depdata_check.py compares each open-arm merge with the depositor's own data, per resolution
shell, using the deposited model as the common yardstick: the rank correlation of our IMEAN with
|Fc|^2 minus that of the deposited intensities (or F^2), on the reflections both carry (d < 4 A,
eight equal-count shells), with the data carried into the model's setting by model_check's
change-of-basis search. New row keys dep_cc_delta_all, dep_cc_delta_outer (two outermost common
shells), dep_beyond_cc / dep_beyond_d (our correlation with |Fc|^2 past the deposited data's
limit), dep_kind, dep_d_min, dep_n_common, dep_status, dep_reason. gemmi only, no CCP4; runs on
every open-arm set with a model, and `report` fills it in for older runs (four processes).
Reported in its own report section and the per-set table, never scored.
Rank rather than Pearson correlation: on the phase-1 run a handful of gross outliers (I/sigma
above 1000 at 2.4 A, or ~1000x the shell median at 1.41 A) decided the outer-shell Pearson CC of
several merges on their own.
On the phase-1 run (38 of 40 open-arm sets compared; the two without are the lattice failures)
the outer-shell delta has median -0.012; 22 s for the whole report fill-in.
model_check.py: REFMAC's mmCIF reader stopped with "rdaniso_cif: Atom symbol mismatch" on 12 of 35
entries whose atoms carry ANISOU only in part. The model is now written in the PDB format where it
fits (under 100000 atoms, chain names of at most two characters), where each ANISOU follows its
own ATOM line; all 12 then score. R-factors of the entries that worked before move by < 0.001.
The runner also records model_check's baseline note (e.g. an intensity-only deposition) in
refmac_reason instead of leaving it empty.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5.5
9b7a91d521