Hi Young-Jin,
While I am trying to deposit, I am faced with several things that I am not sure: FYI. I am in the <Refinement Statistics> section (Auto Dep Input Tool) in the PDB bank. Most values are came from pdb file that was made from phenix.refine but it asks me "R-factor (all)" that satisfy the limits established by high & low resolution cut off and "number of unique reflections (all)". My simple question is if phenix has those kind of information, if so where I can find them.
phenix.refine and phenix.model_vs_data report Rfree and Rwork computed for all reflections used in refinement (which may be different from the number of reflections in your input file, because of Iobs to Fobs conversion and outliers filtering). They do not report R(all) since I believe it is a useless number given that both, Rfree and Rwork, are reported. If you really want it you can compute it using a MTZ file created by phenix.refine, since it contains Fobs used in refinement and Fmodel, so the R-factor is simply R = SUM ||Fobs|-scale*|Fmodel|| / SUM |Fobs| and scale = SUM ( |Fobs|*|Fmodel| )/SUM |Fmodel|**2
Another question is if I changed water (deletion or changed occupancy) based on 'precheck', should I run phenix.refine again to get R/Rfree values in correct?
Yes, definitely, preferably with "ordered_solvent=true" flag. And having a look at this paper: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43, 677-685 (2010). is also a good idea in this case, since it explains how bad a post-refinement manipulation of PDB or data files can be. All the best! Pavel.