Dear All, Thank you all for you valuable suggestions. I have checked the pdb and found Mg is there. Now I will try according to your suggestions.
- Mubinur On 15.6.2017, at 20.47, Pavel Afonine <pafon...@gmail.com<mailto: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<mailto: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
