On Tue, Jul 22, 2014 at 10:01 AM, Aleksandar Bijelic <aleksandar.bijelic@univie.ac.at> wrote:

Thank you very much. Indeed, I started from a good search model (maybe) explaining this low Rfree value. Unfortunately I am now confused, I copied the Rfree flags from my old mtz.file to my new one (as described by you), but Phenix giving me still the error saying that this flags were already used in previous runs ..... is this usual?

Yes, if you are starting refinement from a previous phenix.refine output, it will have the md5 hash corresponding to the old R-free array (at lower resolution), which will not match with the new extended R-free flags. It's fine to ignore the error message in this case.

The funny thing is when I change the refinement by unchecking "update water" Phenix is running without complainig ... why?

That is not normal - are you certain this is the only change?

-Nat