I also have the same problem in some local refinement jobs, with masks created using volume tools (after segmentation in ChimeraX). The masks are unlikely to be the problem, since local refinement jobs with different particle subsets, but the same mask, sometimes work.
The problem occurs when:
- use pose/shift gaussian prior during alignment = TRUE
- minimize over per-particle scale = TRUE
The job then runs after either setting minimize over per-particle scale = FALSE or reset input per-particle scale = TRUE
Also, a local refinement on the same particle set with another mask works without problems.
Actually, so far I’ve encountered this problem only with the smallest mask I’m using (encompassing roughly 90 kDa).