[phenixbb] Positive density at metal ions

Hi everyone, I work on a structure of about 3 A resolution. The structure is almost done except for 3 metal ions which remain positive in the density. The metal is clearly Mn (refinement works fine for an other very similar structure) and has been set at full occupancy. I tried to reset the B factor at lower values, which solves the problem for 2 metal ions but not the 3rd one. Is there anything else I can do? Jan