•  -ignore_unrecognized_res
• Generally, this can be used if you want ignore residues that Rosetta can't or shouldn't load (for instance, you are interested in a different region than where the ligand is it, etc etc

•  -ignore_zero_occupancy false
• Rosetta will ignore any residues/atoms that have an occupancy of 0. Typically this means that the atom or residue was not resolved well enough in the structure. In order to load these residues/atoms into Rosetta anyway (for modeling, design, etc etc.), pass this option.