[phenixbb] Group B factor refinement not working for low resolution data

Phoebe A. Rice price at uchicago.edu
Thu Mar 12 08:18:48 PDT 2015

I've been refining a 3.4A structure (now using dev-1951) and find that anything besides TLS (with multiple groups at least) makes Rs go up.  A lot.  And I am asking it to optimize weights.


Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago

PRice at uchicago.edu<mailto:PRice at uchicago.edu>
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine [pafonine at lbl.gov]
Sent: Thursday, March 12, 2015 12:35 AM
To: 李翔; PHENIX user mailing list
Subject: Re: [phenixbb] Group B factor refinement not working for low resolution data

Hello Xiang,

short answer: try refining with all defaults plus weight optimization. If that does not go well please send me data and model files and I will do my best to make it work.

Longer answer: the way B-factor restraints are implemented in phenix.refine (that you can learn about in corresponding paper) allows refining individual Bs at any resolution. So this is why this is the first choice to try. If that does not work it's best to a) let us know and b) try group B refinement.


On 3/11/15 7:30 PM, 李翔 wrote:

I am working on my ~6A data with molecular replacement method. The MR works out and after rigid body and xyz refinement the result is OK. However, when I tried the ADP refinement with Group B factor option in PHENIX GUI, the R factor significantly increased as well as the B-factor. Any expert can help me to take a look and give some suggestions please?

Thank you very much for your help!


Li Xiang
Department of chemistry,
University of Michigan
Email:lixiang1642 at gmail.com<mailto:lixiang1642 at gmail.com>

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