ShiftField

Until now ShiftField is rarely used because the output rmsd is too large. The idea is to attach a fast refmac/phenix.refine after shift field to not destroy the geometry.

we also wanted to test the shift field of just the bfactors instead of coordinates.

I think it is worth that @dhs37 and I, go over the code. OI am sure he has plenty of suggestions to make better use of it.