// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
// SPDX-License-Identifier: GPL-3.0-only

#include "ModelValidation.h"

#include <algorithm>
#include <cmath>
#include <complex>
#include <array>
#include <numeric>
#include <random>
#include <string>
#include <utility>
#include <vector>
#include <unordered_map>

#include <gemmi/mmread_gz.hpp> // read_structure_gz
#include <gemmi/gz.hpp>        // MaybeGzipped
#include <gemmi/it92.hpp>      // IT92 x-ray form factors
#include <gemmi/dencalc.hpp>   // DensityCalculator
#include <gemmi/fourier.hpp>   // transform_map_to_f_phi, get_f_phi_on_grid, transform_f_phi_grid_to_map
#include <gemmi/solmask.hpp>   // SolventMasker
#include <gemmi/scaling.hpp>   // Scaling (bulk solvent + anisotropic B)
#include <gemmi/ccp4.hpp>      // Ccp4 map I/O
#include <gemmi/mtz.hpp>       // Mtz (map-coefficient output)

#include "../common/JFJochMath.h"   // PI (M_PI is not standard, and MSVC does not define it)
#include "../common/Logger.h"
#include "../common/ParallelFor.h"  // ParallelFor
#include "../image_analysis/scale_merge/ReindexAmbiguity.h"   // ReindexReflections
#include "RigidBodyRefine.h"
#include "SigmaA.h"

namespace {

using Table = gemmi::IT92<float>;

// Stable key for a Miller index reduced into the ASU (indices are small, well within +/-512).
long hkl_key(const gemmi::Miller &h) {
    return (h[0] + 512L) * 1048576 + (h[1] + 512L) * 1024 + (h[2] + 512L);
}

// FFT ASU map coefficients into a real-space map.
gemmi::Grid<float> map_from_coefficients(gemmi::AsuData<std::complex<float>> &coef) {
    coef.ensure_sorted();
    std::array<int, 3> size = gemmi::get_size_for_hkl(coef, {{0, 0, 0}}, 3.0);
    return gemmi::transform_f_phi_grid_to_map(gemmi::get_f_phi_on_grid<float>(coef, size, true));
}

// Write a map as CCP4; return its RMS (the sigma the map is read in).
double write_ccp4(const gemmi::Grid<float> &map, const std::string &path) {
    gemmi::Ccp4<float> ccp4;
    ccp4.grid = map;
    ccp4.update_ccp4_header(2);
    ccp4.write_ccp4_map(path);
    return ccp4.hstats.rms;
}

// Cubic, not the default linear, for reading a map at a point. The maps are sampled every d_min/3,
// and a peak that sharp read by trilinear interpolation comes out up to a quarter low - unevenly
// enough to reorder the anomalous sites.
constexpr int MAP_INTERPOLATION_ORDER = 3;

// How deep a trough at an atom has to be before the anomalous map is called inverted. Well clear of
// the couple of sigma a map with no anomalous signal reaches at its noisiest atom.
constexpr double ANOMALOUS_INVERSION_SIGMA = 5.0;

// How many anomalous sites the report names. The strongest few are what says whether the anomalous
// signal is there and what carries it; a full site list is what the map file is for.
constexpr size_t MAX_ANOMALOUS_SITES = 10;

// How many random placements of the same model the real fit is compared against. The verdict is
// (real - mean)/sd of this sample, so what matters is not the mean but how well the SPREAD is
// pinned: the relative error on an sd from n draws is 1/sqrt(2(n-1)), and a sample that happens to
// come out narrow is what turns a model that does not fit into one that appears to. Measured on the
// case that sits closest to the gate - a model of an unrelated protein, 1.83 sigma against a
// threshold of 3 - the chance of it reading over the gate on a different seed is 31% at n=3, 17% at
// n=5, 6% at n=9.
//
// Nine rather than five because the replicates run concurrently: the null costs the SLOWEST of them
// rather than their sum, and the slowest of nine is barely above the slowest of five, so the extra
// four are close to free in wall clock (measured 2.5 s against 2.6 s) up to the thread count.
constexpr int NULL_REPLICATES = 9;

// Fixed, so the same data and the same model give the same verdict on every run.
constexpr unsigned NULL_SEED = 20260902;

// How far above its own null a fit has to sit before the model is allowed to decide anything. The cut
// is in sigma of that null and not in R: measured, the R a model that explains nothing reaches moves
// with the model's atom count and B-factors as much as with the data, so no value of R separates the
// two on its own. Measured at nine replicates, the crystal's own model reads +17.7 sigma and an
// unrelated protein +1.7, so the cut sits in a gap an order of magnitude wider than the sd it is
// measured in.
constexpr double MODEL_FIT_SIGMA = 3.0;

// Mean and sample standard deviation of a small sample.
std::pair<double, double> mean_sd(const std::vector<double> &v) {
    if (v.size() < 2)
        return {v.empty() ? 0.0 : v.front(), 0.0};
    const double mean = std::accumulate(v.begin(), v.end(), 0.0) / static_cast<double>(v.size());
    double s2 = 0;
    for (double x : v)
        s2 += (x - mean) * (x - mean);
    return {mean, std::sqrt(s2 / static_cast<double>(v.size() - 1))};
}

// A rotation drawn uniformly from SO(3), through a uniform random unit quaternion.
// Following Shoemake (1992) Graphics Gems III, 124-132
gemmi::Mat33 random_rotation(std::mt19937 &rng) {
    std::uniform_real_distribution<double> u(0.0, 1.0);
    const double u1 = u(rng), t2 = 2 * PI * u(rng), t3 = 2 * PI * u(rng);
    const double r1 = std::sqrt(1 - u1), r2 = std::sqrt(u1);
    const double x = r1 * std::sin(t2), y = r1 * std::cos(t2), z = r2 * std::sin(t3), w = r2 * std::cos(t3);
    return {1 - 2 * (y * y + z * z), 2 * (x * y - z * w),     2 * (x * z + y * w),
            2 * (x * y + z * w),     1 - 2 * (x * x + z * z), 2 * (y * z - x * w),
            2 * (x * z - y * w),     2 * (y * z + x * w),     1 - 2 * (x * x + y * y)};
}

// Everything one fit moves: the model itself, and the structure factors that follow it. The real
// model has one of these and every null replicate gets a copy of its own, which is what lets the
// replicates run at the same time without stepping on each other.
struct ModelState {
    gemmi::Structure st;
    gemmi::AsuData<std::complex<float>> fcalc, fmask;
};

// Turn the model about its own centroid, so it keeps its place in the cell and loses its orientation.
void reorient_about_centroid(gemmi::Model &model, const gemmi::Mat33 &rot) {
    std::vector<gemmi::Position> pos = ModelPositions(model);
    if (pos.empty())
        return;
    gemmi::Vec3 centre;
    for (const gemmi::Position &p : pos)
        centre += p;
    centre *= 1.0 / static_cast<double>(pos.size());
    for (gemmi::Position &p : pos)
        p = gemmi::Position(rot.multiply(gemmi::Vec3(p) - centre) + centre);
    SetModelPositions(model, pos);
}

}  // namespace

ModelValidationResult ValidateAgainstModel(const std::vector<MergedReflection> &merged,
                                           const UnitCell &cell,
                                           const std::string &model_path,
                                           const std::string &output_prefix,
                                           Logger &logger,
                                           const gemmi::SpaceGroup *data_space_group,
                                           bool probe_indexing_ambiguity,
                                           size_t nthreads,
                                           double wavelength_A) {
    ModelValidationResult result;
    result.model_path = model_path;

    // --- read the atomic model ---
    ModelState mdl;
    gemmi::Structure &st = mdl.st;   // the real model, the one the maps and the report describe
    try {
        // Detect, not the default: without it GEMMI picks the format from the extension and only
        // falls back to the content when it does not recognise one. A model arrives named however
        // whoever produced it named it, so the file itself is the better authority.
        st = gemmi::read_structure_gz(model_path, gemmi::CoorFormat::Detect);
    } catch (const std::exception &e) {
        result.failure_reason = fmt::format("cannot read model {}: {}", model_path, e.what());
        logger.Error("Model validation: {}", result.failure_reason);
        return result;
    }
    if (st.models.empty() || !st.cell.is_crystal()) {
        result.failure_reason = fmt::format("model {} has no atoms or no unit cell", model_path);
        logger.Error("Model validation: {}", result.failure_reason);
        return result;
    }
    const gemmi::SpaceGroup *sg = st.find_spacegroup();
    if (!sg) {
        result.failure_reason = fmt::format("model {} has no usable space group", model_path);
        logger.Error("Model validation: {}", result.failure_reason);
        return result;
    }
    result.model_space_group_number = sg->number;

    // If the data was indexed in the enantiomorph of the model's space group (e.g. data P4(1)2(1)2,
    // model P4(3)2(1)2 - the merged intensities cannot tell them apart), the model's group is a
    // CANDIDATE for the label the reflections are written under. Only a candidate: this is arithmetic
    // on two group numbers and says nothing about whether the model belongs to this crystal, and a
    // model that does not is exactly as capable of rewriting the label as one that does. Whether it is
    // taken up is settled at the end, on the fit against its own null and on the anomalous map.
    //
    // It is tempting to reindex by the change-of-hand operator instead, and that is wrong. The two
    // groups of an enantiomorphic pair have the same rotation operations - only their translations
    // differ - so they transform hkl identically, share a reciprocal ASU, and split into Bijvoet
    // hands identically: the label carries no handedness at all, and nothing about it needs undoing.
    // What does carry the hand is the indexing the data already have, from the diffraction geometry,
    // and with it the sign of every anomalous difference. The change-of-hand operator is the
    // inversion, so reindexing by it swaps I(+) with I(-) - it does not correct the hand, it flips
    // it, on the strength of a label the space-group search itself reports as undetermined. Where
    // the model really is the wrong enantiomorph for this crystal, that flip does not reveal the
    // disagreement but manufactures agreement. The anomalous difference map below is the only honest
    // arbiter, and it is used to report the disagreement rather than to bury it.
    const std::vector<MergedReflection> &obs = merged;
    if (data_space_group && data_space_group->number != sg->number) {
        if (data_space_group->is_enantiomorphic() && sg->is_enantiomorphic()) {
            gemmi::GroupOps eops = data_space_group->operations();
            eops.change_basis_forward(data_space_group->change_of_hand_op());
            const gemmi::SpaceGroup *enant = gemmi::find_spacegroup_by_ops(eops);
            if (enant && enant->number == sg->number) {
                result.model_enantiomorph_candidate = true;
                logger.Info("Model validation: data space group {} is the enantiomorph of the model {}; "
                            "the model's group is a candidate for the label, pending the fit - a change "
                            "of label only, since the two groups index identically and reindexing would "
                            "flip the anomalous differences",
                            data_space_group->short_name(), sg->hm);
            }
        }
    }

    // Resolution limit from the data (the merged set is already resolution-trimmed).
    double d_min = 0.0;
    for (const MergedReflection &r : obs)
        if (r.d > 0 && (d_min == 0.0 || r.d < d_min))
            d_min = r.d;
    if (d_min <= 0.0) {
        result.failure_reason = "the merged reflections carry no resolution";
        logger.Error("Model validation: {}", result.failure_reason);
        return result;
    }

    // Re-fractionalize the model into the data cell (rigid cell adjustment; no refinement).
    const gemmi::UnitCell data_cell = cell;  // UnitCell -> gemmi::UnitCell
    if (data_cell.is_crystal()) {
        gemmi::UnitCell old = st.cell;
        for (gemmi::Model &m : st.models)
            for (gemmi::Chain &ch : m.chains)
                for (gemmi::Residue &r : ch.residues)
                    for (gemmi::Atom &a : r.atoms)
                        a.pos = data_cell.orthogonalize(old.fractionalize(a.pos));
        st.cell = data_cell;
    }
    st.setup_cell_images();
    const gemmi::UnitCell &ucell = st.cell;

    logger.Info("Model validation: {} atoms, cell a={:.2f} b={:.2f} c={:.2f}, sg {}, to {:.2f} A",
                gemmi::count_atom_sites(st.models[0]), ucell.a, ucell.b, ucell.c, sg->hm, d_min);

    // --- Fcalc (atomic) via electron density on a grid + FFT, plus a flat bulk-solvent mask -> Fmask.
    // A lambda because the rigid-body step below moves the model and then needs both again, and it
    // takes the state to work on so that a null replicate can run it on its own copy. ---
    auto compute_model_factors = [&](ModelState &ms) {
        gemmi::DensityCalculator<Table, float> dc;
        dc.d_min = d_min;
        dc.rate = 1.5;
        dc.set_grid_cell_and_spacegroup(ms.st);
        dc.set_refmac_compatible_blur(ms.st.models[0]);
        dc.put_model_density_on_grid(ms.st.models[0]);
        ms.fcalc = gemmi::transform_map_to_f_phi(dc.grid, true)
                       .prepare_asu_data(dc.d_min, dc.blur, false, false, false);

        // Refmac radii give a slightly lower R than the Cctbx set on our test cases, at no cost.
        gemmi::SolventMasker masker(gemmi::AtomicRadiiSet::Refmac);
        gemmi::Grid<float> mask_grid;
        mask_grid.unit_cell = dc.grid.unit_cell;
        mask_grid.spacegroup = dc.grid.spacegroup;
        mask_grid.set_size_from_spacing(dc.requested_grid_spacing(), gemmi::GridSizeRounding::Up);
        masker.put_mask_on_grid(mask_grid, ms.st.models[0]);
        ms.fmask = gemmi::transform_map_to_f_phi(mask_grid, true).prepare_asu_data(dc.d_min, 0);
    };
    compute_model_factors(mdl);

    gemmi::GroupOps gops = sg->operations();
    gemmi::ReciprocalAsu asu(sg);

    // --- fit the (scaled, solvent-corrected) model to one observed set and score it ---
    // Factored into a lambda so we can probe indexing (merohedral) ambiguities: run the same scale +
    // R computation on each reindexing of the observed reflections and keep the lowest-R-free one.
    struct Fit {
        gemmi::AsuData<std::complex<float>> fmodel;
        gemmi::AsuData<gemmi::ValueSigma<float>> fobs;                 // what it was fitted to
        std::unordered_map<long, std::pair<double, bool>> obs_by_hkl;  // hkl -> (Fobs, is_free)
        double r_work = 1, r_free = 1, k_sol = 0, b_sol = 0, k_overall = 0;
        int n_w = 0, n_f = 0;
    };
    auto fit_model = [&](ModelState &ms, const std::vector<MergedReflection> &obs_in) -> Fit {
        Fit out;
        out.fmodel = ms.fcalc;   // copy the atomic structure factors; scaling mutates them in place

        // --- observed amplitudes into the model ASU, keyed by hkl (also remember free flag) ---
        // Observed amplitudes are the French-Wilson |F| already computed at the end of the merge
        // (MergedReflection.F), so the model R-free / maps use exactly the same amplitudes as the
        // written reflection file.
        gemmi::AsuData<gemmi::ValueSigma<float>> &fobs = out.fobs;
        fobs.unit_cell_ = ucell;
        fobs.spacegroup_ = sg;
        for (const MergedReflection &r : obs_in) {
            if (std::isnan(r.F)) continue;
            gemmi::Miller h{{r.h, r.k, r.l}};
            if (!asu.is_in(h)) h = asu.to_asu(h, gops).first;
            fobs.v.push_back({h, {r.F, 1.0f}});
            out.obs_by_hkl[hkl_key(h)] = {r.F, r.rfree_flag};
        }
        fobs.ensure_asu();
        fobs.ensure_sorted();

        // --- scale Fmodel(+solvent) to Fobs: k_overall, anisotropic B, k_sol, b_sol ---
        gemmi::Scaling<float> scaling(ucell, sg);
        scaling.use_solvent = true;
        scaling.prepare_points(out.fmodel, fobs, &ms.fmask);
        scaling.fit_isotropic_b_approximately();
        scaling.fit_parameters();
        scaling.scale_data(out.fmodel, &ms.fmask);   // out.fmodel now holds the scaled, solvent-corrected Fmodel
        out.k_sol = scaling.k_sol;
        out.b_sol = scaling.b_sol;
        out.k_overall = scaling.k_overall;

        // The model is scaled to the data with an overall scale, an anisotropic B and a flat bulk
        // solvent only - the standard, few-parameter model that refinement programs use. A dataset-
        // specific free-form per-resolution-shell rescale would lower this dataset's R a little, but
        // it reshapes each map's radial amplitude profile differently, so a batch of maps would no
        // longer be directly comparable. For a fragment-screening / PanDDA campaign, comparable maps
        // across datasets matter more than the last bit of per-dataset R, so it is deliberately omitted.
        // (The sigma_A weighting further down is a different thing and does not reopen this: it never
        // rescales Fobs, and it leaves the R-factors below untouched. It does weight the map
        // coefficients per shell and per dataset - see the note where it is computed.)

        // --- R-work / R-free ---
        double num_w = 0, den_w = 0, num_f = 0, den_f = 0;
        for (const auto &hv : out.fmodel.v) {
            auto it = out.obs_by_hkl.find(hkl_key(hv.hkl));
            if (it == out.obs_by_hkl.end()) continue;
            double Fo = it->second.first;
            double Fc = std::abs(hv.value);
            if (it->second.second) { num_f += std::fabs(Fo - Fc); den_f += Fo; ++out.n_f; }
            else                   { num_w += std::fabs(Fo - Fc); den_w += Fo; ++out.n_w; }
        }
        out.r_work = den_w > 0 ? num_w / den_w : 1;
        out.r_free = den_f > 0 ? num_f / den_f : 1;
        return out;
    };

    // --- the model placed against one observed set: fit, then a rigid-body placement ---
    // The real model and every null replicate below go through this same lambda, so the two are
    // comparable - a null that was not placed would be the null of a weaker procedure than the one it
    // is there to judge. It leaves the model where it ends up, and the caller puts it back.
    struct Placement {
        Fit fit;
        bool rb_applied = false;
        double rb_angle_deg = 0, rb_shift_A = 0, r_free_before_rb = 0;
    };
    auto place_and_fit = [&](ModelState &ms, const std::vector<MergedReflection> &obs_in) -> Placement {
        Placement out;
        out.fit = fit_model(ms, obs_in);

        // --- rigid-body placement of the model in the data cell ---
        // Re-fractionalizing the model above puts it in the right box but not in the right place: a
        // non-isomorphous cell squeezes the box without moving the body inside it, and the body's own
        // position differs from crystal to crystal anyway. Six parameters recover that - a rotation about
        // the model's centroid and a translation - which is all a fragment-screening model needs, since it
        // arrives already solved. The step is committed only if the FREE reflections, which the refinement
        // never saw, agree that it helped; on data the model cannot be placed against, the model stays
        // exactly where it was read.
        gemmi::AsuData<gemmi::ValueSigma<float>> fobs_work;
        fobs_work.unit_cell_ = ucell;
        fobs_work.spacegroup_ = sg;
        for (const auto &hv : out.fit.fobs.v) {
            const auto it = out.fit.obs_by_hkl.find(hkl_key(hv.hkl));
            if (it != out.fit.obs_by_hkl.end() && !it->second.second)
                fobs_work.v.push_back(hv);
        }
        const std::vector<gemmi::Position> before = ModelPositions(ms.st.models[0]);
        const RigidBodyRefineResult rb =
            RefineRigidBody(ms.st.models[0], ucell, *sg, fobs_work, d_min, logger);
        if (!rb.converged) {
            // RefineRigidBody leaves the model wherever the solver left it, usable answer or not, so
            // the restore cannot be conditional on the same flag the re-fit is.
            SetModelPositions(ms.st.models[0], before);
            return out;
        }
        {
            compute_model_factors(ms);
            Fit moved = fit_model(ms, obs_in);
            const bool commit = moved.r_free < out.fit.r_free;
            logger.Info("Model validation: rigid body held-out R-free {:.4f} -> {:.4f} => {}",
                        out.fit.r_free, moved.r_free, commit ? "committed" : "rejected, model put back");
            if (commit) {
                out.rb_applied = true;
                out.rb_angle_deg = rb.angle_deg;
                out.rb_shift_A = rb.shift_A;
                out.r_free_before_rb = out.fit.r_free;
                out.fit = std::move(moved);
            } else {
                SetModelPositions(ms.st.models[0], before);
                compute_model_factors(ms);
            }
        }
        return out;
    };

    // --- indexing (merohedral) ambiguity ---
    // When a reference MTZ was supplied, the data were already reindexed to agree with the reference
    // intensities (at the merge stage for rotation data, per image in stills scaling), and that
    // choice is authoritative - we keep it. Only with a model and NO reference do we resolve the
    // ambiguity here, as a fallback, by fitting each candidate reindexing and keeping the lowest
    // R-free. A no-op either way for a holohedral crystal (no twin laws). The
    // enantiomorph/screw ambiguity is never probed by R-free: |Fcalc| is the same for both hands, so
    // it cannot distinguish them - that is taken from the model hand above.
    //
    // The candidates are a property of the DATA's lattice and point group: it is the observed
    // intensities that are relabelled. Asking the model's group instead enumerates nothing at all
    // wherever the two groups differ - measured, a model in P4(3)2(1)2 against data merged in P4(3)
    // probes zero operators - which is exactly the case the probe exists for.
    const gemmi::SpaceGroup &ambiguity_sg = data_space_group != nullptr ? *data_space_group : *sg;
    const std::vector<gemmi::Op> reindex_ops =
        probe_indexing_ambiguity ? ReindexAmbiguityOperators(cell, ambiguity_sg)
                                 : std::vector<gemmi::Op>{};

    struct IndexingProbe {
        gemmi::Op op = gemmi::Op::identity();   // the lowest-R-free relabelling
        double margin = 0;                      // by how much in R-free it leads the runner-up
    };
    auto probe_indexing = [&](ModelState &ms) {
        IndexingProbe out;
        std::vector<double> r_free{fit_model(ms, obs).r_free};   // identity first, then the twin laws
        double best_r_free = r_free.front();
        for (const auto &op : reindex_ops) {
            const double cand = fit_model(ms, ReindexReflections(obs, op)).r_free;
            r_free.push_back(cand);
            if (cand < best_r_free) {
                best_r_free = cand;
                out.op = op;
            }
        }
        // The runner-up as well as the winner: the margin between them is what says whether the choice
        // was made on evidence, and on weak data the two can come out within noise.
        std::sort(r_free.begin(), r_free.end());
        out.margin = r_free[1] - r_free[0];
        return out;
    };

    const std::vector<gemmi::Position> as_read = ModelPositions(st.models[0]);

    IndexingProbe indexing;
    std::vector<MergedReflection> reindexed;
    const std::vector<MergedReflection> *obs_model = &obs;
    if (!reindex_ops.empty()) {
        indexing = probe_indexing(mdl);
        if (!(indexing.op == gemmi::Op::identity())) {
            reindexed = ReindexReflections(obs, indexing.op);
            obs_model = &reindexed;
        }
    }
    Placement real = place_and_fit(mdl, *obs_model);

    // --- is there anything for the model to decide? ---
    // There are only two: the space-group label, where the model asserts the other enantiomorph, and
    // the indexing, where a relabelling of the data fits it better. A model that asserts neither -
    // already in the group the data were merged in, and preferring their indexing - has made no claim
    // that needs arbitrating, and the null below would be several seconds spent gating a decision
    // nobody is making. That is the isomorphous case a screening campaign is made of, and it is the
    // one that has to be fast. Nothing else changes: the R-factors, the maps and the placement are
    // computed and reported exactly as in every other case.
    const bool decision_pending = result.model_enantiomorph_candidate
                                  || !(indexing.op == gemmi::Op::identity());
    // A null that cannot be built is a question that could not be put, and this design already has a
    // state for that. Without this the run dies here - model validation runs BEFORE the reflection
    // files are written, so one failed replicate would take the .mtz, .cif, .hkl and _unmerged.mtz
    // with it, after the merge has already been paid for. The replicates are rotated models fed to a
    // scaling path that throws on data it cannot pair up, so this is the adversarial input for it.
    try {
    if (decision_pending) {
        // --- the null: this model, this data, in random orientations ---
        // An R-factor on its own says nothing about whether a model belongs to a crystal. What a model
        // that explains nothing reaches against these data depends on its atom count and its B-factors as
        // much as on the data, so a threshold on R calibrated on one dataset misjudges the next; and the
        // classical random-structure value does not apply either, because the scale here is fitted to
        // minimise the very sum the R is made of. The only null that fits is made of the same model: it is
        // reoriented about its own centroid and run through the identical fit and rigid-body placement,
        // and the real fit is asked how far above the resulting distribution it sits.
        //
        // R-work, not R-free. Not because nothing is refined against it - the placement's six parameters
        // are, and the scale's four - but because every null replicate is placed and scaled the same
        // way, so whatever that optimism is worth is bought on both sides and cancels in
        // (mean - real)/sd. R-work is then decided on an order of magnitude more reflections.
        //
        // The replicates are fitted to the data as merged even where a reindexing won above: a reindexing
        // is a relabelling of the same intensities, and a model in a random orientation has no more to do
        // with one labelling than with the other.
        logger.Info("Model validation: scoring the fit against a null of {} random placements of the same "
                    "model", NULL_REPLICATES);
        // The orientations are drawn here, up front and in order, and not inside the loop: the
        // replicates run at the same time below, and a draw taken on whichever thread reached the
        // generator first would make the answer depend on the scheduling. Replicate i gets rotation i
        // on every run, so the sigma reported is a property of the data and not of the machine.
        std::vector<gemmi::Mat33> null_rotation;
        {
            std::mt19937 rng(NULL_SEED);
            for (int i = 0; i < NULL_REPLICATES; i++)
                null_rotation.push_back(random_rotation(rng));
        }
        // Each replicate works on its own copy of the model and of its structure factors, and the
        // replicates share nothing else, so they run concurrently and the real model - which the
        // maps and the atom-density readout below are still taken from - is never moved.
        std::vector<double> null_r_work(NULL_REPLICATES), null_margin(NULL_REPLICATES);
        ParallelFor(NULL_REPLICATES, nthreads, [&](int i) {
            ModelState rep;
            rep.st = mdl.st;
            SetModelPositions(rep.st.models[0], as_read);
            reorient_about_centroid(rep.st.models[0], null_rotation[i]);
            compute_model_factors(rep);
            if (!reindex_ops.empty())
                null_margin[i] = probe_indexing(rep).margin;
            null_r_work[i] = place_and_fit(rep, obs).fit.r_work;
        });
        const auto [null_mean, null_sd] = mean_sd(null_r_work);
        result.fit_tested = true;
        result.null_replicates = NULL_REPLICATES;
        result.null_r_work_mean = null_mean;
        result.null_r_work_sd = null_sd;

        auto record_fit = [&](const Placement &p) {
            // Guarded at a floor, not at zero: sd == 0 and sd == 1e-7 are one ulp apart and land on
            // opposite verdicts, and a null with no spread - a model too small or too symmetric for a
            // rotation about its own centroid to move |Fcalc| - is the case that produces it. Measured
            // nulls sit near 0.60 with sd ~0.009, so this is nowhere near anything genuine.
            constexpr double NULL_SD_FLOOR = 1e-3;
            result.r_work_sigma =
                null_sd >= NULL_SD_FLOOR ? (null_mean - p.fit.r_work) / null_sd : 0.0;
            result.model_fits = result.r_work_sigma >= MODEL_FIT_SIGMA;
        };
        record_fit(real);

        // --- does the model get to decide anything? ---
        // The R-factors, the maps and the rigid-body placement are statements about the MODEL and are
        // always computed and always reported, fit or no fit: a model that does not describe these data
        // still has an R against them, and that is the negative result. What the gate below controls is
        // the two decisions that rewrite the DATA - the space-group label and the indexing - which a
        // wrong model must not be able to make.
        if (!reindex_ops.empty()) {
            result.indexing_probed = true;
            result.indexing_margin = indexing.margin;
            const auto [margin_mean, margin_sd] = mean_sd(null_margin);
            result.indexing_margin_null_mean = margin_mean;
            result.indexing_margin_null_sd = margin_sd;
            constexpr double MARGIN_SD_FLOOR = 1e-4;
            result.indexing_margin_sigma =
                margin_sd >= MARGIN_SD_FLOOR ? (indexing.margin - margin_mean) / margin_sd : 0.0;
            // The margin is judged against the margin a random placement produces, not against a value.
            // A random model also picks a winner, and on these data it picks one by a comparable lead
            // (measured), so the raw margin says nothing on its own.
            const bool decided = result.model_fits && result.indexing_margin_sigma >= MODEL_FIT_SIGMA;
            if (decided)
                result.indexing_op = indexing.op;
            logger.Info("Model validation: probed {} indexing solution(s) against the model; the winner "
                        "leads the runner-up by {:.4f} in R-free, against {:.4f} +- {:.4f} for a random "
                        "placement of the same model ({:+.2f} sigma) => {}",
                        reindex_ops.size() + 1, indexing.margin, margin_mean, margin_sd,
                        result.indexing_margin_sigma,
                        !decided ? "not decided; the data keep the indexing they were merged in"
                                 : (result.indexing_op == gemmi::Op::identity()
                                    ? "kept the current indexing" : "reindexed to the model's"));
            if (!decided && !(indexing.op == gemmi::Op::identity())) {
                // The R-factors and the maps have to describe the reflections the files carry, and those
                // are now the ones the merge produced, so the fit is remade on them.
                SetModelPositions(st.models[0], as_read);
                compute_model_factors(mdl);
                real = place_and_fit(mdl, obs);
                record_fit(real);
            }
        }
        logger.Info("Model validation: R-work {:.4f} against a null of {:.4f} +- {:.4f} = {:+.2f} sigma "
                    "=> the model {} these data",
                    real.fit.r_work, null_mean, null_sd, result.r_work_sigma,
                    result.model_fits ? "FITS" : "DOES NOT FIT");
    } else {
        logger.Info("Model validation: the model asserts no other enantiomorph for these data and "
                    "prefers the indexing they were merged in, so it claims nothing about the written "
                    "reflections and no null was run; R-work {:.4f}, R-free {:.4f}",
                    real.fit.r_work, real.fit.r_free);
    }
    } catch (const std::exception &e) {
        // The null could not be built, so no decision is licensed and none is taken - which is the
        // NOT_TESTED state, not a failure of the run. If the indexing probe had already won on a
        // relabelling, the fit that survives describes those reflections and the files will not carry
        // them, so it is remade on the data as merged.
        logger.Warning("Model validation: the null could not be built ({}), so the model decides "
                       "nothing; the reflections keep the group and the indexing they were merged in",
                       e.what());
        result.fit_tested = false;
        result.model_fits = false;
        result.indexing_probed = false;
        result.indexing_op = gemmi::Op::identity();
        result.r_work_sigma = 0.0;
        SetModelPositions(st.models[0], as_read);
        compute_model_factors(mdl);
        real = place_and_fit(mdl, obs);
    }

    Fit &best = real.fit;
    result.rigid_body_applied = real.rb_applied;
    result.rigid_body_angle_deg = real.rb_angle_deg;
    result.rigid_body_shift_A = real.rb_shift_A;
    result.r_free_before_rigid_body = real.r_free_before_rb;

    gemmi::AsuData<std::complex<float>> &fmodel = best.fmodel;
    std::unordered_map<long, std::pair<double, bool>> &obs_by_hkl = best.obs_by_hkl;

    result.r_work = best.r_work;
    result.r_free = best.r_free;
    result.n_work = best.n_w;
    result.n_free = best.n_f;
    result.k_sol = best.k_sol;
    result.b_sol = best.b_sol;
    result.k_overall = best.k_overall;

    // --- sigma_A weighting: the maps are 2mFo-DFc and mFo-DFc, not 2Fo-Fc and Fo-Fc ---
    // m and D come from a maximum-likelihood sigma_A per resolution shell, so a shell the model
    // describes badly is damped rather than carried into the map at full weight, and the difference
    // map is correspondingly less biased towards the model that made its phases.
    //
    // m and D are estimated on THIS dataset, so two datasets of one crystal form get slightly
    // different weights, and to that extent their maps are no longer scaled identically - the same
    // property the scaling above deliberately protects. It is kept anyway: the difference between two
    // datasets' sigma_A curves is the difference in how well the model explains each of them, which is
    // real and is what a screening campaign is looking for, and a PanDDA-style analysis consumes
    // 2mFo-DFc maps and normalizes each dataset's map against the ensemble before comparing them. The
    // per-reflection FOM is written to the MTZ so the weighting can be undone.
    // Following Read (1986) Acta Cryst. A42, 140-149
    struct MapTerm { gemmi::Miller hkl; double fo, fc, phi; bool free, centric; };
    std::vector<MapTerm> terms;
    std::vector<SigmaAReflection> sa_input;
    for (const auto &hv : fmodel.v) {
        const auto it = obs_by_hkl.find(hkl_key(hv.hkl));
        if (it == obs_by_hkl.end()) continue;
        const double Fo = it->second.first;
        const double Fc = std::abs(hv.value);
        const bool centric = gops.is_reflection_centric(hv.hkl);
        terms.push_back({hv.hkl, Fo, Fc, std::arg(hv.value), it->second.second, centric});
        sa_input.push_back({Fo, Fc, ucell.calculate_1_d2(hv.hkl), gops.epsilon_factor(hv.hkl),
                            centric, it->second.second});
    }
    const SigmaAResult sigma_a = EstimateSigmaA(sa_input, ucell);
    result.mean_fom = sigma_a.mean_fom;
    result.sigma_a_shells = sigma_a.shells;

    gemmi::AsuData<std::complex<float>> map2fofc, mapfofc;
    map2fofc.unit_cell_ = ucell; map2fofc.spacegroup_ = sg;
    mapfofc.unit_cell_ = ucell;  mapfofc.spacegroup_ = sg;
    std::vector<float> fwt(terms.size()), delfwt(terms.size());
    for (size_t i = 0; i < terms.size(); i++) {
        const double m = sigma_a.weight[i].m, D = sigma_a.weight[i].d;
        // A centric reflection's phase is either exactly right or 180 degrees wrong, never in
        // between, so its bias-free coefficient is mFo and not 2mFo - DFc.
        fwt[i] = static_cast<float>(terms[i].centric ? m * terms[i].fo
                                                     : 2 * m * terms[i].fo - D * terms[i].fc);
        delfwt[i] = static_cast<float>(m * terms[i].fo - D * terms[i].fc);
        const std::complex<float> ph = std::polar(1.0f, static_cast<float>(terms[i].phi));
        map2fofc.v.push_back({terms[i].hkl, fwt[i] * ph});
        mapfofc.v.push_back({terms[i].hkl, delfwt[i] * ph});
    }

    // --- write the maps and score the 2mFo-DFc map at atom centres (a real map peaks there) ---
    const gemmi::Grid<float> grid2fofc = map_from_coefficients(map2fofc);
    const double rms2 = write_ccp4(grid2fofc, output_prefix + "_2fofc.ccp4");
    write_ccp4(map_from_coefficients(mapfofc), output_prefix + "_fofc.ccp4");
    {
        double s = 0; int n = 0;
        for (gemmi::Model &m : st.models)
            for (gemmi::Chain &ch : m.chains)
                for (gemmi::Residue &r : ch.residues)
                    for (gemmi::Atom &a : r.atoms) { s += grid2fofc.interpolate_value(a.pos, MAP_INTERPOLATION_ORDER); ++n; }
        result.mean_atom_density_sigma = (n > 0 && rms2 > 0) ? (s / n) / rms2 : 0;
    }

    // --- anomalous difference map, where the merge kept the Bijvoet split ---
    // Coefficients F(+) - F(-) carried on the model phase turned back by 90 degrees. Its peaks sit on
    // the anomalous scatterers, so reading the map at each of the model's own atoms names them,
    // rather than leaving a list of coordinates for someone to look up.
    // Following ANODE, Thorn & Sheldrick (2011) J. Appl. Cryst. 44, 1285-1287
    {
        // Read from the merged reflections as they came in, and carry each one into the model's frame
        // here: the hand each Bijvoet difference belongs to is a property of the frame the merge was
        // made in, and both operators can change it. F(+) and F(-) are attached to the + index of the
        // Friedel ASU of that frame, so an anomalous merge - which keeps each mate as a row of its own,
        // both carrying the same pair - is read on its + rows only. Taking the - rows as well would
        // give one reflection both signs of its difference, and the last row written would decide.
        const gemmi::SpaceGroup *data_sg = data_space_group != nullptr ? data_space_group : sg;
        const gemmi::ReciprocalAsu data_asu(data_sg);
        const gemmi::GroupOps data_gops = data_sg->operations();

        std::unordered_map<long, float> danom_by_hkl;
        for (const MergedReflection &r : merged) {
            if (!std::isfinite(r.F_plus) || !std::isfinite(r.F_minus))
                continue;
            gemmi::Op::Miller h{{r.h, r.k, r.l}};
            if (data_gops.is_reflection_centric(h))   // a centric reflection has no anomalous difference
                continue;
            if (!data_asu.to_asu_sign(h, data_gops).second)
                continue;
            if (!(result.indexing_op == gemmi::Op::identity()))
                h = result.indexing_op.apply_to_hkl(h);
            const auto [hasu, plus] = asu.to_asu_sign(h, gops);
            danom_by_hkl[hkl_key(hasu)] = plus ? r.F_plus - r.F_minus : r.F_minus - r.F_plus;
        }

        gemmi::AsuData<std::complex<float>> mapanom;
        mapanom.unit_cell_ = ucell;
        mapanom.spacegroup_ = sg;
        for (const auto &hv : fmodel.v) {
            const auto it = danom_by_hkl.find(hkl_key(hv.hkl));
            if (it == danom_by_hkl.end())
                continue;
            const auto phi = static_cast<float>(std::arg(hv.value) - PI / 2);
            mapanom.v.push_back({hv.hkl, it->second * std::polar(1.0f, phi)});
        }
        result.anomalous_pairs = static_cast<int>(mapanom.v.size());

        if (!mapanom.v.empty()) {
            const gemmi::Grid<float> grid = map_from_coefficients(mapanom);
            const double rms = write_ccp4(grid, output_prefix + "_anom.ccp4");
            std::vector<ModelValidationResult::AnomalousSite> sites;
            for (gemmi::Model &m : st.models)
                for (gemmi::Chain &ch : m.chains)
                    for (gemmi::Residue &r : ch.residues)
                        for (gemmi::Atom &a : r.atoms) {
                            if (a.is_hydrogen())   // hydrogen scatters no anomalous signal
                                continue;
                            sites.push_back({fmt::format("{} {} {}{}", a.name, r.name, ch.name,
                                                         r.seqid.str()),
                                             rms > 0 ? grid.interpolate_value(a.pos, MAP_INTERPOLATION_ORDER) / rms
                                                     : 0.0});
                        }
            std::sort(sites.begin(), sites.end(),
                      [](const auto &x, const auto &y) { return x.sigma > y.sigma; });

            // A model and a dataset in opposite hands turn every anomalous peak into a trough, so a
            // map whose deepest hole at an atom is both deep and deeper than its highest peak says
            // the two disagree about the hand. That is worth reporting: it is real evidence about
            // the crystal, and the alternative - reindexing until the two agree - would erase it.
            if (!sites.empty()) {
                const auto &deepest = sites.back();
                if (deepest.sigma < -ANOMALOUS_INVERSION_SIGMA && -deepest.sigma > sites.front().sigma) {
                    result.anomalous_hands_disagree = true;
                    result.anomalous_deepest_site = deepest.label;
                    result.anomalous_deepest_sigma = deepest.sigma;
                }
            }

            if (sites.size() > MAX_ANOMALOUS_SITES)
                sites.resize(MAX_ANOMALOUS_SITES);
            result.anomalous_sites = std::move(sites);
        }
    }

    // --- the enantiomorph, now that there is something to decide it on ---
    // Two things have to hold before the model's hand is written on these data. The model has to
    // describe them at all - the label is an assertion about the crystal, and a model that fits no
    // better than its own random placements is in no position to make one. And the anomalous map, the
    // only measurement here that is sensitive to the hand at all, must not contradict it: R-free
    // cannot (measured, inverting the model through the origin moves R-work by less than 1e-4, because
    // |F(h)| of the inverted structure is |F(-h)| = |F(h)| on Friedel-averaged data), so where the
    // anomalous differences do say something they say it alone, and they get a veto.
    result.adopted_model_enantiomorph = result.model_enantiomorph_candidate && result.model_fits
                                        && !result.anomalous_hands_disagree;
    if (result.model_enantiomorph_candidate && !result.adopted_model_enantiomorph)
        logger.Warning("Model validation: the model asserts the enantiomorph {} against the data's {}, "
                       "and that assertion is NOT taken up: {}. The reflections are written in the "
                       "group they were merged in",
                       sg->hm, data_space_group != nullptr ? data_space_group->hm : "?",
                       result.anomalous_hands_disagree
                           ? "the anomalous density at the model's atoms is inverted"
                           : "the model does not fit these data");

    // --- MTZ of map coefficients so the maps can be re-opened / rebuilt in Coot etc. ---
    try {
        gemmi::Mtz mtz(true);
        // The group the REFLECTIONS end up in, which is the model's only where its hand was adopted -
        // AdoptModelFrame decides this the same way a few lines below. An enantiomorphic pair indexes
        // identically, so the coefficients are the same numbers either way and only the label moves;
        // but the two groups have different screw translations, so a reader that expands symmetry out
        // of this file works in the wrong one if the label disagrees with the .mtz beside it.
        mtz.spacegroup = result.adopted_model_enantiomorph
                             ? sg
                             // No data group means the caller merged in P1, and P1 is what the
                             // reflection files beside this one carry - not the model's group.
                             : (data_space_group != nullptr ? data_space_group
                                                            : gemmi::find_spacegroup_by_number(1));
        mtz.set_cell_for_all(ucell);
        mtz.add_dataset("model_validation");
        mtz.datasets.back().wavelength = wavelength_A;
        mtz.add_column("FP", 'F', -1, -1, false);
        mtz.add_column("FC", 'F', -1, -1, false);
        mtz.add_column("PHIC", 'P', -1, -1, false);
        mtz.add_column("FWT", 'F', -1, -1, false);
        mtz.add_column("PHWT", 'P', -1, -1, false);
        mtz.add_column("DELFWT", 'F', -1, -1, false);
        mtz.add_column("PHDELWT", 'P', -1, -1, false);
        // The figure of merit the coefficients carry, so the weighting can be read off - and undone -
        // from the file rather than having to be taken on trust.
        mtz.add_column("FOM", 'W', -1, -1, false);
        mtz.add_column("FREE", 'I', -1, -1, false);
        std::vector<float> data;
        for (size_t i = 0; i < terms.size(); i++) {
            // [0, 360), the convention the MTZ 'P' columns carried before sigma_A weighting: std::arg
            // returns (-180, 180] and a P column is not supposed to.
            const double phi_wrapped = terms[i].phi * 180.0 / PI;
            const auto phi_deg = static_cast<float>(phi_wrapped < 0 ? phi_wrapped + 360.0 : phi_wrapped);
            data.insert(data.end(), {static_cast<float>(terms[i].hkl[0]), static_cast<float>(terms[i].hkl[1]),
                                     static_cast<float>(terms[i].hkl[2]),
                                     static_cast<float>(terms[i].fo), static_cast<float>(terms[i].fc),
                                     phi_deg,
                                     fwt[i], phi_deg,
                                     delfwt[i], phi_deg,
                                     static_cast<float>(sigma_a.weight[i].m),
                                     terms[i].free ? 0.0f : 1.0f});
        }
        mtz.nreflections = static_cast<int>(terms.size());
        mtz.data = std::move(data);
        mtz.write_to_file(output_prefix + "_maps.mtz");
    } catch (const std::exception &e) {
        logger.Warning("Model validation: could not write map MTZ: {}", e.what());
    }

    result.ok = true;
    result.maps_prefix = output_prefix;
    // The placed coordinates, for the caller to write out beside the maps once the frame is settled.
    result.placed_model = std::make_shared<gemmi::Structure>(st);
    logger.Info("Model validation: R-work={:.4f} ({} refl)  R-free={:.4f} ({} refl)  "
                "[overall + anisotropic B + bulk solvent]",
                result.r_work, result.n_work, result.r_free, result.n_free);
    logger.Info("Model validation: bulk solvent k_sol={:.3f} b_sol={:.1f}, k_overall={:.3f}",
                result.k_sol, result.b_sol, result.k_overall);
    logger.Info("Model validation: mean 2mFo-DFc density at atom centres = {:.2f} sigma", result.mean_atom_density_sigma);
    logger.Info("Model validation: sigma_A weighting over {} resolution shell(s) (estimated on the {} "
                "free reflections): sigma_A {:.2f} at low resolution, {:.2f} at high, mean FOM {:.3f}",
                sigma_a.shells, sigma_a.free_reflections, sigma_a.sigma_a_lowest_shell,
                sigma_a.sigma_a_highest_shell, sigma_a.mean_fom);
    if (!result.anomalous_sites.empty()) {
        std::string sites;
        for (const auto &s : result.anomalous_sites)
            sites += fmt::format("{}{} {:.1f}", sites.empty() ? "" : ", ", s.label, s.sigma);
        logger.Info("Model validation: anomalous difference map from {} Bijvoet pairs; strongest "
                    "density at the model's atoms (sigma): {}", result.anomalous_pairs, sites);
    }
    if (result.anomalous_hands_disagree)
        logger.Warning("Model validation: the anomalous density at the model's atoms is inverted "
                       "({} reads {:.1f} sigma, deeper than the highest peak): the data and the model "
                       "are in opposite hands. The reflections have NOT been reindexed to make them "
                       "agree - either the model is the wrong enantiomorph for this crystal, or the "
                       "data were indexed in the wrong hand, and reindexing would hide which",
                       result.anomalous_deepest_site, result.anomalous_deepest_sigma);
    logger.Info("Model validation: wrote {}_2fofc.ccp4, {}_fofc.ccp4{}, {}_maps.mtz",
                output_prefix, output_prefix,
                result.anomalous_sites.empty() ? "" : ", " + output_prefix + "_anom.ccp4",
                output_prefix);
    if (result.fit_tested && !result.model_fits)
        logger.Info("Model validation: the model was rejected, so nothing downstream moved - the "
                    "reflection files are byte for byte the ones a run with no model would have "
                    "written. The R-factors and the maps above still describe this model against "
                    "these data, and are the negative result rather than a failure");
    return result;
}

namespace {

// The reindexing operator as it reads on Miller indices ("k,h,-l" rather than "y,x,-z").
std::string hkl_triplet(const gemmi::Op &op) {
    std::string t = op.triplet();
    std::replace(t.begin(), t.end(), 'x', 'h');
    std::replace(t.begin(), t.end(), 'y', 'k');
    std::replace(t.begin(), t.end(), 'z', 'l');
    return t;
}

}  // namespace

const gemmi::SpaceGroup *AdoptModelFrame(const ModelValidationResult &validation,
                                         std::vector<MergedReflection> &merged,
                                         const gemmi::SpaceGroup &data_space_group,
                                         bool merge_friedel,
                                         Logger &logger) {
    const gemmi::SpaceGroup *space_group = &data_space_group;
    // A model that could not be read, or that did not fit, decides nothing: the reflections are
    // written exactly as a run with no model at all would have written them. Both flags are already
    // folded into the fields below, and the guard states the rule where the frame is actually adopted.
    if (!validation.ok || !validation.model_fits)
        return space_group;

    // Adopting the model's enantiomorph is a change of the space-group LABEL and nothing else. The
    // two groups have the same rotation operations, so the same reflections, indexed the way they
    // already are, are as good a description of one group as of the other; what the file gains is a
    // group that agrees with the model it will be refined against. Reindexing here would swap the
    // Bijvoet mates and so change the data - see the note in ValidateAgainstModel.
    if (validation.adopted_model_enantiomorph && validation.model_space_group_number > 0) {
        space_group = gemmi::find_spacegroup_by_number(validation.model_space_group_number);
        logger.Info("Model validation: the written reflections take the model's enantiomorph, {} ({}), "
                    "as a label - no reflection moved",
                    space_group ? space_group->short_name() : "?", validation.model_space_group_number);
    }

    // The alternative indexing, by contrast, is metric- and group-preserving: only the labels move.
    if (!(validation.indexing_op == gemmi::Op::identity())) {
        merged = ReindexMergedIntoAsu(merged, validation.indexing_op, *space_group, merge_friedel);
        logger.Info("Model validation: the written reflections take the model's indexing, reindexed by {}",
                    hkl_triplet(validation.indexing_op));
    }
    return space_group;
}

std::vector<MergedReflection> ModelReferenceIntensities(const std::string &model_path,
                                                        const std::optional<UnitCell> &cell,
                                                        const gemmi::SpaceGroup *space_group,
                                                        double d_min,
                                                        Logger &logger) {
    std::vector<MergedReflection> out;
    if (!(d_min > 0.0)) {
        logger.Warning("Model reference: no resolution limit to compute the model intensities to");
        return out;
    }

    gemmi::Structure st;
    try {
        // Detect, not the default: without it GEMMI picks the format from the extension and only
        // falls back to the content when it does not recognise one. A model arrives named however
        // whoever produced it named it, so the file itself is the better authority.
        st = gemmi::read_structure_gz(model_path, gemmi::CoorFormat::Detect);
    } catch (const std::exception &e) {
        logger.Error("Model reference: cannot read model {}: {}", model_path, e.what());
        return out;
    }
    if (st.models.empty() || !st.cell.is_crystal()) {
        logger.Error("Model reference: model {} has no atoms or no unit cell", model_path);
        return out;
    }

    // Put the model in the cell and group the run works in, where it knows them, so the reference is
    // indexed the way the data are. The correlation that consumes this matches on hkl, so a small cell
    // difference costs nothing; the space group is what has to agree.
    if (cell.has_value()) {
        const gemmi::UnitCell target = *cell;
        if (target.is_crystal()) {
            const gemmi::UnitCell old = st.cell;
            for (gemmi::Model &m : st.models)
                for (gemmi::Chain &ch : m.chains)
                    for (gemmi::Residue &r : ch.residues)
                        for (gemmi::Atom &a : r.atoms)
                            a.pos = target.orthogonalize(old.fractionalize(a.pos));
            st.cell = target;
        }
    }
    if (space_group != nullptr)
        st.spacegroup_hm = space_group->xhm();
    const gemmi::SpaceGroup *sg = st.find_spacegroup();
    if (!sg) {
        logger.Error("Model reference: model {} has no usable space group", model_path);
        return out;
    }
    st.setup_cell_images();

    gemmi::DensityCalculator<Table, float> dc;
    dc.d_min = d_min;
    dc.rate = 1.5;
    dc.set_grid_cell_and_spacegroup(st);
    dc.set_refmac_compatible_blur(st.models[0]);
    dc.put_model_density_on_grid(st.models[0]);
    gemmi::AsuData<std::complex<float>> fcalc =
        gemmi::transform_map_to_f_phi(dc.grid, true).prepare_asu_data(dc.d_min, dc.blur, false, false, false);

    // Flat bulk solvent at the standard constants. Nothing here is fitted - there are no observations
    // yet - but without it the few lowest-resolution reflections are the largest and the most wrong,
    // and a correlation on raw intensities would be led by them.
    constexpr double K_SOL = 0.35;
    constexpr double B_SOL = 46.0;
    gemmi::SolventMasker masker(gemmi::AtomicRadiiSet::Refmac);
    gemmi::Grid<float> mask_grid;
    mask_grid.unit_cell = dc.grid.unit_cell;
    mask_grid.spacegroup = dc.grid.spacegroup;
    mask_grid.set_size_from_spacing(dc.requested_grid_spacing(), gemmi::GridSizeRounding::Up);
    masker.put_mask_on_grid(mask_grid, st.models[0]);
    gemmi::AsuData<std::complex<float>> fmask =
        gemmi::transform_map_to_f_phi(mask_grid, true).prepare_asu_data(dc.d_min, 0);

    std::unordered_map<long, std::complex<float>> mask_by_hkl;
    mask_by_hkl.reserve(fmask.v.size());
    for (const auto &hv : fmask.v)
        mask_by_hkl[hkl_key(hv.hkl)] = hv.value;

    const gemmi::UnitCell &ucell = st.cell;
    out.reserve(fcalc.v.size());
    for (const auto &hv : fcalc.v) {
        const double d = ucell.calculate_d(hv.hkl);
        if (!(d > 0.0))
            continue;
        std::complex<float> f = hv.value;
        const auto it = mask_by_hkl.find(hkl_key(hv.hkl));
        if (it != mask_by_hkl.end())
            f += static_cast<float>(K_SOL * std::exp(-B_SOL / (4.0 * d * d))) * it->second;
        const double F = std::abs(f);
        out.push_back(MergedReflection{.h = hv.hkl[0], .k = hv.hkl[1], .l = hv.hkl[2],
                                       .I = static_cast<float>(F * F),
                                       .d = static_cast<float>(d)});
    }

    logger.Info("Model reference: {} intensities computed from {} to {:.2f} A, space group {}",
                out.size(), model_path, d_min, sg->short_name());
    return out;
}