Every rung of the old ladders (6 positional, then 3 B) was a full 10-cycle refinement from the placed model, so
~90% of the evaluations were thrown away and the kept trajectory had 100 iterations. The run is now:
1. a ladder from the placed model, 2 macro-cycles per trial: three positional weights (w0/1024, /128, /16), each
with the B factors held and refined (adp = 4 w), chosen by the old rule (tighter first, a later trial wins only
within the geometry bounds and by more than the R-free tie);
2. a trajectory of steps from where the last one ended, each two trials side by side - the weights as they are and
the X-ray term raised, in turn the positions' (x2, at most w0/8) and the B factors' (x4) - until a step lowers
neither R-work nor R-free by more than the tie (at most 8 steps);
3. a final ladder from there at x1/2, x1, x2.
A macro-cycle is 30 positional and 20 B iterations (the minimiser's memory kept within a trial). A trial starts
from the scale, solvent and likelihood fit its predecessor ended with (the same computation, so result-neutral),
and the slots that run share the threads.
On 5 battery MD starts (start 1 of 5f6m 1.09 A, 8dqb 2.04, 7arr 0.92, 11if 1.37, 7d98 3.32; R-free by rugnux's
scorer, REFMAC 0-cycle within 0.002), previous commit -> this, against REFMAC run to convergence (40-100 cycles):
5f6m 0.215 -> 0.167 (REFMAC 0.168), 8dqb 0.341 -> 0.290 (0.284), 7arr 0.356 -> 0.289 (0.288), 11if 0.295 ->
0.236 (0.244), 7d98 0.393 -> 0.337 (0.360). Time 5.4 / 8.6 / 7.3 / 3.9 / 10.0 s on the RTX 5080 (base 6-7 s).
Halving a weight during the trajectory never won in the logs, so steps only try raising it; the final ladder
can lower it.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 2bfb84bc4f3c72e8da37e54b728839b65a636519)
leonarski_f
6369a263b1