Dear Florian,
Maybe you are using phenix-dev-1311 or earlier?
I am afraid that you have experienced the bug that overall B-factor is
not applied to individual atomic B-factors in certain cases, which I
have also experienced recently. That bug was fixed in dev-1312 if I
recall correctly.
Hope it helps,
Keitaro
2013/3/19 Florian Brückner
Dear all
I am refining a structure at 3.2 A with phenix.refine using automatic optimization of target weights, solved by molecular replacement with a 2.1A structure of the same crystal form. Rwork=26%, Rfree=28%. I use individual atomic B-factor refinement. The obtained distribution of B-factors after refinement looks reasonable and quite similar to the distribution in the higher resolution model, which I suppose would be expected, since it is the same crystal form. However, the average B-factor does not change substantially, i.e. if I start with the B-factors from the high resolution model (average B-factor around 32 A**2) after 6 macrocycles the average B-factor is still around 32 A**2. If I set all B-factors to the Wilson B-factor determined by phenix.refine (66 A**2), after 6 macrocycles the distribution of B-factors looks again very similar to the high resolution MR model, but the average B-factor is still around 65 A**2. What should I make of this? Is this an expected behavior at this resolution, i.e. the fact that the absolute values of B-factors cannot be determined during refinement, although a reasonable distribution can be obtained as judged by plotting average B-factors vs. residue#? Since the average B-factor does not change much during refinement, which average B-factor should I start refinement with to end up with reasonable absolute values? I have manually determined the Wilson B-factor from the linear part of the Wilson plot (4.5-3.2 A) to be 97 A**2. This seems high to me. Would that be expected for the given resolution, given that the 2.1A structure of the same crystal form has 32 A**2? I should add, that there is not a substantial effect of the average refined B-factor on Rfree.
Thanks for any comments or suggestions.
Best regards
Florian
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Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland
Tel.: +41-(0)56-310-2332 Email: [email protected]
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