R_WORK and R_FREE score the data against a model scaled by k_overall, a
symmetry-constrained anisotropic B and a flat bulk solvent. That scale is
deliberate - a free per-shell rescale would reshape each map's radial
amplitude profile and a batch of maps would no longer be comparable - but it
can only bend one way with resolution, so whatever a dataset's own radial
profile does that k*exp(-B s^2) cannot follow is reported as R. Two reductions
of one crystal whose amplitudes differ radially therefore differ in R_FREE for
a reason that has nothing to do with either fitting the model: measured on one
such pair of runs, R_FREE moved a median +0.042 over eleven sets where
phenix.model_vs_data, which scales per shell, moved +0.002.
Report a second reading of the same fit: R_MODEL_SHELL_SCALED, one free scale
per resolution shell of the merge table, with R_MODEL as the same sum without
it and MODEL_RADIAL_MISFIT (RMS of ln k_shell) as the size of the rescale, so
the reason a comparison is or is not readable is on the page. Over all the
reflections, not the free 5%: nothing here is refined, so work and free
estimate the same quantity and the split only costs precision.
Nothing is written from it. On two sets, every output file - both maps, the
anomalous map, the map coefficients, the MTZ, the HKL and the CIF - is byte
for byte what the same commit produced without this change, and R_WORK and
R_FREE are unchanged.
On the pair above, the new R moves a median +0.0005 and holds every set
inside 0.0065 except the one that is a real regression, which it puts first
at +0.0174 where the old metric ranked it seventh. The battery reports it
beside R_free, and scores neither.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
leonarski_fandClaude Opus 5
8364cfbc40