[phenixbb] Refinement of B-factors at low resolution

Florian Brückner florian.brueckner at psi.ch
Thu Mar 21 01:00:15 PDT 2013

Dear Pavel

yes, the refinement did converge. I did 6 macrocycles and in separate runs started from different average atomic B-factors of 32, 66 and 97 keeping the distribution as in the original high resolution molecular replacement model from the same crystal form (i.e. adding 0, 34 and 65 to all atomic B-factors in the starting pdb). In all cases after 6 macrocycles I get an almost identical distribution of B-factors and also average B-factor of about 52. Also setting all B-factors to the same value of 66 gave a similar distribution after refinement with an average of 52. However, in the latter case the R-free was about 2% higher compared to starting from the original distribution, but it dropped by about 1% during refinement.

Best regards


Am 21.03.2013 um 06:40 schrieb Pavel Afonine <pafonine at lbl.gov>:

> 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?
> Pavel
> 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>:
>>> 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>:
>>>> 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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Dr. Florian Brückner
Laboratory of Biomolecular Research (LBR)
Paul Scherrer Institut
CH-5232 Villigen PSI

Tel.:		+41-(0)56-310-2332
Email: 	florian.brueckner at psi.ch

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