Hi, I refined a structure using phenix.refine. The R/R free decreased slightly from 13.46/15.87 to 13.0/15.6. But, molprobity said there were 3 CB outliers (starting from 0). I looked at those residues in COOT. I could NOT really see a different between the refined and initial model. In addition I looked at COOT validate-->density fit analysis I cannot see ANY difference in the peak heights (same numerical value too). I looked at RSCC (using phenix validate tools as well). I still can't see a difference in the plots. I am not sure how to get rid of the 3 CB outliers that have crept in since I can't pick them out as worse off in the refined model. I ask since in another case > 3 CB outliers, with the same results in picking them out in COOT/RSCC. I am wondering if there is another way I can see the deviation and fix it? Thank you, George