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    1) The dock_mcm flags refer to the full atom (high-res) phase. It would not surprise me if the defaults were changed at some point.

    2) local_refine will skip the centroid/perturb/low-res step. I believe dock_pert is perturbation WITHIN 3deg/8ang, not of 3deg/8ang. So, maybe 2 degrees and 5 angstroms is what you actually get. (I’m not sure about this).

    3) You should be ok here.