[phenixbb] unrealistic low clashscore in phenix.refine

I’m using phenix 2.0-5936 on my M1 Mac. I notice in phenix.refine that the run status reports a realistic clashscore (7.5) for my structure, but in the Molprobity tab of phenix.refine the reported clashscore is 0.77, with only 4 clashes identified with a maximum overlap of 0.472 Å. Running Comprehensive Validation (X-rayNeutron) gives a full list of 76 overlapping pairs, maximum overlap 0.705 Å, and a clashscore of 7.65. -- 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