Hi, Basically I have the same observation. My structure looks good (1.7A, R=19.6 free=22.5; strategy=individual_sites+individual_adp+tls; twin fr. 0.47) with nice geometry and density, but the clashscore in Molprobity is terrible. Almost all residues form clashes. It is improved only slightly if I add hydrogens at riding positions. So I am also curious where the problem is... Karolina Dnia 11-02-2008, pon o godzinie 13:02 +0000, Simon Kolstoe napisał(a):
Dear Phenix community,
I am using phenix.refine version 2007_08_18_1856 to refine a 2.65A structure (with individual_sites, group_adp, TLS & NCS, wxc_scale=0.1). After refinement I am running the pdb file through the Molprobity server. Molprobity gives a clash score of 33.78 indicating the number of steric clashes (within 0.4A) per 1000 atoms.
I am slightly concerned that a refinement program seems happy to allow such clashes. Is this a problem with the version of phenix.refine I am running, or is there a more obvious explanation that I have missed?
Thanks,
Simon _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb