Hi Oliver, can you try the latest Phenix: http://www.phenix-online.org/download/nightly_builds.cgi Let me know if this does not fix your problem. Pavel 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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