[phenixbb] positive density around heavy metals

Hi everyone, I have refined a protein with a metal-chelate complex at 1.4 resolution and saw positive density around some metals that are on a two fold. I refined those chelator complexes with fixed occupancy to avoid the negative density seen around it as they are partially occupied. Also I had to avoid xyz refinement after fixing them on special position, to avoid moving away from two fold. I have attached a figure of one of those complexes. If I increase occupancy then it shows negative density. How can I get rid of this positive density. Thanks in advance for the help Subhani