Five open-arm rows do not reproduce their deposited space group or cell. Four are
scoring rows that disagreed with a published entry with nothing written down about
why, which is not a state a reader should have to discover from the manifest.
A tetragonal row whose deposited asymmetric unit holds two chains related by the very
two-fold the higher group adds, to 0.16 A CA RMSD - coordinate error at its
resolution - is overridden to the higher group. Merging there costs 0.0006 in R_meas
for 1.75x the multiplicity and correlates better with the deposited model, and an
independent reference implementation reads the same point group on our own P1 merge.
The refinement comparison is recorded as SPLIT: one purpose-built program makes the
higher group better at half the parameters and calls the deposited assignment
incorrect, an independent restrained refinement on a symmetry-consistent free set
makes the lower group better, and the gap between refinement protocols exceeds the
difference being measured.
One trigonal row becomes unscored rather than overridden: the evidence points at a
higher point group but the deposited copies differ by more than coordinate error, and
a purpose-built program settles on a different supergroup whose operators these data
do not support. The set runs; it is not scored.
Two trigonal rows had already been overridden, by editing the reference itself, with
no reason recorded. The deposition is restored verbatim to ref and the change moved
into ref_override, which leaves the effective reference and every verdict unchanged.
One of them carries strong centric-zone evidence; the other is marked OPEN, because
the one test that separates real symmetry from pseudo-symmetry reads against the
promotion the row is scored on, and may belong unscored instead.
The documentation frames all of these as open questions rather than as errors in the
PDB, and states the limit that applies to every one of them: a merohedral twin at a
fraction of exactly one half and a crystal that genuinely has the higher symmetry
predict identical intensities, so no test available to us can show that an operator
holds exactly rather than very nearly.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
leonarski_fandClaude Opus 5
2f453e018f
