I am refining a structure with a resolution of 2.1 Angstroem using Phenix. The spacegroup is P 31 2 1 (No. 152) with a twin fraction of 0.37 and twin law -h,-k,l.
In the refinement procedure the NCS (4 chains) constraints are on, using individual sites, ADP and occupancy refinement.
Just a suggestion to quickly try out... What happens if you turn off the NCS restraints and do some refinement without using NCS (with and/or without optimizing the weights)? I know it depends on many factors, but I've seen a good number of cases at around 2A resolution where the refinement was better if NCS is not used.
I can't not respond: I've never had a case where *careful* evaluation and assignment of NCS groups did /not/ allow me to tighten NCS restraints (without screwing Rfree, of course). But of course, it requires work: the default procedures aren't good enough yet. phx