[phenixbb] Ligand refinement - geometry does not fit density

Dear all, I am refining a structure with a simple ligand in phenix 1.14. The ligand is present in 2 conformations at approx. equal occupancy. Refinement of the 2 conformations runs smoothly, but 2 problems occur 1. One of the ligand atoms is placed out of the electron density after refinement. The geometry file (via elbow) is present during refinement. The atom is not in an extreme position or clashes with anything else. 2. After refinement the ligand conformation cannot be changed in coot, although I import the cif dictionary. Any advise ? Best, Eike