[phenixbb] maximum allowable B-factor value

Pavel Afonine pafonine at lbl.gov
Wed Oct 27 09:45:42 PDT 2010

  Hi Christian,

what is the resolution? You may want to tighten up the B-factor 
refinement restraints manually, by making wxu_scale parameter smaller 
(try several values until the refined B-factors "make sense" and the 
R-factors are still ok). Alternatively, you may try group B-factor 
refinement (again, if the resolution is low enough to make individual 
B-factor refinement not favorable).

Also, the high B-factors may simply reflect the fact that those atoms do 
not have a good density. In this case making the B-factors of bad atoms 
to be similar to the B-factors of good atoms (by tightening the 
restraints) is not a good idea.

So, as you can see there is a number of nuances that you need to consider.


On 10/27/10 11:26 AM, Christian Roth wrote:
> Dear all,
> I did a refinement run with a built in ligand. Within the ligand the B-factor
> jumps between two connected atoms from 60 up ~110, which is i think a bit too
> much. Is there a way to restrain the B-factors that they could not jump so
> much. I would accept negative difference density for the atom. Maybe the ligand
> is a bit degraded.
> Best regards
> Christian
> @Pavel Tanks for your suggestions with occupancy refinement and B-factors.

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