I am struggling with a ligand bound structure.

The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet.

As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state.

Hope I did myself clear.

How to deal with this situation ? I am sure that phenix.refine can do it but how ?

What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X

Maybe something specific in a parameter file ?

Thank you for your help