[phenixbb] a question on phenix.real_space_refine

Dear Pavel, By phenix.real_space_refine, I fit a PDB with a 4.0 map. Most of the fitting were nice, but for the Ala residues, it indicates the o of the C=O occupies the density position which should be occupied by the CH3 side chain of the Ala, which also means the CH3 side chain of Ala cannot occupy the density position which clearly should be occupied by the CH3 side chain of Ala. Is any method or restraint to have the CH3 of Ala to ccupy its density position? Smith