[phenixbb] B factor refinement in recent versions of phenix

Pavel Afonine pafonine at lbl.gov
Thu Aug 30 08:52:52 PDT 2012

Hi Oliver,

p.s.: I see you actually tried one of the latest versions (I missed it 
in my previous reply). Can you try this:

1) reset all B-factors to average or simply used the model where 
B-factors are "nomral" (not "too" small); then
2) run phenix.refine with this model.

If this does not help then please send me the inputs so I can reproduce 
this and see what's happening.


On 8/30/12 8:35 AM, "Weiergräber, Oliver H." wrote:
> Hello,
> I am experiencing a weird problem with B factor refinement (individual, isotropic) in phenix.refine.
> The dataset reveals a Wilson B factor of about 23 A². However, if phenix.refine is allowed to run for a number of macrocycles, the mean B value of the model drops continuously to about 9 A². In the end, several atoms are getting values of 0.00!
> There are no obvious abnormalities in the electron density, and R values are quite good.
> I was able to dig out an old phenix version (1.7.1) and found that this one behaves perfectly well: mean B around 26 A² (slightly above Wilson B, as is observed frequently) and minimum B around 10 A².
> So obviously something has happened between versions 1.7.1 and 1.8 ... The latest dev release (1143) shows the same behavior as version 1.8.
> I should say that this structure is somewhat peculiar (pseudomerohedral twinning plus twofold NCS), but again, the old phenix version handles that without problems.
> Moreover, the tendency for unreasonably low B factors has been observed recently for a more "conventional" structure in our lab.
> Any ideas what might be causing this and how to revert to the original behavior?
> Thanks in advance
> Oliver
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