Hi Scott,
So in my example below the SM atom is ~2.5? from OE1 of GLU313, but it is also ~2.5? from OE1 of GLU285 of a symmetry related protein. The problem is that in my particular choice of symmetry equivalent atoms GLU285 is really more like 20-30? away, and phenix.refine does NOT like that.
You can fix the problem like this: bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 285" symmetry_operation = -x,y,-z+.5 distance_ideal = 2.5 sigma = 0.2 } The symmetry operation above is just an example and most likely not the one you need. The find out the proper one, use Coot to draw the symmetry copy of your molecule (near the SM), then click on the symmetry-equivalent OE1. Coot should show you the symmetry operation that was used to draw the atom. Simply copy it into the phenix.refine parameter file. Ralf