 000000000..ecef5ae40
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/THR.cif
@@ -0,0 +1,208 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+THR THR THREONINE peptide 17 8 .
+
+data_comp_THR
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+THR N N NT3 1 36.284 31.964 31.738
+THR CA C CH1 0 35.016 31.199 31.745
+THR C C C 0 34.952 30.333 30.501
+THR O O O 0 35.086 30.909 29.398
+THR CB C CH1 0 33.833 32.166 31.829
+THR OG1 O OH1 0 34.044 32.962 32.993
+THR CG2 C CH3 0 32.493 31.457 31.927
+THR OXT O OC -1 34.770 29.107 30.668
+THR H H H 0 36.319 32.492 31.007
+THR H2 H H 0 36.984 31.395 31.731
+THR H3 H H 0 36.331 32.480 32.477
+THR HA H H 0 35.006 30.619 32.537
+THR HB H H 0 33.830 32.749 31.033
+THR HG1 H H 0 34.002 32.475 33.707
+THR HG21 H H 0 32.588 30.657 32.470
+THR HG22 H H 0 32.191 31.210 31.037
+THR HG23 H H 0 31.841 32.050 32.336
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+THR N n/a CA START
+THR H N . .
+THR H2 N . .
+THR H3 N . .
+THR CA N C .
+THR HA CA . .
+THR CB CA CG2 .
+THR HB CB . .
+THR OG1 CB HG1 .
+THR HG1 OG1 . .
+THR CG2 CB HG23 .
+THR HG21 CG2 . .
+THR HG22 CG2 . .
+THR HG23 CG2 . .
+THR C CA . END
+THR O C . .
+THR OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+THR N N(CCCH)(H)3
+THR CA C(CCHO)(NH3)(COO)(H)
+THR C C(CCHN)(O)2
+THR O O(CCO)
+THR CB C(CCHN)(CH3)(OH)(H)
+THR OG1 O(CCCH)(H)
+THR CG2 C(CCHO)(H)3
+THR OXT O(CCO)
+THR H H(NCHH)
+THR H2 H(NCHH)
+THR H3 H(NCHH)
+THR HA H(CCCN)
+THR HB H(CCCO)
+THR HG1 H(OC)
+THR HG21 H(CCHH)
+THR HG22 H(CCHH)
+THR HG23 H(CCHH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+THR N CA SINGLE n 1.480 0.0122 1.480 0.0122
+THR CA C SINGLE n 1.515 0.0129 1.515 0.0129
+THR CA CB SINGLE n 1.528 0.0100 1.528 0.0100
+THR C O DOUBLE n 1.251 0.0183 1.251 0.0183
+THR C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+THR CB OG1 SINGLE n 1.424 0.0100 1.424 0.0100
+THR CB CG2 SINGLE n 1.518 0.0100 1.518 0.0100
+THR N H SINGLE n 1.018 0.0520 0.902 0.0102
+THR N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+THR N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+THR CA HA SINGLE n 1.092 0.0100 0.982 0.0200
+THR CB HB SINGLE n 1.092 0.0100 0.987 0.0100
+THR OG1 HG1 SINGLE n 0.972 0.0180 0.864 0.0200
+THR CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156
+THR CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156
+THR CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+THR CA N H 109.577 1.50
+THR CA N H2 109.577 1.50
+THR CA N H3 109.577 1.50
+THR H N H2 109.032 3.00
+THR H N H3 109.032 3.00
+THR H2 N H3 109.032 3.00
+THR N CA C 109.121 1.50
+THR N CA CB 109.645 1.84
+THR N CA HA 108.639 1.50
+THR C CA CB 111.778 1.58
+THR C CA HA 109.055 1.50
+THR CB CA HA 108.870 1.50
+THR CA C O 117.098 1.50
+THR CA C OXT 117.098 1.50
+THR O C OXT 125.804 1.50
+THR CA CB OG1 105.245 3.00
+THR CA CB CG2 112.544 1.50
+THR CA CB HB 109.595 2.39
+THR OG1 CB CG2 109.974 3.00
+THR OG1 CB HB 109.323 1.86
+THR CG2 CB HB 109.170 2.61
+THR CB OG1 HG1 109.544 3.00
+THR CB CG2 HG21 109.532 1.50
+THR CB CG2 HG22 109.532 1.50
+THR CB CG2 HG23 109.532 1.50
+THR HG21 CG2 HG22 109.425 1.50
+THR HG21 CG2 HG23 109.425 1.50
+THR HG22 CG2 HG23 109.425 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+THR chi1 N CA CB CG2 -60.000 10.0 3
+THR hh1 CA CB OG1 HG1 -60.000 10.0 3
+THR hh2 CA CB CG2 HG23 -60.000 10.0 3
+THR sp3_sp3_1 C CA N H 180.000 10.0 3
+THR sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+THR chir_1 CA N C CB positive
+THR chir_2 CB OG1 CA CG2 negative
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+THR plan-1 C 0.020
+THR plan-1 CA 0.020
+THR plan-1 O 0.020
+THR plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+THR SMILES ACDLabs 10.04 O=C(O)C(N)C(O)C
+THR SMILES_CANONICAL CACTVS 3.341 C[C@@H](O)[C@H](N)C(O)=O
+THR SMILES CACTVS 3.341 C[CH](O)[CH](N)C(O)=O
+THR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H]([C@@H](C(=O)O)N)O
+THR SMILES "OpenEye OEToolkits" 1.5.0 CC(C(C(=O)O)N)O
+THR InChI InChI 1.03 InChI=1S/C4H9NO3/c1-2(6)3(5)4(7)8/h2-3,6H,5H2,1H3,(H,7,8)/t2-,3+/m1/s1
+THR InChIKey InChI 1.03 AYFVYJQAPQTCCC-GBXIJSLDSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+THR acedrg 278 "dictionary generator"
+THR acedrg_database 12 "data source"
+THR rdkit 2019.09.1 "Chemoinformatics tool"
+THR refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/TRP.cif b/image_analysis/structure_refinement/monomers/TRP.cif
new file mode 100644
index 000000000..8c24a618c
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/TRP.cif
@@ -0,0 +1,301 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+TRP TRP TRYPTOPHAN peptide 27 15 .
+
+data_comp_TRP
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+TRP N N NT3 1 75.046 60.221 32.550
+TRP CA C CH1 0 74.659 61.570 32.056
+TRP C C C 0 73.758 61.438 30.822
+TRP O O O 0 72.787 62.222 30.736
+TRP CB C CH2 0 75.903 62.411 31.737
+TRP CG C CR5 0 76.760 62.727 32.935
+TRP CD1 C CR15 0 77.836 62.019 33.383
+TRP CD2 C CR56 0 76.605 63.839 33.843
+TRP NE1 N NR15 0 78.364 62.608 34.501
+TRP CE2 C CR56 0 77.632 63.725 34.809
+TRP CE3 C CR16 0 75.707 64.913 33.936
+TRP CZ2 C CR16 0 77.780 64.645 35.849
+TRP CZ3 C CR16 0 75.854 65.821 34.965
+TRP CH2 C CR16 0 76.878 65.687 35.909
+TRP OXT O OC -1 74.059 60.555 29.988
+TRP H H H 0 75.680 59.865 32.016
+TRP H2 H H 0 74.332 59.671 32.560
+TRP H3 H H 0 75.369 60.277 33.391
+TRP HA H H 0 74.147 62.030 32.775
+TRP HB3 H H 0 75.613 63.253 31.325
+TRP HB2 H H 0 76.446 61.928 31.078
+TRP HD1 H H 0 78.177 61.234 32.984
+TRP HE1 H H 0 79.056 62.317 34.946
+TRP HE3 H H 0 75.014 65.011 33.305
+TRP HZ2 H H 0 78.468 64.556 36.485
+TRP HZ3 H H 0 75.254 66.545 35.034
+TRP HH2 H H 0 76.954 66.321 36.599
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+TRP N n/a CA START
+TRP H N . .
+TRP H2 N . .
+TRP H3 N . .
+TRP CA N C .
+TRP HA CA . .
+TRP CB CA CG .
+TRP HB3 CB . .
+TRP HB2 CB . .
+TRP CG CB CD1 .
+TRP CD1 CG NE1 .
+TRP HD1 CD1 . .
+TRP NE1 CD1 CE2 .
+TRP HE1 NE1 . .
+TRP CE2 NE1 CD2 .
+TRP CD2 CE2 CE3 .
+TRP CE3 CD2 CZ3 .
+TRP HE3 CE3 . .
+TRP CZ3 CE3 CH2 .
+TRP HZ3 CZ3 . .
+TRP CH2 CZ3 CZ2 .
+TRP HH2 CH2 . .
+TRP CZ2 CH2 HZ2 .
+TRP HZ2 CZ2 . .
+TRP C CA . END
+TRP O C . .
+TRP OXT C . .
+TRP CD2 CG . ADD
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+TRP N N(CCCH)(H)3
+TRP CA C(CC[5a]HH)(NH3)(COO)(H)
+TRP C C(CCHN)(O)2
+TRP O O(CCO)
+TRP CB C(C[5a]C[5a,6a]C[5a])(CCHN)(H)2
+TRP CG C[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]N[5a]H)(CCHH){2|C<3>,2|H<1>}
+TRP CD1 C[5a](C[5a]C[5a,6a]C)(N[5a]C[5a,6a]H)(H){2|C<3>}
+TRP CD2 C[5a,6a](C[5a,6a]C[6a]N[5a])(C[5a]C[5a]C)(C[6a]C[6a]H){1|C<3>,4|H<1>}
+TRP NE1 N[5a](C[5a,6a]C[5a,6a]C[6a])(C[5a]C[5a]H)(H){1|C<4>,1|H<1>,2|C<3>}
+TRP CE2 C[5a,6a](C[5a,6a]C[5a]C[6a])(C[6a]C[6a]H)(N[5a]C[5a]H){1|C<3>,1|C<4>,3|H<1>}
+TRP CE3 C[6a](C[5a,6a]C[5a,6a]C[5a])(C[6a]C[6a]H)(H){1|C<4>,1|H<1>,1|N<3>,2|C<3>}
+TRP CZ2 C[6a](C[5a,6a]C[5a,6a]N[5a])(C[6a]C[6a]H)(H){2|H<1>,3|C<3>}
+TRP CZ3 C[6a](C[6a]C[5a,6a]H)(C[6a]C[6a]H)(H){1|H<1>,2|C<3>}
+TRP CH2 C[6a](C[6a]C[5a,6a]H)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|N<3>}
+TRP OXT O(CCO)
+TRP H H(NCHH)
+TRP H2 H(NCHH)
+TRP H3 H(NCHH)
+TRP HA H(CCCN)
+TRP HB3 H(CC[5a]CH)
+TRP HB2 H(CC[5a]CH)
+TRP HD1 H(C[5a]C[5a]N[5a])
+TRP HE1 H(N[5a]C[5a,6a]C[5a])
+TRP HE3 H(C[6a]C[5a,6a]C[6a])
+TRP HZ2 H(C[6a]C[5a,6a]C[6a])
+TRP HZ3 H(C[6a]C[6a]2)
+TRP HH2 H(C[6a]C[6a]2)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+TRP N CA SINGLE n 1.486 0.0100 1.486 0.0100
+TRP CA C SINGLE n 1.532 0.0129 1.532 0.0129
+TRP CA CB SINGLE n 1.535 0.0100 1.535 0.0100
+TRP C O DOUBLE n 1.251 0.0183 1.251 0.0183
+TRP C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+TRP CB CG SINGLE n 1.506 0.0100 1.506 0.0100
+TRP CG CD1 DOUBLE y 1.364 0.0100 1.364 0.0100
+TRP CG CD2 SINGLE y 1.445 0.0100 1.445 0.0100
+TRP CD1 NE1 SINGLE y 1.369 0.0100 1.369 0.0100
+TRP CD2 CE2 DOUBLE y 1.412 0.0100 1.412 0.0100
+TRP CD2 CE3 SINGLE y 1.399 0.0100 1.399 0.0100
+TRP NE1 CE2 SINGLE y 1.370 0.0100 1.370 0.0100
+TRP CE2 CZ2 SINGLE y 1.393 0.0100 1.393 0.0100
+TRP CE3 CZ3 DOUBLE y 1.377 0.0100 1.377 0.0100
+TRP CZ2 CH2 DOUBLE y 1.376 0.0101 1.376 0.0101
+TRP CZ3 CH2 SINGLE y 1.394 0.0120 1.394 0.0120
+TRP N H SINGLE n 1.018 0.0520 0.902 0.0102
+TRP N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+TRP N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+TRP CA HA SINGLE n 1.092 0.0100 0.995 0.0200
+TRP CB HB3 SINGLE n 1.092 0.0100 0.981 0.0100
+TRP CB HB2 SINGLE n 1.092 0.0100 0.981 0.0100
+TRP CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0195
+TRP NE1 HE1 SINGLE n 1.013 0.0120 0.873 0.0200
+TRP CE3 HE3 SINGLE n 1.085 0.0150 0.942 0.0199
+TRP CZ2 HZ2 SINGLE n 1.085 0.0150 0.942 0.0181
+TRP CZ3 HZ3 SINGLE n 1.085 0.0150 0.943 0.0167
+TRP CH2 HH2 SINGLE n 1.085 0.0150 0.941 0.0176
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+TRP CA N H 109.786 3.00
+TRP CA N H2 109.786 3.00
+TRP CA N H3 109.786 3.00
+TRP H N H2 109.032 3.00
+TRP H N H3 109.032 3.00
+TRP H2 N H3 109.032 3.00
+TRP N CA C 109.790 1.50
+TRP N CA CB 110.346 1.50
+TRP N CA HA 108.404 1.50
+TRP C CA CB 111.156 1.50
+TRP C CA HA 108.682 1.50
+TRP CB CA HA 108.429 1.50
+TRP CA C O 117.155 2.01
+TRP CA C OXT 117.155 2.01
+TRP O C OXT 125.691 1.50
+TRP CA CB CG 113.870 1.50
+TRP CA CB HB3 108.522 1.50
+TRP CA CB HB2 108.522 1.50
+TRP CG CB HB3 108.877 1.50
+TRP CG CB HB2 108.877 1.50
+TRP HB3 CB HB2 107.959 3.00
+TRP CB CG CD1 126.940 2.13
+TRP CB CG CD2 126.837 1.66
+TRP CD1 CG CD2 106.223 1.50
+TRP CG CD1 NE1 110.303 1.50
+TRP CG CD1 HD1 125.325 2.99
+TRP NE1 CD1 HD1 124.372 1.81
+TRP CG CD2 CE2 106.978 1.50
+TRP CG CD2 CE3 134.327 1.50
+TRP CE2 CD2 CE3 118.695 1.50
+TRP CD1 NE1 CE2 109.057 1.50
+TRP CD1 NE1 HE1 125.366 3.00
+TRP CE2 NE1 HE1 125.577 3.00
+TRP CD2 CE2 NE1 107.438 1.50
+TRP CD2 CE2 CZ2 122.273 1.50
+TRP NE1 CE2 CZ2 130.289 1.50
+TRP CD2 CE3 CZ3 118.811 1.50
+TRP CD2 CE3 HE3 120.479 1.50
+TRP CZ3 CE3 HE3 120.709 1.50
+TRP CE2 CZ2 CH2 117.418 1.50
+TRP CE2 CZ2 HZ2 121.196 1.50
+TRP CH2 CZ2 HZ2 121.386 1.50
+TRP CE3 CZ3 CH2 121.228 1.50
+TRP CE3 CZ3 HZ3 119.424 1.50
+TRP CH2 CZ3 HZ3 119.348 1.50
+TRP CZ2 CH2 CZ3 121.574 1.50
+TRP CZ2 CH2 HH2 119.154 1.50
+TRP CZ3 CH2 HH2 119.272 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+TRP chi1 N CA CB CG -60.000 10.0 3
+TRP chi2 CA CB CG CD1 90.000 10.0 6
+TRP CONST_1 CB CG CD1 NE1 0.000 0.0 1
+TRP CONST_2 CG CD1 NE1 CE2 0.000 0.0 1
+TRP CONST_3 NE1 CE2 CD2 CE3 0.000 0.0 1
+TRP CONST_4 CE2 CD2 CE3 CZ3 0.000 0.0 1
+TRP CONST_5 CD1 NE1 CE2 CD2 0.000 0.0 1
+TRP CONST_6 CD2 CE3 CZ3 CH2 0.000 0.0 1
+TRP CONST_7 CZ3 CH2 CZ2 CE2 0.000 0.0 1
+TRP CONST_8 CE3 CZ3 CH2 CZ2 0.000 0.0 1
+TRP sp3_sp3_1 C CA N H 180.000 10.0 3
+TRP const_33 CE2 CD2 CG CD1 0.000 0.0 1
+TRP const_17 CD2 CE2 CZ2 CH2 0.000 0.0 1
+TRP sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+TRP chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+TRP plan-1 CD2 0.020
+TRP plan-1 CE2 0.020
+TRP plan-1 CE3 0.020
+TRP plan-1 CG 0.020
+TRP plan-1 CH2 0.020
+TRP plan-1 CZ2 0.020
+TRP plan-1 CZ3 0.020
+TRP plan-1 HE3 0.020
+TRP plan-1 HH2 0.020
+TRP plan-1 HZ2 0.020
+TRP plan-1 HZ3 0.020
+TRP plan-1 NE1 0.020
+TRP plan-2 CB 0.020
+TRP plan-2 CD1 0.020
+TRP plan-2 CD2 0.020
+TRP plan-2 CE2 0.020
+TRP plan-2 CE3 0.020
+TRP plan-2 CG 0.020
+TRP plan-2 CZ2 0.020
+TRP plan-2 HD1 0.020
+TRP plan-2 HE1 0.020
+TRP plan-2 NE1 0.020
+TRP plan-3 C 0.020
+TRP plan-3 CA 0.020
+TRP plan-3 O 0.020
+TRP plan-3 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+TRP SMILES ACDLabs 10.04 "O=C(O)C(N)Cc2c1ccccc1nc2"
+TRP SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1c[nH]c2ccccc12)C(O)=O"
+TRP SMILES CACTVS 3.341 "N[CH](Cc1c[nH]c2ccccc12)C(O)=O"
+TRP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N"
+TRP SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc2c(c1)c(c[nH]2)CC(C(=O)O)N"
+TRP InChI InChI 1.03 "InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1"
+TRP InChIKey InChI 1.03 QIVBCDIJIAJPQS-VIFPVBQESA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+TRP acedrg 278 "dictionary generator"
+TRP acedrg_database 12 "data source"
+TRP rdkit 2019.09.1 "Chemoinformatics tool"
+TRP refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/TYR.cif b/image_analysis/structure_refinement/monomers/TYR.cif
new file mode 100644
index 000000000..f1a4e5bee
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/TYR.cif
@@ -0,0 +1,268 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+TYR TYR TYROSINE peptide 24 13 .
+
+data_comp_TYR
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+TYR N N NT3 1 5.311 5.160 15.589
+TYR CA C CH1 0 5.358 6.374 16.456
+TYR C C C 0 4.823 7.578 15.662
+TYR O O O 0 3.988 8.305 16.245
+TYR CB C CH2 0 6.763 6.679 16.994
+TYR CG C CR6 0 7.348 5.630 17.938
+TYR CD1 C CR16 0 7.096 5.672 19.314
+TYR CD2 C CR16 0 8.161 4.597 17.458
+TYR CE1 C CR16 0 7.628 4.720 20.176
+TYR CE2 C CR16 0 8.697 3.641 18.313
+TYR CZ C CR6 0 8.431 3.702 19.674
+TYR OH O OH1 0 8.982 2.738 20.476
+TYR OXT O OC -1 5.248 7.759 14.496
+TYR H H H 0 5.552 4.421 16.046
+TYR H2 H H 0 5.856 5.257 14.876
+TYR H3 H H 0 4.470 5.038 15.288
+TYR HA H H 0 4.756 6.220 17.232
+TYR HB3 H H 0 6.733 7.543 17.464
+TYR HB2 H H 0 7.369 6.788 16.227
+TYR HD1 H H 0 6.552 6.358 19.667
+TYR HD2 H H 0 8.350 4.543 16.534
+TYR HE1 H H 0 7.444 4.765 21.099
+TYR HE2 H H 0 9.240 2.953 17.971
+TYR HH H H 0 8.782 2.828 21.308
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+TYR N n/a CA START
+TYR H N . .
+TYR H2 N . .
+TYR H3 N . .
+TYR CA N C .
+TYR HA CA . .
+TYR CB CA CG .
+TYR HB3 CB . .
+TYR HB2 CB . .
+TYR CG CB CD1 .
+TYR CD1 CG CE1 .
+TYR HD1 CD1 . .
+TYR CE1 CD1 CZ .
+TYR HE1 CE1 . .
+TYR CZ CE1 CE2 .
+TYR OH CZ HH .
+TYR HH OH . .
+TYR CE2 CZ CD2 .
+TYR HE2 CE2 . .
+TYR CD2 CE2 HD2 .
+TYR HD2 CD2 . .
+TYR C CA . END
+TYR O C . .
+TYR OXT C . .
+TYR CD2 CG . ADD
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+TYR N N(CCCH)(H)3
+TYR CA C(CC[6a]HH)(NH3)(COO)(H)
+TYR C C(CCHN)(O)2
+TYR O O(CCO)
+TYR CB C(C[6a]C[6a]2)(CCHN)(H)2
+TYR CG C[6a](C[6a]C[6a]H)2(CCHH){1|C<3>,2|H<1>}
+TYR CD1 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>}
+TYR CD2 C[6a](C[6a]C[6a]C)(C[6a]C[6a]H)(H){1|C<3>,1|H<1>,1|O<2>}
+TYR CE1 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>}
+TYR CE2 C[6a](C[6a]C[6a]H)(C[6a]C[6a]O)(H){1|C<3>,1|C<4>,1|H<1>}
+TYR CZ C[6a](C[6a]C[6a]H)2(OH){1|C<3>,2|H<1>}
+TYR OH O(C[6a]C[6a]2)(H)
+TYR OXT O(CCO)
+TYR H H(NCHH)
+TYR H2 H(NCHH)
+TYR H3 H(NCHH)
+TYR HA H(CCCN)
+TYR HB3 H(CC[6a]CH)
+TYR HB2 H(CC[6a]CH)
+TYR HD1 H(C[6a]C[6a]2)
+TYR HD2 H(C[6a]C[6a]2)
+TYR HE1 H(C[6a]C[6a]2)
+TYR HE2 H(C[6a]C[6a]2)
+TYR HH H(OC[6a])
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+TYR N CA SINGLE n 1.489 0.0100 1.489 0.0100
+TYR CA C SINGLE n 1.531 0.0171 1.531 0.0171
+TYR CA CB SINGLE n 1.532 0.0100 1.532 0.0100
+TYR C O DOUBLE n 1.251 0.0183 1.251 0.0183
+TYR C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+TYR CB CG SINGLE n 1.523 0.0100 1.523 0.0100
+TYR CG CD1 DOUBLE y 1.390 0.0116 1.390 0.0116
+TYR CG CD2 SINGLE y 1.390 0.0116 1.390 0.0116
+TYR CD1 CE1 SINGLE y 1.385 0.0100 1.385 0.0100
+TYR CD2 CE2 DOUBLE y 1.385 0.0100 1.385 0.0100
+TYR CE1 CZ DOUBLE y 1.383 0.0100 1.383 0.0100
+TYR CE2 CZ SINGLE y 1.383 0.0100 1.383 0.0100
+TYR CZ OH SINGLE n 1.365 0.0137 1.365 0.0137
+TYR N H SINGLE n 1.018 0.0520 0.902 0.0102
+TYR N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+TYR N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+TYR CA HA SINGLE n 1.092 0.0100 0.994 0.0200
+TYR CB HB3 SINGLE n 1.092 0.0100 0.983 0.0163
+TYR CB HB2 SINGLE n 1.092 0.0100 0.983 0.0163
+TYR CD1 HD1 SINGLE n 1.085 0.0150 0.944 0.0143
+TYR CD2 HD2 SINGLE n 1.085 0.0150 0.944 0.0143
+TYR CE1 HE1 SINGLE n 1.085 0.0150 0.942 0.0174
+TYR CE2 HE2 SINGLE n 1.085 0.0150 0.942 0.0174
+TYR OH HH SINGLE n 0.966 0.0059 0.858 0.0200
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+TYR CA N H 109.791 3.00
+TYR CA N H2 109.791 3.00
+TYR CA N H3 109.791 3.00
+TYR H N H2 109.032 3.00
+TYR H N H3 109.032 3.00
+TYR H2 N H3 109.032 3.00
+TYR N CA C 109.085 1.50
+TYR N CA CB 109.965 3.00
+TYR N CA HA 108.547 1.50
+TYR C CA CB 111.980 3.00
+TYR C CA HA 108.746 1.50
+TYR CB CA HA 108.686 1.50
+TYR CA C O 117.219 3.00
+TYR CA C OXT 117.219 3.00
+TYR O C OXT 125.562 1.50
+TYR CA CB CG 114.693 2.05
+TYR CA CB HB3 108.494 1.50
+TYR CA CB HB2 108.494 1.50
+TYR CG CB HB3 108.859 1.50
+TYR CG CB HB2 108.859 1.50
+TYR HB3 CB HB2 107.843 2.16
+TYR CB CG CD1 121.060 1.50
+TYR CB CG CD2 121.060 1.50
+TYR CD1 CG CD2 117.879 1.50
+TYR CG CD1 CE1 121.468 1.50
+TYR CG CD1 HD1 119.327 1.50
+TYR CE1 CD1 HD1 119.205 1.50
+TYR CG CD2 CE2 121.468 1.50
+TYR CG CD2 HD2 119.327 1.50
+TYR CE2 CD2 HD2 119.205 1.50
+TYR CD1 CE1 CZ 119.794 1.50
+TYR CD1 CE1 HE1 120.177 1.50
+TYR CZ CE1 HE1 120.029 1.50
+TYR CD2 CE2 CZ 119.794 1.50
+TYR CD2 CE2 HE2 120.177 1.50
+TYR CZ CE2 HE2 120.029 1.50
+TYR CE1 CZ CE2 119.597 1.50
+TYR CE1 CZ OH 120.202 3.00
+TYR CE2 CZ OH 120.202 3.00
+TYR CZ OH HH 109.970 3.00
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+TYR chi1 N CA CB CG -60.000 10.0 3
+TYR chi2 CA CB CG CD1 90.000 10.0 6
+TYR CONST_1 CB CG CD1 CE1 0.000 0.0 1
+TYR CONST_2 CG CD1 CE1 CZ 0.000 0.0 1
+TYR CONST_3 CZ CE2 CD2 CG 0.000 0.0 1
+TYR CONST_4 CD1 CE1 CZ CE2 0.000 0.0 1
+TYR CONST_5 CE1 CZ CE2 CD2 0.000 0.0 1
+TYR hh1 CE1 CZ OH HH 0.000 5.0 2
+TYR sp3_sp3_1 C CA N H 180.000 10.0 3
+TYR const_21 CE2 CD2 CG CD1 0.000 0.0 1
+TYR sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+TYR chir_1 CA N C CB positive
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+TYR plan-1 CB 0.020
+TYR plan-1 CD1 0.020
+TYR plan-1 CD2 0.020
+TYR plan-1 CE1 0.020
+TYR plan-1 CE2 0.020
+TYR plan-1 CG 0.020
+TYR plan-1 CZ 0.020
+TYR plan-1 HD1 0.020
+TYR plan-1 HD2 0.020
+TYR plan-1 HE1 0.020
+TYR plan-1 HE2 0.020
+TYR plan-1 OH 0.020
+TYR plan-2 C 0.020
+TYR plan-2 CA 0.020
+TYR plan-2 O 0.020
+TYR plan-2 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+TYR SMILES ACDLabs 10.04 "O=C(O)C(N)Cc1ccc(O)cc1"
+TYR SMILES_CANONICAL CACTVS 3.341 "N[C@@H](Cc1ccc(O)cc1)C(O)=O"
+TYR SMILES CACTVS 3.341 "N[CH](Cc1ccc(O)cc1)C(O)=O"
+TYR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1C[C@@H](C(=O)O)N)O"
+TYR SMILES "OpenEye OEToolkits" 1.5.0 "c1cc(ccc1CC(C(=O)O)N)O"
+TYR InChI InChI 1.03 "InChI=1S/C9H11NO3/c10-8(9(12)13)5-6-1-3-7(11)4-2-6/h1-4,8,11H,5,10H2,(H,12,13)/t8-/m0/s1"
+TYR InChIKey InChI 1.03 OUYCCCASQSFEME-QMMMGPOBSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+TYR acedrg 278 "dictionary generator"
+TYR acedrg_database 12 "data source"
+TYR rdkit 2019.09.1 "Chemoinformatics tool"
+TYR refmac5 5.8.0419 "optimization tool"
+TYR servalcat 0.4.57 'optimization tool'
diff --git a/image_analysis/structure_refinement/monomers/U.cif b/image_analysis/structure_refinement/monomers/U.cif
new file mode 100644
index 000000000..608cab6db
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/U.cif
@@ -0,0 +1,248 @@
+#
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+U     U       "URIDINE-5'-MONOPHOSPHATE"     RNA     32     21     .     
+#
+data_comp_U
+#
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+U       OP3     O       OP      -1      28.643      1.174       0.256       
+U       P       P       P       0       28.819      1.986       -1.013      
+U       OP1     O       O       0       28.329      1.258       -2.251      
+U       OP2     O       OP      -1      30.224      2.536       -1.171      
+U       "O5'"   O       O2      0       27.859      3.273       -0.849      
+U       "C5'"   C       CH2     0       26.439      3.063       -0.635      
+U       "C4'"   C       CH1     0       25.718      4.389       -0.671      
+U       "O4'"   O       O2      0       26.311      5.305       0.281       
+U       "C3'"   C       CH1     0       25.778      5.166       -1.991      
+U       "O3'"   O       OH1     0       24.835      4.654       -2.925      
+U       "C2'"   C       CH1     0       25.458      6.596       -1.533      
+U       "O2'"   O       OH1     0       24.071      6.867       -1.498      
+U       "C1'"   C       CH1     0       26.019      6.633       -0.106      
+U       N1      N       NR6     0       27.258      7.450       0.002       
+U       C2      C       CR6     0       27.205      8.658       0.693       
+U       O2      O       O       0       26.192      9.093       1.231       
+U       N3      N       NR16     0       28.393      9.351       0.740       
+U       C4      C       CR6     0       29.603      8.978       0.180       
+U       O4      O       O       0       30.583      9.712       0.310       
+U       C5      C       CR16    0       29.578      7.725       -0.520      
+U       C6      C       CR16    0       28.433      7.023       -0.585      
+U       "H5'"   H       H       0       26.293      2.630       0.242       
+U       "H5''"  H       H       0       26.078      2.471       -1.340      
+U       "H4'"   H       H       0       24.781      4.238       -0.422      
+U       "H3'"   H       H       0       26.692      5.130       -2.374      
+U       "HO3'"  H       H       0       24.819      5.164       -3.604      
+U       "H2'"   H       H       0       25.919      7.246       -2.101      
+U       "HO2'"  H       H       0       23.948      7.707       -1.488      
+U       "H1'"   H       H       0       25.334      6.986       0.500       
+U       H3      H       H       0       28.372      10.124      1.182       
+U       H5      H       H       0       30.354      7.400       -0.928      
+U       H6      H       H       0       28.431      6.206       -1.045      
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+U       OP3           P      SINGLE       n     1.517  0.0192     1.517  0.0192
+U         P         OP1      DOUBLE       n     1.517  0.0192     1.517  0.0192
+U         P         OP2      SINGLE       n     1.517  0.0192     1.517  0.0192
+U         P       "O5'"      SINGLE       n     1.614  0.0178     1.614  0.0178
+U     "O5'"       "C5'"      SINGLE       n     1.450  0.0166     1.450  0.0166
+U     "C5'"       "C4'"      SINGLE       n     1.509  0.0100     1.509  0.0100
+U     "C4'"       "O4'"      SINGLE       n     1.451  0.0111     1.451  0.0111
+U     "C4'"       "C3'"      SINGLE       n     1.535  0.0100     1.535  0.0100
+U     "O4'"       "C1'"      SINGLE       n     1.412  0.0100     1.412  0.0100
+U     "C3'"       "O3'"      SINGLE       n     1.422  0.0100     1.422  0.0100
+U     "C3'"       "C2'"      SINGLE       n     1.533  0.0109     1.533  0.0109
+U     "C2'"       "O2'"      SINGLE       n     1.412  0.0100     1.412  0.0100
+U     "C2'"       "C1'"      SINGLE       n     1.529  0.0100     1.529  0.0100
+U     "C1'"          N1      SINGLE       n     1.476  0.0133     1.476  0.0133
+U        N1          C2      SINGLE       y     1.383  0.0100     1.383  0.0100
+U        N1          C6      SINGLE       y     1.375  0.0106     1.375  0.0106
+U        C2          O2      DOUBLE       n     1.224  0.0111     1.224  0.0111
+U        C2          N3      SINGLE       y     1.372  0.0112     1.372  0.0112
+U        N3          C4      SINGLE       y     1.381  0.0100     1.381  0.0100
+U        C4          O4      DOUBLE       n     1.231  0.0100     1.231  0.0100
+U        C4          C5      SINGLE       y     1.434  0.0100     1.434  0.0100
+U        C5          C6      DOUBLE       y     1.342  0.0100     1.342  0.0100
+U     "C5'"       "H5'"      SINGLE       n     1.089  0.0100     0.989  0.0200
+U     "C5'"      "H5''"      SINGLE       n     1.089  0.0100     0.989  0.0200
+U     "C4'"       "H4'"      SINGLE       n     1.089  0.0100     0.981  0.0200
+U     "C3'"       "H3'"      SINGLE       n     1.089  0.0100     0.992  0.0200
+U     "O3'"      "HO3'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+U     "C2'"       "H2'"      SINGLE       n     1.089  0.0100     0.978  0.0200
+U     "O2'"      "HO2'"      SINGLE       n     0.970  0.0120     0.849  0.0200
+U     "C1'"       "H1'"      SINGLE       n     1.089  0.0100     0.981  0.0118
+U        N3          H3      SINGLE       n     1.016  0.0100     0.889  0.0200
+U        C5          H5      SINGLE       n     1.082  0.0130     0.935  0.0100
+U        C6          H6      SINGLE       n     1.082  0.0130     0.938  0.0107
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+U       OP3           P         OP1     112.864    1.69
+U       OP3           P         OP2     112.864    1.69
+U       OP3           P       "O5'"     105.808    2.07
+U       OP1           P         OP2     112.864    1.69
+U       OP1           P       "O5'"     105.808    2.07
+U       OP2           P       "O5'"     105.808    2.07
+U         P       "O5'"       "C5'"     118.783    1.50
+U     "O5'"       "C5'"       "C4'"     109.342    1.50
+U     "O5'"       "C5'"       "H5'"     109.845    1.50
+U     "O5'"       "C5'"      "H5''"     109.845    1.50
+U     "C4'"       "C5'"       "H5'"     109.624    1.50
+U     "C4'"       "C5'"      "H5''"     109.624    1.50
+U     "H5'"       "C5'"      "H5''"     108.472    1.50
+U     "C5'"       "C4'"       "O4'"     109.615    1.50
+U     "C5'"       "C4'"       "C3'"     116.008    1.52
+U     "C5'"       "C4'"       "H4'"     108.268    1.50
+U     "O4'"       "C4'"       "C3'"     104.439    1.50
+U     "O4'"       "C4'"       "H4'"     108.698    1.50
+U     "C3'"       "C4'"       "H4'"     109.363    1.86
+U     "C4'"       "O4'"       "C1'"     109.578    1.50
+U     "C4'"       "C3'"       "O3'"     111.281    2.46
+U     "C4'"       "C3'"       "C2'"     102.071    1.50
+U     "C4'"       "C3'"       "H3'"     110.452    2.54
+U     "O3'"       "C3'"       "C2'"     111.993    3.00
+U     "O3'"       "C3'"       "H3'"     110.380    1.67
+U     "C2'"       "C3'"       "H3'"     110.108    1.66
+U     "C3'"       "O3'"      "HO3'"     108.744    3.00
+U     "C3'"       "C2'"       "O2'"     112.861    2.52
+U     "C3'"       "C2'"       "C1'"     101.269    1.50
+U     "C3'"       "C2'"       "H2'"     110.799    1.82
+U     "O2'"       "C2'"       "C1'"     109.476    3.00
+U     "O2'"       "C2'"       "H2'"     111.022    1.77
+U     "C1'"       "C2'"       "H2'"     110.760    1.63
+U     "C2'"       "O2'"      "HO2'"     109.449    1.85
+U     "O4'"       "C1'"       "C2'"     106.825    1.50
+U     "O4'"       "C1'"          N1     108.667    1.50
+U     "O4'"       "C1'"       "H1'"     109.327    1.50
+U     "C2'"       "C1'"          N1     112.859    1.50
+U     "C2'"       "C1'"       "H1'"     109.776    1.83
+U        N1       "C1'"       "H1'"     109.166    1.50
+U     "C1'"          N1          C2     117.109    1.50
+U     "C1'"          N1          C6     121.471    1.52
+U        C2          N1          C6     121.419    1.50
+U        N1          C2          O2     122.841    1.50
+U        N1          C2          N3     114.848    1.50
+U        O2          C2          N3     122.311    1.50
+U        C2          N3          C4     126.992    1.50
+U        C2          N3          H3     115.772    1.79
+U        C4          N3          H3     117.236    1.73
+U        N3          C4          O4     119.401    1.50
+U        N3          C4          C5     114.659    1.50
+U        O4          C4          C5     125.940    1.50
+U        C4          C5          C6     119.525    1.50
+U        C4          C5          H5     120.151    1.50
+U        C6          C5          H5     120.325    1.50
+U        N1          C6          C5     122.557    1.50
+U        N1          C6          H6     118.477    1.50
+U        C5          C6          H6     118.966    1.50
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+U       C2e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+U       C2e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     340.700       6.300     1     
+U       C2e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     32.800        4.900     1     
+U       C2e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     326.9         3.600     1     
+U       C2e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     22.600        4.500     1     
+U       C2e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     357.700       6.100     1     
+U       C3e-chi         "O4'"     "C1'"     N1        C2        210.000       10.000    6     
+U       C3e-nyu0        "C4'"     "O4'"     "C1'"     "C2'"     2.8           6.100     1     
+U       C3e-nyu1        "O4'"     "C1'"     "C2'"     "C3'"     335.00        4.900     1     
+U       C3e-nyu2        "C1'"     "C2'"     "C3'"     "C4'"     35.9          2.800     1     
+U       C3e-nyu3        "C2'"     "C3'"     "C4'"     "O4'"     324.700       3.100     1     
+U       C3e-nyu4        "C3'"     "C4'"     "O4'"     "C1'"     20.500        5.100     1     
+U       alpha           "C5'"     "O5'"     P         OP3       -60.000       10.00     3     
+U       beta            P         "O5'"     "C5'"     "C4'"     180.000       10.00     3     
+U       epsi            "C4'"     "C3'"     "O3'"     "HO3'"    180.000       10.00     3     
+U       gamma           "O5'"     "C5'"     "C4'"     "C3'"     180.000       10.00     3     
+U       sp3_sp3_52      "C3'"     "C2'"     "O2'"     "HO2'"    180.000       10.00     3     
+U       const_sp2_sp2_4          O2          C2          N1       "C1'"       0.000     5.0     2
+U              const_22          C5          C6          N1       "C1'"     180.000    10.0     2
+U       const_sp2_sp2_7          O2          C2          N3          C4     180.000     5.0     2
+U              const_11          O4          C4          N3          C2     180.000    10.0     2
+U              const_15          O4          C4          C5          C6     180.000    10.0     2
+U              const_17          C4          C5          C6          N1       0.000    10.0     2
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+U  chir_1    P    "O5'"    OP3    OP2    both
+U  chir_2    "C4'"    "O4'"    "C3'"    "C5'"    negative
+U  chir_3    "C3'"    "O3'"    "C4'"    "C2'"    positive
+U  chir_4    "C2'"    "O2'"    "C1'"    "C3'"    negative
+U  chir_5    "C1'"    "O4'"    N1    "C2'"    negative
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+U  plan-1       "C1'"   0.020
+U  plan-1          C2   0.020
+U  plan-1          C4   0.020
+U  plan-1          C5   0.020
+U  plan-1          C6   0.020
+U  plan-1          H3   0.020
+U  plan-1          H5   0.020
+U  plan-1          H6   0.020
+U  plan-1          N1   0.020
+U  plan-1          N3   0.020
+U  plan-1          O2   0.020
+U  plan-1          O4   0.020
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+U           SMILES              ACDLabs 10.04                                                                                                         O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
+U SMILES_CANONICAL               CACTVS 3.341                                                                                      O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
+U           SMILES               CACTVS 3.341                                                                                             O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
+U SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0                                                                                     C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
+U           SMILES "OpenEye OEToolkits" 1.5.0                                                                                                       C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
+U            InChI                InChI  1.03 InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
+U         InChIKey                InChI  1.03                                                                                                                       DJJCXFVJDGTHFX-XVFCMESISA-N
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+U   acedrg               243         "dictionary generator"                  
+U   acedrg_database      11          "data source"                           
+U   rdkit                2017.03.2   "Chemoinformatics tool"
+U   refmac5              5.8.0238    "optimization tool"                     
diff --git a/image_analysis/structure_refinement/monomers/VAL.cif b/image_analysis/structure_refinement/monomers/VAL.cif
new file mode 100644
index 000000000..af42ed1b8
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/VAL.cif
@@ -0,0 +1,221 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+VAL VAL VALINE peptide 19 8 .
+
+data_comp_VAL
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+VAL N N NT3 1 11.307 2.990 48.522
+VAL CA C CH1 0 10.346 4.137 48.590
+VAL C C C 0 9.715 4.163 49.994
+VAL O O O 0 9.179 3.107 50.398
+VAL CB C CH1 0 9.259 4.073 47.494
+VAL CG1 C CH3 0 8.396 5.334 47.475
+VAL CG2 C CH3 0 9.849 3.802 46.112
+VAL OXT O OC -1 9.782 5.237 50.630
+VAL H H H 0 11.930 3.145 47.888
+VAL H2 H H 0 10.867 2.229 48.319
+VAL H3 H H 0 11.735 2.877 49.308
+VAL HA H H 0 10.853 4.963 48.468
+VAL HB H H 0 8.670 3.315 47.717
+VAL HG11 H H 0 8.964 6.117 47.567
+VAL HG12 H H 0 7.763 5.306 48.212
+VAL HG13 H H 0 7.907 5.387 46.637
+VAL HG21 H H 0 10.555 4.444 45.928
+VAL HG22 H H 0 9.155 3.884 45.436
+VAL HG23 H H 0 10.217 2.902 46.084
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+VAL N n/a CA START
+VAL H N . .
+VAL H2 N . .
+VAL H3 N . .
+VAL CA N C .
+VAL HA CA . .
+VAL CB CA CG2 .
+VAL HB CB . .
+VAL CG1 CB HG13 .
+VAL HG11 CG1 . .
+VAL HG12 CG1 . .
+VAL HG13 CG1 . .
+VAL CG2 CB HG23 .
+VAL HG21 CG2 . .
+VAL HG22 CG2 . .
+VAL HG23 CG2 . .
+VAL C CA . END
+VAL O C . .
+VAL OXT C . .
+
+loop_
+_chem_comp_acedrg.comp_id
+_chem_comp_acedrg.atom_id
+_chem_comp_acedrg.atom_type
+VAL N N(CCCH)(H)3
+VAL CA C(CCCH)(NH3)(COO)(H)
+VAL C C(CCHN)(O)2
+VAL O O(CCO)
+VAL CB C(CCHN)(CH3)2(H)
+VAL CG1 C(CCCH)(H)3
+VAL CG2 C(CCCH)(H)3
+VAL OXT O(CCO)
+VAL H H(NCHH)
+VAL H2 H(NCHH)
+VAL H3 H(NCHH)
+VAL HA H(CCCN)
+VAL HB H(CC3)
+VAL HG11 H(CCHH)
+VAL HG12 H(CCHH)
+VAL HG13 H(CCHH)
+VAL HG21 H(CCHH)
+VAL HG22 H(CCHH)
+VAL HG23 H(CCHH)
+
+loop_
+_chem_comp_bond.comp_id
+_chem_comp_bond.atom_id_1
+_chem_comp_bond.atom_id_2
+_chem_comp_bond.type
+_chem_comp_bond.aromatic
+_chem_comp_bond.value_dist_nucleus
+_chem_comp_bond.value_dist_nucleus_esd
+_chem_comp_bond.value_dist
+_chem_comp_bond.value_dist_esd
+VAL N CA SINGLE n 1.495 0.0100 1.495 0.0100
+VAL CA C SINGLE n 1.538 0.0100 1.538 0.0100
+VAL CA CB SINGLE n 1.541 0.0101 1.541 0.0101
+VAL C O DOUBLE n 1.251 0.0183 1.251 0.0183
+VAL C OXT SINGLE n 1.251 0.0183 1.251 0.0183
+VAL CB CG1 SINGLE n 1.524 0.0131 1.524 0.0131
+VAL CB CG2 SINGLE n 1.524 0.0131 1.524 0.0131
+VAL N H SINGLE n 1.018 0.0520 0.902 0.0102
+VAL N H2 SINGLE n 1.018 0.0520 0.902 0.0102
+VAL N H3 SINGLE n 1.018 0.0520 0.902 0.0102
+VAL CA HA SINGLE n 1.092 0.0100 0.977 0.0200
+VAL CB HB SINGLE n 1.092 0.0100 0.986 0.0184
+VAL CG1 HG11 SINGLE n 1.092 0.0100 0.972 0.0156
+VAL CG1 HG12 SINGLE n 1.092 0.0100 0.972 0.0156
+VAL CG1 HG13 SINGLE n 1.092 0.0100 0.972 0.0156
+VAL CG2 HG21 SINGLE n 1.092 0.0100 0.972 0.0156
+VAL CG2 HG22 SINGLE n 1.092 0.0100 0.972 0.0156
+VAL CG2 HG23 SINGLE n 1.092 0.0100 0.972 0.0156
+
+loop_
+_chem_comp_angle.comp_id
+_chem_comp_angle.atom_id_1
+_chem_comp_angle.atom_id_2
+_chem_comp_angle.atom_id_3
+_chem_comp_angle.value_angle
+_chem_comp_angle.value_angle_esd
+VAL CA N H 109.990 2.80
+VAL CA N H2 109.990 2.80
+VAL CA N H3 109.990 2.80
+VAL H N H2 109.032 3.00
+VAL H N H3 109.032 3.00
+VAL H2 N H3 109.032 3.00
+VAL N CA C 108.738 1.50
+VAL N CA CB 111.627 2.88
+VAL N CA HA 108.328 1.50
+VAL C CA CB 111.231 1.50
+VAL C CA HA 108.550 1.50
+VAL CB CA HA 108.536 1.50
+VAL CA C O 117.155 1.50
+VAL CA C OXT 117.155 1.50
+VAL O C OXT 125.690 1.50
+VAL CA CB CG1 111.834 1.50
+VAL CA CB CG2 111.834 1.50
+VAL CA CB HB 107.069 1.50
+VAL CG1 CB CG2 110.700 1.76
+VAL CG1 CB HB 107.681 2.06
+VAL CG2 CB HB 107.681 2.06
+VAL CB CG1 HG11 109.510 1.50
+VAL CB CG1 HG12 109.510 1.50
+VAL CB CG1 HG13 109.510 1.50
+VAL HG11 CG1 HG12 109.390 1.50
+VAL HG11 CG1 HG13 109.390 1.50
+VAL HG12 CG1 HG13 109.390 1.50
+VAL CB CG2 HG21 109.510 1.50
+VAL CB CG2 HG22 109.510 1.50
+VAL CB CG2 HG23 109.510 1.50
+VAL HG21 CG2 HG22 109.390 1.50
+VAL HG21 CG2 HG23 109.390 1.50
+VAL HG22 CG2 HG23 109.390 1.50
+
+loop_
+_chem_comp_tor.comp_id
+_chem_comp_tor.id
+_chem_comp_tor.atom_id_1
+_chem_comp_tor.atom_id_2
+_chem_comp_tor.atom_id_3
+_chem_comp_tor.atom_id_4
+_chem_comp_tor.value_angle
+_chem_comp_tor.value_angle_esd
+_chem_comp_tor.period
+VAL chi1 N CA CB CG2 -60.000 10.0 3
+VAL hh1 CA CB CG1 HG13 180.000 10.0 3
+VAL hh2 CA CB CG2 HG23 -60.000 10.0 3
+VAL sp3_sp3_1 C CA N H 180.000 10.0 3
+VAL sp2_sp3_1 O C CA N 0.000 10.0 6
+
+loop_
+_chem_comp_chir.comp_id
+_chem_comp_chir.id
+_chem_comp_chir.atom_id_centre
+_chem_comp_chir.atom_id_1
+_chem_comp_chir.atom_id_2
+_chem_comp_chir.atom_id_3
+_chem_comp_chir.volume_sign
+VAL chir_1 CA N C CB positive
+VAL chir_2 CB CA CG1 CG2 both
+
+loop_
+_chem_comp_plane_atom.comp_id
+_chem_comp_plane_atom.plane_id
+_chem_comp_plane_atom.atom_id
+_chem_comp_plane_atom.dist_esd
+VAL plan-1 C 0.020
+VAL plan-1 CA 0.020
+VAL plan-1 O 0.020
+VAL plan-1 OXT 0.020
+
+loop_
+_pdbx_chem_comp_descriptor.comp_id
+_pdbx_chem_comp_descriptor.type
+_pdbx_chem_comp_descriptor.program
+_pdbx_chem_comp_descriptor.program_version
+_pdbx_chem_comp_descriptor.descriptor
+VAL SMILES ACDLabs 10.04 O=C(O)C(N)C(C)C
+VAL SMILES_CANONICAL CACTVS 3.341 CC(C)[C@H](N)C(O)=O
+VAL SMILES CACTVS 3.341 CC(C)[CH](N)C(O)=O
+VAL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)[C@@H](C(=O)O)N
+VAL SMILES "OpenEye OEToolkits" 1.5.0 CC(C)C(C(=O)O)N
+VAL InChI InChI 1.03 InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m0/s1
+VAL InChIKey InChI 1.03 KZSNJWFQEVHDMF-BYPYZUCNSA-N
+
+loop_
+_pdbx_chem_comp_description_generator.comp_id
+_pdbx_chem_comp_description_generator.program_name
+_pdbx_chem_comp_description_generator.program_version
+_pdbx_chem_comp_description_generator.descriptor
+VAL acedrg 278 "dictionary generator"
+VAL acedrg_database 12 "data source"
+VAL rdkit 2019.09.1 "Chemoinformatics tool"
+VAL refmac5 5.8.0419 "optimization tool"
diff --git a/image_analysis/structure_refinement/monomers/ZN.cif b/image_analysis/structure_refinement/monomers/ZN.cif
new file mode 100644
index 000000000..aada536e8
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ZN.cif
@@ -0,0 +1,30 @@
+data_comp_list
+loop_
+_chem_comp.id
+_chem_comp.three_letter_code
+_chem_comp.name
+_chem_comp.group
+_chem_comp.number_atoms_all
+_chem_comp.number_atoms_nh
+_chem_comp.desc_level
+ZN ZN 'ZINC ION                            ' NON-POLYMER 1 1 .
+
+data_comp_ZN
+loop_
+_chem_comp_atom.comp_id
+_chem_comp_atom.atom_id
+_chem_comp_atom.type_symbol
+_chem_comp_atom.type_energy
+_chem_comp_atom.partial_charge
+_chem_comp_atom.x
+_chem_comp_atom.y
+_chem_comp_atom.z
+ZN ZN ZN ZN 2.000 0.000 0.000 0.000
+
+loop_
+_chem_comp_tree.comp_id
+_chem_comp_tree.atom_id
+_chem_comp_tree.atom_back
+_chem_comp_tree.atom_forward
+_chem_comp_tree.connect_type
+ZN ZN n/a . END
diff --git a/image_analysis/structure_refinement/monomers/ener_lib.cif b/image_analysis/structure_refinement/monomers/ener_lib.cif
new file mode 100644
index 000000000..717864eb2
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/ener_lib.cif
@@ -0,0 +1,219 @@
+data_energy
+loop_
+_lib_atom.type
+_lib_atom.weight
+_lib_atom.hb_type
+_lib_atom.vdw_radius
+_lib_atom.vdwh_radius
+_lib_atom.ion_radius
+_lib_atom.element
+_lib_atom.valency
+_lib_atom.sp
+CSP 12.01150 N 1.700 1.700 . C 4 1
+CSP1 12.01150 N 1.700 1.700 . C 4 1
+C 12.01150 N 1.700 1.750 . C 4 2
+C1 12.01150 N 1.700 1.820 . C 4 2
+C2 12.01150 N 1.700 1.800 . C 4 2
+CR1 12.01150 N 1.700 1.800 . C 4 2
+CR2 12.01150 N 1.700 1.800 . C 4 2
+CR1H 12.01150 N 1.700 1.800 . C 4 2
+CR15 12.01150 N 1.700 1.740 . C 4 2
+CR5 12.01150 N 1.700 1.740 . C 4 2
+CR56 12.01150 N 1.700 1.740 . C 4 2
+CR55 12.01150 N 1.700 1.740 . C 4 2
+CR16 12.01150 N 1.700 1.820 . C 4 2
+CR6 12.01150 N 1.700 1.740 . C 4 2
+CR66 12.01150 N 1.700 1.740 . C 4 2
+CH1 12.01150 N 1.700 1.950 . C 4 3
+CH2 12.01150 N 1.700 1.920 . C 4 3
+CH3 12.01150 N 1.700 1.940 . C 4 3
+CT 12.01150 N 1.700 1.850 . C 4 3
+NS 14.00670 A 1.550 1.600 1.32 N 3 1
+NSP 14.00670 A 1.550 1.600 1.32 N 3 1
+NS1 14.00670 D 1.550 1.600 1.32 N 3 1
+NSP1 14.00670 D 1.550 1.600 1.32 N 3 1
+N 14.00670 N 1.550 1.600 1.32 N 3 2
+NC1 14.00670 D 1.550 1.600 1.32 N 3 2
+NH0 14.00670 N 1.550 1.600 1.32 N 3 2
+NH1 14.00670 D 1.550 1.600 1.32 N 3 2
+NC2 14.00670 D 1.550 1.600 1.32 N 3 2
+NH2 14.00670 D 1.550 1.600 1.32 N 3 2
+NC3 14.00670 D 1.550 1.600 1.32 N 3 2
+N20 14.00670 A 1.550 1.600 1.32 N 3 2
+N21 14.00670 B 1.550 1.600 1.32 N 3 2
+NT 14.00670 N 1.550 1.600 1.32 N 3 3
+NT1 14.00670 D 1.550 1.600 1.32 N 3 3
+NT2 14.00670 D 1.550 1.600 1.32 N 3 3
+NT3 14.00670 D 1.550 1.600 1.32 N 3 3
+NT4 14.00670 D 1.550 1.600 1.32 N 3 3
+N30 14.00670 A 1.550 1.600 1.32 N 3 3
+N31 14.00670 B 1.550 1.600 1.32 N 3 3
+N32 14.00670 B 1.550 1.600 1.32 N 3 3
+N33 14.00670 B 1.550 1.600 1.32 N 3 3
+NPA 14.00670 A 1.550 1.600 1.32 N 3 2
+NPB 14.00670 A 1.550 1.600 1.32 N 3 2
+NR5 14.00670 A 1.550 1.600 1.32 N 3 2
+NR15 14.00670 D 1.550 1.600 1.32 N 3 2
+NRD5 14.00670 A 1.550 1.600 1.32 N 3 2
+NR56 14.00670 N 1.550 1.600 1.32 N 3 2
+NR55 14.00670 N 1.550 1.600 1.32 N 3 2
+NR6 14.00670 A 1.550 1.600 1.32 N 3 2
+NR66 14.00670 N 1.550 1.600 1.32 N 3 2
+NR16 14.00670 D 1.550 1.600 1.32 N 3 2
+NRD6 14.00670 A 1.550 1.600 1.32 N 3 2
+OS 15.99940 A 1.520 1.520 1.28 O 2 2
+O 15.99940 A 1.520 1.520 1.28 O 2 2
+AF 15.99940 A 1.520 1.520 1.28 AF 2 2
+O2 15.99940 A 1.520 1.520 1.28 O 2 3
+OH1 15.99940 B 1.520 1.520 1.28 O 2 3
+OH2 15.99940 B 1.520 1.520 1.28 O 2 3
+OHA 15.99940 B 1.520 1.680 1.28 O 2 3
+OHB 15.99940 B 1.520 1.680 1.28 O 2 3
+OHC 15.99940 B 1.520 1.680 1.28 O 2 3
+OC2 15.99940 A 1.520 1.520 1.28 O 2 2
+OC 15.99940 A 1.520 1.520 1.28 O 2 2
+OP 15.99940 A 1.520 1.520 1.28 O 2 2
+OB 15.99940 A 1.520 1.520 1.28 O 2 2
+P 30.97380 N 1.800 1.88 1.79 P 5 .
+P1 30.97380 N 1.800 1.88 1.79 P 5 .
+PS 30.97380 N 1.800 1.90 1.79 P 5 .
+S 32.06400 A 1.800 1.88 1.7 S 2 .
+S3 32.06400 A 1.800 1.88 1.7 S 4 .
+S2 32.06400 A 1.800 1.88 1.7 S 2 .
+S1 32.06400 A 1.800 1.88 1.7 S 2 .
+ST 32.06400 A 1.800 1.88 1.7 S 6 3
+SH1 32.06400 B 1.800 1.950 1.7 S 2 .
+H 1.00800 N 1.200 . . H 1 .
+HCH 1.00800 N 1.200 . . H 1 .
+HCH1 1.00800 N 1.200 . . H 1 .
+HCH2 1.00800 N 1.200 . . H 1 .
+HCH3 1.00800 N 1.200 . . H 1 .
+HCR1 1.00800 N 1.200 . . H 1 .
+HC2 1.00800 N 1.200 . . H 1 .
+HC1 1.00800 N 1.200 . . H 1 .
+HC2 1.00800 N 1.200 . . H 1 .
+HCR5 1.00800 N 1.200 . . H 1 .
+HCR6 1.00800 N 1.200 . . H 1 .
+HNC1 1.00800 H 1.200 . . H 1 .
+HNC2 1.00800 H 1.200 . . H 1 .
+HNH1 1.00800 H 1.200 . . H 1 .
+HNH2 1.00800 H 1.200 . . H 1 .
+HNR5 1.00800 H 1.200 . . H 1 .
+HNR6 1.00800 H 1.200 . . H 1 .
+HNT1 1.00800 H 1.200 . . H 1 .
+HNT2 1.00800 H 1.200 . . H 1 .
+HNT3 1.00800 H 1.200 . . H 1 .
+HOH1 1.00800 H 1.200 . . H 1 .
+HOH2 1.00800 H 1.200 . . H 1 .
+HOHA 1.00800 H 1.200 . . H 1 .
+HOHB 1.00800 H 1.200 . . H 1 .
+HOHC 1.00800 H 1.200 . . H 1 .
+HSH1 1.00800 H 1.200 . . H 1 .
+SI 28.0855 N 2.10 . 0.40 SI 4 3
+SI1 28.0855 N 2.10 . 0.40 SI 4 .
+GE 72.59 N 2.10 . 0.40 GE 1 .
+GE1 72.59 N 2.10 . 0.40 GE 1 .
+SN 118.69 N 2.17 . 0.69 SN 1 .
+PB 207.2 N 2.02 . 0.79 PB 1 .
+LI 6.941 N 1.82 . 0.73 LI 1 .
+NA 22.990 N 2.27 . 1.13 NA 1 .
+K 30.0983 N 2.75 . 1.51 K 1 .
+RB 85.468 N 2.00 . 1.48 RB 1 .
+CS 132.905 N 2.98 . 1.81 CS 1 .
+FR 223.0 N . . 1.94 FR 1 .
+BE 9.0123 N 1.12 . 0.41 BE 1 .
+MG 24.30500 N 1.73 . 0.71 MG 1 .
+CA 40.08000 N 1.94 . 1.14 CA 1 .
+SR 87.62 N 2.19 . 1.32 SR 1 .
+BA 137.33 N 2.53 . 1.49 BA 1 .
+RA 226.025 N 2.15 . 1.62 RA 1 .
+SC 44.9559 N 1.60 . 0.885 SC 1 .
+Y 88.9059 N 1.80 . 1.04 Y 1 .
+LA 138.9055 N 1.95 . 1.172 LA 1 .
+CE 140.12 N 1.85 . 1.01 CE 1 .
+PR 140.9077 N 1.85 . 0.99 PR 1 .
+ND 144.24 N 1.85 . 1.123 ND 1 .
+PM . N . . 1.11 PM 1 .
+SM 150.36 N 1.85 . 1.098 SM 1 .
+EU 151.96 N 1.85 . 1.087 EU 1 .
+GD 157.25 N 1.80 . 1.078 GD 1 .
+TB 158.9254 N 1.75 . 0.90 TB 1 .
+DY 162.50 N 1.75 . 1.052 DY 1 .
+HO 164.9304 N 1.75 . 1.041 HO 1 .
+ER 167.26 N 1.75 . 1.03 ER 1 .
+TM 168.9342 N 1.75 . 1.02 TM 1 .
+YB 173.04 N 1.75 . 1.008 YB 1 .
+LU 174.967 N 1.75 . 1.001 LU 1 .
+AC 227.028 N 1.95 . 1.26 AC 1 .
+TH 232.0 N 1.80 . 1.08 TH 1 .
+PA 231.0 N 1.80 . 0.92 PA 1 .
+U 238.0 N 1.86 . 0.66 U 1 .
+NP 237.0 N 1.75 . 0.85 NP 1 .
+PU 239.0 N 1.75 . 0.85 PU 1 .
+AM 241.0 N 1.75 . 0.99 AM 1 .
+CM 244.0 N . . 0.99 CM 1 .
+BK 249.0 N . . 0.97 BK 1 .
+CF 252.0 N . . 0.961 CF 1 .
+ES 253.0 N . . . ES 1 .
+FM 257.0 N . . . FM 1 .
+MD 256.0 N . . . MD 1 .
+NO 255.0 N . . . NO 1 .
+LR 256.0 N . . . LR 1 .
+TI 47.88 N 1.40 . 0.56 TI 1 .
+ZR 91.22 N 1.55 . 0.73 ZR 1 .
+HF 178.49 N 1.55 . 0.72 HF 1 .
+RF . N . . . RF 1 .
+V 50.9415 N 1.35 . 0.68 V 1 .
+NB 92.9064 N 1.45 . 0.62 NB 1 .
+TA 180.9479 N 1.45 . 0.78 TA 1 .
+DB . N . . . DB 1 .
+CR 51.996 N 1.40 . 0.53 CR 1 .
+MO 95.94 N 1.45 . 0.55 MO 1 .
+W 183.85 N 1.35 . 0.56 W 1 .
+SG . N . . . SG 1 .
+MN 54.938 N 1.40 . 0.46 MN 1 .
+TC 98.906 N 1.35 . 0.51 TC 1 .
+RE 186.207 N 1.35 . 0.52 RE 1 .
+BH . N . . . BH 1 .
+FE 55.847 N 1.40 . 0.68 FE 1 .
+RU 101.07 N 1.30 . 0.52 RU 1 .
+OSE 190.2 N 1.30 . 0.53 OS 1 .
+HS . N . . . HS 1 .
+CO 58.9332 N 1.35 . 0.54 CO 1 .
+RH 102.9055 N 1.35 . 0.69 RH 1 .
+IR 192.22 N 1.35 . 0.71 IR 1 .
+MT . N . . . MT 1 .
+NI 58.69 N 1.63 . 0.63 NI 1 .
+PD 106.42 N 1.63 . 0.78 PD 1 .
+PT 195.08 N 1.75 . 0.71 PT 1 .
+CU 63.546 N 1.40 . 0.71 CU 1 .
+AG 107.868 N 1.72 . 0.81 AG 1 .
+AU 196.9665 N 1.66 . 0.71 AU 1 .
+ZN 65.38 N 1.39 . 0.74 ZN 1 .
+CD 112.41 N 1.58 . 0.92 CD 1 .
+HG 200.59 N 1.55 . 1.10 HG 1 .
+B 10.81 N 0.85 . 0.25 B 1 .
+AL 26.98154 N 1.25 . 0.53 AL 1 .
+GA 69.72 N 1.87 . 0.61 GA 1 .
+IN 114.82 N 1.93 . 0.76 IN 1 .
+TL 204.383 N 1.96 . 0.89 TL 1 .
+AS 74.9216 N 1.85 . 0.475 AS 1 .
+AS1 74.9216 N 1.85 . 0.475 AS 1 .
+SB 121.75 N 1.8 . 0.90 SB 1 .
+BI 208.9804 N 1.8 . 0.90 BI 1 .
+SE 78.96 N 1.90 . 0.42 SE 1 .
+TE 127.60 N 2.06 . 0.57 TE 1 .
+PO 210.0 N 2.0 . 0.81 PO 1 .
+F 18.998 B 1.47 . 1.19 F 1 .
+CL 35.453 A 1.75 . 1.67 CL 1 .
+BR 79.904 N 1.85 . 0.73 BR 1 .
+I 126.9045 N 1.98 . 0.56 I 1 .
+AT 210.0 N 1.80 . 0.76 AT 1 .
+HE 4.0026 N 1.40 . . HE 1 .
+NE 20.179 N 1.54 . 1.12 NE 1 .
+AR 39.948 N 1.88 . 1.54 AR 1 .
+KR 83.80 N 2.02 . 1.69 KR 1 .
+XE 131.29 N 2.16 . 1.90 XE 1 .
+RN 222.0 N 2.20 . 2.0 RN 1 .
+DUM 16.0 N 0.6 0.6 0.6 O . .
+. . B 1.7 1.5 1.7 C 4 3
diff --git a/image_analysis/structure_refinement/monomers/links_and_mods.cif b/image_analysis/structure_refinement/monomers/links_and_mods.cif
new file mode 100644
index 000000000..132bf6afb
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/links_and_mods.cif
@@ -0,0 +1,5506 @@
+data_link_list
+loop_
+_chem_link.id
+_chem_link.comp_id_1
+_chem_link.mod_id_1
+_chem_link.group_comp_1
+_chem_link.comp_id_2
+_chem_link.mod_id_2
+_chem_link.group_comp_2
+_chem_link.name
+DNA-SER . DEL_OP3 DNA/RNA SER SERm1 peptide DNA-SER
+DNA-TYR . DEL_OP3 DNA/RNA TYR TYRmod5 peptide DNA-TYR
+SS . CYS-SS peptide . CYS-SS peptide SS-bridge
+disulf CYS CYS-SS peptide CYS CYS-SS peptide SS-bridge
+TRANS . DEL-OXT peptide . DEL-HN1 peptide TRANS
+CIS . DEL-OXT peptide . DEL-HN1 peptide CIS
+PTRANS . DEL-OXT peptide . DEL-HNP P-peptide PTRANS
+PCIS . DEL-OXT peptide . DEL-HNP P-peptide PCIS
+NMTRANS . DEL-OXT1 peptide . DEL-NMH M-peptide NMTRANS
+NMCIS . DEL-OXT1 peptide . DEL-NMH M-peptide NMCIS
+gap . . . . . . gap-link
+p . DEL_HO3p DNA/RNA . DEL_OP3 DNA/RNA default-DNA/RNA-link
+AA-RNA . DEL-OXT peptide . DEL_HO3p DNA/RNA aminoacyl-RNA
+ZN-CYS ZN . NON-POLYMER CYS CYSmod1 peptide bond_ZN_=_CYS-SG
+ZN-HISND ZN . NON-POLYMER HIS DEL-HD1 peptide bond_ZN_=_HIS-ND1
+ZN-HISNE ZN . NON-POLYMER HIS DEL-HE2 peptide bond_ZN_=_HIS-NE2
+HEC-CYS1 CYS CYSmod1 peptide HEC HECmod1 NON-POLYMER HEC_CAC-CYS1
+HEC-CYS2 CYS CYSmod1 peptide HEC HECmod2 NON-POLYMER HEC_CAB-CYS2
+FE-CYS FE . NON-POLYMER CYS CYSmod1 peptide bond_FE_=_CYS-SG
+FE-HISND FE . NON-POLYMER HIS DEL-HD1 peptide bond_FE_=_HIS-ND1
+FE-HISNE FE . NON-POLYMER HIS DEL-HE2 peptide bond_FE_=_HIS-NE2
+symmetry . . . . . . dummy_link
+CYS-FAD CYS CYSmod2 peptide FAD FADmod1 NON-POLYMER CYS-FAD
+HIS-FAD1 HIS HISmod1 peptide FAD FADmod2 NON-POLYMER HIS-FAD1
+HIS-FAD2 HIS HISmod2 peptide FAD FADmod3 NON-POLYMER HIS-FAD2
+GTP-p GTP GTPmod1 NON-POLYMER . DEL_OP3 DNA/RNA GTP-p
+CYS-HEMB CYS CYSmod1 peptide HEM HEMmod2 NON-POLYMER CYS-HEMB
+CYS-HEMC CYS CYSmod1 peptide HEM HEMmod3 NON-POLYMER CYS-HEMC
+HIS_TYR1 HIS HISmod1 peptide TYR TYRmod1 peptide HIS_TYR1
+HIS_TYR2 HIS HISmod3 peptide TYR TYRmod2 peptide HIS_TYR2
+LYS-CYS LYS LYSmod1 peptide CYS CYSmod1 peptide LYS-CYS
+LYS-ASN LYS LYSmod3 peptide ASN ASNmod1 peptide LYS-ASN
+MET-TYR MET METmod1 peptide TYR TYRmod3 peptide MET-TYR
+TRP-TYR TRP TRPmod1 peptide TYR TYRmod4 peptide TRP-TYR
+
+data_mod_list
+loop_
+_chem_mod.id
+_chem_mod.name
+_chem_mod.comp_id
+_chem_mod.group_id
+SERm1 SERINE SER peptide
+CYS-SS HG-deletete CYS peptide
+CYSmod1 CYS-HG-delete_with_atom_type CYS peptide
+NH3 NH3-terminus . peptide
+NH1 NH1-terminus . peptide
+NH2 NH2-terminus_for_proline . peptide
+NH2N NH2-terminus_proline_type_with_CN . peptide
+COO COO-terminus . peptide
+AA-STAND AA_to_residue_modification . peptide
+AA-STPRO AA_to_residue_modification_for_proline . peptide
+NA-STAND DNA/RNA_to_residue_modification . DNA/RNA
+5*END DNA/RNA-5*-terminus . DNA/RNA
+3*END DNA/RNA-3*-terminus . DNA/RNA
+p5*END DNA/RNA-p5*-terminus . DNA/RNA
+p3*END DNA/RNA-p3*-terminus . DNA/RNA
+DEL_OP3 DN/RNA-OP3-delete . DNA/RNA
+DEL_HO3p DNA/RNA-OP3-delete . DNA/RNA
+FOR-N N-terminus_of_formyl . .
+FOR-C C-terminus_of_formyl . .
+G-N2 delete_N2_from_guanosine . DNA/RNA
+DEL-HD1 delete_HD1_from_HIS HIS peptide
+DEL-HE2 delete_HE2_from_HIS HIS peptide
+DEL-OXT delete_OXT_from_peptide . peptide
+DEL-OXT1 delete_OXT_from_peptide . peptide
+DEL-HN1 delete_Hs_from_peptide . peptide
+DEL-NMH delete_Hs_from_NMpeptide . peptide
+DEL-HNP delete_Hs_from_peptide . peptide
+PEPT-D change_peptide_to_D . peptide
+1MA N1-metyl_of_adenosine . DNA/RNA
+1MG N1-metyl_of_guanosine . DNA/RNA
+2MG N2-metyl_of_guanosine . DNA/RNA
+M2G N2-dimetyl_of_guanosine . DNA/RNA
+O2*MET O2*_metyl . DNA/RNA
+C5MET C5_metyl . DNA/RNA
+N7MET N7_metyl . DNA/RNA
+RNA-O2* delete_O2*_from_RNA . DNA/RNA
+XYS-O1 delete_O1_from_XYS . .
+B2C replace_B_to_C . peptide
+B2C_D replace_B_to_C_for_D-peptide . peptide
+RENAME change_monomer"s_name . .
+TERMINUS chain_terminus_without_modification . .
+DEL-HD22 delete_HD22_from_ASN ASN peptide
+DEL-HG delete_HG_from_SER SER peptide
+DEL-HG1 delete_HG1_from_THR THR peptide
+HECmod1 'HEME C CAB-C3B bond order           ' HEC NON-POLYMER
+HECmod2 'HEME C CAC-C3C bond order           ' HEC NON-POLYMER
+FADmod1 "FLAVIN-ADENINE DINUCLEOTIDE" FAD NON-POLYMER
+HISmod1 HISTIDINE HIS peptide
+FADmod2 "FLAVIN-ADENINE DINUCLEOTIDE" FAD NON-POLYMER
+HISmod2 HISTIDINE HIS peptide
+FADmod3 "FLAVIN-ADENINE DINUCLEOTIDE" FAD NON-POLYMER
+GTPmod1 "GUANOSINE-5'-TRIPHOSPHATE" GTP NON-POLYMER
+HEMmod2 "PROTOPORPHYRIN IX CONTAINING FE" HEM NON-POLYMER
+HEMmod3 "PROTOPORPHYRIN IX CONTAINING FE" HEM NON-POLYMER
+TYRmod1 TYROSINE TYR peptide
+HISmod3 HISTIDINE HIS peptide
+TYRmod2 TYROSINE TYR peptide
+LYSmod1 LYSINE LYS peptide
+CYSmod2 CYSTEINE CYS peptide
+LYSmod2 LYSINE LYS peptide
+LYSmod3 LYSINE LYS peptide
+ASNmod1 ASPARAGINE ASN peptide
+METmod1 METHIONINE MET peptide
+TYRmod3 TYROSINE TYR peptide
+LEUmod1 LEUCINE LEU peptide
+LYSmod4 LYSINE LYS peptide
+TRPmod1 TRYPTOPHAN TRP peptide
+TYRmod4 TYROSINE TYR peptide
+TYRmod5 TYROSINE TYR peptide
+LYSmod5 LYSINE LYS peptide
+MS6mod2 DEL-HN1_equiv_for_MS6-pept . peptide
+ASPprot "Protonation of ASP" ASP peptide
+GLUprot "Protonation of GLU" GLU peptide
+HISprot1 HISTIDINE HIS peptide
+HISprot2 HISTIDINE HIS peptide
+
+data_link_DNA-SER
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+DNA-SER 1 P 2 OG SINGLE 1.607 0.0108
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+DNA-SER 1 OP1 1 P 2 OG 107.777 3.00
+DNA-SER 1 OP2 1 P 2 OG 107.777 3.00
+DNA-SER 1 "O5'" 1 P 2 OG 103.482 3.00
+DNA-SER 2 CB 2 OG 1 P 119.008 2.40
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+DNA-SER sp3_sp3_1 2 CB 2 OG 1 P 1 OP1 60.000 10.0 3
+DNA-SER sp3_sp3_2 2 CA 2 CB 2 OG 1 P 180.000 10.0 3
+
+loop_
+_chem_link_chir.link_id
+_chem_link_chir.atom_centre_comp_id
+_chem_link_chir.atom_id_centre
+_chem_link_chir.atom_1_comp_id
+_chem_link_chir.atom_id_1
+_chem_link_chir.atom_2_comp_id
+_chem_link_chir.atom_id_2
+_chem_link_chir.atom_3_comp_id
+_chem_link_chir.atom_id_3
+_chem_link_chir.volume_sign
+DNA-SER 1 P 1 "O5'" 2 OG 1 OP2 both
+
+data_link_DNA-TYR
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+DNA-TYR 1 P 2 OH SINGLE 1.618 0.0100
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+DNA-TYR 1 OP1 1 P 2 OH 108.075 3.00
+DNA-TYR 1 OP2 1 P 2 OH 108.075 3.00
+DNA-TYR 1 "O5'" 1 P 2 OH 101.281 3.00
+DNA-TYR 2 CZ 2 OH 1 P 121.950 3.00
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+DNA-TYR sp3_sp3_1 1 OP1 1 P 2 OH 2 CZ 180.000 10.0 3
+DNA-TYR sp2_sp2_1 2 CE1 2 CZ 2 OH 1 P 180.000 5.0 2
+
+loop_
+_chem_link_chir.link_id
+_chem_link_chir.atom_centre_comp_id
+_chem_link_chir.atom_id_centre
+_chem_link_chir.atom_1_comp_id
+_chem_link_chir.atom_id_1
+_chem_link_chir.atom_2_comp_id
+_chem_link_chir.atom_id_2
+_chem_link_chir.atom_3_comp_id
+_chem_link_chir.atom_id_3
+_chem_link_chir.volume_sign
+DNA-TYR 1 P 1 "O5'" 2 OH 1 OP2 both
+
+data_link_SS
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+SS 1 SG 2 SG single 2.031 .020
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
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+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+SS 1 CB 1 SG 2 SG 103.800 1.800
+SS 1 SG 2 SG 2 CB 103.800 1.800
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
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+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+SS ss 1 CB 1 SG 2 SG 2 CB 90.00 10.0 2
+
+data_link_disulf
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+disulf 1 SG 2 SG single 2.031 .020
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+disulf 1 CB 1 SG 2 SG 103.800 1.800
+disulf 1 SG 2 SG 2 CB 103.800 1.800
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+disulf ss 1 CB 1 SG 2 SG 2 CB 90.00 10.0 2
+
+data_link_TRANS
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+TRANS 1 C 2 N SINGLE 1.337 0.011
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+TRANS 1 CA 1 C 2 N 115.917 1.50
+TRANS 1 O 1 C 2 N 123.469 1.50
+TRANS 1 C 2 N 2 CA 122.095 1.76
+TRANS 1 C 2 N 2 H 119.176 1.83
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+TRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
+TRANS omega 1 CA 1 C 2 N 2 CA 180.00 5.0 0
+TRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
+_chem_link_plane.dist_esd
+TRANS plan-1 1 CA 0.020
+TRANS plan-1 1 C 0.020
+TRANS plan-1 2 N 0.020
+TRANS plan-1 1 O 0.020
+TRANS plan-2 2 CA 0.020
+TRANS plan-2 1 C 0.020
+TRANS plan-2 2 H 0.020
+TRANS plan-2 2 N 0.020
+
+data_link_CIS
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+CIS 1 C 2 N SINGLE 1.337 0.011
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+CIS 1 CA 1 C 2 N 115.917 1.50
+CIS 1 O 1 C 2 N 123.469 1.50
+CIS 1 C 2 N 2 CA 122.095 1.76
+CIS 1 C 2 N 2 H 119.176 1.83
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+CIS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
+CIS omega 1 CA 1 C 2 N 2 CA 0.00 5.0 0
+CIS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
+_chem_link_plane.dist_esd
+CIS plan-1 1 CA 0.020
+CIS plan-1 1 C 0.020
+CIS plan-1 2 N 0.020
+CIS plan-1 1 O 0.020
+CIS plan-2 2 CA 0.020
+CIS plan-2 1 C 0.020
+CIS plan-2 2 H 0.020
+CIS plan-2 2 N 0.020
+
+data_link_PTRANS
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+PTRANS 1 C 2 N SINGLE 1.352 0.010
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+PTRANS 1 CA 1 C 2 N 118.415 1.50
+PTRANS 1 O 1 C 2 N 121.016 1.53
+PTRANS 2 CA 2 N 1 C 120.469 1.50
+PTRANS 2 CD 2 N 1 C 124.005 1.50
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+PTRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
+PTRANS omega 1 CA 1 C 2 N 2 CA 180.00 5.0 0
+PTRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
+_chem_link_plane.dist_esd
+PTRANS plan-1 1 CA 0.020
+PTRANS plan-1 1 C 0.020
+PTRANS plan-1 2 N 0.020
+PTRANS plan-1 1 O 0.020
+PTRANS plan-2 1 C .020
+PTRANS plan-2 2 N .020
+PTRANS plan-2 2 CA .020
+PTRANS plan-2 2 CD .020
+
+data_link_PCIS
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+PCIS 1 C 2 N SINGLE 1.352 0.010
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+PCIS 1 CA 1 C 2 N 118.415 1.50
+PCIS 1 O 1 C 2 N 121.016 1.53
+PCIS 2 CA 2 N 1 C 120.469 1.50
+PCIS 2 CD 2 N 1 C 124.005 1.50
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+PCIS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
+PCIS omega 1 CA 1 C 2 N 2 CA 0.00 5.0 0
+PCIS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
+_chem_link_plane.dist_esd
+PCIS plan-1 1 CA 0.020
+PCIS plan-1 1 C 0.020
+PCIS plan-1 2 N 0.020
+PCIS plan-1 1 O 0.020
+PCIS plan-2 1 C .020
+PCIS plan-2 2 N .020
+PCIS plan-2 2 CA .020
+PCIS plan-2 2 CD .020
+
+data_link_NMTRANS
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+NMTRANS 1 C 2 N SINGLE 1.346 0.020
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+NMTRANS 1 CA 1 C 2 N 118.492 1.50
+NMTRANS 1 O 1 C 2 N 121.426 2.26
+NMTRANS 2 CA 2 N 1 C 121.862 2.35
+NMTRANS 2 CN 2 N 1 C 121.178 3.00
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+NMTRANS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
+NMTRANS omega 1 CA 1 C 2 N 2 CA 180.00 5.0 0
+NMTRANS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
+_chem_link_plane.dist_esd
+NMTRANS plan-2 1 CA 0.020
+NMTRANS plan-2 1 C 0.020
+NMTRANS plan-2 2 N 0.020
+NMTRANS plan-2 1 O 0.020
+NMTRANS plan-3 2 CA 0.020
+NMTRANS plan-3 2 CN 0.020
+NMTRANS plan-3 1 C 0.020
+NMTRANS plan-3 2 N 0.020
+
+data_link_NMCIS
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+NMCIS 1 C 2 N single 1.329 .014
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+NMCIS 1 O 1 C 2 N 123.000 1.600
+NMCIS 1 CA 1 C 2 N 116.200 2.000
+NMCIS 1 C 2 N 2 CN 124.300 3.000
+NMCIS 1 C 2 N 2 CA 121.700 1.800
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
+_chem_link_tor.atom_2_comp_id
+_chem_link_tor.atom_id_2
+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+NMCIS psi 1 N 1 CA 1 C 2 N 160.00 30.0 2
+NMCIS omega 1 CA 1 C 2 N 2 CA .00 5.0 0
+NMCIS phi 1 C 2 N 2 CA 2 C 60.00 20.0 3
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
+_chem_link_plane.dist_esd
+NMCIS plane1 1 CA .020
+NMCIS plane1 1 C .020
+NMCIS plane1 1 O .020
+NMCIS plane1 2 N .020
+NMCIS plane2 1 C .050
+NMCIS plane2 2 N .050
+NMCIS plane2 2 CA .050
+NMCIS plane2 2 CN .050
+
+data_link_gap
+
+data_link_p
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+p 1 "O3'" 2 P SINGLE 1.607 0.0100
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
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+_chem_link_angle.atom_3_comp_id
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+p 2 "O5'" 2 P 1 "O3'" 100.661 3.00
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+
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+
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+
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+_chem_link_bond.value_dist_esd
+GTP-p 1 "O3'" 2 P SINGLE 1.607 0.0100
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
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+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+GTP-p 1 "C3'" 1 "O3'" 2 P 121.082 1.50
+GTP-p 2 OP1 2 P 1 "O3'" 109.493 3.00
+GTP-p 2 OP2 2 P 1 "O3'" 109.493 3.00
+GTP-p 2 "O5'" 2 P 1 "O3'" 100.661 3.00
+
+loop_
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+GTP-p sp3_sp3_1 1 "C3'" 1 "O3'" 2 P 2 OP1 60.000 10.0 3
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+
+loop_
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+
+data_link_CYS-HEMB
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+
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+CYS-HEMB 1 CB 1 SG 2 CAB 101.808 3.00
+CYS-HEMB 2 C3B 2 CAB 1 SG 111.652 3.00
+CYS-HEMB 2 CBB 2 CAB 1 SG 110.252 3.00
+CYS-HEMB 1 SG 2 CAB 2 HAB 107.856 1.89
+
+loop_
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+CYS-HEMB sp3_sp3_3 1 CA 1 CB 1 SG 2 CAB 180.000 10.0 3
+
+loop_
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+
+data_link_CYS-HEMC
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+
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+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+CYS-HEMC 1 CB 1 SG 2 CAC 101.808 3.00
+CYS-HEMC 2 C3C 2 CAC 1 SG 111.652 3.00
+CYS-HEMC 2 CBC 2 CAC 1 SG 110.252 3.00
+CYS-HEMC 1 SG 2 CAC 2 HAC 107.856 1.89
+
+loop_
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+CYS-HEMC sp3_sp3_1 2 CBC 2 CAC 1 SG 1 CB 60.000 10.0 3
+CYS-HEMC sp3_sp3_2 1 SG 2 CAC 2 CBC 2 HBC 60.000 10.0 3
+CYS-HEMC sp3_sp3_3 1 CA 1 CB 1 SG 2 CAC 180.000 10.0 3
+
+loop_
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+_chem_link_chir.atom_id_centre
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+_chem_link_chir.atom_3_comp_id
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+_chem_link_chir.volume_sign
+CYS-HEMC 2 CAC 1 SG 2 C3C 2 CBC both
+
+data_link_HIS_TYR1
+loop_
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+HIS_TYR1 1 ND1 2 CB SINGLE 1.479 0.0100
+
+loop_
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+_chem_link_angle.atom_id_3
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+_chem_link_angle.value_angle_esd
+HIS_TYR1 1 CG 1 ND1 2 CB 126.908 3.00
+HIS_TYR1 1 CE1 1 ND1 2 CB 124.367 2.36
+HIS_TYR1 2 CA 2 CB 1 ND1 111.116 3.00
+HIS_TYR1 2 CG 2 CB 1 ND1 110.829 1.95
+HIS_TYR1 1 ND1 2 CB 2 HB2 106.371 1.50
+
+loop_
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+_chem_link_tor.period
+HIS_TYR1 sp2_sp3_1 1 CG 1 ND1 2 CB 2 CA 150.000 10.0 6
+HIS_TYR1 const_24_1 1 CB 1 CG 1 ND1 2 CB 0.000 0.0 2
+
+loop_
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+
+loop_
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+HIS_TYR1 plan-2 2 CB 0.020
+HIS_TYR1 plan-2 1 CB 0.020
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+HIS_TYR1 plan-2 1 CE1 0.020
+HIS_TYR1 plan-2 1 HD2 0.020
+HIS_TYR1 plan-2 1 HE1 0.020
+HIS_TYR1 plan-2 1 HE2 0.020
+HIS_TYR1 plan-2 1 NE2 0.020
+HIS_TYR1 plan-2 1 ND1 0.020
+
+data_link_HIS_TYR2
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+HIS_TYR2 1 NE2 2 CE2 SINGLE 1.447 0.0100
+
+loop_
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+_chem_link_angle.atom_id_3
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+HIS_TYR2 1 CD2 1 NE2 2 CE2 126.913 1.60
+HIS_TYR2 1 CE1 1 NE2 2 CE2 124.723 2.73
+HIS_TYR2 2 CD2 2 CE2 1 NE2 119.776 1.50
+HIS_TYR2 2 CZ 2 CE2 1 NE2 120.443 1.51
+
+loop_
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+
+loop_
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+HIS_TYR2 plan-1 2 CD1 0.020
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+HIS_TYR2 plan-1 2 CZ 0.020
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+HIS_TYR2 plan-1 2 HD2 0.020
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+HIS_TYR2 plan-1 1 NE2 0.020
+HIS_TYR2 plan-1 2 OH 0.020
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+HIS_TYR2 plan-2 1 CB 0.020
+HIS_TYR2 plan-2 1 CG 0.020
+HIS_TYR2 plan-2 1 CD2 0.020
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+HIS_TYR2 plan-2 1 HD2 0.020
+HIS_TYR2 plan-2 1 HE1 0.020
+HIS_TYR2 plan-2 1 NE2 0.020
+HIS_TYR2 plan-2 1 ND1 0.020
+
+data_link_LYS-CYS
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+_chem_link_bond.link_id
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+LYS-CYS 1 NZ 2 SG SINGLE 1.682 0.0176
+
+loop_
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+_chem_link_angle.atom_3_comp_id
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+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+LYS-CYS 1 CE 1 NZ 2 SG 116.537 1.50
+LYS-CYS 2 SG 1 NZ 1 HZ1 110.707 3.00
+LYS-CYS 2 CB 2 SG 1 NZ 109.471 3.00
+
+loop_
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+_chem_link_tor.period
+LYS-CYS sp3_sp3_1 1 CE 1 NZ 2 SG 2 CB 60.000 10.00 3
+
+loop_
+_chem_link_chir.link_id
+_chem_link_chir.atom_centre_comp_id
+_chem_link_chir.atom_id_centre
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+_chem_link_chir.atom_2_comp_id
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+_chem_link_chir.atom_3_comp_id
+_chem_link_chir.atom_id_3
+_chem_link_chir.volume_sign
+LYS-CYS 1 NZ 2 SG 1 CE 1 HZ1 both
+
+data_link_LYS-ASN
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
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+LYS-ASN 1 NZ 2 CG SINGLE 1.337 0.0118
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
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+_chem_link_angle.atom_2_comp_id
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+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+LYS-ASN 1 CE 1 NZ 2 CG 124.480 2.27
+LYS-ASN 2 CG 1 NZ 1 HZ1 117.279 2.10
+LYS-ASN 2 CB 2 CG 1 NZ 116.603 1.50
+LYS-ASN 2 OD1 2 CG 1 NZ 121.996 1.50
+
+loop_
+_chem_link_tor.link_id
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+_chem_link_tor.value_angle
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+_chem_link_tor.period
+LYS-ASN sp2_sp2_1 2 CB 2 CG 1 NZ 1 CE 180.000 5.00 2
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
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+LYS-ASN plan-4 2 CB 0.020
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+LYS-ASN plan-4 1 NZ 0.020
+LYS-ASN plan-4 2 OD1 0.020
+LYS-ASN plan-1 1 CE 0.020
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+LYS-ASN plan-1 1 HZ1 0.020
+LYS-ASN plan-1 1 NZ 0.020
+
+data_link_MET-TYR
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+MET-TYR 1 SD 2 CE1 SINGLE 1.780 0.0200
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
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+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+MET-TYR 1 CG 1 SD 2 CE1 103.903 1.50
+MET-TYR 1 CE 1 SD 2 CE1 103.843 3.00
+MET-TYR 2 CD1 2 CE1 1 SD 120.241 3.00
+MET-TYR 2 CZ 2 CE1 1 SD 120.124 3.00
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
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+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+MET-TYR sp2_sp3_1 2 CD1 2 CE1 1 SD 1 CG 150.000 10.0 6
+MET-TYR sp2_sp2_1 2 CG 2 CD1 2 CE1 1 SD 180.000 0.0 2
+
+loop_
+_chem_link_chir.link_id
+_chem_link_chir.atom_centre_comp_id
+_chem_link_chir.atom_id_centre
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+_chem_link_chir.atom_2_comp_id
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+_chem_link_chir.atom_3_comp_id
+_chem_link_chir.atom_id_3
+_chem_link_chir.volume_sign
+MET-TYR 1 SD 2 CE1 1 CG 1 CE both
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
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+MET-TYR plan-1 2 CB 0.020
+MET-TYR plan-1 2 CG 0.020
+MET-TYR plan-1 2 CD1 0.020
+MET-TYR plan-1 2 CD2 0.020
+MET-TYR plan-1 2 CE1 0.020
+MET-TYR plan-1 2 CE2 0.020
+MET-TYR plan-1 2 CZ 0.020
+MET-TYR plan-1 2 HD1 0.020
+MET-TYR plan-1 2 HD2 0.020
+MET-TYR plan-1 2 HE2 0.020
+MET-TYR plan-1 2 OH 0.020
+MET-TYR plan-1 1 SD 0.020
+
+data_link_TRP-TYR
+loop_
+_chem_link_bond.link_id
+_chem_link_bond.atom_1_comp_id
+_chem_link_bond.atom_id_1
+_chem_link_bond.atom_2_comp_id
+_chem_link_bond.atom_id_2
+_chem_link_bond.type
+_chem_link_bond.value_dist
+_chem_link_bond.value_dist_esd
+TRP-TYR 1 CH2 2 CE2 SINGLE 1.492 0.0125
+
+loop_
+_chem_link_angle.link_id
+_chem_link_angle.atom_1_comp_id
+_chem_link_angle.atom_id_1
+_chem_link_angle.atom_2_comp_id
+_chem_link_angle.atom_id_2
+_chem_link_angle.atom_3_comp_id
+_chem_link_angle.atom_id_3
+_chem_link_angle.value_angle
+_chem_link_angle.value_angle_esd
+TRP-TYR 1 CZ2 1 CH2 2 CE2 120.507 2.02
+TRP-TYR 1 CZ3 1 CH2 2 CE2 120.338 2.79
+TRP-TYR 2 CD2 2 CE2 1 CH2 120.621 2.79
+TRP-TYR 2 CZ 2 CE2 1 CH2 121.366 3.00
+
+loop_
+_chem_link_tor.link_id
+_chem_link_tor.id
+_chem_link_tor.atom_1_comp_id
+_chem_link_tor.atom_id_1
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+_chem_link_tor.atom_3_comp_id
+_chem_link_tor.atom_id_3
+_chem_link_tor.atom_4_comp_id
+_chem_link_tor.atom_id_4
+_chem_link_tor.value_angle
+_chem_link_tor.value_angle_esd
+_chem_link_tor.period
+TRP-TYR sp2_sp2_1 1 CZ2 1 CH2 2 CE2 2 CD2 180.000 5.0 2
+
+loop_
+_chem_link_plane.link_id
+_chem_link_plane.plane_id
+_chem_link_plane.atom_comp_id
+_chem_link_plane.atom_id
+_chem_link_plane.dist_esd
+TRP-TYR plan-1 1 CE2 0.020
+TRP-TYR plan-1 1 CE3 0.020
+TRP-TYR plan-1 1 CZ2 0.020
+TRP-TYR plan-1 1 CZ3 0.020
+TRP-TYR plan-1 1 CH2 0.020
+TRP-TYR plan-1 2 CE2 0.020
+TRP-TYR plan-1 1 CG 0.020
+TRP-TYR plan-1 1 CD2 0.020
+TRP-TYR plan-1 1 HE3 0.020
+TRP-TYR plan-1 1 HZ2 0.020
+TRP-TYR plan-1 1 HZ3 0.020
+TRP-TYR plan-1 1 NE1 0.020
+TRP-TYR plan-2 1 CH2 0.020
+TRP-TYR plan-2 2 CB 0.020
+TRP-TYR plan-2 2 CG 0.020
+TRP-TYR plan-2 2 CD1 0.020
+TRP-TYR plan-2 2 CD2 0.020
+TRP-TYR plan-2 2 CE1 0.020
+TRP-TYR plan-2 2 CE2 0.020
+TRP-TYR plan-2 2 CZ 0.020
+TRP-TYR plan-2 2 HD1 0.020
+TRP-TYR plan-2 2 HD2 0.020
+TRP-TYR plan-2 2 HE1 0.020
+TRP-TYR plan-2 2 OH 0.020
+
+data_mod_SERm1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+SERm1 delete HG . H H 0
+SERm1 change OG . O O2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+SERm1 delete OG HG single . . . .
+SERm1 change CA CB single 1.516 0.0100 1.516 0.0100
+SERm1 change CB OG single 1.438 0.0200 1.438 0.0200
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+SERm1 delete CB OG HG . .
+SERm1 change CA CB OG 108.381 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+SERm1 delete CA CB OG HG . . . 3
+SERm1 change OG CB CA N sp3_sp3_199 180.000 10.0 3
+
+data_mod_CYS-SS
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+CYS-SS delete HG . . . .000
+
+data_mod_CYSmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+CYSmod1 delete HG . H HSH1 0
+CYSmod1 change SG . S S2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+CYSmod1 delete SG HG single . . . .
+CYSmod1 change CB HB3 single 0.980 0.0104 1.089 0.0100
+CYSmod1 change CB HB2 single 0.980 0.0104 1.089 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+CYSmod1 delete CB SG HG . .
+CYSmod1 change N CA CB 109.354 2.20
+CYSmod1 change C CA CB 110.419 3.00
+CYSmod1 change CA CB SG 114.974 2.42
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+CYSmod1 delete CA CB SG HG . . . 0
+CYSmod1 change N CA CB SG sp3_sp3_19 180.000 10.0 3
+
+data_mod_NH3
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+NH3 change N N . NT3 -1.000
+NH3 add H H H HNT3 .000
+NH3 add . H2 H HNT3 .000
+NH3 add . H3 H HNT3 .000
+NH3 delete HN1 . . . .000
+NH3 delete HN2 . . . .000
+NH3 delete HN3 . . . .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+NH3 change N n/a . CA START
+NH3 add H N . . .
+NH3 add H2 N . . .
+NH3 add H3 N . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+NH3 add N H2 single 0.914 0.010 1.036 0.016
+NH3 add N H3 single 0.914 0.010 1.036 0.016
+NH3 change N CA single 1.491 .021 1.491 .021
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+NH3 add H2 N H3 109.470 3.000
+NH3 add H3 N CA 109.470 3.000
+NH3 add H2 N CA 109.470 3.000
+NH3 add H N H2 109.470 3.000
+NH3 add H N H3 109.470 3.000
+NH3 change H N CA 109.470 3.000
+
+data_mod_NH1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+NH1 change N N . NH1 .000
+NH1 add . H H HNH1 .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+NH1 change N n/a . CA START
+NH1 add H N . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+NH1 add N H single 0.914 0.010 1.036 0.016
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+NH1 add H N CA 109.307 3.000
+NH1 add H N CD 106.136 2.250
+
+data_mod_NH2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+NH2 change N N . NH1 .000
+NH2 add . H H HNH1 .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+NH2 change N n/a . CA START
+NH2 add H N . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+NH2 add N H single 0.914 0.010 1.036 0.016
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+NH2 add H N CA 109.307 3.000
+NH2 add H N CD 106.136 2.250
+
+data_mod_NH2N
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+NH2N change N N . NH2 .000
+
+data_mod_COO
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+COO change C C . C .000
+COO change O O . OC -.500
+COO add . OXT O OC -.500
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+COO add OXT C . . END
+COO change C n/a . OXT .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+COO change C O deloc 1.231 .020 1.231 .020
+COO add C OXT deloc 1.231 .020 1.231 .020
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+COO change CA C O 121.000 3.000
+COO add CA C OXT 121.000 3.000
+COO add O C OXT 118.000 3.000
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.id
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+COO add psi N CA C OXT 160.00 30.0 2
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+COO add oxt C .020
+COO add oxt CA .020
+COO add oxt O .020
+COO add oxt OXT .020
+
+data_mod_AA-STAND
+
+data_mod_AA-STPRO
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+AA-STPRO delete HN . . . .000
+
+data_mod_NA-STAND
+
+data_mod_5*END
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+5*END delete P . . . .000
+5*END delete OP1 . . . .000
+5*END delete OP2 . . . .000
+5*END delete OP3 . . . .000
+5*END change 'O5'' 'O5'' . OH1 0.000
+5*END add . 'HO5'' H HOH1 0.000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+5*END delete P n/a . . .
+5*END delete O1P n/a . . .
+5*END delete O2P n/a . . .
+5*END change 'O5'' n/a . 'C5'' START
+5*END add 'HO5'' 'O5'' . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+5*END add 'O5'' 'HO5'' single 0.839 0.010 0.970 0.012
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+5*END add 'C5'' 'O5'' 'HO5'' 120.000 3.000
+
+data_mod_3*END
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+3*END change 'O3'' 'O3'' . OH1 0.000
+3*END add . 'HO3'' H HOH1 0.000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+3*END change 'O3'' 'C3'' . . END
+3*END add 'HO3'' 'O3'' . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+3*END add 'O3'' 'HO3'' single 0.839 0.010 0.970 0.012
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+3*END add 'C3'' 'O3'' 'HO3'' 120.000 3.000
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.id
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+3*END add hh 'C4'' 'C3'' 'O3'' 'HO3'' .00 30.0 3
+
+data_mod_p5*END
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+p5*END change OP3 OP3 O OP -.330
+
+data_mod_p3*END
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+p3*END change 'O3'' 'O3'' . OH1 0.000
+p3*END add . 'HO3'' H HOH1 0.000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+p3*END change 'O3'' 'C3'' . . END
+p3*END add 'HO3'' 'O3'' . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+p3*END add 'O3'' 'HO3'' single 0.839 0.010 0.970 0.012
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+p3*END add 'C3'' 'O3'' 'HO3'' 120.000 3.000
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.id
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+p3*END add hh 'C4'' 'C3'' 'O3'' 'HO3'' .00 30.0 3
+
+data_mod_DEL_OP3
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL_OP3 delete OP3 . O OP -1
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL_OP3 delete OP3 P single . . . .
+DEL_OP3 change P OP1 double 1.491 0.0100 1.491 0.0100
+DEL_OP3 change P OP2 single 1.491 0.0100 1.491 0.0100
+DEL_OP3 change P "O5'" single 1.599 0.0103 1.599 0.0103
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL_OP3 delete OP3 P OP1 . .
+DEL_OP3 delete OP3 P OP2 . .
+DEL_OP3 delete OP3 P "O5'" . .
+DEL_OP3 change OP1 P OP2 118.304 1.50
+DEL_OP3 change OP1 P "O5'" 108.008 3.00
+DEL_OP3 change OP2 P "O5'" 108.008 3.00
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+DEL_OP3 delete "C5'" "O5'" P OP3 . .
+
+data_mod_DEL_HO3p
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL_HO3p delete "HO3'" . H H 0
+DEL_HO3p change "O3'" . O O2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL_HO3p delete "O3'" "HO3'" single . . . .
+DEL_HO3p change "C3'" "O3'" single 1.421 0.0119 1.421 0.0119
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL_HO3p delete "C3'" "O3'" "HO3'" . .
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+DEL_HO3p delete "C4'" "C3'" "O3'" "HO3'" . .
+
+data_mod_FOR-N
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+FOR-N add . H H HC1 .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+FOR-N add H C . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+FOR-N add C H single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+FOR-N add H C O 121.000 3.000
+
+data_mod_FOR-C
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+FOR-C change O O . OC -0.500
+FOR-C add . OXT O OC -0.500
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+FOR-C add OXT C . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+FOR-C change C O deloc 1.231 .020 1.231 .020
+FOR-C add C OXT deloc 1.231 .020 1.231 .020
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+FOR-C add O C OXT 120.000 3.000
+
+data_mod_G-N2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+G-N2 delete N2 . . . .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+G-N2 delete N2 n/a . . .
+
+data_mod_DEL-HD1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+DEL-HD1 delete HD1 . . . .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+DEL-HD1 change ND1 n/a . . END
+
+data_mod_DEL-HE2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+DEL-HE2 delete HE2 . . . .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+DEL-HE2 change NE2 n/a . . END
+
+data_mod_DEL-OXT
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-OXT delete OXT . O OC -1
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-OXT delete C OXT single . . . .
+DEL-OXT change CA C single 1.526 0.010 1.526 0.010
+DEL-OXT change C O double 1.229 0.012 1.229 0.012
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-OXT delete CA C OXT . .
+DEL-OXT delete O C OXT . .
+DEL-OXT change CA C O 120.614 1.50
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+DEL-OXT delete plan-1 C 0.020
+DEL-OXT delete plan-1 CA 0.020
+DEL-OXT delete plan-1 O 0.020
+DEL-OXT delete plan-1 OXT 0.020
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+DEL-OXT delete O C CA N 0.000 10.0
+
+data_mod_DEL-OXT1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-OXT1 delete OXT . O OC -1
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-OXT1 delete C OXT single . . . .
+DEL-OXT1 change CA C single 1.526 0.010 1.526 0.010
+DEL-OXT1 change C O double 1.232 0.010 1.232 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-OXT1 delete CA C OXT . .
+DEL-OXT1 delete O C OXT . .
+DEL-OXT1 change CA C O 120.082 1.50
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+DEL-OXT1 delete plan-1 C 0.020
+DEL-OXT1 delete plan-1 CA 0.020
+DEL-OXT1 delete plan-1 O 0.020
+DEL-OXT1 delete plan-1 OXT 0.020
+
+data_mod_DEL-HN1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-HN1 delete H2 . H H 0
+DEL-HN1 delete H3 . H H 0
+DEL-HN1 change N . N NH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-HN1 delete N H2 single . . . .
+DEL-HN1 delete N H3 single . . . .
+DEL-HN1 change CA N single 1.453 0.010 1.453 0.010
+DEL-HN1 change N H single 0.914 0.010 1.036 0.016
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-HN1 delete CA N H2 . .
+DEL-HN1 delete CA N H3 . .
+DEL-HN1 delete H N H2 . .
+DEL-HN1 delete H N H3 . .
+DEL-HN1 delete H2 N H3 . .
+DEL-HN1 change CA N H 118.729 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+DEL-HN1 delete C CA N H 180 10
+
+data_mod_DEL-NMH
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-NMH delete H . H H 0
+DEL-NMH change N . N N 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-NMH delete N H single . . . .
+DEL-NMH change N CN single 1.450 0.0200 1.450 0.0200
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-NMH delete CN N H . .
+DEL-NMH delete CA N H . .
+DEL-NMH change CN N CA 118.119 2.78
+DEL-NMH change N CA C 111.097 3.00
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+DEL-NMH change CN N CA C sp2_sp3_13 0.000 10.0 6
+DEL-NMH change CA N CN HN1 sp2_sp3_7 0.000 10.0 6
+
+loop_
+_chem_mod_chir.mod_id
+_chem_mod_chir.function
+_chem_mod_chir.atom_id_centre
+_chem_mod_chir.atom_id_1
+_chem_mod_chir.atom_id_2
+_chem_mod_chir.atom_id_3
+_chem_mod_chir.new_volume_sign
+DEL-NMH delete N CA CN H .
+
+data_mod_DEL-HNP
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-HNP delete H . H H 0
+DEL-HNP delete H2 . H H 0
+DEL-HNP change N . N NH0 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-HNP delete N H single . . . .
+DEL-HNP delete N H2 single . . . .
+DEL-HNP change N CA single 1.459 0.0100 1.459 0.0100
+DEL-HNP change N CD single 1.472 0.0100 1.472 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-HNP delete CA N H . .
+DEL-HNP delete CA N H2 . .
+DEL-HNP delete CD N H . .
+DEL-HNP delete CD N H2 . .
+DEL-HNP delete H N H2 . .
+DEL-HNP change CA N CD 112.597 1.50
+DEL-HNP change N CA C 113.251 1.50
+DEL-HNP change N CD CG 102.887 1.50
+
+data_mod_PEPT-D
+loop_
+_chem_mod_chir.mod_id
+_chem_mod_chir.function
+_chem_mod_chir.atom_id_centre
+_chem_mod_chir.atom_id_1
+_chem_mod_chir.atom_id_2
+_chem_mod_chir.atom_id_3
+_chem_mod_chir.new_volume_sign
+PEPT-D change CA N CB C positiv
+
+data_mod_1MA
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+1MA change N1 . . NR6 .000
+1MA add . C1 C CH3 .000
+1MA add . H11 H HCH .000
+1MA add . H12 H HGH .000
+1MA add . H13 H HCH .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+1MA add C1 N1 . H13 .
+1MA add H11 C1 . . .
+1MA add H12 C1 . . .
+1MA add H13 C1 . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+1MA add C1 N1 single 1.465 .020 1.465 .020
+1MA add C1 H11 single 0.988 0.010 1.089 0.010
+1MA add C1 H12 single 0.988 0.010 1.089 0.010
+1MA add C1 H13 single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+1MA add N1 C1 H11 109.470 3.000
+1MA add N1 C1 H12 109.470 3.000
+1MA add N1 C1 H13 109.470 3.000
+1MA add H12 C1 H11 109.470 3.000
+1MA add H13 C1 H11 109.470 3.000
+1MA add H13 C1 H12 109.470 3.000
+
+data_mod_1MG
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+1MG change N1 . . NR6 .000
+1MG add . C1A C CH3 .000
+1MG add . H1A1 H HCH .000
+1MG add . H1A2 H HGH .000
+1MG add . H1A3 H HCH .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+1MG add C1A N1 . H1A3 .
+1MG add H1A1 C1A . . .
+1MG add H1A2 C1A . . .
+1MG add H1A3 C1A . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+1MG add C1A N1 single 1.465 .020 1.465 .020
+1MG add C1A H1A1 single 0.988 0.010 1.089 0.010
+1MG add C1A H1A2 single 0.988 0.010 1.089 0.010
+1MG add C1A H1A3 single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+1MG add N1 C1A H1A1 109.470 3.000
+1MG add N1 C1A H1A2 109.470 3.000
+1MG add N1 C1A H1A3 109.470 3.000
+1MG add H1A2 C1A H1A1 109.470 3.000
+1MG add H1A3 C1A H1A1 109.470 3.000
+1MG add H1A3 C1A H1A2 109.470 3.000
+
+data_mod_2MG
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+2MG change N2 . . NH1 .000
+2MG add . C2A C CH3 .000
+2MG add . H2A1 H HCH .000
+2MG add . H2A2 H HGH .000
+2MG add . H2A3 H HCH .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+2MG change N2 C2 . C2A .
+2MG add C2A N2 . H2A3 .
+2MG add H2A1 C2A . . .
+2MG add H2A2 C2A . . .
+2MG add H2A3 C2A . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+2MG add C2A N2 single 1.465 .020 1.465 .020
+2MG add C2A H2A1 single 0.988 0.010 1.089 0.010
+2MG add C2A H2A2 single 0.988 0.010 1.089 0.010
+2MG add C2A H2A3 single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+2MG add C2 N2 C2A 115.000 3.000
+2MG add N2 C2A H2A1 109.470 3.000
+2MG add N2 C2A H2A2 109.470 3.000
+2MG add N2 C2A H2A3 109.470 3.000
+2MG add H2A2 C2A H2A1 109.470 3.000
+2MG add H2A3 C2A H2A1 109.470 3.000
+2MG add H2A3 C2A H2A2 109.470 3.000
+
+data_mod_M2G
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+M2G change N2 . . N .000
+M2G add . C2A C CH3 .000
+M2G add . H2A1 H HCH .000
+M2G add . H2A2 H HGH .000
+M2G add . H2A3 H HCH .000
+M2G add . C2B C CH3 .000
+M2G add . H2B1 H HCH .000
+M2G add . H2B2 H HGH .000
+M2G add . H2B3 H HCH .000
+M2G delete H21 . . . .000
+M2G delete H22 . . . .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+M2G change N2 C2 . C2A .
+M2G add C2A N2 . H2A3 .
+M2G add H2A1 C2A . . .
+M2G add H2A2 C2A . . .
+M2G add H2A3 C2A . . .
+M2G add C2B N2 . H2B3 .
+M2G add H2B1 C2B . . .
+M2G add H2B2 C2B . . .
+M2G add H2B3 C2B . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+M2G add C2A N2 single 1.465 .020 1.465 .020
+M2G add C2A H2A1 single 0.988 0.010 1.089 0.010
+M2G add C2A H2A2 single 0.988 0.010 1.089 0.010
+M2G add C2A H2A3 single 0.988 0.010 1.089 0.010
+M2G add C2B N2 single 1.465 .020 1.465 .020
+M2G add C2B H2B1 single 0.988 0.010 1.089 0.010
+M2G add C2B H2B2 single 0.988 0.010 1.089 0.010
+M2G add C2B H2B3 single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+M2G add C2 N2 C2A 118.000 3.000
+M2G add C2 N2 C2B 118.000 3.000
+M2G add C2A N2 C2B 124.000 3.000
+M2G add N2 C2A H2A1 109.470 3.000
+M2G add N2 C2A H2A2 109.470 3.000
+M2G add N2 C2A H2A3 109.470 3.000
+M2G add H2A2 C2A H2A1 109.470 3.000
+M2G add H2A3 C2A H2A1 109.470 3.000
+M2G add H2A3 C2A H2A2 109.470 3.000
+M2G add N2 C2B H2B1 109.470 3.000
+M2G add N2 C2B H2B2 109.470 3.000
+M2G add N2 C2B H2B3 109.470 3.000
+M2G add H2B2 C2B H2B1 109.470 3.000
+M2G add H2B3 C2B H2B1 109.470 3.000
+M2G add H2B3 C2B H2B2 109.470 3.000
+
+data_mod_O2*MET
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+O2*MET change 'O2'' . . OC2 .000
+O2*MET delete 'HO2'' . . . .000
+O2*MET add . C2A C CH3 .000
+O2*MET add . H2A1 H HCH .000
+O2*MET add . H2A2 H HGH .000
+O2*MET add . H2A3 H HCH .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+O2*MET change 'O2'' 'C2'' . C2A .
+O2*MET add C2A 'O2'' . H2A3 .
+O2*MET add H2A1 C2A . . .
+O2*MET add H2A2 C2A . . .
+O2*MET add H2A3 C2A . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+O2*MET add 'O2'' C2A single 1.420 .020 1.420 .020
+O2*MET add C2A H2A1 single 0.988 0.010 1.089 0.010
+O2*MET add C2A H2A2 single 0.988 0.010 1.089 0.010
+O2*MET add C2A H2A3 single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+O2*MET add 'C2'' 'O2'' C2A 120.000 3.000
+O2*MET add 'O2'' C2A H2A1 109.470 3.000
+O2*MET add 'O2'' C2A H2A2 109.470 3.000
+O2*MET add 'O2'' C2A H2A3 109.470 3.000
+O2*MET add H2A2 C2A H2A1 109.470 3.000
+O2*MET add H2A3 C2A H2A1 109.470 3.000
+O2*MET add H2A3 C2A H2A2 109.470 3.000
+
+data_mod_C5MET
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+C5MET change C5 . . CR6 .000
+C5MET add . C5A C CH3 .000
+C5MET add . H5A1 H HCH .000
+C5MET add . H5A2 H HGH .000
+C5MET add . H5A3 H HCH .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+C5MET add C5A C5 . H5A3 .
+C5MET add H5A1 C5A . . .
+C5MET add H5A2 C5A . . .
+C5MET add H5A3 C5A . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+C5MET add C5A C5 single 1.500 .020 1.500 .020
+C5MET add C5A H5A1 single 0.988 0.010 1.089 0.010
+C5MET add C5A H5A2 single 0.988 0.010 1.089 0.010
+C5MET add C5A H5A3 single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+C5MET add C4 C5 C5A 122.000 3.000
+C5MET add C6 C5 C5A 118.000 3.000
+C5MET add C5 C5A H5A2 109.470 3.000
+C5MET add C5 C5A H5A3 109.470 3.000
+C5MET add H5A2 C5A H5A1 109.470 3.000
+C5MET add H5A3 C5A H5A1 109.470 3.000
+C5MET add H5A3 C5A H5A2 109.470 3.000
+
+data_mod_N7MET
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+N7MET change N7 . . NR5 .000
+N7MET add . C7 C CH3 .000
+N7MET add . H71 H HCH .000
+N7MET add . H72 H HGH .000
+N7MET add . H73 H HCH .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+N7MET add C7 N7 . H73 .
+N7MET add H71 C7 . . .
+N7MET add H72 C7 . . .
+N7MET add H73 C7 . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+N7MET add C7 N7 single 1.465 .020 1.465 .020
+N7MET add C7 H71 single 0.988 0.010 1.089 0.010
+N7MET add C7 H72 single 0.988 0.010 1.089 0.010
+N7MET add C7 H73 single 0.988 0.010 1.089 0.010
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+N7MET add C5 N7 C7 126.000 3.000
+N7MET add C8 N7 C7 126.000 3.000
+N7MET add N7 C7 H71 109.470 3.000
+N7MET add N7 C7 H72 109.470 3.000
+N7MET add N7 C7 H73 109.470 3.000
+N7MET add H72 C7 H71 109.470 3.000
+N7MET add H73 C7 H71 109.470 3.000
+N7MET add H73 C7 H72 109.470 3.000
+
+data_mod_RNA-O2*
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+RNA-O2* delete 'O2'' . . . .000
+RNA-O2* delete 'HO2'' . . . .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+RNA-O2* delete 'O2'' n/a . . .
+RNA-O2* delete 'HO2'' n/a . . .
+
+data_mod_XYS-O1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+XYS-O1 delete O1 . . . .000
+XYS-O1 delete HO1 . . . .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+XYS-O1 delete O1 n/a . . .
+XYS-O1 delete HO1 n/a . . .
+
+data_mod_B2C
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+B2C change N N . NT3 -1.000
+B2C add . H1 H HNT3 0.000
+B2C add . H2 H HNT3 0.000
+B2C add . H3 H HNT3 0.000
+B2C delete H . . . .000
+B2C change C B B B .000
+B2C change O O1 O O .000
+B2C add . O2 O O .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+B2C change N n/a . CA START
+B2C add H1 N . . .
+B2C add H2 N . . .
+B2C add H3 N . . .
+B2C change B CA . . END
+B2C change CA N . B .
+B2C change O1 B . . .
+B2C add O2 B . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+B2C add N H1 single 0.914 0.010 1.036 0.016
+B2C add N H2 single 0.914 0.010 1.036 0.016
+B2C add N H3 single 0.914 0.010 1.036 0.016
+B2C change N CA single 1.491 .021 1.491 .021
+B2C change B CA single 1.560 .020 1.560 .020
+B2C change B O1 deloc 1.480 .020 1.480 .020
+B2C add B O2 deloc 1.480 .020 1.480 .020
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+B2C add H2 N H3 109.470 3.000
+B2C add H3 N CA 109.470 3.000
+B2C add H2 N CA 109.470 3.000
+B2C add H1 N H2 109.470 3.000
+B2C add H1 N H3 109.470 3.000
+B2C add H1 N CA 109.470 3.000
+B2C add O1 B O2 112.000 3.000
+B2C change CA B O1 126.000 3.000
+B2C add CA B O2 126.000 3.000
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.id
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+B2C add hhb N CA B O2 .00 30.0 3
+
+loop_
+_chem_mod_chir.mod_id
+_chem_mod_chir.function
+_chem_mod_chir.atom_id_centre
+_chem_mod_chir.atom_id_1
+_chem_mod_chir.atom_id_2
+_chem_mod_chir.atom_id_3
+_chem_mod_chir.new_volume_sign
+B2C change CA N CB B negativ
+
+data_mod_B2C_D
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_partial_charge
+B2C_D change N N . NT3 -1.000
+B2C_D add . H1 H HNT3 0.000
+B2C_D add . H2 H HNT3 0.00
+B2C_D add . H3 H HNT3 0.00
+B2C_D delete H . . . .000
+B2C_D change C B B B .000
+B2C_D change O O1 O O .000
+B2C_D add . O2 O O .000
+
+loop_
+_chem_mod_tree.mod_id
+_chem_mod_tree.function
+_chem_mod_tree.atom_id
+_chem_mod_tree.atom_back
+_chem_mod_tree.back_type
+_chem_mod_tree.atom_forward
+_chem_mod_tree.connect_type
+B2C_D change N n/a . CA START
+B2C_D add H1 N . . .
+B2C_D add H2 N . . .
+B2C_D add H3 N . . .
+B2C_D change B CA . . END
+B2C_D change CA N . B .
+B2C_D change O1 B . . .
+B2C_D add O2 B . . .
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+B2C_D add N H1 single 0.914 0.010 1.036 0.016
+B2C_D add N H2 single 0.914 0.010 1.036 0.016
+B2C_D add N H3 single 0.914 0.010 1.036 0.016
+B2C_D change N CA single 1.491 .021 1.491 .021
+B2C_D change B CA single 1.560 .020 1.560 .020
+B2C_D change B O1 deloc 1.480 .020 1.480 .020
+B2C_D add B O2 deloc 1.480 .020 1.480 .020
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+B2C_D add H2 N H3 109.470 3.000
+B2C_D add H3 N CA 109.470 3.000
+B2C_D add H2 N CA 109.470 3.000
+B2C_D add H1 N H2 109.470 3.000
+B2C_D add H1 N H3 109.470 3.000
+B2C_D add H1 N CA 109.470 3.000
+B2C_D add O1 B O2 112.000 3.000
+B2C_D change CA B O1 126.000 3.000
+B2C_D add CA B O2 126.000 3.000
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.id
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+B2C_D add hhb N CA B O2 .00 30.0 3
+
+loop_
+_chem_mod_chir.mod_id
+_chem_mod_chir.function
+_chem_mod_chir.atom_id_centre
+_chem_mod_chir.atom_id_1
+_chem_mod_chir.atom_id_2
+_chem_mod_chir.atom_id_3
+_chem_mod_chir.new_volume_sign
+B2C_D change CA N CB B positiv
+
+data_mod_RENAME
+
+data_mod_TERMINUS
+
+data_mod_DEL-HD22
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-HD22 delete HD22 . H H 0
+DEL-HD22 change ND2 . N NH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-HD22 delete ND2 HD22 single . . . .
+DEL-HD22 change CB CG single 1.520 0.0174 1.520 0.0174
+DEL-HD22 change CG OD1 double 1.227 0.0138 1.227 0.0138
+DEL-HD22 change ND2 HD21 single 0.863 0.0200 1.013 0.0120
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-HD22 delete CG ND2 HD22 . .
+DEL-HD22 delete HD21 ND2 HD22 . .
+DEL-HD22 change CA CB CG 112.357 3.00
+DEL-HD22 change OD1 CG ND2 123.445 2.69
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+DEL-HD22 delete CB CG ND2 HD22 . . . 2
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+DEL-HD22 delete plan-3 CG 0.020
+DEL-HD22 delete plan-3 HD21 0.020
+DEL-HD22 delete plan-3 HD22 0.020
+DEL-HD22 delete plan-3 ND2 0.020
+
+data_mod_DEL-HG
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-HG delete HG . H H 0
+DEL-HG change OG . O O2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-HG delete OG HG single . . . .
+DEL-HG change CA CB single 1.518 0.0126 1.518 0.0126
+DEL-HG change CB OG single 1.426 0.0176 1.426 0.0176
+DEL-HG change CB HB3 single 0.982 0.0125 1.092 0.0100
+DEL-HG change CB HB2 single 0.982 0.0125 1.092 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-HG delete CB OG HG . .
+DEL-HG change N CA CB 113.399 3.00
+DEL-HG change C CA CB 111.339 3.00
+DEL-HG change CA CB OG 109.581 3.00
+DEL-HG change OG CB HB3 109.634 2.46
+DEL-HG change OG CB HB2 109.634 2.46
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+DEL-HG delete CA CB OG HG . . . 3
+
+data_mod_DEL-HG1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+DEL-HG1 delete HG1 . H H 0
+DEL-HG1 change OG1 . O O2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+DEL-HG1 delete OG1 HG1 single . . . .
+DEL-HG1 change CA CB single 1.538 0.0100 1.538 0.0100
+DEL-HG1 change CB OG1 single 1.440 0.0100 1.440 0.0100
+DEL-HG1 change CB CG2 single 1.508 0.0200 1.508 0.0200
+DEL-HG1 change CB HB single 0.993 0.0134 1.092 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+DEL-HG1 delete CB OG1 HG1 . .
+DEL-HG1 change N CA CB 113.399 3.00
+DEL-HG1 change C CA CB 111.339 3.00
+DEL-HG1 change CA CB OG1 111.145 1.50
+DEL-HG1 change CA CB CG2 110.837 3.00
+DEL-HG1 change CG2 CB HB 109.492 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+DEL-HG1 delete CA CB OG1 HG1 . . . 3
+
+data_mod_HECmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HECmod1 change CAC . C CH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HECmod1 change C2C C3C single 1.375 0.0200 1.375 0.0200
+HECmod1 change C3C CAC single 1.503 0.0100 1.503 0.0100
+HECmod1 change CAC CBC single 1.513 0.0121 1.513 0.0121
+HECmod1 change CAC HAC single 0.990 0.0200 1.092 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HECmod1 change NC C4C C3C 108.743 1.50
+HECmod1 change C3C CAC CBC 112.400 1.50
+HECmod1 change C3C CAC HAC 108.177 1.50
+HECmod1 change CBC CAC HAC 108.549 2.04
+HECmod1 change HBC1 CBC HBC2 109.460 1.50
+HECmod1 change HBC1 CBC HBC3 109.460 1.50
+HECmod1 change HBC2 CBC HBC3 109.460 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+HECmod1 delete C3C CAC CBC HBC1 . . . 3
+HECmod1 change C2C C3C CAC CBC sp2_sp3_8 150.000 20.0 6
+
+data_mod_HECmod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HECmod2 change CAB . C CH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HECmod2 change C2B C3B double 1.375 0.0200 1.375 0.0200
+HECmod2 change C3B CAB single 1.503 0.0100 1.503 0.0100
+HECmod2 change CAB CBB single 1.513 0.0121 1.513 0.0121
+HECmod2 change CAB HAB single 0.990 0.0200 1.092 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HECmod2 change NB C4B C3B 108.743 1.50
+HECmod2 change C3B CAB CBB 112.400 1.50
+HECmod2 change C3B CAB HAB 108.177 1.50
+HECmod2 change CBB CAB HAB 108.549 2.04
+HECmod2 change HBB1 CBB HBB2 109.460 1.50
+HECmod2 change HBB1 CBB HBB3 109.460 1.50
+HECmod2 change HBB2 CBB HBB3 109.460 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+HECmod2 delete C3B CAB CBB HBB1 . . . 3
+HECmod2 change C2B C3B CAB CBB sp2_sp3_6 150.000 20.0 6
+
+data_mod_FADmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+FADmod1 delete HM83 . H H 0
+FADmod1 change C8M . C CH2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+FADmod1 delete C8M HM83 single . . . .
+FADmod1 change C7 C8 single 1.401 0.0100 1.401 0.0100
+FADmod1 change C8 C8M single 1.516 0.0100 1.516 0.0100
+FADmod1 change C8 C9 double 1.377 0.0162 1.377 0.0162
+FADmod1 change C8M HM81 single 0.982 0.0200 1.089 0.0100
+FADmod1 change C8M HM82 single 0.982 0.0200 1.089 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+FADmod1 delete C8 C8M HM83 . .
+FADmod1 delete HM81 C8M HM83 . .
+FADmod1 delete HM82 C8M HM83 . .
+FADmod1 change C7 C8 C8M 120.426 2.23
+FADmod1 change C8M C8 C9 120.074 3.00
+
+data_mod_HISmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HISmod1 delete HD1 . H H 0
+HISmod1 change ND1 . N NR5 1
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HISmod1 delete ND1 HD1 single . . . .
+HISmod1 change CB CG single 1.491 0.0100 1.491 0.0100
+HISmod1 change CG ND1 single 1.352 0.0200 1.352 0.0200
+HISmod1 change CG CD2 double 1.357 0.0100 1.357 0.0100
+HISmod1 change ND1 CE1 double 1.351 0.0200 1.351 0.0200
+HISmod1 change CE1 HE1 single 0.939 0.0134 1.082 0.0130
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HISmod1 delete CG ND1 HD1 . .
+HISmod1 delete CE1 ND1 HD1 . .
+HISmod1 change CB CG ND1 123.044 1.50
+HISmod1 change CG CD2 HD2 126.231 1.50
+HISmod1 change ND1 CE1 HE1 125.433 1.50
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+HISmod1 delete plan-1 CB 0.020
+HISmod1 delete plan-1 CD2 0.020
+HISmod1 delete plan-1 CE1 0.020
+HISmod1 delete plan-1 CG 0.020
+HISmod1 delete plan-1 HD1 0.020
+HISmod1 delete plan-1 HD2 0.020
+HISmod1 delete plan-1 HE1 0.020
+HISmod1 delete plan-1 HE2 0.020
+HISmod1 delete plan-1 ND1 0.020
+HISmod1 delete plan-1 NE2 0.020
+
+data_mod_FADmod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+FADmod2 delete HM83 . H H 0
+FADmod2 change C8M . C CH2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+FADmod2 delete C8M HM83 single . . . .
+FADmod2 change C7 C8 single 1.398 0.0119 1.398 0.0119
+FADmod2 change C8 C8M single 1.514 0.0100 1.514 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+FADmod2 delete C8 C8M HM83 . .
+FADmod2 delete HM81 C8M HM83 . .
+FADmod2 delete HM82 C8M HM83 . .
+FADmod2 change C7 C8 C8M 120.918 3.00
+FADmod2 change C8M C8 C9 119.582 3.00
+
+data_mod_HISmod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HISmod2 delete HE2 . H H 0
+HISmod2 change NE2 . N NR5 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HISmod2 delete NE2 HE2 single . . . .
+HISmod2 change CG CD2 double 1.366 0.0178 1.366 0.0178
+HISmod2 change ND1 CE1 double 1.344 0.0200 1.344 0.0200
+HISmod2 change CE1 NE2 single 1.322 0.0100 1.322 0.0100
+HISmod2 change CD2 HD2 single 0.949 0.0120 1.082 0.0130
+HISmod2 change CE1 HE1 single 0.939 0.0134 1.082 0.0130
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HISmod2 delete CD2 NE2 HE2 . .
+HISmod2 delete CE1 NE2 HE2 . .
+HISmod2 change NE2 CD2 HD2 125.717 1.62
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+HISmod2 delete plan-1 CB 0.020
+HISmod2 delete plan-1 CD2 0.020
+HISmod2 delete plan-1 CE1 0.020
+HISmod2 delete plan-1 CG 0.020
+HISmod2 delete plan-1 HD1 0.020
+HISmod2 delete plan-1 HD2 0.020
+HISmod2 delete plan-1 HE1 0.020
+HISmod2 delete plan-1 HE2 0.020
+HISmod2 delete plan-1 ND1 0.020
+HISmod2 delete plan-1 NE2 0.020
+
+data_mod_FADmod3
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+FADmod3 delete HM83 . H H 0
+FADmod3 change C8M . C CH2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+FADmod3 delete C8M HM83 single . . . .
+FADmod3 change C7 C8 single 1.398 0.0119 1.398 0.0119
+FADmod3 change C8 C8M single 1.514 0.0100 1.514 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+FADmod3 delete C8 C8M HM83 . .
+FADmod3 delete HM81 C8M HM83 . .
+FADmod3 delete HM82 C8M HM83 . .
+FADmod3 change C7 C8 C8M 120.918 3.00
+FADmod3 change C8M C8 C9 119.582 3.00
+
+data_mod_GTPmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+GTPmod1 delete "HO3'" . H H 0
+GTPmod1 change "O3'" . O O2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+GTPmod1 delete "O3'" "HO3'" single . . . .
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+GTPmod1 delete "C3'" "O3'" "HO3'" . .
+GTPmod1 change "C5'" "C4'" "C3'" 114.817 2.32
+GTPmod1 change "C3'" "C4'" "H4'" 109.150 1.50
+GTPmod1 change "C2'" "C3'" "H3'" 110.368 2.92
+GTPmod1 change "C3'" "C2'" "H2'" 110.368 2.92
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+GTPmod1 delete "C4'" "C3'" "O3'" "HO3'" . . . 0
+
+data_mod_HEMmod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HEMmod2 change CAB . C CH1 0
+HEMmod2 change CBB . C CH3 0
+HEMmod2 add . H31 H H 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HEMmod2 change C2B C3B double 1.375 0.0200 1.375 0.0200
+HEMmod2 change C3B C4B single 1.381 0.0200 1.381 0.0200
+HEMmod2 change C3B CAB single 1.503 0.0100 1.503 0.0100
+HEMmod2 change CAB CBB single 1.513 0.0121 1.513 0.0121
+HEMmod2 change CAB HAB single 0.990 0.0200 1.092 0.0100
+HEMmod2 add CBB H31 single 0.960 0.0100 1.092 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HEMmod2 change C3B C4B NB 108.743 1.50
+HEMmod2 change C3B CAB CBB 112.400 1.50
+HEMmod2 change C3B CAB HAB 108.177 1.50
+HEMmod2 change CBB CAB HAB 108.549 2.04
+HEMmod2 change CAB CBB HBB 109.518 1.50
+HEMmod2 change CAB CBB HBBA 109.518 1.50
+HEMmod2 change HBB CBB HBBA 109.460 1.50
+HEMmod2 add CAB CBB H31 109.518 1.50
+HEMmod2 add HBB CBB H31 109.460 1.50
+HEMmod2 add HBBA CBB H31 109.460 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+HEMmod2 delete C3B CAB CBB HBB . . . 2
+HEMmod2 change C2B C3B CAB CBB sp2_sp3_9 150.000 20.0 6
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+HEMmod2 delete plan-10 C3B 0.020
+HEMmod2 delete plan-10 CAB 0.020
+HEMmod2 delete plan-10 CBB 0.020
+HEMmod2 delete plan-10 HAB 0.020
+HEMmod2 delete plan-11 CAB 0.020
+HEMmod2 delete plan-11 CBB 0.020
+HEMmod2 delete plan-11 HBB 0.020
+HEMmod2 delete plan-11 HBBA 0.020
+
+data_mod_HEMmod3
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HEMmod3 change CAC . C CH1 0
+HEMmod3 change CBC . C CH3 0
+HEMmod3 add . H32 H H 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HEMmod3 change C2C C3C single 1.375 0.0200 1.375 0.0200
+HEMmod3 change C3C C4C double 1.381 0.0200 1.381 0.0200
+HEMmod3 change C3C CAC single 1.503 0.0100 1.503 0.0100
+HEMmod3 change CAC CBC single 1.513 0.0121 1.513 0.0121
+HEMmod3 change CAC HAC single 0.990 0.0200 1.092 0.0100
+HEMmod3 add CBC H32 single 0.960 0.0100 1.092 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HEMmod3 change C3C C4C NC 108.743 1.50
+HEMmod3 change C3C CAC CBC 112.400 1.50
+HEMmod3 change C3C CAC HAC 108.177 1.50
+HEMmod3 change CBC CAC HAC 108.549 2.04
+HEMmod3 change CAC CBC HBC 109.518 1.50
+HEMmod3 change CAC CBC HBCA 109.518 1.50
+HEMmod3 change HBC CBC HBCA 109.460 1.50
+HEMmod3 add CAC CBC H32 109.518 1.50
+HEMmod3 add HBC CBC H32 109.460 1.50
+HEMmod3 add HBCA CBC H32 109.460 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+HEMmod3 delete C3C CAC CBC HBC . . . 2
+HEMmod3 change C2C C3C CAC CBC sp2_sp3_9 150.000 20.0 6
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+HEMmod3 delete plan-12 C3C 0.020
+HEMmod3 delete plan-12 CAC 0.020
+HEMmod3 delete plan-12 CBC 0.020
+HEMmod3 delete plan-12 HAC 0.020
+HEMmod3 delete plan-13 CAC 0.020
+HEMmod3 delete plan-13 CBC 0.020
+HEMmod3 delete plan-13 HBC 0.020
+HEMmod3 delete plan-13 HBCA 0.020
+
+data_mod_TYRmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+TYRmod1 delete HB3 . H H 0
+TYRmod1 change CB . C CH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+TYRmod1 delete CB HB3 single . . . .
+TYRmod1 change CA C single 1.533 0.0111 1.533 0.0111
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+TYRmod1 delete CA CB HB3 . .
+TYRmod1 delete CG CB HB3 . .
+TYRmod1 delete HB3 CB HB2 . .
+TYRmod1 change N CA CB 113.399 3.00
+TYRmod1 change CA C O 117.156 1.94
+TYRmod1 change CA C OXT 117.156 1.94
+TYRmod1 change CA CB CG 113.308 3.00
+TYRmod1 change CA CB HB2 106.713 1.50
+TYRmod1 change CG CB HB2 107.067 3.00
+TYRmod1 change CB CG CD1 120.731 3.00
+TYRmod1 change CB CG CD2 120.731 3.00
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+TYRmod1 change N CA CB CG sp3_sp3_28 180.000 10.0 3
+TYRmod1 change CD1 CG CB CA sp2_sp3_19 150.000 10.0 6
+
+data_mod_HISmod3
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HISmod3 delete HE2 . H H 0
+HISmod3 change NE2 . N NR5 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HISmod3 delete NE2 HE2 single . . . .
+HISmod3 change CG CD2 double 1.364 0.0129 1.364 0.0129
+HISmod3 change ND1 CE1 double 1.351 0.0200 1.351 0.0200
+HISmod3 change CD2 NE2 single 1.376 0.0100 1.376 0.0100
+HISmod3 change CE1 NE2 single 1.338 0.0162 1.338 0.0162
+HISmod3 change CD2 HD2 single 0.947 0.0141 1.082 0.0130
+HISmod3 change CE1 HE1 single 0.928 0.0133 1.082 0.0130
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HISmod3 delete CD2 NE2 HE2 . .
+HISmod3 delete CE1 NE2 HE2 . .
+HISmod3 change CG ND1 CE1 108.905 3.00
+HISmod3 change CG CD2 NE2 108.374 2.83
+HISmod3 change CG CD2 HD2 126.805 1.50
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+HISmod3 delete plan-1 CB 0.020
+HISmod3 delete plan-1 CD2 0.020
+HISmod3 delete plan-1 CE1 0.020
+HISmod3 delete plan-1 CG 0.020
+HISmod3 delete plan-1 HD1 0.020
+HISmod3 delete plan-1 HD2 0.020
+HISmod3 delete plan-1 HE1 0.020
+HISmod3 delete plan-1 HE2 0.020
+HISmod3 delete plan-1 ND1 0.020
+HISmod3 delete plan-1 NE2 0.020
+
+data_mod_TYRmod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+TYRmod2 delete HE2 . H H 0
+TYRmod2 change CE2 . C CR6 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+TYRmod2 delete CE2 HE2 single . . . .
+TYRmod2 change CG CD2 single 1.374 0.0100 1.374 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+TYRmod2 delete CD2 CE2 HE2 . .
+TYRmod2 delete CZ CE2 HE2 . .
+TYRmod2 change CB CG CD2 121.348 2.28
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+TYRmod2 delete plan-1 CB 0.020
+TYRmod2 delete plan-1 CD1 0.020
+TYRmod2 delete plan-1 CD2 0.020
+TYRmod2 delete plan-1 CE1 0.020
+TYRmod2 delete plan-1 CE2 0.020
+TYRmod2 delete plan-1 CG 0.020
+TYRmod2 delete plan-1 CZ 0.020
+TYRmod2 delete plan-1 HD1 0.020
+TYRmod2 delete plan-1 HD2 0.020
+TYRmod2 delete plan-1 HE1 0.020
+TYRmod2 delete plan-1 HE2 0.020
+TYRmod2 delete plan-1 OH 0.020
+
+data_mod_LYSmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+LYSmod1 delete HZ2 . H H 0
+LYSmod1 delete HZ3 . H H 0
+LYSmod1 change NZ . N NT1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+LYSmod1 delete NZ HZ2 single . . . .
+LYSmod1 delete NZ HZ3 single . . . .
+LYSmod1 change CE NZ single 1.468 0.0134 1.468 0.0134
+LYSmod1 change NZ HZ1 single 0.914 0.010 1.036 0.016
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+LYSmod1 delete CE NZ HZ2 . .
+LYSmod1 delete CE NZ HZ3 . .
+LYSmod1 delete HZ1 NZ HZ2 . .
+LYSmod1 delete HZ1 NZ HZ3 . .
+LYSmod1 delete HZ2 NZ HZ3 . .
+LYSmod1 change CE NZ HZ1 111.861 3.00
+
+data_mod_CYSmod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+CYSmod2 delete HG . H HSH1 0
+CYSmod2 change SG . S S2 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+CYSmod2 delete SG HG single . . . .
+CYSmod2 change CB SG single 1.805 0.0100 1.805 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+CYSmod2 delete CB SG HG . .
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+CYSmod2 delete CA CB SG HG . .
+
+data_mod_LYSmod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+LYSmod2 delete HZ1 . H H 0
+LYSmod2 delete HZ2 . H H 0
+LYSmod2 delete HZ3 . H H 0
+LYSmod2 change NZ . N N 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+LYSmod2 delete NZ HZ1 single . . . .
+LYSmod2 delete NZ HZ2 single . . . .
+LYSmod2 delete NZ HZ3 single . . . .
+LYSmod2 change CE NZ single 1.480 0.0168 1.480 0.0168
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+LYSmod2 delete CE NZ HZ1 . .
+LYSmod2 delete CE NZ HZ2 . .
+LYSmod2 delete CE NZ HZ3 . .
+LYSmod2 delete HZ1 NZ HZ2 . .
+LYSmod2 delete HZ1 NZ HZ3 . .
+LYSmod2 delete HZ2 NZ HZ3 . .
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+LYSmod2 delete CD CE NZ HZ3 . .
+
+data_mod_LYSmod3
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+LYSmod3 delete HZ2 . H H 0
+LYSmod3 delete HZ3 . H H 0
+LYSmod3 change NZ . N NH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+LYSmod3 delete NZ HZ2 single . . . .
+LYSmod3 delete NZ HZ3 single . . . .
+LYSmod3 change CE NZ single 1.456 0.0109 1.456 0.0109
+LYSmod3 change NZ HZ1 single 0.914 0.010 1.036 0.016
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+LYSmod3 delete CE NZ HZ2 . .
+LYSmod3 delete CE NZ HZ3 . .
+LYSmod3 delete HZ1 NZ HZ2 . .
+LYSmod3 delete HZ1 NZ HZ3 . .
+LYSmod3 delete HZ2 NZ HZ3 . .
+LYSmod3 change CE NZ HZ1 118.241 1.90
+
+data_mod_ASNmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+ASNmod1 delete ND2 . N NH2 0
+ASNmod1 delete HD21 . H H 0
+ASNmod1 delete HD22 . H H 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+ASNmod1 delete CG ND2 single . . . .
+ASNmod1 delete ND2 HD21 single . . . .
+ASNmod1 delete ND2 HD22 single . . . .
+ASNmod1 change CB CG single 1.508 0.0116 1.508 0.0116
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+ASNmod1 delete CB CG ND2 . .
+ASNmod1 delete OD1 CG ND2 . .
+ASNmod1 delete CG ND2 HD21 . .
+ASNmod1 delete CG ND2 HD22 . .
+ASNmod1 delete HD21 ND2 HD22 . .
+ASNmod1 change CB CG OD1 121.400 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+ASNmod1 delete CB CG ND2 HD21 . .
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+ASNmod1 delete plan-2 CB 0.020
+ASNmod1 delete plan-2 CG 0.020
+ASNmod1 delete plan-2 ND2 0.020
+ASNmod1 delete plan-2 OD1 0.020
+ASNmod1 delete plan-3 CG 0.020
+ASNmod1 delete plan-3 HD21 0.020
+ASNmod1 delete plan-3 HD22 0.020
+ASNmod1 delete plan-3 ND2 0.020
+
+data_mod_METmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+METmod1 change SD . S S3 1
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+METmod1 change CG SD single 1.808 0.0100 1.808 0.0100
+METmod1 change CE HE3 single 0.967 0.0100 1.089 0.0100
+METmod1 change CE HE2 single 0.967 0.0100 1.089 0.0100
+METmod1 change CE HE1 single 0.967 0.0100 1.089 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+METmod1 change CA CB CG 114.058 2.21
+METmod1 change CG CB HB3 108.377 2.40
+METmod1 change CG CB HB2 108.377 2.40
+METmod1 change CB CG SD 110.122 1.50
+METmod1 change CB CG HG3 108.661 3.00
+METmod1 change CB CG HG2 108.661 3.00
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+METmod1 change CA CB CG SD sp3_sp3_19 180.000 10.0 3
+METmod1 change CB CG SD CE sp3_sp3_28 180.000 10.0 3
+
+data_mod_TYRmod3
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+TYRmod3 delete HE1 . H H 0
+TYRmod3 change CE1 . C CR6 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+TYRmod3 delete CE1 HE1 single . . . .
+TYRmod3 change CE1 CZ double 1.395 0.0152 1.395 0.0152
+TYRmod3 change CD1 HD1 single 0.940 0.0104 1.082 0.0130
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+TYRmod3 delete CD1 CE1 HE1 . .
+TYRmod3 delete CZ CE1 HE1 . .
+TYRmod3 change CB CG CD1 121.186 2.28
+TYRmod3 change CG CD1 HD1 119.873 2.79
+TYRmod3 change CD1 CE1 CZ 119.634 2.58
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+TYRmod3 change CB CG CD1 CE1 const_sp2_sp2_3 180.000 0.0 2
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+TYRmod3 delete plan-1 CB 0.020
+TYRmod3 delete plan-1 CD1 0.020
+TYRmod3 delete plan-1 CD2 0.020
+TYRmod3 delete plan-1 CE1 0.020
+TYRmod3 delete plan-1 CE2 0.020
+TYRmod3 delete plan-1 CG 0.020
+TYRmod3 delete plan-1 CZ 0.020
+TYRmod3 delete plan-1 HD1 0.020
+TYRmod3 delete plan-1 HD2 0.020
+TYRmod3 delete plan-1 HE1 0.020
+TYRmod3 delete plan-1 HE2 0.020
+TYRmod3 delete plan-1 OH 0.020
+
+data_mod_LEUmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+LEUmod1 delete OXT . O OC -1
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+LEUmod1 delete C OXT single . . . .
+LEUmod1 change CA C single 1.527 0.0100 1.527 0.0100
+LEUmod1 change C O double 1.229 0.0102 1.229 0.0102
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+LEUmod1 delete CA C OXT . .
+LEUmod1 delete O C OXT . .
+LEUmod1 change CA C O 121.041 1.50
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+LEUmod1 delete plan-1 C 0.020
+LEUmod1 delete plan-1 CA 0.020
+LEUmod1 delete plan-1 O 0.020
+LEUmod1 delete plan-1 OXT 0.020
+
+data_mod_LYSmod4
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+LYSmod4 delete HZ1 . H H 0
+LYSmod4 delete HZ2 . H H 0
+LYSmod4 delete HZ3 . H H 0
+LYSmod4 change NZ . N N 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+LYSmod4 delete NZ HZ1 single . . . .
+LYSmod4 delete NZ HZ2 single . . . .
+LYSmod4 delete NZ HZ3 single . . . .
+LYSmod4 change CE NZ single 1.462 0.0100 1.462 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+LYSmod4 delete CE NZ HZ1 . .
+LYSmod4 delete CE NZ HZ2 . .
+LYSmod4 delete CE NZ HZ3 . .
+LYSmod4 delete HZ1 NZ HZ2 . .
+LYSmod4 delete HZ1 NZ HZ3 . .
+LYSmod4 delete HZ2 NZ HZ3 . .
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+LYSmod4 delete CD CE NZ HZ1 . .
+
+data_mod_TRPmod1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+TRPmod1 delete HH2 . H H 0
+TRPmod1 change CH2 . C CR6 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+TRPmod1 delete CH2 HH2 single . . . .
+TRPmod1 change CE2 CZ2 single 1.395 0.0185 1.395 0.0185
+TRPmod1 change CE3 CZ3 double 1.379 0.0158 1.379 0.0158
+TRPmod1 change CZ2 CH2 double 1.391 0.0100 1.391 0.0100
+TRPmod1 change CZ3 CH2 single 1.412 0.0100 1.412 0.0100
+TRPmod1 change CZ2 HZ2 single 0.950 0.0100 1.082 0.0130
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+TRPmod1 delete CZ2 CH2 HH2 . .
+TRPmod1 delete CZ3 CH2 HH2 . .
+TRPmod1 change CE2 CZ2 CH2 119.258 1.50
+TRPmod1 change CZ2 CH2 CZ3 119.154 1.50
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+TRPmod1 delete plan-1 CD2 0.020
+TRPmod1 delete plan-1 CE2 0.020
+TRPmod1 delete plan-1 CE3 0.020
+TRPmod1 delete plan-1 CG 0.020
+TRPmod1 delete plan-1 CH2 0.020
+TRPmod1 delete plan-1 CZ2 0.020
+TRPmod1 delete plan-1 CZ3 0.020
+TRPmod1 delete plan-1 HE3 0.020
+TRPmod1 delete plan-1 HH2 0.020
+TRPmod1 delete plan-1 HZ2 0.020
+TRPmod1 delete plan-1 HZ3 0.020
+TRPmod1 delete plan-1 NE1 0.020
+
+data_mod_TYRmod4
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+TYRmod4 delete HE2 . H H 0
+TYRmod4 change CE2 . C CR6 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+TYRmod4 delete CE2 HE2 single . . . .
+TYRmod4 change CG CD2 single 1.391 0.0149 1.391 0.0149
+TYRmod4 change CD2 CE2 double 1.396 0.0127 1.396 0.0127
+TYRmod4 change CE2 CZ single 1.400 0.0131 1.400 0.0131
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+TYRmod4 delete CD2 CE2 HE2 . .
+TYRmod4 delete CZ CE2 HE2 . .
+TYRmod4 change CB CG CD2 121.325 2.28
+TYRmod4 change CD1 CG CD2 117.170 2.83
+TYRmod4 change CG CD2 CE2 123.240 3.00
+TYRmod4 change CD2 CE2 CZ 118.013 1.50
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+TYRmod4 delete plan-1 CB 0.020
+TYRmod4 delete plan-1 CD1 0.020
+TYRmod4 delete plan-1 CD2 0.020
+TYRmod4 delete plan-1 CE1 0.020
+TYRmod4 delete plan-1 CE2 0.020
+TYRmod4 delete plan-1 CG 0.020
+TYRmod4 delete plan-1 CZ 0.020
+TYRmod4 delete plan-1 HD1 0.020
+TYRmod4 delete plan-1 HD2 0.020
+TYRmod4 delete plan-1 HE1 0.020
+TYRmod4 delete plan-1 HE2 0.020
+TYRmod4 delete plan-1 OH 0.020
+
+data_mod_TYRmod5
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+TYRmod5 delete HH . H H 0
+TYRmod5 change OH . O O 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+TYRmod5 delete OH HH single . . . .
+TYRmod5 change CZ OH single 1.410 0.0100 1.410 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+TYRmod5 delete CZ OH HH . .
+TYRmod5 change CE1 CZ CE2 121.469 1.50
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+TYRmod5 delete CE1 CZ OH HH . . . 0
+
+data_mod_LYSmod5
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+LYSmod5 delete HZ2 . H H 0
+LYSmod5 delete HZ3 . H H 0
+LYSmod5 change NZ . N NH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+LYSmod5 delete NZ HZ2 single . . . .
+LYSmod5 delete NZ HZ3 single . . . .
+LYSmod5 change CE NZ single 1.456 0.0109 1.456 0.0109
+LYSmod5 change NZ HZ1 single 0.914 0.010 1.036 0.016
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+LYSmod5 delete CE NZ HZ2 . .
+LYSmod5 delete CE NZ HZ3 . .
+LYSmod5 delete HZ1 NZ HZ2 . .
+LYSmod5 delete HZ1 NZ HZ3 . .
+LYSmod5 delete HZ2 NZ HZ3 . .
+LYSmod5 change CE NZ HZ1 118.176 1.90
+
+data_mod_MS6mod2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+MS6mod2 delete H2 . H H 0
+MS6mod2 delete H3 . H H 0
+MS6mod2 change N . N NH1 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+MS6mod2 delete N H2 single . . . .
+MS6mod2 delete N H3 single . . . .
+MS6mod2 change N CA single 1.454 0.0100 1.454 0.0100
+MS6mod2 change N H single 0.871 0.0200 1.016 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+MS6mod2 delete CA N H2 . .
+MS6mod2 delete CA N H3 . .
+MS6mod2 delete H N H2 . .
+MS6mod2 delete H N H3 . .
+MS6mod2 delete H2 N H3 . .
+MS6mod2 change CA N H 119.298 3.00
+MS6mod2 change N CA C 111.439 3.00
+
+data_mod_ASPprot
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+ASPprot change OD2 . O OH1 0
+ASPprot add . HD2 H H 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+ASPprot change CB CG single 1.505 0.0100 1.505 0.0100
+ASPprot change CG OD1 double 1.217 0.0198 1.217 0.0198
+ASPprot change CG OD2 single 1.308 0.0191 1.308 0.0191
+ASPprot add OD2 HD2 single 0.876 0.0200 0.966 0.0059
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+ASPprot change CA CB CG 113.488 1.82
+ASPprot change CG CB HB3 108.725 1.50
+ASPprot change CG CB HB2 108.725 1.50
+ASPprot change CB CG OD1 123.540 1.50
+ASPprot change CB CG OD2 113.234 2.02
+ASPprot add CG OD2 HD2 110.209 3.00
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+ASPprot add CB CG OD2 HD2 sp2_sp2_1 180.000 5.0 2
+
+data_mod_GLUprot
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+GLUprot change OE2 . O OH1 0
+GLUprot add . HE2 H H 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+GLUprot change CG CD single 1.504 0.0100 1.504 0.0100
+GLUprot change CD OE1 double 1.217 0.0198 1.217 0.0198
+GLUprot change CD OE2 single 1.308 0.0191 1.308 0.0191
+GLUprot add OE2 HE2 single 0.876 0.0200 0.966 0.0059
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+GLUprot change CG CD OE1 123.741 1.99
+GLUprot change CG CD OE2 113.306 2.95
+GLUprot add CD OE2 HE2 110.209 3.00
+
+loop_
+_chem_mod_tor.mod_id
+_chem_mod_tor.function
+_chem_mod_tor.atom_id_1
+_chem_mod_tor.atom_id_2
+_chem_mod_tor.atom_id_3
+_chem_mod_tor.atom_id_4
+_chem_mod_tor.id
+_chem_mod_tor.new_value_angle
+_chem_mod_tor.new_value_angle_esd
+_chem_mod_tor.new_period
+GLUprot add CG CD OE2 HE2 sp2_sp2_1 180.000 5.0 2
+
+data_mod_HISprot1
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HISprot1 delete HD1 . H H 0
+HISprot1 change ND1 . N NRD5 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HISprot1 delete ND1 HD1 single . . . .
+HISprot1 change CB CG single 1.491 0.0100 1.491 0.0100
+HISprot1 change CG CD2 double 1.359 0.0100 1.359 0.0100
+HISprot1 change CD2 NE2 single 1.373 0.0100 1.373 0.0100
+HISprot1 change CE1 NE2 single 1.335 0.0127 1.335 0.0127
+HISprot1 change CB HB3 single 0.981 0.0100 1.092 0.0100
+HISprot1 change CB HB2 single 0.981 0.0100 1.092 0.0100
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HISprot1 delete CG ND1 HD1 . .
+HISprot1 delete CE1 ND1 HD1 . .
+HISprot1 change CA N H 109.786 3.00
+HISprot1 change CA N H2 109.786 3.00
+HISprot1 change CA N H3 109.786 3.00
+HISprot1 change N CA HA 108.404 1.50
+HISprot1 change CB CA HA 109.001 1.50
+HISprot1 change CA C O 117.155 2.01
+HISprot1 change CA C OXT 117.155 2.01
+HISprot1 change HB3 CB HB2 107.622 1.50
+HISprot1 change CB CG ND1 121.338 1.81
+HISprot1 change ND1 CG CD2 108.617 1.58
+HISprot1 change CG ND1 CE1 105.858 1.50
+HISprot1 change ND1 CE1 NE2 111.595 1.50
+HISprot1 change ND1 CE1 HE1 124.330 1.50
+HISprot1 change NE2 CE1 HE1 124.075 2.88
+HISprot1 change CD2 NE2 CE1 107.204 3.00
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+HISprot1 delete plan-1 CB 0.020
+HISprot1 delete plan-1 CD2 0.020
+HISprot1 delete plan-1 CE1 0.020
+HISprot1 delete plan-1 CG 0.020
+HISprot1 delete plan-1 HD1 0.020
+HISprot1 delete plan-1 HD2 0.020
+HISprot1 delete plan-1 HE1 0.020
+HISprot1 delete plan-1 HE2 0.020
+HISprot1 delete plan-1 ND1 0.020
+HISprot1 delete plan-1 NE2 0.020
+HISprot1 add plan-1 CB 0.020
+HISprot1 add plan-1 CD2 0.020
+HISprot1 add plan-1 CE1 0.020
+HISprot1 add plan-1 CG 0.020
+HISprot1 add plan-1 HD2 0.020
+HISprot1 add plan-1 HE1 0.020
+HISprot1 add plan-1 HE2 0.020
+HISprot1 add plan-1 ND1 0.020
+HISprot1 add plan-1 NE2 0.020
+
+data_mod_HISprot2
+loop_
+_chem_mod_atom.mod_id
+_chem_mod_atom.function
+_chem_mod_atom.atom_id
+_chem_mod_atom.new_atom_id
+_chem_mod_atom.new_type_symbol
+_chem_mod_atom.new_type_energy
+_chem_mod_atom.new_charge
+HISprot2 delete HE2 . H H 0
+HISprot2 change ND1 . N NR15 0
+HISprot2 change NE2 . N NRD5 0
+
+loop_
+_chem_mod_bond.mod_id
+_chem_mod_bond.function
+_chem_mod_bond.atom_id_1
+_chem_mod_bond.atom_id_2
+_chem_mod_bond.new_type
+_chem_mod_bond.new_value_dist
+_chem_mod_bond.new_value_dist_esd
+_chem_mod_bond.new_value_dist_nucleus
+_chem_mod_bond.new_value_dist_nucleus_esd
+HISprot2 delete NE2 HE2 single . . . .
+HISprot2 change CB CG single 1.494 0.0100 1.494 0.0100
+HISprot2 change CG CD2 double 1.356 0.0100 1.356 0.0100
+HISprot2 change ND1 CE1 single 1.346 0.0100 1.346 0.0100
+HISprot2 change CD2 NE2 single 1.380 0.0100 1.380 0.0100
+HISprot2 change CE1 NE2 double 1.308 0.0100 1.308 0.0100
+HISprot2 change CB HB3 single 0.981 0.0100 1.092 0.0100
+HISprot2 change CB HB2 single 0.981 0.0100 1.092 0.0100
+HISprot2 change ND1 HD1 single 0.919 0.0200 1.013 0.0120
+HISprot2 change CD2 HD2 single 0.929 0.0143 1.085 0.0150
+
+loop_
+_chem_mod_angle.mod_id
+_chem_mod_angle.function
+_chem_mod_angle.atom_id_1
+_chem_mod_angle.atom_id_2
+_chem_mod_angle.atom_id_3
+_chem_mod_angle.new_value_angle
+_chem_mod_angle.new_value_angle_esd
+HISprot2 delete CD2 NE2 HE2 . .
+HISprot2 delete CE1 NE2 HE2 . .
+HISprot2 change CA N H 109.786 3.00
+HISprot2 change CA N H2 109.786 3.00
+HISprot2 change CA N H3 109.786 3.00
+HISprot2 change N CA HA 108.404 1.50
+HISprot2 change CB CA HA 109.001 1.50
+HISprot2 change CA C O 117.155 2.01
+HISprot2 change CA C OXT 117.155 2.01
+HISprot2 change HB3 CB HB2 107.622 1.50
+HISprot2 change CB CG CD2 132.429 1.50
+HISprot2 change CG ND1 CE1 107.807 1.50
+HISprot2 change CG CD2 NE2 110.147 1.50
+HISprot2 change CG CD2 HD2 124.943 1.50
+HISprot2 change ND1 CE1 NE2 111.530 1.50
+HISprot2 change ND1 CE1 HE1 123.708 1.50
+HISprot2 change NE2 CE1 HE1 124.763 3.00
+HISprot2 change CD2 NE2 CE1 105.756 3.00
+
+loop_
+_chem_mod_plane_atom.mod_id
+_chem_mod_plane_atom.function
+_chem_mod_plane_atom.plane_id
+_chem_mod_plane_atom.atom_id
+_chem_mod_plane_atom.new_dist_esd
+HISprot2 delete plan-1 CB 0.020
+HISprot2 delete plan-1 CD2 0.020
+HISprot2 delete plan-1 CE1 0.020
+HISprot2 delete plan-1 CG 0.020
+HISprot2 delete plan-1 HD1 0.020
+HISprot2 delete plan-1 HD2 0.020
+HISprot2 delete plan-1 HE1 0.020
+HISprot2 delete plan-1 HE2 0.020
+HISprot2 delete plan-1 ND1 0.020
+HISprot2 delete plan-1 NE2 0.020
+HISprot2 add plan-1 CB 0.020
+HISprot2 add plan-1 CD2 0.020
+HISprot2 add plan-1 CE1 0.020
+HISprot2 add plan-1 CG 0.020
+HISprot2 add plan-1 HD1 0.020
+HISprot2 add plan-1 HD2 0.020
+HISprot2 add plan-1 HE1 0.020
+HISprot2 add plan-1 ND1 0.020
+HISprot2 add plan-1 NE2 0.020
diff --git a/image_analysis/structure_refinement/monomers/metals.cif b/image_analysis/structure_refinement/monomers/metals.cif
new file mode 100644
index 000000000..ef6358c3c
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/metals.cif
@@ -0,0 +1,197 @@
+data_metal_coordination
+loop_
+_metal_coordination.metal
+_metal_coordination.ligand
+_metal_coordination.coordination
+_metal_coordination.distance
+_metal_coordination.std
+_metal_coordination.count
+Ca O 4 2.3410 0.0508 11
+Ca O 5 2.3739 0.0757 42
+Ca O 6 2.3394 0.0530 1553
+Ca O 8 2.4677 0.0959 1383
+Ca O 10 2.6507 0.0849 20
+Ca O 11 2.2922 0.0000 1
+Ca O 12 2.3827 0.0231 12
+Ca O 13 2.4900 0.0362 9
+Ca N 4 2.3575 0.0404 16
+Ca N 5 2.3958 0.0865 27
+Ca N 6 2.4784 0.0664 88
+Ca N 8 2.5801 0.0620 140
+Ca N 9 2.2771 0.0055 2
+Ca N 12 2.5812 0.0464 4
+Ca S 8 2.9364 0.0301 64
+Cd O 4 2.2696 0.0541 1231
+Cd O 5 2.3075 0.0823 1290
+Cd O 6 2.3098 0.0733 9252
+Cd O 8 2.4498 0.1269 995
+Cd N 2 2.0928 0.0679 4
+Cd N 4 2.2704 0.0584 1034
+Cd N 5 2.3182 0.0729 978
+Cd N 6 2.3420 0.0567 7948
+Cd N 8 2.4168 0.0730 251
+Cd S 4 2.5344 0.0403 865
+Cd S 5 2.6051 0.0822 139
+Cd S 6 2.7112 0.0790 651
+Cd S 8 2.7723 0.0830 22
+Co O 2 1.8382 0.0023 4
+Co O 3 1.9027 0.0645 25
+Co O 4 1.9674 0.0748 2524
+Co O 5 2.0540 0.1288 2442
+Co O 6 2.0794 0.0873 31908
+Co O 8 2.0525 0.1404 23
+Co O 12 2.0981 0.0038 36
+Co N 2 1.8597 0.0228 19
+Co N 3 1.9920 0.0856 235
+Co N 4 1.9857 0.0829 3126
+Co N 5 2.0660 0.1097 2890
+Co N 6 2.0556 0.1079 23780
+Co N 7 1.8744 0.0681 30
+Co N 8 1.9732 0.0457 57
+Co N 9 1.9558 0.0000 1
+Co N 10 2.0748 0.0032 2
+Co N 12 1.9696 0.0309 12
+Co S 3 2.5588 0.1295 8
+Co S 4 2.2766 0.0681 327
+Co S 5 2.2863 0.1133 230
+Co S 6 2.3645 0.1482 797
+Co S 7 2.1350 0.0240 62
+Co S 8 2.2357 0.0388 110
+Co S 9 2.2874 0.0020 2
+Cu O 2 1.8209 0.0270 17
+Cu O 3 2.1634 0.2038 278
+Cu O 4 1.9484 0.0691 9401
+Cu O 5 2.0597 0.1858 18517
+Cu O 6 2.1733 0.2472 18687
+Cu N 2 1.8821 0.0563 144
+Cu N 3 1.9652 0.0713 2191
+Cu N 4 2.0018 0.0671 13836
+Cu N 5 2.0314 0.0969 20631
+Cu N 6 2.0861 0.1672 13385
+Cu N 7 2.0480 0.0464 10
+Cu S 2 2.1481 0.0143 21
+Cu S 3 2.2507 0.0481 651
+Cu S 4 2.3296 0.0931 2190
+Cu S 5 2.4463 0.2184 425
+Cu S 6 2.5901 0.2628 147
+Fe O 2 1.8469 0.0002 2
+Fe O 3 1.9645 0.1260 120
+Fe O 4 1.9111 0.0994 1017
+Fe O 5 1.9840 0.1333 1160
+Fe O 6 2.0322 0.0892 18340
+Fe O 7 2.0055 0.0302 14
+Fe O 8 2.2664 0.1337 37
+Fe N 2 1.8946 0.0223 22
+Fe N 3 1.9782 0.0914 396
+Fe N 4 1.9621 0.1558 1500
+Fe N 5 2.0733 0.1352 2715
+Fe N 6 2.0641 0.1154 22783
+Fe N 7 2.0293 0.1030 17
+Fe N 8 2.0743 0.1851 201
+Fe N 10 2.0233 0.0311 38
+Fe S 3 2.3024 0.0660 15
+Fe S 4 2.3269 0.0592 294
+Fe S 5 2.2888 0.0897 323
+Fe S 6 2.3543 0.1142 752
+Fe S 7 2.3237 0.0000 1
+Fe S 8 2.2729 0.0686 31
+Fe S 11 2.1977 0.0000 1
+K O 2 2.9059 0.5750 8
+K O 3 2.8089 0.1893 36
+K O 4 2.6188 0.0582 34
+K O 6 2.7546 0.1389 722
+K O 8 2.8184 0.0605 4680
+K O 9 2.8434 0.0817 18
+K O 10 2.8835 0.0759 87
+K O 11 2.6983 0.0465 4
+K O 12 2.8222 0.1108 16
+K O 16 2.7728 0.0428 16
+K N 3 2.8173 0.0237 3
+K N 4 2.7418 0.0241 3
+K N 6 2.8734 0.1215 408
+K N 8 2.9957 0.0534 1141
+K N 12 3.0862 0.0013 2
+K S 3 3.1901 0.0274 9
+K S 4 3.3220 0.1171 8
+K S 6 3.2685 0.0823 18
+K S 8 3.2406 0.1292 41
+Mg O 2 2.0554 0.0097 4
+Mg O 3 1.9937 0.0918 12
+Mg O 4 1.9685 0.0894 352
+Mg O 5 2.0575 0.0846 285
+Mg O 6 2.0741 0.0443 5665
+Mg O 8 2.0342 0.0034 2
+Mg O 12 2.0810 0.0003 12
+Mg N 2 2.0210 0.0000 2
+Mg N 3 2.0244 0.0434 50
+Mg N 4 2.0668 0.0526 431
+Mg N 5 2.1362 0.0752 213
+Mg N 6 2.1893 0.0689 532
+Mg N 7 2.0256 0.0253 12
+Mg S 4 2.4449 0.0066 4
+Mg S 6 2.6233 0.0847 18
+Mn O 3 2.1300 0.0000 1
+Mn O 4 1.9886 0.1364 712
+Mn O 5 2.0454 0.1325 2352
+Mn O 6 2.1235 0.1389 24192
+Mn O 8 2.3379 0.1153 187
+Mn N 2 1.9518 0.0006 2
+Mn N 3 2.1064 0.0836 30
+Mn N 4 2.1247 0.0998 452
+Mn N 5 2.1128 0.1560 1294
+Mn N 6 2.1915 0.1254 12485
+Mn N 7 2.0334 0.0117 8
+Mn N 8 2.1638 0.2290 63
+Mn S 4 2.4160 0.0516 82
+Mn S 5 2.3974 0.1473 65
+Mn S 6 2.5308 0.1543 759
+Mn S 8 2.7530 0.4496 4
+Na O 2 2.7451 0.2229 9
+Na O 3 2.5148 0.2189 356
+Na O 4 2.3601 0.1126 936
+Na O 5 2.3785 0.0889 1964
+Na O 6 2.4167 0.0890 10682
+Na O 8 2.5803 0.1583 1174
+Na O 11 2.4729 0.0682 11
+Na O 12 2.4485 0.0245 12
+Na O 16 2.4544 0.0868 64
+Na N 3 2.3817 0.0468 19
+Na N 4 2.4397 0.0763 110
+Na N 5 2.4662 0.0916 162
+Na N 6 2.5158 0.0858 535
+Na N 8 2.6107 0.1369 108
+Na S 3 3.0905 0.0704 9
+Na S 4 2.8085 0.0742 22
+Na S 5 2.9437 0.0994 24
+Na S 6 2.9463 0.0887 217
+Na S 8 3.0014 0.0301 8
+Ni O 2 1.7925 0.0333 3
+Ni O 3 2.0494 0.0771 147
+Ni O 4 1.8650 0.0474 1934
+Ni O 5 2.0181 0.1088 684
+Ni O 6 2.0680 0.0569 22549
+Ni N 2 1.8330 0.1294 18
+Ni N 3 1.9148 0.0996 263
+Ni N 4 1.9086 0.0578 7110
+Ni N 5 2.0509 0.0767 1323
+Ni N 6 2.0921 0.0531 18876
+Ni N 7 1.8852 0.1013 24
+Ni S 3 2.1662 0.0390 33
+Ni S 4 2.1727 0.0306 4582
+Ni S 5 2.2907 0.0973 198
+Ni S 6 2.4548 0.0691 1081
+Ni S 7 2.1761 0.0533 15
+Zn O 2 2.1082 0.0000 1
+Zn O 3 2.0096 0.0923 171
+Zn O 4 1.9578 0.0451 15632
+Zn O 5 2.0414 0.0799 10506
+Zn O 6 2.1095 0.0766 13008
+Zn N 2 1.8575 0.0462 21
+Zn N 3 2.0281 0.0767 383
+Zn N 4 2.0304 0.0529 10112
+Zn N 5 2.1003 0.0802 7734
+Zn N 6 2.1602 0.0689 6819
+Zn S 3 2.4083 0.0793 16
+Zn S 4 2.3391 0.0545 1189
+Zn S 5 2.4363 0.1220 308
+Zn S 6 2.5526 0.0669 103
diff --git a/image_analysis/structure_refinement/monomers/update_monomers.py b/image_analysis/structure_refinement/monomers/update_monomers.py
new file mode 100644
index 000000000..dfd8a3a04
--- /dev/null
+++ b/image_analysis/structure_refinement/monomers/update_monomers.py
@@ -0,0 +1,133 @@
+#!/usr/bin/env python3
+# SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+# SPDX-License-Identifier: GPL-3.0-only
+"""Copy the subset of the CCP4 Monomer Library (https://github.com/MonomerLibrary/monomers, LGPL-3.0)
+that rugnux's restrained refinement carries in its binary into this directory.
+
+    update_monomers.py /path/to/monomers
+
+COMPOUNDS below is THE list: a compound named there is restrained by the refinement, everything else
+is held fixed. To add one, add its code and run this again; CMake embeds every .cif of this directory
+(MonomerLibrary.cpp), so nothing else needs to change.
+
+The compound files are copied verbatim. links_and_mods.cif is cut down to the links and modifications
+that can apply to these compounds (the polymer links, the termini, the disulfide, ...), and ener_lib.cif
+to its atom-type table (_lib_atom: the van der Waals and ion radii and the hydrogen-bond types).
+metals.json, the library's statistics of metal-ligand distances, becomes metals.cif: for each metal ion of
+COMPOUNDS and each donor element of METAL_LIGANDS, the distance per coordination number (the restraints of
+metal sites the links of links_and_mods.cif do not describe).
+Requires the gemmi Python module."""
+
+import json
+import os
+import shutil
+import sys
+
+import gemmi
+
+AMINO_ACIDS = ["ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", "GLY", "HIS", "ILE",
+               "LEU", "LYS", "MET", "PHE", "PRO", "SER", "THR", "TRP", "TYR", "VAL", "MSE"]
+NUCLEOTIDES = ["DA", "DC", "DG", "DT", "A", "C", "G", "U"]
+# The modified nucleotides of tRNA and rRNA most often met, polymer residues joined by the same backbone link.
+MODIFIED_NUCLEOTIDES = ["PSU", "5MC", "1MA", "OMG", "OMC", "OMU", "H2U", "M2G", "7MG", "2MG", "5MU"]
+NUCLEOTIDE_LIGANDS = ["ATP", "ADP", "AMP", "GTP", "GDP", "GMP"]
+# The cofactors most often met, and the oxygen a heme iron binds. (Not carbon monoxide: CMO.cif has C-O at 1.25 A,
+# where bound CO is near 1.15 A.)
+COFACTORS = ["NAD", "NAI", "NAP", "NDP", "FAD", "FMN", "HEM", "HEC", "SAM", "SAH", "OXY"]
+ADDITIVES = ["DMS", "PEG", "PGE", "PG4", "1PE", "GOL", "EDO", "SO4", "PO4", "ACT", "MPD"]
+WATER_AND_IONS = ["HOH", "NA", "K", "MG", "CA", "ZN", "MN", "FE", "FE2", "NI", "CU", "CO", "CD",
+                  "CL", "BR", "IOD"]
+COMPOUNDS = (AMINO_ACIDS + NUCLEOTIDES + MODIFIED_NUCLEOTIDES + NUCLEOTIDE_LIGANDS + COFACTORS + ADDITIVES +
+             WATER_AND_IONS)
+# The donor elements of metal sites whose distances metals.cif carries.
+METAL_LIGANDS = ["O", "N", "S"]
+
+# Groups of the polymers above; links and modifications of other groups (sugars) are left out.
+GROUPS = {".", "peptide", "P-peptide", "M-peptide", "DNA/RNA", "NON-POLYMER"}
+
+
+def compound_path(lib, code):
+    return os.path.join(lib, code[0].lower(), code + ".cif")
+
+
+def applies(comp, group):
+    return (comp == "." or comp in COMPOUNDS) and group in GROUPS
+
+
+def trim_links_and_mods(lib, out):
+    doc = gemmi.cif.read(os.path.join(lib, "links_and_mods.cif"))
+    links = doc.find_block("link_list").find("_chem_link.", ["id", "comp_id_1", "mod_id_1", "group_comp_1",
+                                                             "comp_id_2", "mod_id_2", "group_comp_2", "name"])
+    mods = doc.find_block("mod_list").find("_chem_mod.", ["id", "name", "comp_id", "group_id"])
+    keep_links = [list(r) for r in links if applies(r[1], r[3]) and applies(r[4], r[6])]
+    keep_mods = [list(r) for r in mods if applies(r[2], r[3])]
+    keep = {"link_" + r[0] for r in keep_links} | {"mod_" + r[0] for r in keep_mods}
+
+    new = gemmi.cif.Document()
+    for name, tag, rows in (("link_list", "_chem_link.", keep_links), ("mod_list", "_chem_mod.", keep_mods)):
+        block = new.add_new_block(name)
+        old = doc.find_block(name).find_loop_item(tag + "id").loop
+        loop = block.init_loop(tag, [t[len(tag):] for t in old.tags])
+        for r in rows:
+            loop.add_row(r)
+    for block in doc:
+        if block.name in keep:
+            new.add_copied_block(block)
+    new.write_file(out)
+    return len(keep_links), len(keep_mods)
+
+
+def trim_ener_lib(lib, out):
+    doc = gemmi.cif.read(os.path.join(lib, "ener_lib.cif"))
+    atoms = doc[0].find_loop_item("_lib_atom.type").loop
+    new = gemmi.cif.Document()
+    block = new.add_new_block(doc[0].name)
+    loop = block.init_loop("_lib_atom.", [t[len("_lib_atom."):] for t in atoms.tags])
+    for i in range(atoms.length()):
+        loop.add_row([atoms[i, j] for j in range(atoms.width())])
+    new.write_file(out)
+
+
+def trim_metals(lib, out):
+    """metals.json -> metals.cif: one row per metal ion of COMPOUNDS, ligand element and coordination number,
+    with the mean distance, its standard deviation and the number of sites behind it."""
+    with open(os.path.join(lib, "metals.json")) as f:
+        table = json.load(f)["metal_coordination"]
+    metals = set()
+    for code in WATER_AND_IONS:
+        for atom in gemmi.make_chemcomp_from_block(gemmi.cif.read(compound_path(lib, code))[-1]).atoms:
+            if atom.el.is_metal:
+                metals.add(atom.el.name)
+    new = gemmi.cif.Document()
+    block = new.add_new_block("metal_coordination")
+    loop = block.init_loop("_metal_coordination.", ["metal", "ligand", "coordination", "distance", "std", "count"])
+    n = 0
+    for metal in sorted(metals):
+        for ligand in METAL_LIGANDS:
+            for row in table.get(metal, {}).get(ligand, []):
+                loop.add_row([metal, ligand, str(row["coord"]), "%.4f" % row["mean"], "%.4f" % row["std"],
+                              str(row["count"])])
+                n += 1
+    new.write_file(out)
+    return n
+
+
+def main():
+    if len(sys.argv) != 2:
+        sys.exit(__doc__)
+    lib = sys.argv[1]
+    here = os.path.dirname(os.path.abspath(__file__))
+    for f in os.listdir(here):
+        if f.endswith(".cif"):
+            os.remove(os.path.join(here, f))
+    for code in COMPOUNDS:
+        shutil.copyfile(compound_path(lib, code), os.path.join(here, code + ".cif"))
+    n_links, n_mods = trim_links_and_mods(lib, os.path.join(here, "links_and_mods.cif"))
+    trim_ener_lib(lib, os.path.join(here, "ener_lib.cif"))
+    n_metal_rows = trim_metals(lib, os.path.join(here, "metals.cif"))
+    shutil.copyfile(os.path.join(lib, "COPYING"), os.path.join(here, "COPYING"))
+    print(f"{len(COMPOUNDS)} compounds, {n_links} links, {n_mods} modifications, {n_metal_rows} metal distances")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/licenses/COLLECT.sh b/licenses/COLLECT.sh
index 772ff0748..014dcfa5d 100644
--- a/licenses/COLLECT.sh
+++ b/licenses/COLLECT.sh
@@ -48,7 +48,6 @@ copy_license libtiff.txt             "$(find_dep tiff-src/LICENSE.md)"
 copy_license fftw.txt                "$(find_dep fftw-src/COPYING)"
 copy_license ceres-solver.txt        "$(find_dep ceres-src/LICENSE)"
 copy_license abseil.txt              "$(find_dep ceres-src/third_party/abseil-cpp/LICENSE)"
-copy_license fast-feedback-indexer.txt "$(find_dep fast-indexer-src/LICENSE.md)"
 copy_license eigen.txt               "$(find_dep eigen3-src/COPYING.MPL2)"
 copy_license eigen-README.txt        "$(find_dep eigen3-src/COPYING.README)"
 copy_license zlib.txt                "$(find_dep zlib-src/LICENSE.md)"
@@ -75,6 +74,8 @@ copy_license bitshuffle-hperf.txt    compression/bitshuffle_hperf/LICENSE-APACHE
 copy_license lz4.txt                 compression/lz4/LICENSE
 copy_license xilinx-hls-headers.txt  fpga/include/LICENSE.HLS_Headers
 copy_license gemmi.txt               gemmi_gph/LICENSE.txt
+copy_license fast-feedback-indexer.txt image_analysis/indexing/fast-feedback-indexer/LICENSE.md
+copy_license ccp4-monomer-library.txt image_analysis/structure_refinement/monomers/COPYING
 # GEMMI bundles six third-party headers under its own include tree, each under its own licence
 # (see THIRD_PARTY_NOTICES.md). Only PEGTL ships a LICENSE file; sajson, fast_float, half, pocketfft
 # and tinydir carry their terms in a comment at the top of the header, so licenses/sajson.txt,
diff --git a/licenses/ccp4-monomer-library.txt b/licenses/ccp4-monomer-library.txt
new file mode 100644
index 000000000..3f7b8b1e5
--- /dev/null
+++ b/licenses/ccp4-monomer-library.txt
@@ -0,0 +1,166 @@
+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions. 
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version. 
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
+
diff --git a/reader/HDF5MetadataSource.cpp b/reader/HDF5MetadataSource.cpp
index 8b2299cee..d53bee837 100644
--- a/reader/HDF5MetadataSource.cpp
+++ b/reader/HDF5MetadataSource.cpp
@@ -944,6 +944,8 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
                 .beta = tmp[4],
                 .gamma = tmp[5]
             });
+        if (const auto e = master_file->ReadOptVector<float>("/entry/sample/unit_cell_esd"); e.size() == 6)
+            dataset->unit_cell_esd = UnitCell{.a = e[0], .b = e[1], .c = e[2], .alpha = e[3], .beta = e[4], .gamma = e[5]};
         // The name carries the setting, the number cannot ("R 3:R" reads back as "R 3:H"), so the
         // name is preferred; the number is the fallback for a file written before it was recorded.
         if (const auto *sg = gemmi::find_spacegroup_by_name(master_file->GetString("/entry/sample/space_group")))
@@ -957,6 +959,18 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
         if (const auto m = master_file->ReadOptVector<int32_t>("/entry/MX/reindexMatrix"); m.size() == 9)
             dataset->reindex_matrix = std::array<int32_t, 9>{m[0], m[1], m[2], m[3], m[4],
                                                              m[5], m[6], m[7], m[8]};
+        if (const auto f = master_file->ReadOptVector<double>("/entry/MX/stillsRockingWidthFormula"); f.size() == 3) {
+            StillsRunWidth w{.gamma0 = f[0], .gamma_e = f[1], .bandwidth_sigma = f[2]};
+            if (const auto r = master_file->ReadOptVector<double>("/entry/MX/stillsRadialScale"); r.size() == 1)
+                w.radial_scale = r[0];
+            w.table_dstar = master_file->ReadOptVector<double>("/entry/MX/stillsRockingWidthTableDstar");
+            w.table_s = master_file->ReadOptVector<double>("/entry/MX/stillsRockingWidthTable");
+            if (w.table_dstar.size() != w.table_s.size()) {
+                w.table_dstar.clear();
+                w.table_s.clear();
+            }
+            dataset->stills_run_width = w;
+        }
         dataset->experiment.SampleName(master_file->GetString("/entry/sample/name"));
 
 
diff --git a/reader/JFJochReaderDataset.h b/reader/JFJochReaderDataset.h
index 9d82b2b5a..53c898d33 100644
--- a/reader/JFJochReaderDataset.h
+++ b/reader/JFJochReaderDataset.h
@@ -12,6 +12,7 @@
 
 #include "../common/DiffractionGeometry.h"
 #include "../common/DiffractionExperiment.h"
+#include "../common/StillsRunWidth.h"
 #include "../common/PixelMask.h"
 #include "../common/AzimuthalIntegrationMapping.h"
 
@@ -41,6 +42,11 @@ struct JFJochReaderDataset {
     // /entry/MX/reindexMatrix; the reader applies it, so everything this class hands out is already in
     // the cell's setting.
     std::optional<std::array<int32_t, 9>> reindex_matrix;
+    // The e.s.d.s of the experiment's unit cell, a b c alpha beta gamma (/entry/sample/unit_cell_esd); empty
+    // where the file has none.
+    std::optional<UnitCell> unit_cell_esd;
+    // Stills: the rocking curve the run's partialities were computed from (/entry/MX/stillsRockingWidth*).
+    std::optional<StillsRunWidth> stills_run_width;
 
     std::vector<float> az_int_bin_to_q;
     std::vector<float> az_int_bin_to_phi;
diff --git a/receiver/JFJochReceiver.cpp b/receiver/JFJochReceiver.cpp
index 516f48900..8ecc77425 100644
--- a/receiver/JFJochReceiver.cpp
+++ b/receiver/JFJochReceiver.cpp
@@ -210,6 +210,9 @@ void JFJochReceiver::SendEndMessage() {
     message.merged.reset();
     message.map_coefficients.reset();
     message.placed_model.reset();
+    message.refined_model.reset();
+    message.refined_map_coefficients.reset();
+    message.blobs.reset();
 
     if (zmq_metadata_socket != nullptr)
         zmq_metadata_socket->EndDataCollection(message);
diff --git a/receiver/JFJochReceiverRugnux.cpp b/receiver/JFJochReceiverRugnux.cpp
index 955cd1820..08cab131f 100644
--- a/receiver/JFJochReceiverRugnux.cpp
+++ b/receiver/JFJochReceiverRugnux.cpp
@@ -96,6 +96,90 @@ namespace {
     }
 }
 
+namespace {
+    // A score the status carries only where it is a number: JSON has no NaN or infinity (nlohmann writes null)
+    void SetIfFinite(std::optional<double> &out, double v) {
+        if (std::isfinite(v))
+            out = v;
+    }
+}
+
+std::optional<RugnuxLiveModel> LiveModel(const ProcessResult &result) {
+    if (!result.model_validation && !result.model_prior)
+        return std::nullopt;
+    RugnuxLiveModel m;
+    m.placement = result.model_placement;
+    if (result.model_prior) {
+        const MolecularReplacementResult &mr = *result.model_prior;
+        m.model_name = mr.model_name;
+        m.predicted = mr.predicted_model;
+        m.mr_decision = mr.decision;
+        if (!mr.ok)
+            m.reason = mr.failure_reason;
+        if (mr.chosen >= 0) {
+            const MRCandidate &c = mr.candidates[mr.chosen];
+            m.mr_space_group = c.space_group.xhm();
+            m.copies = c.copies;
+            SetIfFinite(m.tf_z, c.tf_z);
+            SetIfFinite(m.rf_z, c.rf_z);
+            SetIfFinite(m.llg_z, c.llg_z);
+            SetIfFinite(m.fit_sigma, c.null_sigma);
+            SetIfFinite(m.mr_d_min, mr.d_min_search);
+        }
+    }
+    if (result.model_validation) {
+        const ModelValidationResult &v = *result.model_validation;
+        if (!v.model_name.empty())
+            m.model_name = v.model_name;
+        if (!v.ok) {
+            if (m.reason.empty())
+                m.reason = v.failure_reason;
+        } else {
+            SetIfFinite(m.r_work, v.r_work);
+            SetIfFinite(m.r_free, v.r_free);
+            SetIfFinite(m.cc_model, v.cc_model_overall);
+            if (v.fit_tested)
+                SetIfFinite(m.fit_sigma, v.r_work_sigma);
+            SetIfFinite(m.map_atom_sigma, v.mean_atom_density_sigma);
+            if (v.rigid_body_applied) {
+                SetIfFinite(m.rigid_body_angle_deg, v.rigid_body_angle_deg);
+                SetIfFinite(m.rigid_body_shift_A, v.rigid_body_shift_A);
+            }
+            if (!v.anomalous_sites.empty()) {
+                m.anomalous_site = v.anomalous_sites.front().label;
+                SetIfFinite(m.anomalous_site_sigma, v.anomalous_sites.front().sigma);
+            }
+        }
+    }
+    if (result.refinement) {
+        const RefinementResult &rf = *result.refinement;
+        RugnuxLiveRefinement r;
+        r.performed = rf.ok;
+        r.cancelled = rf.cancelled;
+        r.reason = rf.failure_reason;
+        r.on_gpu = rf.on_gpu;
+        r.seconds = rf.seconds;
+        if (rf.ok) {
+            SetIfFinite(r.r_work, rf.restrained ? rf.r_work : rf.r_work_placement);
+            SetIfFinite(r.r_free, rf.restrained ? rf.r_free : rf.r_free_placement);
+            if (rf.restrained) {
+                SetIfFinite(r.rmsd_bonds_A, rf.geometry.rmsd_bonds);
+                SetIfFinite(r.rmsd_angles_deg, rf.geometry.rmsd_angles);
+            }
+        }
+        r.blob_count = static_cast<int64_t>(rf.blobs.size());
+        for (size_t i = 0; i < std::min(rf.blobs.size(), RugnuxLiveRefinement::MAX_BLOBS); i++) {
+            const DensityBlob &b = rf.blobs[i];
+            RugnuxLiveBlob blob{DensityBlobKindName(b.kind), b.centroid.x, b.centroid.y, b.centroid.z, b.peak_sigma,
+                                b.volume, b.nearest_atom, std::nullopt};
+            SetIfFinite(blob.nearest_atom_distance_A, b.nearest_atom_distance);   // infinite: no atom near
+            r.blobs.push_back(blob);
+        }
+        m.refinement = std::move(r);
+    }
+    return m;
+}
+
 JFJochReceiverRugnux::JFJochReceiverRugnux(const DiffractionExperiment &in_experiment,
                                            const PixelMask &in_pixel_mask,
                                            ImagePuller &in_image_puller,
@@ -159,7 +243,7 @@ JFJochReceiverRugnux::~JFJochReceiverRugnux() {
 }
 
 void JFJochReceiverRugnux::MeasurementThread() {
-    std::future<void> rugnux_done, probe_done;
+    std::future<void> rugnux_done, rugnux_out, probe_done;
     try {
         // Waiting for the start message, as JFJochReceiverLite::MeasurementThread.
         std::optional<std::chrono::steady_clock::time_point> give_up_at;
@@ -201,7 +285,7 @@ void JFJochReceiverRugnux::MeasurementThread() {
             logger.Error("{}", skipped_warning);
             live_status.Finish(RugnuxLiveState::Skipped, "the image buffer cannot hold the whole collection");
         } else
-            StartRugnux(rugnux_done, probe_done);
+            StartRugnux(rugnux_done, rugnux_out, probe_done);
         measurement_started.count_down();
     } catch (const JFJochException &e) {
         logger.ErrorException(e);
@@ -226,12 +310,12 @@ void JFJochReceiverRugnux::MeasurementThread() {
     logger.Info("Receiving finished, {} images", images_collected.load());
 
     std::optional<double> done_s;
-    if (rugnux_done.valid()) {
+    if (rugnux_out.valid()) {
         // The fixed cutoff: the analysis gets deadline_s after the last image, then gives what it has.
-        if (deadline_s > 0 && rugnux_done.wait_for(std::chrono::duration<double>(deadline_s))
+        if (deadline_s > 0 && rugnux_out.wait_for(std::chrono::duration<double>(deadline_s))
                               == std::future_status::timeout)
             Cut("deadline");
-        rugnux_done.wait();
+        rugnux_out.wait();
         if (last_image)
             done_s = SecondsSince(last_image.value());
     }
@@ -251,7 +335,7 @@ void JFJochReceiverRugnux::MeasurementThread() {
     }
     if (push_images_to_writer)
         writer_error = image_pusher.Finalize();
-    if (rugnux_done.valid()) {
+    if (rugnux_out.valid()) {
         // The run's outcome, in one line: its results are in the live status, the end message and the files.
         const auto live = live_status.Get();
         std::string outcome = "rugnux live: " + StateName(live.state);
@@ -272,13 +356,17 @@ void JFJochReceiverRugnux::MeasurementThread() {
         }
         logger.Info("{}", outcome);
     }
+    // The run's teardown, which went on beside the end message and the writer.
+    if (rugnux_done.valid())
+        rugnux_done.wait();
 
     end_time = std::chrono::system_clock::now();
     current_status.SetProgress({});
     current_status.SetStatus(GetStatus());
 }
 
-void JFJochReceiverRugnux::StartRugnux(std::future<void> &rugnux_done, std::future<void> &probe_done) {
+void JFJochReceiverRugnux::StartRugnux(std::future<void> &rugnux_done, std::future<void> &rugnux_out,
+                                       std::future<void> &probe_done) {
     // A failure here costs the analysis only: the images go on to the writer as they would without it.
     try {
         // The start message as the writer gets it, so rugnux sees the dataset an HDF5 master states.
@@ -286,6 +374,7 @@ void JFJochReceiverRugnux::StartRugnux(std::future<void> &rugnux_done, std::futu
         image_buffer.GetStartMessage(start_cbor);
         reader.Open(CBORStream2Deserialize(start_cbor)->start_message.value());
         rugnux_done = std::async(std::launch::async, &JFJochReceiverRugnux::RugnuxThread, this);
+        rugnux_out = rugnux_published.get_future();
         probe_done = std::async(std::launch::async, &JFJochReceiverRugnux::ProbeThread, this);
     } catch (const std::exception &e) {
         logger.Error("rugnux live: cannot start - {}", e.what());
@@ -294,6 +383,7 @@ void JFJochReceiverRugnux::StartRugnux(std::future<void> &rugnux_done, std::futu
 }
 
 void JFJochReceiverRugnux::RugnuxThread() {
+    bool published = false;
     try {
         const auto dataset = reader.GetDataset();
         RugnuxLiveSetup setup = MakeRugnuxLiveSetup(*dataset, rugnux_nthreads, model);
@@ -313,12 +403,13 @@ void JFJochReceiverRugnux::RugnuxThread() {
             }
         });
         LiveObserver observer(plots, scan_result, *az_int_mapping, live_status);
-        ProcessResult result;
-        {
-            Rugnux process(reader, setup.experiment, *dataset->pixel_mask, setup.config);
-            Reachable reachable(rugnux_m, rugnux, process, cut, cancelled);
-            result = process.Run(&observer);
-        }
+        // The run goes - with the pinned buffers its engines kept - once its results are out (below), beside
+        // the end message, which reads only the result: a value of its own, no part of the run.
+        std::optional<Rugnux> process;
+        process.emplace(reader, setup.experiment, *dataset->pixel_mask, setup.config);
+        std::optional<Reachable> reachable;
+        reachable.emplace(rugnux_m, rugnux, *process, cut, cancelled);
+        ProcessResult result = process->Run(&observer);
         // The verdict and summary of the report a `rugnux` run writes, without writing it.
         const ReportDocument doc = BuildReportDocument(experiment.GetFilePrefix(), experiment.GetFilePrefix(),
                                                        setup.experiment, result);
@@ -326,24 +417,55 @@ void JFJochReceiverRugnux::RugnuxThread() {
         for (const auto &w: doc.warnings)
             if (!w.developer_only)
                 warnings.push_back(w.text);
-        live_status.Result(doc.verdict, doc.verdict_text, doc.summary_rows, warnings);
-        // The placed model and a copy of its map coefficients (the end message takes the originals), for
-        // the broker's viewer routes.
+        const double cc_anom = result.merge_statistics.overall.cc_anom;
+        live_status.Result(doc.verdict, doc.verdict_text, doc.summary_rows, warnings,
+                           std::isfinite(cc_anom) && cc_anom > CC_ANOM_SIGNAL);
+        if (const auto m = LiveModel(result))
+            live_status.Model(*m);
+        // The numbers the summary's Space group, Resolution and Signal rows give
+        std::optional<double> d_min, isa;
+        if (result.has_merge_statistics)
+            SetIfFinite(d_min, result.merge_statistics.overall.d_min);
+        if (result.error_model_isa_resolved && result.error_model_isa > 0.0)
+            isa = result.error_model_isa;
+        live_status.Headline(result.space_group ? result.space_group->xhm() : "", d_min, isa);
+        // The placed model and a copy of its map coefficients (the end message takes the originals), and the
+        // refined model with its own, for the broker's viewer routes.
         if (result.outputs && result.outputs->placed_model) {
-            const PlacedModelOutput &p = *result.outputs->placed_model;
+            const RugnuxOutputs &o = *result.outputs;
+            const PlacedModelOutput &p = *o.placed_model;
             std::optional<MtzTable> coefficients;
-            if (result.outputs->maps)
-                coefficients = result.outputs->maps->coefficients;
+            if (o.maps)
+                coefficients = o.maps->coefficients;
+            std::shared_ptr<const RugnuxStructure> refined;
+            if (o.refined_model) {
+                std::optional<MtzTable> refined_coefficients;
+                if (o.refined_maps)
+                    refined_coefficients = o.refined_maps->coefficients;
+                refined = std::make_shared<RugnuxStructure>(o.refined_model->model, o.refined_model->cell,
+                                                            o.refined_model->space_group,
+                                                            std::move(refined_coefficients));
+            }
             live_status.Structure(std::make_shared<RugnuxStructure>(p.model, p.cell, p.space_group,
-                                                                    std::move(coefficients)));
+                                                                    std::move(coefficients)),
+                                  std::move(refined));
         }
         live_status.Finish(result.cancelled ? RugnuxLiveState::Cancelled : RugnuxLiveState::Done);
-        std::unique_lock ul(rugnux_m);
-        rugnux_result = std::move(result);
+        reachable.reset();
+        {
+            std::unique_lock ul(rugnux_m);
+            rugnux_result = std::move(result);
+        }
+        published = true;
+        rugnux_published.set_value();
+        process.reset();
+        Rugnux::ReleasePinnedPool();
     } catch (const std::exception &e) {
         logger.Error("rugnux live: {}", e.what());
         live_status.Finish(RugnuxLiveState::Failed, e.what());
     }
+    if (!published)
+        rugnux_published.set_value();
 }
 
 void JFJochReceiverRugnux::ProbeThread() {
@@ -409,6 +531,7 @@ void JFJochReceiverRugnux::AddToEndMessage(EndMessage &message) {
         message.rotation_lattice_type = r.rotation_lattice_type;
         message.rotation_extra_lattices = r.rotation_extra_lattices;
         message.unit_cell = r.unit_cell;
+        message.unit_cell_esd = r.unit_cell_esd;
         message.space_group_name = r.space_group_name;
         message.space_group_number = r.space_group_number;
         message.reindex_matrix = r.reindex_matrix;
@@ -430,6 +553,14 @@ void JFJochReceiverRugnux::AddToEndMessage(EndMessage &message) {
         if (o.placed_model)
             message.placed_model = PlacedModelFromStructure(*o.placed_model->model, o.placed_model->cell,
                                                             o.placed_model->space_group.xhm());
+        // And the refinement's, as the CLI writes them (_refined_model.cif, _refined_maps.mtz, _blobs.json).
+        if (o.refined_model)
+            message.refined_model = PlacedModelFromStructure(*o.refined_model->model, o.refined_model->cell,
+                                                             o.refined_model->space_group.xhm());
+        if (o.refined_maps)
+            message.refined_map_coefficients = std::move(o.refined_maps->coefficients);
+        if (o.blobs)
+            message.blobs = DensityBlobsToMessage(*o.blobs);
 
         // Every pusher serialises END into a buffer of MESSAGE_SIZE_FOR_START_END, and an END that does
         // not fit there fails the collection. So it is serialised here first, into a buffer of the same
@@ -440,7 +571,7 @@ void JFJochReceiverRugnux::AddToEndMessage(EndMessage &message) {
         try {
             serializer.SerializeSequenceEnd(message);
         } catch (const JFJochException &e) {
-            const std::string text = fmt::format("the merged data, map coefficients and placed model do not "
+            const std::string text = fmt::format("the merged data, map coefficients and models do not "
                                                  "fit in the end message ({} MiB) and are not written",
                                                  MESSAGE_SIZE_FOR_START_END / (1024 * 1024));
             logger.Error("rugnux live: {} - {}", text, e.what());
@@ -448,12 +579,18 @@ void JFJochReceiverRugnux::AddToEndMessage(EndMessage &message) {
             message.merged.reset();
             message.map_coefficients.reset();
             message.placed_model.reset();
+            message.refined_model.reset();
+            message.refined_map_coefficients.reset();
+            message.blobs.reset();
         }
     } catch (const std::exception &e) {
         logger.Error("rugnux live: the end message goes without the analysis results - {}", e.what());
         message.merged.reset();
         message.map_coefficients.reset();
         message.placed_model.reset();
+        message.refined_model.reset();
+        message.refined_map_coefficients.reset();
+        message.blobs.reset();
     }
 }
 
diff --git a/receiver/JFJochReceiverRugnux.h b/receiver/JFJochReceiverRugnux.h
index ee795c049..dabd7f6e5 100644
--- a/receiver/JFJochReceiverRugnux.h
+++ b/receiver/JFJochReceiverRugnux.h
@@ -12,6 +12,9 @@
 #include "../rugnux/Rugnux.h"
 #include "RugnuxLiveStatus.h"
 
+// What the run made of the model it was given, for the live status; none where no model was given.
+std::optional<RugnuxLiveModel> LiveModel(const ProcessResult &result);
+
 // A DECTRIS rotation collection forwarded to the writer as JFJochReceiverLite does, but analysed by
 // rugnux while it arrives instead of image by image: the forward threads put each image into the
 // image buffer and send it on, and one rugnux thread reads the collection back from that buffer. The
@@ -44,13 +47,15 @@ class JFJochReceiverRugnux : public JFJochReceiver {
     Rugnux *rugnux = nullptr;   // while it runs, for Cut
     Rugnux *probe = nullptr;    // the same for the lattice probe
     std::optional<ProcessResult> rugnux_result;
+    std::promise<void> rugnux_published;   // rugnux_result is in place, or the run has failed (RugnuxThread)
     bool cut = false;
     std::atomic<bool> images_done{false};   // the forward threads have ended
 
     void MeasurementThread();
     // Opens the reader on the collection and starts the rugnux and probe threads; a failure is the
-    // analysis's alone (live status Failed), never the collection's.
-    void StartRugnux(std::future<void> &rugnux_done, std::future<void> &probe_done);
+    // analysis's alone (live status Failed), never the collection's. rugnux_out is ready once the run's
+    // result is in place, rugnux_done once the run is gone as well.
+    void StartRugnux(std::future<void> &rugnux_done, std::future<void> &rugnux_out, std::future<void> &probe_done);
     void ForwardThread(uint32_t id);
     void RugnuxThread();
     void ProbeThread();
diff --git a/receiver/RugnuxLiveStatus.cpp b/receiver/RugnuxLiveStatus.cpp
index f8341653e..f0467352c 100644
--- a/receiver/RugnuxLiveStatus.cpp
+++ b/receiver/RugnuxLiveStatus.cpp
@@ -69,12 +69,26 @@ void RugnuxLiveStatus::Finish(RugnuxLiveState state, const std::string &message)
 
 void RugnuxLiveStatus::Result(const std::string &verdict, const std::string &verdict_text,
                               const std::vector<std::pair<std::string, std::string>> &summary,
-                              const std::vector<std::string> &warnings) {
+                              const std::vector<std::string> &warnings, bool anomalous_signal) {
     std::unique_lock ul(m);
     s.verdict = verdict;
     s.verdict_text = verdict_text;
     s.summary = summary;
     s.warnings = warnings;
+    s.anomalous_signal = anomalous_signal;
+}
+
+void RugnuxLiveStatus::Model(const RugnuxLiveModel &model) {
+    std::unique_lock ul(m);
+    s.model = model;
+}
+
+void RugnuxLiveStatus::Headline(const std::string &space_group, std::optional<double> d_min,
+                                std::optional<double> isa) {
+    std::unique_lock ul(m);
+    s.space_group = space_group;
+    s.d_min = d_min;
+    s.isa = isa;
 }
 
 void RugnuxLiveStatus::Latency(double last_image_to_written_s) {
@@ -106,9 +120,11 @@ void RugnuxLiveStatus::Warning(const std::string &text) {
     s.warnings.push_back(text);
 }
 
-void RugnuxLiveStatus::Structure(std::shared_ptr<const RugnuxStructure> structure) {
+void RugnuxLiveStatus::Structure(std::shared_ptr<const RugnuxStructure> structure,
+                                 std::shared_ptr<const RugnuxStructure> refined_structure) {
     std::unique_lock ul(m);
     s.structure = std::move(structure);
+    s.refined_structure = std::move(refined_structure);
 }
 
 void RugnuxLiveStatus::Clear() {
diff --git a/receiver/RugnuxLiveStatus.h b/receiver/RugnuxLiveStatus.h
index 5d3b0b9af..01e76643a 100644
--- a/receiver/RugnuxLiveStatus.h
+++ b/receiver/RugnuxLiveStatus.h
@@ -30,6 +30,58 @@ struct RugnuxLiveStep {
     std::vector<std::string> notes;
 };
 
+// A blob of the refined model's mFo-DFc map it leaves unexplained (DensityBlob), with its likely reading.
+struct RugnuxLiveBlob {
+    std::string kind;                     // DensityBlobKindName: WATER | ION | LIGAND | MODEL_ERROR | UNASSIGNED
+    double x = 0, y = 0, z = 0;           // the centroid, A, in the refined model's frame
+    double peak_sigma = 0;
+    double volume_A3 = 0;
+    std::string nearest_atom;
+    std::optional<double> nearest_atom_distance_A;   // unset where no atom is within reach
+};
+
+// The placed model refined (ProcessResult::refinement), in the numbers of the report's REFINE_ keys.
+struct RugnuxLiveRefinement {
+    // The strongest blobs the status lists; blob_count says how many there are
+    static constexpr size_t MAX_BLOBS = 50;
+    bool performed = false;
+    bool cancelled = false;                // cut short by the deadline or a cancel: the trials that ran
+    std::string reason;                    // why it did not run to the end
+    bool on_gpu = false;
+    double seconds = 0;
+    // After the restrained stage, else after the rigid body and grouped B
+    std::optional<double> r_work, r_free;
+    std::optional<double> rmsd_bonds_A, rmsd_angles_deg;   // where the restrained stage ran
+    int64_t blob_count = 0;
+    std::vector<RugnuxLiveBlob> blobs;     // strongest first
+};
+
+// What the run made of the model it was given (ProcessResult::model_validation and ::model_prior), in the
+// numbers the report's MODEL VALIDATION section gives. Unset values were not computed: the model was not
+// placed, or the placement was not by molecular replacement.
+struct RugnuxLiveModel {
+    std::string placement;                 // RIGID_BODY | MR | NOT_PLACED
+    std::string model_name;
+    bool predicted = false;                // searched as a predicted model
+    std::string reason;                    // why it was not placed or not validated
+    // The placed model against the merge, with nothing refined: coordinates and B factors as given
+    std::optional<double> r_work, r_free;
+    std::optional<double> cc_model;        // CC(model, data) of the intensities, all reflections
+    std::optional<double> fit_sigma;       // R-work above its random-orientation null, in sd
+    std::optional<double> map_atom_sigma;  // mean 2mFo-DFc at the atom centres, in sigma
+    std::optional<double> rigid_body_angle_deg, rigid_body_shift_A;
+    // Molecular replacement's choice
+    std::string mr_decision;
+    std::string mr_space_group;
+    std::optional<int64_t> copies;
+    std::optional<double> tf_z, rf_z, llg_z;
+    std::optional<double> mr_d_min;        // the search's high-resolution limit
+    // The strongest peak of the anomalous difference map at the model's atoms
+    std::string anomalous_site;
+    std::optional<double> anomalous_site_sigma;
+    std::optional<RugnuxLiveRefinement> refinement;
+};
+
 struct RugnuxLiveSnapshot {
     RugnuxLiveState state = RugnuxLiveState::Idle;
     std::string message;                  // why it failed or was skipped
@@ -54,8 +106,16 @@ struct RugnuxLiveSnapshot {
     std::string verdict_text;
     std::vector<std::pair<std::string, std::string>> summary;
     std::vector<std::string> warnings;
-    // The placed model and its maps, once the run has placed one; for the viewer routes.
+    bool anomalous_signal = false;        // the summary's "Anomalous" row says the data carry usable signal
+    std::optional<RugnuxLiveModel> model; // where a model was given
+    // The headline numbers of the result, once the run is over
+    std::string space_group;
+    std::optional<double> d_min;          // of the merge
+    std::optional<double> isa;            // where the error model determined it
+    // The placed model and its maps, once the run has placed one, and the refined model and its maps, once the
+    // run has refined it; for the viewer routes.
     std::shared_ptr<const RugnuxStructure> structure;
+    std::shared_ptr<const RugnuxStructure> refined_structure;
 };
 
 class RugnuxLiveStatus {
@@ -79,14 +139,17 @@ public:
     void Finish(RugnuxLiveState state, const std::string &message = "");
     void Result(const std::string &verdict, const std::string &verdict_text,
                 const std::vector<std::pair<std::string, std::string>> &summary,
-                const std::vector<std::string> &warnings);
+                const std::vector<std::string> &warnings, bool anomalous_signal = false);
+    void Model(const RugnuxLiveModel &model);
+    void Headline(const std::string &space_group, std::optional<double> d_min, std::optional<double> isa);
     void Latency(double last_image_to_written_s);
     // The collection is over: last_image_s is set, and the last image's time is returned (none if no image came).
     std::optional<std::chrono::steady_clock::time_point> LastImage();
     void Cut(const std::string &reason);
     void Probe(const std::string &text);
     void Warning(const std::string &text);
-    void Structure(std::shared_ptr<const RugnuxStructure> structure);
+    void Structure(std::shared_ptr<const RugnuxStructure> structure,
+                   std::shared_ptr<const RugnuxStructure> refined_structure = nullptr);
     // Back to Idle with nothing of the last run, as before any collection.
     void Clear();
     RugnuxLiveSnapshot Get() const;
diff --git a/rugnux/CMakeLists.txt b/rugnux/CMakeLists.txt
index e0696c1b3..396d610f5 100644
--- a/rugnux/CMakeLists.txt
+++ b/rugnux/CMakeLists.txt
@@ -21,6 +21,8 @@ ADD_LIBRARY(JFJochRugnux STATIC
         RugnuxDefaults.h
         RugnuxLive.cpp
         RugnuxLive.h
+        RugnuxRefine.cpp
+        RugnuxRefine.h
         Rugnux.h
         RugnuxCommandLine.cpp
         RugnuxCommandLine.h
@@ -38,8 +40,8 @@ TARGET_LINK_LIBRARIES(JFJochRugnux JFJochReader JFJochImageAnalysis JFJochPrevie
 
 # The files of a run, written by the programs that run one (rugnux, the viewer) from what JFJochRugnux
 # returns: the library itself writes none.
-ADD_LIBRARY(JFJochRugnuxOutput STATIC RugnuxOutputFiles.cpp RugnuxOutputFiles.h)
-TARGET_LINK_LIBRARIES(JFJochRugnuxOutput JFJochRugnux JFJochWriter JFJochModelWriter)
+ADD_LIBRARY(JFJochRugnuxOutput STATIC RugnuxOutputFiles.cpp RugnuxOutputFiles.h RugnuxInputKind.cpp RugnuxInputKind.h)
+TARGET_LINK_LIBRARIES(JFJochRugnuxOutput JFJochRugnux JFJochWriter JFJochModelWriter ZLIB::ZLIB)
 
 # rugnux is the single offline analysis CLI; --mode picks what it does: mx (the full pipeline, the
 # default), azint, scale (re-scale/merge stored reflections) or calibration (powder-ring geometry).
diff --git a/rugnux/ResultReport.cpp b/rugnux/ResultReport.cpp
index a172fc49e..0596612a9 100644
--- a/rugnux/ResultReport.cpp
+++ b/rugnux/ResultReport.cpp
@@ -44,6 +44,8 @@ namespace {
     // 16: FILE_DIRECT_BEAM / BACKGROUND_DIRECT_BEAM / BEAM_CENTRE_SHIFT / BEAM_CENTRE_TOLERANCE in
     //    section 1 and the BEAM_CENTRE_OFF flag - the file's beam centre against the refined one;
     //    the XDS GEOMETRY KEYWORDS section; OVERLOADED_* / OVERLAPPED_* and the OVERLOADS / OVERLAPS flags.
+    // 17: INDEXING_AMBIGUITY_RESOLVED and the AMBIGUITY_* keys in section 2 - serial stills, the
+    //    indexing ambiguity resolved from the data alone (or measured against the reference's answer).
     // 8: every line that is not `KEY= value` and not blank starts with `#`, warnings included
     //    (`# WARNING:`); the header gains RUGNUX_DOWNLOAD and BUILD_CXX_FLAGS, and RUGNUX_GIT is
     //    the full build-time hash.
@@ -413,25 +415,10 @@ namespace {
         }
         return 0.0;
     }
-}
 
-// ---------------------------------------------------------------------------- the emitter
-// Populates the document. Nothing here writes to a stream: the order of the FILE is the renderer's
-// business, which is what lets the SUMMARY sit above the sections whose warnings it reports.
-ReportDocument BuildReportDocument(const std::string &output_prefix,
-                                   const std::string &input_file,
-                                   const DiffractionExperiment &experiment,
-                                   const ProcessResult &result,
-                                   const RunProvenance &provenance) {
-    ReportDocument doc;
-    const bool rotation = experiment.IsRotationIndexing();
-    const bool merged = result.has_merge_statistics;
-    doc.warnings = result.warnings;
-    // SUMMARY rows filled by the sections that measure them; empty leaves the row out.
-    std::string beam_centre_row, overload_row, overlap_row;
-
-    // ------------------------------------------------------------------ header block
-    {
+    // The header block of every report: the version, the build, the input and how the run was invoked.
+    ReportSection HeaderSection(const std::string &output_prefix, const std::string &input_file,
+                                const RunProvenance &provenance) {
         ReportSection h;
         Add(h, KeyInt("REPORT_VERSION", REPORT_VERSION));
         Add(h, KeyText("RUGNUX_VERSION", jfjoch_version()));
@@ -465,9 +452,140 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
             if (!provenance.gpu_description.empty())
                 Add(h, KeyText("GPU", provenance.gpu_description));
         }
-        doc.sections.push_back(std::move(h));
+        return h;
     }
 
+    // The refinement's keys (Refinement.h): REFINE_ of the refinement of a placed model and of --mode refine, with every term of the
+    // score of the model as given under REFINE_SCORE_.
+    void AddRefinementKeys(ReportSection &s, const RefinementResult &rf, const std::string &output_prefix) {
+        Add(s, Blank());
+        if (!rf.ok) {
+            Add(s, KeyEnum("REFINE", "NOT_PERFORMED", {"PERFORMED", "NOT_PERFORMED"}));
+            Add(s, KeyText("REFINE_REASON", rf.failure_reason));
+        } else {
+            Add(s, KeyEnum("REFINE", "PERFORMED", {"PERFORMED", "NOT_PERFORMED"}));
+            Add(s, KeyText("REFINE_DEVICE", rf.on_gpu ? "GPU" : "CPU", true));
+            Add(s, KeyReal("REFINE_SECONDS", rf.seconds, "{:.1f}", true));
+            Add(s, KeyReal("REFINE_D_MIN", rf.d_min, "{:.2f}"));
+            Add(s, KeyReal("REFINE_R_WORK_START", rf.r_work_start, "{:.4f}"));
+            Add(s, KeyReal("REFINE_R_FREE_START", rf.r_free_start, "{:.4f}"));
+            Add(s, KeyInt("REFINE_RIGID_BODIES", rf.rigid_bodies));
+            Add(s, KeyReal("REFINE_R_WORK_PLACEMENT", rf.r_work_placement, "{:.4f}"));
+            Add(s, KeyReal("REFINE_R_FREE_PLACEMENT", rf.r_free_placement, "{:.4f}"));
+            if (rf.restrained) {
+                Add(s, KeyReal("REFINE_R_WORK", rf.r_work, "{:.4f}"));
+                Add(s, KeyReal("REFINE_R_FREE", rf.r_free, "{:.4f}"));
+                Add(s, KeyReal("REFINE_RMSD_BONDS", rf.geometry.rmsd_bonds, "{:.4f}"));
+                if (rf.geometry.metal_bonds > 0)
+                    Add(s, KeyReal("REFINE_RMSD_METAL_BONDS", rf.geometry.rmsd_metal, "{:.4f}"));
+                Add(s, KeyReal("REFINE_RMSD_ANGLES", rf.geometry.rmsd_angles, "{:.2f}"));
+                Add(s, KeyReal("REFINE_RMSD_BONDS_START", rf.geometry_start.rmsd_bonds, "{:.4f}", true));
+                Add(s, KeyReal("REFINE_RMSD_ANGLES_START", rf.geometry_start.rmsd_angles, "{:.2f}", true));
+                Add(s, KeyInt("REFINE_CLASHES", rf.geometry.clashes));
+                Add(s, KeyReal("REFINE_XRAY_WEIGHT", rf.weight, "{:.4g}", true));
+                Add(s, KeyInt("REFINE_ATOMS", rf.atoms));
+                Add(s, KeyInt("REFINE_ATOMS_REFINED", rf.refined_atoms));
+                Add(s, KeyInt("REFINE_RESIDUES_FIXED", rf.fixed_residues));
+                if (!rf.fixed_names.empty()) {
+                    std::string names;
+                    for (const std::string &n : rf.fixed_names)
+                        names += (names.empty() ? "" : " ") + n;
+                    Add(s, KeyText("REFINE_RESIDUES_FIXED_NAMES", names));
+                }
+            }
+            Add(s, KeyReal("REFINE_BULK_SOLVENT_K_SOL", rf.k_sol, "{:.3f}", true));
+            Add(s, KeyReal("REFINE_BULK_SOLVENT_B_SOL", rf.b_sol, "{:.1f}", true));
+            int kinds[5] = {0, 0, 0, 0, 0};
+            for (const DensityBlob &b : rf.blobs)
+                kinds[static_cast<int>(b.kind)]++;
+            Add(s, KeyInt("REFINE_BLOBS", static_cast<int64_t>(rf.blobs.size())));
+            Add(s, KeyInt("REFINE_BLOBS_LIGAND", kinds[static_cast<int>(DensityBlob::Kind::Ligand)]));
+            Add(s, KeyInt("REFINE_BLOBS_WATER", kinds[static_cast<int>(DensityBlob::Kind::Water)]));
+            Add(s, KeyInt("REFINE_BLOBS_ION", kinds[static_cast<int>(DensityBlob::Kind::Ion)]));
+            Add(s, KeyInt("REFINE_BLOBS_MODEL_ERROR", kinds[static_cast<int>(DensityBlob::Kind::ModelError)]));
+            std::string top;
+            for (size_t i = 0; i < std::min<size_t>(rf.blobs.size(), 5); i++) {
+                const DensityBlob &b = rf.blobs[i];
+                top += fmt::format("\n  {:<11} peak {:5.1f} sigma, {:6.1f} A^3, at {:7.2f} {:7.2f} {:7.2f}, {:.1f} A from {}",
+                                   DensityBlobKindName(b.kind), b.peak_sigma, b.volume, b.centroid.x, b.centroid.y,
+                                   b.centroid.z, b.nearest_atom_distance, b.nearest_atom);
+            }
+            Add(s, Prose(fmt::format(
+                    " The placed model was refined against these data: each chain as a rigid body and\n"
+                    " one B per residue, then every atom restrained by the dictionary carried in rugnux, the\n"
+                    " X-ray weight chosen by R-free with the geometry held within bounds. REFINE_ keys describe\n"
+                    " the refined model, which is written as {}_refined_model.cif with its maps; R_WORK and\n"
+                    " R_FREE above remain the model as given. The refinement decided nothing about the\n"
+                    " processing. The strongest unexplained blobs of its difference map ({}_blobs.json):{}",
+                    output_prefix, output_prefix, top.empty() ? std::string(" none") : top)));
+        }
+        if (rf.ok) {
+            const RefinementScore &sc = rf.score_start;
+            Add(s, KeyReal("REFINE_SCORE_R_WORK", sc.r_work, "{:.4f}"));
+            Add(s, KeyReal("REFINE_SCORE_R_FREE", sc.r_free, "{:.4f}"));
+            Add(s, KeyInt("REFINE_SCORE_N_WORK", sc.n_work));
+            Add(s, KeyInt("REFINE_SCORE_N_FREE", sc.n_free));
+            Add(s, KeyReal("REFINE_SCORE_K_OVERALL", sc.k_overall, "{:.5g}", true));
+            Add(s, KeyReal("REFINE_SCORE_B_ISO", sc.b_iso, "{:.2f}", true));
+            Add(s, KeyText("REFINE_SCORE_B_ANISO", fmt::format("{:.2f} {:.2f} {:.2f} {:.2f} {:.2f} {:.2f}", sc.b_aniso[0],
+                                                              sc.b_aniso[1], sc.b_aniso[2], sc.b_aniso[3], sc.b_aniso[4],
+                                                              sc.b_aniso[5]), true));
+            Add(s, KeyReal("REFINE_SCORE_K_SOL", sc.k_sol, "{:.4f}", true));
+            Add(s, KeyReal("REFINE_SCORE_B_SOL", sc.b_sol, "{:.2f}", true));
+            Add(s, KeyReal("REFINE_SCORE_MASK_SPACING", sc.mask_spacing, "{:.3f}", true));
+            Add(s, KeyInt("REFINE_SCORE_HYDROGENS", sc.hydrogens, true));
+            Add(s, KeyReal("REFINE_SCORE_NLL_WORK", sc.nll_work, "{:.1f}", true));
+            Add(s, KeyReal("REFINE_SCORE_NLL_FREE", sc.nll_free, "{:.1f}", true));
+            Add(s, KeyReal("REFINE_SCORE_FOM", sc.fom, "{:.4f}", true));
+            Add(s, KeyReal("REFINE_SCORE_RMSD_BONDS", rf.geometry_start.rmsd_bonds, "{:.4f}", true));
+            Add(s, KeyReal("REFINE_SCORE_RMSZ_BONDS", rf.geometry_start.rmsz_bonds, "{:.3f}", true));
+            Add(s, KeyReal("REFINE_SCORE_RMSD_METAL_BONDS", rf.geometry_start.rmsd_metal, "{:.4f}", true));
+            Add(s, KeyReal("REFINE_SCORE_RMSD_BONDS_ALL", rf.geometry_start.RmsdAllBonds(), "{:.4f}", true));
+            Add(s, KeyReal("REFINE_SCORE_RMSD_ANGLES", rf.geometry_start.rmsd_angles, "{:.3f}", true));
+            Add(s, KeyReal("REFINE_SCORE_RMSZ_ANGLES", rf.geometry_start.rmsz_angles, "{:.3f}", true));
+            if (!sc.shells.empty()) {
+                ReportEntry e;
+                e.kind = ReportEntry::Kind::Table;
+                e.developer_only = true;
+                e.table.columns = {"D_MAX", "D_MIN", "N_WORK", "N_FREE", "R_WORK", "R_FREE"};
+                e.table.text_header = "   D_MAX   D_MIN  N_WORK  N_FREE  R_WORK  R_FREE";
+                for (const RefinementShell &sh : sc.shells) {
+                    e.table.text_rows.push_back(fmt::format("{:8.2f}{:8.2f}{:8d}{:8d}{:8.4f}{:8.4f}", sh.d_max, sh.d_min,
+                                                            sh.n_work, sh.n_free, sh.r_work, sh.r_free));
+                    std::vector<ReportValue> row;
+                    for (double v : {sh.d_max, sh.d_min, double(sh.n_work), double(sh.n_free), sh.r_work, sh.r_free}) {
+                        ReportValue rv;
+                        rv.type = ReportValue::Type::Real;
+                        rv.real = v;
+                        rv.text = fmt::format("{}", v);
+                        row.push_back(rv);
+                    }
+                    e.table.cells.push_back(std::move(row));
+                }
+                Add(s, std::move(e));
+            }
+        }
+    }
+}
+
+// ---------------------------------------------------------------------------- the emitter
+// Populates the document. Nothing here writes to a stream: the order of the FILE is the renderer's
+// business, which is what lets the SUMMARY sit above the sections whose warnings it reports.
+ReportDocument BuildReportDocument(const std::string &output_prefix,
+                                   const std::string &input_file,
+                                   const DiffractionExperiment &experiment,
+                                   const ProcessResult &result,
+                                   const RunProvenance &provenance) {
+    ReportDocument doc;
+    const bool rotation = experiment.IsRotationIndexing();
+    const bool merged = result.has_merge_statistics;
+    doc.warnings = result.warnings;
+    // SUMMARY rows filled by the sections that measure them; empty leaves the row out.
+    std::string beam_centre_row, overload_row, overlap_row;
+
+    // ------------------------------------------------------------------ header block
+    doc.sections.push_back(HeaderSection(output_prefix, input_file, provenance));
+
     // ------------------------------------------------- 1. DATA SET AND GEOMETRY
     {
         ReportSection s;
@@ -752,8 +870,40 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
         Add(s, KeyBool("LATTICE_FOUND", result.consensus_cell.has_value()));
         if (!result.indexing_ambiguity_operators.empty())
             Add(s, KeyText("INDEXING_AMBIGUITY_OPERATORS", result.indexing_ambiguity_operators));
+        // Serial stills: the indexing ambiguity from the data alone - deciding the merge where no reference
+        // or model was given, otherwise measured against the reference's answer (REINDEXED is then the
+        // number of crystals on which the two disagree).
+        if (result.ambiguity_reference_free) {
+            Add(s, KeyText("INDEXING_AMBIGUITY_RESOLVED",
+                           result.ambiguity_reference_free_applied ? "data" : "reference"));
+            Add(s, KeyInt("AMBIGUITY_CRYSTALS", static_cast<int64_t>(result.ambiguity_crystals)));
+            Add(s, KeyInt(result.ambiguity_reference_free_applied ? "AMBIGUITY_REINDEXED"
+                                                                  : "AMBIGUITY_DATA_DISAGREES",
+                          static_cast<int64_t>(result.ambiguity_reindexed)));
+            Add(s, KeyReal("AMBIGUITY_SEPARATION_SIGMA", result.ambiguity_separation_sigma, "{:.2f}"));
+            Add(s, KeyReal("AMBIGUITY_DECIDED_FRACTION", result.ambiguity_decided_fraction, "{:.3f}"));
+            Add(s, KeyReal("AMBIGUITY_TIME_S", result.ambiguity_time_s, "{:.3f}", /*dev=*/true));
+        }
         if (result.consensus_cell.has_value())
             Add(s, KeyText("UNIT_CELL_CONSTANTS", CellString(*result.consensus_cell)));
+        // The cell's e.s.d.s as XDS's E.S.D. OF CELL PARAMETERS (CellEsd.h): the written one (the .ins's
+        // ZERR, the mmCIF's _cell.*_esd) is per parameter the larger of the least-squares e.s.d. and the
+        // scatter of the cells fitted on blocks of frames.
+        if (result.cell_esd.has_value()) {
+            const CellEsd &e = *result.cell_esd;
+            const auto esd_string = [](const std::array<double, 6> &v) {
+                return fmt::format("{:.2E} {:.2E} {:.2E} {:.2E} {:.2E} {:.2E}", v[0], v[1], v[2], v[3], v[4], v[5]);
+            };
+            Add(s, KeyText("CELL_ESD", esd_string(e.esd)));
+            Add(s, KeyText("CELL_ESD_LSQ", esd_string(e.esd_lsq)));
+            if (e.esd_blocks)
+                Add(s, KeyText("CELL_ESD_BLOCKS", esd_string(*e.esd_blocks)));
+            Add(s, KeyInt("CELL_ESD_BLOCK_COUNT", e.blocks));
+            Add(s, KeyInt("CELL_ESD_REFLECTIONS", e.reflections));
+            Add(s, KeyInt("CELL_ESD_OBSERVATIONS", e.observations, /*dev=*/true));
+            Add(s, KeyText("CELL_ESD_THETA_RANGE_DEG", fmt::format("{:.2f} {:.2f}", e.theta_min_deg, e.theta_max_deg)));
+            Add(s, KeyText("CELL_DSPACING_FIT", CellString(e.fitted), /*dev=*/true));
+        }
         // Kabsch's sigma_M, the Gaussian e.s.d. of the rocking width in degrees - XDS's
         // REFLECTING_RANGE_E.S.D. - that the merge computed partiality from.
         if (std::isfinite(result.mosaicity_deg)) {
@@ -2739,6 +2889,10 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
                         mp.t_rotation, mp.t_translation, mp.t_rescore, mp.t_null, mp.t_domains, mp.hand_check.seconds), true));
             }
         }
+        // The placed model refined (Refinement.h; always, where a model is placed). Keys of their own: R_WORK / R_FREE above stay the
+        // unrefined model's.
+        if (result.refinement.has_value())
+            AddRefinementKeys(s, *result.refinement, output_prefix);
         doc.sections.push_back(std::move(s));
     }
 
@@ -2926,7 +3080,7 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
                     sig += fmt::format("   ISa {:.1f}", result.error_model_isa);
                 row("Signal", sig);
                 if (std::isfinite(o.cc_anom))
-                    row("Anomalous", o.cc_anom > 0.15
+                    row("Anomalous", o.cc_anom > CC_ANOM_SIGNAL
                             ? fmt::format("signal present (CC_anom {:.2f})", o.cc_anom)
                             : fmt::format("no usable signal (CC_anom {:.2f})", o.cc_anom));
                 const auto &an = result.merge_statistics.anisotropy;
@@ -3062,6 +3216,42 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
 // -------------------------------------------------------------------------- the text rendering
 // Reads only from the document. Nothing here decides what the report SAYS; it decides only how the
 // text file looks, which is what makes a second rendering a second function rather than a fork.
+// --mode refine: the header, what the input was and what had to be made of it, and the refinement's keys.
+ReportDocument BuildRefineReportDocument(const std::string &output_prefix, const std::string &input_file,
+                                         const std::string &model_file, const RefineOnlyResult &r,
+                                         const RunProvenance &provenance) {
+    ReportDocument doc;
+    doc.sections.push_back(HeaderSection(output_prefix, input_file, provenance));
+    const RefinementResult &rf = r.refinement;
+    ReportSection s;
+    s.title = "1. REFINEMENT";
+    Add(s, KeyText("MODEL_FILE", model_file));
+    Add(s, KeyText("SPACE_GROUP", r.space_group));
+    Add(s, KeyReal("WAVELENGTH", r.wavelength_A, "{:.5f}"));
+    Add(s, KeyInt("REFINE_REFLECTIONS", r.reflections));
+    Add(s, KeyInt("REFINE_FREE_REFLECTIONS", r.free_reflections));
+    Add(s, KeyBool("REFINE_FRENCH_WILSON", r.french_wilson));
+    Add(s, KeyEnum("REFINE_FREE_FLAGS", r.free_flags_generated ? "GENERATED" : "FILE", {"FILE", "GENERATED"}));
+    if (r.d_min_limit > 0)
+        Add(s, KeyReal("REFINE_D_MIN_LIMIT", r.d_min_limit, "{:.3f}"));
+    AddRefinementKeys(s, rf, output_prefix);
+    doc.sections.push_back(std::move(s));
+    doc.verdict = rf.ok ? "OK" : "FAILED";
+    if (!rf.ok)
+        doc.verdict_text = "Refinement did not run: " + rf.failure_reason;
+    else if (r.score_only)
+        doc.verdict_text = fmt::format("Scored as given, nothing refined: R-work {:.4f}, R-free {:.4f}.",
+                                       rf.r_work_start, rf.r_free_start);
+    else
+        doc.verdict_text = fmt::format("Refined: R-work {:.4f}, R-free {:.4f} (as given {:.4f}, {:.4f}).",
+                                       rf.restrained ? rf.r_work : rf.r_work_placement,
+                                       rf.restrained ? rf.r_free : rf.r_free_placement, rf.r_work_start, rf.r_free_start);
+    Add(doc.sections.back(), KeyEnum("VERDICT", doc.verdict, {"OK", "WARNINGS", "UNUSABLE", "FAILED"}));
+    Add(doc.sections.back(), KeyText("VERDICT_TEXT", doc.verdict_text));
+    doc.summary_rows.push_back({"Refinement", doc.verdict_text});
+    return doc;
+}
+
 std::string RenderReportText(const ReportDocument &doc, bool developer) {
     std::ostringstream os;
     // Everything that is not a `KEY= value` line and not blank is written as a `#` comment, so a
diff --git a/rugnux/ResultReport.h b/rugnux/ResultReport.h
index bdbbe1b72..5078a22cf 100644
--- a/rugnux/ResultReport.h
+++ b/rugnux/ResultReport.h
@@ -9,6 +9,7 @@
 #include "../common/Logger.h"
 #include "ReportDocument.h"
 #include "Rugnux.h"
+#include "RugnuxRefine.h"
 
 // <prefix>_report.txt - what the run DETERMINED, written next to the .mtz/.cif/.hkl on every run
 // that has an output prefix. Modelled on XDS's CORRECT.LP: prose and tables a crystallographer
@@ -55,6 +56,9 @@ inline constexpr const char *RUGNUX_ACKNOWLEDGEMENT =
         "are credited in ACKNOWLEDGEMENT.md, with the licence terms in LICENSE and\n"
         "THIRD_PARTY_NOTICES.md - all three ship with this package.";
 
+// The overall CC_anom above which the summary says the data carry anomalous signal.
+inline constexpr double CC_ANOM_SIGNAL = 0.15;
+
 // The emitter. Populates the result object every rendering reads from; it writes no text itself.
 ReportDocument BuildReportDocument(const std::string &output_prefix,
                                    const std::string &input_file,
@@ -62,6 +66,11 @@ ReportDocument BuildReportDocument(const std::string &output_prefix,
                                    const ProcessResult &result,
                                    const RunProvenance &provenance = {});
 
+// --mode refine's report: the header, the input as read and the REFINE_ keys.
+ReportDocument BuildRefineReportDocument(const std::string &output_prefix, const std::string &input_file,
+                                         const std::string &model_file, const RefineOnlyResult &result,
+                                         const RunProvenance &provenance = {});
+
 // The text rendering of that document - XDS-style prose, tables and `KEY= value` lines. Reads only
 // from the document, so a second rendering is a second function of the same input.
 std::string RenderReportText(const ReportDocument &doc, bool developer);
diff --git a/rugnux/Rugnux.cpp b/rugnux/Rugnux.cpp
index e7aa66f59..6eb5ee2f4 100644
--- a/rugnux/Rugnux.cpp
+++ b/rugnux/Rugnux.cpp
@@ -147,7 +147,14 @@ RotationScaleWalk WalkRotationScale(double first_fit,
     for (int round = 0; round < max_rounds && next != walk.scale; ++round) {
         const ValidationSpotEvidence e = index_at(next);
         walk.trail += fmt::format(", {:.5f}: {:.1f}%", next, score(e));
-        if (!ValidationEvidencePrefers(walk.evidence, e))
+        // The stored angles are left only where the validation frames prefer the fit. Once they are
+        // left, the refit is the estimate and the frames only guard it: a first pass indexes through a
+        // degree of drift late in the sweep, so they can score two scales alike while integration at
+        // the less refitted one loses half its signal. A refit step is refused only where they score
+        // it worse.
+        const bool refused = walk.scale == 1.0f ? !ValidationEvidencePrefers(walk.evidence, e)
+                                                : ValidationEvidencePrefers(e, walk.evidence);
+        if (refused)
             break;
         const double step = next - walk.scale;
         walk.scale = next;
@@ -493,14 +500,19 @@ ProcessResult Rugnux::Run(RugnuxObserver *observer) {
     if (result.consensus_cell)
         header_experiment.SetUnitCell(*result.consensus_cell);
     result.beam_centre_need_pxl = BeamCenterNeed_pxl(header_experiment);
-#ifdef JFJOCH_USE_CUDA
-    // The engines went with their passes; the pinned buffers they kept for each other go with the run.
-    const size_t pinned_bytes = cuda_release_pinned_pool();
-    Logger("Rugnux").Debug("Pinned host memory kept between engines, released: {:.1f} MB", pinned_bytes / 1e6);
-#endif
     return result;
 }
 
+void Rugnux::ReleasePinnedPool() {
+#ifdef JFJOCH_USE_CUDA
+    Logger logger("Rugnux");
+    TimingMark mark(logger, "pinned pool release");
+    const size_t bytes = cuda_release_pinned_pool();
+    mark.Stop();
+    logger.Debug("Pinned host memory kept between engines, released: {:.1f} MB", bytes / 1e6);
+#endif
+}
+
 void Rugnux::StartNearTieRecheck(std::shared_ptr<Rugnux> run, bool geometry_prepass) {
     // The pass again, up to its first pass, as the probe it would be: the same inputs, no memo to
     // answer from, nothing started beside it.
@@ -780,6 +792,8 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
     ProcessResult result;
     TimingMark pass_mark(logger, geometry_prepass ? "pass (geometry pre-pass)"
                                  : write_output ? "pass (output)" : "pass (probe)");
+    // Started where the pass returns: the time its locals - engines, indexers, outcomes - take to go.
+    std::optional<TimingMark> teardown_mark;
     // Only a pass that makes the result is shown as steps; a probe pass is part of the step that ran it.
     steps_ = (write_output || geometry_prepass) ? observer : nullptr;
 
@@ -1118,6 +1132,16 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
     std::atomic<uint64_t> total_uncompressed_bytes = 0;
     EndMessage end_msg;
     std::future<MtzTable> unmerged_mtz;
+    // The pass's integrated observations - gigabytes, in mappings of their own (ReflectionArena) - are handed
+    // back on a thread of their own as the pass returns: nothing after it reads them, and unmapping them was most
+    // of the time the pass took to end. The unmerged table made from them beside the refinement goes first.
+    const auto retire_outcomes = [&] {
+        retired_outcomes_ = std::async(std::launch::async,
+                [i = std::move(indexer), u = std::move(unmerged_mtz)]() mutable {
+            u = {};
+            i.reset();
+        }).share();
+    };
     PipelineLocals p{
             .logger = logger, .result = result, .observer = observer,
             .geometry_prepass = geometry_prepass, .full = full, .calibration = calibration,
@@ -1203,8 +1227,11 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
             for (const auto &note : p.postrefine_notes)
                 Note(note);
         }
-        if (finished)
+        if (finished) {
+            retire_outcomes();
+            teardown_mark.emplace(logger, "pass teardown");
             return result;
+        }
     }
 
     TimingMark output_mark(logger, "outputs");
@@ -1298,6 +1325,12 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
         end_msg.image_scale_mosaicity = scaling.mosaicity_deg;
     }
 
+    if (result.cell_esd) {
+        const std::array<double, 6> &e = result.cell_esd->esd;
+        end_msg.unit_cell_esd = UnitCell{static_cast<float>(e[0]), static_cast<float>(e[1]), static_cast<float>(e[2]),
+                                         static_cast<float>(e[3]), static_cast<float>(e[4]), static_cast<float>(e[5])};
+    }
+
     if (sink)
         sink->End(end_msg);
     result.end_message = end_msg;
@@ -1341,5 +1374,7 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
         TimingMark mark(logger, "leftover-lattice census wait");
         result.leftover_lattices = census_future.get();
     }
+    retire_outcomes();
+    teardown_mark.emplace(logger, "pass teardown");
     return result;
 }
diff --git a/rugnux/Rugnux.h b/rugnux/Rugnux.h
index 1441847a7..8ce4222a2 100644
--- a/rugnux/Rugnux.h
+++ b/rugnux/Rugnux.h
@@ -30,10 +30,13 @@
 #include "../image_analysis/scale_merge/Merge.h"   // MergeStatistics
 #include "../image_analysis/scale_merge/TwinningAnalysis.h"   // TwinningAnalysisResult
 #include "../image_analysis/scale_merge/CentreOfSymmetry.h"   // CentreOfSymmetryResult
+#include "../image_analysis/scale_merge/StillsPartialityRefine.h"   // StillsPartialityRefine::RunWidth
 #include "../image_analysis/scale_merge/TranslationalNCS.h"   // TranslationalNCSResult
 #include "../image_analysis/indexing/HarmonicContamination.h"  // HarmonicContaminationResult
+#include "../image_analysis/geom_refinement/CellEsd.h"   // CellEsd
 #include "../image_analysis/structure_refinement/ModelValidation.h"                  // ModelValidationResult
 #include "../image_analysis/structure_refinement/MolecularReplacement.h"            // MolecularReplacementResult
+#include "../image_analysis/structure_refinement/Refinement.h"                      // RefinementResult
 #include "../image_analysis/indexing/LeftoverLattices.h"                 // LeftoverLatticeCensus
 #include "ReportDocument.h"                   // ReportWarning, PathologyCode
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"   // SearchSpaceGroupResult
@@ -260,6 +263,13 @@ struct ProcessConfig {
     // did not place, is searched for anyway.
     bool force_mr = false;
 
+    // A placed model refined against the merge it was placed on - each chain as a rigid body and a B per residue,
+    // then every atom restrained (Refinement.h) - and what it leaves in the difference map listed (DensityBlobs.h).
+    // Reported in keys of its own; it decides nothing about the processing or the files the run writes otherwise.
+    // On in the rugnux CLI (--no-refine turns it off), the viewer and the broker's live mode: giving a model is the
+    // opt-in.
+    bool refine = false;
+
     // --finalist-ledger: report-only symmetry evidence table (and the twin-immune zones), folded from
     // a merge of its own in P1 that only this flag makes.
     bool finalist_ledger = false;
@@ -330,7 +340,8 @@ std::pair<double, double> ValidationEvidenceDifference(const ValidationSpotEvide
 // stops them tracking the rest, so one fit reads only part of the error. So: index the lattice under
 // the fitted scale and under the angles in hand; where the fitted one scores better on the validation
 // frames (ValidationEvidencePrefers), adopt it, fit again there and repeat. The stored angles (k = 1)
-// are the first hypothesis, and stand unless the evidence moves the run off them.
+// are the first hypothesis, and stand unless the evidence moves the run off them; once off them, a
+// refit step is taken unless the frames score it worse.
 //   index_at(k): the validation evidence of the lattice indexed with the stored angles scaled by k
 //   refit_at(k): the scale the post-refinement fits on reflections integrated at k, relative to k;
 //                empty where it fitted none
@@ -383,6 +394,7 @@ struct MergedOutput {
     ErrorModelReport error_model;
     TwinningAnalysisResult twinning;             // a twin hypothesis' law and fraction, for its mmCIF
     std::vector<ScaledFull> scaled_fulls;        // the .hkl's records, where the merge made them (rotation)
+    std::optional<CellEsd> cell_esd;             // the cell's e.s.d.s: the mmCIF's _cell.*_esd and the .ins's ZERR
 };
 
 // An atomic model as placed against the data (<prefix>_model.cif, WritePlacedModel): `cell` and
@@ -403,6 +415,9 @@ struct RugnuxOutputs {
     std::shared_ptr<ModelMaps> model_prior_maps;              // the same at <prefix>_mr
     std::optional<PlacedModelOutput> placed_model;            // <prefix>_model.cif/.pdb
     std::optional<PlacedModelOutput> model_prior_placed_model;   // <prefix>_mr_model.cif/.pdb
+    std::optional<PlacedModelOutput> refined_model;           // <prefix>_refined_model.cif/.pdb (ProcessConfig::refine)
+    std::shared_ptr<ModelMaps> refined_maps;                  // <prefix>_refined_maps.mtz
+    std::optional<std::vector<DensityBlob>> blobs;            // <prefix>_blobs.json
     std::optional<MtzTable> unmerged;                         // <prefix>_unmerged.mtz
     std::optional<MtzTable> unmerged_partials;                // <prefix>_unmerged_partials.mtz
     std::string detector_jpeg;                                // <prefix>_detector.jpg; empty: none drawn
@@ -469,6 +484,8 @@ struct ProcessResult {
     // file's. The report's XDS keyword block reads it. Empty on stills.
     std::optional<Coord> used_rotation_axis;
     std::optional<UnitCell> consensus_cell;
+    // The e.s.d.s of consensus_cell (CellEsd.h); rotation only.
+    std::optional<CellEsd> cell_esd;
     // The centring `consensus_cell` is written in; empty when nothing named one (the stills path
     // averages per-image cells and has no lattice search behind them). A conventional cell says
     // nothing about size on its own - a centred one is an exact integer multiple of its primitive
@@ -646,6 +663,18 @@ struct ProcessResult {
     // it matters only against other data. Empty where there is none, or where it was resolved.
     std::string indexing_ambiguity_operators;
 
+    // Serial stills: the indexing ambiguity resolved from the data alone (ReferenceFreeReindex.h), where
+    // the cell and space group admit one. Without a reference or model it decides the merge; with one, it
+    // is only measured against the reference's answer (ambiguity_reference_free_applied = false, and
+    // ambiguity_reindexed is then the number of crystals on which the two disagree).
+    bool ambiguity_reference_free = false;
+    bool ambiguity_reference_free_applied = false;
+    size_t ambiguity_crystals = 0;
+    size_t ambiguity_reindexed = 0;
+    double ambiguity_separation_sigma = NAN;
+    double ambiguity_decided_fraction = NAN;
+    double ambiguity_time_s = NAN;
+
     // The same analysis measured BEFORE the space group was decided, on the subgroup merge the search
     // was given. It is the only twinning number a promotion cannot contaminate: once a higher Laue
     // class is adopted, its own twinning test can say no more than "no twin law exists inside this
@@ -711,6 +740,8 @@ struct ProcessResult {
     std::string model_placement;
     // What molecular replacement found, where it ran; failure_reason says why where it could not.
     std::optional<MolecularReplacementResult> model_prior;
+    // What refinement made of the placed model; unset where nothing was placed (or refine was off).
+    std::optional<RefinementResult> refinement;
     // The file suffix the model's choice of another group or the twin hypothesis' subgroup is written under
     // (_mr), and that group; empty where nothing was.
     std::string model_prior_file_suffix;
@@ -934,6 +965,8 @@ class Rugnux {
         CancelFlag &operator=(bool v) { flag->store(v); return *this; }
         // A flag of its own that cancelling the run still sets.
         CancelFlag Own() const { CancelFlag f; f.run = flag; return f; }
+        // The flag Cancel() on the run sets, for work that takes a plain atomic (RefinementSettings::cancel).
+        const std::atomic<bool> *RunFlag() const { return run ? run.get() : flag.get(); }
     };
     CancelFlag cancelled_;
     // fast_live: the last pass that ran to its end. Where a cancel cuts the pass after it short, Run()
@@ -964,6 +997,11 @@ class Rugnux {
     // describes neither geometry. The two travel together or not at all.
     std::optional<std::array<float, 5>> prepass_detector_geometry_;
 
+    // The space group a search of the geometry pre-pass's P1 merge finds. A prediction only: the canonical
+    // pass merges in it ahead, on a copy of its engine, and keeps that merge only where its own decision
+    // lands on the same group on the same ingest (ScaleMergeAndSymmetry). It decides nothing.
+    std::shared_future<std::optional<gemmi::SpaceGroup>> predicted_group_;
+
     // The goniometer rotation scale the run adopted (WalkRotationScale, in RunAllPasses), applied to the
     // second pass's goniometer - and, while the walk runs, the scale its current probe pass is at.
     // Empty where the stored angles stand.
@@ -1074,6 +1112,9 @@ class Rugnux {
     // The pixels the pre-scan's own frames show to be defective (HotPixelFinder) are measured once,
     // on the pre-scan that also measures the width, and stay in pixel_mask_ for every pass after it.
     bool hot_pixels_measured_ = false;
+    // The polarization the pre-scan took from the background where it turned the stated plane, kept with
+    // the shadow it was decided with (PreScan).
+    std::optional<float> polarization_from_background_;
     // The integration radii in force before the measured spot width widened them, so a widening that
     // turns out to cost data can be given back exactly rather than to a written-down default.
     std::optional<BraggIntegrationSettings> bragg_before_adaptive_;
@@ -1449,6 +1490,12 @@ class Rugnux {
     // Stills: the cell the user gave (-C / reference), kept apart from the one the geometry refinement
     // writes into experiment_. See RefineStillsGeometry.
     std::optional<UnitCell> stills_user_cell_;
+    // Stills: the rocking width measured before the image pass, on a sample of its frames, which every
+    // frame is then predicted through (ImagePass) and the partialities are computed from (ScaleMerge).
+    std::optional<StillsPartialityRefine::RunWidth> stills_run_width_;
+    static constexpr double STILLS_WINDOW_SIGMAS = 2.0;   // the window's half-width, in rocking widths
+    static constexpr int STILLS_WINDOW_MIN_FRAMES = 2000;  // the sample: a tenth of the run, at least this
+    static constexpr int STILLS_WINDOW_FRACTION = 10;
     // Stills: where the frames' pixel values pile up, against the file's saturation limit (see there).
     static constexpr int SATURATION_SAMPLE_FRAMES = 40;
     saturation_ceiling::Histogram SampleSaturation(int start_image, int images_to_process);
@@ -1566,6 +1613,12 @@ public:
 
     // Runs the configured workflow to completion or until Cancel(). Throws on setup failure.
     ProcessResult Run(RugnuxObserver *observer = nullptr);
+
+    // The pinned host buffers the engines of a run kept for each other (CUDAMemHelpers.h), handed back to the
+    // driver. Not part of Run: a process that outlives the run (the broker, the viewer) calls it once the
+    // results are out, as it takes a tenth of a second the user would otherwise wait for; one that ends
+    // after the run does not need it.
+    static void ReleasePinnedPool();
     // The pre-scan's powder measurement, for a report on a run that ended without a result.
     const PowderRings &GetPowderRings() const { return powder_; }
 
@@ -1575,4 +1628,8 @@ public:
     // pass cut short gives way to the last complete one.
     void Cancel() { cancelled_ = true; }
     bool IsCancelled() const { return cancelled_; }
+
+private:
+    // The last pass's integrated observations being handed back (RunPipeline); last, so it is waited for first.
+    std::shared_future<void> retired_outcomes_;
 };
diff --git a/rugnux/RugnuxCommandLine.cpp b/rugnux/RugnuxCommandLine.cpp
index 9bdb53dd1..52167a8ea 100644
--- a/rugnux/RugnuxCommandLine.cpp
+++ b/rugnux/RugnuxCommandLine.cpp
@@ -86,6 +86,8 @@ std::string RugnuxCommandLine(const ProcessConfig &config,
         }
         if (config.model)
             add(config.force_mr ? "--mr" : "--model", config.model->name);
+        if (config.model && !config.refine)
+            args.emplace_back("--no-refine");
     }
     if (config.start_image != 0)
         add("-s", std::to_string(config.start_image));
diff --git a/rugnux/RugnuxDefaults.cpp b/rugnux/RugnuxDefaults.cpp
index 352e11050..8ef13bbb4 100644
--- a/rugnux/RugnuxDefaults.cpp
+++ b/rugnux/RugnuxDefaults.cpp
@@ -11,6 +11,10 @@ namespace {
     constexpr double SMOOTH_G_DEG = 5.0;
     // Per-observation outlier rejection for the rotation combine, in sigma.
     constexpr double REJECT_OUTLIERS_NSIGMA = 6.0;
+    // The same for the stills merge, set wider: a still's partials scatter with heavier tails than the
+    // error model's normal band, and what has to go - a powder grain or a neighbour's spot in the box - sits
+    // tens to hundreds of sigma out.
+    constexpr double REJECT_OUTLIERS_NSIGMA_STILLS = 10.0;
 }
 
 void ApplyRugnuxExperimentDefaults(DiffractionExperiment &experiment) {
@@ -52,12 +56,20 @@ ScalingSettings RugnuxDefaultScalingSettings(bool rotation) {
     // I/sigma floor and falls back to P1.
     s.MinCapturedFraction(rotation ? 0.7 : 0.0);
 
+    // A still's intensity is divided by the partiality its excitation error gives. Below about one half
+    // the error of that model (the run's curve is an average over crystals, and mis-oriented crystals
+    // leave a floor far out on its tail) dominates, and dividing by a small p turns it into a bias that
+    // no variance term weights away. So stills merge only the reflections the model calls at least half
+    // recorded; rotation sums its partials into fulls and keeps the permissive floor.
+    s.MinPartiality(rotation ? 0.02 : 0.5);
+
     // Capture-aware systematic sigma: down-weights the over-extrapolated under-captured fulls.
     s.CaptureUncertaintyCoeff(rotation ? 1.0 : 0.0);
 
     // A single un-rejected artifact wrecks the intensity-correlation and second-moment statistics the
-    // space-group and twinning tests are built on.
-    s.OutlierRejectNsigma(rotation ? REJECT_OUTLIERS_NSIGMA : 0.0);
+    // space-group and twinning tests are built on. On stills one powder grain or neighbour's spot in a
+    // reflection's box can be its whole merged intensity, whatever its multiplicity.
+    s.OutlierRejectNsigma(rotation ? REJECT_OUTLIERS_NSIGMA : REJECT_OUTLIERS_NSIGMA_STILLS);
 
     // Run the de-novo space-group search a second time on a merge of only the well-measured
     // observations and keep whichever found more symmetry. It cannot lose symmetry, so an imperfect cut
diff --git a/rugnux/RugnuxFirstPass.h b/rugnux/RugnuxFirstPass.h
index f055a6e11..024164fc9 100644
--- a/rugnux/RugnuxFirstPass.h
+++ b/rugnux/RugnuxFirstPass.h
@@ -80,6 +80,8 @@ struct Rugnux::FirstPassRun {
     FirstPass SubLatticeHypothesis(FirstPass best);
     FirstPass TwinCompositeHypothesis(FirstPass best);
     FirstPass Pass1Fallback(FirstPass best);
+    // Pass 1's lattice refit at the rotation scale the pass runs at (see Pass1Fallback).
+    RotationIndexerResult RefitAtScale(RotationIndexerResult pass1_lattice);
     std::optional<FirstPass> FirstPassLadder(int score_before, int min_gain, int min_score);
 
     // The pooled spots of the validation frames on the lattice the pass ended on, and their share.
diff --git a/rugnux/RugnuxFirstPassRescues.cpp b/rugnux/RugnuxFirstPassRescues.cpp
index 554ca3fb3..9784a8464 100644
--- a/rugnux/RugnuxFirstPassRescues.cpp
+++ b/rugnux/RugnuxFirstPassRescues.cpp
@@ -11,6 +11,7 @@
 #include "../image_analysis/hot_pixels/HotPixels.h"
 #include "../image_analysis/SensorAbsorption.h"
 #include "DiagnosticOutput.h"
+#include "../image_analysis/geom_refinement/XtalOptimizer.h"
 
 #include <algorithm>
 #include <atomic>
@@ -1009,6 +1010,55 @@ auto Rugnux::FirstPassRun::SubLatticeHypothesis(FirstPass best) -> FirstPass {
     return best;
 }
 
+// Pass 1's lattice refit at the rotation scale this pass runs at (see Pass1Fallback): cell and
+// orientation, at pass 1's detector geometry and with the detector and the axis held, on the spots of
+// the validation frames of the whole sweep.
+auto Rugnux::FirstPassRun::RefitAtScale(RotationIndexerResult pass1_lattice) -> RotationIndexerResult {
+    const UnitCell before = pass1_lattice.lattice.GetUnitCell();
+    const std::vector<int> frames = AllValidationFrames();
+    PrefetchSpots(frames);
+    // XtalOptimizer reads a frame's angle off its place in the list, so the list is indexed by image.
+    std::vector<std::vector<SpotToSave>> spots;
+    for (const int f : frames) {
+        if (f >= static_cast<int>(spots.size()))
+            spots.resize(f + 1);
+        spots[f] = spot_cache.at(f);
+    }
+    XtalOptimizerData d{
+        .geom = pass1_lattice.geom,
+        .latt = pass1_lattice.lattice,
+        .crystal_system = pass1_lattice.search_result.system == gemmi::CrystalSystem::Trigonal
+                          ? gemmi::CrystalSystem::Hexagonal : pass1_lattice.search_result.system,
+        .min_spots = rx.experiment_.GetIndexingSettings().GetViableCellMinSpots(),
+        .max_length_A = 1.2f * static_cast<float>(std::max({before.a, before.b, before.c})),
+        // The indexers' bounds, as RotationIndexer::RefineConstrained sets them.
+        .min_angle_deg = 30.0f,
+        .max_angle_deg = 150.0f,
+        .refine_beam_center = false,
+        .refine_detector_angles = false,
+        .refine_rotation_axis = false,
+        .index_ice_rings = false,
+        .max_iterations = 50,
+        .axis = pass1_lattice.axis
+    };
+    if (!XtalOptimizer(d, spots, 4)) {
+        logger.Info("Two-pass: pass-1's lattice refit at rotation scale {:.5f} on {} validation frames did not "
+                    "converge - pass-1's lattice is kept as it is", *rx.prepass_rotation_scale_, frames.size());
+        return pass1_lattice;
+    }
+    RotationIndexerResult refit = pass1_lattice;
+    refit.lattice = d.latt;
+    const int n_before = CountIndexed(*indexer, pass1_lattice, frames);
+    const int n_after = CountIndexed(*indexer, refit, frames);
+    const UnitCell uc = d.latt.GetUnitCell();
+    logger.Info("Two-pass: pass-1's lattice refit at rotation scale {:.5f} on {} validation frames: {:.3f} {:.3f} "
+                "{:.3f} {:.2f} {:.2f} {:.2f} from {:.3f} {:.3f} {:.3f} {:.2f} {:.2f} {:.2f}, indexing {} of them "
+                "against {} - {}", *rx.prepass_rotation_scale_, frames.size(), uc.a, uc.b, uc.c, uc.alpha, uc.beta,
+                uc.gamma, before.a, before.b, before.c, before.alpha, before.beta, before.gamma, n_after, n_before,
+                n_after >= n_before ? "taken" : "refused");
+    return n_after >= n_before ? refit : pass1_lattice;
+}
+
 // A lattice that indexes almost none of the validation frames is not this crystal's lattice.
 // Forcing it anyway integrates every image against it; the few partials that survive yield no
 // fulls in the 3D combine, and the run then dies inside the merge complaining about resolution -
@@ -1033,6 +1083,13 @@ auto Rugnux::FirstPassRun::Pass1Fallback(FirstPass best) -> FirstPass {
     // uncorrected angles back (the same repair as the supercell re-run in RunAllPasses).
     if (rx.prepass_rotation_scale_ && pass1_lattice.axis)
         pass1_lattice.axis = ScaleRotation(*pass1_lattice.axis, *rx.prepass_rotation_scale_);
+    // Pass 1's cell and orientation were fitted at the angles pass 1 ran at, and where the run now
+    // tries another rotation scale, a stage that turned at the wrong rate has put part of that error
+    // into the cell: carried as it is, the cell undoes the scale it is integrated at. So refit them at
+    // the angles this pass uses, on the validation frames of the whole sweep - the lattice pass 1
+    // chose, not a new one - and keep the refit where it indexes no fewer of those frames.
+    if (rx.prepass_rotation_scale_ && pass1_lattice.axis)
+        pass1_lattice = RefitAtScale(std::move(pass1_lattice));
     // Pass 1's lattice was FITTED at pass 1's detector distance, and this pass
     // integrates at the post-refined one. Re-scoring it here is not the same as
     // re-fitting it: a real-space cell is measured against the distance the spots were
diff --git a/rugnux/RugnuxImagePass.cpp b/rugnux/RugnuxImagePass.cpp
index 24cee59e4..92edbe15f 100644
--- a/rugnux/RugnuxImagePass.cpp
+++ b/rugnux/RugnuxImagePass.cpp
@@ -255,7 +255,27 @@ void Rugnux::ImagePass(PipelineLocals &p) {
     // A pre-pass of the pre-pass subset (prepass_subset_only_) integrates its frames and no other.
     const std::vector<bool> subset = prepass_subset_only_ ? PrepassSubset(prepass_images) : std::vector<bool>();
 
-    auto full_worker = [&]() {
+    // Stills: the window each frame predicts through. Twice the frame's own profile radius is one width at
+    // every resolution and differs eightfold between frames, while the rocking curve widens with d*: it
+    // predicted five to eight widths at low resolution, mostly empty, and cut the curve at one or two at
+    // high resolution, so the partials there were never integrated. So the run's width is measured first,
+    // on a sample of the frames integrated the old way (MeasureRunWidth, as the merge measures it), and
+    // every frame is then predicted through STILLS_WINDOW_SIGMAS of it.
+    std::vector<int> window_frames;
+    const bool stills_window = full && per_image_analysis && !calibration && !geometry_prepass && indexer
+                               && !experiment_.IsRotationIndexing() && config_.spot_finding.indexing
+                               && experiment_.GetScalingSettings().GetStillsPartialityRefine();
+    if (stills_window) {
+        stills_run_width_.reset();
+        indexer->SetStillsWindow(std::nullopt);
+        const int n_sample = std::min(images_to_process,
+                                      std::max(STILLS_WINDOW_MIN_FRAMES, images_to_process / STILLS_WINDOW_FRACTION));
+        for (int j = 0; j < n_sample; ++j)
+            window_frames.push_back(static_cast<int>(static_cast<int64_t>(j) * images_to_process / n_sample));
+    }
+    std::atomic<size_t> next_window_frame = 0;
+
+    auto full_worker_impl = [&](bool measure) {
         pin_gpu();   // round-robin per worker thread; must precede engine construction
         // Before the analysis engine, which page-locks these bytes for its uploads and unregisters
         // them when it is destroyed: it must not outlive the buffer it was given.
@@ -272,7 +292,13 @@ void Rugnux::ImagePass(PipelineLocals &p) {
             analysis.CountCrowdingAt(*crowding_at);
 
         while (!cancelled_) {
-            const int ordinal = next_ordinal.fetch_add(1);
+            int ordinal;
+            if (measure) {
+                const size_t j = next_window_frame.fetch_add(1);
+                if (j >= window_frames.size()) break;
+                ordinal = window_frames[j];
+            } else
+                ordinal = next_ordinal.fetch_add(1);
             const int image_idx = start_image + ordinal * config_.stride;
             if (image_idx >= loop_end) break;
             if (!subset.empty() && !subset[ordinal])
@@ -320,6 +346,8 @@ void Rugnux::ImagePass(PipelineLocals &p) {
             // rather than merge what the machine dropped.
             indexer->RethrowIndexerError();
             pinned.reset();
+            if (measure)
+                continue;
             msg.processing_time_s = std::chrono::duration<float>(std::chrono::steady_clock::now() - t0).count();
             msg.run_number = experiment_.GetRunNumber();
             msg.run_name = experiment_.GetRunName();
@@ -353,6 +381,8 @@ void Rugnux::ImagePass(PipelineLocals &p) {
             if (observer) observer->OnProgress(done, images_to_process);
         }
 
+        if (measure)
+            return;
         {
             std::lock_guard lock(harmonic_m);
             harmonic_evidence.Add(worker_harmonic);
@@ -375,6 +405,7 @@ void Rugnux::ImagePass(PipelineLocals &p) {
         bragg_overlapped_major += bragg.overlapped_major;
         bragg_overloads_kept += bragg.overloads_kept;
     };
+    auto full_worker = [&]() { full_worker_impl(false); };
 
     if (observer) {
         observer->OnPhase("Processing images");
@@ -403,6 +434,33 @@ void Rugnux::ImagePass(PipelineLocals &p) {
     std::vector<std::future<void> > futures;
     futures.reserve(image_workers);
     const auto image_loop_start = std::chrono::steady_clock::now();
+    if (!window_frames.empty()) {
+        // The sample is integrated, scaled against its own merge and measured; then it is forgotten, and
+        // its frames are integrated again in the pass proper like every other.
+        for (int i = 0; i < image_workers; ++i)
+            futures.push_back(std::async(std::launch::async, [&] { full_worker_impl(true); }));
+        for (auto &f: futures)
+            f.get();
+        futures.clear();
+        auto &outcomes = indexer->GetIntegrationOutcome();
+        indexer->ScaleAllImages(MergeAll(experiment_, outcomes, config_.nthreads, stills_user_cell_), config_.nthreads);
+        const StillsPartialityRefine refine(experiment_);
+        double radial_scale = 1.0;
+        for (int i = 0; i < 3; ++i)
+            radial_scale = refine.MeasureRadialScale(outcomes, stills_user_cell_, radial_scale);
+        stills_run_width_ = refine.MeasureRunWidth(outcomes, stills_user_cell_, radial_scale);
+        for (const int o: window_frames)
+            outcomes[o] = IntegrationOutcome{};
+        if (stills_run_width_) {
+            const auto k = static_cast<float>(STILLS_WINDOW_SIGMAS);
+            indexer->SetStillsWindow(StillsWindow{.c0 = k * static_cast<float>(stills_run_width_->gamma0),
+                                                  .ang = k * static_cast<float>(stills_run_width_->gamma_e),
+                                                  .bw = k * static_cast<float>(stills_run_width_->bandwidth_sigma),
+                                                  .q_scale = static_cast<float>(stills_run_width_->radial_scale)});
+            Note(fmt::format("prediction window {:.1f} x the rocking width measured on {} frames, centred at "
+                             "radial scale {:+.2e}", STILLS_WINDOW_SIGMAS, window_frames.size(), radial_scale - 1.0));
+        }
+    }
     for (int i = 0; i < image_workers; ++i)
         futures.push_back(std::async(std::launch::async, worker));
     for (auto &f: futures)
diff --git a/rugnux/RugnuxInputKind.cpp b/rugnux/RugnuxInputKind.cpp
new file mode 100644
index 000000000..565ead494
--- /dev/null
+++ b/rugnux/RugnuxInputKind.cpp
@@ -0,0 +1,137 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "RugnuxInputKind.h"
+
+#include <algorithm>
+#include <filesystem>
+#include <optional>
+#include <stdexcept>
+
+#include <zlib.h>
+
+const char *RugnuxInputKindName(RugnuxInputKind kind) {
+    switch (kind) {
+        case RugnuxInputKind::Images: return "images";
+        case RugnuxInputKind::Model: return "model";
+        case RugnuxInputKind::Reflections: return "reflections";
+        case RugnuxInputKind::Ambiguous: return "ambiguous";
+    }
+    return "?";
+}
+
+namespace {
+    // The record names a PDB file starts with (its first line that is not blank)
+    constexpr const char *PDB_RECORDS[] = {"HEADER", "TITLE ", "COMPND", "SOURCE", "KEYWDS", "EXPDTA", "AUTHOR",
+                                           "REVDAT", "REMARK", "SEQRES", "CRYST1", "MODEL ", "ATOM  ", "HETATM"};
+
+    // The rule, fed one line at a time; done() once the answer cannot change.
+    class Sniffer {
+        enum class Text { Unknown, Cif, Pdb } text = Text::Unknown;
+        bool atoms = false, reflections = false;
+        std::optional<RugnuxInputKind> decided;
+    public:
+        explicit Sniffer(const std::string &head) {
+            if (head.starts_with("MTZ "))
+                decided = RugnuxInputKind::Reflections;
+            else if (head.starts_with("\x89HDF\r\n\x1a\n") || head.starts_with("###CBF")
+                     || head.find('\0') != std::string::npos)
+                decided = RugnuxInputKind::Images;
+        }
+        bool done() const { return decided.has_value(); }
+        void line(const std::string &l) {
+            if (decided)
+                return;
+            if (text == Text::Unknown) {
+                const size_t i = l.find_first_not_of(" \t\r");
+                if (i == std::string::npos || l[i] == '#')
+                    return;
+                if (l.compare(i, 5, "data_") == 0)
+                    text = Text::Cif;
+                else if (std::any_of(std::begin(PDB_RECORDS), std::end(PDB_RECORDS),
+                                     [&](const char *r) { return l.starts_with(r); }))
+                    text = Text::Pdb;
+                else
+                    decided = RugnuxInputKind::Images;   // not a model nor reflections: for the image readers
+            }
+            if (text == Text::Pdb && (l.starts_with("ATOM  ") || l.starts_with("HETATM")))
+                decided = RugnuxInputKind::Model;
+            if (text == Text::Cif) {
+                if (l.starts_with("_array_data"))
+                    decided = RugnuxInputKind::Images;   // a CBF without its ###CBF line
+                atoms = atoms || l.starts_with("_atom_site.");
+                reflections = reflections || l.starts_with("_refln.") || l.starts_with("_diffrn_refln.");
+            }
+        }
+        RugnuxInputKind kind() const {
+            if (decided)
+                return *decided;
+            if (atoms && reflections)
+                return RugnuxInputKind::Ambiguous;
+            if (atoms)
+                return RugnuxInputKind::Model;
+            if (reflections)
+                return RugnuxInputKind::Reflections;
+            return RugnuxInputKind::Images;
+        }
+    };
+
+    // A text line is shorter than this
+    constexpr int MAX_LINE = 4096;
+    constexpr int HEAD = 16;
+}
+
+RugnuxInputKind ClassifyRugnuxInputContent(const std::string &head, const std::vector<std::string> &lines) {
+    Sniffer s(head);
+    for (const auto &l : lines)
+        s.line(l);
+    return s.kind();
+}
+
+RugnuxInputKind ClassifyRugnuxInput(const std::string &path) {
+    gzFile f = gzopen(path.c_str(), "rb");
+    if (f == nullptr)
+        throw std::runtime_error("cannot open " + path);
+    std::string head(HEAD, '\0');
+    head.resize(std::max(gzread(f, head.data(), HEAD), 0));
+    Sniffer s(head);
+    gzrewind(f);
+    std::string buf(MAX_LINE, '\0');
+    while (!s.done() && gzgets(f, buf.data(), MAX_LINE) != nullptr) {
+        std::string l(buf.c_str());
+        if (!l.empty() && l.back() == '\n')
+            l.pop_back();
+        s.line(l);
+    }
+    gzclose(f);
+    return s.kind();
+}
+
+RugnuxPositionalInputs SplitRugnuxInputs(const std::vector<std::string> &paths) {
+    RugnuxPositionalInputs out;
+    for (const std::string &p : paths) {
+        // what is not a file (a missing path, a broker URL) is left to the image readers to report
+        const RugnuxInputKind kind = std::filesystem::is_regular_file(p) ? ClassifyRugnuxInput(p)
+                                                                        : RugnuxInputKind::Images;
+        switch (kind) {
+            case RugnuxInputKind::Images:
+                out.images.push_back(p);
+                break;
+            case RugnuxInputKind::Model:
+                if (!out.model.empty())
+                    throw std::runtime_error("two atomic models given, " + out.model + " and " + p + "; give one");
+                out.model = p;
+                break;
+            case RugnuxInputKind::Reflections:
+                if (!out.reflections.empty())
+                    throw std::runtime_error("two reflection files given, " + out.reflections + " and " + p
+                                             + "; give one");
+                out.reflections = p;
+                break;
+            case RugnuxInputKind::Ambiguous:
+                throw std::runtime_error(p + " holds both atomic coordinates (_atom_site) and reflections (_refln); "
+                                         "give it with --model or -z");
+        }
+    }
+    return out;
+}
diff --git a/rugnux/RugnuxInputKind.h b/rugnux/RugnuxInputKind.h
new file mode 100644
index 000000000..a34d23809
--- /dev/null
+++ b/rugnux/RugnuxInputKind.h
@@ -0,0 +1,37 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+// What a file given to rugnux as a positional argument holds, read from its contents, never its name, so that
+// `rugnux <images> <model> <reflections>` works in any order without --model or -z:
+//   Reflections  MTZ (the "MTZ " magic), or an mmCIF with a _refln or _diffrn_refln loop (a PDB -sf.cif)
+//   Model        PDB (a file starting with a PDB record, with an ATOM or HETATM record), or an mmCIF with an
+//                _atom_site loop
+//   Images       anything else - HDF5, CBF (an mmCIF-like file starting ###CBF, or with _array_data), and every
+//                other format the readers take, which then decide. A file whose first line is neither "data_"
+//                nor a PDB record is decided on that line, so an image file is not read through.
+// An mmCIF holding both atoms and reflections is Ambiguous: it has to be given with --model or -z. Gzipped files
+// are read through.
+enum class RugnuxInputKind { Images, Model, Reflections, Ambiguous };
+
+const char *RugnuxInputKindName(RugnuxInputKind kind);
+
+// Classifies a file (reads it, gunzipping where it is gzipped)
+RugnuxInputKind ClassifyRugnuxInput(const std::string &path);
+
+// The rule itself, on decompressed content: `head` is the first 16 bytes, `lines` the lines from the start.
+RugnuxInputKind ClassifyRugnuxInputContent(const std::string &head, const std::vector<std::string> &lines);
+
+// The positional inputs of a rugnux command line, split by what they hold
+struct RugnuxPositionalInputs {
+    std::vector<std::string> images;
+    std::string model;          // empty: none
+    std::string reflections;    // empty: none
+};
+
+// Throws std::runtime_error (with a message for the user) on two models, two reflection files or an ambiguous file.
+RugnuxPositionalInputs SplitRugnuxInputs(const std::vector<std::string> &paths);
diff --git a/rugnux/RugnuxLive.cpp b/rugnux/RugnuxLive.cpp
index 886db699c..90cf5f755 100644
--- a/rugnux/RugnuxLive.cpp
+++ b/rugnux/RugnuxLive.cpp
@@ -56,6 +56,8 @@ RugnuxLiveSetup MakeRugnuxLiveSetup(const JFJochReaderDataset &dataset, int nthr
     c.measure_spot_budget = true;
     c.run_scaling = true;
     c.model = std::move(model);
+    // The placed model is refined, as in `rugnux`: the uploaded model is the opt-in.
+    c.refine = true;
     c.live = true;
     c.fast_live = true;
     // Decided late, on the whole sweep, as it re-checks its radius there - which fast_live does not.
diff --git a/rugnux/RugnuxOutputFiles.cpp b/rugnux/RugnuxOutputFiles.cpp
index ea118d3fd..e7d3e7a4e 100644
--- a/rugnux/RugnuxOutputFiles.cpp
+++ b/rugnux/RugnuxOutputFiles.cpp
@@ -12,6 +12,17 @@
 
 namespace {
 
+// The unexplained blobs of the refined model's difference map (DensityBlobs.h), strongest first.
+void WriteDensityBlobs(const std::vector<DensityBlob> &blobs, const std::string &path, Logger &logger) {
+    std::ofstream f(path, std::ofstream::out | std::ofstream::trunc);
+    if (!f) {
+        logger.Warning("Cannot open {} for writing", path);
+        return;
+    }
+    f << DensityBlobsJson(DensityBlobsToMessage(blobs));
+    logger.Info("Difference-map blobs written to {}", path);
+}
+
 // The files of one output pass at `prefix`, all but its _process.h5.
 void WriteOutputs(const RugnuxOutputs &o, const std::string &prefix, const OutputProvenance &provenance,
                   size_t nthreads, Logger &logger) {
@@ -30,6 +41,13 @@ void WriteOutputs(const RugnuxOutputs &o, const std::string &prefix, const Outpu
     if (o.model_prior_placed_model)
         WritePlacedModel(*o.model_prior_placed_model->model, o.model_prior_placed_model->cell,
                          o.model_prior_placed_model->space_group, prefix + "_mr", logger);
+    if (o.refined_model)
+        WritePlacedModel(*o.refined_model->model, o.refined_model->cell, o.refined_model->space_group,
+                         prefix + "_refined", logger);
+    if (o.refined_maps)
+        WriteModelMaps(*o.refined_maps, prefix + "_refined", logger);
+    if (o.blobs)
+        WriteDensityBlobs(*o.blobs, prefix + "_blobs.json", logger);
     if (o.unmerged) {
         WriteMtz(*o.unmerged, prefix + "_unmerged.mtz");
         logger.Info("Unmerged observations written to {}_unmerged.mtz", prefix);
@@ -105,20 +123,24 @@ void WriteRugnuxOutputs(const ProcessResult &result, const std::string &prefix,
 
 void WriteMergedOutput(const MergedOutput &merged, const std::string &prefix, const OutputProvenance &provenance,
                        size_t nthreads, bool hkl) {
-    // An MTZ, an mmCIF and a SHELX HKLF-4 .hkl - each has its uses downstream (MTZ for the CCP4 / phenix
+    // An MTZ, an mmCIF and a SHELX HKLF-4 .hkl with its .ins - each has its uses downstream (MTZ for the CCP4 / phenix
     // reflection tools, mmCIF for deposition and as the self-describing native format, HKLF-4 for SHELXL
     // refinement and SHELXC / ANODE substructure solution). The .hkl holds the unmerged scaled fulls where the
     // merge provides them (rotation), the merged reflections otherwise (stills).
     const std::string file = prefix + merged.suffix;
     WriteMtz(merged.mtz, file + ".mtz");
+    const CellEsd *esd = merged.cell_esd ? &*merged.cell_esd : nullptr;
     WriteMmcifReflections(merged.reflections, merged.cell, merged.experiment, merged.statistics, merged.error_model,
-                          merged.twinning, provenance, file + ".cif", nthreads);
+                          merged.twinning, provenance, file + ".cif", nthreads, esd);
     if (!hkl)
         return;
     if (!merged.scaled_fulls.empty())
         WriteShelxHklReflections(merged.scaled_fulls, file + ".hkl", nthreads);
     else
         WriteShelxHklReflections(merged.reflections, merged.experiment, file + ".hkl", nthreads);
+    // The SHELX instructions beside it, with the cell's e.s.d.s as ZERR where the run measured them.
+    WriteShelxIns(merged.cell, esd, merged.experiment, std::filesystem::path(file).filename().string(),
+                  file + ".ins");
 }
 
 void WriteModelMaps(const ModelMaps &maps, const std::string &prefix, Logger &logger) {
@@ -156,3 +178,29 @@ ReportDocument WriteResultReport(const std::string &output_prefix,
     }
     return doc;
 }
+
+ReportDocument WriteRefineOutputs(const RefineOnlyResult &result, const std::string &prefix,
+                                  const std::string &input_file, const std::string &model_file, Logger &logger,
+                                  const RunProvenance &provenance) {
+    ReportDocument doc = BuildRefineReportDocument(prefix, input_file, model_file, result, provenance);
+    if (prefix.empty())
+        return doc;
+    const RefinementResult &rf = result.refinement;
+    if (rf.ok) {
+        const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name(result.space_group);
+        const gemmi::UnitCell &c = rf.model->cell;
+        const UnitCell cell{static_cast<float>(c.a), static_cast<float>(c.b), static_cast<float>(c.c),
+                            static_cast<float>(c.alpha), static_cast<float>(c.beta), static_cast<float>(c.gamma)};
+        WritePlacedModel(*rf.model, cell, *sg, prefix + "_refined", logger);
+        WriteModelMaps(*rf.maps, prefix + "_refined", logger);
+        WriteDensityBlobs(rf.blobs, prefix + "_blobs.json", logger);
+    }
+    try {
+        std::ofstream file(prefix + "_report.txt");
+        file.exceptions(std::ios::failbit | std::ios::badbit);
+        file << RenderReportText(doc, provenance.developer);
+    } catch (const std::exception &e) {
+        logger.Warning("Could not write the results report {}_report.txt: {}", prefix, e.what());
+    }
+    return doc;
+}
diff --git a/rugnux/RugnuxOutputFiles.h b/rugnux/RugnuxOutputFiles.h
index 5821bd21c..ee3cab6af 100644
--- a/rugnux/RugnuxOutputFiles.h
+++ b/rugnux/RugnuxOutputFiles.h
@@ -42,6 +42,12 @@ void WriteMergedOutput(const MergedOutput &merged, const std::string &prefix, co
 // A model validation's map coefficients at `prefix`: _maps.mtz.
 void WriteModelMaps(const ModelMaps &maps, const std::string &prefix, Logger &logger);
 
+// --mode refine's files under `prefix`: <prefix>_refined_model.cif, <prefix>_refined_maps.mtz, <prefix>_blobs.json
+// and <prefix>_report.txt; returns the report's document. Writes nothing when the prefix is empty.
+ReportDocument WriteRefineOutputs(const RefineOnlyResult &result, const std::string &prefix,
+                                  const std::string &input_file, const std::string &model_file, Logger &logger,
+                                  const RunProvenance &provenance = {});
+
 // <prefix>_plot.txt (PerImagePlotText).
 void WritePerImagePlot(const std::string &prefix, const PerImagePlot &plot);
 
diff --git a/rugnux/RugnuxPreScan.cpp b/rugnux/RugnuxPreScan.cpp
index 9534da056..582eb6294 100644
--- a/rugnux/RugnuxPreScan.cpp
+++ b/rugnux/RugnuxPreScan.cpp
@@ -199,6 +199,10 @@ void Rugnux::PreScan(int start_image, int images_to_process, int frame_count, Ru
     const bool have_shadow = std::any_of(current.begin(), current.end(),
                                          [](uint32_t v) { return (v & (1u << PixelMask::BeamStopPixelBit)) != 0; });
     const bool want_shadow = config_.detect_beam_stop.has_value() && !have_shadow;
+    // The plane was decided with that shadow; a pass that starts again from an experiment taken before
+    // the decision (the measured-centre arm, the no-lattice pass) carries it on rather than the stated one.
+    if (have_shadow && polarization_from_background_)
+        experiment_.PolarizationFactor(polarization_from_background_);
     // The spot width is a property of the crystal, not of the geometry, so the second pass reuses the
     // radius the first one measured rather than re-reading the frames.
     const bool want_width = config_.adaptive_integration_radius && !spot_width_measured_;
@@ -978,6 +982,7 @@ void Rugnux::PreScan(int start_image, int images_to_process, int frame_count, Ru
     // Where the scattered background puts the beam, when the projection exists to say so.
     std::optional<std::pair<float, float>> ring_centre;
     std::vector<uint32_t> opaque_shadow;
+    std::vector<uint32_t> dead_pixels;   // reported by the shadow finder, counted nothing (below)
     // The mean projection, taken once and shared read-only by everything below that reads it - the
     // ring-centre fit here, and the diagnostic picture and the beam-centre capture on threads of
     // their own. It is 4 bytes a pixel, and a copy for each of them was a copy on this thread.
@@ -1028,6 +1033,12 @@ void Rugnux::PreScan(int start_image, int images_to_process, int frame_count, Ru
             shadow = finder->GetMask(config_.nthreads);
             shadow_frames = finder->GetFrameCount();
             polarization = finder->GetAppliedPolarization();
+            if (const auto e = finder->GetPlaneEvidence())
+                logger.Info("Polarization plane: the background's cos 2phi harmonic has correlation {:+.3f} and "
+                            "modulation {:+.3f} against a polarized source's (positive towards the plane turned by "
+                            "90 degrees from lab x; the plane follows the background beyond {} and {}, the "
+                            "modulation under {})", e->correlation, e->modulation, shadow_finder::PLANE_CORRELATION,
+                            shadow_finder::PLANE_MODULATION, shadow_finder::PLANE_MODULATION_MAX);
             finder.reset();
 
             BeamStopMemo::Entry entry{shadow_key, {}, projection, ring_centre, centre_line, frames_read.load(),
@@ -1051,7 +1062,24 @@ void Rugnux::PreScan(int start_image, int images_to_process, int frame_count, Ru
                         *polarization);
             Note("polarization plane taken from the background, turned by 90 degrees");
             experiment_.PolarizationFactor(polarization);
+            polarization_from_background_ = polarization;
         }
+        // A pixel whose mean is negative holds the detector's own mark for no data - a module gap a PILATUS
+        // CBF leaves at -1 - and is the darkest pixel there is, so the shadow finder reports it. It is dead
+        // rather than shadowed, and goes to the defective pixels (after MaskDefectivePixels below), so that
+        // the shadow bit holds only what something in the beam shadowed: what the share reported here
+        // counts, and what the integration's shadow test reads (MXAnalysisWithoutFPGA::DropShadowClipped).
+        // A mean of zero is not enough: a deep shadow on a low background counts nothing in the frames
+        // projected, and on a still it often does.
+        dead_pixels.assign(shadow.size(), 0);
+        for (size_t i = 0; i < shadow.size(); i++)
+            if (shadow[i] != 0 && !((*projection)[i] > -0.5f)) {
+                shadow[i] = 0;
+                dead_pixels[i] = 1;
+            }
+        if (const auto dead = std::count(dead_pixels.begin(), dead_pixels.end(), 1u); dead > 0)
+            logger.Info("Beam stop: {} pixels reading the detector's no-data mark in {} images are masked as dead, "
+                        "not as shadow", dead, shadow_frames);
         const auto shadowed = std::count_if(shadow.begin(), shadow.end(), [](uint32_t v) { return v != 0; });
         pixel_mask_.LoadBeamStopMask(experiment_, shadow);
         opaque_shadow = shadow;
@@ -1107,6 +1135,12 @@ void Rugnux::PreScan(int start_image, int images_to_process, int frame_count, Ru
             measured.emplace();
         MaskDefectivePixels(start_image, shadow_sample, ring_centre, frame, measured->defects);
     }
+    if (!dead_pixels.empty()) {
+        const auto &m = pixel_mask_.GetMask();
+        for (size_t i = 0; i < m.size(); i++)
+            dead_pixels[i] |= (m[i] >> PixelMask::HotPixelBit) & 1u;
+        pixel_mask_.LoadHotPixelMask(experiment_, dead_pixels);
+    }
 
     // The centre is fitted with the shadow masked but NOT the transmitting pieces the shadow finder
     // adds after it. Their dimming is multiplicative in azimuth, which the fit's per-sector amplitude
diff --git a/rugnux/RugnuxRefine.cpp b/rugnux/RugnuxRefine.cpp
new file mode 100644
index 000000000..8d897eab6
--- /dev/null
+++ b/rugnux/RugnuxRefine.cpp
@@ -0,0 +1,59 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "RugnuxRefine.h"
+
+#include <cmath>
+
+#include "../common/UnitCell.h"
+#include "../image_analysis/scale_merge/FrenchWilson.h"
+#include "../image_analysis/scale_merge/RfreeFlags.h"
+
+RefineOnlyResult RunRefineOnly(RugnuxReflections data, const gemmi::Structure &model, double d_min_limit,
+                               const RefinementSettings &settings, Logger &logger) {
+    RefineOnlyResult out;
+    out.d_min_limit = d_min_limit;
+    out.score_only = settings.score_only;
+    const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name(data.space_group);
+    if (sg == nullptr) {
+        out.refinement.failure_reason = "unknown space group " + data.space_group;
+        return out;
+    }
+    out.space_group = sg->xhm();
+    out.wavelength_A = data.wavelength_A > 0 ? data.wavelength_A : 1.0;
+    std::vector<MergedReflection> &refl = data.reflections;
+    if (d_min_limit > 0)
+        std::erase_if(refl, [&](const MergedReflection &r) { return r.d < d_min_limit; });
+    if (!data.amplitudes) {
+        FrenchWilsonOptions fw;
+        fw.num_threads = static_cast<int>(settings.nthreads);
+        ApplyFrenchWilson(refl, *sg, fw);
+        out.french_wilson = true;
+    }
+    std::erase_if(refl, [](const MergedReflection &r) { return !std::isfinite(r.F); });
+    if (data.free_column.empty()) {
+        const UnitCell cell{static_cast<float>(data.cell.a), static_cast<float>(data.cell.b),
+                            static_cast<float>(data.cell.c), static_cast<float>(data.cell.alpha),
+                            static_cast<float>(data.cell.beta), static_cast<float>(data.cell.gamma)};
+        AssignRfreeFlags(refl, *sg, 0.05, 500, cell, settings.nthreads);
+        out.free_flags_generated = true;
+    }
+    out.reflections = static_cast<int>(refl.size());
+    for (const MergedReflection &r : refl)
+        out.free_reflections += r.rfree_flag;
+    logger.Info("Refinement input: {} ({}), {} {} in {}, {} free ({}){}", data.name, data.source, refl.size(),
+                data.amplitudes ? "amplitudes " + data.value_column
+                                : "amplitudes by French-Wilson from " + data.value_column,
+                out.space_group, out.free_reflections,
+                out.free_flags_generated ? "drawn here, the file has no free set" : "column " + data.free_column,
+                d_min_limit > 0 ? fmt::format(", to {:.2f} A", d_min_limit) : std::string());
+    if (const gemmi::SpaceGroup *msg = model.find_spacegroup(); msg != nullptr && msg->number != sg->number)
+        logger.Warning("The model names space group {}, the data {}: refined in the data's", msg->xhm(), sg->xhm());
+    try {
+        out.refinement = RefineModel(model, refl, data.cell, *sg, out.wavelength_A, logger, settings);
+    } catch (const std::exception &e) {
+        out.refinement = RefinementResult();
+        out.refinement.failure_reason = std::string("refinement failed: ") + e.what();
+    }
+    return out;
+}
diff --git a/rugnux/RugnuxRefine.h b/rugnux/RugnuxRefine.h
new file mode 100644
index 000000000..78e2bf2af
--- /dev/null
+++ b/rugnux/RugnuxRefine.h
@@ -0,0 +1,31 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <string>
+
+#include "gemmi/model.hpp"
+
+#include "../common/Logger.h"
+#include "../image_analysis/structure_refinement/Refinement.h"
+#include "../writer/RugnuxReflectionFile.h"
+
+// rugnux --mode refine: a model refined against merged structure factors it is given, nothing processed. The
+// reflections and the model come in parsed (RugnuxReflectionFile.h, RugnuxModelFile.h); the refinement and what
+// had to be made of the input to run it go out. No file is read or written here.
+struct RefineOnlyResult {
+    RefinementResult refinement;
+    std::string space_group;         // the data's, which the model is refined in
+    double wavelength_A = 0;         // the file's, or 1 A where it states none
+    bool french_wilson = false;      // amplitudes made here from the file's intensities
+    bool free_flags_generated = false;   // the file has no free set: one was drawn here (AssignRfreeFlags)
+    int reflections = 0;             // amplitudes refined against, after the resolution limit
+    int free_reflections = 0;
+    double d_min_limit = 0;          // the limit asked for (0: none)
+    bool score_only = false;         // the model only scored (RefinementSettings::score_only)
+};
+
+// `data` as parsed; `d_min_limit`: leave out reflections finer than this (0: keep all).
+RefineOnlyResult RunRefineOnly(RugnuxReflections data, const gemmi::Structure &model, double d_min_limit,
+                               const RefinementSettings &settings, Logger &logger);
diff --git a/rugnux/RugnuxScaleMerge.cpp b/rugnux/RugnuxScaleMerge.cpp
index 815b0edec..fc1cc42de 100644
--- a/rugnux/RugnuxScaleMerge.cpp
+++ b/rugnux/RugnuxScaleMerge.cpp
@@ -76,6 +76,7 @@
 #include "../image_analysis/scale_merge/ScaleOnTheFly.h"
 #include "../image_analysis/scale_merge/StillsPartialityRefine.h"
 #include "../image_analysis/scale_merge/SublatticeRelabel.h"
+#include "../image_analysis/scale_merge/ReferenceFreeReindex.h"
 #include "../image_analysis/WriteReflections.h"
 #include "../image_analysis/bragg_integration/CalcISigma.h"
 #include "../common/Definitions.h"
@@ -88,6 +89,73 @@
 using namespace rugnux_internal;
 
 namespace {
+    // The space-group search's resolution cut on a P1 merge: where the best non-increasing fit of its
+    // thin-shell <I/sigma> drops under 1 (0: no cut). See the search below.
+    double SearchCut(const std::vector<MergedReflection> &merged) {
+        double d_min_search = 0.0;
+        std::vector<std::pair<float, float>> rs;   // (d, I/sigma) over the full P1 merge
+        rs.reserve(merged.size());
+        for (const auto &m : merged)
+            if (std::isfinite(m.I) && std::isfinite(m.sigma) && m.sigma > 0.0f &&
+                std::isfinite(m.d) && m.d > 0.0f)
+                rs.emplace_back(m.d, m.I / m.sigma);
+        if (rs.size() >= 400) {
+            std::sort(rs.begin(), rs.end(),
+                      [](const auto &a, const auto &b) { return a.first > b.first; });   // low -> high res
+            const int bins = std::clamp(static_cast<int>(rs.size() / 100), 1, 40);
+            const size_t per = (rs.size() + bins - 1) / static_cast<size_t>(bins);
+            // The shell means, then their best NON-INCREASING fit (pool adjacent violators, weighted
+            // by shell size). The cut is where the FIT drops under 1, not where the first shell
+            // does: on a merge whose <I/sigma> is flat near 1 - its ISa has collapsed - the first
+            // single shell to dip under 1 is a coin toss that moved the cut from 0.85 to 1.19 A
+            // between two compiler flags on one crystal, and the coarser cut left its glide zones
+            // too few absences to be judged. The fit moves by as much as its input does.
+            std::vector<double> mean, weight;
+            for (size_t lo = 0; lo < rs.size(); lo += per) {
+                const size_t hi = std::min(rs.size(), lo + per);
+                double sum = 0.0;
+                for (size_t j = lo; j < hi; ++j) sum += rs[j].second;
+                mean.push_back(sum / static_cast<double>(hi - lo));
+                weight.push_back(static_cast<double>(hi - lo));
+            }
+            std::vector<double> block_mean, block_weight;
+            std::vector<size_t> block_size;
+            for (size_t b = 0; b < mean.size(); ++b) {
+                block_mean.push_back(mean[b]); block_weight.push_back(weight[b]); block_size.push_back(1);
+                while (block_mean.size() > 1 && block_mean[block_mean.size() - 2] < block_mean.back()) {
+                    const size_t k = block_mean.size() - 1;
+                    const double w = block_weight[k - 1] + block_weight[k];
+                    block_mean[k - 1] = (block_mean[k - 1] * block_weight[k - 1] + block_mean[k] * block_weight[k]) / w;
+                    block_weight[k - 1] = w;
+                    block_size[k - 1] += block_size[k];
+                    block_mean.pop_back(); block_weight.pop_back(); block_size.pop_back();
+                }
+            }
+            std::vector<double> fit;
+            for (size_t k = 0; k < block_mean.size(); ++k)
+                fit.insert(fit.end(), block_size[k], block_mean[k]);
+            for (size_t b = 0; b < fit.size(); ++b) {
+                const size_t lo = b * per;
+                if (fit[b] < 1.0) {
+                    // Cut the noise-dominated high-res shells. When even the lowest-res shell fails,
+                    // keep that shell alone rather than abandoning the cut. The bound is absolute
+                    // while the merged I/sigma it tests saturates at the merge's own ISa (times the
+                    // square root of the multiplicity), so a merge whose ISa has collapsed towards 1
+                    // can fail it in every shell - and that is exactly the merge the search must not
+                    // be handed whole, since the noise which drove ISa down is what the cut exists to
+                    // remove. Abandoning it feeds back: more noise into the search, a weaker operator
+                    // statistic, and a lost symmetry.
+                    if (b > 0)
+                        d_min_search = rs[lo].first;
+                    else if (per >= 400)
+                        d_min_search = rs[per - 1].first;
+                    break;
+                }
+            }
+        }
+        return d_min_search;
+    }
+
     // How precisely the measured beam centre has to be placed before the post-refinement takes it as a
     // second place the centre is believed to be (the bound on its beam move). The ceiling is the larger
     // of this and what the geometry asks of the centre (BeamCenterNeed_pxl).
@@ -469,6 +537,9 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     };
     phase("Scaling and merging");
     Step(geometry_prepass ? "Scaling and post-refinement" : "Scaling and merging");
+    // Whether the reflections the engine ingested are still indexed as they were (the final merge made
+    // ahead, below): every change of basis of the integrated reflections clears it.
+    bool spec_same_ingest = true;
 
     // Ice-ring handling (--detect-ice-rings): flag reflections sitting on a hexagonal-ice powder
     // ring. Their integrated intensity is contaminated by the strong, variable ice background, so
@@ -505,8 +576,32 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     // drops the whole rocking event) - they are the strongest reflections, mostly at low resolution,
     // and what a model's low-resolution terms rest on. The ice flags are set in the same sweep. Integer
     // counts, one image per task: the totals do not depend on the split.
+    TimingMark ends_mark(logger, "sweep ends, overloads, ice rings");
+    // One walk over the reflections, per frame, for all three: what the sweep ends are decided on, the
+    // overload counts and the ice flags. The counts are added up below over the frames still in.
+    auto &outcomes = indexer->GetIntegrationOutcome();
+    struct FrameCounts { int64_t all = 0, low = 0, over = 0, over_low = 0, on_ice = 0; };
+    std::vector<SweepEndTally> tally(outcomes.size());
+    std::vector<FrameCounts> counts(outcomes.size());
+    ParallelFor(static_cast<int>(outcomes.size()), config_.nthreads, [&](int o) {
+        tally[o] = TallySweepEnd(outcomes[o]);
+        FrameCounts &c = counts[o];
+        for (auto &r : outcomes[o].reflections) {
+            const bool low_res = r.d >= OVERLOAD_LOW_RES_A;
+            ++c.all;
+            c.low += low_res;
+            if (r.overloaded) {
+                ++c.over;
+                c.over_low += low_res;
+            }
+            if (flag_ice) {
+                r.on_ice_ring = IsOnIceRing(r.d, ice_width);
+                c.on_ice += r.on_ice_ring;
+            }
+        }
+    });
     if (experiment_.IsRotationIndexing()) {
-        const auto [at_start, at_end] = TrimBlankSweepEnds(indexer->GetIntegrationOutcome(), config_.nthreads);
+        const auto [at_start, at_end] = TrimBlankSweepEnds(outcomes, tally);
         result.blank_start_frames = at_start;
         result.blank_end_frames = at_end;
         if (at_start + at_end > 0)
@@ -516,7 +611,6 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     // Stills given a cell: only the frames whose refined cell belongs to its population are merged
     // (see GivenCellPopulation) - a second crystal form, fitted to the same cell, is left out.
     if (!experiment_.IsRotationIndexing() && stills_user_cell_) {
-        auto &outcomes = indexer->GetIntegrationOutcome();
         const double given = CrystalLattice(*stills_user_cell_).CalcVolume();
         std::vector<double> rel;
         for (const auto &o : outcomes)
@@ -548,25 +642,13 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     }
     size_t ice_flagged = 0, ice_total = 0;
     {
-        auto &outcomes = indexer->GetIntegrationOutcome();
-        std::atomic<int64_t> n_all{0}, n_low{0}, n_over{0}, n_over_low{0}, n_ice{0};
-        ParallelFor(static_cast<int>(outcomes.size()), config_.nthreads, [&](int o) {
-            int64_t all = 0, low = 0, over = 0, over_low = 0, on_ice = 0;
-            for (auto &r : outcomes[o].reflections) {
-                const bool low_res = r.d >= OVERLOAD_LOW_RES_A;
-                ++all;
-                low += low_res;
-                if (r.overloaded) {
-                    ++over;
-                    over_low += low_res;
-                }
-                if (flag_ice) {
-                    r.on_ice_ring = IsOnIceRing(r.d, ice_width);
-                    on_ice += r.on_ice_ring;
-                }
-            }
-            n_all += all; n_low += low; n_over += over; n_over_low += over_low; n_ice += on_ice;
-        });
+        int64_t n_all = 0, n_low = 0, n_over = 0, n_over_low = 0, n_ice = 0;
+        for (size_t o = 0; o < outcomes.size(); ++o) {
+            if (outcomes[o].reflections.empty())   // a frame left out above counts nothing
+                continue;
+            const FrameCounts &c = counts[o];
+            n_all += c.all; n_low += c.low; n_over += c.over; n_over_low += c.over_low; n_ice += c.on_ice;
+        }
         result.integrated_reflections += n_all;
         result.integrated_reflections_low_res += n_low;
         result.overloaded_reflections += n_over;
@@ -584,6 +666,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                         result.integrated_reflections_low_res, OVERLOAD_LOW_RES_A);
     }
 
+    ends_mark.Stop();
     if (experiment_.IsDetectIceRings() && !ice_present) {
         logger.Info("Ice-ring handling: measured ice score {:.2f} < {:.2f} and spot ratio {:.2f} < "
                     "{:.2f}, no ice detected - ice-ring handling skipped entirely",
@@ -671,6 +754,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                 r.l = static_cast<int32_t>(std::lround(reindex.a[2][0]*h + reindex.a[2][1]*k + reindex.a[2][2]*l));
             }
         }
+        spec_same_ingest = false;
         result.consensus_cell = cand.conventional.GetUnitCell();
         result.consensus_centering = cand.centering;
         end_msg.unit_cell = result.consensus_cell;
@@ -697,6 +781,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                 r.h = h[0]; r.k = h[1]; r.l = h[2];
             }
         });
+        spec_same_ingest = false;
         result.consensus_cell = CellInBasis(*result.consensus_cell, cob);
         end_msg.unit_cell = result.consensus_cell;
         if (end_msg.rotation_lattice.has_value())
@@ -1207,6 +1292,40 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     // a search that turns out not to need it (no point group from the first arm) does not read it.
     // Declared before the future, which waits for the merge when it goes, so the engine outlives it.
     std::unique_ptr<RotationScaleMerge> rsm_all;
+    // The final merge made ahead: copies of the engine merging, beside the P1 merges, the search and the
+    // decisions, in the groups the run is expected to adopt - the one a search of the geometry pre-pass's
+    // merge predicted (predicted_group_), and the first arm's where that differs - each on a spare card
+    // (cards_ahead). Taken where the decision lands on that group on this ingest: no merge depends on the
+    // merges before it (RunArm), so it is the merge the engine would make. A decision that re-indexes the
+    // reflections clears spec_same_ingest. A deque, so that a second one does not move the first under its
+    // thread; declared before anything a merge reads, as rsm_all.
+    struct MergeAhead {
+        gemmi::SpaceGroup group;
+        std::unique_ptr<RotationScaleMerge> rsm;
+        Logger log = Logger::Buffered();
+        // ... with the intensity statistics for the centre on it (below), which read that merge alone.
+        std::future<std::pair<RotationScaleMerge::Result, CentreOfSymmetryResult>> ahead;
+    };
+    std::deque<MergeAhead> merges_ahead;
+    std::vector<int32_t> cards_ahead;   // the cards one may go on, in the order they are taken (below)
+    const auto merge_ahead = [&](const gemmi::SpaceGroup &g) {
+        MergeAhead &m = merges_ahead.emplace_back();
+        m.group = g;
+        m.rsm = rsm->CloneIngest(cards_ahead[merges_ahead.size() - 1], m.log);
+        // As scale_and_merge sets them for the merge that may be written.
+        m.rsm->SetExportScaledFulls(write_output && config_.write_merged);
+        m.rsm->SetFrenchWilson(false);
+        m.rsm->IngestDevice(&*rsm);
+        m.ahead = std::async(std::launch::async, [&m, nthreads = config_.nthreads] {
+            pin_gpu(m.rsm->GetGpuDevice());
+            TimingMark mark(m.log, "merge " + m.group.short_name() + " (ahead)");
+            auto r = m.rsm->Run(/*for_search=*/false, /*full_stats=*/true,
+                                /*measure_cc_before_corrections=*/false, &m.group);
+            mark.Stop();
+            CentreOfSymmetryResult centre = AnalyzeCentreOfSymmetry(r.merged, m.group, nthreads);
+            return std::make_pair(std::move(r), std::move(centre));
+        });
+    };
     Logger all_arm_log = Logger::Buffered();
     std::future<RotationScaleMerge::Result> all_arm_ahead;
     const auto start_all_arm = [&rsm_all, &all_arm_log] {
@@ -1323,6 +1442,72 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             p.postrefine_ahead.wait();
             postrefine_beside = false;
         }
+        // The cards for the merges made ahead (merges_ahead), decided here from the card count so that a run
+        // on one card is exactly what it is without them: spare cards only - card 3 from four cards up, then
+        // card 2, the all-observation arm's, whose merge is done when a second one is asked for; on two or
+        // three cards the last card, beside the engine already there, where one more engine fits its total
+        // memory. And only where one more merge fits the host budget. GPU engines only: on the host it would
+        // take the threads the chain runs on.
+        if (!geometry_prepass && !experiment_.GetGemmiSpaceGroup().has_value() && config_.reference_data.empty()
+            && write_output && cards >= 2 && rsm->OnGPU()) {
+            const bool host_fits = host_engine + (all_arm ? 3 : 2) * host_merge
+                                   + (postrefine_beside ? host_postrefine : 0) <= host_budget_;
+            if (cards >= 4)
+                cards_ahead = {3, 2};
+            else if ((2 + (all_arm && all_arm_device == cards - 1 ? 1 : 0)) * rsm->DeviceBytes() + CARD_BYTES_RESERVED
+                     <= get_gpu_total_memory(cards - 1))
+                cards_ahead = {cards - 1};
+            if (!host_fits)
+                cards_ahead.clear();
+            logger.Debug("Final merge ahead: {}", !host_fits ? "no room on the host" : cards_ahead.empty()
+                         ? "no room on a card" : fmt::format("on card {}, {} at most", cards_ahead.front(), cards_ahead.size()));
+        }
+        if (!cards_ahead.empty() && p.gpu_merge)
+            p.gpu_merge->Holds(((all_arm ? 2 : 1) + cards_ahead.size()) * rsm->DeviceBytes());
+        // The geometry pre-pass decides no group, but a search of a P1 merge of ALL its observations predicts
+        // the one the canonical pass will most likely adopt, and that pass merges in it ahead (merges_ahead).
+        // All observations, on a copy of the engine, because the pre-pass's own merge is Lorentz-filtered and
+        // a screw axis is read on the weak reflections the filter discards: searched on that merge a 4(1)
+        // crystal was predicted as its symmorphic group every time. On the last card, beside the rest of the
+        // pre-pass and the second pass, under the same card and host rule as a merge ahead; set up as the
+        // canonical search is. It decides nothing.
+        if (geometry_prepass && !experiment_.GetGemmiSpaceGroup().has_value() && config_.reference_data.empty()
+            && cards >= 2 && rsm->OnGPU() && rsm->GetSearchMinZeta() > 0.0
+            && host_engine + 2 * host_merge + (postrefine_beside ? host_postrefine : 0) <= host_budget_
+            && (cards >= 4 || 2 * rsm->DeviceBytes() + CARD_BYTES_RESERVED <= get_gpu_total_memory(cards - 1))) {
+            struct Prediction {
+                Logger log = Logger::Buffered();
+                std::unique_ptr<RotationScaleMerge> rsm;
+            };
+            auto prediction = std::make_shared<Prediction>();
+            prediction->rsm = rsm->CloneIngest(cards - 1, prediction->log);
+            prediction->rsm->SetSearchMinZeta(0.0);
+            prediction->rsm->SetExportScaledFulls(false);
+            prediction->rsm->SetFrenchWilson(false);
+            prediction->rsm->IngestDevice(&*rsm);
+            SearchSpaceGroupOptions o;
+            o.nthreads = static_cast<size_t>(std::max(1, config_.nthreads));
+            o.merge_friedel = experiment_.GetScalingSettings().GetMergeFriedel();
+            if (end_msg.rotation_lattice_type.has_value()) {
+                o.lattice_system = end_msg.rotation_lattice_type->crystal_system;
+                o.lattice_centring = end_msg.rotation_lattice_type->centering;
+            }
+            if (result.consensus_cell.has_value())
+                o.cell = gemmi::UnitCell(*result.consensus_cell);
+            o.enumerate_all_settings = true;
+            o.enumerate_all_rotation_sets = true;
+            const double d_manual = experiment_.GetScalingSettings().GetHighResolutionLimit_A().value_or(0.0);
+            predicted_group_ = std::async(std::launch::async, [prediction, o, d_manual]() mutable
+                                                              -> std::optional<gemmi::SpaceGroup> {
+                pin_gpu(prediction->rsm->GetGpuDevice());
+                auto merge = prediction->rsm->Run(/*for_search=*/true, /*full_stats=*/false,
+                                                  /*measure_cc_before_corrections=*/false);
+                prediction.reset();   // the card is given back before the search
+                o.d_min_limit_A = std::max(SearchCut(merge.merged), d_manual);
+                o.merge_isa = merge.isa;
+                return SearchSpaceGroup(merge.merged, o).best_space_group;
+            }).share();
+        }
         bool all_arm_beside = false;
         if (all_arm) {
             rsm_all = rsm->CloneIngest(all_arm_device, all_arm_log);
@@ -1346,6 +1531,19 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             if (all_arm_beside)
                 all_arm_ahead = start_all_arm();
         }
+        // The pre-pass's prediction, where it is in: a search still running is one the merge is not waited for.
+        if (!cards_ahead.empty() && predicted_group_.valid()
+            && predicted_group_.wait_for(std::chrono::seconds(0)) == std::future_status::ready) {
+            std::optional<gemmi::SpaceGroup> predicted;
+            try {
+                predicted = predicted_group_.get();
+            } catch (const std::exception &e) {
+                logger.Debug("Final merge ahead: the pre-pass search failed ({})", e.what());
+            }
+            logger.Debug("Final merge ahead: the pre-pass predicts {}", predicted ? predicted->xhm() : "no group");
+            if (predicted)
+                merge_ahead(*predicted);
+        }
     }
 
     // The geometry pre-pass reads the per-image reflections exactly twice more: they were just
@@ -1427,7 +1625,8 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             phase("Partiality post-refine (" + label + ")");
             TimingMark refine_mark(logger, "stills partiality post-refine " + label);
             StillsPartialityRefine refiner(experiment_);
-            const double mean_tilt = refiner.Run(indexer->GetIntegrationOutcome(), config_.nthreads, result.consensus_cell);
+            const double mean_tilt = refiner.Run(indexer->GetIntegrationOutcome(), config_.nthreads, result.consensus_cell,
+                                                 stills_run_width_, &end_msg.stills_run_width);
             logger.Info("Stills partiality post-refine: mean |dpsi| = {:.3f} deg", mean_tilt);
             // The refine fits its OWN per-image scale, with no floor, and adopts it unconditionally
             // when the image has no prior CC - which is exactly the state the guard above leaves. So
@@ -1493,6 +1692,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         {   // stills: no asymptote tier, and its ISa already IS the whole-range 1/b
             const auto em = ToXdsErrorModel(merge_engine.ErrorModelA(), merge_engine.ErrorModelB());
             result.error_model_isa = em.isa;
+            result.error_model_isa_resolved = merge_engine.ErrorModelBResolved();
             result.error_model_a = em.a;
             result.error_model_b = em.b;
         }
@@ -1507,6 +1707,25 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     const bool guard_beside = merge_first_part && guard_ahead.valid();
     if (guard_beside)
         rsm->SetWriteBackPerFrameScale(false);
+    // Stills with a reference or a model: each image was put into the indexing that agrees best with it,
+    // image by image. Where the crystals' own cells decide an indexing, those cells come first, and the
+    // reference decides only the crystals they leave open. Before the relabel below, which changes axes.
+    if (!rsm && ambiguity_reference && result.consensus_cell && experiment_.GetUnitCell()
+        && experiment_.GetGemmiSpaceGroup()) {
+        const auto ops = ReindexAmbiguityOperators(*experiment_.GetUnitCell(), experiment_.GetSpaceGroupOrP1());
+        if (!ops.empty()) {
+            const auto anchored = AnchorReferenceReindex(indexer->GetIntegrationOutcome(), *result.consensus_cell,
+                                                         ops);
+            for (size_t i = 0; i < ops.size(); ++i)
+                logger.Info("Indexing ambiguity {}: {:.1f}% of the crystals' own cells fit better as indexed{}",
+                            IndexTriplet(ops[i]), 100.0 * anchored.metric_preference[i],
+                            anchored.metric_preference[i] >= METRIC_DECIDED
+                                ? " - the cells decide it; the reference decides only crystals whose cell does not"
+                                : "");
+            logger.Info("Indexing ambiguity: {} crystal(s) the reference had put against their own cell kept "
+                        "in an indexing the cell allows", anchored.overruled);
+        }
+    }
     // Stills: a crystal indexed in a lattice that contains the run's - an axis multiple, or the run's in
     // another setting - is put on the run's cell before anything is scaled, rather than left out.
     if (!rsm && result.consensus_cell) {
@@ -1517,6 +1736,47 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                     relabel.frames, relabel.reflections_kept, relabel.reflections_dropped);
     }
     const auto initial_sg = experiment_.GetGemmiSpaceGroup();
+    // Stills in a group whose lattice admits alternative indexings: each crystal was indexed in one of
+    // them at random. With a reference or a model each image has already been put into the reference's
+    // (IndexAndRefine::ScaleImage); without one the indexings are made consistent here, from the data
+    // alone, before anything is scaled. With one, the same is done only to measure it against the
+    // reference's answer.
+    if (!rsm && initial_sg && result.consensus_cell) {
+        const auto ops = ReindexAmbiguityOperators(*result.consensus_cell, *initial_sg);
+        if (!ops.empty()) {
+            const auto t0 = std::chrono::steady_clock::now();
+            const auto rf = ResolveReindexReferenceFree(indexer->GetIntegrationOutcome(), experiment_,
+                                                        *result.consensus_cell, ops, config_.nthreads,
+                                                        /*apply=*/!ambiguity_reference);
+            result.ambiguity_time_s = std::chrono::duration<double>(std::chrono::steady_clock::now() - t0).count();
+            for (size_t i = 0; i < ops.size(); ++i)
+                logger.Info("Indexing ambiguity {}: {:.1f}% of the crystals' own cells fit better as indexed{}",
+                            IndexTriplet(ops[i]), 100.0 * rf.metric_preference[i],
+                            rf.metric_preference[i] >= METRIC_DECIDED
+                                ? " - the cells decide it; only crystals whose cell does not are decided by "
+                                  "the intensities" : "");
+            result.ambiguity_reference_free = true;
+            result.ambiguity_reference_free_applied = !ambiguity_reference;
+            result.ambiguity_crystals = rf.crystals;
+            result.ambiguity_reindexed = rf.reindexed;
+            result.ambiguity_separation_sigma = rf.median_sigma;
+            result.ambiguity_decided_fraction = rf.decided_fraction;
+            if (!ambiguity_reference)
+                logger.Info("Indexing ambiguity resolved from the data: {} of {} crystals reindexed; median "
+                            "separation {:.1f} sigma, {:.0f}% of crystals decided at over 3 sigma (CC with the "
+                            "rest {:.3f} as chosen, {:.3f} otherwise); {} sweeps, {:.2f} s",
+                            rf.reindexed, rf.crystals, rf.median_sigma, 100.0 * rf.decided_fraction,
+                            rf.cc_chosen, rf.cc_other, rf.sweeps, result.ambiguity_time_s);
+            else
+                logger.Info("Indexing ambiguity from the data alone, against the reference's: it would put {} "
+                            "of {} crystals into another indexing; median separation {:.1f} sigma, {:.0f}% of "
+                            "crystals decided at over 3 sigma; {:.2f} s", rf.reindexed, rf.crystals,
+                            rf.median_sigma, 100.0 * rf.decided_fraction, result.ambiguity_time_s);
+            Note(fmt::format("indexing ambiguity from the data: {} of {} crystals {}", rf.reindexed, rf.crystals,
+                             ambiguity_reference ? "disagree with the reference" : "reindexed"));
+            ambiguity_reference = true;
+        }
+    }
     auto sm = scale_and_merge(initial_sg ? initial_sg->short_name() : "P1", !initial_sg.has_value(),
                               /*measure_cc=*/true);
     if (guard_beside) {
@@ -1695,66 +1955,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
 
     double d_min_search = 0.0;
     if (search_space_group) {
-        std::vector<std::pair<float, float>> rs;   // (d, I/sigma) over the full P1 merge
-        rs.reserve(sm.merged.size());
-        for (const auto &m : sm.merged)
-            if (std::isfinite(m.I) && std::isfinite(m.sigma) && m.sigma > 0.0f &&
-                std::isfinite(m.d) && m.d > 0.0f)
-                rs.emplace_back(m.d, m.I / m.sigma);
-        if (rs.size() >= 400) {
-            std::sort(rs.begin(), rs.end(),
-                      [](const auto &a, const auto &b) { return a.first > b.first; });   // low -> high res
-            const int bins = std::clamp(static_cast<int>(rs.size() / 100), 1, 40);
-            const size_t per = (rs.size() + bins - 1) / static_cast<size_t>(bins);
-            // The shell means, then their best NON-INCREASING fit (pool adjacent violators, weighted
-            // by shell size). The cut is where the FIT drops under 1, not where the first shell
-            // does: on a merge whose <I/sigma> is flat near 1 - its ISa has collapsed - the first
-            // single shell to dip under 1 is a coin toss that moved the cut from 0.85 to 1.19 A
-            // between two compiler flags on one crystal, and the coarser cut left its glide zones
-            // too few absences to be judged. The fit moves by as much as its input does.
-            std::vector<double> mean, weight;
-            for (size_t lo = 0; lo < rs.size(); lo += per) {
-                const size_t hi = std::min(rs.size(), lo + per);
-                double sum = 0.0;
-                for (size_t j = lo; j < hi; ++j) sum += rs[j].second;
-                mean.push_back(sum / static_cast<double>(hi - lo));
-                weight.push_back(static_cast<double>(hi - lo));
-            }
-            std::vector<double> block_mean, block_weight;
-            std::vector<size_t> block_size;
-            for (size_t b = 0; b < mean.size(); ++b) {
-                block_mean.push_back(mean[b]); block_weight.push_back(weight[b]); block_size.push_back(1);
-                while (block_mean.size() > 1 && block_mean[block_mean.size() - 2] < block_mean.back()) {
-                    const size_t k = block_mean.size() - 1;
-                    const double w = block_weight[k - 1] + block_weight[k];
-                    block_mean[k - 1] = (block_mean[k - 1] * block_weight[k - 1] + block_mean[k] * block_weight[k]) / w;
-                    block_weight[k - 1] = w;
-                    block_size[k - 1] += block_size[k];
-                    block_mean.pop_back(); block_weight.pop_back(); block_size.pop_back();
-                }
-            }
-            std::vector<double> fit;
-            for (size_t k = 0; k < block_mean.size(); ++k)
-                fit.insert(fit.end(), block_size[k], block_mean[k]);
-            for (size_t b = 0; b < fit.size(); ++b) {
-                const size_t lo = b * per;
-                if (fit[b] < 1.0) {
-                    // Cut the noise-dominated high-res shells. When even the lowest-res shell fails,
-                    // keep that shell alone rather than abandoning the cut. The bound is absolute
-                    // while the merged I/sigma it tests saturates at the merge's own ISa (times the
-                    // square root of the multiplicity), so a merge whose ISa has collapsed towards 1
-                    // can fail it in every shell - and that is exactly the merge the search must not
-                    // be handed whole, since the noise which drove ISa down is what the cut exists to
-                    // remove. Abandoning it feeds back: more noise into the search, a weaker operator
-                    // statistic, and a lost symmetry.
-                    if (b > 0)
-                        d_min_search = rs[lo].first;
-                    else if (per >= 400)
-                        d_min_search = rs[per - 1].first;
-                    break;
-                }
-            }
-        }
+        d_min_search = SearchCut(sm.merged);
         const double d_manual = experiment_.GetScalingSettings().GetHighResolutionLimit_A().value_or(0.0);
         if (rsm && d_min_search > d_manual) {
             logger.Info("Space-group search: re-scaling the P1 pass at {:.2f} A (<I/sigma> >= 1)", d_min_search);
@@ -1852,6 +2053,11 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         // else. Whether the all-observation arm is wanted at all is known only from the first arm
         // (below), so nothing of it reaches the run before then. A merge that failed beside the
         // others is made again where it is wanted, in series, as it would have been without it.
+        // The first arm's search runs beside the wait for that merge and the search on it.
+        TimingMark first_arm_mark(logger, "SearchSpaceGroup (first arm)");
+        auto first_search_ahead = std::async(std::launch::async, [&merged = sm.merged, sg_opts] {
+            return SearchSpaceGroup(merged, sg_opts);
+        });
         std::optional<RotationScaleMerge::Result> all_merge;
         std::future<SearchSpaceGroupResult> all_search_ahead;
         if (rsm_all && !all_arm_ahead.valid())
@@ -1866,6 +2072,29 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             }
             wait_mark.Stop();
         }
+        // The twinning evidence measured before any promotion (see the decisions below), on the merge the arms
+        // carry forward - the all-observation one wherever it is there. Where the final merge is being made
+        // ahead, nothing else is left to hide that measurement behind, so it starts here, on a copy of the
+        // all-observation merge, beside the searches, and is taken below where that merge is carried forward
+        // in the same cell and centring.
+        const auto pre_promotion_analysis = [nthreads = config_.nthreads](const std::vector<MergedReflection> &merged,
+                                                                          std::optional<UnitCell> cell, char centring) {
+            TranslationalNCSResult tncs;
+            if (cell)
+                tncs = AnalyzeTranslationalNCS(merged, gemmi::UnitCell(*cell), nullptr, 30, 0, nthreads);
+            auto twinning = AnalyzeTwinning(merged, nullptr, 20, TranslationalNCSVectorForLTest(tncs), centring);
+            return std::make_pair(tncs, twinning);
+        };
+        const std::optional<UnitCell> early_cell = result.consensus_cell;
+        const char early_centring = end_msg.rotation_lattice_type.has_value()
+                                    ? end_msg.rotation_lattice_type->centering : 'P';
+        std::future<std::pair<TranslationalNCSResult, TwinningAnalysisResult>> pre_promotion_early;
+        bool all_merge_carried = false;
+        if (all_merge && !cards_ahead.empty())
+            pre_promotion_early = std::async(std::launch::async, [pre_promotion_analysis, merged = all_merge->merged,
+                                                                  early_cell, early_centring] {
+                return pre_promotion_analysis(merged, early_cell, early_centring);
+            });
         if (all_merge) {
             SearchSpaceGroupOptions all_opts = sg_opts;
             all_opts.merge_isa = all_merge->isa;   // as take_merge leaves it below
@@ -1873,9 +2102,18 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                 return SearchSpaceGroup(merged, all_opts);
             });
         }
-        TimingMark first_arm_mark(logger, "SearchSpaceGroup (first arm)");
-        auto sg_search = SearchSpaceGroup(sm.merged, sg_opts);
+        auto sg_search = first_search_ahead.get();
         first_arm_mark.Stop();
+        // The first arm's group, merged ahead as well where it is not the one the pre-pass predicted and a card
+        // is left for it: the pre-pass's merge is of a third of the frames, and a screw axis its few axial
+        // reflections could not settle is read here on all of them. Where the first arm has no group either,
+        // nothing is merged ahead - the decisions are what will make one.
+        if (sg_search.best_space_group && merges_ahead.size() < cards_ahead.size()
+            && std::none_of(merges_ahead.begin(), merges_ahead.end(), [&](const MergeAhead &m) {
+                   return std::strcmp(m.group.hall, sg_search.best_space_group->hall) == 0; })) {
+            logger.Debug("Final merge ahead: the first arm finds {}", sg_search.best_space_group->xhm());
+            merge_ahead(*sg_search.best_space_group);
+        }
 
         // The Lorentz-filtered arm's merge, kept past the point where the all-observation one
         // replaces it. The metric re-ask below is a search like any other and answers to the same
@@ -2073,6 +2311,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             // second opinion reported above.
             merged_filtered = std::move(sm.merged);
             sm = std::move(sm_all);
+            all_merge_carried = all_merge.has_value();
         }
 
         // The arm merged beside the search is done with - or was not needed - before anything below
@@ -2110,15 +2349,12 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         // cell is taken now: a change of basis committed below replaces it.
         const char lattice_centring = end_msg.rotation_lattice_type.has_value()
                                       ? end_msg.rotation_lattice_type->centering : 'P';
-        auto pre_promotion = std::async(std::launch::async,
-                                        [&merged = sm.merged, cell = result.consensus_cell,
-                                         lattice_centring, nthreads = config_.nthreads] {
-            TranslationalNCSResult tncs;
-            if (cell)
-                tncs = AnalyzeTranslationalNCS(merged, gemmi::UnitCell(*cell), nullptr, 30, 0, nthreads);
-            auto twinning = AnalyzeTwinning(merged, nullptr, 20, TranslationalNCSVectorForLTest(tncs),
-                                            lattice_centring);
-            return std::make_pair(tncs, twinning);
+        auto pre_promotion = pre_promotion_early.valid() && all_merge_carried && early_cell == result.consensus_cell
+                             && early_centring == lattice_centring
+                ? std::move(pre_promotion_early)
+                : std::async(std::launch::async, [&merged = sm.merged, cell = result.consensus_cell, lattice_centring,
+                                                  pre_promotion_analysis] {
+            return pre_promotion_analysis(merged, cell, lattice_centring);
         });
         TranslationalNCSResult pre_tncs;
         const auto join_pre_promotion = [&] {
@@ -2706,6 +2942,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                                         static_cast<int>(config_.scaling_iter),
                                         config_.nthreads, logger, config_.observation_dump);
                             rsm->Ingest();
+                            spec_same_ingest = false;
                         }
                         const auto &uc = *result.consensus_cell;
                         logger.Info("{} names a cell of {}x the volume of its reference setting: the "
@@ -2945,6 +3182,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                                         result.consensus_cell, static_cast<int>(config_.scaling_iter),
                                         config_.nthreads, logger, config_.observation_dump);
                             rsm->Ingest();
+                            spec_same_ingest = false;
                         }
                     }
                 }
@@ -2959,6 +3197,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                     for (auto &r : io.reflections)
                         reindex_hkl(r, *commit_reindex);
                 }
+                spec_same_ingest = false;
                 result.consensus_cell = commit_cell;
                 result.consensus_centering = commit_lattice_type->centering;
                 end_msg.unit_cell = commit_cell;
@@ -2972,6 +3211,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                                 static_cast<int>(config_.scaling_iter),
                                 config_.nthreads, logger, config_.observation_dump);
                     rsm->Ingest();
+                    spec_same_ingest = false;
                 }
             }
             experiment_.SetSpaceGroup(sg);
@@ -2980,15 +3220,52 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             result.space_group = sg;
             decisions_mark.Stop();
             phase("Re-scaling in space group " + sg.short_name());
-            auto adopted = scale_and_merge(sg.short_name(), false);
+            // The merge made ahead in this group on this ingest is taken, with its per-frame scales and its
+            // partial-scaling choice, which the merges after it keep as they would on this engine. The others
+            // are left to end on their own (merges_ahead reaps them when the step is over): one started at the
+            // first arm's answer is still merging here, and waiting for it put the whole of it on the critical
+            // path - 0.9 s of a 2.8 s step on a four-card server.
+            std::optional<std::pair<RotationScaleMerge::Result, CentreOfSymmetryResult>> ahead;
+            for (MergeAhead &m : merges_ahead) {
+                if (!spec_same_ingest || std::strcmp(m.group.hall, sg.hall) != 0) {
+                    logger.Debug("Final merge ahead: made in {}, the run adopts {}{} - not taken", m.group.xhm(),
+                                 sg.xhm(), spec_same_ingest ? "" : " on a new ingest");
+                    continue;
+                }
+                TimingMark mark(logger, "merge " + sg.short_name() + " (made ahead, wait)");
+                try {
+                    ahead = m.ahead.get();
+                } catch (const std::exception &e) {
+                    logger.Warning("The final merge made ahead failed ({}); it is made again", e.what());
+                }
+                mark.Stop();
+                m.log.ReplayInto(logger);
+                if (ahead) {
+                    m.rsm->WriteBackPerFrameScale();
+                    rsm->TakeScalePartialsChoice(*m.rsm);
+                }
+                m.rsm.reset();
+            }
+            ScaleMergeResult adopted;
+            if (ahead) {
+                logger.Info("Final merge: made ahead in {}", sg.xhm());
+                adopted = take_merge(sg.short_name(), false, std::move(ahead->first));
+            } else {
+                adopted = scale_and_merge(sg.short_name(), false);
+            }
+            TimingMark pre_promotion_mark(logger, "pre-promotion analyses wait");
             join_pre_promotion();
+            pre_promotion_mark.Stop();
             sm = std::move(adopted);
 
             // The intensity statistics for the centre, on this merge - the full one, resolution-cut and
             // corrected, in the adopted group. Read on every run and reported, Sohncke groups included,
             // so a chiral small molecule's reader sees them too; they decide only between a glide
             // group and its partner with the same absences (see above).
-            result.centre_statistics = AnalyzeCentreOfSymmetry(sm.merged, sg);
+            {
+                TimingMark centre_mark(logger, "centre-of-symmetry statistics");
+                result.centre_statistics = ahead ? ahead->second : AnalyzeCentreOfSymmetry(sm.merged, sg, config_.nthreads);
+            }
             if (centre_partner && sg.is_centrosymmetric() && result.centre_statistics->reads_acentric
                 && result.centre_twinning_excluded) {
                 logger.Info("Centre of symmetry: {} and {} predict the same absences; the intensity "
@@ -3604,7 +3881,9 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
 
     // Diffraction anisotropy (see where it is reported, below), made beside the analyses that come
     // before it: it reads the merge, the integrated observations and the per-frame scales the merge
-    // wrote back, none of which they change, and most of it is gathering the observations.
+    // wrote back, none of which they change, and most of it is gathering the observations. It runs on
+    // beside the molecular replacement too (finish_analyses), so it takes its own copy of the group: the
+    // enantiomorph relabelling there changes the experiment's.
     std::future<decltype(sm.statistics.anisotropy)> anisotropy;
     if (!geometry_prepass && !superseded && result.consensus_cell) {
         AnisotropyRunInfo aniso_run;
@@ -3612,14 +3891,16 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             aniso_run.observed_rotation_deg = sm.statistics.sweep_quality.sweep_deg;
         aniso_run.dose_term_in_scale_model = experiment_.GetScalingSettings().GetCorrectionSurfaces();
         aniso_run.radiation_damage_relative_b = sm.statistics.radiation_damage_delta_b;
+        aniso_run.nthreads = config_.nthreads;
         const float wedge_deg = experiment_.GetGoniometer() ? experiment_.GetGoniometer()->GetWedge_deg() : 0.0f;
         anisotropy = std::async(std::launch::async,
-                [&, aniso_run, wedge_deg, cell = *result.consensus_cell,
+                [&, aniso_run, wedge_deg, cell = *result.consensus_cell, sg = twin_sg_opt,
                  rotation = experiment_.IsRotationIndexing()] {
+            const gemmi::SpaceGroup *g = sg ? &*sg : nullptr;
             return AnalyzeAnisotropy(sm.merged,
-                                     ScaledObservations(indexer->GetIntegrationOutcome(), rotation, twin_sg,
+                                     ScaledObservations(indexer->GetIntegrationOutcome(), rotation, g,
                                                         wedge_deg, 0.5, config_.nthreads),
-                                     cell, twin_sg, aniso_run);
+                                     cell, g, aniso_run);
         });
     }
     // fast_live, cut (the broker's deadline or a cancel): the model is left out, and the files are written
@@ -3758,6 +4039,47 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                                         report_shell_d_min, first_schedule);
         });
     }
+    // The molecular replacement (below): the search started on the geometry pre-pass's merge, where there is one,
+    // taken over where it holds on this one - not where the twin hypothesis' merge is searched too, as that search
+    // is this merge's own - and this merge searched itself where it does not.
+    const auto search_model = [&](const std::vector<MRMerge> &merges, Logger &log) {
+        if (early_mr_ && merges.size() == 1) {
+            TimingMark early_mark(log, "early molecular replacement wait");
+            try {
+                MolecularReplacementResult early = early_mr_->run.get();
+                early_mark.Stop();
+                early_mr_->log.ReplayInto(log);
+                if (auto carried = CarryMolecularReplacement(
+                        early, {"geometry pre-pass's merge", &early_mr_->merged, early_mr_->cell, early_mr_->space_group},
+                        merges[0], log, static_cast<size_t>(config_.nthreads), merge_on_card))
+                    return std::move(*carried);
+            } catch (const std::exception &e) {
+                log.Warning("Molecular replacement on the geometry pre-pass's merge failed ({}) - searched again",
+                            e.what());
+            }
+        }
+        return RunMolecularReplacement(*config_.model, merges, log, static_cast<size_t>(config_.nthreads),
+                                       merge_on_card);
+    };
+    // A prediction, or --mr, has no validation to start here, but the search reads of the merge only its amplitudes
+    // too. Where there is no twin hypothesis' merge to search beside it and no reference to take the free set from,
+    // nothing up to the search changes the merge or the group, so it starts here the same way, beside the analyses,
+    // on a copy given the same amplitudes. Its log is held, and printed where it is taken.
+    Logger model_search_log = Logger::Buffered();
+    std::future<MolecularReplacementResult> model_search_run;
+    if (model_run && (model_predicted || config_.force_mr) && !twin_merge && !model_twin_merge
+        && config_.reference_data.empty()) {
+        model_merged = sm.merged;
+        model_search_run = std::async(std::launch::async,
+                [&, device = get_gpu(), sg = experiment_.GetSpaceGroupOrP1()] {
+            set_gpu(device);
+            FrenchWilsonOptions fw_opts;
+            fw_opts.num_threads = config_.nthreads;
+            fw_opts.anisotropy_hkl = AnisotropyPriorHKL(model_merged, gemmi::UnitCell(*result.consensus_cell), twin_sg);
+            ApplyFrenchWilson(model_merged, sg, fw_opts);
+            return search_model({{"MERGE", &model_merged, *result.consensus_cell, sg}}, model_search_log);
+        });
+    }
     // Not on the geometry pre-pass, nor on a superseded one: the analysis goes into that pass's
     // statistics text and its written reflections, and neither survives the run. The promotion flag
     // below is a different thing - it is what the SEARCH did, the second pass reads it, and it is
@@ -3766,9 +4088,11 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         // Translational pseudo-symmetry first: its verdict is an input to the twinning analysis,
         // which must not read its own L-test when a non-half-integer pseudo-translation has biased
         // it. Reporting only - no reflection and no merge depends on the outcome.
+        TimingMark tncs_mark(logger, "analyses/tNCS");
         if (result.consensus_cell)
             result.tncs = AnalyzeTranslationalNCS(sm.merged, gemmi::UnitCell(*result.consensus_cell),
                                                   twin_sg, 30, 0, config_.nthreads);
+        tncs_mark.Stop();
         if (result.tncs.detected)
             logger.Warning("Translational pseudo-symmetry: Patterson off-origin peak {:.1f}% of the "
                            "origin at ({:.3f}, {:.3f}, {:.3f}), {:.1f} A - declare it to the "
@@ -3786,9 +4110,11 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                                      ? end_msg.rotation_lattice_type->centering : 'P';
         const std::optional<gemmi::UnitCell> twin_cell =
                 result.consensus_cell ? std::optional<gemmi::UnitCell>(*result.consensus_cell) : std::nullopt;
+        TimingMark twinning_mark(logger, "analyses/twinning");
         result.twinning = AnalyzeTwinning(sm.merged, twin_sg, 20,
                                          TranslationalNCSVectorForLTest(result.tncs), twin_centring,
                                          twin_cell ? &*twin_cell : nullptr);
+        twinning_mark.Stop();
         // Set on the struct the text below is rendered from. AnalyzeTwinning returns a fresh result
         // with this flag clear, so setting it only afterwards left the statistics text asserting
         // "No twinning: the Laue class is holohedral" as a fact while the report, rendering the same
@@ -3963,13 +4289,17 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                 const std::string msg = fmt::format(
                     "Indexing ambiguity: this cell / space group admits alternative indexing "
                     "(reindex operator(s): {}). Serial-stills crystals are indexed in one hand at random, "
-                    "and rugnux can only break this against an external reference. WITHOUT one the merge "
-                    "mixes the hands and CC1/2 is degraded; a reference MTZ (-z) or a model (--model, "
-                    "which needs -C and -S here) resolves it.", laws);
+                    "and rugnux makes them consistent from the data only where the space group is given: "
+                    "here it was determined by the run, so the merge mixes the hands and CC1/2 is degraded. "
+                    "Giving the space group (-S) resolves it from the data; a reference MTZ (-z) or a model "
+                    "(--model, which needs -C and -S here) resolves it against them.", laws);
                 logger.Warning("{}", msg);
                 ambiguity_warning_text = "  !! " + msg + "\n\n";
                 stats_text << ambiguity_warning_text;
                 result.warnings.push_back({PathologyCode::INDEXING_AMBIGUITY, msg});
+            } else if (result.ambiguity_reference_free_applied) {
+                logger.Info("Indexing ambiguity present (reindex operator(s): {}); resolved "
+                            "from the data.", laws);
             } else {
                 logger.Info("Indexing ambiguity present (reindex operator(s): {}); resolved "
                             "against the supplied reference.", laws);
@@ -3998,15 +4328,16 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         // tensor directions the symmetry forbids - the only place a dataset measures its own
         // systematic error - are identically zero in it.
         if (anisotropy.valid()) {
-            sm.statistics.anisotropy = anisotropy.get();
-            stats_text << AnisotropyToText(sm.statistics.anisotropy) << "\n";
             // The amplitudes are the one place the tensor is used: French-Wilson with the Wilson
             // prior of each reflection taken along its own direction. The intensities and
-            // everything measured on them above are left as they are.
+            // everything measured on them above are left as they are. The tensor is the analysis'
+            // own, fitted to the merge alone (AnisotropyPriorHKL), so the model work does not wait for
+            // the rest of the analysis, which is taken once that is done (finish_analyses). The analysis
+            // reads the intensities only; French-Wilson writes the amplitudes only.
             FrenchWilsonOptions fw_opts;
             fw_opts.num_threads = config_.nthreads;
-            fw_opts.anisotropy_hkl = AnisotropyTensorHKL(sm.statistics.anisotropy,
-                                                         gemmi::UnitCell(*result.consensus_cell));
+            fw_opts.anisotropy_hkl = AnisotropyPriorHKL(sm.merged, gemmi::UnitCell(*result.consensus_cell),
+                                                        twin_sg);
             ApplyFrenchWilson(sm.merged, experiment_.GetSpaceGroupOrP1(), fw_opts);
         } else if (rsm) {
             // No tensor: the isotropic prior. The rotation merge leaves its amplitudes to here.
@@ -4016,10 +4347,21 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         }
     }
 
-    stats_text << sm.statistics;
-    result.merge_statistics_text = stats_text.str();
-    result.has_merge_statistics = true;
-    result.merge_statistics = sm.statistics;
+    // The anisotropy and the statistics text it ends, once the model work has gone ahead: before the
+    // validation below, which edits the text and moves the merge to the model's frame, or after the
+    // molecular replacement.
+    const auto finish_analyses = [&] {
+        if (anisotropy.valid()) {
+            TimingMark anisotropy_mark(logger, "analyses/anisotropy wait");
+            sm.statistics.anisotropy = anisotropy.get();
+            anisotropy_mark.Stop();
+            stats_text << AnisotropyToText(sm.statistics.anisotropy) << "\n";
+        }
+        stats_text << sm.statistics;
+        result.merge_statistics_text = stats_text.str();
+        result.has_merge_statistics = true;
+        result.merge_statistics = sm.statistics;
+    };
     result.reference_merge_statistics = sm.reference_statistics;
     result.reference_isa = sm.reference_isa;
 
@@ -4353,6 +4695,8 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     std::optional<ModelPriorFile> model_prior_file;
     // The coordinates that go with the maps beside the answer's files, kept once the model is done.
     std::optional<PlacedModelOutput> placed_model_out;
+    // The merge that placement was made against, which refinement refines it against.
+    const std::vector<MergedReflection> *placed_merged = nullptr;
     // The twin hypothesis the model is asked about: its own subgroup's merge where it has one, the data's
     // otherwise - and whether that merge was made only for the model, so is written only where it chooses it.
     std::optional<TwinFile> &model_twin = model_twin_merge ? model_twin_file : twin_file;
@@ -4364,7 +4708,10 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
     // for by molecular replacement below.
     bool placed_by_rigid_body = false;
     bool twin_chosen_by_model = false;
-    if (model_run && !model_predicted && !config_.force_mr) {
+    const bool validated_first = model_run && !model_predicted && !config_.force_mr;
+    if (validated_first)
+        finish_analyses();
+    if (validated_first) {
         phase("Validating against model");
         Step("Model validation");
         TimingMark mark(logger, "model validation");
@@ -4532,8 +4879,10 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                                               twin_validation.r_free_twin, twin_validation.twin_fraction)
                                 : std::string(),
                         maps_from_twin ? "the merge in " + mt.space_group.xhm() : "the answer's merge");
-            if (maps_from_twin && twin_validation.placed_model)
+            if (maps_from_twin && twin_validation.placed_model) {
                 placed_model_out = PlacedModelOutput{twin_validation.placed_model, mt.cell, mt.space_group};
+                placed_merged = &mt.merged;
+            }
             // The model placed there and fitting better there chooses the subgroup: its files, <prefix>_mr. They
             // carry the model's own group where it has the subgroup's rotations - the screws and the hand are the
             // model's, as the coordinates beside them are, unless the anomalous map at its atoms is inverted - and
@@ -4559,9 +4908,11 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
             mt_report.maps_from_this_merge = maps_from_twin;
             mt_report.model_validation = std::move(twin_validation);
         }
-        if (validation.placed_model && !maps_from_twin)
+        if (validation.placed_model && !maps_from_twin) {
             placed_model_out = PlacedModelOutput{validation.placed_model, *result.consensus_cell,
                                                experiment_.GetSpaceGroupOrP1()};
+            placed_merged = &sm.merged;
+        }
     }
     prepare_twin_file();
 
@@ -4581,31 +4932,19 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         if (!ledger_ahead.valid())
             rsm.reset();
         const size_t merge_on_card = rsm && rsm->OnGPU() ? rsm->DeviceBytes() : 0;
-        std::vector<MRMerge> merges{{"MERGE", &sm.merged, *result.consensus_cell, experiment_.GetSpaceGroupOrP1()}};
-        if (model_twin)
-            merges.push_back({"TWIN_SUBGROUP_MERGE", &model_twin->merged, model_twin->cell, model_twin->space_group,
-                              model_twin->law});
-        // The search started on the geometry pre-pass's merge, where there is one, taken over where it holds on
-        // this one. Not where the twin hypothesis' merge is searched too: that search is this merge's own.
-        std::optional<MolecularReplacementResult> carried;
-        if (early_mr_ && !model_twin) {
-            TimingMark early_mark(logger, "early molecular replacement wait");
-            try {
-                MolecularReplacementResult early = early_mr_->run.get();
-                early_mark.Stop();
-                early_mr_->log.ReplayInto(logger);
-                carried = CarryMolecularReplacement(
-                        early, {"geometry pre-pass's merge", &early_mr_->merged, early_mr_->cell, early_mr_->space_group},
-                        merges[0], logger, static_cast<size_t>(config_.nthreads), merge_on_card);
-            } catch (const std::exception &e) {
-                logger.Warning("Molecular replacement on the geometry pre-pass's merge failed ({}) - searched again",
-                               e.what());
-            }
+        MolecularReplacementResult mr;
+        if (model_search_run.valid()) {
+            TimingMark wait_mark(logger, "molecular replacement (beside the analyses) wait");
+            mr = model_search_run.get();
+            wait_mark.Stop();
+            model_search_log.ReplayInto(logger);
+        } else {
+            std::vector<MRMerge> merges{{"MERGE", &sm.merged, *result.consensus_cell, experiment_.GetSpaceGroupOrP1()}};
+            if (model_twin)
+                merges.push_back({"TWIN_SUBGROUP_MERGE", &model_twin->merged, model_twin->cell,
+                                  model_twin->space_group, model_twin->law});
+            mr = search_model(merges, logger);
         }
-        MolecularReplacementResult mr = carried ? std::move(*carried)
-                                                : RunMolecularReplacement(*config_.model, merges, logger,
-                                                                          static_cast<size_t>(config_.nthreads),
-                                                                          merge_on_card);
         if (mr.chosen >= 0) {
             const MRCandidate &c = mr.candidates[mr.chosen];
             if (mr.decision == "ENANTIOMORPH")
@@ -4665,13 +5004,46 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                 }
                 if (own)
                     model_prior_file->placed = v.placed_model;
-                else
+                else {
                     placed_model_out = PlacedModelOutput{v.placed_model, cell, data_sg};
+                    placed_merged = &sm.merged;
+                }
                 result.model_validation = std::move(v);
             }
         }
         result.model_prior = std::move(mr);
     }
+    if (!validated_first)
+        finish_analyses();
+
+    // The cell's e.s.d.s (CellEsd.h), from the same integrated observations and at the same point as the
+    // unmerged MTZ below: the indexing and the group are final here, once the model has been read. Rotation
+    // only - a stills run keeps no per-image reflections to the end, and its crystals' cells differ by more than
+    // any one is measured to. Made beside the refinement, which reads neither.
+    std::future<std::optional<CellEsd>> cell_esd;
+    if (is_rotation && !geometry_prepass && !superseded && result.consensus_cell)
+        cell_esd = std::async(std::launch::async, [&outcomes = indexer->GetIntegrationOutcome(),
+                                                   sg = experiment_.GetSpaceGroupOrP1(),
+                                                   wavelength = experiment_.GetWavelength_A(),
+                                                   nthreads = config_.nthreads, &logger = logger] {
+            TimingMark mark(logger, "cell e.s.d.");
+            return EstimateCellEsd(GatherCellObservations(outcomes, nthreads), sg, wavelength);
+        });
+
+    // The unmerged MTZ (kept with the other outputs, see there) is built from here on, beside the
+    // refinement and the reflection files: the indexing and the group it is written in are final once the
+    // model has been read, and nothing after this changes the integrated observations it reads. It gets its
+    // own copy of the experiment.
+    if (full && write_output && !geometry_prepass && !superseded && result.consensus_cell
+        && config_.export_unmerged) {
+        unmerged_mtz = std::async(std::launch::async,
+                                  [&outcomes = indexer->GetIntegrationOutcome(),
+                                   cell = *result.consensus_cell, x = experiment_,
+                                   &provenance = config_.provenance, nthreads = config_.nthreads] {
+            return UnmergedMtzTable(outcomes, cell, x, true, provenance, nthreads);
+        });
+    }
+
     if (model_run) {
         result.model_placement = placed_by_rigid_body ? "RIGID_BODY"
                                  : result.model_prior && result.model_prior->chosen >= 0 ? "MR" : "NOT_PLACED";
@@ -4692,20 +5064,75 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
         if (model_prior_file)
             result.model_prior_file_space_group = model_prior_file->space_group.xhm();
         result.outputs->placed_model = placed_model_out;
+        // The outcome, as notes of the step that decided it
+        if (result.model_prior) {
+            const MolecularReplacementResult &mp = *result.model_prior;
+            if (mp.chosen >= 0) {
+                const MRCandidate &c = mp.candidates[mp.chosen];
+                Note(fmt::format("placed {} {} in {}: TFZ {:.1f}, RFZ {:.1f}", c.copies, c.copies == 1 ? "copy" : "copies",
+                                 c.space_group.xhm(), c.tf_z, c.rf_z));
+            } else
+                Note(mp.ok ? mp.decision : "not searched: " + mp.failure_reason);
+        }
+        if (result.model_validation && result.model_validation->ok) {
+            const ModelValidationResult &v = *result.model_validation;
+            std::string note = fmt::format("R-work {:.3f}, R-free {:.3f} (unrefined)", v.r_work, v.r_free);
+            if (std::isfinite(v.cc_model_overall))
+                note += fmt::format(", CC(model, data) {:.3f}", v.cc_model_overall);
+            Note(note);
+            if (v.rigid_body_applied)
+                Note(fmt::format("rigid body: {:.2f} deg, {:.2f} A", v.rigid_body_angle_deg, v.rigid_body_shift_A));
+        }
+        // The placed model refined against the merge it was placed on, after everything above has been decided,
+        // so that nothing reads what it finds - and after the notes above, which belong to the step that placed
+        // the model. Only a model that was placed: one the rigid body rejected and molecular replacement did not
+        // place has nothing to refine. Left out, as the model is, on a cut.
+        const bool refine_cut = config_.fast_live && cancelled_;
+        if (refine_cut && config_.refine && result.model_placement != "NOT_PLACED")
+            Note("cut: the refinement is left out");
+        if (config_.refine && !refine_cut && result.model_placement != "NOT_PLACED" && placed_model_out
+            && placed_merged != nullptr && result.model_validation && result.model_validation->ok) {
+            phase("Refining the model");
+            Step("Refinement");
+            TimingMark mark(logger, "refinement");
+            RefinementSettings settings;
+            settings.nthreads = static_cast<size_t>(config_.nthreads);
+            settings.gpu_resident_bytes = rsm && rsm->OnGPU() ? rsm->DeviceBytes() : 0;
+            // A cut (the broker's deadline or cancel, Ctrl+C) cuts a running refinement short, keeping what it has
+            settings.cancel = cancelled_.RunFlag();
+            const PlacedModelOutput &p = *placed_model_out;
+            // processing-inert: a refinement that fails is reported, and the run goes on to its other outputs
+            RefinementResult refined;
+            try {
+                refined = RefineModel(*p.model, *placed_merged, gemmi::UnitCell(p.cell), p.space_group,
+                                      experiment_.GetWavelength_A(), logger, settings);
+            } catch (const std::exception &e) {
+                refined = RefinementResult();
+                refined.failure_reason = std::string("refinement failed: ") + e.what();
+            }
+            if (refined.ok) {
+                result.outputs->refined_model = PlacedModelOutput{refined.model, p.cell, p.space_group};
+                result.outputs->refined_maps = refined.maps;
+                result.outputs->blobs = refined.blobs;
+                Note(fmt::format("refined{}: R-work {:.3f}, R-free {:.3f}, rmsd bonds {:.3f} A, {} blobs",
+                                 refined.cancelled ? " (cut short)" : "", refined.r_work, refined.r_free,
+                                 refined.geometry.rmsd_bonds, refined.blobs.size()));
+            } else
+                logger.Warning("Refinement did not run: {}", refined.failure_reason);
+            result.refinement = std::move(refined);
+        }
     }
 
-    // The unmerged MTZ (kept with the other outputs, see there) is built from here on, beside the
-    // reflection files: the indexing and the group it is written in are final once the model has been
-    // read, and nothing after this changes the integrated observations it reads. It gets its own copy of
-    // the experiment.
-    if (full && write_output && !geometry_prepass && !superseded && result.consensus_cell
-        && config_.export_unmerged) {
-        unmerged_mtz = std::async(std::launch::async,
-                                  [&outcomes = indexer->GetIntegrationOutcome(),
-                                   cell = *result.consensus_cell, x = experiment_,
-                                   &provenance = config_.provenance, nthreads = config_.nthreads] {
-            return UnmergedMtzTable(outcomes, cell, x, true, provenance, nthreads);
-        });
+    if (cell_esd.valid()) {
+        result.cell_esd = cell_esd.get();
+        if (result.cell_esd) {
+            const CellEsd &e = *result.cell_esd;
+            logger.Info("Cell e.s.d.s from {} observations of {} reflections: {:.5f} {:.5f} {:.5f} {:.4f} {:.4f} {:.4f}"
+                        " (least squares {:.5f} {:.5f} {:.5f} {:.4f} {:.4f} {:.4f}, {} frame blocks)",
+                        e.observations, e.reflections, e.esd[0], e.esd[1], e.esd[2], e.esd[3], e.esd[4], e.esd[5],
+                        e.esd_lsq[0], e.esd_lsq[1], e.esd_lsq[2], e.esd_lsq[3], e.esd_lsq[4], e.esd_lsq[5],
+                        e.blocks);
+        }
     }
 
     // Not on the geometry pre-pass, and not on a pass that is going to be re-run. Pass 1 exists to
@@ -4735,6 +5162,7 @@ bool Rugnux::ScaleMergeAndSymmetry(PipelineLocals &p) {
                                                                  config_.provenance),
                                               sm.merged, *result.consensus_cell, experiment_, sm.statistics,
                                               em_report, result.twinning, std::move(sm.scaled_fulls)};
+        result.outputs->merged->cell_esd = result.cell_esd;
         if (keep_merged_reflections_)
             result.merged_reflections = sm.merged;
         // The twin hypothesis beside it (see prepare_twin_file): the reflection files only, with the
diff --git a/rugnux/RugnuxStills.cpp b/rugnux/RugnuxStills.cpp
index 29872e86b..1911dadc6 100644
--- a/rugnux/RugnuxStills.cpp
+++ b/rugnux/RugnuxStills.cpp
@@ -61,6 +61,7 @@
 #include "../image_analysis/image_preprocessing/ImagePreprocessorBufferGPU.h"
 #include "../image_analysis/spot_finding/AdaptiveSpotFinderGPU.h"
 #endif
+#include "../image_analysis/scale_merge/CellPopulation.h"
 #include "../image_analysis/scale_merge/Merge.h"
 #include "../image_analysis/scale_merge/RfreeFlags.h"
 #include "../image_analysis/scale_merge/RotationScaleMerge.h"
@@ -304,6 +305,29 @@ void Rugnux::RefineStillsGeometry(int start_image, int end_image, int images_to_
     if (cancelled_)
         return;
 
+    // A sample holding two crystal forms indexes both against the given cell, and a fit on both puts the
+    // cell, and with it the distance, between them. Only the frames of the given cell's population are
+    // fitted, the population the merge keeps (GivenCellPopulation); a run of one form keeps every frame.
+    // The population is told from the strong frames, whose cells are refined well enough to show the
+    // valley between two forms: at the start geometry, a weak frame's cell spreads across it.
+    {
+        const double given = CrystalLattice(*cell).CalcVolume();
+        std::vector<double> rel;
+        for (const auto &f : frames)
+            if (static_cast<int>(f.spots.size()) >= MIN_STRONG_SPOTS)
+                rel.push_back(f.lattice.CalcVolume() / given - 1.0);
+        const auto [low, high] = GivenCellPopulation(rel);
+        const size_t before = frames.size();
+        std::erase_if(frames, [&](const GeomRefineFrame &f) {
+            const double r = f.lattice.CalcVolume() / given - 1.0;
+            return r < low || r > high;
+        });
+        if (frames.size() != before)
+            logger.Info("Geometry refinement: {} of {} sampled frames refined to a cell outside the given cell's "
+                        "population ({:+.1f}% to {:+.1f}% in volume) and are not fitted",
+                        before - frames.size(), before, 100 * low, 100 * high);
+    }
+
     // Keep the strongest frames (most indexed spots) for the bundle - the true cell indexes many
     // spots per frame, and orientation diversity comes for free from independent serial stills.
     std::vector<GeomRefineFrame> strong;
diff --git a/rugnux/rugnux_cli.cpp b/rugnux/rugnux_cli.cpp
index c7b3e8fd7..938e87c92 100644
--- a/rugnux/rugnux_cli.cpp
+++ b/rugnux/rugnux_cli.cpp
@@ -77,11 +77,14 @@
 #include "Rugnux.h"
 #include "RugnuxDefaults.h"
 #include "../image_analysis/structure_refinement/ModelValidation.h"
+#include "../writer/RugnuxReflectionFile.h"
+#include "RugnuxRefine.h"
 #include "../writer/WriteModel.h"
 #include "../writer/RugnuxModelFile.h"
 #include "ResultReport.h"
 #include "RugnuxOutputFiles.h"
 #include "RugnuxConsole.h"
+#include "RugnuxInputKind.h"
 #ifdef __APPLE__
 #include "../image_analysis/bragg_integration/BraggIntegrationEngineMetal.h"
 #endif
@@ -95,7 +98,7 @@ constexpr double RELATIVE_B_DEFAULT_DEG = 10.0;
 
 // What the run does (--mode). Each of these was once a flag of its own; one option keeps them
 // mutually exclusive by construction.
-enum class RugnuxMode { MX, Azint, Scale, Calibration };
+enum class RugnuxMode { MX, Azint, Scale, Calibration, Refine };
 
 // Azimuthal sectors used by --mode calibration --calibration rings when --azim-phi-bins was not given.
 // The default of 1 is a plain radial profile, in which a ring has been averaged over every direction so
@@ -113,6 +116,12 @@ void print_usage() {
                  "together, the indexing rate reported per master as well; these must share the detector, "
                  "wavelength, distance and beam centre. Several inputs must be one format; rotation sweeps (name "
                  "one frame of a CBF/marCCD/SMV sweep), --mode other than mx and following a broker take one" << std::endl;
+    std::cout << "   An atomic model and a reference reflection file can be given among the inputs, in any order, instead of "
+                 "--model and -z: each file is told by its contents, not its name - an MTZ (the MTZ magic) or an mmCIF "
+                 "with a _refln or _diffrn_refln loop is reflections (-z; the input itself in --mode refine), a PDB file "
+                 "or an mmCIF with an _atom_site loop is a model (--model), anything else is images. An mmCIF holding "
+                 "both coordinates and reflections has to be given with --model or -z. At most one of each, also "
+                 "counting --model/--mr and -z; gzipped or not. E.g. rugnux data_master.h5 model.cif" << std::endl;
     std::cout << "   With a broker URL (http://host:port/) and no <input.h5> on disk yet, follows the broker's current "
                  "collection while it is written: <input.h5> must be the path its master file will have, the data "
                  "files are read next to it as the broker reports them closed, and the run ends with the images the "
@@ -151,6 +160,13 @@ void print_usage() {
     std::cout << "        azint         Only azimuthal integration (no spot finding/indexing); writes <prefix>_process.h5" << std::endl;
     std::cout << "        scale         Only re-scale/merge the already-integrated reflections in <input> (no re-integration)" << std::endl;
     std::cout << "        calibration   Determine the detector geometry from powder rings; writes <prefix>.poni for pyFAI and <prefix>.json, whose dataset_settings member is a jfjoch_broker dataset_settings body as it stands" << std::endl;
+    std::cout << "        refine        Refine the --model against merged structure factors: <input> is an MTZ or a structure-factor mmCIF (gzipped or not), nothing is processed. As a placed model is refined after a merge, and written alike: <prefix>_refined_model.cif, <prefix>_refined_maps.mtz, <prefix>_blobs.json and REFINE_ keys in <prefix>_report.txt" << std::endl;
+    std::cout << std::endl;
+
+    std::cout << "  Refinement (--mode refine)" << std::endl;
+    std::cout << "   The columns are found, not named: amplitudes with their sigmas (F/SIGF, FP/SIGFP, ...) where the file has them, else intensities (IMEAN/SIGIMEAN, I/SIGI, ...) made into amplitudes by French-Wilson, else the mean of the anomalous pairs; the free set from a FreeR_flag-like column (0 the test set, or the minority value where 0 is the majority, as phenix writes it), drawn here where the file has none. The model is taken as placed in the data's cell, and refined in the data's space group" << std::endl;
+    std::cout << "   --refine-score-only              Score the model as given and refine nothing: R-work/R-free, the scale, the bulk solvent, the likelihood and the geometry, each term under REFINE_SCORE_ (--developer prints them all)" << std::endl;
+    std::cout << "   --refine-d-min <num>             Leave out reflections finer than this (A)" << std::endl;
     std::cout << std::endl;
 
     std::cout << "  Calibration (--mode calibration)" << std::endl;
@@ -167,7 +183,7 @@ void print_usage() {
     std::cout << "  Detector mask" << std::endl;
     std::cout << "   --mask-good [<file>:]<dataset>[@<bits>] HDF5/CXI stills: a mask array in the frames' own layout (as stored, before the panels are placed) - in <file>, or without it in each data file (a per-frame mask stored beside the frames); a pixel is usable only where it is non-zero, or with <bits> only where it has all of them. May be given more than once" << std::endl;
     std::cout << "   --mask-bad [<file>:]<dataset>[@<bits>] As --mask-good, but a pixel is unusable where the array is non-zero, or with <bits> where it has any of them (e.g. @0xfeff)" << std::endl;
-    std::cout << "   --detect-beam-stop[=N|off]       Find the beam stop and its holder in a projection of N images and add them to the pixel mask (bit 9), so nothing shadowed by them is integrated. ON by default (60 images); =off disables. Reflections behind the stop are attenuated but not flagged, so they are integrated low with a plausible sigma and no existing rejection catches them" << std::endl;
+    std::cout << "   --detect-beam-stop[=N|off]       Find the beam stop and its holder in a projection of N images and add them to the pixel mask (bit 9), so nothing shadowed by them is integrated. ON by default (60 images); =off disables. A reflection whose signal disk reaches into the shadow is not integrated: the rest of such a disk lies in the stop's half-shadow and reads low. Pixels the finder reports that hold the detector's no-data mark (a PILATUS gap) are masked as dead instead" << std::endl;
     std::cout << "   --beam-center-check[=off]        Measure the beam centre from the isotropy of the scattered background on EVERY run, report how far the file's value is from it, and index a second first pass with it to see whether the two centres give the same lattice. The fit reads the projection --detect-beam-stop already builds, so it costs no extra frames. On a run that indexes, the measured centre is adopted where the file's centre indexes nothing and the measured one indexes a majority, and where the two centres return cells related by an integer volume factor, in either direction, and the measured centre's lattice carries materially more of the pooled spots against its own chance level - the axis harmonic a centre error along the spindle produces, which nothing downstream repairs. Where the indexing cannot tell the two centres apart - the same cell with a different metric symmetry, or the same lattice found at both only by reading less of each frame - the first pass is run at both and the run keeps the one that merges better (on the same lattice: the one that measures more reflections at I/sigma >= 2). ON by default; =off disables On stills, where there is no first pass, the file's centre, the measured one and the point-symmetry capture's are each indexed on a sample of frames and the run takes the one that puts materially more spots on the lattice of their frame; with a reference cell (-C) the detector distance is searched too, over 30-3000 mm at every centre, the file's value being one hypothesis, before the stills geometry refinement" << std::endl;
     std::cout << std::endl;
 
@@ -199,10 +215,10 @@ void print_usage() {
                  "CPU (FFTW); cuFFT and FFTW name one implementation each, and cuFFT needs a GPU. FFBIDX is the known-cell "
                  "fast-feedback indexer for stills, likewise on the GPU where there is one and otherwise on the CPU; "
                  "Auto picks it for stills whenever a cell is known" << std::endl;
-    std::cout << "   -S, --space-group <num|symbol>   Space group number (96) or symbol (P43212) - for indexing and scaling" << std::endl;
+    std::cout << "   -S, --space-group <num|symbol>   Space group number (96) or symbol (P43212) - for indexing and scaling; on serial stills where the space group admits two indexings, the crystals are put on one from the data (or from --model/-z when given)" << std::endl;
     std::cout << "   -C, --unit-cell <cell>           Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
     std::cout << "   --fft-min-unit-cell <num>        Shortest cell axis the FFT search accepts, in A (default: 10). A candidate with a shorter axis is discarded, but a de-novo rotation run also tries a second first-pass hypothesis with the floor at 5 A, so a small-molecule cell is indexed without this flag; -C lowers it on its own to cover the cell given" << std::endl;
-    std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|flex); flex tries all three per image and keeps whichever indexes the most spots (alias: multi)" << std::endl;
+    std::cout << "   -r, --geom-refine <txt>          Geometry refinement algorithm (none|orientation|beam_and_lattice|flex); flex tries all three per image and keeps whichever indexes the most spots (alias: multi)" << std::endl;
     std::cout << "   --refine-geometry[=N|off]        Stills: extra first pass that bundle-adjusts the shared beam/distance/cell from N strongly-indexed frames (default: 200) then re-indexes (lifts weak-stills indexing). Default ON for stills when a reference cell is given (-C / reference MTZ); =off disables" << std::endl;
     std::cout << "   --refine-modules[=on|off|diagnose] Stills, in that bundle adjustment: a detector of several modules (the input's own - NXdetector_module groups, SACLA sensors, geometry-file panels - or --module-geometry) has each placed as a rigid block - shift and in-plane turn - where that predicts the spots better on frames held out of the fit (default: on). Used from there on for the panels of a foreign detector (SACLA sensors, geometry-file panels); for a JUNGFRAU measured and reported only. The placement is written to <prefix>_modules.h5" << std::endl;
     std::cout << "   --module-geometry <file>         Where the detector's modules are: an NXmx file with one NXdetector_module group per module (module_0, module_1, ...; what a run writes as <prefix>_modules.h5), or a CrystFEL geometry file whose panels are laid on the image (fs = column, ss = row). Replaces the input's own modules" << std::endl;
@@ -222,26 +238,27 @@ void print_usage() {
     std::cout << "   --no-expected-variance-merge    stills: disable the default expected-variance merge weighting (which rebuilds each weak observation's signal variance at the reflection mean to de-bias the inverse-variance merge); restores observed-sigma weighting" << std::endl;
     std::cout << "   -A, --anomalous                 Anomalous mode (don't merge Friedel pairs)" << std::endl;
     std::cout << "   --scaling-high-resolution <num> High resolution limit for scaling/merging (manual override; default: no limit)" << std::endl;
-    std::cout << "   --scaling-low-resolution <num>  Low resolution limit for scaling/merging, in A (default: 50, also XDS's own default; 0 = no limit). The beam stop suppresses air scatter well beyond the shadow the beam-stop mask covers, so reflections coarser than this are measured on a depressed background and mostly integrate negative; masking does not reach them" << std::endl;
+    std::cout << "   --scaling-low-resolution <num>  Low resolution limit of the scale fit, in A (default: 50, also XDS's own default; 0 = no limit). Coarser reflections are merged and written, but kept out of the scale model, which a few of them on a large cell can bend" << std::endl;
     std::cout << "   --resolution-cutoff <txt>       Automatic high-resolution cutoff for the written reflections + reported shells: cc-logistic|off (default: cc-logistic; ignored when --scaling-high-resolution is set)" << std::endl;
     std::cout << "   --resolution-cc-target <num>    CC1/2 target defining the cc-logistic fall-off (default: 0.30)" << std::endl;
     std::cout << "   --resolution-shells <num>       Number of resolution shells in the reported statistics table (default: 9, as XDS)" << std::endl;
     std::cout << "   --report-resolution <dmin>[,<dmax>] Also report the merging statistics over this resolution range (A, either order; dmax defaults to the run's own low-resolution limit) as a second table beside the run's own - the REFRES_* keys of the report - binned from the same merged reflections, so a run can be read against another program's table at that program's range. Report-only: the cut, the scaling, the error model and every decision stay the run's own, and shells finer than the run's own limit are empty rather than filled from data the run did not keep" << std::endl;
     std::cout << "   --ice-min-score <num>           Ice-presence gate: measured ice score (1 = no ice) a run must reach before ANY ice handling is applied - the flagging and the exclusion from scaling (default: 1.5). The eleven hexagonal bands cover 16-26% of the unique reflections whether or not the crystal has ice, so handling ice on a clean crystal is a pure loss. 0 = no gate (always handle ice)" << std::endl;
     std::cout << "   --ice-min-spot-ratio <num>      Second ice-presence channel: found spots on the hexagonal rings over the same q width of ice-free flanks beside them (1 = spots spread evenly). Ice in large crystallites diffracts as discrete spots and leaves the radial profile flat, so --ice-min-score alone is blind to it. Default 2.0; 0 disables this channel" << std::endl;
-    std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02)" << std::endl;
+    std::cout << "   --min-partiality <num>          Minimum partiality to accept reflection (default: 0.02 for rotation, 0.5 for stills)" << std::endl;
     std::cout << "   --capture-uncertainty <num>     Systematic sigma num*(1-captured fraction)*<I>: on rot3d fulls, the share of the rocking curve not captured; on stills, the share of each partial its partiality does not see (default: 1.0 for rot3d, 0 otherwise)" << std::endl;
     std::cout << "   --min-captured-fraction <num>   rot3d: drop a combined full whose rocking curve was captured below this fraction (edge-of-sweep truncated fulls) (default: 0.7 for rotation, 0 otherwise; 0 = off)" << std::endl;
     std::cout << "   --mosaicity <num>               Diagnostic: fix the scaling mosaicity (deg) instead of the per-image seed" << std::endl;
     std::cout << "   --prediction-mosaicity <num>    Diagnostic: fix the rocking width the PREDICTION window opens to (deg), leaving the partiality on the per-image sigma_M. Prediction and partiality are one number by default, so a sigma_M that moves takes the integrated reflection population with it" << std::endl;
-    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median, the systematic part of the band multiplicative (default: 6 for rot3d, XDS/DIALS-style; 0 = off)" << std::endl;
+    std::cout << "   --reject-outliers <num>         Per-observation merge outlier rejection, N sigma from the per-reflection median, the systematic part of the band multiplicative on rotation and linear on stills (default: 6 for rotation, XDS/DIALS-style, and 10 for stills; 0 = off)" << std::endl;
     std::cout << "   --search-min-zeta <num>         De-novo space-group search only: also search a merge of just the observations whose Lorentz geometry |zeta| reaches this, and report both answers (default: 0.85 for rotation, 0 = single search). Reflections crossing the Ewald sphere near-tangentially are measured worst and can make a real symmetry operator look like a twin law; where the two searches disagree, the merge of ALL the observations decides" << std::endl;
     std::cout << "   --min-image-cc <num>            Per-image CC limit in percent (default: no limit)" << std::endl;
     std::cout << "   --scaling-iterations <num>      Cap on the per-frame scaling iterations; the loop stops earlier once the scales settle (default: 100)" << std::endl;
     std::cout << "   -z, --reference <file>          Reference data of the same crystal form: an MTZ, or a PDB structure-factor mmCIF (e.g. 1abc-sf.cif, first merged block with a usable column; R-free set from _refln.status f/o, else pdbx_r_free_flag). Gzipped or not, recognised by content. --reference-mtz is the same option" << std::endl;
     std::cout << "   --reference-column <label>      Reference column to use, by MTZ label; an mmCIF is read under the labels gemmi cif2mtz gives it (IMEAN, FP, I(+), FC, F-model, ...) (default: auto - F-model, else IMEAN/I, else FP/FOBS/F)" << std::endl;
-    std::cout << "   --model <file>                  After merging, validate vs this atomic model: R-free, sigma_A-weighted 2mFo-DFc/mFo-DFc maps, the model as placed (written beside them), and - where the merge kept the Bijvoet split - an anomalous difference map with the strongest anomalous scatterers named by the atom they sit on. PDB or mmCIF, gzipped or not, recognised by content rather than by extension. A prediction (AlphaFold or ModelCIF, pLDDT in the B column), or an experimental structure the rigid body does not place against its null, is placed by molecular replacement instead (see --mr)" << std::endl;
+    std::cout << "   --model <file>                  After merging, validate vs this atomic model: R-free, sigma_A-weighted 2mFo-DFc/mFo-DFc maps, the model as placed (written beside them), and - where the merge kept the Bijvoet split - an anomalous difference map with the strongest anomalous scatterers named by the atom they sit on. PDB or mmCIF, gzipped or not, recognised by content rather than by extension. A prediction (AlphaFold or ModelCIF, pLDDT in the B column), or an experimental structure the rigid body does not place against its null, is placed by molecular replacement instead (see --mr). A model that is placed is then refined against the merge it was placed on - each chain as a rigid body and one B per residue, then every atom's position and B restrained by the dictionary carried in rugnux against a maximum-likelihood target, the X-ray weight chosen by R-free within geometry bounds - and the unexplained blobs of its difference map are listed: <prefix>_refined_model.cif, <prefix>_refined_maps.mtz, <prefix>_blobs.json, REFINE_ keys in the report. R_WORK, R_FREE and every other key stay those of the model as placed; the refinement decides nothing about the processing. It costs seconds on a GPU and typically 2-15 minutes on the CPU (no GPU, or --no-gpu); --no-refine skips it" << std::endl;
     std::cout << "   --mr <file>                     As --model, but placed by molecular replacement straight away, without the rigid-body placement first: as many copies as the cell holds, in every space group the merge cannot tell apart and in the twin hypothesis' subgroup. A prediction is trimmed to the residues of pLDDT 70 and above, and where the AlphaFold DB's predicted-aligned-error JSON sits beside it under its own name it is cut into rigid domains; any other PDB or mmCIF is taken as an experimental structure, its polymer only (no waters, ligands, hydrogens or alternative conformers). Which of the two it is is read from the file. It may relabel the enantiomorph of the answer, and a different space group it chooses is written beside the answer as <prefix>_mr.mtz/.cif with the placed model <prefix>_mr_model.pdb. --mode mx only" << std::endl;
+    std::cout << "   --no-refine                     Do not refine the placed model (for debugging): by default a model that --model or --mr places is refined (see --model)" << std::endl;
     std::cout << "   --export-unmerged               Write <prefix>_unmerged.mtz, an unmerged MTZ (POINTLESS column layout) of the integrated observations, for aimless / pointless / careless. On by default, whenever there is an output prefix. On a rotation run the partials of each reflection are summed into one full, written at the batch its rocking curve is centred on, with the summed rocking-curve fraction in FRACTIONCALC; an event that caught less of its rocking curve than --min-captured-fraction (or --min-partiality) is not written, exactly as in the merge, since a full is what the reading program is told these rows are. Intensities carry the deterministic per-reflection corrections and nothing else - Lorentz and polarization in the LP column, the sensor's angle-dependent efficiency in QE and the flight path's attenuation in FLIGHT, so raw counts are I / LP * QE * FLIGHT - while the partiality is not divided out and the per-image scale is not applied at all, since those programs scale the data themselves. Written in --mode mx and --mode scale, and with --no-merge" << std::endl;
     std::cout << "   --no-export-unmerged            Do not write <prefix>_unmerged.mtz. It is the largest file a run produces, so a run whose observations are not going to another scaling program - a regression battery, say - can skip writing it" << std::endl;
     std::cout << "   --export-unmerged-partials      Write <prefix>_unmerged_partials.mtz, the same observations with each partial as its own row (one batch per image) flagged for the reading program to sum, instead of summed here. Off by default and independent of --export-unmerged; both can be written in one run" << std::endl;
@@ -331,6 +348,7 @@ enum {
     OPT_MODEL,
     OPT_CRYSTFEL_GEOMETRY,
     OPT_MR,
+    OPT_NO_REFINE,
     OPT_EXPORT_UNMERGED,
     OPT_NO_EXPORT_UNMERGED,
     OPT_EXPORT_UNMERGED_PARTIALS,
@@ -386,7 +404,9 @@ enum {
     OPT_DETECTOR_QUARTER_TURNS,
     OPT_FFT_MIN_UNIT_CELL,
     OPT_POLARIZATION,
-    OPT_NO_REFINE_TILT
+    OPT_NO_REFINE_TILT,
+    OPT_REFINE_SCORE_ONLY,
+    OPT_REFINE_D_MIN
 };
 
 static option long_options[] = {
@@ -405,6 +425,9 @@ static option long_options[] = {
     {"model", required_argument, nullptr, OPT_MODEL},
     {"crystfel-geometry", required_argument, nullptr, OPT_CRYSTFEL_GEOMETRY},
     {"mr", required_argument, nullptr, OPT_MR},
+    {"no-refine", no_argument, nullptr, OPT_NO_REFINE},
+    {"refine-score-only", no_argument, nullptr, OPT_REFINE_SCORE_ONLY},
+    {"refine-d-min", required_argument, nullptr, OPT_REFINE_D_MIN},
     {"export-unmerged", no_argument, nullptr, OPT_EXPORT_UNMERGED},
     {"no-export-unmerged", no_argument, nullptr, OPT_NO_EXPORT_UNMERGED},
     {"export-unmerged-partials", no_argument, nullptr, OPT_EXPORT_UNMERGED_PARTIALS},
@@ -428,7 +451,7 @@ static option long_options[] = {
     {"relative-b", optional_argument, nullptr, OPT_RELATIVE_B},
     {"no-scaling-corrections", no_argument, nullptr, OPT_NO_SCALING_CORRECTIONS},
     {"no-expected-variance-merge", no_argument, nullptr, OPT_NO_EXPECTED_VARIANCE_MERGE},
-    {"refine", required_argument, nullptr, 'r'},
+    {"geom-refine", required_argument, nullptr, 'r'},
 
     {"two-pass-rotation", optional_argument, nullptr, 'R'},
     {"single-pass-rotation", optional_argument, nullptr, OPT_SINGLE_PASS_ROTATION},
@@ -1037,10 +1060,13 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
     std::string crystfel_geometry;   // --crystfel-geometry: read the input as CrystFEL would with this geometry
     std::string model_pdb;           // --model: PDB to validate merged intensities against (R-free + maps)
     std::string mr_model;            // --mr: --model, placed by molecular replacement straight away
+    bool refine_model = true;        // --no-refine: a placed model is refined unless it is given
+    bool refine_score_only = false;  // --refine-score-only
+    double refine_d_min = 0;         // --refine-d-min
     bool export_unmerged = true;            // on by default; --no-export-unmerged turns it off
     bool export_unmerged_partials = false;  // --export-unmerged-partials: the same, one row per image
     std::string dump_observations;   // diagnostic: dump unmerged -P rot3d fulls to this path
-    double min_partiality = 0.02;
+    std::optional<double> min_partiality_arg;   // --min-partiality; default per mode (RugnuxDefaultScalingSettings)
     std::optional<double> min_captured_fraction_arg;   // explicit --min-captured-fraction; default depends on rotation
     std::optional<double> capture_uncertainty_arg;   // explicit --capture-uncertainty; default depends on rot3d
     std::optional<double> forced_mosaicity_arg;      // diagnostic: fix the scaling mosaicity (deg) instead of the per-image seed
@@ -1279,6 +1305,15 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
         case OPT_MR:
             mr_model = optarg;
             break;
+        case OPT_NO_REFINE:
+            refine_model = false;
+            break;
+        case OPT_REFINE_SCORE_ONLY:
+            refine_score_only = true;
+            break;
+        case OPT_REFINE_D_MIN:
+            refine_d_min = parse_number_arg<double>(optarg, "--refine-d-min", logger, 0.1, 100.0);
+            break;
         case OPT_EXPORT_UNMERGED:
             export_unmerged = true;
             break;
@@ -1375,8 +1410,9 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
             else if (m == "azint") mode = RugnuxMode::Azint;
             else if (m == "scale") mode = RugnuxMode::Scale;
             else if (m == "calibration") mode = RugnuxMode::Calibration;
+            else if (m == "refine") mode = RugnuxMode::Refine;
             else {
-                logger.Error("Invalid --mode: {} (expected mx|azint|scale|calibration)", m);
+                logger.Error("Invalid --mode: {} (expected mx|azint|scale|calibration|refine)", m);
                 return 1;
             }
             break;
@@ -1468,7 +1504,7 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
             no_scaling_corrections = true;
             break;
         case OPT_MIN_PARTIALITY:
-            min_partiality = parse_double_arg(optarg, "--min-partiality", logger);
+            min_partiality_arg = parse_double_arg(optarg, "--min-partiality", logger);
             break;
         case OPT_CAPTURE_UNCERTAINTY:
             capture_uncertainty_arg = parse_double_arg(optarg, "--capture-uncertainty", logger);
@@ -1712,6 +1748,31 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
         broker_url = input_files.back();
         input_files.pop_back();
     }
+    // The inputs in any order: an atomic model and a reflection file are told from the images by their contents
+    // (RugnuxInputKind.h), and taken as --model and -z are - as the input of --mode refine, its reflections.
+    try {
+        RugnuxPositionalInputs split = SplitRugnuxInputs(input_files);
+        if (!split.model.empty()) {
+            if (!model_pdb.empty() || !mr_model.empty()) {
+                logger.Error("Two models: {} and {}; give one", model_pdb.empty() ? mr_model : model_pdb, split.model);
+                exit(EXIT_FAILURE);
+            }
+            model_pdb = split.model;
+        }
+        if (!split.reflections.empty()) {
+            if (mode == RugnuxMode::Refine)
+                split.images.insert(split.images.begin(), split.reflections);
+            else if (!ref_mtz.empty()) {
+                logger.Error("Two reference reflection files: {} and {}; give one", ref_mtz, split.reflections);
+                exit(EXIT_FAILURE);
+            } else
+                ref_mtz = split.reflections;
+        }
+        input_files = std::move(split.images);
+    } catch (const std::exception &e) {
+        logger.Error("{}", e.what());
+        exit(EXIT_FAILURE);
+    }
     if (input_files.empty()) {
         logger.Error("Input file not specified");
         print_usage();
@@ -1746,6 +1807,10 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
         logger.Error("--model and --mr both name the model; give one");
         exit(EXIT_FAILURE);
     }
+    if (mode == RugnuxMode::Refine && model_pdb.empty()) {
+        logger.Error("--mode refine refines a model: give it with --model");
+        exit(EXIT_FAILURE);
+    }
     // Read before anything runs: a file that holds no model ends the run here rather than after it.
     std::shared_ptr<const RugnuxModel> model;
     if (const std::string path = mr_model.empty() ? model_pdb : mr_model; !path.empty()) {
@@ -1807,6 +1872,39 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
     } else
         logger.Info("Threads: {}{}", nthreads, nthreads_auto ? " (the CPUs this run may use)" : " (-N)");
 
+    // --mode refine: the model against the structure factors given, nothing processed.
+    if (mode == RugnuxMode::Refine) {
+        console->Field("Input", input_file);
+        console->Field("Output", log_file.empty() ? output_prefix + "_*"
+                                                  : fmt::format("{}_*   (full log in {})", output_prefix, log_file));
+        console->Rule('-');
+        console->OnStep("Reading the reflections");
+        RugnuxReflections data;
+        try {
+            data = ReadRugnuxReflectionFile(input_file);
+        } catch (const std::exception &e) {
+            logger.Error("Cannot read the reflections {}: {}", input_file, e.what());
+            exit(EXIT_FAILURE);
+        }
+        console->OnStep(refine_score_only ? "Scoring the model" : "Refining the model");
+        RefinementSettings settings;
+        settings.nthreads = static_cast<size_t>(nthreads);
+        settings.gpu = !no_gpu;
+        settings.score_only = refine_score_only;
+        const RefineOnlyResult refined = RunRefineOnly(std::move(data), model->structure, refine_d_min, settings,
+                                                       logger);
+        if (!refined.refinement.ok)
+            logger.Error("Refinement did not run: {}", refined.refinement.failure_reason);
+        console->OnStep("Writing files");
+        provenance.wall_time_s = std::chrono::duration<double>(
+                std::chrono::steady_clock::now() - invocation_start).count();
+        const ReportDocument doc = WriteRefineOutputs(refined, output_prefix, input_file, model_pdb, logger,
+                                                      provenance);
+        console->Finish();
+        PrintSummary(*console, doc, output_prefix, files_since, provenance.wall_time_s);
+        return refined.refinement.ok ? 0 : 1;
+    }
+
     std::string input_list;
     for (const auto &f: input_files)
         input_list += (input_list.empty() ? "" : ", ") + f;
@@ -2260,7 +2358,7 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
                 ParseReportResolution(*report_resolution_arg, scaling_settings, logger));
         // Rotation merges decide with Friedel mates merged, -A or not (see the Rugnux constructor).
         scaling_settings.MergeFriedel(!anomalous_mode || rot);
-        scaling_settings.MinPartiality(min_partiality);
+        scaling_settings.MinPartiality(min_partiality_arg.value_or(scaling_settings.GetMinPartiality()));
         scaling_settings.MinCapturedFraction(
             min_captured_fraction_arg.value_or(scaling_settings.GetMinCapturedFraction()));
         scaling_settings.CaptureUncertaintyCoeff(
@@ -2468,14 +2566,33 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
             // against a foreign dataset injects cross-dataset systematics and is a worse reference than
             // the data's own merge. The per-image scale G is the exact one-pass solution, so one pass
             // (iterating a self-rebuilt reference only re-fits the freshly-scaled noise on weak stills).
+            // The file holds each still as it was merged - with its post-refined partiality - and not the
+            // excitation errors its prediction made. Put every reflection back where the prediction left it,
+            // at p = 1 and with the excitation error of the stored lattice and geometry, so that the scaling
+            // and the post-refinement start from the state they start from in the full pipeline.
+            for (auto &o: reflections) {
+                const Coord S0 = o.geom.GetScatteringVector();
+                const double inv_lambda = 1.0 / o.geom.GetWavelength_A();
+                for (auto &r: o.reflections) {
+                    const Coord S = o.latt.Astar() * static_cast<float>(r.h) + o.latt.Bstar() * static_cast<float>(r.k)
+                                    + o.latt.Cstar() * static_cast<float>(r.l) + S0;
+                    r.dist_ewald = static_cast<float>(std::fabs(std::sqrt(S.x * S.x + S.y * S.y + S.z * S.z) - inv_lambda));
+                    r.partiality = 1.0f;
+                }
+            }
             ScaleOnTheFly(experiment, MergeAll(experiment, reflections, nthreads, experiment.GetUnitCell())).Scale(reflections, nthreads);
             // Physical partiality post-refinement (default on; --simple-stills disables): refine a per-crystal
             // orientation tilt against the merge and recompute each reflection's partiality + scale correction
             // (no re-integration), then merge with the improved corrections.
             if (experiment.GetScalingSettings().GetStillsPartialityRefine()) {
                 StillsPartialityRefine refiner(experiment);
-                const double mean_tilt = refiner.Run(reflections, nthreads, experiment.GetUnitCell());
+                // The curve the mx run computed its partialities from (and predicted the frames through),
+                // where the file carries it: measured again on frames predicted through it, it is another.
+                const double mean_tilt = refiner.Run(reflections, nthreads, experiment.GetUnitCell(),
+                                                     dataset->stills_run_width);
                 logger.Info("Stills partiality post-refine: mean |dpsi| = {:.3f} deg", mean_tilt);
+                // As in the full pipeline: the refine fits its own per-image scale, with no floor.
+                ScaleOnTheFly::RejectCollapsedScales(reflections);
             }
             MergeOnTheFly merge_engine(experiment);
             merge_engine.Threads(nthreads);
@@ -2514,6 +2631,7 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
             {   // stills: no asymptote tier, and its ISa already IS the whole-range 1/b
                 const auto em = ToXdsErrorModel(merge_engine.ErrorModelA(), merge_engine.ErrorModelB());
                 error_model_isa = em.isa;
+                error_model_isa_resolved = merge_engine.ErrorModelBResolved();
                 error_model_a = em.a;
                 error_model_b = em.b;
             }
@@ -3273,7 +3391,7 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
         scaling_settings.ReportResolutionRange_A(
             ParseReportResolution(*report_resolution_arg, scaling_settings, logger));
     scaling_settings.MergeFriedel(!anomalous_mode);
-    scaling_settings.MinPartiality(min_partiality);
+    scaling_settings.MinPartiality(min_partiality_arg.value_or(scaling_settings.GetMinPartiality()));
     // Drop edge-of-sweep truncated fulls (rocking curve captured < this fraction) from the rot3d combine.
     // Defaults ON (0.7) for rotation - removes the low-capture fulls that inflate low-res R-meas and
     // slightly bias accuracy; off for non-rot3d (no combine). 0.7 (rather than 0.5) also strips the
@@ -3517,6 +3635,7 @@ static int RunRugnux(int argc, char **argv, bool no_gpu) {
     config.export_unmerged_partials = export_unmerged_partials;
     config.model = model;
     config.force_mr = !mr_model.empty();
+    config.refine = refine_model;   // a placed model is refined unless --no-refine
     // When merging, the merged reflections (.mtz/.cif) are the wanted output; skip the large
     // _process.h5 unless explicitly requested. Without merging, the _process.h5 is the only output.
     std::optional<ProcessFileSink> sink;
diff --git a/tests/BraggIntegrationEngineCPUTest.cpp b/tests/BraggIntegrationEngineCPUTest.cpp
index c89320728..46d2f30b5 100644
--- a/tests/BraggIntegrationEngineCPUTest.cpp
+++ b/tests/BraggIntegrationEngineCPUTest.cpp
@@ -13,6 +13,8 @@
 #include "../common/DiffractionExperiment.h"
 #include "../common/JFJochMath.h"
 #include "../common/Reflection.h"
+#include "../common/PixelMask.h"
+#include "../image_analysis/MXAnalysisWithoutFPGA.h"
 #include "../image_analysis/bragg_integration/BraggIntegrationEngineCPU.h"
 #include "../image_analysis/image_preprocessing/ImagePreprocessorBuffer.h"
 
@@ -540,3 +542,33 @@ TEST_CASE("BraggIntegrationEngineCPU_AduIntegratesAsPhotons", "[Integration][por
         }
     }
 }
+
+// A reflection is left out only when its signal disk reaches the beam-stop shadow: a shadow pixel just
+// outside the disk, or a pixel masked for any other reason inside it, keeps it.
+TEST_CASE("DropShadowClipped_SignalDiskTouchingTheShadow", "[Integration][portable]") {
+    const int W = 64, H = 32;
+    const float r1 = 4.0f;
+    std::vector<uint32_t> mask(W * H, 0);
+    for (int y = 0; y < H; y++)
+        mask[y * W + 30] = 1u << PixelMask::BeamStopPixelBit;   // a shadow column at x = 30
+    mask[16 * W + 10] = 1u << PixelMask::ModuleGapPixelBit;      // a gap pixel at (10, 16)
+
+    auto at = [](float x, float y) {
+        Reflection r{};
+        r.predicted_x = x;
+        r.predicted_y = y;
+        return r;
+    };
+    std::vector<Reflection> refl = {at(10.0f, 16.0f),    // a gap pixel at its centre: kept
+                                    at(26.5f, 16.0f),    // 3.5 px from the shadow: dropped
+                                    at(25.0f, 16.0f),    // 5 px from it: kept
+                                    at(33.9f, 5.0f),     // 3.9 px on the other side: dropped
+                                    at(34.0f, 5.0f),     // 4 px, the disk's own edge: kept
+                                    at(1.0f, 1.0f)};     // near the image corner: kept
+    DropShadowClipped(refl, mask, W, H, r1);
+    REQUIRE(refl.size() == 4);
+    CHECK(refl[0].predicted_x == 10.0f);
+    CHECK(refl[1].predicted_x == 25.0f);
+    CHECK(refl[2].predicted_x == 34.0f);
+    CHECK(refl[3].predicted_x == 1.0f);
+}
diff --git a/tests/CBORTest.cpp b/tests/CBORTest.cpp
index 05b2e1790..76cbe36ce 100644
--- a/tests/CBORTest.cpp
+++ b/tests/CBORTest.cpp
@@ -578,6 +578,33 @@ TEST_CASE("CBORSerialize_End_SpaceGroup", "[CBOR]") {
     CHECK(*out.space_group_number == static_cast<uint64_t>(sg->number));
 }
 
+TEST_CASE("CBORSerialize_End_UnitCellEsd", "[CBOR]") {
+    std::vector<uint8_t> buffer(1024 * 1024);
+    CBORStream2Serializer serializer(buffer.data(), buffer.size());
+
+    EndMessage message{};
+    message.max_image_number = 0;
+    message.unit_cell = UnitCell{.a = 40, .b = 50, .c = 60, .alpha = 90, .beta = 101.5f, .gamma = 90};
+    message.unit_cell_esd = UnitCell{.a = 0.002f, .b = 0.003f, .c = 0.004f, .alpha = 0, .beta = 0.011f, .gamma = 0};
+    REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(message));
+
+    auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
+    REQUIRE(deserialized);
+    REQUIRE(deserialized->end_message);
+    const EndMessage &out = *deserialized->end_message;
+    REQUIRE(out.unit_cell_esd.has_value());
+    CHECK(*out.unit_cell_esd == *message.unit_cell_esd);
+    CHECK(*out.unit_cell == *message.unit_cell);
+
+    // Absent stays absent: a stills run has no e.s.d.s.
+    message.unit_cell_esd.reset();
+    CBORStream2Serializer serializer2(buffer.data(), buffer.size());
+    REQUIRE_NOTHROW(serializer2.SerializeSequenceEnd(message));
+    auto deserialized2 = CBORStream2Deserialize(buffer.data(), serializer2.GetBufferSize());
+    REQUIRE(deserialized2->end_message);
+    CHECK_FALSE(deserialized2->end_message->unit_cell_esd.has_value());
+}
+
 TEST_CASE("CBORSerialize_End_SpaceGroupNumberOnly", "[CBOR]") {
     // A sender written before the name existed fills in only the number; the message still arrives
     // and the missing name is absent rather than empty, so a reader can tell it apart.
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index cecfe9c5a..2f50cb2ab 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -47,8 +47,7 @@ ENDIF()
 
 # The CPU vs GPU test of the fast-feedback indexer reads the library's own test spot lists
 IF (JFJOCH_CUDA_AVAILABLE)
-    FetchContent_GetProperties(fast-indexer SOURCE_DIR FFBIDX_SOURCE_DIR)
-    SET(FFBIDX_SIMPLE_DATA_DIR "${FFBIDX_SOURCE_DIR}/data/simple/files")
+    SET(FFBIDX_SIMPLE_DATA_DIR "${CMAKE_SOURCE_DIR}/image_analysis/indexing/fast-feedback-indexer/data")
     TARGET_COMPILE_DEFINITIONS(jfjoch_portable_test PRIVATE FFBIDX_SIMPLE_DATA_DIR="${FFBIDX_SIMPLE_DATA_DIR}")
 ENDIF()
 
@@ -138,6 +137,7 @@ ADD_EXECUTABLE(jfjoch_test
         ResultReportTest.cpp
         DiagnosticOutputTest.cpp
         PostRefineTest.cpp
+        CellEsdTest.cpp
         RotationScaleWalkTest.cpp
         AndersonMixingTest.cpp
         RugnuxLargeTest.cpp
@@ -184,6 +184,8 @@ ADD_EXECUTABLE(jfjoch_test
         MolecularReplacementTest.cpp
         ModelMaskGPUTest.cpp
         ModelDensityGPUTest.cpp
+        RefinementTest.cpp
+        RefineOnlyTest.cpp
         SearchSpaceGroupTest.cpp
         SearchSpaceGroupTwinTest.cpp
         SyntheticMergedReflections.h
@@ -207,6 +209,7 @@ ADD_EXECUTABLE(jfjoch_test
         LoadReferenceSfCifTest.cpp
         WriteReflectionsTest.cpp
         RugnuxResultFilesTest.cpp
+        RugnuxInputKindTest.cpp
         UnitCellTest.cpp
         CCTest.cpp
         MultiLatticeSearchTest.cpp
diff --git a/tests/CalcBraggPredictionTest.cpp b/tests/CalcBraggPredictionTest.cpp
index 918ef1abd..22d65dc01 100644
--- a/tests/CalcBraggPredictionTest.cpp
+++ b/tests/CalcBraggPredictionTest.cpp
@@ -13,6 +13,7 @@
 #include <set>
 #include <random>
 #include <algorithm>
+#include <iterator>
 
 // The flight-path term is a zero-parameter prediction: a NIST attenuation coefficient, the stated
 // sample-to-detector distance, and Beer-Lambert. Nothing about it is fitted, so it can be checked
@@ -387,6 +388,69 @@ namespace {
     }
 }
 
+TEST_CASE("BraggPrediction_WindowFollowsResolution", "[portable]") {
+    // A still's window as a curve in d*, sqrt(c0^2 + (ang d*)^2 + (bw |q_z|)^2): it replaces the one
+    // half-width, so the window is narrower than that half-width at low resolution and wider at high
+    // resolution, and what is predicted is exactly what the curve takes out of a much wider prediction.
+    DiffractionExperiment experiment(DetJF4M());
+    experiment.DetectorDistance_mm(100.0).BeamX_pxl(1500.0).BeamY_pxl(1000.0).IncidentEnergy_keV(12.0);
+    const CrystalLattice lattice(Coord{30, 10, 0}, Coord{-15, 45, 0}, Coord{0, 0, 150});
+
+    BraggPredictionSettings wide{.high_res_A = 1.8, .ewald_dist_cutoff = 0.01f,
+                                 .max_h = 40, .max_k = 40, .max_l = 90};
+    BraggPredictionSettings curve = wide;
+    curve.ewald_dist_cutoff = 0.0003f;   // ignored once the curve is set
+    curve.window_c0 = 1e-4f;
+    curve.window_ang = 0.06f * static_cast<float>(PI) / 180.0f;
+    curve.window_bw = 0.006f;
+
+    auto window = [&](const Reflection &r) {
+        const auto recip = r.h * lattice.Astar() + r.k * lattice.Bstar() + r.l * lattice.Cstar();
+        const float wb = curve.window_bw * std::fabs(recip.z);
+        return std::sqrt(curve.window_c0 * curve.window_c0
+                         + curve.window_ang * curve.window_ang * (recip * recip) + wb * wb);
+    };
+
+    BraggPrediction pred_wide, pred_curve;
+    const int n_wide = pred_wide.Calc(experiment, lattice, wide);
+    const int n_curve = pred_curve.Calc(experiment, lattice, curve);
+    REQUIRE(n_curve > 0);
+
+    std::set<std::tuple<int, int, int>> expected, got;
+    for (int i = 0; i < n_wide; ++i) {
+        const auto &r = pred_wide.GetReflections()[i];
+        if (r.dist_ewald <= window(r))
+            expected.insert({r.h, r.k, r.l});
+    }
+    int beyond_cutoff = 0, low_res = 0;
+    for (int i = 0; i < n_curve; ++i) {
+        const auto &r = pred_curve.GetReflections()[i];
+        got.insert({r.h, r.k, r.l});
+        CHECK(r.dist_ewald <= window(r));
+        if (r.dist_ewald > curve.ewald_dist_cutoff) ++beyond_cutoff;
+        if (r.d > 6.0f) ++low_res;
+    }
+    CHECK(got == expected);
+    CHECK(beyond_cutoff > 0);   // wider than the old half-width at high resolution
+    CHECK(low_res > 0);
+
+    // Centred on a scaled reciprocal lattice: the window is taken about the excitation error of q * scale,
+    // while dist_ewald stays the lattice's own.
+    curve.window_q_scale = 1.003f;
+    const int n_scaled = pred_curve.Calc(experiment, lattice, curve);
+    REQUIRE(n_scaled > 0);
+    const Coord S0 = experiment.GetDiffractionGeometry().GetScatteringVector();
+    const float inv_lambda = 1.0f / experiment.GetWavelength_A();
+    std::set<std::tuple<int, int, int>> got_scaled;
+    for (int i = 0; i < n_scaled; ++i) {
+        const auto &r = pred_curve.GetReflections()[i];
+        got_scaled.insert({r.h, r.k, r.l});
+        const auto q = (r.h * lattice.Astar() + r.k * lattice.Bstar() + r.l * lattice.Cstar()) * curve.window_q_scale;
+        CHECK(std::fabs((q + S0).Length() - inv_lambda) <= window(r) * 1.0001f);
+    }
+    CHECK(got_scaled != got);
+}
+
 TEST_CASE("BraggPrediction_GrowsPastStartingCapacity", "[portable]") {
     // A frame predicting more than the buffer starts with must come back whole - the same reflections a
     // buffer large enough from the outset returns - and not as whichever the h/k/l walk reached first.
@@ -531,6 +595,7 @@ TEST_CASE("BraggPredictionRot_ColumnRangeKeepsEveryReflection", "[portable]") {
 #include "../image_analysis/bragg_prediction/BraggPredictionRot.h"
 #include <map>
 #include <algorithm>
+#include <iterator>
 
 TEST_CASE("BraggPredictionGPU") {
     if (get_gpu_count() == 0)
@@ -771,6 +836,41 @@ TEST_CASE("BraggPrediction_CPU_GPU_consistency_tilted") {
     CHECK(max_flight > 1.0f);
 }
 
+TEST_CASE("BraggPrediction_CPU_GPU_consistency_window") {
+    if (get_gpu_count() == 0)
+        SKIP("No CUDA GPU present");
+    // The still's window curve (BraggPredictionSettings::window_*) takes the same reflections on both.
+    DiffractionExperiment experiment(DetJF4M());
+    experiment.DetectorDistance_mm(100.0).BeamX_pxl(1500.0).BeamY_pxl(1000.0).IncidentEnergy_keV(12.0);
+    const CrystalLattice lattice(Coord{30, 10, 0}, Coord{-15, 45, 0}, Coord{0, 0, 150});
+    BraggPredictionSettings settings{.high_res_A = 1.8, .ewald_dist_cutoff = 0.0003f,
+                                     .max_h = 40, .max_k = 40, .max_l = 90};
+    settings.window_c0 = 1e-4f;
+    settings.window_ang = 0.06f * static_cast<float>(PI) / 180.0f;
+    settings.window_bw = 0.006f;
+
+    BraggPrediction cpu_pred;
+    BraggPredictionGPU gpu_pred;
+    const int cpu_count = cpu_pred.Calc(experiment, lattice, settings);
+    const int gpu_count = gpu_pred.Calc(experiment, lattice, settings);
+    REQUIRE(cpu_count > 0);
+
+    std::set<std::tuple<int, int, int>> cpu_set, gpu_set;
+    for (int i = 0; i < cpu_count; ++i) {
+        const auto &r = cpu_pred.GetReflections()[i];
+        cpu_set.insert({r.h, r.k, r.l});
+    }
+    for (int i = 0; i < gpu_count; ++i) {
+        const auto &r = gpu_pred.GetReflections()[i];
+        gpu_set.insert({r.h, r.k, r.l});
+    }
+    std::vector<std::tuple<int, int, int>> differ;
+    std::set_symmetric_difference(cpu_set.begin(), cpu_set.end(), gpu_set.begin(), gpu_set.end(),
+                                  std::back_inserter(differ));
+    // Float rounding may move a reflection sitting exactly on the edge, nothing more.
+    CHECK(differ.size() <= cpu_set.size() / 1000 + 2);
+}
+
 TEST_CASE("BraggPredictionRot_CPU_GPU_consistency_tilted") {
     if (get_gpu_count() == 0)
         SKIP("No CUDA GPU present");
diff --git a/tests/CellEsdTest.cpp b/tests/CellEsdTest.cpp
new file mode 100644
index 000000000..3ef7f3a47
--- /dev/null
+++ b/tests/CellEsdTest.cpp
@@ -0,0 +1,264 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+
+#include <filesystem>
+#include <fstream>
+#include <random>
+#include <sstream>
+
+#include <gemmi/read_cif.hpp>
+
+#include "../image_analysis/geom_refinement/CellEsd.h"
+#include "../image_analysis/WriteReflections.h"
+#include "../image_analysis/scale_merge/Merge.h"
+#include "../image_analysis/scale_merge/TwinningAnalysis.h"
+
+namespace {
+    Eigen::Matrix3d ReciprocalMetric(double a, double b, double c, double al, double be, double ga) {
+        const gemmi::UnitCell cell(a, b, c, al, be, ga);
+        Eigen::Matrix3d g;
+        for (int i = 0; i < 3; i++)
+            for (int j = 0; j < 3; j++)
+                g(i, j) = cell.frac.mat[i][0] * cell.frac.mat[j][0] + cell.frac.mat[i][1] * cell.frac.mat[j][1]
+                          + cell.frac.mat[i][2] * cell.frac.mat[j][2];   // a*_i . a*_j, a*_i a row
+        return g;
+    }
+
+    // The basis coordinates of G* (the basis is orthonormal over g11, g22, g33, g12, g13, g23), and
+    // how far G* lies outside the basis' span.
+    Eigen::VectorXd Coordinates(const std::vector<Eigen::Matrix3d> &basis, const Eigen::Matrix3d &g,
+                                double &residual) {
+        const auto vec = [](const Eigen::Matrix3d &m) {
+            Eigen::Matrix<double, 6, 1> v;
+            v << m(0, 0), m(1, 1), m(2, 2), m(0, 1), m(0, 2), m(1, 2);
+            return v;
+        };
+        Eigen::VectorXd p(basis.size());
+        Eigen::Matrix<double, 6, 1> rest = vec(g);
+        for (size_t k = 0; k < basis.size(); k++) {
+            p(k) = vec(basis[k]).dot(vec(g));
+            rest -= p(k) * vec(basis[k]);
+        }
+        residual = rest.norm() / vec(g).norm();
+        return p;
+    }
+
+    const gemmi::SpaceGroup &Sg(const char *name) { return *gemmi::find_spacegroup_by_name(name); }
+
+    // The e.s.d.s of the cell under a covariance of the metric's coordinates, against the scatter of
+    // the cells of metrics drawn from it.
+    void CheckAgainstSampling(const char *sg, double a, double b, double c, double al, double be, double ga) {
+        const auto basis = MetricBasis(Sg(sg));
+        double residual = 0.0;
+        const Eigen::VectorXd p0 = Coordinates(basis, ReciprocalMetric(a, b, c, al, be, ga), residual);
+        REQUIRE(residual < 1e-12);
+        const int n = static_cast<int>(basis.size());
+        Eigen::MatrixXd cov = Eigen::MatrixXd::Zero(n, n);
+        for (int k = 0; k < n; k++)
+            cov(k, k) = std::pow(1e-5 * p0.norm() * (k + 1), 2);
+        if (n > 1)
+            cov(0, 1) = cov(1, 0) = 0.3 * std::sqrt(cov(0, 0) * cov(1, 1));
+        const auto esd = CellEsdFromCovariance(basis, p0, cov);
+
+        const Eigen::MatrixXd chol = cov.llt().matrixL();
+        std::mt19937 rng(7);
+        std::normal_distribution<double> normal;
+        constexpr int SAMPLES = 20000;
+        std::array<double, 6> sum{}, sum2{};
+        for (int s = 0; s < SAMPLES; s++) {
+            Eigen::VectorXd z(n);
+            for (int k = 0; k < n; k++)
+                z(k) = normal(rng);
+            const Eigen::VectorXd p = p0 + chol * z;
+            Eigen::Matrix3d g = Eigen::Matrix3d::Zero();
+            for (int k = 0; k < n; k++)
+                g += p(k) * basis[k];
+            const auto cell = CellFromReciprocalMetric(g);
+            for (int j = 0; j < 6; j++) {
+                sum[j] += cell[j];
+                sum2[j] += cell[j] * cell[j];
+            }
+        }
+        for (int j = 0; j < 6; j++) {
+            const double mean = sum[j] / SAMPLES;
+            const double sd = std::sqrt(std::max(0.0, sum2[j] / SAMPLES - mean * mean));
+            if (esd[j] < CELL_ESD_FIXED)
+                CHECK(sd < 1e-7);
+            else
+                CHECK(sd == Catch::Approx(esd[j]).epsilon(0.03));
+        }
+    }
+}
+
+TEST_CASE("CellEsd: the metric basis has the free parameters of each crystal system", "[cell_esd]") {
+    CHECK(MetricBasis(Sg("P 1")).size() == 6);
+    CHECK(MetricBasis(Sg("P 1 21 1")).size() == 4);
+    CHECK(MetricBasis(Sg("C 1 2/c 1")).size() == 4);
+    CHECK(MetricBasis(Sg("P 21 21 21")).size() == 3);
+    CHECK(MetricBasis(Sg("I 41/a")).size() == 2);
+    CHECK(MetricBasis(Sg("P 61 2 2")).size() == 2);
+    CHECK(MetricBasis(Sg("R 3 :H")).size() == 2);
+    CHECK(MetricBasis(Sg("R 3 :R")).size() == 2);
+    CHECK(MetricBasis(Sg("I a -3 d")).size() == 1);
+}
+
+TEST_CASE("CellEsd: the metric basis spans the reciprocal metric of a cell of the group", "[cell_esd]") {
+    // R G* R^T, not R^T G* R: only the right one keeps a hexagonal G* (g12* = +a*^2/2) in the span.
+    double residual = 1.0;
+    Coordinates(MetricBasis(Sg("P 61 2 2")), ReciprocalMetric(5.5, 5.5, 56.0, 90, 90, 120), residual);
+    CHECK(residual < 1e-12);
+    Coordinates(MetricBasis(Sg("R 3 :R")), ReciprocalMetric(7.0, 7.0, 7.0, 80, 80, 80), residual);
+    CHECK(residual < 1e-12);
+    Coordinates(MetricBasis(Sg("P 1 21 1")), ReciprocalMetric(10.0, 7.0, 12.0, 90, 100, 90), residual);
+    CHECK(residual < 1e-12);
+    // and nothing outside it
+    Coordinates(MetricBasis(Sg("P 1 21 1")), ReciprocalMetric(10.0, 7.0, 12.0, 91, 100, 90), residual);
+    CHECK(residual > 1e-4);
+}
+
+TEST_CASE("CellEsd: e.s.d.s from a covariance follow the constraints and match sampling", "[cell_esd]") {
+    CheckAgainstSampling("P 1", 7.1, 8.3, 9.2, 81.0, 76.0, 69.0);
+    CheckAgainstSampling("P 1 21 1", 10.0, 7.0, 12.0, 90.0, 100.0, 90.0);
+    CheckAgainstSampling("P 21 21 21", 8.0, 9.5, 27.0, 90.0, 90.0, 90.0);
+    CheckAgainstSampling("P 61 2 2", 5.5, 5.5, 56.0, 90.0, 90.0, 120.0);
+    CheckAgainstSampling("R 3 :R", 7.0, 7.0, 7.0, 80.0, 80.0, 80.0);
+
+    // Tetragonal: a and b share one e.s.d., the angles have none.
+    const auto basis = MetricBasis(Sg("I -4 2 d"));
+    double residual = 0.0;
+    const Eigen::VectorXd p = Coordinates(basis, ReciprocalMetric(7.5, 7.5, 7.0, 90, 90, 90), residual);
+    const auto esd = CellEsdFromCovariance(basis, p, Eigen::MatrixXd::Identity(2, 2) * 1e-12);
+    CHECK(esd[0] > 0.0);
+    CHECK(esd[0] == Catch::Approx(esd[1]).epsilon(1e-9));
+    for (int j = 3; j < 6; j++)
+        CHECK(esd[j] < CELL_ESD_FIXED);
+}
+
+TEST_CASE("CellEsd: the d-spacing fit recovers the cell, and its e.s.d. is its scatter", "[cell_esd]") {
+    const double a = 10.0, b = 7.0, c = 12.0, beta = 100.0;   // synthetic
+    const Eigen::Matrix3d gstar = ReciprocalMetric(a, b, c, 90, beta, 90);
+    std::vector<CellObservation> clean;
+    for (int h = -8; h <= 8; h++)
+        for (int k = -5; k <= 5; k++)
+            for (int l = -8; l <= 8; l++) {
+                const Eigen::Vector3d v(h, k, l);
+                const double q = std::sqrt(v.dot(gstar * v));
+                if (q > 0.0 && q < 1.0 / 1.0)
+                    clean.push_back(CellObservation{h, k, l, static_cast<float>(q),
+                                                    static_cast<int32_t>(clean.size() * 37 % 100)});
+            }
+    REQUIRE(clean.size() > 2500);
+
+    const auto &sg = Sg("P 1 21 1");
+    std::mt19937 rng(11);
+    std::normal_distribution<double> noise(0.0, 2e-4);   // e.s.d. on q, 1/A
+    std::vector<double> fitted_a, fitted_beta;
+    std::vector<CellEsd> fits;
+    for (int trial = 0; trial < 40; trial++) {
+        std::vector<CellObservation> obs = clean;
+        for (auto &o : obs)
+            o.q = static_cast<float>(o.q + noise(rng));
+        // One gross outlier, which the 4-sigma rejection takes out.
+        obs[17].q *= 1.05f;
+        const auto e = EstimateCellEsd(obs, sg, 0.62);
+        REQUIRE(e.has_value());
+        // a 4-sigma tail of 3000 Gaussian residuals may lose one or two more
+        CHECK(e->observations <= static_cast<int64_t>(obs.size()) - 1);
+        CHECK(e->observations >= static_cast<int64_t>(obs.size()) - 4);
+        fitted_a.push_back(e->fitted.a);
+        fitted_beta.push_back(e->fitted.beta);
+        fits.push_back(*e);
+    }
+    const auto sd = [](const std::vector<double> &v) {
+        double m = 0, s = 0;
+        for (double x : v) m += x / v.size();
+        for (double x : v) s += (x - m) * (x - m) / (v.size() - 1);
+        return std::sqrt(s);
+    };
+    const CellEsd &e = fits.front();
+    CHECK(sd(fitted_a) == Catch::Approx(e.esd_lsq[0]).epsilon(0.3));
+    CHECK(sd(fitted_beta) == Catch::Approx(e.esd_lsq[4]).epsilon(0.3));
+    CHECK(std::abs(e.fitted.a - a) < 5 * e.esd_lsq[0] + 1e-4);   // float cell
+    CHECK(e.esd_lsq[3] < CELL_ESD_FIXED);
+    CHECK(e.esd_lsq[5] < CELL_ESD_FIXED);
+    // Pure centroid noise: the blocks agree with the least squares, and the larger of the two is written.
+    REQUIRE(e.esd_blocks.has_value());
+    CHECK(e.blocks == 8);
+    CHECK((*e.esd_blocks)[0] == Catch::Approx(e.esd_lsq[0]).epsilon(0.8));
+    for (int j = 0; j < 6; j++)
+        CHECK(e.esd[j] == std::max(e.esd_lsq[j], (*e.esd_blocks)[j]));
+    CHECK(e.theta_max_deg == Catch::Approx(std::asin(0.62 / 2.0) * 180.0 / M_PI).margin(0.1));
+}
+
+TEST_CASE("CellEsd: the SHELX .ins carries CELL, ZERR, LATT and SYMM", "[cell_esd][write_reflections]") {
+    CellEsd esd;
+    esd.esd = {0.0014, 0.0013, 0.0012, 0.0, 0.0034, 0.0};
+    const UnitCell cell{10.0f, 7.0f, 12.0f, 90.0f, 100.0f, 90.0f};   // synthetic
+    const auto path = (std::filesystem::temp_directory_path() / "rugnux_cell_esd_test.ins").string();
+    const auto read_ins = [&](int sg_number, const CellEsd *e) {
+        DiffractionExperiment x;
+        x.IncidentEnergy_keV(20.0f);
+        x.SpaceGroupNumber(sg_number);
+        WriteShelxIns(cell, e, x, "p", path);
+        std::ifstream in(path);
+        std::stringstream ss;
+        ss << in.rdbuf();
+        std::filesystem::remove(path);
+        return ss.str();
+    };
+
+    // P 21/c: centrosymmetric with -1 at the origin, so LATT +1 and one operator of each pair.
+    std::string ins = read_ins(14, &esd);
+    CHECK(ins.find("TITL p in P 1 21/c 1\n") == 0);
+    CHECK(ins.find(" 10.00000 7.00000 12.00000 90.0000 100.0000 90.0000\n") != std::string::npos);
+    CHECK(ins.find("\nCELL 0.6199") != std::string::npos);
+    CHECK(ins.find("\nZERR 4 0.00140 0.00130 0.00120 0.0000 0.0034 0.0000\n") != std::string::npos);
+    CHECK(ins.find("\nLATT 1\n") != std::string::npos);
+    CHECK(ins.find("\nSYMM -X,Y+1/2,-Z+1/2\n") != std::string::npos);
+    CHECK(ins.find("\nSYMM X,-Y+1/2,Z+1/2\n") == std::string::npos);
+    CHECK(ins.find("\nHKLF 4\nEND\n") != std::string::npos);
+
+    // P 21 21 21: no inversion, LATT -1 and three operators.
+    ins = read_ins(19, nullptr);
+    CHECK(ins.find("\nLATT -1\n") != std::string::npos);
+    CHECK(ins.find("\nZERR") == std::string::npos);
+    size_t symm = 0;
+    for (size_t pos = ins.find("SYMM"); pos != std::string::npos; pos = ins.find("SYMM", pos + 1))
+        symm++;
+    CHECK(symm == 3);
+
+    // C 2/c: the C centring, centrosymmetric, Z = 8.
+    ins = read_ins(15, &esd);
+    CHECK(ins.find("\nLATT 7\n") != std::string::npos);
+    CHECK(ins.find("\nZERR 8 ") != std::string::npos);
+}
+
+TEST_CASE("CellEsd: the mmCIF carries the e.s.d.s, '.' where the symmetry fixes the parameter",
+          "[cell_esd][write_reflections]") {
+    DiffractionExperiment x;
+    x.IncidentEnergy_keV(20.0f);
+    x.SpaceGroupNumber(4);
+    const UnitCell cell{10.0f, 7.0f, 12.0f, 90.0f, 100.0f, 90.0f};   // synthetic
+    x.SetUnitCell(cell);
+    CellEsd esd;
+    esd.esd = {0.0014, 0.0013, 0.0012, 0.0, 0.0034, 0.0};
+    esd.reflections = 1234;
+    esd.theta_min_deg = 1.5;
+    esd.theta_max_deg = 18.0;
+    std::vector<MergedReflection> refl(1);
+    refl[0].h = 1; refl[0].I = 10.0f; refl[0].sigma = 1.0f; refl[0].d = 5.0f;
+    const auto path = (std::filesystem::temp_directory_path() / "rugnux_cell_esd_test.cif").string();
+    WriteMmcifReflections(refl, cell, x, MergeStatistics{}, ErrorModelReport{}, TwinningAnalysisResult{},
+                          OutputProvenance{}, path, 1, &esd);
+    gemmi::cif::Document doc = gemmi::read_cif_gz(path);
+    std::filesystem::remove(path);
+    gemmi::cif::Block &block = doc.blocks[0];
+    CHECK(*block.find_value("_cell.length_a") == "10.0000");
+    CHECK(*block.find_value("_cell.length_a_esd") == "0.00140");
+    CHECK(*block.find_value("_cell.angle_beta_esd") == "0.0034");
+    CHECK(*block.find_value("_cell.angle_alpha_esd") == ".");
+    CHECK(*block.find_value("_cell_measurement.reflns_used") == "1234");
+    CHECK(*block.find_value("_cell_measurement.theta_max") == "18.00");
+}
diff --git a/tests/CellPopulationTest.cpp b/tests/CellPopulationTest.cpp
index 31335a5e1..6fb81e0f1 100644
--- a/tests/CellPopulationTest.cpp
+++ b/tests/CellPopulationTest.cpp
@@ -58,6 +58,25 @@ TEST_CASE("CellPopulation_GivenCellOffTheCrystal", "[CellPopulation][portable]")
     CHECK(kept >= 2000);
 }
 
+TEST_CASE("CellPopulation_StrayFramesBeyondTheTail", "[CellPopulation][portable]") {
+    // Two forms, the given cell at the smaller one, and a few misindexed frames far out beyond its tail.
+    // Each stray frame is a local maximum of the histogram with no valley of its own; it is not a
+    // population, and must not stand for "everything", both forms included.
+    const auto block = [](double mu, double w, int n, std::vector<double> &r) {
+        for (int i = 0; i < n; i++) r.push_back(mu + w * ((i + 0.5) / n - 0.5));
+    };
+    std::vector<double> r;
+    block(-0.055, 0.0582, 400, r);
+    block(0.02, 0.0194, 220, r);
+    for (double x : {0.0748, 0.0442, 0.0423, 0.8394, 0.7456}) r.push_back(x);
+    const auto [low, high] = GivenCellPopulation(r);
+    size_t kept_other = 0, kept_given = 0;
+    for (int i = 0; i < 400; i++) kept_other += (r[i] >= low && r[i] <= high);
+    for (int i = 400; i < 620; i++) kept_given += (r[i] >= low && r[i] <= high);
+    CHECK(kept_given == 220);
+    CHECK(kept_other < 10);
+}
+
 TEST_CASE("CellPopulation_TooFewFrames", "[CellPopulation][portable]") {
     const auto [low, high] = GivenCellPopulation({0.0, 0.1, 0.2});
     CHECK(std::isinf(low));
diff --git a/tests/JFJochReaderTest.cpp b/tests/JFJochReaderTest.cpp
index 0f7b952f1..24953b013 100644
--- a/tests/JFJochReaderTest.cpp
+++ b/tests/JFJochReaderTest.cpp
@@ -2776,6 +2776,109 @@ TEST_CASE("JFJochReader_ReadReflections_Reindex", "[HDF5][Full]") {
     REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
 }
 
+// A stills run's rocking curve (the one its partialities were computed from) goes to the master file and
+// comes back whole, so --mode scale merges with it instead of measuring another; a file without it reads
+// back without one.
+TEST_CASE("JFJochReader_StillsRunWidth", "[HDF5][Full]") {
+    for (const bool with_width: {true, false}) {
+        DiffractionExperiment x(DetJF(1));
+        x.FilePrefix("read_stills_run_width")
+         .ImagesPerTrigger(1)
+         .ImagesPerFile(1)
+         .OverwriteExistingFiles(true)
+         .BitDepthImage(16)
+         .PixelSigned(true)
+         .SetFileWriterFormat(FileWriterFormat::NXmxVDS)
+         .Compression(CompressionAlgorithm::NO_COMPRESSION);
+
+        const StillsRunWidth w{.gamma0 = 1.25e-4, .gamma_e = 6.1e-4, .bandwidth_sigma = 1.7e-3,
+                               .radial_scale = 1.0 + 3.3e-4,
+                               .table_dstar = {0.1, 0.25, 0.4}, .table_s = {1.1e-4, 1.4e-4, 2.2e-4}};
+        RegisterHDF5Filter();
+        {
+            StartMessage start_message;
+            x.FillMessage(start_message);
+            FileWriter writer(start_message);
+            std::vector<int16_t> image(x.GetPixelsNum(), 0);
+            DataMessage message{};
+            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+            message.number = 0;
+            REQUIRE_NOTHROW(writer.WriteHDF5(message));
+            EndMessage end_message;
+            end_message.max_image_number = 1;
+            if (with_width)
+                end_message.stills_run_width = w;
+            writer.WriteHDF5(end_message);
+            writer.Finalize();
+        }
+        {
+            JFJochHDF5Reader reader;
+            REQUIRE_NOTHROW(reader.ReadFile("read_stills_run_width_master.h5"));
+            const auto &got = reader.GetDataset()->stills_run_width;
+            REQUIRE(got.has_value() == with_width);
+            if (with_width) {
+                CHECK(got->gamma0 == w.gamma0);
+                CHECK(got->gamma_e == w.gamma_e);
+                CHECK(got->bandwidth_sigma == w.bandwidth_sigma);
+                CHECK(got->radial_scale == w.radial_scale);
+                CHECK(got->table_dstar == w.table_dstar);
+                CHECK(got->table_s == w.table_s);
+            }
+        }
+        remove("read_stills_run_width_master.h5");
+        remove("read_stills_run_width_data_000001.h5");
+    }
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
+TEST_CASE("JFJochReader_UnitCellEsd", "[HDF5][Full]") {
+    for (const bool with_esd: {true, false}) {
+        DiffractionExperiment x(DetJF(1));
+        x.FilePrefix("read_unit_cell_esd")
+         .ImagesPerTrigger(1)
+         .ImagesPerFile(1)
+         .OverwriteExistingFiles(true)
+         .BitDepthImage(16)
+         .PixelSigned(true)
+         .SetFileWriterFormat(FileWriterFormat::NXmxVDS)
+         .Compression(CompressionAlgorithm::NO_COMPRESSION);
+
+        const UnitCell cell{.a = 61.2f, .b = 61.2f, .c = 97.5f, .alpha = 90, .beta = 90, .gamma = 120};
+        const UnitCell esd{.a = 0.0031f, .b = 0.0031f, .c = 0.0074f, .alpha = 0, .beta = 0, .gamma = 0};
+        RegisterHDF5Filter();
+        {
+            StartMessage start_message;
+            x.FillMessage(start_message);
+            FileWriter writer(start_message);
+            std::vector<int16_t> image(x.GetPixelsNum(), 0);
+            DataMessage message{};
+            message.image = CompressedImage(image, x.GetXPixelsNum(), x.GetYPixelsNum());
+            message.number = 0;
+            REQUIRE_NOTHROW(writer.WriteHDF5(message));
+            EndMessage end_message;
+            end_message.max_image_number = 1;
+            end_message.unit_cell = cell;
+            if (with_esd)
+                end_message.unit_cell_esd = esd;
+            writer.WriteHDF5(end_message);
+            writer.Finalize();
+        }
+        {
+            JFJochHDF5Reader reader;
+            REQUIRE_NOTHROW(reader.ReadFile("read_unit_cell_esd_master.h5"));
+            const auto dataset = reader.GetDataset();
+            REQUIRE(dataset->experiment.GetUnitCell().has_value());
+            CHECK(dataset->experiment.GetUnitCell()->c == cell.c);
+            REQUIRE(dataset->unit_cell_esd.has_value() == with_esd);
+            if (with_esd)
+                CHECK(*dataset->unit_cell_esd == esd);
+        }
+        remove("read_unit_cell_esd_master.h5");
+        remove("read_unit_cell_esd_data_000001.h5");
+    }
+    REQUIRE(H5Fget_obj_count(H5F_OBJ_ALL, H5F_OBJ_ALL) == 0);
+}
+
 static std::vector<SpotToSave> MakeTestSpots(int i) {
     return {
         SpotToSave{
diff --git a/tests/MergeScaleTest.cpp b/tests/MergeScaleTest.cpp
index 04ba3bb63..1e9050001 100644
--- a/tests/MergeScaleTest.cpp
+++ b/tests/MergeScaleTest.cpp
@@ -162,19 +162,25 @@ namespace {
         return out;
     }
 
+    // The statistics over a declared low-resolution bound (--report-resolution), or over the whole sphere
+    // without one: the scaling's own low-resolution limit bounds the scale fit, not the merge.
     MergeStatistics StatsWithLowLimit(const gemmi::SpaceGroup &sg, const std::optional<UnitCell> &cell,
                                       const std::vector<MergedReflection> &merged,
                                       std::optional<double> low_limit, bool merge_friedel) {
         DiffractionExperiment x;
         x.SetSpaceGroup(sg);
         ScalingSettings s = x.GetScalingSettings();
-        s.LowResolutionLimit_A(low_limit);
         s.MergeFriedel(merge_friedel);
         x.ImportScalingSettings(s);
 
         MergeOnTheFly merge(x);
         merge.ReferenceCell(cell);
-        return merge.MergeStats(merged, {});
+        const auto own = merge.MergeStats(merged, {});
+        if (!low_limit)
+            return own;
+        // Down to the data's own d_min, padded as MergeStats pads it.
+        return merge.MergeStats(merged, {}, {}, std::nullopt,
+                                ReportResolutionRange{.d_min = own.overall.d_min * 0.999, .d_max = *low_limit});
     }
 
     double Completeness(const MergeStatisticsShell &s) {
@@ -528,10 +534,37 @@ TEST_CASE("ErrorModel_BNotMeasuredOnWeakData") {
     const auto fit = FitErrorModel(pool, scratch, 4);
     REQUIRE(fit.active);
     CHECK(!fit.b_measured);
+    CHECK(!fit.b_resolved);   // b held at zero is not a b to report 1/b of
     CHECK(fit.b2 == 0.0);
     CHECK(fit.a == Catch::Approx(0.9).epsilon(0.03));
 }
 
+// Nearly half the observations repeat their mates to the bit (an input read twice): the bins' median deviations
+// sit near zero, their 1/bd2^2 weights take the fit, and both terms are pulled towards zero. a stops on
+// its lower bound while b^2 goes on to a remainder whose 1/b is an I/sigma in the hundreds or thousands. Beside a
+// clamped a the b^2 is not the solution of any fit, so it is left unresolved and no ISa is printed.
+TEST_CASE("ErrorModel_HalfTheMatesIdenticalLeavesISaUndetermined") {
+    std::mt19937 rng(1);
+    std::uniform_real_distribution<double> u(0.0, 1.0);
+    std::normal_distribution<double> z(0.0, 1.0);
+    std::vector<ErrorModelSample> pool;
+    for (int i = 0; i < 200000; ++i) {
+        const double s2 = std::pow(10.0, 2.0 * u(rng));
+        const double snr = 300.0 * std::pow(10.0, -4.0 * u(rng));
+        const double I2 = snr * snr * s2;
+        const double e = z(rng);
+        double dev2 = (1.3 * s2 + 0.03 * 0.03 * I2) * e * e;
+        if (u(rng) < 0.48) dev2 = 0.0;
+        pool.push_back({s2, I2, dev2, 2.0f});
+    }
+    std::vector<ErrorModelBinned> scratch;
+    const auto fit = FitErrorModel(pool, scratch, 4);
+    REQUIRE(fit.active);
+    CHECK(fit.a == 0.25);
+    CHECK(1.0 / std::sqrt(fit.b2) > 100.0);
+    CHECK(!fit.b_resolved);
+}
+
 #ifdef JFJOCH_USE_CUDA
 #include "../common/CUDAWrapper.h"
 #include "../image_analysis/scale_merge/ErrorModelGPU.h"
@@ -789,6 +822,78 @@ namespace {
     }
 }
 
+// A reciprocal lattice scaled by (1 + eps) - a wavelength or cell a little off, which the spot positions
+// cannot see - centres every crystal's rocking curve at eps lambda d*^2 / 2 instead of zero. The windows are
+// cut symmetrically about the stored lattice's sphere, as prediction cuts them; the run's radial scale has
+// to come back from where the recorded intensity sits within them.
+TEST_CASE("StillsPartialityRefine_MeasureRadialScale") {
+    constexpr float CELL = 50.0f, WAVELENGTH = 1.0f, D_MIN = 2.0f;
+    constexpr double EPS = 4e-3, GAMMA0 = 2e-4, WINDOW = 1e-3;
+    DiffractionExperiment x;
+    x.SetSpaceGroup(gemmi::get_spacegroup_by_name("P 1"));
+    DiffractionGeometry geom;
+    geom.Wavelength_A(WAVELENGTH);
+    const Coord S0 = geom.GetScatteringVector();
+
+    std::mt19937 rng(13);
+    std::normal_distribution<double> gauss(0.0, 1.0);
+    std::uniform_real_distribution<double> unit(0.0, 1.0);
+    std::exponential_distribution<double> wilson(1.0);
+    std::vector<IntegrationOutcome> outcomes(100);
+    const int hmax = static_cast<int>(CELL / D_MIN);
+    for (auto &o: outcomes) {
+        const auto axes = TurnedAxes(UnitCell(CELL, CELL, CELL, 90, 90, 90));
+        // a different orientation per crystal: turn the turned axes about a random axis
+        const double ax = gauss(rng), ay = gauss(rng), az = gauss(rng), n = std::sqrt(ax * ax + ay * ay + az * az);
+        const double angle = 2.0 * M_PI * unit(rng), c = std::cos(angle), s = std::sin(angle);
+        auto turn = [&](const Coord &v) {
+            const double k[3] = {ax / n, ay / n, az / n};
+            const double dot = k[0] * v.x + k[1] * v.y + k[2] * v.z;
+            const double cr[3] = {k[1] * v.z - k[2] * v.y, k[2] * v.x - k[0] * v.z, k[0] * v.y - k[1] * v.x};
+            return Coord(static_cast<float>(v.x * c + cr[0] * s + k[0] * dot * (1 - c)),
+                         static_cast<float>(v.y * c + cr[1] * s + k[1] * dot * (1 - c)),
+                         static_cast<float>(v.z * c + cr[2] * s + k[2] * dot * (1 - c)));
+        };
+        o.geom = geom;
+        o.latt = CrystalLattice(turn(axes[0]), turn(axes[1]), turn(axes[2]));
+        o.image_scale_g = 0.5 + unit(rng);
+        for (int h = -hmax; h <= hmax; ++h)
+            for (int k = -hmax; k <= hmax; ++k)
+                for (int l = -hmax; l <= hmax; ++l) {
+                    const Coord q = o.latt.Astar() * h + o.latt.Bstar() * k + o.latt.Cstar() * l;
+                    const float dstar = q.Length();
+                    if (dstar == 0.0f || dstar > 1.0f / D_MIN)
+                        continue;
+                    const double de_stored = (q + S0).Length() - 1.0 / WAVELENGTH;
+                    if (std::fabs(de_stored) > WINDOW)
+                        continue;
+                    const double de_true = (q * static_cast<float>(1.0 + EPS) + S0).Length() - 1.0 / WAVELENGTH;
+                    Reflection r{};
+                    r.h = h; r.k = k; r.l = l;
+                    r.d = 1.0f / dstar;
+                    r.dist_ewald = static_cast<float>(std::fabs(de_stored));
+                    r.I = static_cast<float>(*o.image_scale_g * 1000.0 * wilson(rng)
+                                             * std::exp(-0.5 * de_true * de_true / (GAMMA0 * GAMMA0)));
+                    r.sigma = 1.0f;
+                    r.prescaling_corr = 1.0f;
+                    r.partiality = 1.0f;
+                    o.reflections.push_back(r);
+                }
+    }
+    const StillsPartialityRefine refine(x);
+    double scale = 1.0;
+    for (int i = 0; i < 3; ++i)
+        scale = refine.MeasureRadialScale(outcomes, std::nullopt, scale);
+    CHECK(scale - 1.0 == Catch::Approx(EPS).epsilon(0.15));
+
+    // and a lattice that is right stays put
+    for (auto &o: outcomes)
+        for (auto &r: o.reflections)
+            r.I = static_cast<float>(*o.image_scale_g * 1000.0);
+    CHECK(std::fabs(refine.MeasureRadialScale(outcomes, std::nullopt, 1.0) - 1.0) < 5e-4);
+}
+
+
 // A frame indexed with its c axis doubled: its reciprocal lattice holds every node of the true one plus
 // the planes in between. Relabelling keeps exactly the true nodes, each at the same scattering vector,
 // and gives the frame the true cell.
@@ -957,6 +1062,91 @@ TEST_CASE("StillsPartialityRefine_MeasureRunWidth") {
     CHECK(width->bandwidth_sigma < 1e-3);
 }
 
+// Frames predicted through a much wider window whose intensities do not follow the curve (a wrong lattice
+// on the frame) must not decide the measured width: pooled with the others they hold most of the de^2, and
+// the run's width then read as their window. Measured per group of similar window, they are a group whose
+// curve looks wider than its window, which is left out.
+TEST_CASE("StillsPartialityRefine_MeasureRunWidth_WideWindowFramesIgnored") {
+    constexpr double GAMMA0 = 1.0e-4, GAMMA_E = 0.035 * M_PI / 180.0;
+    DiffractionExperiment x;
+    x.SetSpaceGroup(gemmi::get_spacegroup_by_name("P 1"));
+
+    std::mt19937 rng(7);
+    std::uniform_real_distribution<double> unit(0.0, 1.0);
+    std::exponential_distribution<double> wilson(1.0);
+    std::normal_distribution<double> gauss(0.0, 1.0);
+    std::vector<IntegrationOutcome> outcomes(400);
+    for (size_t f = 0; f < outcomes.size(); ++f) {
+        auto &o = outcomes[f];
+        const bool wide = f % 4 == 3;
+        o.image_scale_g = 0.5 + unit(rng);
+        for (int j = 0; j < 200; ++j) {
+            const double d = 1.5 + 8.0 * unit(rng);
+            const double dstar = 1.0 / d;
+            const double s = std::sqrt(GAMMA0 * GAMMA0 + GAMMA_E * GAMMA_E * dstar * dstar);
+            const double window = (wide ? 20.0 : 4.0) * std::sqrt(GAMMA0 * GAMMA0 + GAMMA_E * GAMMA_E / (1.5 * 1.5));
+            const double de = window * (2.0 * unit(rng) - 1.0);
+            const double p = wide ? 1.0 : std::exp(-0.5 * de * de / (s * s));
+            Reflection r{};
+            r.h = j; r.k = 1; r.l = 1;
+            r.d = static_cast<float>(d);
+            r.dist_ewald = static_cast<float>(std::fabs(de));
+            r.I = static_cast<float>(*o.image_scale_g * 1000.0 * wilson(rng) * p + 5.0 * gauss(rng));
+            r.sigma = 5.0f;
+            r.prescaling_corr = 1.0f;
+            r.partiality = 1.0f;
+            r.image_scale_corr = static_cast<float>(1.0 / *o.image_scale_g);
+            o.reflections.push_back(r);
+        }
+    }
+    const auto width = StillsPartialityRefine(x).MeasureRunWidth(outcomes, std::nullopt);
+    REQUIRE(width.has_value());
+    CHECK(width->gamma0 == Catch::Approx(GAMMA0).epsilon(0.3));
+    CHECK(width->gamma_e == Catch::Approx(GAMMA_E).epsilon(0.15));
+}
+
+// Frames predicted through the run's width (2 sigma(d*) of its formula) have a window at every reflection's
+// own resolution; measured with that window, the table gives the width back at each shell.
+TEST_CASE("StillsPartialityRefine_MeasureRunWidth_WindowAtReflectionResolution") {
+    constexpr double GAMMA0 = 1.0e-4, GAMMA_E = 0.035 * M_PI / 180.0;
+    DiffractionExperiment x;
+    x.SetSpaceGroup(gemmi::get_spacegroup_by_name("P 1"));
+    const StillsPartialityRefine::RunWidth window{.gamma0 = GAMMA0, .gamma_e = GAMMA_E};
+    auto sigma = [&](double dstar) { return std::sqrt(GAMMA0 * GAMMA0 + GAMMA_E * GAMMA_E * dstar * dstar); };
+
+    std::mt19937 rng(11);
+    std::uniform_real_distribution<double> unit(0.0, 1.0);
+    std::exponential_distribution<double> wilson(1.0);
+    std::normal_distribution<double> gauss(0.0, 1.0);
+    std::vector<IntegrationOutcome> outcomes(400);
+    for (auto &o: outcomes) {
+        o.image_scale_g = 0.5 + unit(rng);
+        for (int j = 0; j < 200; ++j) {
+            const double d = 1.5 + 8.0 * unit(rng);
+            const double s = sigma(1.0 / d);
+            const double de = 2.0 * s * (2.0 * unit(rng) - 1.0);
+            Reflection r{};
+            r.h = j; r.k = 1; r.l = 1;
+            r.d = static_cast<float>(d);
+            r.dist_ewald = static_cast<float>(std::fabs(de));
+            r.I = static_cast<float>(*o.image_scale_g * 1000.0 * wilson(rng) * std::exp(-0.5 * de * de / (s * s))
+                                     + 5.0 * gauss(rng));
+            r.sigma = 5.0f;
+            r.prescaling_corr = 1.0f;
+            r.partiality = 1.0f;
+            r.image_scale_corr = static_cast<float>(1.0 / *o.image_scale_g);
+            o.reflections.push_back(r);
+        }
+    }
+    const auto width = StillsPartialityRefine(x).MeasureRunWidth(outcomes, std::nullopt, 1.0, &window);
+    REQUIRE(width.has_value());
+    REQUIRE(width->table_s.size() >= 3);
+    for (size_t i = 0; i < width->table_s.size(); ++i) {
+        INFO("d* = " << width->table_dstar[i]);
+        CHECK(width->table_s[i] == Catch::Approx(sigma(width->table_dstar[i])).epsilon(0.15));
+    }
+}
+
 // Outlier rejection on the stills merge: one observation at ten times its reflection's intensity among
 // nineteen consistent ones is dropped, and nothing else is.
 TEST_CASE("MergeOnTheFly_RejectsAnOutlierInTheBand") {
@@ -992,6 +1182,45 @@ TEST_CASE("MergeOnTheFly_RejectsAnOutlierInTheBand") {
     CHECK(merge.RejectedCount() == 1);
 }
 
+// Stills: the observations of a reflection spread from near zero to its full intensity (partials), so
+// the spread of ln(I / median) is wide. One powder grain in a weak reflection's box, at 200 times its
+// intensity, must still be rejected - the band is the error model's, n sigma about the median - while
+// none of the partials is.
+TEST_CASE("MergeOnTheFly_StillsRejectsAGrainAmongPartials") {
+    DiffractionExperiment x;
+    x.SetSpaceGroup(gemmi::get_spacegroup_by_name("P 1"));
+    ScalingSettings s = x.GetScalingSettings();
+    s.OutlierRejectNsigma(6.0);
+    x.ImportScalingSettings(s);
+    REQUIRE(!x.IsRotationIndexing());
+
+    std::mt19937 rng(5);
+    std::normal_distribution<float> gauss(0.0f, 1.0f);
+    std::uniform_real_distribution<float> partial(0.1f, 1.0f);
+    std::vector<IntegrationOutcome> outcomes(40);
+    for (size_t i = 0; i < outcomes.size(); ++i) {
+        for (int h = 1; h <= 50; ++h) {
+            Reflection r{};
+            r.h = h; r.k = 2; r.l = 3;
+            r.d = 2.0f;
+            const float I_true = 100.0f * static_cast<float>(h);
+            r.I = I_true * partial(rng) + 3.0f * gauss(rng);
+            if (i == 7 && h == 1)
+                r.I = 200.0f * I_true;
+            r.sigma = 3.0f;
+            r.prescaling_corr = 1.0f;
+            r.partiality = 1.0f;
+            r.image_scale_corr = 1.0f;
+            outcomes[i].reflections.push_back(r);
+        }
+    }
+    MergeOnTheFly merge(x);
+    merge.RefineErrorModel(outcomes);
+    REQUIRE(merge.ErrorModelActive());
+    merge.AddImages(outcomes);
+    CHECK(merge.RejectedCount() == 1);
+}
+
 // The capture term widens the sigma of a partial by (c (1 - p) <I>): a partial merges at a lower weight
 // than a full of the same intensity, and not at all differently with c = 0.
 TEST_CASE("MergeOnTheFly_CaptureTermDownweightsPartials") {
@@ -1028,3 +1257,12 @@ TEST_CASE("MergeOnTheFly_CaptureTermDownweightsPartials") {
     CHECK(with < without);
     CHECK(with < 1.08f);
 }
+
+// The setter checks the value it is given, not the one it replaces.
+TEST_CASE("ScalingSettings_MinPartialityRange") {
+    ScalingSettings s;
+    CHECK_THROWS(s.MinPartiality(1.5));
+    CHECK_THROWS(s.MinPartiality(-0.1));
+    CHECK_NOTHROW(s.MinPartiality(0.5));
+    CHECK(s.GetMinPartiality() == 0.5);
+}
diff --git a/tests/ModelScaleGPUTest.cpp b/tests/ModelScaleGPUTest.cpp
index 3ceb54200..d9e608ce1 100644
--- a/tests/ModelScaleGPUTest.cpp
+++ b/tests/ModelScaleGPUTest.cpp
@@ -392,6 +392,45 @@ TEST_CASE("ModelScaleGPUPool_MatchesFitModelScale", "[ModelValidation][gpu]") {
     }
 }
 
+// Refinement's robust fit (ModelScaleBox::robust) on the card: the reweighting on the device, the answer
+// FitModelScale's to rounding where one reflection in fifty is a gross outlier - and the same, to the bit, run to
+// run and whichever engine a fit got.
+TEST_CASE("ModelScaleGPUPool_RobustMatchesFitModelScale", "[ModelValidation][gpu]") {
+    if (get_gpu_count() == 0)
+        SKIP("No GPU");
+    for (const Case &c : CASES) {
+        INFO(c.name);
+        gemmi::UnitCell cell(c.a, c.b, c.c, c.alpha, c.beta, c.gamma);
+        const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(c.hm);
+        gemmi::Scaling<float> points = MakeScaling(cell, sg, 2.8);
+        for (size_t i = 0; i < points.points.size(); i += 50)
+            points.points[i].fobs *= 4.0f;
+        gemmi::Scaling<float> cpu = points, cpu_plain = points;
+        FitModelScale(cpu, {.robust = true}, 8);
+        FitModelScale(cpu_plain, {}, 8);
+
+        ModelScaleGPUPool pool(0, points.points.size(), 2);
+        std::vector<gemmi::Scaling<float>> gpu(4, points);
+        std::vector<std::future<void>> fits;
+        for (size_t i = 0; i < gpu.size(); i++)
+            fits.push_back(std::async(std::launch::async, [&, i] { pool.Fit(gpu[i], 80.0, 2, true); }));
+        for (auto &f : fits)
+            f.get();
+
+        // the robust answer is not the plain one, and the card's is the host's to rounding
+        CHECK(std::fabs(cpu.k_overall - cpu_plain.k_overall) > 1e-3 * cpu.k_overall);
+        CHECK(gpu[0].k_overall == Catch::Approx(cpu.k_overall).epsilon(1e-3));
+        CHECK(gpu[0].k_sol == Catch::Approx(cpu.k_sol).margin(0.026));
+        CHECK(std::fabs(gpu[0].calculate_r_factor() - cpu.calculate_r_factor()) < 1e-4);
+        for (size_t i = 1; i < gpu.size(); i++) {
+            CHECK(gpu[i].k_sol == gpu[0].k_sol);
+            CHECK(gpu[i].b_sol == gpu[0].b_sol);
+            CHECK(gpu[i].k_overall == gpu[0].k_overall);
+            CHECK(std::memcmp(&gpu[i].b_star, &gpu[0].b_star, sizeof(gpu[0].b_star)) == 0);
+        }
+    }
+}
+
 // ModelScaling fits past a reflection the solvent cancels exactly (ModelScalingTest.cpp), on the card.
 TEST_CASE("ModelScaleGPUPool_FitsPastAReflectionTheSolventCancelsExactly", "[ModelValidation][gpu]") {
     if (get_gpu_count() == 0)
diff --git a/tests/RefineOnlyTest.cpp b/tests/RefineOnlyTest.cpp
new file mode 100644
index 000000000..c98c6e0ba
--- /dev/null
+++ b/tests/RefineOnlyTest.cpp
@@ -0,0 +1,229 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+
+#include <cmath>
+#include <random>
+#include <string>
+#include <vector>
+
+#include <gemmi/dencalc.hpp>
+#include <gemmi/fourier.hpp>
+#include <gemmi/it92.hpp>
+#include <gemmi/mtz.hpp>
+
+#include "../common/Logger.h"
+#include "../rugnux/ResultReport.h"
+#include "../rugnux/RugnuxRefine.h"
+#include "../writer/RugnuxReflectionFile.h"
+
+namespace {
+
+// A small synthetic orthorhombic cell (no real sample) and its reflections h, k, l = 1..6.
+const gemmi::UnitCell test_cell(31.0, 37.0, 43.0, 90.0, 90.0, 90.0);
+
+// An MTZ of `columns` (label, type), every row the hkl followed by values from `value(h, k, l, column)`.
+gemmi::Mtz MakeMtz(const std::vector<std::pair<std::string, char>> &columns,
+                   float (*value)(int h, int k, int l, size_t column)) {
+    gemmi::Mtz mtz(true);
+    mtz.spacegroup = gemmi::find_spacegroup_by_name("P 21 21 21");
+    mtz.set_cell_for_all(test_cell);
+    mtz.add_dataset("test").wavelength = 0.9;
+    for (const auto &[label, type] : columns)
+        mtz.add_column(label, type, -1, -1, false);
+    for (int h = 1; h <= 6; h++)
+        for (int k = 1; k <= 6; k++)
+            for (int l = 1; l <= 6; l++) {
+                mtz.data.insert(mtz.data.end(), {float(h), float(k), float(l)});
+                for (size_t c = 0; c < columns.size(); c++)
+                    mtz.data.push_back(value(h, k, l, c));
+                mtz.nreflections++;
+            }
+    return mtz;
+}
+
+bool InTestSet(int h, int k, int l) { return (h * 7 + k * 13 + l * 17) % 10 == 0; }
+
+// Waters scattered over the test cell, and their own |F|^2 as the data: the model as given scores well.
+void SyntheticRefineInput(gemmi::Structure &st, RugnuxReflections &data) {
+    const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name("P 21 21 21");
+    st.cell = test_cell;
+    st.spacegroup_hm = sg->xhm();
+    st.setup_cell_images();
+    gemmi::Model model(1);
+    gemmi::Chain chain("A");
+    std::mt19937 rng(7);
+    std::uniform_real_distribution<double> frac(0.0, 1.0);
+    for (int i = 0; i < 120; i++) {
+        gemmi::Residue res;
+        res.name = "HOH";
+        res.seqid = gemmi::SeqId(i + 1, ' ');
+        res.het_flag = 'H';
+        gemmi::Atom a;
+        a.name = "O";
+        a.element = gemmi::El::O;
+        a.pos = test_cell.orthogonalize(gemmi::Fractional(frac(rng), frac(rng), frac(rng)));
+        a.b_iso = 15.0f;
+        a.occ = 1.0f;
+        res.atoms.push_back(a);
+        chain.residues.push_back(res);
+    }
+    model.chains.push_back(chain);
+    st.models.push_back(model);
+
+    gemmi::DensityCalculator<gemmi::IT92<float>, float> dc;
+    dc.d_min = 2.0;
+    dc.grid.unit_cell = test_cell;
+    dc.grid.spacegroup = sg;
+    dc.set_refmac_compatible_blur(st.models[0]);
+    dc.put_model_density_on_grid(st.models[0]);
+    const gemmi::AsuData<std::complex<float>> f =
+            gemmi::transform_map_to_f_phi(dc.grid, true).prepare_asu_data(2.0, dc.blur);
+
+    data.name = "synthetic.mtz";
+    data.source = "MTZ";
+    data.cell = test_cell;
+    data.space_group = sg->xhm();
+    data.amplitudes = false;
+    for (const auto &hv : f.v) {
+        if (hv.hkl == gemmi::Miller{{0, 0, 0}})
+            continue;
+        const double fc = std::abs(hv.value);
+        MergedReflection m;
+        m.h = hv.hkl[0];
+        m.k = hv.hkl[1];
+        m.l = hv.hkl[2];
+        m.d = static_cast<float>(test_cell.calculate_d(hv.hkl));
+        m.I = static_cast<float>(fc * fc);
+        m.sigma = static_cast<float>(0.02 * fc * fc + 1.0);
+        data.reflections.push_back(m);
+    }
+}
+
+}  // namespace
+
+TEST_CASE("RugnuxReflectionsFromMtz takes observed amplitudes over map coefficients", "[refine_only]") {
+    // FWT comes first and is an amplitude with a phase after it; FP/SIGFP is what is observed.
+    const gemmi::Mtz mtz = MakeMtz({{"FWT", 'F'}, {"PHWT", 'P'}, {"FP", 'F'}, {"SIGFP", 'Q'}, {"FreeR_flag", 'I'}},
+                                   [](int h, int k, int l, size_t c) -> float {
+                                       switch (c) {
+                                           case 0: return 999.0f;
+                                           case 1: return 10.0f;
+                                           case 2: return 100.0f + h;
+                                           case 3: return 2.0f;
+                                           default: return InTestSet(h, k, l) ? 0.0f : float(1 + (h + k + l) % 19);
+                                       }
+                                   });
+    const RugnuxReflections r = RugnuxReflectionsFromMtz(mtz, "synthetic.mtz");
+    CHECK(r.amplitudes);
+    CHECK(r.value_column == "FP");
+    CHECK(r.sigma_column == "SIGFP");
+    CHECK(r.free_column == "FreeR_flag");
+    CHECK(r.wavelength_A == Catch::Approx(0.9));
+    REQUIRE(r.reflections.size() == 216);
+    int n_free = 0;
+    for (const MergedReflection &m : r.reflections) {
+        CHECK(m.F == Catch::Approx(100.0 + m.h));
+        CHECK(m.rfree_flag == InTestSet(m.h, m.k, m.l));
+        n_free += m.rfree_flag;
+    }
+    CHECK(r.n_free == n_free);
+}
+
+TEST_CASE("RugnuxReflectionsFromMtz falls back to intensities and reads a 1-marks-free flag", "[refine_only]") {
+    const gemmi::Mtz mtz = MakeMtz({{"IMEAN", 'J'}, {"SIGIMEAN", 'Q'}, {"R-free-flags", 'I'}},
+                                   [](int h, int k, int l, size_t c) -> float {
+                                       if (c == 0) return 50.0f * h;
+                                       if (c == 1) return 5.0f;
+                                       return InTestSet(h, k, l) ? 1.0f : 0.0f;
+                                   });
+    const RugnuxReflections r = RugnuxReflectionsFromMtz(mtz, "synthetic.mtz");
+    CHECK_FALSE(r.amplitudes);
+    CHECK(r.value_column == "IMEAN");
+    CHECK(r.free_column == "R-free-flags");
+    for (const MergedReflection &m : r.reflections) {
+        CHECK(m.I == Catch::Approx(50.0 * m.h));
+        CHECK(std::isnan(m.F));
+        CHECK(m.rfree_flag == InTestSet(m.h, m.k, m.l));
+    }
+}
+
+TEST_CASE("RugnuxReflectionsFromMtz without free flags, and without any value column", "[refine_only]") {
+    const gemmi::Mtz plain = MakeMtz({{"F", 'F'}, {"SIGF", 'Q'}},
+                                     [](int h, int, int, size_t c) -> float { return c == 0 ? 10.0f * h : 1.0f; });
+    const RugnuxReflections r = RugnuxReflectionsFromMtz(plain, "synthetic.mtz");
+    CHECK(r.value_column == "F");
+    CHECK(r.free_column.empty());
+    CHECK(r.n_free == 0);
+
+    const gemmi::Mtz calculated = MakeMtz({{"FC", 'F'}, {"PHIC", 'P'}},
+                                          [](int, int, int, size_t) -> float { return 1.0f; });
+    CHECK_THROWS(RugnuxReflectionsFromMtz(calculated, "synthetic.mtz"));
+}
+
+TEST_CASE("ParseRugnuxReflections reads an MTZ from its bytes", "[refine_only]") {
+    const gemmi::Mtz mtz = MakeMtz({{"F", 'F'}, {"SIGF", 'Q'}, {"FreeR_flag", 'I'}},
+                                   [](int h, int k, int l, size_t c) -> float {
+                                       if (c == 0) return 10.0f * h;
+                                       if (c == 1) return 1.0f;
+                                       return InTestSet(h, k, l) ? 0.0f : 1.0f;
+                                   });
+    std::string bytes;
+    mtz.write_to_string(bytes);
+    const RugnuxReflections r = ParseRugnuxReflections(bytes, "synthetic.mtz");
+    CHECK(r.source == "MTZ");
+    CHECK(r.space_group == "P 21 21 21");
+    CHECK(r.reflections.size() == 216);
+    CHECK(r.free_column == "FreeR_flag");
+}
+
+TEST_CASE("RunRefineOnly scores a model against intensities, with amplitudes and free flags made for it",
+          "[refine_only]") {
+    gemmi::Structure st;
+    RugnuxReflections data;
+    SyntheticRefineInput(st, data);
+    RefinementSettings settings;
+    settings.score_only = true;
+    settings.gpu = false;
+    settings.nthreads = 2;
+    Logger logger("RefineOnlyTest");
+    const RefineOnlyResult r = RunRefineOnly(data, st, 2.5, settings, logger);
+    REQUIRE(r.refinement.ok);
+    CHECK(r.french_wilson);
+    CHECK(r.free_flags_generated);
+    CHECK(r.free_reflections > 0);
+    CHECK(r.d_min_limit == 2.5);
+    CHECK(r.refinement.d_min >= 2.5);
+    CHECK(r.refinement.r_work_start < 0.15);
+    CHECK(r.refinement.score_start.r_work == Catch::Approx(r.refinement.r_work_start));
+    CHECK(r.refinement.score_start.shells.size() == 20);
+    CHECK_FALSE(r.refinement.restrained);
+
+    const ReportDocument doc = BuildRefineReportDocument("out", "synthetic.mtz", "model.cif", r);
+    CHECK(doc.verdict == "OK");
+    const std::string text = RenderReportText(doc, true);
+    CHECK(text.find("REFINE= PERFORMED") != std::string::npos);
+    CHECK(text.find("REFINE_SCORE_R_WORK=") != std::string::npos);
+    CHECK(text.find("REFINE_FREE_FLAGS= GENERATED") != std::string::npos);
+    CHECK(text.find("REFINE_FRENCH_WILSON= TRUE") != std::string::npos);
+}
+
+TEST_CASE("RunRefineOnly reports a refinement that throws as not performed, with the reason", "[refine_only]") {
+    // The data's cell, a hundred metres on a side, makes the bulk-solvent mask's grid too large to allocate.
+    gemmi::Structure st;
+    RugnuxReflections data;
+    SyntheticRefineInput(st, data);
+    data.cell = gemmi::UnitCell(1e6, 1e6, 1e6, 90, 90, 90);
+    RefinementSettings settings;
+    settings.gpu = false;
+    settings.nthreads = 2;
+    Logger logger("RefineOnlyTest");
+    RefineOnlyResult r;
+    REQUIRE_NOTHROW(r = RunRefineOnly(data, st, 0.0, settings, logger));
+    CHECK_FALSE(r.refinement.ok);
+    CHECK(r.refinement.failure_reason.find("refinement failed") == 0);
+    const std::string text = RenderReportText(BuildRefineReportDocument("out", "synthetic.mtz", "model.cif", r), true);
+    CHECK(text.find("REFINE= NOT_PERFORMED") != std::string::npos);
+    CHECK(text.find("REFINE_REASON= refinement failed") != std::string::npos);
+}
diff --git a/tests/RefinementTest.cpp b/tests/RefinementTest.cpp
new file mode 100644
index 000000000..6d4c146f3
--- /dev/null
+++ b/tests/RefinementTest.cpp
@@ -0,0 +1,794 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+
+#include <algorithm>
+#include <atomic>
+#include <cmath>
+#include <map>
+#include <random>
+#include <vector>
+
+#include <gemmi/mmread_gz.hpp>
+#include <gemmi/symmetry.hpp>
+
+#include "../common/CUDAWrapper.h"
+#include "../common/Logger.h"
+#include "../image_analysis/structure_refinement/MonomerLibrary.h"
+#include "../image_analysis/structure_refinement/Refinement.h"
+#include "../image_analysis/structure_refinement/RefinementMath.h"
+#include "../image_analysis/structure_refinement/RefinementMinimiser.h"
+#include "../image_analysis/structure_refinement/RefinementRestraints.h"
+#include "../image_analysis/structure_refinement/RefinementXray.h"
+#ifdef JFJOCH_USE_CUDA
+#include "../image_analysis/structure_refinement/RefinementGPU.h"
+#endif
+
+namespace {
+
+// Copies of residue `code` at the embedded dictionary's ideal coordinates (hydrogens left out), each turned and
+// moved to a place of its own in the cell.
+gemmi::Structure residue_crystal(const std::vector<std::string> &codes, const gemmi::UnitCell &cell, const char *group,
+                                 unsigned seed) {
+    std::mt19937 rng(seed);
+    std::uniform_real_distribution<double> frac(0.0, 1.0), angle(-3.1, 3.1);
+    gemmi::Structure st;
+    st.cell = cell;
+    st.spacegroup_hm = group;
+    st.setup_cell_images();
+    gemmi::Model model(1);
+    gemmi::Chain chain("A");
+    int seq = 1;
+    for (const std::string &code : codes) {
+        const gemmi::ChemComp &cc = EmbeddedMonomerLibrary().monomers.at(code);
+        gemmi::Residue res;
+        res.name = code;
+        res.seqid = gemmi::SeqId(seq++, ' ');
+        res.het_flag = 'H';
+        res.entity_type = gemmi::EntityType::NonPolymer;
+        const gemmi::Position centre = cell.orthogonalize(gemmi::Fractional(frac(rng), frac(rng), frac(rng)));
+        const double ax = angle(rng), ay = angle(rng), az = angle(rng);
+        const gemmi::Mat33 rot = gemmi::Mat33(1, 0, 0, 0, std::cos(ax), -std::sin(ax), 0, std::sin(ax), std::cos(ax))
+                                     .multiply(gemmi::Mat33(std::cos(ay), 0, std::sin(ay), 0, 1, 0, -std::sin(ay), 0, std::cos(ay)))
+                                     .multiply(gemmi::Mat33(std::cos(az), -std::sin(az), 0, std::sin(az), std::cos(az), 0, 0, 0, 1));
+        for (const gemmi::ChemComp::Atom &ca : cc.atoms) {
+            if (ca.is_hydrogen())
+                continue;
+            gemmi::Atom a;
+            a.name = ca.id;
+            a.element = ca.el;
+            a.pos = gemmi::Position(rot.multiply(ca.xyz)) + centre;
+            a.b_iso = 20.0f;
+            a.occ = 1.0f;
+            res.atoms.push_back(a);
+        }
+        chain.residues.push_back(res);
+    }
+    model.chains.push_back(chain);
+    st.models.push_back(model);
+    return st;
+}
+
+// Atoms of a few elements scattered over the cell.
+gemmi::Structure random_crystal(const gemmi::UnitCell &cell, const char *group, int n, unsigned seed) {
+    std::mt19937 rng(seed);
+    std::uniform_real_distribution<double> frac(0.0, 1.0), b(10.0, 40.0);
+    const gemmi::El elements[] = {gemmi::El::C, gemmi::El::N, gemmi::El::O, gemmi::El::S};
+    gemmi::Structure st;
+    st.cell = cell;
+    st.spacegroup_hm = group;
+    st.setup_cell_images();
+    gemmi::Model model(1);
+    gemmi::Chain chain("A");
+    gemmi::Residue res;
+    res.name = "UNK";
+    res.seqid = gemmi::SeqId(1, ' ');
+    for (int i = 0; i < n; i++) {
+        gemmi::Atom a;
+        a.name = "X";
+        a.element = elements[i % 4];
+        a.pos = cell.orthogonalize(gemmi::Fractional(frac(rng), frac(rng), frac(rng)));
+        a.b_iso = static_cast<float>(b(rng));
+        a.occ = 1.0f;
+        res.atoms.push_back(a);
+    }
+    chain.residues.push_back(res);
+    model.chains.push_back(chain);
+    st.models.push_back(model);
+    return st;
+}
+
+// Every reflection of the group's ASU to d_min, amplitude 1, one in twenty free.
+std::vector<MergedReflection> asu_reflections(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min) {
+    std::vector<MergedReflection> out;
+    const gemmi::ReciprocalAsu asu(&sg);
+    const gemmi::GroupOps gops = sg.operations();
+    const gemmi::Miller lim = cell.get_hkl_limits(d_min);
+    int i = 0;
+    for (int h = -lim[0]; h <= lim[0]; h++)
+        for (int k = -lim[1]; k <= lim[1]; k++)
+            for (int l = -lim[2]; l <= lim[2]; l++) {
+                const gemmi::Miller m{{h, k, l}};
+                if ((h == 0 && k == 0 && l == 0) || !asu.is_in(m) || gops.is_systematically_absent(m))
+                    continue;
+                const double d = cell.calculate_d(m);
+                if (d < d_min)
+                    continue;
+                MergedReflection r;
+                r.h = h;
+                r.k = k;
+                r.l = l;
+                r.d = static_cast<float>(d);
+                r.F = 1.0f;
+                r.sigmaF = 0.05f;
+                r.rfree_flag = (i++ % 20) == 0;
+                out.push_back(r);
+            }
+    return out;
+}
+
+// The observations set to |F| of `truth`, and a row model with no scale, no solvent and the likelihood's
+// parameters estimated against `model`.
+void set_observations(RefinementEngine &engine, RefinementReflections &refl, const gemmi::Model &truth,
+                      const gemmi::Model &model) {
+    std::vector<std::complex<float>> f;
+    engine.Fcalc(truth, f);
+    for (size_t m = 0; m < refl.Size(); m++)
+        refl.fo[m] = std::abs(f[m]);
+    engine.Fcalc(model, f);
+    XrayRowModel rows;
+    rows.k_total.assign(refl.Size(), 1.0f);
+    rows.fmask.assign(refl.Size(), {0, 0});
+    EstimateLikelihoodParameters(refl, f, rows);
+    engine.SetRowModel(rows);
+}
+
+gemmi::Model shaken(const gemmi::Model &model, double sigma, double b_sigma, unsigned seed) {
+    std::mt19937 rng(seed);
+    std::normal_distribution<double> d(0, sigma), db(0, b_sigma);
+    gemmi::Model out = model;
+    for (gemmi::Chain &ch : out.chains)
+        for (gemmi::Residue &r : ch.residues)
+            for (gemmi::Atom &a : r.atoms) {
+                a.pos += gemmi::Position(d(rng), d(rng), d(rng));
+                a.b_iso = static_cast<float>(std::max(5.0, a.b_iso + db(rng)));
+            }
+    return out;
+}
+
+std::vector<gemmi::Atom *> atoms_of(gemmi::Model &model) {
+    std::vector<gemmi::Atom *> out;
+    for (gemmi::Chain &ch : model.chains)
+        for (gemmi::Residue &r : ch.residues)
+            for (gemmi::Atom &a : r.atoms)
+                out.push_back(&a);
+    return out;
+}
+
+// The engine's gradient of a few atoms against central differences of its own target.
+void check_xray_gradient(RefinementEngine &engine, gemmi::Model model, double tolerance) {
+    std::vector<std::array<double, 4>> grad;
+    engine.Evaluate(model, &grad);
+    std::vector<gemmi::Atom *> atoms = atoms_of(model);
+    const double hx = 2e-3, hb = 2e-2;
+    double max_g = 0;
+    for (const auto &g : grad)
+        for (int c = 0; c < 4; c++)
+            max_g = std::max(max_g, std::fabs(g[c]));
+    for (size_t i = 0; i < atoms.size(); i += atoms.size() / 7) {
+        for (int c = 0; c < 4; c++) {
+            const gemmi::Position p0 = atoms[i]->pos;
+            const float b0 = atoms[i]->b_iso;
+            const double h = c < 3 ? hx : hb;
+            auto set = [&](double s) {
+                atoms[i]->pos = p0;
+                atoms[i]->b_iso = b0;
+                if (c < 3)
+                    atoms[i]->pos.at(c) += s;
+                else
+                    atoms[i]->b_iso = static_cast<float>(b0 + s);
+            };
+            set(h);
+            const double fp = engine.Evaluate(model, nullptr);
+            set(-h);
+            const double fm = engine.Evaluate(model, nullptr);
+            set(0);
+            const double fd = (fp - fm) / (2 * h);
+            CAPTURE(i, c, fd, grad[i][c], max_g);
+            CHECK(std::fabs(fd - grad[i][c]) < tolerance * std::max(std::fabs(fd), 0.05 * max_g));
+        }
+    }
+}
+
+}  // namespace
+
+TEST_CASE("RefinementLikelihood_derivative", "[Refinement]") {
+    for (bool centric : {false, true})
+        for (double fc : {0.3, 2.0, 9.0}) {
+            double dfc = 0, dummy = 0;
+            const double f0 = refine_math::AmplitudeNegLogLikelihood<double>(4.0, fc, 0.8, 2.5, centric, dfc);
+            const double h = 1e-5;
+            const double fp = refine_math::AmplitudeNegLogLikelihood<double>(4.0, fc + h, 0.8, 2.5, centric, dummy);
+            const double fm = refine_math::AmplitudeNegLogLikelihood<double>(4.0, fc - h, 0.8, 2.5, centric, dummy);
+            CAPTURE(centric, fc, f0);
+            CHECK(dfc == Catch::Approx((fp - fm) / (2 * h)).epsilon(1e-5));
+        }
+    // the Bessel approximation on both sides of its switch
+    double l0, r0, l1, r1;
+    refine_math::BesselI0I1(3.75 * (1 - 1e-12), l0, r0);
+    refine_math::BesselI0I1(3.75 * (1 + 1e-12), l1, r1);
+    CHECK(l0 == Catch::Approx(l1).epsilon(1e-5));
+    CHECK(r0 == Catch::Approx(r1).epsilon(1e-5));
+}
+
+TEST_CASE("RefinementMonomerLibrary_embedded", "[Refinement]") {
+    const gemmi::MonLib &monlib = EmbeddedMonomerLibrary();
+    for (const char *code : {"ALA", "PRO", "MSE", "DA", "U", "ATP", "GOL", "SO4", "HOH", "ZN"})
+        CHECK(InEmbeddedMonomerLibrary(code));
+    CHECK_FALSE(InEmbeddedMonomerLibrary("XYZ"));
+    for (const char *link : {"TRANS", "CIS", "PTRANS", "p", "SS"})
+        CHECK(monlib.links.count(link) == 1);
+    CHECK(monlib.modifications.count("NH3") == 1);
+    CHECK(monlib.ener_lib.atoms.count("CH1") == 1);
+}
+
+TEST_CASE("RefinementRestraints_ideal_residues", "[Refinement]") {
+    const gemmi::UnitCell cell(60, 65, 70, 90, 90, 90);
+    gemmi::Structure st = residue_crystal({"PHE", "DA", "ATP", "HOH", "ZN"}, cell, "P 21 21 21", 3);
+    const RefinementTopology topo = BuildRefinementTopology(st);
+    CHECK(topo.restrained_residues == 5);
+    CHECK(topo.fixed_residues == 0);
+    CHECK(topo.bonds > 60);
+    CHECK(topo.planes >= 3);
+    CHECK(topo.chirals >= 4);
+    std::vector<std::array<double, 4>> xyzb;
+    for (gemmi::Atom *a : atoms_of(st.models[0]))
+        xyzb.push_back({a->pos.x, a->pos.y, a->pos.z, a->b_iso});
+    const GeometryStatistics g = MeasureGeometry(topo.geometry, {}, xyzb);
+    CHECK(g.rmsd_bonds < 0.02);
+    CHECK(g.rmsd_angles < 2.5);
+    CHECK(g.rmsd_chirals < 0.2);
+}
+
+// A zinc bound by four cysteines (the dictionary's own ZN-CYS link) and a magnesium by six waters (links made from
+// the library's metal-site statistics), both from LINK records: the bonds come out at the expected distances,
+// and a metal set off its site returns there under them alone.
+TEST_CASE("RefinementRestraints_metal_links", "[Refinement]") {
+    const gemmi::UnitCell cell(40, 40, 40, 90, 90, 90);
+    gemmi::Structure st = residue_crystal({"CYS", "CYS", "CYS", "CYS", "ZN", "HOH", "HOH", "HOH", "HOH", "HOH", "HOH",
+                                           "MG"}, cell, "P 1", 11);
+    double mg_o = 0, mg_sigma = 0;
+    REQUIRE(EmbeddedMetalDistance(gemmi::El::Mg, gemmi::El::O, 6, mg_o, mg_sigma));
+    CHECK(mg_o == Catch::Approx(2.07).margin(0.02));   // Mg-O of an octahedral site
+    constexpr double ZN_S = 2.34;                      // the ZN-CYS link
+    std::vector<gemmi::Residue> &res = st.models[0].chains[0].residues;
+    // the donors on a tetrahedron and an octahedron around their sites, each residue moved as a whole
+    const gemmi::Position zn_site(10, 10, 10), mg_site(25, 25, 25);
+    const double t = 1.0 / std::sqrt(3.0);
+    const gemmi::Position tetra[4] = {{t, t, t}, {t, -t, -t}, {-t, t, -t}, {-t, -t, t}};
+    const gemmi::Position octa[6] = {{1, 0, 0}, {-1, 0, 0}, {0, 1, 0}, {0, -1, 0}, {0, 0, 1}, {0, 0, -1}};
+    auto donor_to = [](gemmi::Residue &r, const std::string &atom, const gemmi::Position &target) {
+        const gemmi::Position shift = target - r.find_atom(atom, '*')->pos;
+        for (gemmi::Atom &a : r.atoms)
+            a.pos += shift;
+    };
+    for (int k = 0; k < 4; k++)
+        donor_to(res[k], "SG", zn_site + tetra[k] * ZN_S);
+    for (int k = 0; k < 6; k++)
+        donor_to(res[5 + k], "O", mg_site + octa[k] * mg_o);
+    // the metals off their sites by 0.3 A
+    res[4].atoms[0].pos = zn_site + gemmi::Position(0.2, -0.15, 0.17);
+    res[11].atoms[0].pos = mg_site + gemmi::Position(-0.1, 0.25, 0.12);
+    auto link = [&](int metal, int donor, const char *atom) {
+        gemmi::Connection c;
+        c.type = gemmi::Connection::MetalC;
+        c.asu = gemmi::Asu::Same;
+        c.partner1 = gemmi::AtomAddress("A", res[donor].seqid, res[donor].name, atom);
+        c.partner2 = gemmi::AtomAddress("A", res[metal].seqid, res[metal].name, res[metal].atoms[0].name);
+        st.connections.push_back(c);
+    };
+    for (int k = 0; k < 4; k++)
+        link(4, k, "SG");
+    for (int k = 0; k < 6; k++)
+        link(11, 5 + k, "O");
+
+    const RefinementTopology topo = BuildRefinementTopology(st);
+    CHECK(topo.metal_links == 6);   // the Mg-O links; Zn-S is the dictionary's
+    std::vector<gemmi::Atom *> atoms = atoms_of(st.models[0]);
+    const int zn = static_cast<int>(std::find(atoms.begin(), atoms.end(), &res[4].atoms[0]) - atoms.begin());
+    const int mg = static_cast<int>(std::find(atoms.begin(), atoms.end(), &res[11].atoms[0]) - atoms.begin());
+    // the metals' bonds kept apart from the covalent ones, none left among them
+    for (const RestraintRecord &r : topo.geometry.records)
+        CHECK_FALSE((r.kind == static_cast<int>(RestraintKind::Bond) &&
+                     (r.atom[0] == zn || r.atom[1] == zn || r.atom[0] == mg || r.atom[1] == mg)));
+    const RestraintSet &metal_bonds = topo.metal_bonds;
+    REQUIRE(metal_bonds.records.size() == 10);
+    for (const RestraintRecord &r : metal_bonds.records) {
+        const bool is_zn = r.atom[0] == zn || r.atom[1] == zn;
+        CHECK((is_zn || r.atom[0] == mg || r.atom[1] == mg));
+        CHECK(r.ideal == Catch::Approx(is_zn ? ZN_S : mg_o).margin(1e-4));
+    }
+
+    // the two metals moved down the gradient of their bonds, everything else held
+    std::vector<std::array<double, 4>> xyzb;
+    for (gemmi::Atom *a : atoms)
+        xyzb.push_back({a->pos.x, a->pos.y, a->pos.z, a->b_iso});
+    double e = EvaluateRestraints(metal_bonds, xyzb, nullptr), step = 1e-4;
+    for (int it = 0; it < 2000 && step > 1e-12; it++) {
+        std::vector<std::array<double, 4>> grad(xyzb.size(), {0, 0, 0, 0}), trial = xyzb;
+        EvaluateRestraints(metal_bonds, xyzb, &grad);
+        for (int a : {zn, mg})
+            for (int k = 0; k < 3; k++)
+                trial[a][k] -= step * grad[a][k];
+        const double e_trial = EvaluateRestraints(metal_bonds, trial, nullptr);
+        if (e_trial < e) {
+            xyzb = trial;
+            e = e_trial;
+            step *= 1.5;
+        } else
+            step *= 0.5;
+    }
+    for (const RestraintRecord &r : metal_bonds.records)
+        CHECK(RestraintValue(metal_bonds, r, xyzb) == Catch::Approx(r.ideal).margin(0.005));
+}
+
+// Deposited models cut down to a ligand and the residues within 4.2 A of it (test_data/ligands, from the PDB entries
+// their names start with; the tRNA as its modified nucleotides and their neighbours in the chain): every ligand is
+// restrained, its own restraints included, the deposited geometry agrees with the dictionary, and the links the
+// ligands need are made - the RNA backbone to and from each modified nucleotide, the iron of a heme to its histidine
+// (and a heme C's to its methionine) from the LINK records, and a heme C's two thioethers to its cysteines.
+TEST_CASE("RefinementRestraints_deposited_ligands", "[Refinement]") {
+    const std::vector<std::string> modified_nucleotides = {"PSU", "5MC", "1MA", "OMG", "OMC", "H2U", "M2G", "7MG",
+                                                           "2MG", "5MU"};
+    const std::vector<std::pair<std::string, std::vector<std::string>>> cases = {
+        {"1ehz_psu", modified_nucleotides}, {"8bkh_hem", {"HEM"}}, {"6k9i_hec", {"HEC"}}, {"2w3v_ndp", {"NDP"}},
+        {"5vml_nap", {"NAP"}}, {"6f3p_nad", {"NAD"}}, {"8con_nai", {"NAI"}}, {"3tk0_fad", {"FAD"}},
+        {"7tcd_fmn", {"FMN"}}, {"6w4h_sam", {"SAM"}}, {"5epe_sah", {"SAH"}}};
+    for (const auto &[name, ligands] : cases) {
+        DYNAMIC_SECTION(name) {
+            gemmi::Structure st = gemmi::read_structure_gz("../../tests/test_data/ligands/" + name + ".pdb.gz");
+            const RefinementTopology topo = BuildRefinementTopology(st);
+            std::vector<gemmi::Atom *> atoms = atoms_of(st.models[0]);
+            std::vector<const gemmi::Residue *> residue_of;
+            for (const gemmi::Chain &ch : st.models[0].chains)
+                for (const gemmi::Residue &r : ch.residues)
+                    for (size_t k = 0; k < r.atoms.size(); k++)
+                        residue_of.push_back(&r);
+            auto index_of = [&](const gemmi::Residue &r, const char *atom) {
+                const gemmi::Atom *a = r.find_atom(atom, '*');
+                return a == nullptr ? -1 : static_cast<int>(std::find(atoms.begin(), atoms.end(), a) - atoms.begin());
+            };
+            auto bonded = [&](const RestraintSet &set, int i, int j) {
+                for (const RestraintRecord &r : set.records)
+                    if (r.kind == static_cast<int>(RestraintKind::Bond) &&
+                        ((r.atom[0] == i && r.atom[1] == j) || (r.atom[0] == j && r.atom[1] == i)))
+                        return true;
+                return false;
+            };
+
+            std::map<std::string, int> restraints, found;
+            for (const RestraintRecord &r : topo.geometry.records)
+                if (r.kind != static_cast<int>(RestraintKind::Plane))
+                    restraints[residue_of[r.atom[0]]->name]++;
+            for (size_t i = 0; i < atoms.size(); i++)
+                if (std::find(ligands.begin(), ligands.end(), residue_of[i]->name) != ligands.end()) {
+                    found[residue_of[i]->name]++;
+                    CHECK(topo.refinable[i]);
+                }
+            for (const std::string &code : ligands) {
+                INFO(code);
+                CHECK(found[code] > 0);
+                CHECK(restraints[code] > 0);
+                CHECK(std::find(topo.fixed_names.begin(), topo.fixed_names.end(), code) == topo.fixed_names.end());
+            }
+
+            std::vector<std::array<double, 4>> xyzb;
+            for (gemmi::Atom *a : atoms)
+                xyzb.push_back({a->pos.x, a->pos.y, a->pos.z, a->b_iso});
+            const GeometryStatistics g = MeasureGeometry(topo.geometry, {}, xyzb, &topo.metal_bonds);
+            CHECK(g.rmsd_bonds < 0.03);
+            CHECK(g.rmsd_angles < 3.0);
+            CHECK(g.rmsd_metal < 0.1);
+
+            if (name == "1ehz_psu") {
+                // each modified nucleotide bonded to the residue before it in the chain, where that one is there
+                int links = 0;
+                for (const gemmi::Residue &r : st.models[0].chains[0].residues) {
+                    const gemmi::Residue *prev = &r == &st.models[0].chains[0].residues.front() ? nullptr : &r - 1;
+                    if (prev == nullptr || prev->seqid.num != r.seqid.num - 1 ||
+                        std::find(ligands.begin(), ligands.end(), r.name) == ligands.end())
+                        continue;
+                    INFO(r.name << " " << *r.seqid.num);
+                    CHECK(bonded(topo.geometry, index_of(*prev, "O3'"), index_of(r, "P")));
+                    links++;
+                }
+                CHECK(links >= 10);
+            }
+            if (name == "8bkh_hem" || name == "6k9i_hec") {
+                const gemmi::Residue *heme = nullptr, *his = nullptr;
+                for (const gemmi::Residue &r : st.models[0].chains[0].residues) {
+                    if (r.name == ligands[0])
+                        heme = &r;
+                    if (r.name == "HIS" && r.seqid.num == (name == "8bkh_hem" ? 93 : 18))
+                        his = &r;
+                }
+                REQUIRE(heme != nullptr);
+                REQUIRE(his != nullptr);
+                const int fe = index_of(*heme, "FE");
+                CHECK(topo.metal[fe]);
+                CHECK(topo.metal_links == (name == "8bkh_hem" ? 1 : 2));   // the histidine; and the methionine
+                CHECK(bonded(topo.metal_bonds, fe, index_of(*his, "NE2")));
+                CHECK(bonded(topo.metal_bonds, fe, index_of(*heme, "NA")));   // the porphyrin's own, among the metal's
+                if (name == "6k9i_hec")
+                    for (auto [cys, carbon] : {std::pair{14, "CAB"}, std::pair{17, "CAC"}})
+                        for (const gemmi::Residue &r : st.models[0].chains[0].residues)
+                            if (r.name == "CYS" && r.seqid.num == cys)
+                                CHECK(bonded(topo.geometry, index_of(r, "SG"), index_of(*heme, carbon)));
+            }
+        }
+    }
+}
+
+TEST_CASE("RefinementRestraints_gradient", "[Refinement]") {
+    const gemmi::UnitCell cell(14, 15, 16, 90, 90, 90);
+    gemmi::Structure st = residue_crystal({"TYR", "DG"}, cell, "P 21 21 21", 5);
+    st.models[0] = shaken(st.models[0], 0.15, 3.0, 2);
+    const RefinementTopology topo = BuildRefinementTopology(st);
+    // the geometry, the B similarity and the repulsions (symmetry mates included, at a contact distance that
+    // makes every pair within reach count)
+    RestraintSet set = topo.geometry;
+    set.Append(topo.adp);
+    RefinementTopology wide = topo;
+    for (float &r : wide.vdw_radius)
+        r = 2.5f;
+    std::fill(wide.hbond.begin(), wide.hbond.end(), 0);
+    const RestraintSet rep = BuildRepulsions(wide, st.models[0], cell, *st.find_spacegroup(), 0.0);
+    REQUIRE(rep.records.size() > 10);
+    bool image = false;
+    for (const RestraintRecord &r : rep.records)
+        image = image || r.rot[0] != 1.0f || r.tran[0] != 0.0f || r.tran[1] != 0.0f || r.tran[2] != 0.0f;
+    CAPTURE(rep.records.size());
+    CHECK(image);
+    set.Append(rep);
+    set.Finalize(atoms_of(st.models[0]).size());
+
+    std::vector<std::array<double, 4>> xyzb;
+    for (gemmi::Atom *a : atoms_of(st.models[0]))
+        xyzb.push_back({a->pos.x, a->pos.y, a->pos.z, a->b_iso});
+    // each kind of restraint on its own, against central differences
+    for (int kind = 0; kind <= static_cast<int>(RestraintKind::BSimilarity); kind++) {
+        RestraintSet one;
+        for (const RestraintRecord &r : set.records)
+            if (r.kind == kind) {
+                RestraintRecord copy = r;
+                if (kind == static_cast<int>(RestraintKind::Plane)) {
+                    copy.atom[0] = static_cast<int>(one.plane_atoms.size());
+                    for (int k = 0; k < r.atom[1]; k++)
+                        one.plane_atoms.push_back(set.plane_atoms[r.atom[0] + k]);
+                }
+                one.Add(copy, kind == static_cast<int>(RestraintKind::Plane) ? r.atom[1] : 4);
+            }
+        CAPTURE(kind, one.records.size());
+        std::vector<std::array<double, 4>> grad(xyzb.size(), {0, 0, 0, 0});
+        EvaluateRestraints(one, xyzb, &grad);
+        const double h = 1e-6;
+        for (size_t i = 0; i < xyzb.size(); i++)
+            for (int c = 0; c < 4; c++) {
+                auto x = xyzb;
+                x[i][c] += h;
+                const double fp = EvaluateRestraints(one, x, nullptr);
+                x[i][c] -= 2 * h;
+                const double fm = EvaluateRestraints(one, x, nullptr);
+                CAPTURE(i, c);
+                CHECK(grad[i][c] == Catch::Approx((fp - fm) / (2 * h)).epsilon(1e-4).margin(1e-3));
+            }
+    }
+
+#ifdef JFJOCH_USE_CUDA
+    if (get_gpu_count() > 0) {
+        // the GPU's float evaluation of the same set
+        // (the engine is made for a cell wide enough for its gather; the restraints do not read the cell)
+        const gemmi::UnitCell wide_cell(40, 40, 40, 90, 90, 90);
+        std::vector<MergedReflection> merged = asu_reflections(wide_cell, *st.find_spacegroup(), 3.0);
+        RefinementReflections refl = PrepareRefinementReflections(merged, wide_cell, *st.find_spacegroup(), 3.0);
+        auto gpu = MakeRefinementEngineGPU(0, wide_cell, *st.find_spacegroup(), 3.0, refl, st.models[0], 100.0, SIZE_MAX);
+        REQUIRE(gpu);
+        gpu->SetRestraints(0, set);
+        std::vector<std::array<double, 4>> ggpu;
+        const double egpu = gpu->EvaluateRestraints(0, xyzb, &ggpu);
+        std::vector<std::array<double, 4>> gcpu(xyzb.size(), {0, 0, 0, 0});
+        const double ecpu = EvaluateRestraints(set, xyzb, &gcpu);
+        CHECK(egpu == Catch::Approx(ecpu).epsilon(1e-4));
+        for (size_t i = 0; i < xyzb.size(); i++)
+            for (int c = 0; c < 4; c++)
+                CHECK(ggpu[i][c] == Catch::Approx(gcpu[i][c]).epsilon(2e-3).margin(2e-2));
+    }
+#endif
+}
+
+// Contacts with other copies of the molecule: in P1 two waters 2.4 A apart across the a face (17.6 A apart within
+// the cell) repel each other once, and a water 1.4 A from a 3-fold axis, 2.4 A from its images x -> T x and
+// x -> T^-1 x (one contact per asymmetric unit), repels its image once.
+TEST_CASE("RefinementRestraints_lattice_and_symmetry_contacts", "[Refinement]") {
+    auto oxygens = [](gemmi::Structure &st, const std::vector<gemmi::Fractional> &where) {
+        std::vector<gemmi::Atom *> atoms = atoms_of(st.models[0]);
+        REQUIRE(atoms.size() == where.size());
+        for (size_t i = 0; i < where.size(); i++)
+            atoms[i]->pos = st.cell.orthogonalize(where[i]);
+    };
+    {
+        const gemmi::UnitCell cell(20, 21, 22, 90, 90, 90);
+        gemmi::Structure st = residue_crystal({"HOH", "HOH"}, cell, "P 1", 1);
+        oxygens(st, {gemmi::Fractional(0.01, 0.5, 0.5), gemmi::Fractional(0.89, 0.5, 0.5)});
+        const RefinementTopology topo = BuildRefinementTopology(st);
+        const RestraintSet rep = BuildRepulsions(topo, st.models[0], cell, *st.find_spacegroup(), 0.0);
+        REQUIRE(rep.records.size() == 1);
+        CHECK(rep.records[0].tran[0] == Catch::Approx(-20.0f));
+        CHECK(BuildBContacts(topo, st.models[0], cell, *st.find_spacegroup()).records.size() == 1);
+    }
+    {
+        const gemmi::UnitCell cell(20, 20, 22, 90, 90, 120);
+        gemmi::Structure st = residue_crystal({"HOH"}, cell, "P 3", 1);
+        oxygens(st, {cell.fractionalize(gemmi::Position(1.4, 0.0, 11.0))});
+        const RefinementTopology topo = BuildRefinementTopology(st);
+        const RestraintSet rep = BuildRepulsions(topo, st.models[0], cell, *st.find_spacegroup(), 0.0);
+        CHECK(rep.records.size() == 1);
+    }
+}
+
+// A complete model whose every atom is off by a Gaussian error of sigma_x per axis: D(s) = <cos(2 pi s.dx)> =
+// exp(-2 pi^2 sigma_x^2 s^2) (Luzzati). With a negligible measurement error D comes out at that; with an error of
+// half the rms amplitude of the outermost shell it falls below it there, where the error is a large part of the
+// spread and is counted twice, and stays where the amplitudes are strong.
+TEST_CASE("RefinementLikelihood_D_coordinate_error", "[Refinement]") {
+    const char *group = "P 1";
+    const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(group);
+    const gemmi::UnitCell cell(40, 45, 50, 90, 90, 90);
+    const double d_min = 1.5, sigma_x = 0.25;
+    gemmi::Structure truth = random_crystal(cell, group, 1500, 3);
+    gemmi::Model model = truth.models[0];
+    std::mt19937 rng(4);
+    std::normal_distribution<double> dx(0, sigma_x);
+    for (gemmi::Atom &a : model.chains[0].residues[0].atoms)
+        a.pos += gemmi::Position(dx(rng), dx(rng), dx(rng));
+    RefinementReflections refl = PrepareRefinementReflections(asu_reflections(cell, sg, d_min), cell, sg, d_min);
+    auto cpu = MakeRefinementEngineCPU(cell, sg, d_min, refl, 4);
+    cpu->SetBlur(RefinementBlur(cell, sg, d_min, 5.0));
+    std::vector<std::complex<float>> f;
+    cpu->Fcalc(truth.models[0], f);
+    for (size_t m = 0; m < refl.Size(); m++)
+        refl.fo[m] = std::abs(f[m]);
+    cpu->Fcalc(model, f);
+
+    // mean D and mean Luzzati D in five shells of 1/d^2
+    constexpr int SHELLS = 5;
+    const double s2_max = 1.0 / (d_min * d_min);
+    auto shells = [&](const XrayRowModel &rows, std::vector<double> &d, std::vector<double> &luzzati) {
+        std::vector<int> n(SHELLS, 0);
+        d.assign(SHELLS, 0);
+        luzzati.assign(SHELLS, 0);
+        for (size_t m = 0; m < refl.Size(); m++) {
+            const int k = std::min(SHELLS - 1, static_cast<int>(refl.inv_d2[m] / s2_max * SHELLS));
+            d[k] += rows.d[m];
+            luzzati[k] += std::exp(-2 * M_PI * M_PI * sigma_x * sigma_x * refl.inv_d2[m]);
+            n[k]++;
+        }
+        for (int k = 0; k < SHELLS; k++) {
+            d[k] /= n[k];
+            luzzati[k] /= n[k];
+        }
+    };
+    XrayRowModel rows;
+    rows.k_total.assign(refl.Size(), 1.0f);
+    rows.fmask.assign(refl.Size(), {0, 0});
+    for (float &s : refl.sigma)
+        s = 0.01f;
+    EstimateLikelihoodParameters(refl, f, rows);
+    std::vector<double> d_clean, luzzati;
+    shells(rows, d_clean, luzzati);
+    for (int k = 0; k < SHELLS; k++) {
+        CAPTURE(k, d_clean[k], luzzati[k]);
+        CHECK(std::fabs(d_clean[k] - luzzati[k]) < 0.05);
+    }
+    CHECK(luzzati[SHELLS - 1] < 0.65);
+
+    // a measurement error of half the rms amplitude of the outermost shell
+    double fo2 = 0;
+    int n = 0;
+    for (size_t m = 0; m < refl.Size(); m++)
+        if (refl.inv_d2[m] > s2_max * (SHELLS - 1) / SHELLS) {
+            fo2 += double(refl.fo[m]) * refl.fo[m];
+            n++;
+        }
+    for (float &s : refl.sigma)
+        s = static_cast<float>(0.5 * std::sqrt(fo2 / n));
+    EstimateLikelihoodParameters(refl, f, rows);
+    std::vector<double> d_noisy;
+    shells(rows, d_noisy, luzzati);
+    CHECK(d_noisy[0] > d_clean[0] - 0.03);
+    CHECK(d_noisy[SHELLS - 1] < d_clean[SHELLS - 1] - 0.1);
+}
+
+TEST_CASE("RefinementXray_gradient_CPU", "[Refinement]") {
+    for (const char *group : {"P 1", "P 21 21 21", "C 1 2 1", "P 61 2 2"}) {
+        CAPTURE(group);
+        const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(group);
+        const gemmi::UnitCell cell = sg.crystal_system() == gemmi::CrystalSystem::Hexagonal
+                                         ? gemmi::UnitCell(30, 30, 45, 90, 90, 120)
+                                         : gemmi::UnitCell(28, 31, 34, 90, sg.number == 5 ? 104 : 90, 90);
+        gemmi::Structure truth = random_crystal(cell, group, 240, 7);
+        gemmi::Model model = shaken(truth.models[0], 0.3, 4.0, 8);
+        RefinementReflections refl = PrepareRefinementReflections(asu_reflections(cell, sg, 2.2), cell, sg, 2.2);
+        REQUIRE(refl.Size() > 500);
+        auto cpu = MakeRefinementEngineCPU(cell, sg, 2.2, refl, 4);
+        cpu->SetBlur(RefinementBlur(cell, sg, 2.2, 5.0));
+        set_observations(*cpu, refl, truth.models[0], model);
+        check_xray_gradient(*cpu, model, 0.03);
+    }
+}
+
+#ifdef JFJOCH_USE_CUDA
+TEST_CASE("RefinementXray_gradient_GPU", "[Refinement]") {
+    if (get_gpu_count() == 0)
+        return;
+    for (const char *group : {"P 1", "P 21 21 21", "C 1 2 1", "P 61 2 2"}) {
+        CAPTURE(group);
+        const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name(group);
+        const gemmi::UnitCell cell = sg.crystal_system() == gemmi::CrystalSystem::Hexagonal
+                                         ? gemmi::UnitCell(30, 30, 45, 90, 90, 120)
+                                         : gemmi::UnitCell(28, 31, 34, 90, sg.number == 5 ? 104 : 90, 90);
+        gemmi::Structure truth = random_crystal(cell, group, 240, 7);
+        gemmi::Model model = shaken(truth.models[0], 0.3, 4.0, 8);
+        RefinementReflections refl = PrepareRefinementReflections(asu_reflections(cell, sg, 2.2), cell, sg, 2.2);
+        auto cpu = MakeRefinementEngineCPU(cell, sg, 2.2, refl, 4);
+        cpu->SetBlur(RefinementBlur(cell, sg, 2.2, 5.0));
+        set_observations(*cpu, refl, truth.models[0], model);
+        // the GPU engine sees the same observations: it is made after they are set
+        auto gpu = MakeRefinementEngineGPU(0, cell, sg, 2.2, refl, model, 300.0, SIZE_MAX);
+        REQUIRE(gpu);
+        gpu->SetBlur(RefinementBlur(cell, sg, 2.2, 5.0));
+        std::vector<std::complex<float>> f;
+        cpu->Fcalc(model, f);
+        XrayRowModel rows;
+        rows.k_total.assign(refl.Size(), 1.0f);
+        rows.fmask.assign(refl.Size(), {0, 0});
+        EstimateLikelihoodParameters(refl, f, rows);
+        cpu->SetRowModel(rows);
+        gpu->SetRowModel(rows);
+
+        std::vector<std::complex<float>> fg;
+        gpu->Fcalc(model, fg);
+        double num = 0, den = 0;
+        for (size_t m = 0; m < f.size(); m++) {
+            num += std::abs(f[m] - fg[m]);
+            den += std::abs(f[m]);
+        }
+        CHECK(num / den < 1e-3);
+
+        std::vector<std::array<double, 4>> gc, gg;
+        const double tc = cpu->Evaluate(model, &gc);
+        const double tg = gpu->Evaluate(model, &gg);
+        CHECK(tg == Catch::Approx(tc).epsilon(1e-4));
+        double max_g = 0;
+        for (const auto &g : gc)
+            for (int c = 0; c < 4; c++)
+                max_g = std::max(max_g, std::fabs(g[c]));
+        for (size_t i = 0; i < gc.size(); i++)
+            for (int c = 0; c < 4; c++) {
+                CAPTURE(i, c);
+                CHECK(std::fabs(gg[i][c] - gc[i][c]) < 0.01 * max_g);
+            }
+        check_xray_gradient(*gpu, model, 0.05);
+    }
+}
+#endif
+
+TEST_CASE("RefinementMinimiser_quadratic", "[Refinement]") {
+    // f = sum a_k (x_k - 1)^2 with curvatures spread over two decades
+    const size_t n = 50;
+    std::vector<double> a(n);
+    for (size_t k = 0; k < n; k++)
+        a[k] = std::pow(100.0, static_cast<double>(k) / (n - 1));
+    const RefinementMinimiser::Target target = [&](const std::vector<double> &x, double &f, std::vector<double> &g) {
+        f = 0;
+        for (size_t k = 0; k < n; k++) {
+            f += a[k] * (x[k] - 1) * (x[k] - 1);
+            g[k] = 2 * a[k] * (x[k] - 1);
+        }
+        return true;
+    };
+    auto distance = [&](const std::vector<double> &x) {
+        double d = 0;
+        for (double v : x)
+            d = std::max(d, std::fabs(v - 1));
+        return d;
+    };
+
+    // the exact diagonal: one step
+    RefinementMinimiser exact;
+    std::vector<double> h(n);
+    for (size_t k = 0; k < n; k++)
+        h[k] = 2 * a[k];
+    exact.SetDiagonal(h);
+    std::vector<double> x(n, 0.0);
+    exact.Minimise(target, x, 1, 0.0, 10.0);
+    CHECK(distance(x) < 1e-9);
+
+    // without it, the memory carried from one call to the next does what one long call does
+    RefinementMinimiser split, whole;
+    std::vector<double> xs(n, 0.0), xw(n, 0.0);
+    for (int call = 0; call < 6; call++)
+        split.Minimise(target, xs, 10, 0.0, 10.0);
+    whole.Minimise(target, xw, 60, 0.0, 10.0);
+    CHECK(distance(xw) < 1e-3);
+    for (size_t k = 0; k < n; k++)
+        CHECK(xs[k] == Catch::Approx(xw[k]).margin(1e-12));
+}
+
+TEST_CASE("Refinement_restrained_recovers_model", "[Refinement]") {
+    const gemmi::UnitCell cell(36, 40, 44, 90, 90, 90);
+    const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name("P 21 21 21");
+    gemmi::Structure truth = residue_crystal({"PHE", "TRP", "DA", "DG", "TYR", "HOH", "HOH", "HOH"}, cell,
+                                             "P 21 21 21", 11);
+    gemmi::Structure start = truth;
+    start.models[0] = shaken(truth.models[0], 0.25, 5.0, 12);
+    std::vector<MergedReflection> merged = asu_reflections(cell, sg, 1.8);
+    {
+        RefinementReflections refl = PrepareRefinementReflections(merged, cell, sg, 1.8 * 0.999);
+        auto cpu = MakeRefinementEngineCPU(cell, sg, 1.8 * 0.999, refl, 4);
+        cpu->SetBlur(RefinementBlur(cell, sg, 1.8, 5.0));
+        std::vector<std::complex<float>> f;
+        cpu->Fcalc(truth.models[0], f);
+        std::map<gemmi::Miller, double> amplitude;
+        for (size_t m = 0; m < refl.Size(); m++)
+            amplitude[refl.hkl[m]] = std::abs(f[m]);
+        std::mt19937 rng(3);
+        std::normal_distribution<double> noise(0.0, 0.03);
+        for (MergedReflection &r : merged) {
+            const auto it = amplitude.find(gemmi::Miller{{r.h, r.k, r.l}});
+            r.F = it == amplitude.end() ? NAN : static_cast<float>(it->second * (1 + noise(rng)));
+            r.sigmaF = 0.03f * r.F + 0.01f;
+        }
+    }
+    Logger logger("RefinementTest");
+    for (bool gpu : {false, true}) {
+        if (gpu && get_gpu_count() == 0)
+            continue;
+        CAPTURE(gpu);
+        RefinementSettings settings;
+        settings.gpu = gpu;
+        settings.nthreads = 4;
+        settings.weight_ladder = {0.0625};
+        settings.adp_ladder = {4.0};
+        settings.max_steps = 2;
+        settings.final_ladder = {1.0};
+        settings.riding_hydrogens = false;   // the data were made without them
+        const RefinementResult r = RefineModel(start, merged, cell, sg, 1.0, logger, settings);
+        REQUIRE(r.ok);
+        CHECK(r.on_gpu == gpu);
+        CHECK(r.restrained_residues == 8);
+        CHECK(r.r_free < 0.6 * r.r_free_start);
+        CHECK(r.geometry.rmsd_bonds < r.geometry_start.rmsd_bonds);
+        double rms = 0;
+        std::vector<gemmi::Atom *> refined = atoms_of(r.model->models[0]);
+        std::erase_if(refined, [](const gemmi::Atom *a) { return a->is_hydrogen(); });   // the riding hydrogens
+        const std::vector<gemmi::Atom *> ref = atoms_of(truth.models[0]);
+        REQUIRE(refined.size() == ref.size());
+        for (size_t i = 0; i < ref.size(); i++)
+            rms += refined[i]->pos.dist_sq(ref[i]->pos);
+        rms = std::sqrt(rms / ref.size());
+        CHECK(rms < 0.15);
+
+        // cut short before the first weight trial: the model as placed comes back, no trial chosen
+        const std::atomic<bool> cancel{true};
+        settings.cancel = &cancel;
+        const RefinementResult c = RefineModel(start, merged, cell, sg, 1.0, logger, settings);
+        REQUIRE(c.ok);
+        CHECK(c.cancelled);
+        CHECK_FALSE(c.restrained);
+        CHECK(c.trials.empty());
+        CHECK(c.model != nullptr);
+        CHECK_FALSE(r.cancelled);
+    }
+}
diff --git a/tests/ReindexAmbiguityTest.cpp b/tests/ReindexAmbiguityTest.cpp
index 1f821295f..143b4e9aa 100644
--- a/tests/ReindexAmbiguityTest.cpp
+++ b/tests/ReindexAmbiguityTest.cpp
@@ -3,7 +3,10 @@
 
 #include <catch2/catch_all.hpp>
 
+#include <algorithm>
+#include <array>
 #include <cmath>
+#include <random>
 #include <unordered_map>
 #include <unordered_set>
 #include <vector>
@@ -11,6 +14,7 @@
 #include "../image_analysis/scale_merge/CrystalSetting.h"
 #include "../image_analysis/scale_merge/HKLKey.h"
 #include "../image_analysis/scale_merge/ReindexAmbiguity.h"
+#include "../image_analysis/scale_merge/ReferenceFreeReindex.h"
 #include "../image_analysis/scale_merge/SublatticeRelabel.h"
 
 namespace {
@@ -306,3 +310,248 @@ TEST_CASE("Sublattice: a frame on the given cell in another setting is described
     // An unrelated cell is not put on it.
     CHECK_FALSE(CellOnReference(UnitCell{55.0f, 66.0f, 77.0f, 90.0f, 90.0f, 90.0f}, given, settings).has_value());
 }
+
+TEST_CASE("Reindex: a stills set indexed in random hands is made consistent from the data alone", "[reindex]") {
+    // P4 on a tetragonal lattice: two indexings, related by a twin law. Every crystal records a random
+    // part of the same synthetic structure with its own scale and noise, and half of them, at random,
+    // carry the other indexing.
+    const UnitCell cell = Tetragonal();
+    DiffractionExperiment x;
+    x.SetUnitCell(cell).SpaceGroupNumber(75);
+    const auto laws = ReindexAmbiguityOperators(cell, x.GetSpaceGroupOrP1());
+    REQUIRE(laws.size() == 1);
+
+    const HKLKeyGenerator key(true, x.GetSpaceGroupOrP1());
+    std::mt19937 rng(7);
+    std::exponential_distribution<double> wilson(1.0);
+    std::normal_distribution<double> noise(0.0, 0.3);
+    std::unordered_map<uint64_t, double> structure;
+    std::vector<std::array<int, 3>> hkls;
+    for (int h = -12; h <= 12; ++h)
+        for (int k = -12; k <= 12; ++k)
+            for (int l = -6; l <= 6; ++l) {
+                if (h == 0 && k == 0 && l == 0)
+                    continue;
+                hkls.push_back({h, k, l});
+                structure.try_emplace(key(h, k, l).pack(), wilson(rng));
+            }
+
+    const int n_crystals = 300;
+    std::vector<IntegrationOutcome> outcomes(n_crystals);
+    std::vector<bool> flipped(n_crystals);
+    for (int c = 0; c < n_crystals; ++c) {
+        flipped[c] = rng() % 2;
+        const double scale = 0.5 + (rng() % 1000) / 1000.0;
+        outcomes[c].latt = CrystalLattice(cell);
+        for (int i = 0; i < 150; ++i) {
+            const auto &t = hkls[rng() % hkls.size()];
+            const auto m = flipped[c] ? laws[0].apply_to_hkl({{t[0], t[1], t[2]}}) : gemmi::Op::Miller{{t[0], t[1], t[2]}};
+            Reflection r{};
+            r.h = m[0]; r.k = m[1]; r.l = m[2];
+            r.d = 1.0f / std::sqrt((t[0] * t[0] + t[1] * t[1]) / (cell.a * cell.a) + t[2] * t[2] / (cell.c * cell.c));
+            r.I = static_cast<float>(scale * structure.at(key(t[0], t[1], t[2]).pack()) * (1.0 + noise(rng)));
+            r.sigma = 1.0f;
+            r.partiality = 1.0f;
+            r.prescaling_corr = 1.0f;
+            outcomes[c].reflections.push_back(r);
+        }
+    }
+
+    const auto result = ResolveReindexReferenceFree(outcomes, x, cell, laws, 4, /*apply=*/true);
+    CHECK(result.crystals == n_crystals);
+    // The overall hand is free: either exactly the flipped crystals are reindexed, or exactly the others.
+    int agree = 0;
+    for (int c = 0; c < n_crystals; ++c)
+        agree += (result.choice[c] != 0) == flipped[c];
+    CHECK((agree == n_crystals || agree == 0));
+    const size_t n_flipped = std::count(flipped.begin(), flipped.end(), true);
+    CHECK(result.reindexed == std::min(n_flipped, n_crystals - n_flipped));
+    CHECK(result.reindexed <= n_crystals / 2);   // the overall hand that moves the fewest crystals
+    CHECK(result.decided_fraction > 0.9);
+
+    // Done again on the consistent set, nothing moves.
+    const auto again = ResolveReindexReferenceFree(outcomes, x, cell, laws, 4, /*apply=*/false);
+    CHECK(again.reindexed == 0);
+}
+
+TEST_CASE("Reindex: a holohedral crystal gives the stills resolution nothing to do", "[reindex]") {
+    DiffractionExperiment x;
+    x.SetUnitCell(Tetragonal()).SpaceGroupNumber(89);   // P422
+    std::vector<IntegrationOutcome> outcomes(3);
+    const auto laws = ReindexAmbiguityOperators(Tetragonal(), x.GetSpaceGroupOrP1());
+    const auto result = ResolveReindexReferenceFree(outcomes, x, Tetragonal(), laws, 1, true);
+    CHECK(laws.empty());
+    CHECK(result.reindexed == 0);
+    CHECK(result.crystals == 0);
+}
+
+TEST_CASE("Reindex: an operator the crystals' own cells decide is left to them", "[reindex]") {
+    // Orthorhombic with a and b 3% apart: a twin law of the metric to within the obliquity tolerance,
+    // but every crystal's refined cell says which axis is which - nothing for the data to decide.
+    const UnitCell cell{78.0f, 80.4f, 37.0f, 90.0f, 90.0f, 90.0f};
+    DiffractionExperiment x;
+    x.SetUnitCell(cell).SpaceGroupNumber(16);   // P222
+    const auto laws = ReindexAmbiguityOperators(cell, x.GetSpaceGroupOrP1());
+    REQUIRE_FALSE(laws.empty());
+
+    std::vector<IntegrationOutcome> outcomes(50);
+    std::mt19937 rng(3);
+    for (auto &o : outcomes) {
+        o.latt = CrystalLattice(cell);
+        for (int i = 0; i < 100; ++i) {
+            Reflection r{};
+            r.h = static_cast<int>(rng() % 15) - 7; r.k = static_cast<int>(rng() % 15) - 7; r.l = static_cast<int>(rng() % 7) + 1;
+            r.d = 3.0f; r.I = static_cast<float>(rng() % 1000); r.sigma = 1.0f; r.partiality = 1.0f; r.prescaling_corr = 1.0f;
+            o.reflections.push_back(r);
+        }
+    }
+    const auto result = ResolveReindexReferenceFree(outcomes, x, cell, laws, 1, true);
+    REQUIRE(result.metric_preference.size() == laws.size());
+    for (double p : result.metric_preference)
+        CHECK(p == 1.0);
+    CHECK(result.crystals == 0);
+    CHECK(result.reindexed == 0);
+}
+
+TEST_CASE("Reindex: where the cells decide, the crystals whose cell disagrees are decided by the intensities",
+          "[reindex]") {
+    // As above, a and b 3% apart, but a few crystals were indexed on swapped axes: their own cells say so,
+    // and the intensities, read against the crystals the cells anchor, put them back.
+    const UnitCell cell{78.0f, 80.4f, 37.0f, 90.0f, 90.0f, 90.0f};
+    DiffractionExperiment x;
+    x.SetUnitCell(cell).SpaceGroupNumber(16);   // P222
+    const auto laws = ReindexAmbiguityOperators(cell, x.GetSpaceGroupOrP1());
+    REQUIRE(laws.size() == 1);
+
+    const HKLKeyGenerator key(true, x.GetSpaceGroupOrP1());
+    std::mt19937 rng(11);
+    std::exponential_distribution<double> wilson(1.0);
+    std::normal_distribution<double> noise(0.0, 0.3);
+    std::unordered_map<uint64_t, double> structure;
+    std::vector<std::array<int, 3>> hkls;
+    for (int h = -12; h <= 12; ++h)
+        for (int k = -12; k <= 12; ++k)
+            for (int l = -6; l <= 6; ++l)
+                if (h != 0 || k != 0 || l != 0) {
+                    hkls.push_back({h, k, l});
+                    structure.try_emplace(key(h, k, l).pack(), wilson(rng));
+                }
+
+    const int n_crystals = 300;
+    std::vector<IntegrationOutcome> outcomes(n_crystals);
+    std::vector<bool> swapped(n_crystals, false);
+    for (int c = 0; c < n_crystals; ++c) {
+        swapped[c] = c % 12 == 5;   // 25 of 300: the cells still decide the law
+        outcomes[c].latt = swapped[c] ? ReindexLattice(CrystalLattice(cell), laws[0]) : CrystalLattice(cell);
+        for (int i = 0; i < 150; ++i) {
+            const auto &t = hkls[rng() % hkls.size()];
+            const auto m = swapped[c] ? laws[0].apply_to_hkl({{t[0], t[1], t[2]}}) : gemmi::Op::Miller{{t[0], t[1], t[2]}};
+            Reflection r{};
+            r.h = m[0]; r.k = m[1]; r.l = m[2];
+            r.d = 1.0f / std::sqrt(t[0] * t[0] / (cell.a * cell.a) + t[1] * t[1] / (cell.b * cell.b)
+                                   + t[2] * t[2] / (cell.c * cell.c));
+            r.I = static_cast<float>(structure.at(key(t[0], t[1], t[2]).pack()) * (1.0 + noise(rng)));
+            r.sigma = 0.1f;
+            r.partiality = 1.0f;
+            r.prescaling_corr = 1.0f;
+            outcomes[c].reflections.push_back(r);
+        }
+    }
+
+    const auto result = ResolveReindexReferenceFree(outcomes, x, cell, laws, 4, /*apply=*/true);
+    REQUIRE(result.metric_preference.size() == 1);
+    CHECK(result.metric_preference[0] >= METRIC_DECIDED);
+    CHECK(result.crystals == 25);
+    for (int c = 0; c < n_crystals; ++c)
+        CHECK((result.choice[c] != 0) == swapped[c]);
+}
+
+TEST_CASE("Reindex: with a reference, a crystal its own cell anchors keeps that indexing", "[reindex]") {
+    // a and b 3% apart: the crystals' cells decide the twin law. The reference is written in the other
+    // indexing, so image by image it moves every crystal; afterwards, the crystals whose cell says which
+    // axis is which go back, and only those whose cell cannot tell (a = b) stay where the reference put them.
+    const UnitCell cell{78.0f, 80.4f, 37.0f, 90.0f, 90.0f, 90.0f};
+    const UnitCell undecided{79.2f, 79.2f, 37.0f, 90.0f, 90.0f, 90.0f};
+    DiffractionExperiment x;
+    x.SetUnitCell(cell).SpaceGroupNumber(16);   // P222
+    const auto laws = ReindexAmbiguityOperators(cell, x.GetSpaceGroupOrP1());
+    REQUIRE(laws.size() == 1);
+
+    const HKLKeyGenerator key(true, x.GetSpaceGroupOrP1());
+    std::mt19937 rng(5);
+    std::exponential_distribution<double> wilson(1.0);
+    std::normal_distribution<double> noise(0.0, 0.2);
+    std::unordered_map<uint64_t, double> structure;
+    std::vector<std::array<int, 3>> hkls;
+    for (int h = -12; h <= 12; ++h)
+        for (int k = -12; k <= 12; ++k)
+            for (int l = -6; l <= 6; ++l)
+                if (h != 0 || k != 0 || l != 0) {
+                    hkls.push_back({h, k, l});
+                    structure.try_emplace(key(h, k, l).pack(), wilson(rng));
+                }
+    const auto d_of = [&](const std::array<int, 3> &t) {
+        return 1.0f / std::sqrt(t[0] * t[0] / (cell.a * cell.a) + t[1] * t[1] / (cell.b * cell.b)
+                                + t[2] * t[2] / (cell.c * cell.c));
+    };
+    std::vector<MergedReflection> reference;
+    std::unordered_set<uint64_t> seen;
+    for (const auto &t : hkls) {
+        if (!seen.insert(key(t[0], t[1], t[2]).pack()).second)
+            continue;
+        const auto m = laws[0].apply_to_hkl({{t[0], t[1], t[2]}});
+        MergedReflection r;
+        r.h = t[0]; r.k = t[1]; r.l = t[2];
+        r.I = static_cast<float>(structure.at(key(m[0], m[1], m[2]).pack()));
+        r.sigma = 1.0f;
+        r.d = d_of(t);
+        reference.push_back(r);
+    }
+
+    const int n_crystals = 200;
+    std::vector<IntegrationOutcome> outcomes(n_crystals);
+    std::vector<bool> open(n_crystals);
+    for (int c = 0; c < n_crystals; ++c) {
+        open[c] = c % 10 == 3;
+        outcomes[c].latt = CrystalLattice(open[c] ? undecided : cell);
+        for (int i = 0; i < 150; ++i) {
+            const auto &t = hkls[rng() % hkls.size()];
+            Reflection r{};
+            r.h = t[0]; r.k = t[1]; r.l = t[2];
+            r.d = d_of(t);
+            r.I = static_cast<float>(structure.at(key(t[0], t[1], t[2]).pack()) * (1.0 + noise(rng)));
+            r.sigma = 0.1f;
+            r.partiality = 1.0f;
+            r.prescaling_corr = 1.0f;
+            outcomes[c].reflections.push_back(r);
+        }
+    }
+    const auto as_indexed = outcomes;
+    const auto as_indexed_now = [&](int c) {
+        for (size_t i = 0; i < outcomes[c].reflections.size(); ++i) {
+            const auto &r = outcomes[c].reflections[i], &r0 = as_indexed[c].reflections[i];
+            if (r.h != r0.h || r.k != r0.k || r.l != r0.l)
+                return false;
+        }
+        return true;
+    };
+
+    const ReindexAmbiguityResolver resolver(x, reference);
+    for (auto &o : outcomes) {
+        o.reference_cc = resolver.Resolve(o.reflections, o.latt);
+        REQUIRE(o.reference_cc.size() == 2);
+    }
+    for (int c = 0; c < n_crystals; ++c)
+        REQUIRE_FALSE(as_indexed_now(c));   // the reference moved them all
+
+    const auto result = AnchorReferenceReindex(outcomes, cell, laws);
+    REQUIRE(result.metric_preference.size() == 1);
+    CHECK(result.metric_preference[0] >= METRIC_DECIDED);
+    CHECK(result.overruled == static_cast<size_t>(std::count(open.begin(), open.end(), false)));
+    for (int c = 0; c < n_crystals; ++c) {
+        CHECK(as_indexed_now(c) == !open[c]);
+        CHECK(outcomes[c].reference_cc.empty());
+        if (!open[c])
+            CHECK(outcomes[c].latt.GetUnitCell().b == Catch::Approx(cell.b).epsilon(1e-4));
+    }
+}
diff --git a/tests/RotationIngestGPUTest.cpp b/tests/RotationIngestGPUTest.cpp
index 7b8588480..f0d4f973a 100644
--- a/tests/RotationIngestGPUTest.cpp
+++ b/tests/RotationIngestGPUTest.cpp
@@ -161,7 +161,7 @@ TEST_CASE("RotationIngestGPU_SortAndCutMatchHost", "[RotationScale][gpu]") {
         }
 
         std::vector<float> px(n_keep), py(n_keep);
-        gpu.IngestObservations(ptr.data(), count.data(), 4, flux.data(), px.data(), py.data());
+        gpu.IngestObservations(ptr.data(), count.data(), 4, flux.data(), INFINITY, px.data(), py.data());
         for (int i = 0; i < n; ++i)
             if (keep[i]) {
                 CHECK(px[new_idx[i]] == all[i]->predicted_x);
diff --git a/tests/RotationScaleWalkTest.cpp b/tests/RotationScaleWalkTest.cpp
index ddc2e4867..9b1c83385 100644
--- a/tests/RotationScaleWalkTest.cpp
+++ b/tests/RotationScaleWalkTest.cpp
@@ -81,6 +81,35 @@ TEST_CASE("WalkRotationScale_StopsWhereTheNextStepIsUnderHalfAFrame", "[Rotation
     CHECK(std::fabs(b.scale - 0.97) * 36000 < 1.0);
 }
 
+TEST_CASE("WalkRotationScale_RefitStepTheFramesCannotResolve", "[RotationScale]") {
+    // Validation frames that resolve the first step off the stored angles but score every later one
+    // alike: the refit is followed to its fixed point all the same.
+    struct FlatPastFirstStep : SyntheticSweep {
+        ValidationSpotEvidence IndexAt(float k) {
+            ++index_calls;
+            const double on = k == 1.0f ? 0.37 : 0.42;
+            return ValidationSpotEvidence{spots, std::llround(on * spots), std::llround(0.005 * spots)};
+        }
+    } sweep{{0.98}};
+    const auto walk = WalkRotationScale(sweep.RefitAt(1.0f).value(), [&](float k) { return sweep.IndexAt(k); },
+                                        [&](float k) { return sweep.RefitAt(k); }, 8, 3600);
+    CHECK(walk.scale == Catch::Approx(0.98).margin(0.0005));
+
+    // A refit step the frames score worse is still refused.
+    struct WorseAfterFirstStep : SyntheticSweep {
+        ValidationSpotEvidence IndexAt(float k) {
+            ++index_calls;
+            const double on = k == 1.0f ? 0.37 : (k == first ? 0.42 : 0.30);
+            return ValidationSpotEvidence{spots, std::llround(on * spots), std::llround(0.005 * spots)};
+        }
+        float first = 0.0f;
+    } worse{{0.98}};
+    worse.first = static_cast<float>(worse.RefitAt(1.0f).value());
+    const auto refused = WalkRotationScale(worse.first, [&](float k) { return worse.IndexAt(k); },
+                                           [&](float k) { return worse.RefitAt(k); }, 8, 3600);
+    CHECK(refused.scale == worse.first);
+}
+
 TEST_CASE("WalkRotationScale_StoredAnglesStand", "[RotationScale]") {
     SECTION("A healthy stage: a fit off by noise scores no better than the stored angles") {
         SyntheticSweep sweep{1.0};
diff --git a/tests/RugnuxInputKindTest.cpp b/tests/RugnuxInputKindTest.cpp
new file mode 100644
index 000000000..7eb42fc4f
--- /dev/null
+++ b/tests/RugnuxInputKindTest.cpp
@@ -0,0 +1,79 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <catch2/catch_all.hpp>
+#include <filesystem>
+#include <fstream>
+#include <zlib.h>
+
+#include "../rugnux/RugnuxInputKind.h"
+
+namespace {
+    const std::string MODEL_CIF = "data_test\n#\n_cell.length_a 50.0\nloop_\n_atom_site.group_PDB\n_atom_site.id\n"
+                                  "ATOM 1\n";
+    const std::string SF_CIF = "data_r1abcsf\n_cell.length_a 50.0\nloop_\n_refln.index_h\n_refln.index_k\n"
+                               "_refln.index_l\n_refln.intensity_meas\n1 0 0 10.0\n";
+    const std::string PDB = "HEADER    TEST\nREMARK   1 SYNTHETIC\nCRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1\n"
+                            "ATOM      1  CA  ALA A   1       1.000   2.000   3.000  1.00 10.00           C\nEND\n";
+
+    std::string Write(const std::string &name, const std::string &content) {
+        std::ofstream(name, std::ios::binary) << content;
+        return name;
+    }
+
+    std::string WriteGz(const std::string &name, const std::string &content) {
+        gzFile f = gzopen(name.c_str(), "wb");
+        gzwrite(f, content.data(), static_cast<unsigned>(content.size()));
+        gzclose(f);
+        return name;
+    }
+}
+
+TEST_CASE("RugnuxInputKind_Classify", "[rugnux_inputs]") {
+    using K = RugnuxInputKind;
+    CHECK(ClassifyRugnuxInput(Write("ik_model.cif", MODEL_CIF)) == K::Model);
+    CHECK(ClassifyRugnuxInput(Write("ik_sf.cif", SF_CIF)) == K::Reflections);
+    CHECK(ClassifyRugnuxInput(Write("ik_diffrn.cif", "data_x\nloop_\n_diffrn_refln.index_h\n1\n")) == K::Reflections);
+    CHECK(ClassifyRugnuxInput(Write("ik_model.pdb", PDB)) == K::Model);
+    CHECK(ClassifyRugnuxInput(WriteGz("ik_model.pdb.gz", PDB)) == K::Model);
+    CHECK(ClassifyRugnuxInput(WriteGz("ik_sf.cif.gz", SF_CIF)) == K::Reflections);
+    // the name says nothing: a model in a file called .mtz, reflections in one called .pdb
+    CHECK(ClassifyRugnuxInput(Write("ik_model_named.mtz", MODEL_CIF)) == K::Model);
+    CHECK(ClassifyRugnuxInput(Write("ik_mtz_named.pdb", std::string("MTZ \0\0\0\0", 8) + "binary")) == K::Reflections);
+    CHECK(ClassifyRugnuxInput(Write("ik_image.h5", std::string("\x89HDF\r\n\x1a\n\0\0\0\0", 12))) == K::Images);
+    CHECK(ClassifyRugnuxInput(Write("ik_image.cbf", "###CBF: VERSION 1.5\ndata_image\n_array_data.data\n")) == K::Images);
+    CHECK(ClassifyRugnuxInput(Write("ik_image2.cbf", "data_image\n_array_data.data\n_atom_site.x\n")) == K::Images);
+    CHECK(ClassifyRugnuxInput(Write("ik_image.img", "{\nHEADER_BYTES=  512;\nDIM=2;\n}")) == K::Images);
+    CHECK(ClassifyRugnuxInput(Write("ik_binary", std::string("\0\1\2\3\4\5\6\7\0\0\0\0\0\0\0\0x", 17))) == K::Images);
+    // A PDB file without an atom is not a model
+    CHECK(ClassifyRugnuxInput(Write("ik_noatom.pdb", "HEADER    TEST\nEND\n")) == K::Images);
+    // Both coordinates and reflections: the user has to say
+    CHECK(ClassifyRugnuxInput(Write("ik_both.cif", MODEL_CIF + "loop_\n_refln.index_h\n1\n")) == K::Ambiguous);
+    for (const char *f: {"ik_model.cif", "ik_sf.cif", "ik_diffrn.cif", "ik_model.pdb", "ik_model.pdb.gz", "ik_sf.cif.gz",
+                         "ik_model_named.mtz", "ik_mtz_named.pdb", "ik_image.h5", "ik_image.cbf", "ik_image2.cbf",
+                         "ik_image.img", "ik_binary", "ik_noatom.pdb", "ik_both.cif"})
+        std::filesystem::remove(f);
+}
+
+TEST_CASE("RugnuxInputKind_SplitAnyOrder", "[rugnux_inputs]") {
+    const std::string img = Write("ik_s_image.h5", std::string("\x89HDF\r\n\x1a\n\0\0\0\0", 12));
+    const std::string model = Write("ik_s_model.pdb", PDB);
+    const std::string sf = Write("ik_s_sf.cif", SF_CIF);
+    for (const auto &order: std::vector<std::vector<std::string>>{{img, model, sf}, {model, sf, img}, {sf, img, model}}) {
+        const RugnuxPositionalInputs s = SplitRugnuxInputs(order);
+        CHECK(s.images == std::vector<std::string>{img});
+        CHECK(s.model == model);
+        CHECK(s.reflections == sf);
+    }
+    // image files keep their order; a path that is no file (yet) is left to the image readers
+    const RugnuxPositionalInputs s = SplitRugnuxInputs({"later_master.h5", model, img});
+    CHECK(s.images == std::vector<std::string>{"later_master.h5", img});
+
+    const std::string model2 = Write("ik_s_model2.cif", MODEL_CIF);
+    CHECK_THROWS(SplitRugnuxInputs({img, model, model2}));
+    CHECK_THROWS(SplitRugnuxInputs({sf, img, sf}));
+    const std::string both = Write("ik_s_both.cif", MODEL_CIF + "loop_\n_refln.index_h\n1\n");
+    CHECK_THROWS(SplitRugnuxInputs({img, both}));
+    for (const auto &f: {img, model, sf, model2, both})
+        std::filesystem::remove(f);
+}
diff --git a/tests/RugnuxLiveStatusTest.cpp b/tests/RugnuxLiveStatusTest.cpp
index 24c8be717..b57e19dca 100644
--- a/tests/RugnuxLiveStatusTest.cpp
+++ b/tests/RugnuxLiveStatusTest.cpp
@@ -3,7 +3,11 @@
 
 #include <catch2/catch_all.hpp>
 
+#include <cmath>
+
 #include "../receiver/RugnuxLiveStatus.h"
+#include "../receiver/JFJochReceiverRugnux.h"
+#include "../broker/OpenAPIConvert.h"
 #include "../image_puller/TestImagePuller.h"
 
 using namespace std::chrono_literals;
@@ -86,3 +90,234 @@ TEST_CASE("TestImagePuller_SetsReceiveTime", "[RugnuxLive]") {
     REQUIRE(out);
     CHECK(out->received == given);
 }
+
+TEST_CASE("RugnuxLiveModel_MolecularReplacement", "[RugnuxLive]") {
+    ProcessResult r;
+    CHECK(!LiveModel(r));
+
+    MolecularReplacementResult mr;
+    mr.ok = true;
+    mr.model_name = "model.cif";
+    mr.predicted_model = true;
+    mr.decision = "AGREES";
+    mr.d_min_search = 2.5;
+    MRCandidate c;
+    c.space_group = *gemmi::find_spacegroup_by_name("P 1 21 1");
+    c.copies = 2;
+    c.tf_z = 12.5;
+    c.rf_z = 6.0;
+    c.null_sigma = 20.0;
+    mr.candidates = {MRCandidate{}, c};
+    mr.chosen = 1;
+    r.model_prior = mr;
+    ModelValidationResult v;
+    v.ok = true;
+    v.r_work = 0.38;
+    v.r_free = 0.40;
+    v.cc_model_overall = 0.71;
+    v.mean_atom_density_sigma = 1.6;
+    v.anomalous_sites = {{"SD MET A1", 5.5}};
+    r.model_validation = v;
+    r.model_placement = "MR";
+
+    const auto m = LiveModel(r);
+    REQUIRE(m);
+    CHECK(m->placement == "MR");
+    CHECK(m->predicted);
+    CHECK(m->mr_space_group == "P 1 21 1");
+    CHECK(m->copies.value() == 2);
+    CHECK(m->tf_z.value() == Catch::Approx(12.5));
+    CHECK(!m->llg_z);
+    CHECK(m->fit_sigma.value() == Catch::Approx(20.0));   // MR's null: the rigid body's was not tested
+    CHECK(m->r_free.value() == Catch::Approx(0.40));
+    CHECK(m->cc_model.value() == Catch::Approx(0.71));
+    CHECK(!m->rigid_body_shift_A);
+    CHECK(m->anomalous_site == "SD MET A1");
+
+    RugnuxLiveStatus status;
+    status.Start(10, 1.0, std::chrono::steady_clock::now());
+    status.Result("OK", "fine", {}, {}, true);
+    status.Model(*m);
+    nlohmann::json j = Convert(status.Get());
+    CHECK(j["anomalous_signal"] == true);
+    CHECK(j["model"]["placement"] == "MR");
+    CHECK(j["model"]["copies"] == 2);
+    CHECK(j["model"]["r_free"].get<double>() == Catch::Approx(0.40));
+    CHECK(!j["model"].contains("llg_z"));
+    CHECK(!j["model"].contains("rigid_body_angle_deg"));
+
+    status.Clear();
+    CHECK(!status.Get().model);
+    CHECK(!status.Get().anomalous_signal);
+}
+
+TEST_CASE("RugnuxLiveStatus_Headline", "[RugnuxLive]") {
+    RugnuxLiveStatus status;
+    status.Start(10, 1.0, std::chrono::steady_clock::now());
+    nlohmann::json j = Convert(status.Get());
+    CHECK(!j.contains("space_group"));
+    CHECK(!j.contains("d_min"));
+    CHECK(!j.contains("isa"));
+
+    status.Headline("P 1 21 1", 1.25, 24.2);
+    j = Convert(status.Get());
+    CHECK(j["space_group"] == "P 1 21 1");
+    CHECK(j["d_min"].get<double>() == Catch::Approx(1.25));
+    CHECK(j["isa"].get<double>() == Catch::Approx(24.2));
+
+    // ISa undetermined
+    status.Headline("P 1 21 1", 1.25, std::nullopt);
+    j = Convert(status.Get());
+    CHECK(!j.contains("isa"));
+
+    status.Clear();
+    CHECK(status.Get().space_group.empty());
+    CHECK(!status.Get().d_min);
+}
+
+TEST_CASE("RugnuxLiveModel_Refinement", "[RugnuxLive]") {
+    ProcessResult r;
+    ModelValidationResult v;
+    v.ok = true;
+    v.r_work = 0.38;
+    v.r_free = 0.40;
+    r.model_validation = v;
+    r.model_placement = "RIGID_BODY";
+    CHECK(!LiveModel(r)->refinement);
+
+    RefinementResult rf;
+    rf.ok = true;
+    rf.on_gpu = true;
+    rf.seconds = 3.5;
+    rf.r_work_placement = 0.30;
+    rf.r_free_placement = 0.33;
+    rf.restrained = true;
+    rf.r_work = 0.19;
+    rf.r_free = 0.23;
+    rf.geometry.rmsd_bonds = 0.011;
+    rf.geometry.rmsd_angles = 1.6;
+    DensityBlob b;
+    b.kind = DensityBlob::Kind::Ligand;
+    b.centroid = gemmi::Position(1.0, 2.0, 3.0);
+    b.peak_sigma = 7.5;
+    b.volume = 40.0;
+    b.nearest_atom = "OG1 THR A42";
+    b.nearest_atom_distance = 3.1;
+    rf.blobs.assign(RugnuxLiveRefinement::MAX_BLOBS + 5, b);
+    r.refinement = rf;
+
+    const auto m = LiveModel(r);
+    REQUIRE(m->refinement);
+    const RugnuxLiveRefinement &lr = *m->refinement;
+    CHECK(lr.performed);
+    CHECK(lr.r_free.value() == Catch::Approx(0.23));
+    CHECK(lr.rmsd_bonds_A.value() == Catch::Approx(0.011));
+    CHECK(lr.blob_count == static_cast<int64_t>(RugnuxLiveRefinement::MAX_BLOBS + 5));
+    CHECK(lr.blobs.size() == RugnuxLiveRefinement::MAX_BLOBS);
+    // the placed model's R-factors are untouched
+    CHECK(m->r_free.value() == Catch::Approx(0.40));
+
+    RugnuxLiveStatus status;
+    status.Start(10, 1.0, std::chrono::steady_clock::now());
+    status.Model(*m);
+    nlohmann::json j = Convert(status.Get());
+    CHECK(j["refined_model"] == false);
+    CHECK(j["model"]["r_free"].get<double>() == Catch::Approx(0.40));
+    CHECK(j["model"]["refinement"]["r_free"].get<double>() == Catch::Approx(0.23));
+    CHECK(j["model"]["refinement"]["on_gpu"] == true);
+    CHECK(j["model"]["refinement"]["blob_count"] == RugnuxLiveRefinement::MAX_BLOBS + 5);
+    CHECK(j["model"]["refinement"]["blobs"].size() == RugnuxLiveRefinement::MAX_BLOBS);
+    CHECK(j["model"]["refinement"]["blobs"][0]["kind"] == "LIGAND");
+    CHECK(j["model"]["refinement"]["blobs"][0]["z"].get<double>() == Catch::Approx(3.0));
+
+    // Only the placement stage ran: its R-factors, no geometry
+    rf.restrained = false;
+    r.refinement = rf;
+    const auto p = LiveModel(r);
+    CHECK(p->refinement->r_free.value() == Catch::Approx(0.33));
+    CHECK(!p->refinement->rmsd_bonds_A);
+
+    // Failed
+    RefinementResult failed;
+    failed.failure_reason = "no dictionary";
+    r.refinement = failed;
+    status.Model(*LiveModel(r));
+    j = Convert(status.Get());
+    CHECK(j["model"]["refinement"]["performed"] == false);
+    CHECK(j["model"]["refinement"]["reason"] == "no dictionary");
+    CHECK(!j["model"]["refinement"].contains("r_free"));
+}
+
+TEST_CASE("RugnuxLiveModel_RefinementCancelled", "[RugnuxLive]") {
+    ProcessResult r;
+    ModelValidationResult v;
+    v.ok = true;
+    r.model_validation = v;
+    r.model_placement = "MR";
+    RefinementResult rf;
+    rf.ok = true;
+    rf.cancelled = true;
+    r.refinement = rf;
+    const auto m = LiveModel(r);
+    CHECK(m->refinement->cancelled);
+    RugnuxLiveStatus status;
+    status.Start(10, 1.0, std::chrono::steady_clock::now());
+    status.Model(*m);
+    const nlohmann::json j = Convert(status.Get());
+    CHECK(j["model"]["refinement"]["cancelled"] == true);
+}
+
+// A score that is not a number is left out, not written as null: the page reads every present one as a number.
+TEST_CASE("RugnuxLiveModel_NonFiniteScores", "[RugnuxLive]") {
+    ProcessResult r;
+    MolecularReplacementResult mr;
+    mr.ok = true;
+    mr.d_min_search = NAN;
+    MRCandidate c;
+    c.space_group = *gemmi::find_spacegroup_by_name("P 1 21 1");
+    c.tf_z = NAN;
+    c.rf_z = INFINITY;
+    mr.candidates = {c};
+    mr.chosen = 0;
+    r.model_prior = mr;
+    ModelValidationResult v;
+    v.ok = true;
+    v.r_work = NAN;
+    v.r_free = NAN;
+    v.mean_atom_density_sigma = NAN;
+    r.model_validation = v;
+    r.model_placement = "MR";
+    RefinementResult rf;
+    rf.ok = true;
+    rf.restrained = true;
+    rf.r_work = NAN;
+    rf.r_free = 0.25;
+    rf.geometry.rmsd_bonds = NAN;
+    DensityBlob b;
+    b.nearest_atom_distance = INFINITY;
+    rf.blobs = {b};
+    r.refinement = rf;
+
+    const auto m = LiveModel(r);
+    REQUIRE(m);
+    CHECK(!m->tf_z);
+    CHECK(!m->rf_z);
+    CHECK(!m->mr_d_min);
+    CHECK(!m->r_free);
+    CHECK(!m->map_atom_sigma);
+    CHECK(!m->refinement->r_work);
+    CHECK(m->refinement->r_free.value() == Catch::Approx(0.25));
+    CHECK(!m->refinement->rmsd_bonds_A);
+    CHECK(!m->refinement->blobs.at(0).nearest_atom_distance_A);
+
+    RugnuxLiveStatus status;
+    status.Start(10, 1.0, std::chrono::steady_clock::now());
+    status.Model(*m);
+    const nlohmann::json j = Convert(status.Get());
+    CHECK(!j["model"].contains("tf_z"));
+    CHECK(!j["model"].contains("rf_z"));
+    CHECK(!j["model"].contains("r_free"));
+    CHECK(!j["model"]["refinement"].contains("r_work"));
+    CHECK(!j["model"]["refinement"]["blobs"][0].contains("nearest_atom_distance_A"));
+    CHECK(j.dump().find("null") == std::string::npos);
+}
diff --git a/tests/RugnuxResultFilesTest.cpp b/tests/RugnuxResultFilesTest.cpp
index 8792a465d..a21df3a2c 100644
--- a/tests/RugnuxResultFilesTest.cpp
+++ b/tests/RugnuxResultFilesTest.cpp
@@ -11,11 +11,13 @@
 #include <gemmi/mtz.hpp>
 #include <gemmi/mmread_gz.hpp>
 #include <gemmi/calculate.hpp>  // count_atom_sites
+#include <nlohmann/json.hpp>
 
 #include "../common/Definitions.h"
 #include "../common/DiffractionExperiment.h"
 #include "../common/Logger.h"
 #include "../image_analysis/WriteReflections.h"
+#include "../image_analysis/structure_refinement/DensityBlobs.h"
 #include "../frame_serialize/CBORStream2Serializer.h"
 #include "../frame_serialize/CBORStream2Deserializer.h"
 #include "../writer/WriteModel.h"
@@ -307,3 +309,86 @@ TEST_CASE("RugnuxResultFiles: the input model's metadata reaches _model.cif thro
 
     std::filesystem::remove_all(dir);
 }
+
+TEST_CASE("RugnuxResultFiles: the refinement's model, maps and blobs reach the writer through the END block",
+          "[rugnux_result_files]") {
+    Logger logger("RugnuxResultFiles");
+    const std::filesystem::path dir = std::filesystem::temp_directory_path() / "rugnux_result_files_refined";
+    std::filesystem::remove_all(dir);
+    std::filesystem::create_directories(dir);
+    const std::string original = (dir / "rugnux").string();
+    const std::string written = (dir / "writer").string();
+    const gemmi::SpaceGroup &sg = *gemmi::find_spacegroup_by_name("P 43 21 2");
+
+    // As rugnux writes them (RugnuxOutputFiles.cpp): WritePlacedModel at <prefix>_refined, the maps' MTZ, and
+    // the blobs' JSON.
+    WritePlacedModel(TestModel(), TEST_CELL, sg, original + "_refined", logger);
+    MtzTable maps;
+    maps.unit_cell = TEST_CELL;
+    maps.space_group_name = sg.xhm();
+    maps.datasets = {{"HKL_base", "HKL_base", "HKL_base", 0.0f}, {"refined", "refined", "refined", 1.0f}};
+    for (const auto &[label, type] : std::vector<std::pair<const char *, char>>{
+             {"H", 'H'}, {"K", 'H'}, {"L", 'H'}, {"FWT", 'F'}, {"PHWT", 'P'}, {"DELFWT", 'F'}, {"PHDELWT", 'P'}})
+        maps.columns.push_back({label, type, type == 'H' ? 0 : 1, {}});
+    for (int i = 1; i <= 30; i++) {
+        const float row[] = {static_cast<float>(i % 5), static_cast<float>(i % 7), static_cast<float>(i),
+                             10.0f + i, static_cast<float>((i * 37) % 360), 0.5f * i, static_cast<float>(i)};
+        for (size_t c = 0; c < maps.columns.size(); c++)
+            maps.columns[c].values.push_back(row[c]);
+    }
+    WriteMtz(maps, original + "_refined_maps.mtz");
+    std::vector<DensityBlob> blobs(2);
+    blobs[0] = {.kind = DensityBlob::Kind::Ligand, .centroid = {12.25, -3.5, 40.125}, .peak_sigma = 7.3,
+                .volume = 41.2, .score = 160.4, .nearest_atom_distance = 3.1, .nearest_atom = "OG1 THR A42",
+                .polar_contacts = 2, .metal_contacts = 0, .anomalous_sigma = 0.0};
+    blobs[1] = {.kind = DensityBlob::Kind::Water, .centroid = {1.0 / 3.0, 2.0, 3.0}, .peak_sigma = 4.4,
+                .volume = 2.5, .score = 9.1, .nearest_atom_distance = 2.8, .nearest_atom = "O HOH A101",
+                .polar_contacts = 3, .metal_contacts = 1, .anomalous_sigma = 1.25};
+    { std::ofstream f(original + "_blobs.json"); f << DensityBlobsJson(DensityBlobsToMessage(blobs)); }
+
+    // As the broker puts them in the END message (JFJochReceiverRugnux::AddToEndMessage).
+    EndMessage end{};
+    end.refined_model = PlacedModelFromStructure(TestModel(), TEST_CELL, sg.xhm());
+    end.refined_map_coefficients = maps;
+    end.blobs = DensityBlobsToMessage(blobs);
+    std::vector<uint8_t> buffer(16 * 1024 * 1024);
+    CBORStream2Serializer serializer(buffer.data(), buffer.size());
+    REQUIRE_NOTHROW(serializer.SerializeSequenceEnd(end));
+    auto deserialized = CBORStream2Deserialize(buffer.data(), serializer.GetBufferSize());
+    REQUIRE(deserialized);
+    REQUIRE(deserialized->end_message);
+    const EndMessage &out = *deserialized->end_message;
+    REQUIRE(out.refined_model);
+    REQUIRE(out.refined_map_coefficients);
+    REQUIRE(out.blobs);
+    CHECK(!out.placed_model);
+    CHECK(out.refined_model->x == end.refined_model->x);
+    CHECK(out.blobs->kind == std::vector<std::string>{"LIGAND", "WATER"});
+    CHECK(out.blobs->x == end.blobs->x);
+    CHECK(out.blobs->nearest_atom == end.blobs->nearest_atom);
+    CHECK(out.blobs->metal_contacts == end.blobs->metal_contacts);
+    CHECK(out.blobs->anomalous_sigma == end.blobs->anomalous_sigma);
+
+    WriteRugnuxResultFiles(out, written, false, logger);
+    CHECK(ReadFile(written + "_refined_model.cif") == ReadFile(original + "_refined_model.cif"));
+    CHECK(ReadFile(written + "_refined_model.pdb") == ReadFile(original + "_refined_model.pdb"));
+    CHECK(ReadFile(written + "_refined_maps.mtz") == ReadFile(original + "_refined_maps.mtz"));
+    CHECK(ReadFile(written + "_blobs.json") == ReadFile(original + "_blobs.json"));
+    CHECK(!std::filesystem::exists(written + "_model.cif"));
+    CHECK(!std::filesystem::exists(written + "_blobs.json.tmp"));
+    const auto json = nlohmann::json::parse(ReadFile(written + "_blobs.json"));
+    REQUIRE(json["blobs"].size() == 2);
+    CHECK(json["blobs"][0]["kind"] == "LIGAND");
+    CHECK(json["blobs"][1]["centroid"][0].get<double>() == 1.0 / 3.0);
+
+    // A blobs block whose fields disagree is reported, not written.
+    DensityBlobsMessage bad = *end.blobs;
+    bad.score.pop_back();
+    CHECK_THROWS(DensityBlobsJson(bad));
+    EndMessage bad_end{};
+    bad_end.blobs = bad;
+    REQUIRE_NOTHROW(WriteRugnuxResultFiles(bad_end, written + "_bad", false, logger));
+    CHECK(!std::filesystem::exists(written + "_bad_blobs.json"));
+
+    std::filesystem::remove_all(dir);
+}
diff --git a/tests/RugnuxStructureTest.cpp b/tests/RugnuxStructureTest.cpp
index e6aecfdf0..b7ad2f535 100644
--- a/tests/RugnuxStructureTest.cpp
+++ b/tests/RugnuxStructureTest.cpp
@@ -148,7 +148,11 @@ TEST_CASE("RugnuxLiveStatus_StructureClearedAtStart", "[RugnuxLive]") {
     status.Start(10, 1.0, std::chrono::steady_clock::now());
     CHECK(!status.Get().structure);
     status.Structure(std::make_shared<RugnuxStructure>(OneAtomModel(), TEST_CELL,
+                                                       *gemmi::find_spacegroup_by_name("P 1"), std::nullopt),
+                     std::make_shared<RugnuxStructure>(OneAtomModel(), TEST_CELL,
                                                        *gemmi::find_spacegroup_by_name("P 1"), std::nullopt));
+    CHECK(status.Get().refined_structure);
     status.Clear();
     CHECK(!status.Get().structure);
+    CHECK(!status.Get().refined_structure);
 }
diff --git a/tests/RugnuxTest.cpp b/tests/RugnuxTest.cpp
index 0aa0f08bf..ba3b904f8 100644
--- a/tests/RugnuxTest.cpp
+++ b/tests/RugnuxTest.cpp
@@ -340,6 +340,10 @@ TEST_CASE("RugnuxCommandLine_Full", "[process]") {
     model->name = "model.cif";
     config.model = model;
     CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--model model.cif") != std::string::npos);
+    // A placed model is refined by default: only --no-refine is given back.
+    CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--no-refine") != std::string::npos);
+    config.refine = true;
+    CHECK(RugnuxCommandLine(config, x, "in.h5", "", false).find("--no-refine") == std::string::npos);
     config.force_mr = true;
     const std::string mr_cmd = RugnuxCommandLine(config, x, "in.h5", "", false);
     CHECK(mr_cmd.find("--mr model.cif") != std::string::npos);
diff --git a/tests/ShadowFinderTest.cpp b/tests/ShadowFinderTest.cpp
index 32fff47f7..13a6f35f5 100644
--- a/tests/ShadowFinderTest.cpp
+++ b/tests/ShadowFinderTest.cpp
@@ -541,10 +541,24 @@ TEST_CASE("ShadowFinder_PolarizationPlane", "[ShadowFinder]") {
             }
         return m;
     };
-    CHECK(PolarizationPlane(medians(-1.0, false), amplitude) == 1.0f);   // dim along x: horizontal
-    CHECK(PolarizationPlane(medians(+1.0, false), amplitude) == -1.0f);  // dim along y: vertical
-    CHECK(PolarizationPlane(medians(+1.0, true), amplitude) == -1.0f);   // the shadow along x does not hide it
-    CHECK(PolarizationPlane(medians(0.0, false), amplitude) == 0.0f);    // no modulation: no decision
+    CHECK(PolarizationPlane(medians(-1.0, false), amplitude).plane == 1.0f);   // dim along x: horizontal
+    CHECK(PolarizationPlane(medians(+1.0, false), amplitude).plane == -1.0f);  // dim along y: vertical
+    CHECK(PolarizationPlane(medians(+1.0, true), amplitude).plane == -1.0f);   // the shadow along x does not hide it
+    CHECK(PolarizationPlane(medians(0.0, false), amplitude).plane == 0.0f);    // no modulation: no decision
+    // Three times what a fully polarized source would give these bands: not the source's.
+    std::vector<float> third(amplitude);
+    for (auto &a : third)
+        a /= 3.0f;
+    CHECK(PolarizationPlane(medians(+1.0, false), third).modulation == Catch::Approx(3.0).margin(0.03));
+    CHECK(PolarizationPlane(medians(+1.0, false), third).plane == 0.0f);
+    CHECK(PolarizationPlane(medians(-1.0, false), third).plane == 0.0f);
+    // A fully polarized source's modulation, followed exactly: correlation and scale both 1.
+    const auto vertical = PolarizationPlane(medians(+1.0, false), amplitude);
+    CHECK(vertical.correlation == Catch::Approx(1.0).margin(1e-3));
+    CHECK(vertical.modulation == Catch::Approx(1.0).margin(1e-2));
+    const auto horizontal = PolarizationPlane(medians(-1.0, false), amplitude);
+    CHECK(horizontal.correlation == Catch::Approx(-1.0).margin(1e-3));
+    CHECK(horizontal.modulation == Catch::Approx(-1.0).margin(1e-2));
 }
 
 // The other side of that correction: a polarization factor that is not the beam's. Here the
diff --git a/tests/test_data/ligands/1ehz_psu.pdb.gz b/tests/test_data/ligands/1ehz_psu.pdb.gz
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diff --git a/tests/test_data/ligands/2w3v_ndp.pdb.gz b/tests/test_data/ligands/2w3v_ndp.pdb.gz
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index 000000000..5b4aa2a3c
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diff --git a/tests/test_data/ligands/3tk0_fad.pdb.gz b/tests/test_data/ligands/3tk0_fad.pdb.gz
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diff --git a/tests/test_data/ligands/5epe_sah.pdb.gz b/tests/test_data/ligands/5epe_sah.pdb.gz
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index 000000000..f6f99fa94
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diff --git a/tests/test_data/ligands/5vml_nap.pdb.gz b/tests/test_data/ligands/5vml_nap.pdb.gz
new file mode 100644
index 000000000..0eafacceb
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diff --git a/tests/test_data/ligands/6f3p_nad.pdb.gz b/tests/test_data/ligands/6f3p_nad.pdb.gz
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index 000000000..a910bb1ff
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diff --git a/tests/test_data/ligands/6k9i_hec.pdb.gz b/tests/test_data/ligands/6k9i_hec.pdb.gz
new file mode 100644
index 000000000..8ce3b8364
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diff --git a/tests/test_data/ligands/6w4h_sam.pdb.gz b/tests/test_data/ligands/6w4h_sam.pdb.gz
new file mode 100644
index 000000000..67c476fb0
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diff --git a/tests/test_data/ligands/7tcd_fmn.pdb.gz b/tests/test_data/ligands/7tcd_fmn.pdb.gz
new file mode 100644
index 000000000..58da6ca00
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diff --git a/tests/test_data/ligands/8bkh_hem.pdb.gz b/tests/test_data/ligands/8bkh_hem.pdb.gz
new file mode 100644
index 000000000..4057dd29c
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diff --git a/tests/test_data/ligands/8con_nai.pdb.gz b/tests/test_data/ligands/8con_nai.pdb.gz
new file mode 100644
index 000000000..db2a34f00
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diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index b6754ec31..12c0e427f 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -12,6 +12,15 @@ TARGET_LINK_LIBRARIES(jfjoch_extract_hkl JFJochReader)
 
 # rugnux, the single offline analysis CLI, lives in rugnux/ next to its library.
 
+# Developer utility, not installed: refines a model against a finished run's merged MTZ (Refinement.h), for
+# measuring the refinement on battery outputs without processing anything again.
+ADD_EXECUTABLE(rugnux_refine_test rugnux_refine_test.cpp)
+TARGET_LINK_LIBRARIES(rugnux_refine_test JFJochStructureRefinement JFJochCommon gemmi)
+# Same device-link step as rugnux (see rugnux/CMakeLists.txt): a portable CUDA build links cuFFT statically.
+IF (JFJOCH_PORTABLE_ONLY AND JFJOCH_CUDA_AVAILABLE AND TARGET CUDA::cufft_static)
+    SET_TARGET_PROPERTIES(rugnux_refine_test PROPERTIES CUDA_RESOLVE_DEVICE_SYMBOLS ON)
+ENDIF()
+
 # In-place re-compress /entry/data/data of a _data file from bitshuffle/LZ4 to bitshuffle/zstd.
 ADD_EXECUTABLE(jfjoch_recompress jfjoch_recompress.cpp)
 TARGET_LINK_LIBRARIES(jfjoch_recompress JFJochHDF5Wrappers)
diff --git a/tools/battery/README.md b/tools/battery/README.md
index ed6fcf18b..131a3945b 100644
--- a/tools/battery/README.md
+++ b/tools/battery/README.md
@@ -730,6 +730,7 @@ was run `--unforced`), so its forced XDS-arm rows are left out the same way.
 | `lowres_d`, `lowres_r_meas`, `refres_lowres_d`, `refres_lowres_r_meas`, `lowres_d_ref`, `lowres_r_meas_ref`, `lowres_r_meas_ratio` | the lowest-resolution shell's high-resolution limit and R_meas: rugnux's own table, the reference-range table, XDS's; and refres_lowres_r_meas / lowres_r_meas_ref |
 | `model`, `model_note` | open arm, and in-house sets with a `model`: the coordinates given to `--model`, or why there were none |
 | `rfree`, `rwork`, `cc_model`, `model_fit`, `rfree_deposited`, `rfree_ratio` | any row with a model: R_FREE, R_WORK, CC_MODEL_OVERALL and MODEL_FIT as rugnux reports them (placement-only, own free set: trend fields), the published R-free, and rfree / rfree_deposited |
+| `rfree_refined`, `rwork_refined`, `refine_s` | any row whose model was placed: REFINE_R_FREE, REFINE_R_WORK and REFINE_SECONDS - the placed model refined, which rugnux always does where it places a model. Reported, never scored; `rfree` and every other field stay the unrefined placement's. `refine_s` is included in `rugnux_wall_s`, so a baseline from before refinement was always on reads seconds slower per placed set on a GPU (minutes on the CPU) |
 | `anom_sigma` | any row with a model: ANOMALOUS_SCATTERER_MEAN_SIGMA, the anomalous difference map (F+ - F- on the model's phases) read at every model atom from phosphorus up (S of Met/Cys, metals, Cl, I, ...) and averaged, in map sigma - how much anomalous signal the merge carries; null where the merge kept no Bijvoet split or the model has no such atom |
 | `rmodel`, `rmodel_shell_scaled`, `radial_misfit` | any row with a model: R_MODEL, R_MODEL_SHELL_SCALED and MODEL_RADIAL_MISFIT - R over all the reflections, with and without one free scale per resolution shell, and how big that rescale was. `rmodel_shell_scaled` is the R that compares between runs (below) |
 | `refmac_rfree`, `refmac_rwork`, `refmac_rfree_depflags`, `refmac_rfree_depdata`, `refmac_rfree_ratio`, `refmac_twin`, `refmac_untwinned`, `refmac_status`, `refmac_reason` | the REFMAC check (`--model-check`, open arm; see its section for which R-free is which) |
diff --git a/tools/battery/refine_parity.py b/tools/battery/refine_parity.py
new file mode 100644
index 000000000..a00786b10
--- /dev/null
+++ b/tools/battery/refine_parity.py
@@ -0,0 +1,179 @@
+#!/usr/bin/env python3
+"""refine_parity.py -- rugnux's refinement score against REFMAC's, term by term, on identical inputs.
+
+For one model and one merged MTZ (F, SIGF, FreeR_flag) it scores the model as given, refining nothing, twice:
+
+  * REFMAC 5.8, restrained setup at 0 cycles (`ncyc 0`, `refi bref iso`, riding hydrogens restored as REFMAC
+    does by default), read from its log: R-work / R-free overall and in its 20 resolution bins, the overall
+    scale and B, the anisotropic B, the bulk solvent's k_sol / B_sol, the FOM, -LL / -LLfree and the geometry
+    (rmsd and rmsZ of bonds and angles);
+  * rugnux --mode refine --refine-score-only on the same files, read from its report (REFINE_SCORE_* keys).
+
+The two are printed side by side with their differences, and one JSON line goes to stdout for scripts.
+REFMAC's anisotropic B is printed in the convention exp(-sum B_ij h_i h_j a*_i a*_j), rugnux's in
+exp(-s^T B s / 4); the REFMAC numbers are multiplied by 4 here so that the two columns compare.
+
+Per reflection, REFMAC's model amplitude on the input's scale is recovered from its output MTZ: the output F
+is the input F times REFMAC's overall scale, so FC_ALL_LS * F_in / F_out is the model amplitude R is computed
+with. With --per-reflection the R of each data subset (resolution bins) is recomputed from both programs'
+model amplitudes on the same reflections, rugnux's being FC of its _refined_maps.mtz.
+
+  refine_parity.py --rugnux build/rugnux/rugnux --workdir DIR [--d-min D] [--refmac-extra 'make hydr no'] [--gpu] model data.mtz
+"""
+import argparse
+import json
+import os
+import re
+import subprocess
+
+import gemmi
+import numpy as np
+
+CCP4_SETUP = os.environ.get("CCP4_SETUP", "/opt/xtal/ccp4-9/bin/ccp4.setup-sh")
+
+
+def ccp4_env():
+    out = subprocess.run(["bash", "-c", f"source {CCP4_SETUP} >/dev/null 2>&1; env -0"], capture_output=True).stdout
+    return dict(kv.split("=", 1) for kv in out.decode().split("\0") if "=" in kv)
+
+
+def run_refmac(workdir, model, mtz, d_min, extra):
+    keywords = "labin FP=F SIGFP=SIGF FREE=FreeR_flag\nncyc 0\nweight auto\nrefi bref iso\n" \
+               "make newligand continue\nmake check none\n"
+    if d_min:
+        keywords += f"reso 999 {d_min:.3f}\n"
+    keywords += "".join(line + "\n" for line in extra) + "end\n"
+    log = os.path.join(workdir, "refmac.log")
+    with open(log, "w") as fh:
+        subprocess.run(["nice", "refmac5", "hklin", mtz, "xyzin", model,
+                        "hklout", os.path.join(workdir, "refmac.mtz"), "xyzout", os.path.join(workdir, "refmac.pdb")],
+                       input=keywords.encode(), stdout=fh, stderr=subprocess.STDOUT, cwd=workdir, env=ccp4_env())
+    return parse_refmac(open(log, errors="replace").read())
+
+
+def parse_refmac(text):
+    num = lambda pat: float(re.search(pat, text, re.M).group(1))
+    out = {"r_work": num(r"^Overall R factor\s+=\s+([\d.]+)"), "r_free": num(r"^Free R factor\s+=\s+([\d.]+)")}
+    m = re.search(r"Overall\s+: scale =\s+([-\d.]+), B\s+=\s+([-\d.]+)", text)
+    out["k_overall"], out["b_iso"] = float(m.group(1)), float(m.group(2))
+    m = re.search(r"Partial structure\s+1: scale =\s+([-\d.]+), B\s+=\s+([-\d.]+)", text)
+    if m:
+        out["k_sol"], out["b_sol"] = float(m.group(1)), float(m.group(2))
+    m = re.search(r"B11 =\s*([-\d.]+) B22 =\s*([-\d.]+) B33 =\s*([-\d.]+) B12 =\s*([-\d.]+) B13 =\s*([-\d.]+) "
+                  r"B23 =\s*([-\d.]+)", text)
+    out["b_aniso"] = [4 * float(m.group(i)) for i in range(1, 7)]
+    m = re.search(r"^\s+0\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)"
+                  r"\s+([\d.]+)", text, re.M)
+    if m:
+        (out["fom"], out["nll_work"], out["nll_free"], out["rmsd_bonds"], out["rmsz_bonds"], out["rmsd_angles"],
+         out["rmsz_angles"]) = [float(m.group(i)) for i in range(3, 10)]
+    table = text.split("M(4SSQ/LL) NR_used")[1].split("$$")[2]
+    out["shells"] = []
+    for line in table.strip().splitlines():
+        v = line.split()
+        out["shells"].append({"inv_d2": float(v[0]), "n_work": int(v[1]), "r_work": float(v[5]),
+                              "n_free": int(v[7]), "r_free": float(v[10])})
+    return out
+
+
+def run_rugnux(rugnux, workdir, model, mtz, d_min, gpu=False):
+    prefix = os.path.join(workdir, "rugnux")
+    cmd = ["nice", rugnux, "--mode", "refine", "--refine-score-only", "--developer", "-N", "8", "-o", prefix,
+           "--model", model] + ([] if gpu else ["--no-gpu"])
+    if d_min:
+        cmd += ["--refine-d-min", f"{d_min:.3f}"]
+    subprocess.run(cmd + [mtz], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+    text = open(prefix + "_report.txt").read()
+    key = lambda k: re.search(rf"^{k}=\s*(.+)$", text, re.M).group(1).strip()
+    out = {k: float(key("REFINE_SCORE_" + k.upper())) for k in
+           ("r_work", "r_free", "k_overall", "b_iso", "k_sol", "b_sol", "nll_work", "nll_free", "fom",
+            "rmsd_bonds", "rmsz_bonds", "rmsd_angles", "rmsz_angles")}
+    out["b_aniso"] = [float(x) for x in key("REFINE_SCORE_B_ANISO").split()]
+    out["mask_spacing"] = float(key("REFINE_SCORE_MASK_SPACING"))
+    # REFMAC's bond rmsd counts the metal links among its bonds; rugnux reports them apart
+    out["rmsd_bonds"] = float(key("REFINE_SCORE_RMSD_BONDS_ALL"))
+    return out
+
+
+def per_reflection(workdir, data_mtz):
+    """R per resolution bin of both programs' model amplitudes on the reflections both score."""
+    din = gemmi.read_mtz_file(data_mtz)
+    ref = gemmi.read_mtz_file(os.path.join(workdir, "refmac.mtz"))
+    rug = gemmi.read_mtz_file(os.path.join(workdir, "rugnux_refined_maps.mtz"))
+
+    asu, gops = gemmi.ReciprocalAsu(din.spacegroup), din.spacegroup.operations()
+
+    def table(mtz, labels):
+        a = np.array(mtz, copy=False)
+        cols = {c.label: i for i, c in enumerate(mtz.columns)}
+        out = {}
+        for row in a:
+            h = tuple(asu.to_asu([int(x) for x in row[:3]], gops)[0])
+            out[(h[0] + 512) * 1048576 + (h[1] + 512) * 1024 + h[2] + 512] = row[[cols[l] for l in labels]]
+        return out
+    t_in = table(din, ["F", "FreeR_flag"])
+    t_ref = table(ref, ["F", "FC_ALL_LS"])
+    t_rug = table(rug, ["FC"])
+    rows = []
+    for k, (fo_ref, fc_ref) in t_ref.items():
+        if k in t_in and k in t_rug and fo_ref > 0 and np.isfinite(fc_ref):
+            fo, flag = t_in[k]
+            rows.append((k, fo, flag == 0, fc_ref * fo / fo_ref, t_rug[k][0], 0.0))
+    rows = np.array(rows)
+    if len(rows):
+        h = rows[:, 0].astype(np.int64)
+        hkl = np.stack([h // 1048576 - 512, (h // 1024) % 1024 - 512, h % 1024 - 512], axis=1)
+        rows[:, 5] = [1 / din.cell.calculate_d(list(map(int, x))) ** 2 for x in hkl]
+    return rows
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument("model")
+    ap.add_argument("data")
+    ap.add_argument("--rugnux", required=True)
+    ap.add_argument("--workdir", required=True)
+    ap.add_argument("--d-min", type=float, default=None)
+    ap.add_argument("--refmac-extra", action="append", default=[])
+    ap.add_argument("--no-refmac", action="store_true", help="reuse refmac.log in the workdir")
+    ap.add_argument("--gpu", action="store_true", help="rugnux on the GPU (the default is its CPU engine)")
+    args = ap.parse_args()
+    os.makedirs(args.workdir, exist_ok=True)
+    model, data = os.path.abspath(args.model), os.path.abspath(args.data)
+    if args.no_refmac:
+        ref = parse_refmac(open(os.path.join(args.workdir, "refmac.log"), errors="replace").read())
+    else:
+        ref = run_refmac(args.workdir, model, data, args.d_min, args.refmac_extra)
+    rug = run_rugnux(args.rugnux, args.workdir, model, data, args.d_min, args.gpu)
+    print(f"{'term':<14} {'REFMAC':>10} {'rugnux':>10} {'diff':>10}")
+    for k in ("r_work", "r_free", "k_overall", "b_iso", "k_sol", "b_sol", "fom", "nll_work", "nll_free",
+              "rmsd_bonds", "rmsz_bonds", "rmsd_angles", "rmsz_angles"):
+        a, b = ref.get(k), rug.get(k)
+        if a is None or b is None:
+            continue
+        print(f"{k:<14} {a:10.4f} {b:10.4f} {b - a:+10.4f}")
+    print("b_aniso REFMAC(x4) " + " ".join(f"{x:7.2f}" for x in ref["b_aniso"]))
+    print("b_aniso rugnux     " + " ".join(f"{x:7.2f}" for x in rug["b_aniso"]))
+    rows = per_reflection(args.workdir, data)
+    if len(rows):
+        fo, free, fr, fg = rows[:, 1], rows[:, 2] > 0, rows[:, 3], rows[:, 4]
+        print(f"same reflections ({len(rows)}): R-work REFMAC {np.abs(fo - fr)[~free].sum() / fo[~free].sum():.4f} "
+              f"rugnux {np.abs(fo - fg)[~free].sum() / fo[~free].sum():.4f}; R-free REFMAC "
+              f"{np.abs(fo - fr)[free].sum() / fo[free].sum():.4f} rugnux {np.abs(fo - fg)[free].sum() / fo[free].sum():.4f}")
+        # by resolution, on the work set: R of each and the mean model amplitude of rugnux over REFMAC's
+        s2 = rows[:, 5]
+        edges = np.linspace(s2.min(), s2.max() + 1e-12, 11)
+        print(f"{'d_max':>7} {'d_min':>7} {'n':>6} {'R_REFMAC':>9} {'R_rugnux':>9} {'<Fr/Fref>':>10}")
+        for lo, hi in zip(edges[:-1], edges[1:]):
+            sel = (s2 >= lo) & (s2 < hi) & ~free
+            if sel.sum() == 0:
+                continue
+            print(f"{1 / np.sqrt(lo):7.2f} {1 / np.sqrt(hi):7.2f} {sel.sum():6d} "
+                  f"{np.abs(fo - fr)[sel].sum() / fo[sel].sum():9.4f} {np.abs(fo - fg)[sel].sum() / fo[sel].sum():9.4f} "
+                  f"{fg[sel].sum() / fr[sel].sum():10.4f}")
+    ref_short = {k: v for k, v in ref.items() if k != "shells"}
+    print("JSON " + json.dumps({"refmac": ref_short, "rugnux": rug, "refmac_shells": ref["shells"]}))
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tools/battery/report.py b/tools/battery/report.py
index b670ed609..31618a818 100644
--- a/tools/battery/report.py
+++ b/tools/battery/report.py
@@ -673,6 +673,8 @@ def build(run_dir, baseline=None, allow_incomplete=False):
              ("dep R_free", "rfree_deposited"),
              ("R_free ratio", "rfree_ratio"),
              ("anom. sigma", "anom_sigma")] if any(r.get("rfree") for r in res) else []
+    model += [("refined R_free", "rfree_refined"), ("refine s", "refine_s")] \
+        if any(r.get("rfree_refined") for r in res) else []
     model += [("REFMAC R_free", "refmac_rfree_depflags"), ("REFMAC dep data", "refmac_rfree_depdata"),
               ("REFMAC ratio", "refmac_rfree_ratio")] if any(r.get("refmac_status") for r in res) else []
     model += [("dCC dep. outer", "dep_cc_delta_outer")] if any(r.get("dep_status") for r in res) else []
@@ -691,7 +693,7 @@ def build(run_dir, baseline=None, allow_incomplete=False):
                      pct(r.get("r_meas")), pct(r.get("lowres_r_meas")), f(r.get("cc_half"), "{:.3f}"),
                      f(r.get("isa"), "{:.1f}"),
                      f(r.get("isa_ref"), "{:.1f}"), pct(r.get("indexing_rate"), 0)]
-                    + [f(r.get(k), "{:.3f}") for _, k in model]
+                    + [f(r.get(k), "{:.1f}" if k == "refine_s" else "{:.3f}") for _, k in model]
                     + ([r.get("model_fit") or "-"] if model else [])
                     + [f(r.get("wall_s"), "{:.0f}"), note])
     doc.table(head, rows, num=range(5, len(head) - 1),
diff --git a/tools/battery/score.py b/tools/battery/score.py
index 822fb24e2..0aeed74a9 100644
--- a/tools/battery/score.py
+++ b/tools/battery/score.py
@@ -256,6 +256,10 @@ def judge(entry, rep, run_note):
         # the R to read in a delta table. radial_misfit says how much there was to take out.
         "rmodel": fnum(rep.get("R_MODEL")), "rmodel_shell_scaled": fnum(rep.get("R_MODEL_SHELL_SCALED")),
         "radial_misfit": fnum(rep.get("MODEL_RADIAL_MISFIT")),
+        # the placed model refined (always, wherever a model is placed; its own REFINE_ keys - rfree
+        # above stays the unrefined placement's): reported, never scored; refine_s is part of rugnux_wall_s
+        "rfree_refined": fnum(rep.get("REFINE_R_FREE")), "rwork_refined": fnum(rep.get("REFINE_R_WORK")),
+        "refine_s": fnum(rep.get("REFINE_SECONDS")),
         "sg_label": None, "accepted_alt": None, "accepted_alt_why": None,
         # the groups rugnux could not tell from the one it wrote (and, with an undetermined screw,
         # the screw alternatives), as it lists them
diff --git a/tools/rugnux_refine_test.cpp b/tools/rugnux_refine_test.cpp
new file mode 100644
index 000000000..f45272611
--- /dev/null
+++ b/tools/rugnux_refine_test.cpp
@@ -0,0 +1,200 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+// Refinement (image_analysis/structure_refinement/Refinement.h) of a model against a rugnux merged MTZ, without
+// processing anything: for measuring the refinement on finished runs (a battery run's p.mtz and p_model.cif)
+// against another program on the same files. Prints the outcome, and one JSON line for scripts.
+
+#include <cmath>
+#include <cstdlib>
+#include <iostream>
+#include <sstream>
+
+#include <gemmi/mmread_gz.hpp>
+#include <gemmi/mtz.hpp>
+#include <gemmi/to_cif.hpp>
+#include <gemmi/to_mmcif.hpp>
+#include <fstream>
+#include <nlohmann/json.hpp>
+
+#include "../common/CUDAWrapper.h"
+#include "../common/Logger.h"
+#include "../image_analysis/structure_refinement/Refinement.h"
+
+namespace {
+
+void usage() {
+    std::cout << "Usage: rugnux_refine_test [options] <merged.mtz> <model.cif|.pdb>\n"
+                 "  -N <threads>        CPU threads (default 8)\n"
+                 "  --no-gpu            the CPU engine\n"
+                 "  --placement-only    rigid bodies and group B only\n"
+                 "  --score-only        score the model as given, refine nothing\n"
+                 "  --no-group-b        no B shift per residue in the placement stage\n"
+                 "  --no-hydrogens      no riding hydrogens\n"
+                 "  --ladder <a,b,...>  the first weight trials, times the gradient-balanced weight\n"
+                 "  --adp-ladder <a,..> each with the B factors' weight that weight times these (0: B held)\n"
+                 "  --steps <n>         the trajectory's steps at most\n"
+                 "  --final-ladder <a,..> the final trials, times the trajectory's weights\n"
+                 "  --max-weight <x>    the positions' weight at most, times the gradient-balanced weight\n"
+                 "  --cycles <n>        macro-cycles per weight trial (default as in RefinementSettings)\n"
+                 "  --xyz-iterations <n>, --b-iterations <n>  L-BFGS iterations per macro-cycle\n"
+                 "  -o <file.cif>       write the refined model\n"
+                 "  --dump <file>       with --score-only: h k l |Fcalc| phi |Fmask| phi k_total D var per reflection\n"
+                 "  --trials-at-once <n> at most n weight trials side by side (1: one after another)\n"
+                 "  -v                  debug lines (TIMING per refinement stage)\n";
+}
+
+std::vector<double> ParseList(const std::string &s) {
+    std::vector<double> out;
+    std::stringstream ss(s);
+    std::string item;
+    while (std::getline(ss, item, ','))
+        out.push_back(std::stod(item));
+    return out;
+}
+
+}  // namespace
+
+int main(int argc, char **argv) {
+    RefinementSettings settings;
+    settings.nthreads = 8;
+    std::string out_path, dump_path;
+    bool verbose = false;
+    std::vector<std::string> files;
+    for (int i = 1; i < argc; i++) {
+        const std::string a = argv[i];
+        if (a == "-N" && i + 1 < argc)
+            settings.nthreads = std::stoul(argv[++i]);
+        else if (a == "--no-gpu") {
+            settings.gpu = false;
+            hide_gpus();
+        } else if (a == "--no-group-b")
+            settings.group_b = false;
+        else if (a == "--no-hydrogens")
+            settings.riding_hydrogens = false;
+        else if (a == "--placement-only")
+            settings.restrained = false;
+        else if (a == "--score-only")
+            settings.score_only = true;
+        else if (a == "--cycles" && i + 1 < argc)
+            settings.macro_cycles = std::stoi(argv[++i]);
+        else if (a == "--xyz-iterations" && i + 1 < argc)
+            settings.xyz_iterations = std::stoi(argv[++i]);
+        else if (a == "--adp-ladder" && i + 1 < argc)
+            settings.adp_ladder = ParseList(argv[++i]);
+        else if (a == "--b-iterations" && i + 1 < argc)
+            settings.b_iterations = std::stoi(argv[++i]);
+        else if (a == "--ladder" && i + 1 < argc)
+            settings.weight_ladder = ParseList(argv[++i]);
+        else if (a == "--steps" && i + 1 < argc)
+            settings.max_steps = std::stoi(argv[++i]);
+        else if (a == "--final-ladder" && i + 1 < argc)
+            settings.final_ladder = ParseList(argv[++i]);
+        else if (a == "--max-weight" && i + 1 < argc)
+            settings.max_weight = std::stod(argv[++i]);
+        else if (a == "-v")
+            verbose = true;
+        else if (a == "--trials-at-once" && i + 1 < argc)
+            settings.max_trials_at_once = std::stoul(argv[++i]);
+        else if (a == "--dump" && i + 1 < argc)
+            dump_path = argv[++i];
+        else if (a == "-o" && i + 1 < argc)
+            out_path = argv[++i];
+        else if (!a.empty() && a[0] == '-') {
+            usage();
+            return EXIT_FAILURE;
+        } else
+            files.push_back(a);
+    }
+    if (files.size() != 2) {
+        usage();
+        return EXIT_FAILURE;
+    }
+
+    gemmi::Mtz mtz = gemmi::read_mtz_file(files[0]);
+    const gemmi::SpaceGroup *sg = mtz.spacegroup;
+    if (sg == nullptr) {
+        std::cerr << "No space group in " << files[0] << std::endl;
+        return EXIT_FAILURE;
+    }
+    const int ih = mtz.column_with_label("H")->idx, ik = mtz.column_with_label("K")->idx,
+              il = mtz.column_with_label("L")->idx, iF = mtz.column_with_label("F")->idx,
+              isF = mtz.column_with_label("SIGF")->idx, ifree = mtz.column_with_label("FreeR_flag")->idx;
+    const gemmi::Mtz::Column *fp = mtz.column_with_label("F(+)"), *fm = mtz.column_with_label("F(-)");
+    std::vector<MergedReflection> merged;
+    for (size_t r = 0; r < static_cast<size_t>(mtz.nreflections); r++) {
+        const float *row = &mtz.data[r * mtz.columns.size()];
+        MergedReflection m;
+        m.h = static_cast<int>(row[ih]);
+        m.k = static_cast<int>(row[ik]);
+        m.l = static_cast<int>(row[il]);
+        m.F = row[iF];
+        m.sigmaF = row[isF];
+        m.rfree_flag = row[ifree] == 0;
+        m.d = static_cast<float>(mtz.cell.calculate_d({{m.h, m.k, m.l}}));
+        if (fp != nullptr && fm != nullptr) {
+            m.F_plus = row[fp->idx];
+            m.F_minus = row[fm->idx];
+        }
+        merged.push_back(m);
+    }
+    gemmi::Structure st = gemmi::read_structure_gz(files[1]);
+
+    Logger logger("rugnux_refine_test");
+    logger.Verbose(verbose);
+    const RefinementResult r = RefineModel(st, merged, mtz.cell, *sg, 1.0, logger, settings);
+    if (!r.ok) {
+        std::cerr << "Refinement failed: " << r.failure_reason << std::endl;
+        return EXIT_FAILURE;
+    }
+    if (!out_path.empty())
+    {
+        std::ofstream f(out_path);
+        gemmi::cif::write_cif_to_stream(f, gemmi::make_mmcif_document(*r.model));
+    }
+
+    if (!dump_path.empty()) {
+        std::ofstream f(dump_path);
+        const RefinementScore &sc = r.score_start;
+        for (size_t m = 0; m < sc.hkl.size(); m++)
+            f << sc.hkl[m][0] << " " << sc.hkl[m][1] << " " << sc.hkl[m][2] << " " << std::abs(sc.fcalc[m]) << " "
+              << std::arg(sc.fcalc[m]) << " " << std::abs(sc.fmask[m]) << " " << std::arg(sc.fmask[m]) << " "
+              << sc.k_total[m] << " " << sc.d[m] << " " << sc.var[m] << "\n";
+    }
+    int kinds[5] = {0, 0, 0, 0, 0};
+    for (const DensityBlob &b : r.blobs)
+        kinds[static_cast<int>(b.kind)]++;
+    nlohmann::json blobs = nlohmann::json::array();
+    for (const DensityBlob &b : r.blobs)
+        blobs.push_back({{"kind", DensityBlobKindName(b.kind)}, {"x", b.centroid.x}, {"y", b.centroid.y},
+                         {"z", b.centroid.z}, {"peak", b.peak_sigma}, {"volume", b.volume}, {"score", b.score},
+                         {"nearest", b.nearest_atom}, {"distance", b.nearest_atom_distance},
+                         {"anomalous", b.anomalous_sigma}});
+    nlohmann::json j = {{"d_min", r.d_min}, {"gpu", r.on_gpu}, {"seconds", r.seconds},
+                        {"r_work_start", r.r_work_start}, {"r_free_start", r.r_free_start},
+                        {"r_work_placement", r.r_work_placement}, {"r_free_placement", r.r_free_placement},
+                        {"r_work", r.r_work}, {"r_free", r.r_free}, {"weight", r.weight}, {"adp_weight", r.adp_weight},
+                        {"rmsd_bonds", r.geometry.rmsd_bonds}, {"rmsd_angles", r.geometry.rmsd_angles},
+                        {"rmsd_bonds_start", r.geometry_start.rmsd_bonds},
+                        {"rmsd_angles_start", r.geometry_start.rmsd_angles}, {"clashes", r.geometry.clashes},
+                        {"atoms", r.atoms}, {"refined_atoms", r.refined_atoms}, {"fixed_residues", r.fixed_residues},
+                        {"blobs", blobs}};
+    nlohmann::json trials = nlohmann::json::array();
+    for (const RefinementWeightTrial &t : r.trials)
+        trials.push_back({{"weight", t.weight}, {"adp_weight", t.adp_weight}, {"r_work", t.r_work}, {"r_free", t.r_free},
+                          {"rmsd_bonds", t.geometry.rmsd_bonds}, {"rmsd_angles", t.geometry.rmsd_angles}});
+    j["trials"] = trials;
+    const RefinementScore &sc = r.score_start;
+    nlohmann::json shells = nlohmann::json::array();
+    for (const RefinementShell &sh : sc.shells)
+        shells.push_back({{"d_max", sh.d_max}, {"d_min", sh.d_min}, {"n_work", sh.n_work}, {"n_free", sh.n_free},
+                          {"r_work", sh.r_work}, {"r_free", sh.r_free}});
+    j["score_start"] = {{"k_overall", sc.k_overall}, {"b_iso", sc.b_iso}, {"b_aniso", sc.b_aniso}, {"k_sol", sc.k_sol},
+                        {"b_sol", sc.b_sol}, {"mask_spacing", sc.mask_spacing}, {"r_work", sc.r_work},
+                        {"r_free", sc.r_free}, {"n_work", sc.n_work}, {"n_free", sc.n_free}, {"nll_work", sc.nll_work},
+                        {"nll_free", sc.nll_free}, {"hydrogens", sc.hydrogens}, {"fom", sc.fom}, {"mean_fom", r.mean_fom},
+                        {"rmsz_bonds", r.geometry_start.rmsz_bonds}, {"rmsz_angles", r.geometry_start.rmsz_angles},
+                        {"shells", shells}};
+    std::cout << "JSON " << j.dump() << std::endl;
+    return EXIT_SUCCESS;
+}
diff --git a/viewer/JFJochProcessController.cpp b/viewer/JFJochProcessController.cpp
index d9fd334fd..13e49cdd3 100644
--- a/viewer/JFJochProcessController.cpp
+++ b/viewer/JFJochProcessController.cpp
@@ -137,6 +137,7 @@ void JFJochProcessController::run_(QString file_path, DiffractionExperiment expe
         active_ = nullptr;
         running_ = false;
         emit finished(result, report, checks);
+        Rugnux::ReleasePinnedPool();
     } catch (const std::exception &e) {
         active_ = nullptr;
         running_ = false;
diff --git a/viewer/windows/JFJochProcessingJobsWindow.cpp b/viewer/windows/JFJochProcessingJobsWindow.cpp
index 89689825d..369710075 100644
--- a/viewer/windows/JFJochProcessingJobsWindow.cpp
+++ b/viewer/windows/JFJochProcessingJobsWindow.cpp
@@ -427,6 +427,7 @@ void JFJochProcessingJobsWindow::newJob(ProcessMode mode, CalibrationSelection c
     if (spec.mode == ProcessMode::FullAnalysis && !inputs.model_path.isEmpty()) {
         try {
             config.model = std::make_shared<const RugnuxModel>(ReadRugnuxModelFile(inputs.model_path.toStdString()));
+            config.refine = true;   // as `rugnux` refines a placed model by default
         } catch (const std::exception &e) {
             QMessageBox::warning(this, "Processing", QString("Cannot read the model: %1").arg(e.what()));
             return;
diff --git a/writer/CMakeLists.txt b/writer/CMakeLists.txt
index 003a5eaab..7566823e3 100644
--- a/writer/CMakeLists.txt
+++ b/writer/CMakeLists.txt
@@ -38,10 +38,11 @@ TARGET_LINK_LIBRARIES(JFJochModelWriter JFJochLogger gemmi)
 
 # rugnux's merged MTZ, map-coefficient MTZ and placed model, to and from the structured END-message
 # blocks, so that jfjoch_writer writes them with gemmi alone and no analysis library; and the atomic model
-# a run is given, parsed for it.
+# a run is given and the merged reflections --mode refine is given, parsed for it.
 ADD_LIBRARY(JFJochRugnuxFiles STATIC WriteRugnuxFiles.cpp WriteRugnuxFiles.h
         RugnuxResultBlocks.cpp RugnuxResultBlocks.h
-        RugnuxModelFile.cpp RugnuxModelFile.h)
+        RugnuxModelFile.cpp RugnuxModelFile.h
+        RugnuxReflectionFile.cpp RugnuxReflectionFile.h)
 TARGET_LINK_LIBRARIES(JFJochRugnuxFiles JFJochModelWriter JFJochLogger gemmi ZLIB::ZLIB)
 
 TARGET_LINK_LIBRARIES(JFJochWriter JFJochPreview JFJochLogger JFJochHDF5Wrappers CBORStream2FrameSerialize
diff --git a/writer/HDF5NXmx.cpp b/writer/HDF5NXmx.cpp
index 205652468..8836e4f96 100644
--- a/writer/HDF5NXmx.cpp
+++ b/writer/HDF5NXmx.cpp
@@ -825,6 +825,8 @@ void NXmx::Sample(const StartMessage &start, const EndMessage &end) {
     
     if (unit_cell)
         SaveUnitCell(group, "unit_cell", unit_cell.value());
+    if (end.unit_cell_esd)
+        SaveUnitCell(group, "unit_cell_esd", end.unit_cell_esd.value());
 
     if (input_unit_cell)
         SaveUnitCell(group, "input_unit_cell", input_unit_cell.value());
@@ -1194,6 +1196,19 @@ void NXmx::Finalize(const EndMessage &end) {
             SaveVector(*hdf5_file, "/entry/MX/reindexMatrix",
                        std::vector<int32_t>(end.reindex_matrix->begin(), end.reindex_matrix->end()));
 
+        // Stills: the run's rocking curve, so that --mode scale merges with the curve the frames were
+        // predicted through instead of measuring another on them.
+        if (end.stills_run_width) {
+            const auto &w = *end.stills_run_width;
+            SaveVector(*hdf5_file, "/entry/MX/stillsRockingWidthFormula",
+                       std::vector<double>{w.gamma0, w.gamma_e, w.bandwidth_sigma});
+            SaveScalar(*hdf5_file, "/entry/MX/stillsRadialScale", w.radial_scale);
+            if (!w.table_s.empty()) {
+                SaveVector(*hdf5_file, "/entry/MX/stillsRockingWidthTableDstar", w.table_dstar)->Units("Angstrom^-1");
+                SaveVector(*hdf5_file, "/entry/MX/stillsRockingWidthTable", w.table_s)->Units("Angstrom^-1");
+            }
+        }
+
         if (end.indexing_rate) {
             SaveScalar(*hdf5_file, "/entry/MX/imageIndexedMean", end.indexing_rate.value());
         }
diff --git a/writer/RugnuxModelFile.cpp b/writer/RugnuxModelFile.cpp
index 287872ff4..e43ef1b45 100644
--- a/writer/RugnuxModelFile.cpp
+++ b/writer/RugnuxModelFile.cpp
@@ -53,10 +53,14 @@ std::string ReadFile(const std::string &path) {
 
 }  // namespace
 
+std::string GunzipIfCompressed(const std::string &bytes) {
+    return bytes.size() >= 2 && bytes[0] == '\x1f' && bytes[1] == '\x8b' ? Gunzip(bytes) : bytes;
+}
+
 RugnuxModel ParseRugnuxModel(const std::string &bytes, const std::string &name, const std::string &pae_json) {
     RugnuxModel m;
     m.name = name;
-    std::string text = bytes.size() >= 2 && bytes[0] == '\x1f' && bytes[1] == '\x8b' ? Gunzip(bytes) : bytes;
+    std::string text = GunzipIfCompressed(bytes);
     gemmi::cif::Document doc;
     m.structure = gemmi::read_structure_from_memory(text.data(), text.size(), name, gemmi::CoorFormat::Detect, &doc);
     if (gemmi::count_atom_sites(m.structure) == 0)
diff --git a/writer/RugnuxModelFile.h b/writer/RugnuxModelFile.h
index 5f242e6b1..57f9c304a 100644
--- a/writer/RugnuxModelFile.h
+++ b/writer/RugnuxModelFile.h
@@ -14,6 +14,9 @@
 // atomic model.
 RugnuxModel ParseRugnuxModel(const std::string &bytes, const std::string &name, const std::string &pae_json = {});
 
+// `bytes` inflated where they are a gzip stream (by the magic number), as they are otherwise.
+std::string GunzipIfCompressed(const std::string &bytes);
+
 // The model file at `path`, with the predicted aligned error the AlphaFold DB puts beside it where it is there
 // (PaePathFor). Named by `path`.
 RugnuxModel ReadRugnuxModelFile(const std::string &path);
diff --git a/writer/RugnuxReflectionFile.cpp b/writer/RugnuxReflectionFile.cpp
new file mode 100644
index 000000000..5fd297502
--- /dev/null
+++ b/writer/RugnuxReflectionFile.cpp
@@ -0,0 +1,247 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "RugnuxReflectionFile.h"
+
+#include <algorithm>
+#include <cctype>
+#include <cmath>
+#include <cstring>
+#include <fstream>
+#include <iterator>
+#include <stdexcept>
+
+#include <gemmi/cif2mtz.hpp>
+#include <gemmi/read_cif.hpp>
+#include <gemmi/refln.hpp>
+
+#include "RugnuxModelFile.h"   // GunzipIfCompressed
+
+namespace {
+
+std::string Lower(std::string s) {
+    std::transform(s.begin(), s.end(), s.begin(), [](unsigned char c) { return std::tolower(c); });
+    return s;
+}
+
+// The sigma of column `c`: the type-Q column named SIG<label>, else the type-Q column right after it.
+const gemmi::Mtz::Column *SigmaOf(const gemmi::Mtz &mtz, const gemmi::Mtz::Column &c, char type) {
+    if (const gemmi::Mtz::Column *s = mtz.column_with_label("SIG" + c.label, nullptr, type))
+        return s;
+    if (c.idx + 1 < mtz.columns.size() && mtz.columns[c.idx + 1].type == type)
+        return &mtz.columns[c.idx + 1];
+    return nullptr;
+}
+
+// Labels of amplitudes that are not observations: calculated structure factors and map coefficients.
+bool CalculatedAmplitude(const std::string &label) {
+    const std::string l = Lower(label);
+    for (const char *p : {"fc", "fwt", "delfwt", "2fofc", "fofc", "f-model", "fmodel", "fcalc", "fpart", "fmask",
+                          "fom", "fdiff", "fano", "dano", "fem"})
+        if (l.starts_with(p))
+            return true;
+    return false;
+}
+
+// A value column of `type` with its sigma: the names in `preferred` first, then any (that `accept` takes).
+template <typename Accept>
+std::pair<const gemmi::Mtz::Column *, const gemmi::Mtz::Column *>
+FindPair(const gemmi::Mtz &mtz, char type, std::initializer_list<const char *> preferred, Accept accept) {
+    for (const char *label : preferred)
+        if (const gemmi::Mtz::Column *c = mtz.column_with_label(label, nullptr, type))
+            if (const gemmi::Mtz::Column *s = SigmaOf(mtz, *c, 'Q'))
+                return {c, s};
+    for (const gemmi::Mtz::Column &c : mtz.columns)
+        if (c.type == type && accept(c.label))
+            if (const gemmi::Mtz::Column *s = SigmaOf(mtz, c, 'Q'))
+                return {&c, s};
+    return {nullptr, nullptr};
+}
+
+// The free-set flag column: FreeR_flag and the other usual names first, then any type-I column with "free" in its name.
+const gemmi::Mtz::Column *FindFree(const gemmi::Mtz &mtz) {
+    for (const char *label : {"FreeR_flag", "FREE", "FREER", "RFREE", "R-free-flags", "FreeRflag", "FREE_FLAG"})
+        if (const gemmi::Mtz::Column *c = mtz.column_with_label(label, nullptr, 'I'))
+            return c;
+    for (const gemmi::Mtz::Column &c : mtz.columns)
+        if (c.type == 'I' && Lower(c.label).find("free") != std::string::npos)
+            return &c;
+    return nullptr;
+}
+
+// The anomalous pair of `value_type` (G or K) with sigmas of `sigma_type` (L or M), named X(+) and X(-).
+bool FindAnomalous(const gemmi::Mtz &mtz, char value_type, char sigma_type, const gemmi::Mtz::Column *out[4]) {
+    for (const gemmi::Mtz::Column &c : mtz.columns) {
+        if (c.type != value_type || !c.label.ends_with("(+)"))
+            continue;
+        const std::string base = c.label.substr(0, c.label.size() - 3);
+        const gemmi::Mtz::Column *m = mtz.column_with_label(base + "(-)", nullptr, value_type);
+        const gemmi::Mtz::Column *sp = SigmaOf(mtz, c, sigma_type);
+        const gemmi::Mtz::Column *sm = m != nullptr ? SigmaOf(mtz, *m, sigma_type) : nullptr;
+        if (m != nullptr && sp != nullptr && sm != nullptr) {
+            out[0] = &c;
+            out[1] = sp;
+            out[2] = m;
+            out[3] = sm;
+            return true;
+        }
+    }
+    return false;
+}
+
+// gemmi's SF-mmCIF -> MTZ conversion with _refln.status preferred to _refln.pdbx_r_free_flag for the free set
+// where status marks any reflection free ('f'), as LoadFCalcFromMtz.cpp reads a deposition.
+std::vector<std::string> SfCifSpec(const gemmi::cif::Loop &loop) {
+    bool status_has_free = false;
+    const int status = loop.find_tag("_refln.status");
+    if (status >= 0)
+        for (size_t i = status; i < loop.values.size(); i += loop.width())
+            if (gemmi::cif::as_string(loop.values[i]) == "f") {
+                status_has_free = true;
+                break;
+            }
+    std::vector<std::string> spec;
+    for (const char **line = gemmi::CifToMtz::default_spec(true); *line != nullptr; ++line) {
+        const std::string l = *line;
+        if ((status_has_free && l.starts_with("pdbx_r_free_flag ")) || (!status_has_free && l.starts_with("status ")))
+            continue;
+        spec.push_back(l);
+    }
+    return spec;
+}
+
+}  // namespace
+
+RugnuxReflections RugnuxReflectionsFromMtz(const gemmi::Mtz &mtz, const std::string &name) {
+    RugnuxReflections out;
+    out.name = name;
+    out.cell = mtz.get_cell();
+    if (mtz.spacegroup == nullptr)
+        throw std::runtime_error(name + " names no space group");
+    out.space_group = mtz.spacegroup->xhm();
+    for (const gemmi::Mtz::Dataset &ds : mtz.datasets)
+        if (ds.wavelength > 0)
+            out.wavelength_A = ds.wavelength;
+
+    auto [value, sigma] = FindPair(mtz, 'F', {"F", "FP", "FOBS", "F-obs", "FMEAN", "F_meas", "Fobs"},
+                                   [](const std::string &l) { return !CalculatedAmplitude(l); });
+    if (value == nullptr) {
+        std::tie(value, sigma) = FindPair(mtz, 'J', {"IMEAN", "I", "IOBS", "I-obs", "Iobs", "I_meas"},
+                                          [](const std::string &) { return true; });
+        out.amplitudes = false;
+    }
+    const gemmi::Mtz::Column *anom[4] = {nullptr, nullptr, nullptr, nullptr};
+    if (value == nullptr) {
+        out.amplitudes = FindAnomalous(mtz, 'G', 'L', anom);
+        if (!out.amplitudes && !FindAnomalous(mtz, 'K', 'M', anom))
+            throw std::runtime_error(name + " holds no amplitudes or intensities with their sigmas");
+        out.value_column = anom[0]->label + "," + anom[2]->label;
+        out.sigma_column = anom[1]->label + "," + anom[3]->label;
+    } else {
+        out.value_column = value->label;
+        out.sigma_column = sigma->label;
+    }
+
+    const gemmi::Mtz::Column *free = FindFree(mtz);
+    std::vector<int> raw_free;
+    const size_t stride = mtz.columns.size();
+    for (size_t r = 0; r < static_cast<size_t>(mtz.nreflections); r++) {
+        const float *row = &mtz.data[r * stride];
+        float v = NAN, s = NAN;
+        if (value != nullptr) {
+            v = row[value->idx];
+            s = row[sigma->idx];
+        } else {
+            // the mean of the two hands where both were measured, the one measured otherwise
+            const float vp = row[anom[0]->idx], sp = row[anom[1]->idx], vm = row[anom[2]->idx], sm = row[anom[3]->idx];
+            if (std::isfinite(vp) && std::isfinite(vm)) {
+                v = 0.5f * (vp + vm);
+                s = 0.5f * std::sqrt(sp * sp + sm * sm);
+            } else if (std::isfinite(vp)) {
+                v = vp;
+                s = sp;
+            } else {
+                v = vm;
+                s = sm;
+            }
+        }
+        if (!std::isfinite(v))
+            continue;
+        MergedReflection m;
+        m.h = static_cast<int32_t>(row[0]);
+        m.k = static_cast<int32_t>(row[1]);
+        m.l = static_cast<int32_t>(row[2]);
+        m.d = static_cast<float>(out.cell.calculate_d({{m.h, m.k, m.l}}));
+        if (out.amplitudes) {
+            m.F = v;
+            m.sigmaF = s;
+        } else {
+            m.I = v;
+            m.sigma = s;
+        }
+        out.reflections.push_back(m);
+        if (free != nullptr) {
+            const float f = row[free->idx];
+            raw_free.push_back(std::isfinite(f) ? static_cast<int>(std::lround(f)) : -1);
+        }
+    }
+    if (out.reflections.empty())
+        throw std::runtime_error(name + " holds no reflection with a value in " + out.value_column);
+
+    if (free != nullptr) {
+        size_t zeros = 0, flagged = 0;
+        for (int f : raw_free) {
+            zeros += f == 0;
+            flagged += f >= 0;
+        }
+        const bool free_is_zero = zeros * 2 <= flagged;
+        for (size_t i = 0; i < out.reflections.size(); i++) {
+            const bool is_free = raw_free[i] >= 0 && (raw_free[i] == 0) == free_is_zero;
+            out.reflections[i].rfree_flag = is_free;
+            out.n_free += is_free;
+        }
+        // a column that marks nothing free is no free set
+        if (out.n_free > 0)
+            out.free_column = free->label;
+    }
+    return out;
+}
+
+RugnuxReflections ParseRugnuxReflections(const std::string &bytes, const std::string &name) {
+    const std::string text = GunzipIfCompressed(bytes);
+    if (text.size() >= 4 && std::memcmp(text.data(), "MTZ ", 4) == 0) {
+        gemmi::Mtz mtz;
+        gemmi::MemoryStream stream(text.data(), text.size());
+        mtz.read_stream(stream, true);
+        RugnuxReflections out = RugnuxReflectionsFromMtz(mtz, name);
+        out.source = "MTZ";
+        return out;
+    }
+    gemmi::cif::Document doc = gemmi::read_cif_from_memory(text.data(), text.size(), name.c_str());
+    std::vector<gemmi::ReflnBlock> blocks = gemmi::as_refln_blocks(std::move(doc.blocks));
+    gemmi::Logger logger;
+    std::string why = name + " holds no merged reflection block";
+    for (gemmi::ReflnBlock &rb : blocks) {
+        if (rb.refln_loop == nullptr)
+            continue;
+        gemmi::CifToMtz converter;
+        converter.spec_lines = SfCifSpec(*rb.refln_loop);
+        try {
+            const gemmi::Mtz mtz = converter.convert_block_to_mtz(rb, logger);
+            RugnuxReflections out = RugnuxReflectionsFromMtz(mtz, name);
+            out.source = "mmCIF block " + rb.block.name;
+            return out;
+        } catch (const std::exception &e) {
+            why = e.what();
+        }
+    }
+    throw std::runtime_error(why);
+}
+
+RugnuxReflections ReadRugnuxReflectionFile(const std::string &path) {
+    std::ifstream f(path, std::ios::binary);
+    if (!f)
+        throw std::runtime_error("cannot open " + path);
+    const std::string bytes{std::istreambuf_iterator<char>(f), std::istreambuf_iterator<char>()};
+    return ParseRugnuxReflections(bytes, path);
+}
diff --git a/writer/RugnuxReflectionFile.h b/writer/RugnuxReflectionFile.h
new file mode 100644
index 000000000..08a2de429
--- /dev/null
+++ b/writer/RugnuxReflectionFile.h
@@ -0,0 +1,50 @@
+// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#pragma once
+
+#include <string>
+#include <vector>
+
+#include "gemmi/mtz.hpp"
+#include "gemmi/unitcell.hpp"
+
+#include "../common/Reflection.h"
+
+// Merged reflections a refinement is given (rugnux --mode refine), as their file held them: an MTZ or a
+// structure-factor mmCIF (as the PDB holds them), gzipped or not, the format taken from the content. The
+// columns are found, not named: amplitudes with their sigmas where the file has them, else intensities (the
+// caller turns those into amplitudes), and the free-set flags where there are any. The caller parses; the
+// analysis reads no file.
+struct RugnuxReflections {
+    std::string name;                // what the report calls the file
+    std::string source;              // "MTZ" or "mmCIF block <name>"
+    gemmi::UnitCell cell;
+    std::string space_group;         // extended Hermann-Mauguin symbol
+    double wavelength_A = 0;         // 0: the file does not say
+    // h, k, l and d, with F/sigmaF where amplitudes were read, I/sigma where intensities were; rfree_flag
+    // where the file has free-set flags.
+    std::vector<MergedReflection> reflections;
+    bool amplitudes = true;          // false: intensities, no amplitudes in the file
+    std::string value_column, sigma_column;
+    std::string free_column;         // empty: the file has no free-set flags
+    int n_free = 0;
+};
+
+// The columns of `mtz` (an MTZ, or an mmCIF converted to one), found as RugnuxReflections describes:
+// - amplitudes: a type-F column followed by its type-Q sigma, by the usual names first (F, FP, FOBS, F-obs,
+//   FMEAN, ...), then any such pair that is not a calculated or map coefficient (FC, FWT, DELFWT, F-model ...);
+// - else intensities: a type-J column with its type-Q sigma (IMEAN, I, IOBS, I-obs, ... first); the
+//   anomalous pairs F(+)/F(-) (G/L) or I(+)/I(-) (K/M) averaged where there is nothing else;
+// - free flags: a type-I column named as a free set (FreeR_flag, FREE, R-free-flags, ...: any with "free" in
+//   its name). The test set is flag 0 in the CCP4 convention (0-19 thin shells included); where 0 marks the
+//   majority (1 marks the test set, as phenix and CNS write it), the minority is taken.
+// Throws where there is neither.
+RugnuxReflections RugnuxReflectionsFromMtz(const gemmi::Mtz &mtz, const std::string &name);
+
+// The reflections of a file's bytes, the format from the content (MTZ by its magic, else mmCIF: the first
+// merged block that holds amplitudes or intensities). Throws where the bytes hold none.
+RugnuxReflections ParseRugnuxReflections(const std::string &bytes, const std::string &name);
+
+// The file at `path`, named by it.
+RugnuxReflections ReadRugnuxReflectionFile(const std::string &path);
diff --git a/writer/WriteRugnuxFiles.cpp b/writer/WriteRugnuxFiles.cpp
index a2e16b515..a9516a81c 100644
--- a/writer/WriteRugnuxFiles.cpp
+++ b/writer/WriteRugnuxFiles.cpp
@@ -6,10 +6,12 @@
 #include <chrono>
 #include <stdexcept>
 #include <filesystem>
+#include <fstream>
 
 #include <gemmi/mtz.hpp>
 #include <gemmi/read_cif.hpp>   // cif::read_string
 #include <gemmi/mmcif.hpp>   // make_structure_from_block
+#include <nlohmann/json.hpp>
 
 #include "WriteModel.h"
 #include "../common/Logger.h"
@@ -142,6 +144,28 @@ gemmi::Structure PlacedModelStructure(const PlacedModelMessage &model) {
     return st;
 }
 
+std::string DensityBlobsJson(const DensityBlobsMessage &b) {
+    const size_t n = b.kind.size();
+    for (const size_t size : {b.x.size(), b.y.size(), b.z.size(), b.peak_sigma.size(), b.volume.size(), b.score.size(),
+                              b.nearest_atom.size(), b.nearest_atom_distance.size(), b.polar_contacts.size(),
+                              b.metal_contacts.size(), b.anomalous_sigma.size()})
+        if (size != n)
+            throw std::runtime_error(fmt::format("blobs: a field has {} entries for {} blobs", size, n));
+    nlohmann::json list = nlohmann::json::array();
+    for (size_t i = 0; i < n; i++)
+        list.push_back({{"kind", b.kind[i]},
+                        {"centroid", {b.x[i], b.y[i], b.z[i]}},
+                        {"peak_sigma", b.peak_sigma[i]},
+                        {"volume_A3", b.volume[i]},
+                        {"score_sigma_A3", b.score[i]},
+                        {"nearest_atom", b.nearest_atom[i]},
+                        {"nearest_atom_distance_A", b.nearest_atom_distance[i]},
+                        {"polar_contacts", b.polar_contacts[i]},
+                        {"metal_contacts", b.metal_contacts[i]},
+                        {"anomalous_sigma", b.anomalous_sigma[i]}});
+    return nlohmann::json{{"blobs", list}}.dump(1) + "\n";
+}
+
 namespace {
 
 double WallClockSeconds() {
@@ -159,6 +183,20 @@ void RenameIntoPlace(const std::string &tmp, const std::string &final_name, bool
     logger.Info("{} written, renamed into place at wall clock {:.3f} s", final_name, WallClockSeconds());
 }
 
+// <file_prefix><name>_model.cif (and .pdb) from `model`.
+void WriteModelFiles(const PlacedModelMessage &model, const std::string &file_prefix, const std::string &name,
+                     bool overwrite, Logger &logger) {
+    const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name(model.space_group_name);
+    if (sg == nullptr)
+        throw std::runtime_error("unknown space group '" + model.space_group_name + "'");
+    // WritePlacedModel appends _model.cif and _model.pdb to the prefix it is given.
+    const std::string tmp_prefix = file_prefix + name + ".tmp";
+    WritePlacedModel(PlacedModelStructure(model), model.unit_cell, *sg, tmp_prefix, logger);
+    for (const std::string suffix : {"_model.cif", "_model.pdb"})
+        if (std::filesystem::exists(tmp_prefix + suffix))
+            RenameIntoPlace(tmp_prefix + suffix, file_prefix + name + suffix, overwrite, logger);
+}
+
 }  // namespace
 
 void WriteRugnuxResultFiles(const EndMessage &end, const std::string &file_prefix, bool overwrite,
@@ -181,19 +219,37 @@ void WriteRugnuxResultFiles(const EndMessage &end, const std::string &file_prefi
         logger.Error("Cannot write {}_maps.mtz: {}", file_prefix, e.what());
     }
     try {
-        if (end.placed_model) {
-            const PlacedModelMessage &model = *end.placed_model;
-            const gemmi::SpaceGroup *sg = gemmi::find_spacegroup_by_name(model.space_group_name);
-            if (sg == nullptr)
-                throw std::runtime_error("unknown space group '" + model.space_group_name + "'");
-            // WritePlacedModel appends _model.cif and _model.pdb to the prefix it is given.
-            const std::string tmp_prefix = file_prefix + ".tmp";
-            WritePlacedModel(PlacedModelStructure(model), model.unit_cell, *sg, tmp_prefix, logger);
-            for (const std::string suffix : {"_model.cif", "_model.pdb"})
-                if (std::filesystem::exists(tmp_prefix + suffix))
-                    RenameIntoPlace(tmp_prefix + suffix, file_prefix + suffix, overwrite, logger);
-        }
+        if (end.placed_model)
+            WriteModelFiles(*end.placed_model, file_prefix, "", overwrite, logger);
     } catch (const std::exception &e) {
         logger.Error("Cannot write {}_model.cif: {}", file_prefix, e.what());
     }
+    try {
+        if (end.refined_model)
+            WriteModelFiles(*end.refined_model, file_prefix, "_refined", overwrite, logger);
+    } catch (const std::exception &e) {
+        logger.Error("Cannot write {}_refined_model.cif: {}", file_prefix, e.what());
+    }
+    try {
+        if (end.refined_map_coefficients) {
+            WriteMtz(*end.refined_map_coefficients, file_prefix + "_refined_maps.mtz.tmp");
+            RenameIntoPlace(file_prefix + "_refined_maps.mtz.tmp", file_prefix + "_refined_maps.mtz", overwrite,
+                            logger);
+        }
+    } catch (const std::exception &e) {
+        logger.Error("Cannot write {}_refined_maps.mtz: {}", file_prefix, e.what());
+    }
+    try {
+        if (end.blobs) {
+            const std::string text = DensityBlobsJson(*end.blobs);
+            {
+                std::ofstream f(file_prefix + "_blobs.json.tmp", std::ofstream::out | std::ofstream::trunc);
+                f.exceptions(std::ios::failbit | std::ios::badbit);
+                f << text;
+            }
+            RenameIntoPlace(file_prefix + "_blobs.json.tmp", file_prefix + "_blobs.json", overwrite, logger);
+        }
+    } catch (const std::exception &e) {
+        logger.Error("Cannot write {}_blobs.json: {}", file_prefix, e.what());
+    }
 }
diff --git a/writer/WriteRugnuxFiles.h b/writer/WriteRugnuxFiles.h
index 6d0bdca38..9496d64d8 100644
--- a/writer/WriteRugnuxFiles.h
+++ b/writer/WriteRugnuxFiles.h
@@ -25,9 +25,13 @@ void WriteMtz(const MtzTable &table, const std::string &filename);
 // nor six per atom.
 gemmi::Structure PlacedModelStructure(const PlacedModelMessage &model);
 
-// The three files above, from whichever blocks `end` carries, at <file_prefix>.mtz, _maps.mtz and
-// _model.cif (WritePlacedModel adds _model.pdb where a PDB can hold the cell). Each is written under a
-// temporary name and renamed into place. An existing file is replaced only with `overwrite`; otherwise
-// it is kept and the new one is not written.
+// The text of <prefix>_blobs.json. Throws where a field has another number of entries than kind.
+std::string DensityBlobsJson(const DensityBlobsMessage &blobs);
+
+// The files above, from whichever blocks `end` carries, at <file_prefix>.mtz, _maps.mtz and _model.cif
+// (WritePlacedModel adds _model.pdb where a PDB can hold the cell), and the refinement's
+// _refined_model.cif (.pdb), _refined_maps.mtz and _blobs.json. Each is written under a temporary name and
+// renamed into place. An existing file is replaced only with `overwrite`; otherwise it is kept and the
+// new one is not written.
 void WriteRugnuxResultFiles(const EndMessage &end, const std::string &file_prefix, bool overwrite,
                             Logger &logger);