[phenixbb] Geometry problem with sugars refined in phenix

[Tirumala Kumar Chowdary]

Hi,

I have refined a structure with NAGs linked to ASNs at 3 places in my 
structure. I used the right link definitions and the NAG definitions 
are from Phenix library.

Phenix refined all the sugars right and made the right links between 
the NAGs. However, while submitting, PDB found problem with the 
geometry of NAGs linked to the ASN at two places.

This is the issue
-the atoms around C1 atom of the sugar molecule NAG A #810 and NAG A 
#1670  are on a plane and the C1 atom center is far off to be 
tetrahedral. Please, verify the chirality of C1 and provide the correct 
coordinates if necessary.-

Any ideas on how to fix the geometry of these sugars will be of great help.

Regularization and real space refine in Coot is not working or I don't 
know how to do it. I am looking for alternative ways to fix this 
problem.

Thank You

Tirumal