It's the library: https://doi.org/10.1107/S2059798320013534
And it is not something that is terribly easy to fix. Arginine just has internal clashes so that plane is only flat sometimes. This is a lot of what led to the "Conformation Dependent Library", which I don't think is set up under CCP4.
What I do, is copy $CLIBD/monomers/a/ARG.cif, edit it to increase the sigmas of plan-2 and the NH1-CZ-NH2 angle, and also edit the other two guanidino angles as described in the above paper. Provide this edited cif file as if it were a ligand to your refinement. It helps. Not as good as using CDL, but it helps.
-James Holton MAD Scientist On 6/27/2022 8:38 AM, SUBSCRIBE CCP4BB rkrishnan wrote:
I am refining a structure at 2.2A resolution. I find that all my arginines show distortion after refinement with refmac5 even though they fit into the density really well. This is latest version of ccp4 8.00 running on windows 10. Is my library messed up in refmac5? Any other ideas? ######################################################################## 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/
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