Wenchang,
I had two steps refinement:
1->phenix.refine data.mtz model.pdb xray_data.high_resolution=3 fix_rotamers=true strategy=individual+adp+individual_sites+tls
2->phenix.refine data.mtz model-refined.pdb xray_data.high_resolution=3 fix_rotamers=false strategy=none main.number_of_macro_cycles=1
may I ask why is the step #2 ?
model-refined.pdb is actually from the 1st step, so in principle the R/R-free values should be the same for 1 and 2. However in my case, I had 0.2506/0.2996 for the 1st step but 0.2503/0.2998 for the second.
Well, 0.2506/0.2996 vs 0.2503/0.2998 I would say the same. Ralf made a great comment about this sometime ago - if interested search in phenixbb archives. Something like a tiny rounding while reading out/in makes the scaling to take a route to a slightly different minimum and voila - a slightly different R. Or that same rounding makes density sampling a tiny bit different and here is tiny bit difference. I guess one can imagine a long list of such things.
I use the latest version of phenix, phenix-dev-1009.
As of today the latest is 1054, so you are 45+ days behind -:) Pavel