I apologize if this has already been addressed. I'm trying to deposit a model to the pdb database, but there are a few required values in the Refinement Statistics section that I'm not sure where to find.
1,2) Cut-off sigma (F), Number unique reflections (observed)
Looking at the log file, it appears that the cut-off is 0, which results in 330 reflections being rejected. The pdb header, however, lists the number of reflections at a value corresponding to 352 reflections being rejected. Why are these numbers different and which should I report?
3) R-factor (all)
R-factor (all) includes both the working and test sets in addition to reflections rejected by the sigma cut-off. Does PHENIX calculate this value? I know R-factor (observed), which includes the working and test sets but not rejected reflections, is calculated.
Thanks,
Elwood
