[modeller_usage] ions and non-standard amino acids problem

Dear modeller users,

I have the following problem:

I have to model a metalloenzyme named nitrile hydratase with a cobalt ion as well as two oxidised Cysteines in the active site.

The problems is that once the model is established, the structure of the active site is very different from that of the template.

I want to figure out how to get an accurate protein model with ions or non-standard amino acids in its active site.

Please suggest me any ideas to overcome this problem.

Thanks in advance.

Expecting reply from you guys.