Hi Karolina,
Hi,
Has anyone solved this problem? I am also fighting with extremly low rmsd values. For 1.7A structure I get rmsd 0.004A (bond) 0.733 (angles) (R/Rfree=0.1884/0.2216) with automatic weight calculation. When I want to loose restraints to get more reasonable rmsd I get R/Rfree 0.1814/0.2240). However, at the moment I do not know what "reasonable" means while using phenix.refine. Is seems to me that the program include hydrogen atoms in rmsd calculations.
Put hydrogen atoms issue aside (see my previous email), and even put particular program use aside too, I would still be uncertain about "what reasonable means". There was enough of discussion on this matter in CCP4BB and relatively recent Acta D papers. I'm sure it can be easily criticized, but I would use that X-ray target weight that gives you the best Rfree (this is what "optimize_wxc=true" option in phenix.refine does, and similar for B-factors). And yes, for the moment you can use phenix.model_vs_data to report the final geometry rmsd statistics for a model containing hydrogen atoms: phenix.model_vs_data model.pdb data.mtz Please let me know if you have any questions! Cheers, Pavel.