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
In the PDB they may be considered different with small differences and very small sigmas. 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) 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> wrote: > > Hi Fellows/Garib, > > I notice unexplained discrepancies between the PDB validation report and the > Refmac log file: > 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 > > 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> > hofkristall...@gmail.com <mailto:hofkristall...@gmail.com> > http://www.hofkristallamt.org/ <http://www.hofkristallamt.org/> > > ----------------------------------------------------------------- > Doors and corners – that’s where they get you > ----------------------------------------------------------------- > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <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/
