Hi Jan, it might be helpful to provide some screen shots of the positive density you are observing. I also wonder if you have somehow introduced some model bias into your data.
All the best,John
On Friday, October 2, 2026 at 11:14:34 AM CDT, jan.abendroth--- via phenixbb wrote:
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
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