HI Robbie and all, Here is further recent analysis regarding the geometry of Arg side chains and recommendations for restraints:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709202/ Best, Andy [Black Lives Matter] Dr. P. Andrew Karplus (he, him, his) Distinguished Professor of Biochemistry and Biophysics NIGMS GCE4All Research Center<http://gce4all.oregonstate.edu/> Director of Communications 2133 ALS Building Oregon State University Corvallis, OR 97331 ph. 541-737-3200 andy.karp...@oregonstate.edu<mailto:andy.karp...@oregonstate.edu> “Revealing how life works for the benefit of all!” http://biochem.oregonstate.edu/ https://www.facebook.com/OSUBB From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Robbie Joosten <robbie_joos...@hotmail.com> Reply-To: Robbie Joosten <robbie_joos...@hotmail.com> Date: Thursday, October 20, 2022 at 5:53 AM To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] bond angle deviation listing in refmac log [This email originated from outside of OSU. Use caution with links and attachments.] Hi Garib, Are these related to the side chain of ARG? In the monomer library sigmas are capped from below - 1.5degree. In the PDB these sigmas might be very small and tiny differences could be given as outliers. Another reason might be that in the monomer library these two angles are identical (they are considered graph-equivalent, however, rotating around NE- CZ may make them non-equivalent in 3D space): ARG NE CZ NH1 120.052 1.50 ARG NE CZ NH2 120.052 1.50 The chi-5 angle is not really freely rotatable due to the 1.33 bond order. It does give away more than say, a peptide bond with 1.5 bond order. Anyway, NH2 and NH1 have E/Z differences if you assume the bond is not freely rotatable. In the PDB they may be considered different with small differences and very small sigmas. I'm using ARG NE CZ NH1 121.5 1.00 ARG NE CZ NH2 119.2 0.90 From https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubmed.ncbi.nlm.nih.gov%2F27326702%2F&data=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C07e6e953f28545470f8b08dab299eaf0%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638018672137036416%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ORI09%2BMubqLUxmBcaOrrQwGs%2FyiNeBM4ajxSJYDun3s%3D&reserved=0 I personally do not think that these differences are significant or important. However, to make pdb validation happy you can change the sigmas and make the angles different. Then NH1 and NH2 will become inequivalent and you have to change your coordinates (it could be done automatically if somebody writes a tiny program) Because chi-5 was freely rotatable in O (against convention) there is a check for this in WHAT_CHECK. AFAIK the atom naming is fixed in pdb-redo based on that. We can build in into flipper. Cheers, Robbie If the problem is not related with this then I need more info. Regards Garib On 20 Oct 2022, at 12:33, Bernhard Rupp <hofkristall...@gmail.com<mailto:hofkristall...@gmail.com> <mailto:hofkristall...@gmail.com<mailto:hofkristall...@gmail.com>> > wrote: Hi Fellows/Garib, I notice unexplained discrepancies between the PDB validation report and the Refmac log file: a. If I set in ‘Monitoring and Output Options’ the angle sigma for the log output reporting option to the PDB 5 sigma cutoff, I get zero angle deviations (i.e., no angle deviation printout at all in the log), even at improbably low sigma levels such as 2.0 or 1.0 monitor MANY torsion 5.0 distance 5.0 angle 1.0 plane 5.0 b. PDB informs me that there are up to 10 sigma outliers on multiple (and almost exclusively) ARG N-C-N angles (how to fix this we address later). Garib, I can send you a link to the complete log, below the header for versions (windows) : #CCP4I VERSION CCP4Interface 8.0.005 #CCP4I SCRIPT LOG refmac5 #CCP4I DATE 20 Oct 2022 13:17:07 #CCP4I USER 'UNKNOWN' #CCP4I PROJECT data_mono #CCP4I JOB_ID 13 #CCP4I SCRATCH C:/Users/br/AppData/Local/Temp #CCP4I HOSTNAME BR-WORK #CCP4I PID 10064 <B><FONT COLOR="#FF0000"> <hr><font size="-5"><br></font> </FONT></B> <B><FONT COLOR="#FF0000"> ############################################################### ############################################################ ### ############################################################ ### ### CCP4 8.0.005: Refmac version 5.8.0352 : 05/31/22## ############################################################ ### Thx, BR ----------------------------------------------------------------- Bernhard Rupp k.k. Hofkristallamt 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org<mailto:b...@ruppweb.org> <mailto:b...@ruppweb.org<mailto:b...@ruppweb.org>> hofkristall...@gmail.com<mailto:hofkristall...@gmail.com> <mailto:hofkristall...@gmail.com<mailto:hofkristall...@gmail.com>> https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.hofkristallamt.org%2F&data=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C07e6e953f28545470f8b08dab299eaf0%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638018672137036416%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Nbl%2FTkGV2DXfk%2BIae7ze%2FQAjSG1pcHOWkb%2BS4uzWT8g%3D&reserved=0 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