I am using Phenix 1.8-1069. I am having a problem with phenix refine terminating with an error message. I added several solvent molecules, MPD and bicarbonate in Coot, and ran Phenix ReadySet to generate restraints for them and applied those restraints to all future jobs in that project. When I try to refine it, I get an error message stating that I have too many non-bonded interactions. If I generated my restraints file before running refine, this should not happen (?)
