Hi Tereza, Rather than opting for a technological fix in a reciprocal space refinement program you should look at all the outliers in Coot and see if they are fixable. If they are severe outliers, you need to rebuild by peptide flipping and possibly by more invasive actions. If you have small outliers (just outside the distribution), see if this general fit is okay. If so, just tighten the overall restraints a bit and refine some more. If not, rebuild.
Generally in Refmac you should use local NCS restraints rather that chain-level restraints like you use now. This can be part of the problem. If you insists on solving the problem by automation you can try PDB-REDO which will do peptide flipping for you and will try to optimize settings for Refmac. That may solve some of your outliers, but you really need to look at them in Coot as well. Cheers, Robbie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tereza Skalova Sent: Friday, March 08, 2019 10:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ramachandran outliers Dear all, I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers. Do you have any idea how to reduce the number? I refine in Refmac, using h-bond based Prosmart restraints based on PDB structures (identical molecules with high resolution) and I use NCS, medium between AB (protein 1) and loose between CDE (protein 2). I use overall B-factor and 8 TLS groups. Is it possible to optimize Ramachandran plot directly in Refmac? Thank you Tereza Skalova ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
