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Hi Tongqing,<br>
<br>
can be a number of reasons, including:<br>
<br>
- refinement did not converge (need to run more macro-cycles);<br>
- choice of TLS groups is not optimal;<br>
- side-chains are partially occupied (need to use partial occupancy
or model multiple occupancies);<br>
- see recent discussion on ccp4b about disulfides showing lots of
residual density.<br>
<br>
To tell more I will need to see data and model, focusing on
residues/ligands in question.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/8/14, 5:32 PM, Zhou, Tongqing
(NIH/VRC) [E] wrote:<br>
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<p class="MsoNormal">Dear colleagues,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am refining one structure at 1.94 A with
phenix.refine with individual b, TLS, and xyz. The Rwork and
Rfree are now at 16.1 and 19.8%. But when inspecting the maps,
I noticed that the sidechain tip of some residues showed
positive density and the b-factor for those atoms were very
high while those for the other atoms of the same residues were
normal; The b-factors for newly added ligands were also not
refined well showing high b-value and positive density at the
same time; the disulfide bonds also show positive density and
high B. The occupancy were all set to 1. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Please give suggestions. Thanks!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Best
regards,
<o:p></o:p></span></p>
<p class="MsoNormal"><b><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Tongqing<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><b><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Tongqing
Zhou, Ph.D.<o:p></o:p></span></b></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Staff
Scientist<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Structural
Biology Section<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Vaccine
Research Center, NIAID/NIH<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Building
40, Room 4609B<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">40
Convent Drive, MSC3027<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">Bethesda,
MD 20892<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">(301)
594-8710 (Tel)<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:10.5pt;font-family:"Arial","sans-serif";color:#1F497D">(301)
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