Two decisions in the rotation two-pass flipped whenever the integration
changed, because each compared a raw number with no account of its noise.
The quality guard (RefinedPassIsWorse) counted reflections at I/sigma >= 2 in
each pass's search merge. Across two lattices that count is not like for like:
a header pass on a 7x supercell merges seven times the reflections, six in
seven empty, and their noise reached the strong count - it out-counted the
refined pass on the crystal's own lattice and the run went back to the
supercell, while that merge held more reflections at I/sigma <= -2 than at
>= 2. The guard now reads the signal as the strong count less the count at
<= -2 (the merge's own noise tail), and its dilution clause scales the
reflection count of the smaller lattice by the integer index of one lattice in
the other, so the same lattice (index 1) compares exactly as before. Measured
on 37 sets: no guard decision changes except the supercell case, which now
keeps the refined pass and the crystal's own lattice both in the configuration
that flipped and at HEAD; the axial-row arm still fires on the crystal it was
written for.
The post-refinement commit gate required each residual family to fall by any
amount. The positional family is what sees the detector geometry a commit hands
the next pass, and its sign was a coin toss where it did not move: on 9yzk it
read +7.1 % in one build and -0.14 % (0.1 of its paired noise) in the next, and
the second committed a geometry the positions had no opinion about (R-free
0.382 -> 0.412, radial misfit 0.30 -> 0.39). The gate now asks the positional
residual to fall by more than its paired standard error (both geometries read on
the same held-out reflections) and the excitation residual not to rise by more
than its own. On the 37-set validation this moves five fit decisions: 9yzk
(R-free 0.412 -> 0.394, radial misfit 0.39 -> 0.29, ISa 9.7 -> 7.8), two
canonical-pass probes whose output is unchanged, and one pre-pass commit on 9pbb
whose excitation moved +0.1 of its noise (ISa 14.77 -> 14.54, R-free 0.2353 ->
0.2357, inside the noise). The in-house myob, cytc, lyso and sparse sets are
md5-identical.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
leonarski_fandClaude Opus 5.5
eeeb724890
