Hi Mubinur, I got the same situation while refining my protein complex with Lanthanum ion complex, reducing the occupancy while refining solved the problem. Good luck P.P
On Thu, Jun 15, 2017 at 11:17 PM, Pavel Afonine <pafon...@gmail.com> wrote: > 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 >> >>
