Kevin
All of this arises from a simple miscommunication. The default restraints
for refinement in Phenix is the Conformation Dependent Library. It
basically changes the ideal values for the protein backbone based on the
phi/psi.angles. While Moprobity in Phenix uses the same libraries, it
appears the communication has broken so it's not using the CDL but rather
the single value restraints. As a result, .geo file (which is the gold
standard) is correct and the Molprobity is slightly wrong. As a power user
(you look in the .geo file), I suggest you check the .geo file until I
correct this.
Cheers
Nigel
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Nigel W. Moriarty
Building 91, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : [email protected]
Web : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464
On Tue, Sep 23, 2025 at 12:20 PM Kevin M Jude
I notice inconsistencies in the Molprobity results reported for the same structure from RealSpaceRefine and from ValidationCryoEM. As an example, for bond angle restraints, RSR reports that there are four >4sigma outliers (but does not list the outliers), while ValidationCryoEM reports 0.
RSR CryoEMValidation Number of restraints 13228 13228 RMS(deviation) 0.509 0.51 Max. deviation 9.997 9.998 Min. deviation 0 0 Number of outliers > 4sigma 4 0
Browsing through the .geo file, I don’t see any >4 sigma deviations among the highest residual angles, so I think this is an error.
I also see small discrepancies in Ramachandran favored, rotamer outliers, and clash score which seem to come down to minuscule differences in measurements at the margins.
This is for Phenix 1.21.2-5419. Happy to share files offline.
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s