The published R-free comes from the depositors' own refinement (mostly phenix.refine), while the
battery refines with dimple's 8 REFMAC cycles, so the two are not like-for-like: on LCLS 222 (8TDQ)
the deposited intensities reach 0.1918 under dimple against a published 0.2012.
Every set now carries "R-free deposition (dimple)": the deposition's -sf.cif (intensity_meas, else
the mean of the anomalous pair, else F_meas_au squared) refined with the same refine() as our merge -
same deposited model, the deposition's free set, cut at its resolution. It is computed once per entry
and resolution and kept in the PDB cache (<pdb>-dimple-<d_cut>/reference.json); `run` and `report`
fill in a missing one, `reference` computes or lists them up front. The report gains the difference
(ours minus the deposition's) and a quality verdict (win below -0.01, draw within 0.01, loss
otherwise); the published R-free stays as an informational column.
Reproduces the hand-computed references: 8TDQ 0.1918, 9V3D 0.2220, 31JT 0.1945.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
leonarski_fandClaude Opus 5.5
0bf4bdb9d0