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 [email protected]