<div dir="ltr">Try resetting the B-factors to some suitably low value (i.e. below the minimum for the entire structure), then refining. If they're starting out too high, it may be difficult for the minimizer to bring them down to the true values (but going in the opposite direction is not a problem).<div>
<br></div><div>-Nat</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Feb 27, 2014 at 9:50 AM, Jan <span dir="ltr"><<a href="mailto:jan.abendroth@gmail.com" target="_blank">jan.abendroth@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi all,<div>I am refining a pretty high resolution structure (1.65Å, <i>P</i>1) with two tetramers of the protein in the ASU using Phenix dev 1630.</div>
<div>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</div>
<div><br></div><div>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.</div>
<div><br></div><div>Any ideas? I am happy to share the data. It is a SSGCID target and will be in the PDB shortly anyway.</div><div><br></div><div>Thanks,</div><div>Jan</div><div><br></div><div><br></div><div><br><div>
<span style="border-collapse:separate;border-spacing:0px"><span style="text-indent:0px;letter-spacing:normal;font-variant:normal;font-style:normal;font-weight:normal;line-height:normal;border-collapse:separate;text-transform:none;font-size:medium;white-space:normal;font-family:Helvetica;word-spacing:0px"><div style="word-wrap:break-word">
<div style="font-size:12px">--</div><div style="font-size:12px">Jan Abendroth</div><div style="font-size:12px">Emerald BioStructures</div><div style="font-size:12px">Seattle / Bainbridge Island WA, USA</div><div style="font-size:12px">
<div>home: <a href="http://Jan.Abendroth_at_gmail.com" target="_blank">Jan.Abendroth_at_gmail.com</a></div><div>work: JAbendroth_at_embios.com</div><div><a href="http://www.emeraldbiostructures.com" target="_blank">http://www.emeraldbiostructures.com</a></div>
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