Hi Mubinur, try without "metal restraints" and see if that helps. As others suggested, make sure 2+ is present in rightmost column of PDB file. The side may be partially occupied, so refining occupancy of Mg2+ is not a bad idea.
Pavel On Wed, Jun 14, 2017 at 2:44 PM, Mohammad Rahman <mohammad.rah...@uef.fi> wrote: > Dear All, > > I am trying to refine a tetrameric enzyme structure that was determined at > 2.7 Å. The structure contains a Mg2+ binding site in each monomer. After > refinement, in Mg2+ binding site negative density (red) has been found > as in pictures. I am using Phenix refine, and during refinement, metal > restrains were used. Herewith I have attached the refinement statistics. > > please help me to overcome this problem. > > Thank you > > -Mubinur > >
