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Bernard,
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<div class="">I have experienced this problem too. A workaround is to disable both NQH flips and real space refinement. </div>
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<div class=""> strategy = *individual_sites individual_sites_real_space rigid_body \<br class="">
*individual_adp group_adp *tls occupancies group_anomalous<br class="">
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<div class="">Jack</div>
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<div class="" style="orphans: 2; widows: 2;">John J. Tanner<br class="">
Professor of Biochemistry and Chemistry</div>
<div class="" style="orphans: 2; widows: 2;">Chair, Biochemistry Department Graduate Admissions Committee </div>
<div class="" style="orphans: 2; widows: 2;">Department of Biochemistry</div>
<div class="" style="orphans: 2; widows: 2;">University of Missouri-Columbia<br class="">
117 Schweitzer Hall<br class="">
Columbia, MO 65211<br class="">
Phone: 573-884-1280</div>
<div class="" style="orphans: 2; widows: 2;">Fax: 573-882-5635<br class="">
Email: <a href="mailto:tannerjj@missouri.edu" class="">tannerjj@missouri.edu</a><br class="">
<a href="http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html" class="">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a></div>
<div class="" style="orphans: 2; widows: 2;">Lab: Schlundt Annex rooms 3,6,9, 203B, 203C</div>
<div class="" style="orphans: 2; widows: 2;">Office: Schlundt Annex 203A</div>
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<div class="">On Dec 29, 2015, at 11:57 AM, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" class="">pafonine@lbl.gov</a>> wrote:</div>
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<div class="">Hi Bernhard,<br class="">
<br class="">
If you disable the flips they should not happen during refinement.<br class="">
This is something that I heard before but users were reluctant to provide evidence.<br class="">
Could you please send me data file, and two PDB files (before and after refinement) and indicate residues that are undesirably flipped? In case there are ligands, please send ligand CIF files too.<br class="">
Once I have files I will run refinement myself and see how this behavior may be prevented.<br class="">
<br class="">
Thanks,<br class="">
Pavel<br class="">
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<br class="">
On 12/29/15 09:38, Bernhard Loll wrote:<br class="">
<blockquote type="cite" class="">Dear all,<br class="">
<br class="">
I am currently refining a 1.9 A structure with PHENIX 1.10.1-2155.<br class="">
<br class="">
The problem I am facing is the following:<br class="">
<br class="">
Running the Molprobity server, it suggests me to correct a couple of N/Q/H<br class="">
flips. I perform the flips re-run PHENIX.REFINE with “Automatically<br class="">
correct N/Q/H errors” not ticked. The log file confirms the selection<br class="">
with nqh_flips = False.<br class="">
<br class="">
Nevertheless PHENIX.REFINE again flips these residues and the output PDB<br class="">
file has all previously flipped residues “re-flipped” in comparison to the<br class="">
input PDB file. I am very confident that the automatically flips performed<br class="">
by PHENIX.REFINE (REDEUCE) are wrong, since I have two metal binding<br class="">
sites.<br class="">
<br class="">
Why PHENIX.REFINE rotates side chains by 180 degree even though nqh_flips<br class="">
were set to false?<br class="">
<br class="">
Any help is appreciated.<br class="">
<br class="">
Cheers,<br class="">
<br class="">
Bernhard<br class="">
<br class="">
<br class="">
Dr. Bernhard Loll<br class="">
Freie Universitaet Berlin<br class="">
Fachbereich Biologie, Chemie, Pharmazie<br class="">
Institut fuer Chemie und Biochemie<br class="">
AG Strukturbiochemie<br class="">
Takustr. 6<br class="">
D-14195 Berlin<br class="">
Germany<br class="">
<br class="">
Phone: +49 (0) 30 838-57348<br class="">
Fax: +49 (0) 30 838-454936<br class="">
Email: <a href="mailto:loll@chemie.fu-berlin.de" class="">loll@chemie.fu-berlin.de</a><br class="">
<br class="">
Homepage: <a href="http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/" class="">http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/</a><br class="">
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