I wanted to clarify your question before I attempted an answer. You are trying to build structural models of a protein with 281 amino acids. You have templates( homology models )for part of the protein, but not for an unaligned region( 46 amino acids ).
For residues 84-161 a conformational disorder is induced( is this a result of the alignment in Modeller? )
Ultimately you would like to build structural models of the whole 281 residues and you hope to use RosettaAbinitio to predict residues 84-161?
please give as much detail as possible about your system