Refinement score: the model's structure factors as REFMAC 5.8 scores them at 0 cycles

Three terms of the score of a model - the same F_model at every stage, the as-given start and the
refined end alike - and a breakdown of it:

- Riding hydrogens from the start: the dictionary's hydrogens are added before the model is first
  scored (REFMAC's 0-cycle restores them; they move R by 0.010-0.013 at 1.1 A). The engine is made
  once, with them.
- The bulk-solvent mask on a grid of its own, min(d_min/3, 0.4 A), at most 2^26 points. On the
  density grid (1.1 A at 3.3 A) gemmi's 0.8 A shrink found no grid offset and was skipped, which put
  R 0.015-0.03 high at >= 2.5 A. 0.3 and 0.4 A agree to 0.001.
- The overall scale and anisotropic B by robust least squares (pseudo-Huber, iteratively
  reweighted, c = median |residual|) in the fine pass of the k_sol/b_sol grid (ModelScaleBox::robust,
  refinement only; MR and validation keep the plain fit). Plain least squares on |F| is the exact LS
  optimum but lets a few badly-fitted strong reflections set the scale (1.1 A set: R 0.1706 against
  REFMAC's 0.1600). The scale fit of refinement now runs on the CPU (no ModelScaleGPUPool).

RefinementSettings::score_only scores the model as given and stops; RefinementResult::score_start
carries every term (k, B, anisotropic B, k_sol, b_sol, mask spacing, R in 20 shells, -lnL work/free,
the likelihood FOM, hydrogens; per-reflection terms with score_only). GeometryStatistics gains rmsZ.
rugnux_refine_test: --score-only, --dump.

Measured against REFMAC 5.8.0431 ncyc 0 (refi bref iso) on the same model, data and flags, 14 open-arm
sets 1.1-3.6 A: R-work/R-free within 0.002 on 12 (was +0.003..+0.03); 7n2s and 9yl4 score 0.003/0.005
below REFMAC, which a 0.6-0.8 A mask grid reproduces. REFMAC with ANISOU stripped scores identically,
so isotropic B is not a parity term. Open: the likelihood's D/FOM (ours 0.01-0.11 higher at high
resolution); geometry differs only by REFMAC's metal LINK restraints and residues outside the
embedded dictionary.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 4f94b21611874ad9dcf89e6771fe311a0e10bb06)
(cherry picked from commit 00db6a6f539ac2da515c0a649474335f4c4b07b8)

image_analysis/structure_refinement/RefinementXray.cpp

@@ -228,6 +228,26 @@ RefinementReflections PrepareRefinementReflections(const std::vector<MergedRefle
     return out;
 }
 
+BulkSolventMask::BulkSolventMask(const gemmi::UnitCell &cell, const gemmi::SpaceGroup &sg, double d_min,
+                                 size_t nthreads)
+    : nthreads_(nthreads),
+      spacing_(std::max(std::min(d_min / 3.0, MASK_SPACING_MAX), std::cbrt(cell.volume / MASK_POINTS_MAX))) {
+    grid_.unit_cell = cell;
+    grid_.spacegroup = &sg;
+    grid_.set_size_from_spacing(spacing_, gemmi::GridSizeRounding::Up);
+    orbit_leaders_ = OrbitLeaders(grid_, nthreads);
+}
+
+void BulkSolventMask::Fmask(const gemmi::Model &model, const std::vector<gemmi::Miller> &hkl,
+                            std::vector<std::complex<float>> &f) const {
+    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 : 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();