Hi Breann,
I am currently refining a model of a zinc-binding protein and after refinement there is additional positive Fo-Fc density at the zinc site. This is the fourth independent structure of this particular protein solved in my lab so we are confident the metal is in fact zinc.
- Are you applying any restraints to ZN position? It may be a good idea. In my experience, this usually fixes problems similar to yours. To do so: phenix.metal_coordination model.pdb this will give you a file that defines these restraints. Have a look at it and edit if you find it necessary. Then use this file in refinement. - Try refining occupancy of ZN.
I noticed that after refinement the "residue info" in Coot has two lines for the zinc atom. The first line reads "G/121 ZN/ZN 1.00 44.30" while the second line reads G/121 ZN/ 0.00 0.00.
Can't say anything about it. If you still need more help with this - please send me the data, model files and input parameters you used and I will have a look. Pavel.