Re: [phenixbb] Refinement of B-factors at low resolution

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 mailto:[email protected]>:

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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 mailto:[email protected]>:

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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