The INDEXING_AMBIGUITY warning was suppressed whenever --model was given on
rotation data, decided before the model was read. A model that then decided
nothing - not tested, rejected, or a probe winner that did not beat its own null
- still silenced it, so WARNING_COUNT, PATHOLOGY_FLAGS and possibly VERDICT
differed from a run without the model although the written reflections were
identical.
The warning is now issued exactly as without a model, and withdrawn (from the
warnings and from the statistics text) after model validation only where the
indexing probe decided the indexing: the model fits and the winner's R-free
margin beats the random-placement null (ModelValidationResult::indexing_decided,
set where the decision is taken). A reference MTZ, or the model reference on
serial stills with -C and -S, suppresses it up front as before.
Verified bare vs --model on three open-arm sets: merged MTZ data identical in
all three; warnings identical where the model decided nothing (identity probe
without null; no twin law); withdrawn where the probe decided (+33 sigma).
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5
6a26591786