Hi, this is just a summary.. In a nutshell the problem was following. Assuming total model structure factor is (for simplicity): Fmodel ~ exp(-Boverall_scale) * exp(-Batoms) it's clear that Boverall_scale and Batoms are correlated, and any combination of Boverall_scale and Batoms that maintains Boverall_scale+Batoms=const will not change the the total model structure factors (and therefore R-factors, etc). The new bulk-solvent and overall scaling algorithm that I switched to in April did not care about returning isotropic component of Boverall_scale back to atoms: http://www.phenix-online.org/presentations/PhenixSantaFe2012_PA.pdf In fact (as explained above), the new algorithm does not use analytical form for overall scale at all. Therefore a portion of Batoms was systematically absorbed by Boverall_scale. Not sure if this is a real problem, but to be consistemt with previous versions and expectations, recently (may be a month ago or so) I changed it such that isotropic exponential component of overall scale is added back to atoms. So current version of phenix.refine should not produce these "too small" B-factors anymore. Anyone who experience this problem please try the latest Phenix from nightly builds: http://www.phenix-online.org/download/nightly_builds.cgi If this does not solve the problem please let me know. The most efficient way to let me know is to send me data and model files so I can reproduce and fix the problem. Thanks, 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