[phenixbb] on Phenix refine

Dear All, By rigid body refinement (Phenix) with a searching model (Model A) I got a output PDB (Model B) and output mtz file (MTZ FILE) of a diffraction dataset. In Coot I modify the Model B and saved it as Model C. I want to continue  to optimize Model C by Phenix.refine. In the GUI interface of Phenix.refine input, of course I need to input the MTZ FILE, but for the PDB file, should I only input the PDB of Model C, or all of Model A, Model B and Model C? If I input all of Model A, Model B and ModeC, then how does Phenix.refine distinguish the function of each PDB model? I am looking forward to getting your reply. Cheers, Dialing