Hi all, I have seen this odd behavior with a couple of ligands in phenix 2.2.1-6174: B-factors of some well-defined ligands increase significantly during a refinement, in the range of 2-fold compared with surrounding protein residues. The density hints for full occupancy - just about as strong as for the neighboring residues. As a test, I changed the occupancy of the ligand to 0.8. Phenix refines back to 1.0. If I turn off occupancy refinement, B-factors for the ligand increase even more. While the geometry looks fine, I am left with significant positive difference density. I have refined several structures for both targets with different ligands and never ran into this. Has this been seen before and is there anything I could try? I have already tested versions 6190 and 6048 and see the same behavior. Thanks, Jan