this has probably been discussed many times before, but I just can’t seem to find a solution for my current problem with phenix.refine:

I am trying to refine a protein structure with a rather complex ligand. I’ve generated a .cif file for the ligand with eLBOW, including planarity restraints for its aromatic ring systems. However, phenix.refine keeps on distorting the 6-ring in my indole group, although all respective atoms are included in the plane definition. 

At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar structure on this ligand. 

How can I convince Phenix to not distort my ligand's aromatic rings?

Many thanks for your kind suggestions.

Best regards,

Maike