As I noted above, in my initial reply--
"It may depend on the values used for @xcen, etc. for the MMFP restraint; I suggest trying w/o restraints and then find the protein center. I found that OpenMM in CHARMM seems to shift the Cartesian coordinates such that the minimum corner of the unit cell is at the origin, instead of the origin being the center. Also, since the OpenMM interface is still somewhat developmental, it's not clear if all of the restraints in CHARMM are fully supported; the documentation does not address the issue."