-fast==Fast Protocol: ideal geometry is inserted all at once throughout the structure, which perturbs the conformation leading to a potentially large RMSD to the input structure. Then Rosetta's minimizer is called to optimize the dihedral angles and reduce the coordinate deviations from the input structure. In the "slow" protocol (i.e., without the -fast option), ideal geometry is inserted at a single residue at a time, and torsion angles nearby the idealized residue are minimized to bring the structure back into agreement with the starting structure.
-atom_pair_constraint_weight .01==Sets an optional non-zero weight for atompair constraints. Using atompair constraints results in a significant slow down, but may lead to better preservation of short-range interactions like hydrogen bonds. A reasonable value for this would be ~0.01, but it's worth experimenting with.
-coordinate_constraint_weight==Can be used to toggle the coordinate constraint weight. Default value is 0.01.

