[phenixbb] High B-factors after Phenix restrained refinement

Pavel Afonine pafonine at lbl.gov
Fri Dec 16 08:56:48 PST 2011

I agree, it is a matter of convention. The total ADP is: 
Utotal=Ucryst+Ugroup+Ulocal. You can either output the total Utotal into 
ATOM/ANISOU records or keep Ucryst+Ugroup in REMARKs and output Ulocal 
into ATOMs. Both ways are valid as long as they yield identical Utotal.

For more relevant information, summary and some review, see:

- pages 23-29 here:

- article "On atomic displacement parameters (ADP) and their 
parameterization in PHENIX" here:


On 12/16/11 8:11 AM, Steiner, Roberto wrote:
> Hi Da
> Even if you deposit a structure refined with Refmac the PDB now 
> expects the total B values being present. Have a look at
> http://deposit.rcsb.org/adit/REFMAC.html
> What you call "more" correct does not really make much sense to me if 
> I understand you properly. If you follow the link given above (or use 
> TLSANL directly from the CCP4) and get 'total Bs' from Refmac  I am 
> sure they will be more or less the same and the Bs from phenix.refine.
> R
> On 16 Dec 2011, at 15:54, Da Duan wrote:
>> Hi Nat
>> I was just looking at the average B in the refinement log files from 
>> Refmac and Phenix Refine. Thanks for the clarification on how Refmac 
>> and Phenix calculate the average B. My next question is when 
>> depositing the structure, is it more common to deposit structures 
>> with the "residual" B-factors or B-factors generated by Phenix that 
>> includes the TLS and Ucryst contribution? I also performed sfcheck 
>> and the average B generated by the Wilson plot is ~100 which seems to 
>> suggest that the Phenix average B is probably "more" correct?
>> Thanks again
>> Da
>> On Fri, Dec 16, 2011 at 12:31 AM, Nathaniel Echols <nechols at lbl.gov 
>> <mailto:nechols at lbl.gov>> wrote:
>>     On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <2dd13 at queensu.ca
>>     <mailto:2dd13 at queensu.ca>> wrote:
>>     > I used Phenix AutoMR to solved a structure to 3.3A and after 1
>>     round of
>>     > rigidbody refinement with Phenix Refine I proceeded to restrained
>>     > refinement. The R/Rfree from the refinement decreased nicely as
>>     expected but
>>     > the B average is at ~100 (using Group B factor refinement
>>     option). I took
>>     > the same model and mtz through Refmac and the B average is
>>     about ~40. Has
>>     > anyone experienced this before? I am almost positive it maybe a
>>     setting
>>     > issue in Phenix Refine that i should be looking at to get the B
>>     factors to
>>     > refine correctly.
>>     How are you calculating the average B?  Refmac prints "residual"
>>     B-factors in the B column of ATOM records - these do not include the
>>     contribution from TLS and Ucryst (an overall B-factor for the entire
>>     crystal).  In Phenix, the ATOM records always have the total
>>     isotropic
>>     B-factor, and this will always be higher than the equivalent in
>>     Refmac.  So it's quite likely that both programs are correct, they're
>>     just reporting very different things.  (And for what it's worth, a
>>     mean B-factor of 100 is totally normal at 3.3A resolution.)
>>     -Nat
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>> <ATT00001..c>
> Roberto Steiner, PhD
> Randall Division of Cell and Molecular Biophysics Group Leader
> King's College London
> Room 3.10A
> New Hunt's House
> Guy's Campus
> SE1 1UL, London, UK
> Tel 0044-20-78488216
> Fax 0044-20-78486435
> roberto.steiner at kcl.ac.uk <mailto:roberto.steiner at kcl.ac.uk>
> _______________________________________________
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