I'm running RDC refinement on the NMR structures of several glycopeptides, and in some of the resulting accepted structures the Rhombicity (which, along with Da was allowed to float during the entire SA run) will consistently hit either the upper (0.667) or lower (0.0) limits, as reported in the pdb file for the resulting structure. This indicates to me that there is something wrong with my RDC restraints. Perhaps an RDC restraint on a residue that is experiencing a certain amount of conformational averaging? Da values all look reasonable. When the Rhombicity does hit one of the limits, it will only hit the upper or only the lower limit, but not both for the same construct. Any thoughts as to what this could be?
I am using a slightly modified version of the refine.py script from the 2.18 distribution. NOE, 3J and other torsional restraints are also active. The RDC potential is a square well. I am looking at heteronuclear RDCS (HN and HC) and have ~2 backbone rdcs for each residue (except prolines), and a few sidechain and sugar RDCs as well. Andrew Borgert
