Opt-in. After the model's placement and everything it decides (setting, indexing, enantiomorph, MR, twin
choice), the placed model is refined against the merge it was placed on (RefineModel) and the blobs of the
refined mFo-DFc map are listed (FindDensityBlobs). Nothing reads the outcome: the reflection files, the
space group and R_WORK/R_FREE of the model as given are those of a run without --refine.
Writes <prefix>_refined_model.cif/.pdb, <prefix>_refined_maps.mtz (FP FC PHIC FWT PHWT DELFWT PHDELWT FOM
FREE) and <prefix>_blobs.json; the report's model section gains REFINE_* keys (start, placement and
restrained R-factors, rmsd bonds/angles, clashes, fixed residues, weights, blob counts by kind) and the five
strongest blobs. Documented in RUGNUX_MODEL_AND_REFERENCE.md and CPU_DATA_ANALYSIS.md.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit aaee92711a205bf6a575a47c4db4555d34e7e8fe)
leonarski_f
7759643d4c
