I’m
using 1.6.1 r393. The logfile shows 10 “Mask
optimization: start’ entries in 1 macrocycle total composed of
rigid_body
(2 zones), individual positions and adp refinement.
I see. Yes, the bulk solvent model gets updated during rigid body
refinement but the mask should not be optimized. Looks like it's not
the case. I'm fixing it now and it will be in the next available
nightly build. Thanks for finding this!