On Thu, Oct 11, 2012 at 8:09 PM,
There are some close contacts (hydrogen bonds) in my refined model. Can I just ignore it, delete it or what? I added hydrogen for refinement since the resolution is 1.47 A. Should I remove all these added hydrogens and refine again?
Second question is there are several outilers of torsion angles (6 from Ramachandran plot in coot ). But 16 are outside expected Ramachandran regions from the validation report from PDB bank(ADIT) . What is the cause? And should I re-refine to correct them? Or just go ahead to deposit it?
As Pavel indicates, it's difficult to answer this without more context. But here are several partial answers: 1) Close contacts (in the way the term is used by Probe/Molprobity) are usually okay, hydrogen bonds are good. Significant overlaps (> 0.4Å) are bad (when viewing Probe output in Coot or KiNG, these will be the jagged pink lines). But it's very difficult to remove these entirely; really severe problems need to be fixed, but if the overall clashscore is less than 10 (for this resolution I would aim for < 5) the model is basically okay. If Pavel's suggestion doesn't work, and your clashscore is very low, I wouldn't worry too much - but I can't really say for sure without seeing the specific clashes. 1b) Assuming you're at the end of refinement anyway, leave the hydrogens on (they will improve your R-factors at this resolution) try setting nonbonded_weight=200 and re-refining with XYZ weight optimization. 2) Phenix is using very new Ramachandran distributions from the Richardson lab based on a larger set of reference structures, which changed the boundary between "allowed" and "outlier" slightly. Right now it may still disagree with the Molprobity web server (hopefully this will change very soon); I have no idea what the PDB uses. Additionally, slight differences in the way values are stored and/or interpolated can determine whether a residue is flagged - this is why Phenix often disagrees with Coot on corner cases. Regardless, I would trust the output of Phenix over most other sources, as it is based on the best statistics the Richardson lab has been able to obtain so far, sampled very finely. As always, if you are able to show us the model and data (OFF-LIST - just email Pavel and/or me), we may have a more detailed answer. -Nat