Refinement (Refinement.h) now runs whenever --model or --mr places the model (rigid body fits, or
molecular replacement placed it), on the GPU or the CPU: a run that should not spend the time is
given no model. --no-refine skips it (for debugging); --refine is still accepted and ignored. A
model that was not placed (rejected by the rigid body, not placed by MR - e.g. the battery's
wrong-model null) is no longer refined.
Processing-inert as before: it runs after every decision; R_WORK/R_FREE and every key outside
REFINE_ (section 5), and <prefix>.mtz / _model.cif / _maps.mtz, are unchanged. The block moved
after the placement notes so they stay on the step that placed the model. The viewer's processing
jobs refine too. The equivalent command line gives --no-refine back where refinement was off.
Battery: score.py reads keys exactly, so REFINE_R_FREE cannot alias R_FREE; new report-only
fields rfree_refined, rwork_refined, refine_s (part of rugnux_wall_s), shown in the per-set table.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit b0bb741831f517b553e59152b3b482a3f75d953a)
leonarski_f
7bf906e4a2