The column was written with 1 for the test set and 0 for the working set - the
phenix/CNS numbering - under FreeR_flag, which is CCP4's column name. CCP4's own
freerflag writes 0..19 with 0 as the test bin, and REFMAC5's default FREE 0
reads it that way, so REFMAC5 stopped on every file we wrote: "more than half of
reflections are in free R set", then "Cannot switch free R flag", exit 1.
phenix auto-detects either numbering with equal confidence (measured on both,
score 3 each), and rugnux's own reference-MTZ reader already takes flag 0 as the
test set, so 0 = test is the numbering that works everywhere and the one the
rest of the code assumes.
This changes every merged .mtz we write: a script that reads FreeR_flag == 1 as
the test set has to be inverted. The mmCIF's _refln.status_free is a separate
item with its own convention and is unchanged.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5
47ec939c39