This may not be helpful - but I had a similar thing happen at low resolution a few months ago. It turned out that a couple of residues just "blew out" of the structure for some reason. Their crappy geometries skewed everything else (though I had bad bond angles to go with the bad distances). It took me a while to see it, since everything else (99% of the structure) looked fine. Good luck, Arthur Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA On Sep 14, 2011, at 11:35 AM, Ian Slaymaker wrote:
I am bringing a PDB refined in Refmac back to phenix.refine. After an initial rigid body refinement to compare numbers (one chain per group), the geometry (specifically the bond length rmsd) had surprisingly increased. Phenix.validate confirmed the Refmac (initial) geometry numbers and then afterwards confirmed the distorted geometry. What is strange is that when opened in COOT, the initial and final models are completely super imposed.
REMARK Start: r_work = 0.3375 r_free = 0.3624 bonds = 0.006 angles = 0.768 REMARK Final: r_work = 0.3379 r_free = 0.3626 bonds = 0.145 angles = 1.019
can you help me figure out what is going on here? These are the final few refinements of a 4.1 A structure. Thanks, Ian _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb