Well - some outliers are infix able! There are various reasons - floppy residues like arg or lys In multiple positions; strain due to protein folding constraints, etc.
I use the validation report to check for obvious modelling errors but if you can’t find any, you have to just submit the results of your experiment... On Sat, 23 Sep 2023 at 02:29, Nitin Kulhar < 00009dfccc771c91-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all > > We have refined (Refmac5) a crystallographic structure with Rw/Rf values > 0.19/0.22 (Resln 2.67). However, the deposition has stalled on account of > the wwPDB's preliminary validation report, which indicates map/model and > geometry issues, with each criterion containing a few instances. We tried > to correct these by varying overall geometry restraint weights, e.g. > decreasing overall weights from default value of 1.0, incementally > decreasing sigmas corresponding to the planarity restraint term. This did > not resolve the issues. > > In another approach, real space refinement by hand (against 2fo-fc) in > coot brought the geometry parameters within acceptable limits in addition > to improved apparent agreement with electron density (2fo-fc, sigma=1), but > uploading the resultant coordinates seems to undo the changes made in coot, > as indicated by reappearance of same outliers in the subsequent validation > report. > > I request your kind suggestions in this regard. Please also revert for any > further information. > > Thanks > Nitin Kulhar > PhD student > c/o Dr Rajakumara Eerappa > Macromolecular Structural Biology Group > Department of Biotechnology > Indian Institute of Technology Hyderabad > Kandi, Sangareddy > Telangana, India 502284 > > Disclaimer:- This footer text is to convey that this email is sent by one > of the users of IITH. So, do not mark it as SPAM. > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## 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/
