Beside the good propositions of fixing the environment, flip the peptide, or using PDB_REDO, I would suggest the following additional attempts: Try 1) setting the OCC of the sidechain (CG and further) below 0.3 or mutate directly to Ala. See which ones remain visible in a diff map and bring them back in during the upcoming ref cycles (refine OCCs in Phenix) 2) use simulated CART annealing to get the side chains out of your way 3) use a FEM map against misinterpreted side chains 4) In very nasty cases, I use MOLOC to do real space refinement and give a lot of weight to the H-Bond network. This usually helps to keep weakly defined regions in place.
good luck, matthias >>> Vipul Panchal <panchal.vi...@igib.in> 02.07.17 19.31 Uhr >>> I do agree with Eleanor. When I was solving structure at 2.16A resolution, outlier residues were having stearic clash or required side chain flipping. At 2.76A resolution, hydrogen bonds would be difficult to visulize. I found phenix.refine more user friendly. You may too find it useful. Vipul Panchal, Ph.D. student CSIR-IGIB (M)- 091 7678617949 On 02-Jul-2017 9:14 PM, "Eleanor Dodson" <eleanor.dod...@york.ac.uk> wrote: Just remember - most Ramachandran outliers are due to errors in the environment - eg: maybe some side chains clash hence refinement tries to move things to accommodate that bad feature, etc etc etc... At that resolution it is inevitable you will have some level of mis-interpretation .. 4% outliers does not surprise me. EDSTATS is a useful tool to find things such as pep flips - you can access it most simply from CCP4 GUI2 . But unless the outliers are in a important part of the structure I would suggest checking, then living with them. Eleanor On 2 July 2017 at 16:31, Rajesh Kumar <rsu.iitku...@gmail.com> wrote: 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 10461Tel: 718.430.2777 | Fax: 718.430.8565 On Sun, Jul 2, 2017 at 7:26 AM, Meytal Galilee <meytal.gali...@gmail.com> 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
