Your PDB file contains atoms that are less than 0.001 A apart. This doesn't look like a good model. Please consider fixing it first.
Pavel P.S.: There is Phenix mailing list for Phenix related questions. On Tue, Jan 3, 2017 at 6:10 AM, Vikram Dalal <vikram.dalal...@gmail.com> wrote: > Hi all, > > > I have added the water, EDO and GOL in coot in a protein structure. I got > this error message (Fig 1) after running the phenix refinement. > > > > > > > > > > Thanks & Regards, > > > > > > > >
