Thank you everyone for suggestions.   As it turns out, there is a problem in the 1.20 phenix version that I was using. I updated to 1.21 as suggested by Dorothee, repeated one refinement job and had no more C-beta outliers, so I am guessing I will not have them in other models either. Best, Andrea On Friday, June 14, 2024 21:16 CEST, Nigel Moriarty wrote:   Andrea Can you send me files off-line?   Cheers   Nigel  ---Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : [email protected]  : CCI.LBL.govORCID : orcid.org/0000-0001-8857-9464      On Thu, Jun 13, 2024 at 9:59 AM Andrea Smith wrote:   Hi all,   I am running Phenix v. 1.20.1-4487 on Windows and I keep on getting C-beta outliers of methionine residues after phenix.refine (happened in different data from two different proteins). Even if I correct the methionines in Coot (and they fit perfectly in the density), I get the outliers at the end of refinement again (while these outliers don't fit the density and I can see a green difference map where the C-beta is).   Why is this? Is there a way to tell phenix.refine not to move a specific amino acid during refinement?   Thanks, Andrea _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]