I am using the latest version of phenix 1.8.1-1168

1.8.1-1168 should not have that "problem".

If you suspect there is still a problem, you can send me the data and model
files off list, explain what exactly the problem is, and I will have a look
right away.

FYI: there is Phenix mailing list for Phenix-specific questions, where I
can also explain in great details the behavior with the B-factors you

All the best,

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