<div dir="ltr">Hi Tongqin,<div><br></div><div>It is a bit difficult to diagnose with the information you provided. Could you please answer the following questions?<br><div><br></div><div>- Did you also try to reset the B-factors to similar values than neighboring atoms?</div><div>F.ex. the average B-factor in the model could be 50 A**2, but in the ligand region, it could be lower, let's say 20 A**2. Then the starting value using average B is quite far from the likely B-factor of the ligand.</div><div><br></div><div>- What refinement strategy do you apply? How many macro-cycles? Do you use any non-default parameters for B-factor refinement?</div></div><div><br></div><div>- Which Phenix version are you using?</div><div><br></div><div>Best wishes,</div><div><br></div><div>Dorothee</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Aug 31, 2016 at 7:12 AM, Zhou, Tongqing (NIH/VRC) [E] <span dir="ltr"><<a href="mailto:tzhou@mail.nih.gov" target="_blank">tzhou@mail.nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US" link="#0563C1" vlink="#954F72">
<div>
<p class="MsoNormal">Dear All,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I am refining a structure with diffraction to 2.2A resolution and 95 % overall completeness. Now the Rs are at 18% and 23%, respectively. But the program failed to refine B factors for several ligands, atoms had high B factors while showing
positive Fo-Fc map around them. Occupancy was set to 1 and I also tried to reset B to mean B of the whole PDB. Any of you seeing this phenomenon? Thanks!<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Shown below is HEPES that has high B factor and positive density around it after refinement:<u></u><u></u></p>
<p class="MsoNormal"><img width="303" height="278" style="width:3.1562in;min-height:2.8958in" src="cid:image003.jpg@01D20370.26FD7150"><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Best regards,
<u></u><u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d"><u></u> <u></u></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Tongqing<u></u><u></u></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d"><u></u> <u></u></span></b></p>
<p class="MsoNormal"><b><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Tongqing Zhou, Ph.D.<u></u><u></u></span></b></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Co-head and Staff Scientist<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Structural Biology Section<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Vaccine Research Center, NIAID/NIH<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Building 40, Room 4609B<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">40 Convent Drive, MSC3027<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d">Bethesda, MD 20892<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d"><a href="tel:%28301%29%20761-7068" value="+13017617068" target="_blank">(301) 761-7068</a> (Tel)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d"><a href="tel:%28301%29%20793-0794" value="+13017930794" target="_blank">(301) 793-0794</a> (Cell)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#1f497d"><a href="tel:%28301%29%20480-2658" value="+13014802658" target="_blank">(301) 480-2658</a> (Fax)<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#a6a6a6">******************************<wbr>******************************<wbr>******************<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:#a6a6a6">The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the
original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements
made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:#a6a6a6">******************************<wbr>******************************<wbr>******</span><span style="font-family:"Arial",sans-serif"><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
<br>______________________________<wbr>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/<wbr>mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org">phenixbb-leave@phenix-online.<wbr>org</a><br></blockquote></div><br></div>