[phenixbb] Refinement of B-factors at low resolution

Pavel Afonine pafonine at lbl.gov
Mon Mar 18 09:45:48 PDT 2013

Hi Florian,

interesting observation... I don't have explanation right away, but if 
you send me the data and model then I will have a closer look and may be 
come up with an idea.


On 3/18/13 8:19 AM, Florian Brückner wrote:
> 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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