[phenixbb] Parameters of a metal ion do not change during refinement

I added a Cu(II) ion in a blob of density using Coot (this metal is used in crystallization solution). When I refined using phenix, I noted that occupancy does not change from the arbitrary value that I set in Coot, and negative density remains when refinement is complete. When I manually adjust occupancy to 0.3, phenix changes it to 0.29, and no negative density is seen, however B-factor does not move from my arbitrary setting of 30 in Coot. I worry if something is wrong in my refinement strategy. I thank any suggestion.Some additional information: my mtz is merged F's, resolution is 1.3 A, refinement strategy includes XYZ coordinates, Occupancies and Individual B-factors. Ezequiel