Hello,
I have only started using PHENIX and have made an interesting observation. If I run my model through PHENIX refine (individual sites, individual ADPs, occupancies, optimized X-ray/stereochemistry weight, optimized X-ray/ADP weight options selected) I obtain R/Rfree 0.15/0.18 and very nice geometry values (data is to 1.7A). However, if I now take this refined model and run it through Refmac (without any refinement) I obtain R/Rfree of 0.19/0.21.
sounds good to me, I would be worried otherwise.
Can anyone explain why is there such a big difference? Will this be an issue during PDB submission?
Have a look at this: J. Appl. Cryst. (2010). 43, 669-676 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 and P. D. Adams
Take a look at what phenix.refine reports for the number of reflections used for refinement in the logfile - I believe it will discard reflections that are flagged as suspicious (can't remember the reference, I think it's one of Randy Read's papers),
It is typically from zero to a few dozens of reflections and unless they are ~1.e+9 removing them rarely visible in terms of R-factor (if you just re-compute it). Pavel.