I'm using the standalong version of Rosetta Antibody. I can rebuild the antibodys which are already in PDB, however, for my own sequences, I can not build them for some reasons. I checked the results of the CDR Graft procedure. I found the "FR02.pdb" was distorted. Apparently, the some atoms of H-CDR3 residues were far away from the framework. Besides, I got a "VERY LOW CONFIDENCE PREDICTION" warning on the H3 loop.
I know this is because of the low homology to other antibodies, however, to my knowledge, it should not give me a distorted structrure. Since I got a distorted FR02, I can only build a distorted antibody whose H chain was broken at Q105 (which is the position of the H3 should be grafted to).
For those antibodys whose structures were already resolved, I could build them perfectly with RosettaAntibody