[phenixbb] Refinement of B-factors at low resolution

Pavel Afonine pafonine at lbl.gov
Thu Mar 21 23:09:52 PDT 2013

Hi Florian,

I think it is pretty convincing that refinement went all right and the 
mean B you get is what it actually is. Also I just looked at the files 
that you sent me the other day and I did not notice anything suspicious.


P.S.: Sorry if you received multiple copies of this email: I was trying 
to attach a tiny image with some PDB statistics but our server did not 
let me do it.

On 3/21/13 1:00 AM, Florian Brückner wrote:
> 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
> Florian
> Am 21.03.2013 um 06:40 schrieb Pavel Afonine <pafonine at lbl.gov 
> <mailto: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 
>>> <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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> -------------------------------------------------------------
> 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:florian.brueckner at psi.ch <mailto:florian.brueckner at psi.ch>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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