Your PDB file and your data file have different space groups - usually this means that either the PDB file is missing symmetry entirely and gets treated as a P1 box, or the PDB file specifies the screw axes while the data file only specifies the point group (for instance, P212121 versus P222).  This is something we normally try to handle more automatically but the input handler for the Rosetta refinement is somewhat less flexible at the moment.  I'll fix this, but it should run okay if you ensure that the space group is unambiguously specified in both files.

-Nat