On Mon, May 14, 2012 at 6:37 PM, Michael Thompson
I recently ran into a discrepancy between the MolProbity statistics reported by phenix.refine and the MolProbity statistics reported by the actual MolProbity webserver. I was hoping someone could comment on this and let me know if this is a warning sign that something is amiss. The structure (resolution=2.0A) seems to be correct and well refined, based on R-factors (0.1591/0.1774) and geometry reports from the various validation tools.
Did you refine with explicit hydrogens, and if so, did you skip the step in the MolProbity server where you add hydrogens? The likely explanation is this: 1) You ran phenix.ready_set (or phenix.reduce) to add hydrogens, which were placed at the nuclear distances (approximately 1.1A). 2) phenix.refine shortened the C-H bonds to conform to X-ray scattering distances, i.e. the center of the electron cloud, approximately 1.0A. 3) when you run validation in Phenix, the hydrogens are stripped off and re-added internally, again at 1.1A, and this temporary model is used to calculate the clashscore. 4) when you take the final model with explicit hydrogens and submit it to MolProbity, the hydrogens will all be at X-ray distances, which means they will be as much as 0.2A further apart from each other than they otherwise would be. Since the clashscore counts any overlap > 0.4A, this has a significant effect. So, as a general rule, when running Molprobity you should always let it add new hydrogens. (I'd recommend using the Phenix validation tools anyway, as they will be more consistent with the refinement output, although I suspect both are doing something dumb with hydrogens on ligands.) The number reported by Phenix is the one you want to report in your publication, and since the statistics are spectacular for this resolution it won't be a problem. (I'm not sure about the rotamer discrepancy.) (And yes, someday we'll fix this - the Richardson lab is working on determining appropriate hydrogen parameters that can be used consistently for both refinement and validation. But since Phenix also does neutron refinement, this is another one of those problems that is much more complicated than it initially appears.) -Nat