(1) By the images of various output pdb files, be more clear that these are ones with the ten lowest I_sc (interface energy) scores.
(2) In the instructions, give more details about the differences between local_docking and docking_local_refine protocols.
(3) For each docking_local_refine job, please let every output pdb file listed in score.sf have a unique name and include all these pdb files in the tar archive file for the job.
(4) Please include in score.sf and the spreadsheet for each job the scores for each isolated monomer, Isc, and the total score. Since each pdb file should contain 2 monomers, which can differ from each other, there should be two different isolated monomer scores listed for each pdb file. It would also be nice to have 2 more rms and Fnat values (one for each monomer) for each pdb file to reflect how much each individual monomer has changed shape while docking. These would be in addition to the rms and Fnat values already listed for the overall complex in each pdb file.
(5) In the instructions, it talks about using 2 input pdb files per job, but only 1 input pdb file seems to be allowed per job.