protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER VirtualRoot - root=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AtomCoordinateCstMover - cst=======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - fast-relax=======================
protocols.relax.FastRelax: CMD: repeat 6291.49 0 0 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight 6291.49 0 0 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep 209.191 0 0 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8938 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1471.29 0 0 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -1414.05 0 0 0.02805
protocols.relax.FastRelax: CMD: min -2568.85 0.770356 0.770356 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2568.85 0.770356 0.770356 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1638.15 0.770356 0.770356 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7850 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1663.79 0.770356 0.770356 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1601.95 0.770356 0.770356 0.154
protocols.relax.FastRelax: CMD: min -2194.12 0.571879 0.571879 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2194.12 0.571879 0.571879 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1892.05 0.571879 0.571879 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7766 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1849.92 0.571879 0.571879 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1824.43 0.571879 0.571879 0.31955
protocols.relax.FastRelax: CMD: min -1958.18 0.531052 0.531052 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -1958.18 0.531052 0.531052 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1684.3 0.531052 0.531052 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7643 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1635.24 0.531052 0.531052 0.55
protocols.relax.FastRelax: CMD: min -1752.98 0.544111 0.544111 0.55
protocols.relax.FastRelax: MRP: 0 -1752.98 -1752.98 0.544111 0.544111
protocols.relax.FastRelax: CMD: accept_to_best -1752.98 0.544111 0.544111 0.55
protocols.relax.FastRelax: CMD: endrepeat -1752.98 0.544111 0.544111 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1752.98 0.544111 0.544111 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2182.69 0.544111 0.544111 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8699 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2213.05 0.544111 0.544111 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2200.42 0.544111 0.544111 0.02805
protocols.relax.FastRelax: CMD: min -2647.12 0.816157 0.816157 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2647.12 0.816157 0.816157 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1780.14 0.816157 0.816157 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7947 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1796.69 0.816157 0.816157 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1740.25 0.816157 0.816157 0.154
protocols.relax.FastRelax: CMD: min -2221.44 0.610118 0.610118 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2221.44 0.610118 0.610118 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1917.97 0.610118 0.610118 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7754 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1866.35 0.610118 0.610118 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1840.98 0.610118 0.610118 0.31955
protocols.relax.FastRelax: CMD: min -1978.45 0.551444 0.551444 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -1978.45 0.551444 0.551444 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1709.65 0.551444 0.551444 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7602 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1667.36 0.551444 0.551444 0.55
protocols.relax.FastRelax: CMD: min -1766.44 0.563459 0.563459 0.55
protocols.relax.FastRelax: MRP: 1 -1766.44 -1766.44 0.563459 0.563459
protocols.relax.FastRelax: CMD: accept_to_best -1766.44 0.563459 0.563459 0.55
protocols.relax.FastRelax: CMD: endrepeat -1766.44 0.563459 0.563459 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1766.44 0.563459 0.563459 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2196.94 0.563459 0.563459 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8726 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2232.89 0.563459 0.563459 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2222.55 0.563459 0.563459 0.02805
protocols.relax.FastRelax: CMD: min -2651.27 0.825956 0.825956 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2651.27 0.825956 0.825956 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1797.06 0.825956 0.825956 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7861 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1810.14 0.825956 0.825956 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1753.92 0.825956 0.825956 0.154
protocols.relax.FastRelax: CMD: min -2224.46 0.604729 0.604729 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2224.46 0.604729 0.604729 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1919.45 0.604729 0.604729 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7691 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1896.97 0.604729 0.604729 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1872.12 0.604729 0.604729 0.31955
protocols.relax.FastRelax: CMD: min -1986.3 0.556653 0.556653 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -1986.3 0.556653 0.556653 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1713.23 0.556653 0.556653 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7584 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1697.37 0.556653 0.556653 0.55
protocols.relax.FastRelax: CMD: min -1771.02 0.564642 0.564642 0.55
protocols.relax.FastRelax: MRP: 2 -1771.02 -1771.02 0.564642 0.564642
protocols.relax.FastRelax: CMD: accept_to_best -1771.02 0.564642 0.564642 0.55
protocols.relax.FastRelax: CMD: endrepeat -1771.02 0.564642 0.564642 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1771.02 0.564642 0.564642 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2205.45 0.564642 0.564642 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8709 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2243.07 0.564642 0.564642 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2232.35 0.564642 0.564642 0.02805
protocols.relax.FastRelax: CMD: min -2652.76 0.822974 0.822974 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2652.76 0.822974 0.822974 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1806.45 0.822974 0.822974 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7890 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1828.28 0.822974 0.822974 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1772.45 0.822974 0.822974 0.154
protocols.relax.FastRelax: CMD: min -2235.62 0.615896 0.615896 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2235.62 0.615896 0.615896 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1934.58 0.615896 0.615896 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7696 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1922.14 0.615896 0.615896 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1898.23 0.615896 0.615896 0.31955
protocols.relax.FastRelax: CMD: min -1986.35 0.564516 0.564516 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -1986.35 0.564516 0.564516 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1708.03 0.564516 0.564516 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7609 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1690.25 0.564516 0.564516 0.55
protocols.relax.FastRelax: CMD: min -1775.84 0.572479 0.572479 0.55
protocols.relax.FastRelax: MRP: 3 -1775.84 -1775.84 0.572479 0.572479
protocols.relax.FastRelax: CMD: accept_to_best -1775.84 0.572479 0.572479 0.55
protocols.relax.FastRelax: CMD: endrepeat -1775.84 0.572479 0.572479 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1775.84 0.572479 0.572479 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2209.58 0.572479 0.572479 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8692 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2248.93 0.572479 0.572479 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2238.64 0.572479 0.572479 0.02805
protocols.relax.FastRelax: CMD: min -2666.03 0.836856 0.836856 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2666.03 0.836856 0.836856 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1807.8 0.836856 0.836856 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7856 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1829.79 0.836856 0.836856 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1773.07 0.836856 0.836856 0.154
protocols.relax.FastRelax: CMD: min -2247.05 0.620456 0.620456 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2247.05 0.620456 0.620456 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1945.86 0.620456 0.620456 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7735 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1935.32 0.620456 0.620456 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1911.18 0.620456 0.620456 0.31955
protocols.relax.FastRelax: CMD: min -2002.75 0.569491 0.569491 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -2002.75 0.569491 0.569491 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1730.65 0.569491 0.569491 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7625 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1708.58 0.569491 0.569491 0.55
protocols.relax.FastRelax: CMD: min -1787.85 0.577568 0.577568 0.55
protocols.relax.FastRelax: MRP: 4 -1787.85 -1787.85 0.577568 0.577568
protocols.relax.FastRelax: CMD: accept_to_best -1787.85 0.577568 0.577568 0.55
protocols.relax.FastRelax: CMD: endrepeat -1787.85 0.577568 0.577568 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1787.85 0.577568 0.577568 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2223.09 0.577568 0.577568 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8719 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2252.99 0.577568 0.577568 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2243.25 0.577568 0.577568 0.02805
protocols.relax.FastRelax: CMD: min -2671.94 0.840359 0.840359 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2671.94 0.840359 0.840359 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1806.62 0.840359 0.840359 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7862 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1826.23 0.840359 0.840359 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1768.39 0.840359 0.840359 0.154
protocols.relax.FastRelax: CMD: min -2251.09 0.623128 0.623128 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2251.09 0.623128 0.623128 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1947.19 0.623128 0.623128 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7715 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1935.91 0.623128 0.623128 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1911.53 0.623128 0.623128 0.31955
protocols.relax.FastRelax: CMD: min -2009.27 0.576565 0.576565 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -2009.27 0.576565 0.576565 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1739.17 0.576565 0.576565 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7634 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1710.52 0.576565 0.576565 0.55
protocols.relax.FastRelax: CMD: min -1790.19 0.578418 0.578418 0.55
protocols.relax.FastRelax: MRP: 5 -1790.19 -1790.19 0.578418 0.578418
protocols.relax.FastRelax: CMD: accept_to_best -1790.19 0.578418 0.578418 0.55
protocols.relax.FastRelax: CMD: endrepeat -1790.19 0.578418 0.578418 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1790.19 0.578418 0.578418 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2224.11 0.578418 0.578418 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8746 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2254.55 0.578418 0.578418 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2244.85 0.578418 0.578418 0.02805
protocols.relax.FastRelax: CMD: min -2662.61 0.833988 0.833988 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2662.61 0.833988 0.833988 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1821.14 0.833988 0.833988 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7888 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1841.95 0.833988 0.833988 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1785.78 0.833988 0.833988 0.154
protocols.relax.FastRelax: CMD: min -2251.78 0.620633 0.620633 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2251.78 0.620633 0.620633 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1949.91 0.620633 0.620633 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7751 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1940.23 0.620633 0.620633 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1916.08 0.620633 0.620633 0.31955
protocols.relax.FastRelax: CMD: min -2010.81 0.571941 0.571941 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -2010.81 0.571941 0.571941 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1741.4 0.571941 0.571941 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7622 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1720.31 0.571941 0.571941 0.55
protocols.relax.FastRelax: CMD: min -1790.87 0.583307 0.583307 0.55
protocols.relax.FastRelax: MRP: 6 -1790.87 -1790.87 0.583307 0.583307
protocols.relax.FastRelax: CMD: accept_to_best -1790.87 0.583307 0.583307 0.55
protocols.relax.FastRelax: CMD: endrepeat -1790.87 0.583307 0.583307 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1790.87 0.583307 0.583307 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2228.08 0.583307 0.583307 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8724 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2256.25 0.583307 0.583307 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2245.96 0.583307 0.583307 0.02805
protocols.relax.FastRelax: CMD: min -2665.39 0.838525 0.838525 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2665.39 0.838525 0.838525 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1809.79 0.838525 0.838525 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7892 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1833.11 0.838525 0.838525 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1776.14 0.838525 0.838525 0.154
protocols.relax.FastRelax: CMD: min -2247.72 0.617993 0.617993 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2247.72 0.617993 0.617993 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1945.11 0.617993 0.617993 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7743 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1945.65 0.617993 0.617993 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1921.85 0.617993 0.617993 0.31955
protocols.relax.FastRelax: CMD: min -2010.37 0.573592 0.573592 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -2010.37 0.573592 0.573592 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1740.9 0.573592 0.573592 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7630 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1712.44 0.573592 0.573592 0.55
protocols.relax.FastRelax: CMD: min -1790.87 0.580936 0.580936 0.55
protocols.relax.FastRelax: MRP: 7 -1790.87 -1790.87 0.580936 0.580936
protocols.relax.FastRelax: CMD: accept_to_best -1790.87 0.580936 0.580936 0.55
protocols.relax.FastRelax: CMD: endrepeat -1790.87 0.580936 0.580936 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1790.87 0.580936 0.580936 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2225.5 0.580936 0.580936 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8716 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2245.21 0.580936 0.580936 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2234.62 0.580936 0.580936 0.02805
protocols.relax.FastRelax: CMD: min -2666.18 0.845681 0.845681 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2666.18 0.845681 0.845681 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1781.54 0.845681 0.845681 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7903 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1797.12 0.845681 0.845681 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1738.84 0.845681 0.845681 0.154
protocols.relax.FastRelax: CMD: min -2241.84 0.611895 0.611895 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2241.84 0.611895 0.611895 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1941.57 0.611895 0.611895 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7685 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1941.46 0.611895 0.611895 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1917.82 0.611895 0.611895 0.31955
protocols.relax.FastRelax: CMD: min -2005.37 0.569744 0.569744 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -2005.37 0.569744 0.569744 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1737.4 0.569744 0.569744 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7637 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1704.27 0.569744 0.569744 0.55
protocols.relax.FastRelax: CMD: min -1788.69 0.577947 0.577947 0.55
protocols.relax.FastRelax: MRP: 8 -1788.69 -1790.87 0.580936 0.580936
protocols.relax.FastRelax: CMD: accept_to_best -1788.69 0.577947 0.577947 0.55
protocols.relax.FastRelax: CMD: endrepeat -1788.69 0.577947 0.577947 0.55
protocols.relax.FastRelax: CMD: coord_cst_weight -1788.69 0.577947 0.577947 0.55
protocols.relax.FastRelax: CMD: scale:fa_rep -2219.15 0.577947 0.577947 0.022
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 8731 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -2250.2 0.577947 0.577947 0.022
protocols.relax.FastRelax: CMD: scale:fa_rep -2237.01 0.577947 0.577947 0.02805
protocols.relax.FastRelax: CMD: min -2667.86 0.837579 0.837579 0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight -2667.86 0.837579 0.837579 0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep -1793.36 0.837579 0.837579 0.14575
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7872 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1813.04 0.837579 0.837579 0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep -1755.29 0.837579 0.837579 0.154
protocols.relax.FastRelax: CMD: min -2241.12 0.615365 0.615365 0.154
protocols.relax.FastRelax: CMD: coord_cst_weight -2241.12 0.615365 0.615365 0.154
protocols.relax.FastRelax: CMD: scale:fa_rep -1939.93 0.615365 0.615365 0.30745
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7721 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1938.72 0.615365 0.615365 0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep -1914.98 0.615365 0.615365 0.31955
protocols.relax.FastRelax: CMD: min -1999.81 0.574178 0.574178 0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight -1999.81 0.574178 0.574178 0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep -1727.94 0.574178 0.574178 0.55
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_NAG
core.pack.rotamer_set.RotamerSet_: Using simple Rotamer generation logic for pdb_MAN
core.pack.pack_rotamers: built 7613 rotamers at 639 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack -1694.4 0.574178 0.574178 0.55
protocols.relax.FastRelax: CMD: min -1784.8 0.582392 0.582392 0.55
protocols.relax.FastRelax: MRP: 9 -1784.8 -1790.87 0.580936 0.580936
protocols.relax.FastRelax: CMD: accept_to_best -1784.8 0.582392 0.582392 0.55
protocols.relax.FastRelax: CMD: endrepeat -1784.8 0.582392 0.582392 0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: 3O3P_B_17_5Y10 reported success in 5194 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5194 seconds
basic.citation_manager.CitationManager:
The following Rosetta modules were used during this run of Rosetta, and should be cited:
rosetta_scripts Application's citation(s):
Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, and Baker D. (2011). RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite. PLoS ONE 6(6):e20161. doi: 10.1371/journal.pone.0020161.
FastRelax Mover's citation(s):
*Tyka MD, *Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, and Baker D. (2011). Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol 405(2):607-18. doi: 10.1016/j.jmb.2010.11.008. (*Co-primary authors.)
Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popovic Z, Baker D, and Players F. (2011). Algorithm discovery by protein folding game players. Proc Natl Acad Sci USA 108(47):18949-53. doi: 10.1073/pnas.1115898108.
Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, and Kuhlman B. (2021). Perturbing the energy landscape for improved packing during computational protein design. Proteins 89(4):436-449. doi: 10.1002/prot.26030.
******** (C) Copyright Rosetta Commons Member Institutions. ***************
* Use of Rosetta for commercial purposes may require purchase of a license. *
******** See LICENSE.md or email license@uw.edu for more details. **********
core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.binary.ubuntu.release-371 r371 2024.09+release.06b3cf8ad0 06b3cf8ad0940d628690d0ed6fa2009d72ad2b44 https://www.rosettacommons.org 2024-02-29T01:16:28.135490
core.init: command: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol interface_design.xml -s /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb -no_nstruct_label -out:path:all ./out -overwrite -renumber_pdb -ignore_unrecognized_res -holes:dalphaball /media/lh/data3/masif_seed/rosetta_scripts/DAlpahBall/DAlphaBall.gcc
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1293585145 seed_offset=0 real_seed=1293585145
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1293585145 RG_type=mt19937
core.init: Resolved executable path: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/source/build/src/release/linux/5.15/64/x86/gcc/11/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.593078 seconds.
core.import_pose.import_pose: File '/media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb' automatically determined to be of type PDB
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'NAG' from the PDB components dictionary for residue type 'pdb_NAG'
core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) 'MAN' from the PDB components dictionary for residue type 'pdb_MAN'
core.conformation.Conformation: Found disulfide between residues 321 344
core.conformation.Conformation: Found disulfide between residues 438 451
core.conformation.Conformation: Found disulfide between residues 475 622
core.conformation.Conformation: Found disulfide between residues 501 511
core.conformation.Conformation: Found disulfide between residues 553 600
core.conformation.Conformation: Found disulfide between residues 561 598
core.conformation.Conformation: Found disulfide between residues 569 575
core.conformation.Conformation: Found disulfide between residues 582 587
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=interface_design.xml
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="sfxn" weights="ref2015"/>
<ScoreFunction name="sfxn_design" weights="ref2015">
<Reweight scoretype="approximate_buried_unsat_penalty" weight="10"/>
<Set approximate_buried_unsat_penalty_burial_probe_radius="2.3"/>
<Set approximate_buried_unsat_penalty_burial_atomic_depth="2.5"/>
<Set approximate_buried_unsat_penalty_hbond_energy_threshold="-0.25"/>
<Set approximate_buried_unsat_penalty_oversat_penalty="0"/>
<Reweight scoretype="hbond_sr_bb" weight="1"/>
<Reweight scoretype="hbond_lr_bb" weight="1"/>
<Reweight scoretype="hbond_bb_sc" weight="1"/>
<Reweight scoretype="hbond_sc" weight="1"/>
<Reweight scoretype="coordinate_constraint" weight="1"/>
</ScoreFunction>
</SCOREFXNS>
<RESIDUE_SELECTORS>
<Chain chains="A" name="chainA"/>
<Chain chains="B" name="chainB"/>
<Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chA" selector="chainB"/>
<Neighborhood distance="10.0" include_focus_in_subset="false" name="interface_chB" selector="chainA"/>
<InterfaceByVector cb_dist_cut="11" grp1_selector="interface_chA" grp2_selector="interface_chB" name="AB_interface" nearby_atom_cut="5.5" vector_angle_cut="75" vector_dist_cut="10"/>
<Not name="Not_interface" selector="AB_interface"/>
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<OperateOnResidueSubset name="restrict_to_interface" selector="Not_interface">
<PreventRepackingRLT/>
</OperateOnResidueSubset>
<OperateOnResidueSubset name="restrict_target2repacking" selector="chainB">
<RestrictToRepackingRLT/>
</OperateOnResidueSubset>
<DesignRestrictions name="allowed_aas">
<Action aas="ADEFGHIKLMNQRSTVWY" selector_logic="chainA"/>
</DesignRestrictions>
<IncludeCurrent name="current"/>
<ExtraRotamersGeneric ex1="1" ex2="1" name="ex1_ex2"/>
<ProteinProteinInterfaceUpweighter interface_weight="3" name="upweight_interface"/>
</TASKOPERATIONS>
<FILTERS>
<ShapeComplementarity confidence="0" name="sc" residue_selector1="chainA" residue_selector2="chainB"/>
<PeptideInternalHbondsFilter backbone_backbone="false" backbone_sidechain="true" exclusion_distance="100000" hbond_cutoff="0" name="hbonds" sidechain_sidechain="true"/>
<BuriedUnsatHbonds2 jump_number="1" name="buried_unsat_hbonds"/>
<Ddg confidence="1" jump="1" name="ddg" repack="0" repeats="1" scorefxn="sfxn" threshold="1000"/>
<BuriedUnsatHbonds burial_cutoff_apo="0.2" confidence="0" cutoff="4" dalphaball_sasa="1" ignore_surface_res="false" name="buns_all_heavy_ball_interface" print_out_info_to_pdb="true" probe_radius="1.1" report_all_heavy_atom_unsats="true" scorefxn="sfxn" use_ddG_style="true"/>
<Sasa confidence="1" hydrophobic="0" jump="1" name="sasa" polar="0"/>
</FILTERS>
<MOVERS>
<AtomCoordinateCstMover coord_dev="0.5" name="constrainCA"/>
<FastDesign batch="false" bondangle="false" bondlength="false" cartesian="false" min_type="dfpmin_armijo_nonmonotone" name="FastDesign" ramp_down_constraints="false" relaxscript="no_ref.rosettacon2018.beta_nov16.txt" repeats="1" scorefxn="sfxn_design" task_operations="current,ex1_ex2,restrict_to_interface,restrict_target2repacking,allowed_aas,upweight_interface">
<MoveMap name="MM">
<Chain bb="true" chi="true" number="1"/>
<Chain bb="false" chi="true" number="2"/>
<Jump number="1" setting="true"/>
</MoveMap>
</FastDesign>
<MinMover bb="0" cartesian="false" chi="0" name="chi_min" scorefxn="sfxn" tolerance="0.001" type="lbfgs_armijo_nonmonotone">
<MoveMap name="MM">
<Chain bb="false" chi="true" number="1"/>
<Chain bb="false" chi="true" number="2"/>
<Jump number="1" setting="false"/>
</MoveMap>
</MinMover>
<FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_pre" report_as="ddg_pre"/>
<FilterReportAsPoseExtraScoresMover filter_name="ddg" name="report_ddg_post" report_as="ddg_post"/>
<FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_pre" report_as="hbonds_pre"/>
<FilterReportAsPoseExtraScoresMover filter_name="hbonds" name="report_hbonds_post" report_as="hbonds_post"/>
<FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_pre" report_as="bunsh_pre"/>
<FilterReportAsPoseExtraScoresMover filter_name="buns_all_heavy_ball_interface" name="report_bunsh_post" report_as="bunsh_post"/>
<FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_pre" report_as="bunsh2_pre"/>
<FilterReportAsPoseExtraScoresMover filter_name="buried_unsat_hbonds" name="report_bunsh2_post" report_as="bunsh2_post"/>
<FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_pre" report_as="sasa_pre"/>
<FilterReportAsPoseExtraScoresMover filter_name="sasa" name="report_sasa_post" report_as="sasa_post"/>
<FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_pre" report_as="sc_pre"/>
<FilterReportAsPoseExtraScoresMover filter_name="sc" name="report_sc_post" report_as="sc_post"/>
<InterfaceAnalyzerMover jump="1" name="ia" scorefxn="sfxn"/>
</MOVERS>
<APPLY_TO_POSE/>
<PROTOCOLS>
<Add mover="report_ddg_pre"/>
<Add mover="report_bunsh_pre"/>
<Add mover="report_bunsh2_pre"/>
<Add mover="report_hbonds_pre"/>
<Add mover="report_sasa_pre"/>
<Add mover="report_sc_pre"/>
<Add mover="constrainCA"/>
<Add mover="FastDesign"/>
<Add mover="report_ddg_post"/>
<Add mover="report_bunsh_post"/>
<Add mover="report_bunsh2_post"/>
<Add mover="report_hbonds_post"/>
<Add mover="report_sasa_post"/>
<Add mover="report_sc_post"/>
</PROTOCOLS>
<OUTPUT/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn_design" with weights "ref2015"
protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight approximate_buried_unsat_penalty to 10
protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight hbond_sr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight hbond_lr_bb to 1
protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight hbond_bb_sc to 1
protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight hbond_sc to 1
protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight coordinate_constraint to 1
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_to_interface" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_target2repacking" of type OperateOnResidueSubset
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "allowed_aas" of type DesignRestrictions
core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class.
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ex1_ex2" of type ExtraRotamersGeneric
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "upweight_interface" of type ProteinProteinInterfaceUpweighter
protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.5, interface area < 0 A^2, median distance > 0 will be filtered.
protocols.simple_filters.ShapeComplementarityFilter: Using Jump Selector to define surfaces.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sc" of type ShapeComplementarity
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "hbonds" of type PeptideInternalHbondsFilter
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering VarSolDist SASA Calculator
protocols.buns.BuriedUnsatisfiedPolarsCalculator2: Registering new basic buried unsat calculator.
protocols.buns.BuriedUnsatHbondFilter2: Buried Unsatisfied Hbond filter v2 over jump number 1 with cutoff 20
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buried_unsat_hbonds" of type BuriedUnsatHbonds2
protocols.simple_filters.DdgFilter: ddg filter with threshold 1000 and threshold_min -999999 repeats=1 and scorefxn sfxn extreme_value_removal: 0 and repack 0
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buns_all_heavy_ball_interface" of type BuriedUnsatHbonds
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sasa" of type Sasa
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "constrainCA" of type AtomCoordinateCstMover
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/sampling/relax_scripts/MonomerRelax2019.txt ==================
protocols.relax.RelaxScriptManager: repeat %%nrepeats%%
protocols.relax.RelaxScriptManager: coord_cst_weight 1.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.040
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.051
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.5
protocols.relax.RelaxScriptManager: scale:fa_rep 0.265
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.280
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 0.559
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: scale:fa_rep 0.581
protocols.relax.RelaxScriptManager: min 0.01
protocols.relax.RelaxScriptManager: coord_cst_weight 0.0
protocols.relax.RelaxScriptManager: scale:fa_rep 1
protocols.relax.RelaxScriptManager: repack
protocols.relax.RelaxScriptManager: min 0.00001
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
core.pack.task.xml_util: Object FastDesign reading the following task_operations: Adding the following task operations
current ex1_ex2 restrict_to_interface restrict_target2repacking allowed_aas upweight_interface
protocols.relax.RelaxScriptManager: ================== Reading script file: no_ref.rosettacon2018.beta_nov16.txt ==================
protocols.relax.RelaxScriptManager: repeat 1
protocols.relax.RelaxScriptManager: ramp_repack_min 0.079 0.01 1.0
protocols.relax.RelaxScriptManager: ramp_repack_min 0.295 0.01 0.5
protocols.relax.RelaxScriptManager: ramp_repack_min 0.577 0.01 0.0
protocols.relax.RelaxScriptManager: ramp_repack_min 1 0.00001 0.0
protocols.relax.RelaxScriptManager: accept_to_best
protocols.relax.RelaxScriptManager: endrepeat
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "FastDesign" of type FastDesign
protocols.minimization_packing.MinMover: Options chi, bb: 0, 0 omega: 1
protocols.RosettaScripts.util: [ WARNING ] Ignoring 'default' MoveMapFactory in parse_movemap_factory_legacy(), using existing MoveMapFactory MM instead
core.select.movemap.util: Found MoveMapFactory MM
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "chi_min" of type MinMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_ddg_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_hbonds_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_bunsh2_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sasa_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_pre" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "report_sc_post" of type FilterReportAsPoseExtraScoresMover
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "ia" of type InterfaceAnalyzerMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_ddg_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh2_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_hbonds_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sasa_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sc_pre"
protocols.rosetta_scripts.ParsedProtocol: Added mover "constrainCA"
protocols.rosetta_scripts.ParsedProtocol: Added mover "FastDesign"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_ddg_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_bunsh2_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_hbonds_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sasa_post"
protocols.rosetta_scripts.ParsedProtocol: Added mover "report_sc_post"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy /media/lh/data3/masif_seed/rosetta_scripts/seed_refine/relax/3O3P_B_17_5Y10.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FilterReportAsPoseExtraScoresMover - report_ddg_pre=======================
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/media/lh/data3/masif_seed/real_rosetta/rosetta.binary.ubuntu.release-371/main/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.129239 seconds to load from binary
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FilterReportAsPoseExtraScoresMover - report_bunsh_pre=======================
protocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////
protocols.simple_filters.BuriedUnsatHbondFilter:
protocols.simple_filters.BuriedUnsatHbondFilter: USING DEFAULT BEHAVIOR: filter will report total number of heavy-atom donor/acceptor buried unsats
protocols.simple_filters.BuriedUnsatHbondFilter:
protocols.simple_filters.BuriedUnsatHbondFilter: /////////////////////////////////////////////////////////////////////////////////////////
protocols.simple_filters.BuriedUnsatHbondFilter:
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv
protocols.simple_filters.BuriedUnsatHbondFilter: buried unsats in input pose:
protocols.simple_filters.BuriedUnsatHbondFilter: all_heavy_atom_unsats = 83
protocols.simple_filters.BuriedUnsatHbondFilter: bb_heavy_atom_unsats = 69
protocols.simple_filters.BuriedUnsatHbondFilter: sc_heavy_atom_unsats = 14
protocols.simple_filters.BuriedUnsatHbondFilter: countable_nonheavy_unsats = 48
protocols.simple_filters.BuriedUnsatHbondFilter: use_ddG_style=true: Using ddG style calculation ( will substract unsats in unbound state from those in bound state ):
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing protocol:
File: src/protocols/simple_filters/BuriedUnsatHbondFilter.cc:530
[ ERROR ] UtilityExitException
ERROR: Assertion `symmetric || pose.num_chains() < 4` failed. MSG:ERROR: use_ddG_style not compatible with symmetry or poses with > 3 chains
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 3O3P_B_17_5Y10
protocols.jd2.JobDistributor: [ WARNING ] 3O3P_B_17_5Y10 reported failure and will NOT retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 8 seconds
ERROR: Assertion `symmetric || pose.num_chains() < 4` failed. MSG:ERROR: use_ddG_style not compatible with symmetry or poses with > 3 chains
ERROR:: Exit from: src/protocols/simple_filters/BuriedUnsatHbondFilter.cc line: 530
[ ERROR ]: Caught exception:
File: src/protocols/simple_filters/BuriedUnsatHbondFilter.cc:530
[ ERROR ] UtilityExitException
ERROR: Assertion `symmetric || pose.num_chains() < 4` failed. MSG:ERROR: use_ddG_style not compatible with symmetry or poses with > 3 chains
AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.
---------------------------------------------------------------
[ ERROR ]: Error(s) were encountered when running jobs.
1 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------
I meet this problem when I try to refine the protein, could you please help me?
Thanks a lot again!