Dear Jan and Tim,
two little comments.
If Arg in A clashes with Arg in A* and Arg has multiple conformations, couldn't you just fix the occupancy of the clashing conformation to 0.5? The two will add up to one, and there won't be a clash left. The remaining 0.5 occupancy would be in the other one or more conformations?
I agree with Tim regarding artefacts on symmetry axes. However, please don't remove side chains that are there. I know this is a contentious subject and has been discussed ad nauseam on the CCP4 mailing list, with no consensus emerging. To me it is a no-brainer that if a side chain is present in the protein, it should be part of the model as well, whether at zero occupancy or with mental B values (my preferred way) - though I realize that far from everyone finds this argument convincing. However, for surface charge plots and for molecular dynamics simulations, complete side chains are essential for correct parametrization.
All best.
Andreas