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<div class="moz-cite-prefix">Hi Florian,<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
On 3/18/13 8:19 AM, Florian Brückner wrote:<br>
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Dear all
<div><br>
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<div>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.</div>
<div><br>
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<div>Thanks for any comments or suggestions.</div>
<div><br>
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<div>Best regards</div>
<div><br>
</div>
<div>Florian</div>
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