- New docs/CPU_DATA_ANALYSIS_REFINEMENT.md (§15): the ML amplitude target and its FFT gradient,
scale/robust fit/fine solvent mask, D and the variance (work/free), the embedded Monomer Library
subset and topology, geometry/metal/KL-B restraints, the minimiser, the weight trials, refined maps,
blobs, GPU/CPU, and a "Not yet" list; with its own References. Linked from TECHNICAL.md and
CPU_DATA_ANALYSIS.md; §14 no longer says the structure is never refined.
- RUGNUX_REPORT.md: a Refinement (REFINE_*) section - every REFINE_ and REFINE_SCORE_ key, the
--mode refine input keys and the _blobs.json fields.
- RUGNUX_MODEL_AND_REFERENCE.md: "What it does not do yet"; RUGNUX_ADVANCED.md: --model mentions the
refinement, --no-refine as in the usage, a --mode refine options table; GPU_DATA_ANALYSIS.md: the
refinement's CUDA engines and the missing Metal path.
- ACKNOWLEDGEMENT.md: Brunger, Karplus & Petsko 1989 (gradient-balanced starting weight), Nocedal 1980
(two-loop recursion), Charbonnier et al. 1997 (pseudo-Huber), Jiang & Brunger 1994 (flat solvent
mask), Kullback & Leibler 1951; all DOIs checked against Crossref.
- In-source credit lines: the weight balancing (replacing a "Brunger (1992)-style" line that named the
R-free paper), Nocedal 1980, Charbonnier 1997, Jiang & Brunger 1994, Emsley et al. 2010 at
FindDensityBlobs, Read 1986 at the refined maps. Comments only.
- docs/THIRD_PARTY_NOTICES.md regenerated from the root file with update_version.sh's own step (it
lacked the CCP4 Monomer Library row).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 09375dba351bae0cc73e9a6f0f79455dc92b3a10)
Measured by stripping the deposited ligands and ions of 12 open-arm models (placement-refined, then the
blobs of mFo-DFc): ligands with a blob 34/39, called LIGAND 26/39, LIGAND blobs on a removed ligand or ion
24/33; ions with a blob 23/40. The ligand-size threshold was four resolution spheres, which called no glycan
at 3.3 A and every ion at 1.1 A; it is now one and a half, and never under 8 A^3.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 8e66d58ba87c35119df3ba8779ca193053f5cf00)
RefineModel (Refinement.h) refines a placed model against the merge, reading and writing nothing:
- placement stage (R1): every chain of 50+ atoms as a rigid body at once (L-BFGS on six parameters per
chain, their gradient from the per-atom one through Ceres jets), then one B shift per residue;
- restrained stage (R2): positions and isotropic B of every atom of a residue the embedded dictionary
describes, the rest held fixed but kept in Fcalc and the mask; riding hydrogens added by gemmi's
topology, moved with their parents, re-placed every macro-cycle. Macro-cycles refit the mask, the
scale and bulk solvent (FitModelScale / ModelScaleGPUPool) and the likelihood's D and beta (ML on
the free set in resolution bins), rebuild the repulsion pairs (symmetry mates included), then L-BFGS
on positions and, where chosen, on B.
- weights: a ladder of full refinements at multiples of the gradient-balanced X-ray weight, chosen by
R-free within bond/angle bounds (ties to the tighter geometry), then the B refinement tried at its own
weights and kept only where it beats B held by more than the tie.
The target and its gradient (RefinementXray, RefinementGPU): the Rice/centric amplitude likelihood
(RefinementMath.h, shared host/device code), the gradient by Agarwal's FFT method - the adjoint of the
reciprocal-space symmetry composition into a half-l (CPU) or half-u (cuFFT) spectrum, one inverse real
transform, then each atom's density derivatives (xyz and B) summed over its box. On the GPU everything
per evaluation stays on the device: ModelDensityGPU's gather, r2c, a fused compose + likelihood kernel,
a CSR gather for the adjoint (no atomics), c2r, one warp per atom for the gradient; the restraints are
one kernel per restraint plus a per-atom gather of gradient slots; cub reductions. Deterministic.
Restraints (RefinementRestraints): bonds, angles, torsions (with esd, no phi/psi, no alternative sugar
puckers), chiral volumes, least-squares planes from gemmi's Topo; repulsions beyond 1-4 (vdW radii from
the dictionary's energy library, 2.6 A for H-bond pairs, 1.9 A metal-N/O/S); B similarity of bonded and
angle-related atoms.
DensityBlobs (D1): gemmi's flood-fill blobs of mFo-DFc above 3 sigma peaking above 4 sigma, placed beside
the model and labelled WATER / ION / LIGAND / MODEL_ERROR by distance, contacts, volume and the anomalous
map.
tools/rugnux_refine_test refines a model against a finished run's p.mtz (developer utility, not
installed). Tests: likelihood derivative, the embedded library, restraint values on ideal residues and
every restraint kind's gradient against finite differences (CPU, and the GPU against the CPU), the X-ray
gradient against finite differences in P1, P212121, C2 and P6122 (CPU and GPU), and a synthetic
refinement that recovers a shaken model. Credits in docs/ACKNOWLEDGEMENT.md and at the algorithms.
Measured on the open arm's battery outputs against REFMAC 5.8, 10 cycles, same p.mtz, free set and start
model (R-free): 5reo 0.2228 vs 0.2236, 8dyz 0.1733 vs 0.1651, 9chw 0.1995 vs 0.1969 (CPU engine).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 8efe6f2322b3bfdae580bb34f256e67730dfc3c2)
leonarski_f