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

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.

I think the Wilson B calculated from the linear part (say beyond 3A) should be _lower_ than the average atomic B, because well-ordered parts of the structure contribute disproportionately to the high-resolution scattering and the disordered bits contribute nothing in that range, while the average atomic B weights each atoms contribution the same. Sort of like log(average) is not the same as average(log). But then if Wilson B is 97 I wouldn't expect diffraction to extend much beyond 3A. OK, this is 3.2A data. In that case I think there is no linear part- from the ideal wilson plot that arp-warp shows us, in the region 4-3A the value is coming down off a peak due to secondary structure, and is considerably steeper than in 3-2 A range. So the value of 97 may be an overestimate. Would the following sanity check with another suite make sense? Calculate Fc,Phic from the refined model with sfall, and scale the raw data against that and Fmask,PhiFmask from phenix.refine with ccp4 icoefl program. If the overall B applied to the raw data is far from zero, it suggests something is fishy about the atomic B's? 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

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Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland

Tel.: +41-(0)56-310-2332 Email: [email protected] mailto:[email protected]

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-------------------------------------------------------------

Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland

Tel.:+41-(0)56-310-2332 Email:[email protected] mailto:[email protected]

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