On Thu, Nov 7, 2013 at 12:57 PM, Pavel Afonine <pafonine@lbl.gov> wrote:
Depending which kind of differences you mean (magnitude). Ideally, R-factors should be identical. If it's like 0.1856 vs 0.1858, then it's fine, if larger then some of us here need to investigate what's going on.
Agreed, since the Table 1 program is using phenix.model_vs_data internally, which was designed to reproduce the R-factors from phenix.refine, any major discrepancy is cause for concern. We have seen a handful of cases where they deviate significantly, but it's been very difficult to isolate the cause, so data is always helpful. (Of course this doesn't rule out the possibility that there's simply a bug in my code somewhere, but I don't think the program is doing anything fancy.)