[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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