Dear Tereza, It is highly recommended that you do not attempt to directly optimise the Ramachandran plot during refinement. Doing so would not guarantee you a better model, and would mean that you could no longer use the Ramachandran plot for validation purposes.
I suggest that you inspect each of the residues corresponding to the outliers, and assess the conformation, geometry and density fit of that residue and residues in the surrounding region. There are various tools in Coot to help you with this. It should be clear which regions are in need of attention (outliers that should be fixed) and which "outliers" should be considered acceptable. Indeed, ensuring that there are no Ramachandran outliers is not an objective/requirement for a good model. > I refine in Refmac, using h-bond based Prosmart restraints based on PDB > structures (identical molecules with high resolution) Prosmart h-bond based restraints, and Prosmart restraints based on PDB structures are two different things. Are you using Prosmart h-bond restraints, or Prosmart restraints to a high-resolution homologous model? If you're using restraints to a high-resolution homologue, are you generating restraints for all of your chains, or just some of them? If you're just generating restraints for some of them, then you should ensure that the others are appropriately restrained also. > I use NCS, medium between AB (protein 1) and loose between CDE (protein 2). From your mention of "medium" and "loose" NCS restraints, I'm guessing you're using CCP4i. Why not try using CCP4i2? This is the currently recommended and supported interface for CCP4 software. Don't use manual NCS restraints (medium, loose, etc.). Try using automatically generated local NCS restraints - we find they work better. How are your R/Rfree behaving in refinement? If you're using Prosmart restraints to homologous models then do you need/benefit from the use of NCS restraints too, or are they working against each other? Best regards, Rob > On 8 Mar 2019, at 09:08, Tereza Skalova <t.skalova.c...@gmail.com> wrote: > > 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 > <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
