A good example of such expected outliers can be found in structures of nucleosomes: the validation report always flags almost all DNA bases as geometry outliers. But we have no end of evidence that these structures are correct: for instance, the many ensemble and single-molecule FRET studies of nucleosomes that relied on said structures to design their labeling scheme and to formulate testable hypotheses.
If your map insists on putting some residues in an uncomfortable conformation, it’s possible that this is indeed what is going on in the protein and not necessarily a modeling error. Cheers, Guillaume On 23 Sep 2023, at 21:50, Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: 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<mailto: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 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
