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Dear Meytal, PHENIX-REFINE has an option for Ramachandran outlier refine. If you check this on, it will do the work. But after this refinement, you must check every residues to make sure residues are in the density. Thank you Rajesh ---xxxxx---- With regards Rajesh K. Harijan, Ph.D. Schramm Laboratory Albert Einstein College of Medicine 1300 Morris Park Ave., Bronx, NY 10461 Tel: 718.430.2777 <(718)%20430-2777> | Fax: 718.430.8565 <(718)%20430-8565> On Sun, Jul 2, 2017 at 7:26 AM, Meytal Galilee <[log in to unmask]> wrote: > Dear all, > I am refining a 2.76A structure using refmac5. > I keep fixing the Ramachandran outliers down to 18 (1.9%), however, upon > restrained refinement, the outliers increase back to 35. > Do you have any suggestions how can I fix my structure? > Thanks, > Meytal Galilee > >