[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.
Pavel
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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