I've been learning phenix refinement on a MAD dataset which is already deposited in PDB. There are something I can not get through. Basically 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

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. I compared the resulting pdb and mtz files from the two steps. PDB model were exactly the same but there were little difference in the mtz file. Why there is difference in mtz file and would it be the reason for the difference of R factors? I use the latest version of phenix, phenix-dev-1009.