ModRefiner: How to run more than 1 chain at a time

I am having some trouble with the fact that ModRefiner can only process one chain at a time. Most structures I am working with from the PDB have 2 or more chains, and having to run chains separately and redocking them is not doable.

Is there any feature in ModRefiner that allows for the refinement of multiple chains at a time? If not, how can I refine both chains and then evaluate them afterwards as a single structure?

Thanks