[phenixbb] Refinement of B-factors at low resolution

Pavel Afonine pafonine at lbl.gov
Wed Mar 20 22:40:58 PDT 2013

Hi Florian,

I'm glad it works now. Regarding difference between Wilson B and mean 
refined B: well, it's hard to quantify what's "too low" or "too 
different". Average refined B may deviate from Wilson B and the 
difference in your case does not seem to be terribly large.
Did the refinement converge? What if you do say 10 or 20 macro-cycles 
instead of default 3? Will B-factors further change between macro-cycles?


On 3/19/13 7:37 AM, Florian Brückner wrote:
> Dear Keitaro and Pavel,
> thank you for your suggestions. I have now used the latest nightly 
> build (1326). With this version, the average B-factor converges at 
> about 52 A**2 and also the distribution is very similar, regardless 
> with what B-factors I start the refinement (I tried average B-factors 
> between 32 and 97). So clearly the behavior of this newest version is 
> different from the version I have been using before (1.8.1 stable 
> release 1168) and also from the latest stable release (1.8.2 stable 
> release 1309), which behaves the same as 1168. To me the B-factors 
> still look a bit too low, since the Wilson B-factor calculated by 
> phenix is 66.45, the Wilson B-factor I determined manually from the 
> linear part of the Wilson plot is 97.
> Best regards
> Florian
> Am 19.03.2013 um 00:06 schrieb Keitaro Yamashita 
> <yamashita at castor.sci.hokudai.ac.jp 
> <mailto:yamashita at castor.sci.hokudai.ac.jp>>:
>> 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 <florian.brueckner at psi.ch 
>> <mailto: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

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