Hmm - this is extracted from your log file: it looks more sensible.. 2899: b_iso_mean = 66.62
2907: b_iso_min = 63.50 (limit = 1.00) 2908: b_iso_max = 68.13 (limit = 80.00) 2909: b_iso_mean = 66.62 The average B is 66?? I am more familiar with REFMAC and the fact that the iso_min and iso_max are so close looks odd to me, but maybe that is a PHENIX quirk? But you need to look at the data processing log if you have access to it. The CCP4I2 gives a very useful analysis of your data.. Eleanor On Mon, 4 Jan 2021 at 15:03, Barone, Matthias <bar...@fmp-berlin.de> wrote: > dear silvia, > > apart from the resolution, it would be good to know your current > refinement strategy and if you fed the structure to pdbredo yet. How did > that turn out? the polygon values are picked from structures at similar > resolution afaik. In any case, a better list of B-factors is the one you > find in the refinement tab "Atomic properties", where phenix lists them for > the macromolecules and ligands separately. In that tab you will also find a > list of which atoms cause such high ADPs. I think Eleanor is talking about > such a screenshot > > best, matthias > > > > Dr. Matthias Barone > > AG Kuehne, Rational Drug Design > > Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Eleanor > Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> > *Sent:* Monday, January 4, 2021 3:44:33 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] B-factors very high > > That polygon is not very useful I dont think. The statistics need to be > given separately for structures solved at given resolutions. > Eleanor > > On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > >> Well - you dont give the resolution of your data or the "wilson B" which >> will be recorded in the data processing log. >> If the resolution is 3A or less a) it is hard to refine a B value, and b) >> it certainly should be high.. >> >> So more information is needed. >> Eleanor >> >> On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano < >> silvia.napolit...@mol.biol.ethz.ch> wrote: >> >>> Dear CCP4 Community, >>> I am currently working on the structure of a monomeric protein of 23KDa. >>> The protein is generally quite "loopy" and I think I am mid-way refinement. >>> At the moment I am struggling, among other things, with an extremely >>> high B-factor and I'm not sure how to lower it. >>> Do you have any suggestions on how I can proceed to obtain a lower >>> average B-factor? (I am sorry if the question is rather naive, but I have >>> worked very little on X-ray structures so far) >>> I attached a screenshot of the polygon obtained from the last refinement >>> (the geometry now should be a bit improved, I am running a new job at the >>> moment). I will be happy to provide further files if needed. >>> Many thanks in advance for your precious help! >>> I wish you a nice start to the new year. >>> 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 > > ------------------------------ > > 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/
