[phenixbb] discrepancy in MolProbity statistics
Michael Thompson
miket at chem.ucla.edu
Mon May 14 18:37:17 PDT 2012
Hello All,
I recently ran into a discrepancy between the MolProbity statistics reported by phenix.refine and the MolProbity statistics reported by the actual MolProbity webserver. I was hoping someone could comment on this and let me know if this is a warning sign that something is amiss. The structure (resolution=2.0A) seems to be correct and well refined, based on R-factors (0.1591/0.1774) and geometry reports from the various validation tools.
Remark 3, which was written out to the pdb file by phenix.refine, contains the following:
REMARK 3 MOLPROBITY STATISTICS.
REMARK 3 ALL-ATOM CLASHSCORE : 4.14
REMARK 3 RAMACHANDRAN PLOT:
REMARK 3 OUTLIERS : 0.00 %
REMARK 3 ALLOWED : 2.32 %
REMARK 3 FAVORED : 97.68 %
REMARK 3 ROTAMER OUTLIERS : 1.83 %
REMARK 3 CBETA DEVIATIONS : 0
Remark 40, which was created by and downloaded from the MolProbity web server, contains slightly different statistics:
REMARK 40 MOLPROBITY OUTPUT SCORES:
REMARK 40 ALL-ATOM CLASHSCORE : 0.83
REMARK 40 BAD ROTAMERS : 1.6% 8/510 (TARGET 0-1%)
REMARK 40 RAMACHANDRAN OUTLIERS : 0.0% 0/657 (TARGET 0.2%)
REMARK 40 RAMACHANDRAN FAVORED : 97.7% 642/657 (TARGET 98.0%)
I am mainly concerned about the values of the ALL-ATOM CLASHSCORE, as they are significantly different according to the two calculations.
Thanks in advance for any information/answers!
Mike
--
Michael C. Thompson
Graduate Student
Biochemistry & Molecular Biology Division
Department of Chemistry & Biochemistry
University of California, Los Angeles
miket at chem.ucla.edu
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