--model re-fractionalized the model into the data cell and then left it there.
On a non-isomorphous pair that is a placement error, not a cell error: the box
is squeezed, the body inside it is not moved. Six parameters now recover it -
an angle-axis rotation about the model's centroid and a translation, refined
over a 6 / 4.5 / 3.5 A ladder, the scale (k_overall, anisotropic B, k_sol,
b_sol) re-fitted at every evaluation so the target measures the placement and
not the scale. The refinement sees only the working reflections and the step is
committed only if R-free, on the free set it never saw, drops; otherwise the
model goes back where it was read.
Measured on merged lysozyme data against a deposited lysozyme model whose cell
differs by 3.4% in c: R-work 0.559 -> 0.400, R-free 0.591 -> 0.383. Over the
same 3.5 A range the external arbiter (REFMAC rigid body through dimple) works
in, 0.524 -> 0.330 against REFMAC's 0.522 -> 0.355, and the recovered movement
agrees with REFMAC's to 0.25 deg and 0.03 A (3.05 deg / 1.04 A vs 2.76 / 0.98).
2.4 s of added wall clock, 234 structure-factor evaluations.
The map coefficients become 2mFo-DFc and mFo-DFc. sigma_A is estimated by
maximum likelihood per resolution shell on the free reflections only, with the
number of shells taken from the size of the free set so no shell is thin;
centric and acentric reflections carry their own likelihoods, and a centric
reflection's bias-free coefficient is mFo. Cross-checked against CCP4 SIGMAA
on the same reflections: mean FOM 0.404 against its 0.396, with the same
per-shell structure. The figure of merit is written to _maps.mtz so the
weighting can be undone.
The per-shell scaling refusal in fit_model stands - Fobs is never rescaled and
the R-factors are untouched - but m and D are per-dataset, so maps from one
campaign are no longer scaled identically. That is argued at the code and in
docs/CPU_DATA_ANALYSIS_DECISIONS.md 14.4.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5
6b738713e8