I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å.

The MGD cofactors (molybdopterin guanine dinucleotide) are being refined with a weird distorted geometry causing some clashes. The Fo-Fc maps show that something is going wrong in the aromatic rings interatomic distances.

I'm using the readyset to pick up MGD and metal restraints.

Am I using the right protocol? 

Best regards,

Cristiano Mota