docs: the metal records' decision, one topology for the whole refinement

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQqN9qRD57vnShzTC37

docs/CPU_DATA_ANALYSIS_REFINEMENT.md

@@ -191,9 +191,9 @@ would pull the ion onto that atom; it stays a contact instead. The coordination
 records the metal has within its inner sphere, 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. Which records stay contacts is decided once, on the model as given:
-the solvent build's later refinements keep that decision rather than judge again distances the refinement has
-moved (a record at 2.50 Å refused, the ion slid to 2.39 Å, accepted the next round). The records are written out with the refined model as they were
+left out, as every bond to a symmetry mate is. Which records stay contacts is decided once, on the model as given: one topology serves the whole refinement, its
+solvent build included, so a record is not judged again on a distance the refinement has moved (a record at 2.50 Å
+refused, the ion slid to 2.39 Å, would have been taken). The records are written out with the refined model as they were
 read, without the names of the links made here. 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`).