<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Jan,<br>
<br>
have a look at pages 8-14 here:<br>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/presentations/faq.pdf">http://phenix-online.org/presentations/faq.pdf</a><br>
<br>
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.<br>
<br>
Problem of large B (that Nat mentioned) is a possibility, though
B-factors should be above 100 to cause that sort of problems.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/27/14, 9:50 AM, Jan wrote:<br>
</div>
<blockquote
cite="mid:D87628CC-A657-4B4C-B14F-C230C0C2EF00@gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
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 apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse:
separate; border-spacing: 0px; "><span
class="Apple-style-span" style="border-collapse: separate;
color: rgb(0, 0, 0); font-family: Helvetica; font-style:
normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
text-indent: 0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px;
-webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; font-size: medium; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode:
space; -webkit-line-break: after-white-space; ">
<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: Jan.Abendroth_at_gmail.com</div>
<div>work: JAbendroth_at_embios.com</div>
<div><a moz-do-not-send="true"
href="http://www.emeraldbiostructures.com">http://www.emeraldbiostructures.com</a></div>
</div>
</div>
</span></span>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
<br>
</body>
</html>