[phenixbb] adding hydrogens -> increasing clash score

Hi! I have probably a very naive question - when one includes hydrogens into a refinement of a model build with data at ~3.6A clash score should not go up? I mean I am including hydrogens for a reason of improving the model quality when I cannot fit the sidechains into some density, etc. Can it be true that using default 3 macrocycles on a changed (reduced) model is not enough to minimize it? Thanks, Tanya