[phenixbb] B factor refinement in recent versions of phenix

"Weiergräber, Oliver H." o.h.weiergraeber at fz-juelich.de
Thu Aug 30 08:35:17 PDT 2012


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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