[phenixbb] Refinement of B-factors at low resolution

Keitaro Yamashita yamashita at castor.sci.hokudai.ac.jp
Mon Mar 18 16:06:02 PDT 2013

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,

2013/3/19 Florian Brückner <florian.brueckner at psi.ch>:
> 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
> -------------------------------------------------------------
> 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:  florian.brueckner at psi.ch
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