Hello Banin-- Because your structure has a PNS moiety in addition to the ligated Zinc ion, you must have used a custom-made PSF to generate this structure. I suspect that there may be issues with this PSF, or the associated parameters.
> > I am currently working on the refinement of a protein structure > (refine_170.pdb) using Xplor-NIH version 3.8. Despite several attempts to run > simulated annealing protocols, the structure continues to show significant > outliers in MolProbity. I am specifically struggling with a Zinc-coordination > site that is failing to refine correctly. > > Based on my MolProbity analysis, the following outliers need to be addressed: > > * Clashscore: Significant atomic overlaps exist, particularly in the > region of the active site. The VDW potential in my current scripts > is not effectively resolving these sterics. > > * Ramachandran Outliers: Multiple residues are currently in the "disallowed" > regions. These could be parameter problems. > > * Zinc Coordination Geometry: The Zinc ion (Residue 170) is currently > positioned ~11Å away from its intended ligands (Cys72, His35, > Asp26, Glu28). This sounds like a PSF problem - the ion should be covalently bound to its ligated residues. I don't believe I have a patch for Zinc ion coordination with this combination of residue types. If you could find one in the PDB, I can generate the appropriate patch and parameters. > * Bond and Angle Violations: There are several C-alpha and side-chain bonds > Possibly parameter problems. > The Issue: > > Every time I attempt to load the PDB and initialize the Zinc > topology/structure, Xplor-NIH fails to recognize the Zinc atom or crashes > during the protocol.initStruct phase with "unrecognized command" errors. This indicates a mismatch between the PDB and PSF. You might send me the files you used to generate a structure, and I can make sure things look ok, and that you have decent parameters. best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
