I submitted a job to the ROSIE antibody queue, which ran successfully, but all the result files now have a discontinuity in the backbone 2 residues before the start of CDR L2. No residues are missing. I ran it again without the H3 modeling, and the discontinuity isn't there, so it's something during the high resolution modeling that is causing a problem. Is there anything I can do to prevent this from happening? Should I use the light chain structure from the grafted model as correct, and use the heavy chains from the more rigorous protocol?
I have attached an example PDB which contains the discontinuity.