[phenixbb] unusually high B-factors for selected -heavier- atoms

Pavel Afonine pafonine at lbl.gov
Thu Feb 27 11:13:26 PST 2014

Hi Jan,

have a look at pages 8-14 here:

If this does not help please send me model and data files (as well as 
ligand CIF files, if any) and I will help to solve this problem one way 
or another. This question is quite typical and in most cases the recipe 
above solves the problem.

Problem of large B (that Nat mentioned) is a possibility, though 
B-factors should be above 100 to cause that sort of problems.


On 2/27/14, 9:50 AM, Jan wrote:
> Hi all,
> I am refining a pretty high resolution structure (1.65Å, /P/1) with 
> two tetramers of the protein in the ASU using Phenix dev 1630.
> Refinement statistics looks really good, R=0.16 Rf=0.18, maps are very 
> clear. However, several sulphur atoms of the protein, and in 
> particular the phosphorous atoms of its cofactor NAD have inflated 
> B-factors, along with distinct FoFc peaks. For instance B-factors for 
> a Met with very well defined density: CB=19.7, CG=27.5, SD=62.2, CE=38.4
> For some of the residues it is comparable when I refine with or 
> without TLS groups. I used one group per chain of this compact 
> protein, the cofactor is part of each TLS group. Restraints for NAD 
> were generated via eLBOW. When I refine the structure in refmac, using 
> either the standard cif file or the eLBOW generated one, B-factors 
> remain low.
> Any ideas? I am happy to share the data. It is a SSGCID target and 
> will be in the PDB shortly anyway.
> Thanks,
> Jan
> --
> Jan Abendroth
> Emerald BioStructures
> Seattle / Bainbridge Island WA, USA
> home: Jan.Abendroth_at_gmail.com
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140227/484dd852/attachment-0001.htm>

More information about the phenixbb mailing list