Hello, I think you are at a mid-refinement stage (R-free mid-thirties and map clearly still needing a lot more fitting work to be done on it) so I would not worry too much about the geometry stats at this point! I should pick someone's brains locally on model-building and get the fit to the map as good as possible.
Best wishes, Jon Cooper. jon.b.coo...@protonmail.com -------- Original Message -------- On 6 Aug 2020, 16:39, Silvia Napolitano wrote: > Dear CCP4BB community, > > I am working on a crystal structure and I am a bit stuck with the refinement. > > To build the model I use Coot and to refine I use Phenix. > > First, I noticed that the geometry analysis of exactly the same files is > quite different between Coot 0.8 and Coot 0.9 (see PowerPoint attached, > slides 1 and 2); isn't that a bit strange? > Anyway, I tried to fix the Ramachandran outliers, geometry, and rotamers, > obtaining, I think, a decent model (see PowerPoint attached, slides 3-5). > > However, when I input this model for refinement, the statistics and the > geometry obtained at the end of the refinement cycles are very bad (see > PowerPoint attached, slide 6). I am a very basic user, so I was wondering if > some of you have some suggestions on what I can do and which parameters I can > set for the refinement that might improve the model. I also attached the .log > file and the .eff file of the last refinement I performed. > > Many thanks in advance for your precious help! > > I wish you a nice evening/day. > > Best > > Silvia > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
