[phenixbb] NAG clashes: C2 with ND2

Sam Stampfer Samuel.Stampfer at tufts.edu
Thu Jun 24 08:42:20 PDT 2010


I'm in the process of preparing 4 structures for submission to rcsb, and the
validation server has pointed out numerous issues with the
N-acetyl-glucosamine moieties on my structures.  While I have fixed the
torsion angles accordingly (using CARP from
http://www.glycosciences.de/tools/carp/ as a validation checker) and they
stay fixed after phenix refinement, phenix keeps generating 2-2.2 Angstrom
clashes between ND2 on asparagine with C2 on the NAG (the linkage is ND2-C1
and the usual distances are at least 2.28 Angstroms).  Occasionally, the ND2
to C2 distance is as low as 1.8 Angstroms.  This is happening in all my
structures and happens independently of the setting of wxc_scale (even for
wxc_scale=0.05!)  My NAG groups fit the density well, both pre- and post-

Any suggestions?  Will rcsb care?  These clashes are present in 12 out of 39
NAG moieties.


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