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