Hi Jan, have a look at pages 8-14 here: http://phenix-online.org/presentations/faq.pdf 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. Pavel 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
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