[phenixbb] unwanted N/Q/H flipping in PHENIX.REFINE

Bernhard Loll loll at chemie.fu-berlin.de
Tue Dec 29 09:38:25 PST 2015

Dear all,

I am currently refining a 1.9 A structure with PHENIX 1.10.1-2155.

The problem I am facing is the following:

Running the Molprobity server, it suggests me to correct a couple of N/Q/H
flips. I perform the flips re-run PHENIX.REFINE with  “Automatically
correct N/Q/H  errors” not ticked. The log file confirms the selection
with nqh_flips = False.

Nevertheless PHENIX.REFINE again flips these residues and the output PDB
file has all previously flipped residues “re-flipped” in comparison to the
input PDB file. I am very confident that the automatically flips performed
by PHENIX.REFINE (REDEUCE) are wrong, since I have two metal binding

Why PHENIX.REFINE rotates side chains by 180 degree even though nqh_flips 
were set to false?

Any help is appreciated.



Dr. Bernhard Loll
Freie Universitaet Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut fuer Chemie und Biochemie
AG Strukturbiochemie
Takustr. 6
D-14195 Berlin

Phone: +49 (0) 30 838-57348
Fax:   +49 (0) 30 838-454936
Email: loll at chemie.fu-berlin.de

Homepage: http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/

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