Hi Andy Yes, ARG side chain should not be planar. It was mistakenly restrained to be planar. The same rule applies for peptide planes. Planarity should only be applied (if ever) for aromatic groups. For ARG side chains the bond is sp2-sp2 and rotation around this bond is not as prohibited as rotation within aromatic rings (as far as I know).
Regards Garib > On 21 Oct 2022, at 00:24, Karplus, Andy <[email protected]> wrote: > > 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/ > <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709202/> > > Best, Andy > > <image001.png> > > 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 > [email protected] <mailto:[email protected]> > > “Revealing how life works for the benefit of all!” > http://biochem.oregonstate.edu <http://biochem.oregonstate.edu/>/ > https://www.facebook.com/OSUBB <https://www.facebook.com/OSUBB> > > > > From: CCP4 bulletin board <[email protected] > <mailto:[email protected]>> on behalf of Robbie Joosten > <[email protected] <mailto:[email protected]>> > Reply-To: Robbie Joosten <[email protected] > <mailto:[email protected]>> > Date: Thursday, October 20, 2022 at 5:53 AM > To: "[email protected] <mailto:[email protected]>" > <[email protected] <mailto:[email protected]>> > 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 > > <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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> > 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. 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