[phenixbb] Difference Map positive peaks in release dev-798

I was wondering if anything changed (weights or something) in the way the difference maps are calculated? I just ran refinement on a 1.3 structure and a hexacoordinated Mg2+ ion has significant positive density peak even at occupancy 1.0. I had not noticed that before. My ligand also does have positive peaks, but refine gives it a .91 occupancy. I wonder if I am missing some parameter cif file or some definition that would make the positive peaks decrease? Thank you -- Yuri Pompeu