DDG filter computes binding score for the complex (threshold=0 only allows complexes with negative binding score) (repeats=3 calculates binding score three times and returns average) (repack=1 repack complex in both bound and unbound states to calculate binding score) SASA filter computes interface solvent-accessible surface area (threshold=800 only allows complexes with greater than 800 Å^2 as per Janin et al., Quarterly Reviews of Biophysics, 2008) Designs and repacks interface residues of chain 1 and repacks interface residues of chain 2 Reads command line options Runs local refinement stage of full atom docking Runs protein interface design Runs full atom side-chain and backbone minimization Runs movers and filters in this order