[phenixbb] NAG clashes: C2 with ND2

Sam Stampfer Samuel.Stampfer at tufts.edu
Fri Jun 25 11:50:13 PDT 2010

Does anyone know what file phenix uses to do NAG restraints when the
molecule being refined has NAG groups?  My groups are called "NAG".  I found
data_NAG.cif and NAG-B-D.cif in the phenix folder but can't tell whether
it's using either of those to refine my NAGs (they don't show up in the log

On Thu, Jun 24, 2010 at 11:42 AM, Sam Stampfer <Samuel.Stampfer at tufts.edu>wrote:

> Hi,
> 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-
> refinement.
> Any suggestions?  Will rcsb care?  These clashes are present in 12 out of
> 39 NAG moieties.
> Thanks!
> -Sam
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