Dear all,

 

I am trying to fit Cd in a protein structure using Phenix. However, the refinement returns me a result with DC (2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE) in the validation report and gives me the missing atoms accordingly. When I open the same structure in Coot, it shows me the ion Cd. Also, the .pdb file contains Cd.

 

Cd is present in my crystallization condition and fits well into the density.

 

Can someone suggest what may be wrong?