# qianlei @ mgr in ~zhangyunqi/software/ab_dock_test/ab_dock_pipe_hpc-main/ab_dock_para_NOepi_hpc [0:55:02] $ ./job_prep6_snug_v4.sh /share/home/zhangyunqi/software/ab_dock_test/ab_dock_pipe_hpc-main/ab_dock_para_NOepi_hpc HL_A 2 & [1] 83158 # qianlei @ mgr in ~zhangyunqi/software/ab_dock_test/ab_dock_pipe_hpc-main/ab_dock_para_NOepi_hpc [0:56:05] $ core.init: (1) Checking for fconfig files in pwd and ./rosetta/flags core.init: (1) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (1) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (8) Checking for fconfig files in pwd and ./rosetta/flags core.init: (8) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (8) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (5) Checking for fconfig files in pwd and ./rosetta/flags core.init: (1) Checking for fconfig files in pwd and ./rosetta/flags core.init: (5) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (1) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (1) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (5) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (9) Checking for fconfig files in pwd and ./rosetta/flags core.init: (6) Checking for fconfig files in pwd and ./rosetta/flags core.init: (6) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (6) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (6) Checking for fconfig files in pwd and ./rosetta/flags core.init: (5) Checking for fconfig files in pwd and ./rosetta/flags core.init: (2) Checking for fconfig files in pwd and ./rosetta/flags core.init: (5) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (5) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (2) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (2) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (3) Checking for fconfig files in pwd and ./rosetta/flags core.init: (3) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (3) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (0) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (4) Checking for fconfig files in pwd and ./rosetta/flags core.init: (6) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (9) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (0) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (6) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (9) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (4) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (4) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=-1211953620 seed_offset=0 real_seed=-1211953620 basic.random.init_random_generator: (1) 'RNG device' seed mode, using '/dev/urandom', seed=1901136977 seed_offset=0 real_seed=-1211953619 basic.random.init_random_generator: (4) 'RNG device' seed mode, using '/dev/urandom', seed=-1501405124 seed_offset=0 real_seed=-1211953616 basic.random.init_random_generator: (1) RandomGenerator:init: Normal mode, seed=-1211953619 RG_type=mt19937 basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=-1211953620 RG_type=mt19937 core.init: (1) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (1) Instantiate PDBJobInputter core.init: (0) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database core.init: (7) Checking for fconfig files in pwd and ./rosetta/flags protocols.jd2.PDBJobInputter: (1) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (1) pushed snug_input.pdb nstruct indices 1 - 2 protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs basic.random.init_random_generator: (4) RandomGenerator:init: Normal mode, seed=-1211953616 RG_type=mt19937 core.init: (4) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (4) Instantiate PDBJobInputter core.init: (7) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 protocols.jd2.PDBJobInputter: (0) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (2) 'RNG device' seed mode, using '/dev/urandom', seed=-464590896 seed_offset=0 real_seed=-1211953618 basic.random.init_random_generator: (2) RandomGenerator:init: Normal mode, seed=-1211953618 RG_type=mt19937 core.init: (2) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database core.init: (7) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 basic.random.init_random_generator: (7) 'RNG device' seed mode, using '/dev/urandom', seed=176561004 seed_offset=0 real_seed=-1211953613 protocols.jd2.PDBJobInputter: (4) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (4) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (5) 'RNG device' seed mode, using '/dev/urandom', seed=1525712789 seed_offset=0 real_seed=-1211953615 basic.random.init_random_generator: (5) RandomGenerator:init: Normal mode, seed=-1211953615 RG_type=mt19937 core.init: (5) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database basic.random.init_random_generator: (3) 'RNG device' seed mode, using '/dev/urandom', seed=371326993 seed_offset=0 real_seed=-1211953617 protocols.jd2.PDBJobInputter: (2) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (2) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (2) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (7) RandomGenerator:init: Normal mode, seed=-1211953613 RG_type=mt19937 core.init: (7) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database basic.random.init_random_generator: (3) RandomGenerator:init: Normal mode, seed=-1211953617 RG_type=mt19937 protocols.jd2.PDBJobInputter: (7) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (5) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (5) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (5) pushed snug_input.pdb nstruct indices 1 - 2 core.init: (3) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (3) Instantiate PDBJobInputter basic.random.init_random_generator: (8) 'RNG device' seed mode, using '/dev/urandom', seed=-341860093 seed_offset=0 real_seed=-1211953612 basic.random.init_random_generator: (8) RandomGenerator:init: Normal mode, seed=-1211953612 RG_type=mt19937 core.init: (8) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (7) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (7) pushed snug_input.pdb nstruct indices 1 - 2 protocols.jd2.PDBJobInputter: (8) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (3) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (3) pushed snug_input.pdb nstruct indices 1 - 2 protocols.jd2.PDBJobInputter: (8) PDBJobInputter::fill_jobs basic.random.init_random_generator: (6) 'RNG device' seed mode, using '/dev/urandom', seed=1052970032 seed_offset=0 real_seed=-1211953614 basic.random.init_random_generator: (9) 'RNG device' seed mode, using '/dev/urandom', seed=-1624081599 seed_offset=0 real_seed=-1211953611 basic.random.init_random_generator: (9) RandomGenerator:init: Normal mode, seed=-1211953611 RG_type=mt19937 core.init: (9) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (9) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (9) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (9) pushed snug_input.pdb nstruct indices 1 - 2 protocols.jd2.PDBJobInputter: (8) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (6) RandomGenerator:init: Normal mode, seed=-1211953614 RG_type=mt19937 core.init: (6) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (6) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (6) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (6) pushed snug_input.pdb nstruct indices 1 - 2 core.init: (7) Checking for fconfig files in pwd and ./rosetta/flags core.init: (7) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (7) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (2) Checking for fconfig files in pwd and ./rosetta/flags core.init: (2) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (2) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (9) Checking for fconfig files in pwd and ./rosetta/flags core.init: (9) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (9) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (4) Checking for fconfig files in pwd and ./rosetta/flags core.init: (4) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (4) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 core.init: (0) Checking for fconfig files in pwd and ./rosetta/flags core.init: (8) Checking for fconfig files in pwd and ./rosetta/flags core.init: (8) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (8) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 basic.random.init_random_generator: (1) 'RNG device' seed mode, using '/dev/urandom', seed=1576399124 seed_offset=0 real_seed=1008684662 core.init: (0) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (0) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 basic.random.init_random_generator: (0) 'RNG device' seed mode, using '/dev/urandom', seed=1008684661 seed_offset=0 real_seed=1008684661 basic.random.init_random_generator: (0) RandomGenerator:init: Normal mode, seed=1008684661 RG_type=mt19937 basic.random.init_random_generator: (1) RandomGenerator:init: Normal mode, seed=1008684662 RG_type=mt19937 core.init: (0) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs basic.random.init_random_generator: (4) 'RNG device' seed mode, using '/dev/urandom', seed=2105325233 seed_offset=0 real_seed=1008684665 basic.random.init_random_generator: (5) 'RNG device' seed mode, using '/dev/urandom', seed=1730947737 seed_offset=0 real_seed=1008684666 protocols.jd2.PDBJobInputter: (0) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (7) 'RNG device' seed mode, using '/dev/urandom', seed=429074855 seed_offset=0 real_seed=1008684668 basic.random.init_random_generator: (7) RandomGenerator:init: Normal mode, seed=1008684668 RG_type=mt19937 basic.random.init_random_generator: (2) 'RNG device' seed mode, using '/dev/urandom', seed=205955457 seed_offset=0 real_seed=1008684663 basic.random.init_random_generator: (2) RandomGenerator:init: Normal mode, seed=1008684663 RG_type=mt19937 core.init: (2) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (2) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (2) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (2) pushed snug_input.pdb nstruct indices 1 - 2 core.init: (7) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (7) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (7) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (7) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (4) RandomGenerator:init: Normal mode, seed=1008684665 RG_type=mt19937 core.init: (4) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database basic.random.init_random_generator: (6) 'RNG device' seed mode, using '/dev/urandom', seed=-1739176309 seed_offset=0 real_seed=1008684667 basic.random.init_random_generator: (6) RandomGenerator:init: Normal mode, seed=1008684667 RG_type=mt19937 core.init: (1) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (4) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (4) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (4) pushed snug_input.pdb nstruct indices 1 - 2 core.init: (6) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (6) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (6) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (1) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (6) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (5) RandomGenerator:init: Normal mode, seed=1008684666 RG_type=mt19937 core.init: (5) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (1) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (1) pushed snug_input.pdb nstruct indices 1 - 2 protocols.jd2.PDBJobInputter: (5) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (5) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (5) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (8) 'RNG device' seed mode, using '/dev/urandom', seed=1208952636 seed_offset=0 real_seed=1008684669 basic.random.init_random_generator: (8) RandomGenerator:init: Normal mode, seed=1008684669 RG_type=mt19937 core.init: (8) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (8) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (8) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (8) pushed snug_input.pdb nstruct indices 1 - 2 basic.random.init_random_generator: (9) 'RNG device' seed mode, using '/dev/urandom', seed=-1242507515 seed_offset=0 real_seed=1008684670 basic.random.init_random_generator: (9) RandomGenerator:init: Normal mode, seed=1008684670 RG_type=mt19937 core.init: (9) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (9) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (9) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (9) pushed snug_input.pdb nstruct indices 1 - 2 core.init: (3) Checking for fconfig files in pwd and ./rosetta/flags core.init: (3) Rosetta version: rosetta.source.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:57:38.289184 core.init: (3) command: /share/home/qianlei/Softwares/rosetta_src_2021.16.61629_bundle/main/source/bin/snugdock.mpi.linuxgccrelease @flag_input_snug -partners HL_A -nstruct 2 basic.random.init_random_generator: (3) 'RNG device' seed mode, using '/dev/urandom', seed=-514614864 seed_offset=0 real_seed=1008684664 basic.random.init_random_generator: (3) RandomGenerator:init: Normal mode, seed=1008684664 RG_type=mt19937 core.init: (3) found database environment variable ROSETTA3_DB: /share/home/qianlei/Softwares/rosetta_bin_linux_2021.16.61629_bundle/main/database protocols.jd2.PDBJobInputter: (3) Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: (3) PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: (3) pushed snug_input.pdb nstruct indices 1 - 2 core.chemical.GlobalResidueTypeSet: (3) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 1.14905 seconds. core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (4) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (4) Total time to initialize 1.24304 seconds. core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (2) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 1.18593 seconds. core.import_pose.import_pose: (2) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (3) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (3) Slave Node 3: Requesting new job id from master core.chemical.GlobalResidueTypeSet: (7) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (7) Total time to initialize 1.26618 seconds. core.import_pose.import_pose: (7) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (9) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (9) Total time to initialize 1.2532 seconds. core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (6) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (6) Total time to initialize 1.20116 seconds. core.import_pose.import_pose: (6) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (4) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (4) Slave Node 4: Requesting new job id from master core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 1.19071 seconds. core.import_pose.import_pose: (0) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (3) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 1.29489 seconds. core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (5) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (5) Total time to initialize 1.28757 seconds. core.import_pose.import_pose: (5) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (1) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (0) Total time to initialize 1.19999 seconds. core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 1.27407 seconds. core.chemical.GlobalResidueTypeSet: (2) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (2) Total time to initialize 1.19106 seconds. core.chemical.GlobalResidueTypeSet: (1) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 1.2674 seconds. core.import_pose.import_pose: (0) File 'native_input.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (2) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (5) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (5) Total time to initialize 1.27946 seconds. core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (5) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (8) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (8) Total time to initialize 1.27269 seconds. core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (0) Found disulfide between residues 22 97 core.conformation.Conformation: (0) current variant for 22 CYS core.conformation.Conformation: (0) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.import_pose.import_pose: (8) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (0) current variant for 22 CYD core.chemical.GlobalResidueTypeSet: (4) Finished initializing fa_standard residue type set. Created 984 residue types core.conformation.Conformation: (0) current variant for 97 CYD core.conformation.Conformation: (0) Found disulfide between residues 253 281 core.chemical.GlobalResidueTypeSet: (4) Total time to initialize 1.26413 seconds. core.conformation.Conformation: (0) current variant for 253 CYS core.conformation.Conformation: (0) current variant for 281 CYS core.conformation.Conformation: (0) current variant for 253 CYD core.conformation.Conformation: (0) current variant for 281 CYD core.conformation.Conformation: (0) Found disulfide between residues 143 208 core.chemical.GlobalResidueTypeSet: (7) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (7) Total time to initialize 1.26904 seconds. protocols.evaluation.ChiWellRmsdEvaluatorCreator: (3) Evaluation Creator active ... protocols.evaluation.ChiWellRmsdEvaluatorCreator: (9) Evaluation Creator active ... core.conformation.Conformation: (0) current variant for 143 CYS core.conformation.Conformation: (0) current variant for 208 CYS protocols.jd2.MPIWorkPoolJobDistributor: (9) Slave Node 9: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (3) Slave Node 3: Requesting new job id from master core.conformation.Conformation: (0) current variant for 143 CYD core.conformation.Conformation: (0) current variant for 208 CYD core.conformation.Conformation: (0) Found disulfide between residues 269 295 core.conformation.Conformation: (0) current variant for 269 CYS core.conformation.Conformation: (0) current variant for 295 CYS core.conformation.Conformation: (0) current variant for 269 CYD core.conformation.Conformation: (0) current variant for 295 CYD core.import_pose.import_pose: (7) File 'native_input.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (9) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (9) Total time to initialize 1.27481 seconds. core.chemical.GlobalResidueTypeSet: (8) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (8) Total time to initialize 1.26428 seconds. core.conformation.Conformation: (2) Found disulfide between residues 22 97 core.conformation.Conformation: (2) current variant for 22 CYS core.conformation.Conformation: (2) current variant for 97 CYS core.conformation.Conformation: (2) current variant for 22 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ... core.conformation.Conformation: (2) current variant for 97 CYD core.conformation.Conformation: (2) Found disulfide between residues 253 281 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Getting next job to assign from list id 1 of 2 core.conformation.Conformation: (2) current variant for 253 CYS core.conformation.Conformation: (2) current variant for 281 CYS core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 3 with tag 10 core.conformation.Conformation: (2) current variant for 253 CYD protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 1 to node 3 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Getting next job to assign from list id 2 of 2 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 9 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 2 to node 9 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: No more jobs to assign, setting next job id to zero protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Finished handing out jobs protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 9 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (3) Slave Node 3: Received job id 1 from master. core.conformation.Conformation: (2) current variant for 281 CYD core.conformation.Conformation: (2) Found disulfide between residues 143 208 core.conformation.Conformation: (2) current variant for 143 CYS core.conformation.Conformation: (2) current variant for 208 CYS protocols.jd2.PDBJobInputter: (3) PDBJobInputter::pose_from_job protocols.jd2.MPIWorkPoolJobDistributor: (9) Slave Node 9: Received job id 2 from master. core.conformation.Conformation: (2) current variant for 143 CYD core.conformation.Conformation: (2) current variant for 208 CYD protocols.jd2.PDBJobInputter: (9) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (9) filling pose from PDB snug_input.pdb protocols.jd2.PDBJobInputter: (3) filling pose from PDB snug_input.pdb core.import_pose.import_pose: (8) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (2) Found disulfide between residues 269 295 core.conformation.Conformation: (2) current variant for 269 CYS core.conformation.Conformation: (2) current variant for 295 CYS core.import_pose.import_pose: (9) File 'snug_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (2) current variant for 269 CYD core.conformation.Conformation: (2) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (2) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 2 protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received job id 0 from master. protocols.jd2.JobDistributor: (2) no more batches to process... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 8 slaves to finish jobs protocols.jd2.JobDistributor: (2) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (2) no jobs were attempted, did you forget to pass -overwrite? core.import_pose.import_pose: (3) File 'snug_input.pdb' automatically determined to be of type PDB core.chemical.GlobalResidueTypeSet: (6) Finished initializing fa_standard residue type set. Created 984 residue types core.chemical.GlobalResidueTypeSet: (6) Total time to initialize 1.20066 seconds. core.import_pose.import_pose: (6) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (1) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Requesting new job id from master core.conformation.Conformation: (7) Found disulfide between residues 22 97 core.conformation.Conformation: (7) current variant for 22 CYS core.conformation.Conformation: (7) current variant for 97 CYS core.conformation.Conformation: (7) current variant for 22 CYD core.conformation.Conformation: (7) current variant for 97 CYD core.conformation.Conformation: (7) Found disulfide between residues 253 281 core.conformation.Conformation: (7) current variant for 253 CYS core.conformation.Conformation: (7) current variant for 281 CYS core.conformation.Conformation: (7) current variant for 253 CYD core.conformation.Conformation: (7) current variant for 281 CYD core.conformation.Conformation: (7) Found disulfide between residues 143 208 core.conformation.Conformation: (7) current variant for 143 CYS core.conformation.Conformation: (7) current variant for 208 CYS core.conformation.Conformation: (7) current variant for 143 CYD core.conformation.Conformation: (7) current variant for 208 CYD core.conformation.Conformation: (7) Found disulfide between residues 269 295 core.conformation.Conformation: (7) current variant for 269 CYS core.conformation.Conformation: (7) current variant for 295 CYS core.conformation.Conformation: (7) current variant for 269 CYD core.conformation.Conformation: (7) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (7) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (7) Slave Node 7: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 7 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 7 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 7 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (7) Slave Node 7: Received job id 0 from master. protocols.jd2.JobDistributor: (7) no more batches to process... protocols.jd2.JobDistributor: (7) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (7) no jobs were attempted, did you forget to pass -overwrite? core.conformation.Conformation: (5) Found disulfide between residues 22 97 core.conformation.Conformation: (5) current variant for 22 CYS core.conformation.Conformation: (5) current variant for 97 CYS core.conformation.Conformation: (6) Found disulfide between residues 22 97 core.conformation.Conformation: (5) current variant for 22 CYD core.conformation.Conformation: (5) current variant for 97 CYD core.conformation.Conformation: (6) current variant for 22 CYS core.conformation.Conformation: (6) current variant for 97 CYS core.conformation.Conformation: (5) Found disulfide between residues 253 281 core.conformation.Conformation: (5) current variant for 253 CYS core.conformation.Conformation: (5) current variant for 281 CYS core.conformation.Conformation: (5) current variant for 253 CYD core.conformation.Conformation: (6) current variant for 22 CYD core.conformation.Conformation: (6) current variant for 97 CYD core.conformation.Conformation: (5) current variant for 281 CYD core.conformation.Conformation: (6) Found disulfide between residues 253 281 core.conformation.Conformation: (6) current variant for 253 CYS core.conformation.Conformation: (6) current variant for 281 CYS core.conformation.Conformation: (5) Found disulfide between residues 143 208 core.conformation.Conformation: (5) current variant for 143 CYS core.conformation.Conformation: (5) current variant for 208 CYS core.conformation.Conformation: (5) current variant for 143 CYD core.conformation.Conformation: (5) current variant for 208 CYD core.conformation.Conformation: (6) current variant for 253 CYD core.conformation.Conformation: (5) Found disulfide between residues 269 295 core.conformation.Conformation: (6) current variant for 281 CYD core.conformation.Conformation: (5) current variant for 269 CYS core.conformation.Conformation: (5) current variant for 295 CYS core.conformation.Conformation: (6) Found disulfide between residues 143 208 core.conformation.Conformation: (6) current variant for 143 CYS core.conformation.Conformation: (6) current variant for 208 CYS core.conformation.Conformation: (5) current variant for 269 CYD core.conformation.Conformation: (5) current variant for 295 CYD core.conformation.Conformation: (6) current variant for 143 CYD core.conformation.Conformation: (6) current variant for 208 CYD core.conformation.Conformation: (6) Found disulfide between residues 269 295 core.conformation.Conformation: (6) current variant for 269 CYS core.conformation.Conformation: (6) current variant for 295 CYS core.conformation.Conformation: (6) current variant for 269 CYD core.conformation.Conformation: (6) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (6) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (6) Slave Node 6: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 6 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 6 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 6 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (6) Slave Node 6: Received job id 0 from master. protocols.jd2.JobDistributor: (6) no more batches to process... protocols.jd2.JobDistributor: (6) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (6) no jobs were attempted, did you forget to pass -overwrite? protocols.evaluation.ChiWellRmsdEvaluatorCreator: (5) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (5) Slave Node 5: Requesting new job id from master core.conformation.Conformation: (7) Found disulfide between residues 22 97 core.conformation.Conformation: (7) current variant for 22 CYS core.conformation.Conformation: (7) current variant for 97 CYS core.conformation.Conformation: (7) current variant for 22 CYD core.conformation.Conformation: (7) current variant for 97 CYD core.conformation.Conformation: (7) Found disulfide between residues 253 281 core.conformation.Conformation: (7) current variant for 253 CYS core.conformation.Conformation: (7) current variant for 281 CYS core.conformation.Conformation: (7) current variant for 253 CYD core.conformation.Conformation: (7) current variant for 281 CYD core.conformation.Conformation: (7) Found disulfide between residues 143 208 core.conformation.Conformation: (7) current variant for 143 CYS core.conformation.Conformation: (7) current variant for 208 CYS core.conformation.Conformation: (7) current variant for 143 CYD core.conformation.Conformation: (7) current variant for 208 CYD core.conformation.Conformation: (7) Found disulfide between residues 269 295 core.conformation.Conformation: (7) current variant for 269 CYS core.conformation.Conformation: (7) current variant for 295 CYS core.conformation.Conformation: (7) current variant for 269 CYD core.conformation.Conformation: (7) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (7) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (7) Slave Node 7: Requesting new job id from master core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (9) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (9) Slave Node 9: Requesting new job id from master core.conformation.Conformation: (0) Found disulfide between residues 22 97 core.conformation.Conformation: (0) current variant for 22 CYS core.conformation.Conformation: (0) current variant for 97 CYS core.conformation.Conformation: (0) current variant for 22 CYD core.conformation.Conformation: (0) current variant for 97 CYD core.conformation.Conformation: (0) Found disulfide between residues 253 281 core.conformation.Conformation: (0) current variant for 253 CYS core.conformation.Conformation: (0) current variant for 281 CYS core.conformation.Conformation: (0) current variant for 253 CYD core.conformation.Conformation: (0) current variant for 281 CYD core.conformation.Conformation: (0) Found disulfide between residues 143 208 core.conformation.Conformation: (0) current variant for 143 CYS core.conformation.Conformation: (0) current variant for 208 CYS core.conformation.Conformation: (0) current variant for 143 CYD core.conformation.Conformation: (0) current variant for 208 CYD core.conformation.Conformation: (0) Found disulfide between residues 269 295 core.conformation.Conformation: (0) current variant for 269 CYS core.conformation.Conformation: (0) current variant for 295 CYS core.conformation.Conformation: (0) current variant for 269 CYD core.conformation.Conformation: (0) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Getting next job to assign from list id 1 of 2 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 4 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 1 to node 4 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Getting next job to assign from list id 2 of 2 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for job requests... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending new job id 2 to node 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: No more jobs to assign, setting next job id to zero protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Finished handing out jobs protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 9 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 3 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 3 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 8 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 5 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 5 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 7 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 7 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 7 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 6 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 9 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 9 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 5 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (7) Slave Node 7: Received job id 0 from master. protocols.jd2.JobDistributor: (7) no more batches to process... protocols.jd2.JobDistributor: (7) 2 jobs considered, 0 jobs attempted in 1 seconds protocols.jd2.JobDistributor: (7) no jobs were attempted, did you forget to pass -overwrite? protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received job id 2 from master. protocols.jd2.PDBJobInputter: (1) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (1) filling pose from PDB snug_input.pdb protocols.jd2.MPIWorkPoolJobDistributor: (9) Slave Node 9: Received job id 0 from master. protocols.jd2.JobDistributor: (9) no more batches to process... protocols.jd2.JobDistributor: (9) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (9) no jobs were attempted, did you forget to pass -overwrite? protocols.jd2.MPIWorkPoolJobDistributor: (3) Slave Node 3: Received job id 0 from master. protocols.jd2.JobDistributor: (3) no more batches to process... protocols.jd2.JobDistributor: (3) 2 jobs considered, 0 jobs attempted in 6 seconds protocols.jd2.JobDistributor: (3) no jobs were attempted, did you forget to pass -overwrite? protocols.jd2.MPIWorkPoolJobDistributor: (4) Slave Node 4: Received job id 1 from master. protocols.jd2.PDBJobInputter: (4) PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: (4) filling pose from PDB snug_input.pdb protocols.jd2.MPIWorkPoolJobDistributor: (5) Slave Node 5: Received job id 0 from master. protocols.jd2.JobDistributor: (5) no more batches to process... protocols.jd2.JobDistributor: (5) 2 jobs considered, 0 jobs attempted in 2 seconds protocols.jd2.JobDistributor: (5) no jobs were attempted, did you forget to pass -overwrite? core.import_pose.import_pose: (4) File 'snug_input.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (1) File 'snug_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD protocols.antibody.SnugDockProtocol: (9) Beginning apply function of SnugDockProtocol. protocols.antibody.SnugDockProtocol: (9) Setting up data for SnugDockProtocol. basic.io.database: (9) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: (9) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (9) Antibody CDR definition read successfully antibody.AntibodyInfo: (9) Successfully finished the CDR definition antibody.AntibodyInfo: (9) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (9) ARMGSDYDVWFDYW antibody.AntibodyInfo: (9) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (9) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (9) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 9 Omega: TTTTTTCTT core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (9) Found disulfide between residues 23 88 core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 88 CYD core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 88 CYD core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (9) Found disulfide between residues 23 51 core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 51 CYD core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 51 CYD core.conformation.Conformation: (9) Found disulfide between residues 39 65 core.conformation.Conformation: (9) current variant for 39 CYD core.conformation.Conformation: (9) current variant for 65 CYD core.conformation.Conformation: (9) current variant for 39 CYD core.conformation.Conformation: (9) current variant for 65 CYD core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (8) Found disulfide between residues 22 97 core.conformation.Conformation: (8) current variant for 22 CYS core.conformation.Conformation: (8) current variant for 97 CYS core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (8) current variant for 22 CYD core.conformation.Conformation: (8) current variant for 97 CYD core.conformation.Conformation: (8) Found disulfide between residues 253 281 core.conformation.Conformation: (8) current variant for 253 CYS core.conformation.Conformation: (8) current variant for 281 CYS core.conformation.Conformation: (9) Found disulfide between residues 23 88 core.conformation.Conformation: (8) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 88 CYD core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 88 CYD core.conformation.Conformation: (8) current variant for 281 CYD core.conformation.Conformation: (8) Found disulfide between residues 143 208 core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (8) current variant for 143 CYS core.conformation.Conformation: (8) current variant for 208 CYS core.conformation.Conformation: (9) Found disulfide between residues 23 51 core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 51 CYD core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 51 CYD core.conformation.Conformation: (9) Found disulfide between residues 39 65 core.conformation.Conformation: (9) current variant for 39 CYD core.conformation.Conformation: (9) current variant for 65 CYD core.conformation.Conformation: (9) current variant for 39 CYD core.conformation.Conformation: (9) current variant for 65 CYD core.conformation.Conformation: (8) current variant for 143 CYD core.conformation.Conformation: (8) current variant for 208 CYD core.conformation.Conformation: (8) Found disulfide between residues 269 295 core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (8) current variant for 269 CYS core.conformation.Conformation: (8) current variant for 295 CYS core.conformation.Conformation: (8) current variant for 269 CYD core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (8) current variant for 295 CYD core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (8) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (8) Slave Node 8: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 8 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 8 protocols.jd2.MPIWorkPoolJobDistributor: (8) Slave Node 8: Received job id 0 from master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 4 slaves to finish jobs core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 protocols.jd2.JobDistributor: (8) no more batches to process... protocols.jd2.JobDistributor: (8) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (8) no jobs were attempted, did you forget to pass -overwrite? core.conformation.Conformation: (9) Found disulfide between residues 23 88 core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 88 CYD core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 88 CYD core.kinematics.FoldTree: (9) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (9) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (2) Found disulfide between residues 22 97 core.conformation.Conformation: (9) Found disulfide between residues 23 51 core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 51 CYD core.conformation.Conformation: (9) current variant for 23 CYD core.conformation.Conformation: (9) current variant for 51 CYD core.conformation.Conformation: (9) Found disulfide between residues 39 65 core.conformation.Conformation: (9) current variant for 39 CYD core.conformation.Conformation: (9) current variant for 65 CYD core.conformation.Conformation: (9) current variant for 39 CYD core.conformation.Conformation: (9) current variant for 65 CYD core.conformation.Conformation: (2) current variant for 22 CYS core.conformation.Conformation: (2) current variant for 97 CYS basic.io.database: (9) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt core.conformation.Conformation: (2) current variant for 22 CYD protocols.antibody.AntibodyNumberingParser: (9) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (9) Antibody CDR definition read successfully antibody.AntibodyInfo: (9) Successfully finished the CDR definition antibody.AntibodyInfo: (9) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (9) ARMGSDYDVWFDYW antibody.AntibodyInfo: (9) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (9) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (9) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (9) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (9) Length: 9 Omega: TTTTTTCTT protocols.antibody.SnugDockProtocol: (9) Is my new SnugDock fold tree ok? 1 core.conformation.Conformation: (2) current variant for 97 CYD core.conformation.Conformation: (2) Found disulfide between residues 253 281 core.conformation.Conformation: (2) current variant for 253 CYS core.conformation.Conformation: (2) current variant for 281 CYS core.conformation.Conformation: (2) current variant for 253 CYD core.conformation.Conformation: (2) current variant for 281 CYD core.conformation.Conformation: (2) Found disulfide between residues 143 208 core.conformation.Conformation: (2) current variant for 143 CYS core.conformation.Conformation: (2) current variant for 208 CYS core.conformation.Conformation: (2) current variant for 143 CYD core.conformation.Conformation: (2) current variant for 208 CYD core.conformation.Conformation: (2) Found disulfide between residues 269 295 core.conformation.Conformation: (2) current variant for 269 CYS core.conformation.Conformation: (2) current variant for 295 CYS core.conformation.Conformation: (2) current variant for 269 CYD core.conformation.Conformation: (2) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (2) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 2 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 2 protocols.jd2.MPIWorkPoolJobDistributor: (2) Slave Node 2: Received job id 0 from master. protocols.jd2.JobDistributor: (2) no more batches to process... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 3 slaves to finish jobs protocols.jd2.JobDistributor: (2) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (2) no jobs were attempted, did you forget to pass -overwrite? basic.io.database: (9) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: (9) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (9) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (9) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: (9) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (9) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (9) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (9) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (9) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.scoring.ramachandran: (9) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: (9) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (4) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (4) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (4) Slave Node 4: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 4 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 4 protocols.jd2.MPIWorkPoolJobDistributor: (4) Slave Node 4: Received job id 0 from master. protocols.jd2.JobDistributor: (4) no more batches to process... protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 5 slaves to finish jobs protocols.jd2.JobDistributor: (4) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (4) no jobs were attempted, did you forget to pass -overwrite? core.conformation.Conformation: (8) Found disulfide between residues 22 97 core.conformation.Conformation: (8) current variant for 22 CYS core.conformation.Conformation: (8) current variant for 97 CYS core.conformation.Conformation: (8) current variant for 22 CYD core.conformation.Conformation: (8) current variant for 97 CYD core.conformation.Conformation: (8) Found disulfide between residues 253 281 core.conformation.Conformation: (8) current variant for 253 CYS core.conformation.Conformation: (8) current variant for 281 CYS core.conformation.Conformation: (8) current variant for 253 CYD core.conformation.Conformation: (8) current variant for 281 CYD core.conformation.Conformation: (8) Found disulfide between residues 143 208 core.conformation.Conformation: (8) current variant for 143 CYS core.conformation.Conformation: (8) current variant for 208 CYS core.conformation.Conformation: (8) current variant for 143 CYD core.conformation.Conformation: (8) current variant for 208 CYD core.conformation.Conformation: (8) Found disulfide between residues 269 295 core.conformation.Conformation: (8) current variant for 269 CYS core.conformation.Conformation: (8) current variant for 295 CYS core.conformation.Conformation: (8) current variant for 269 CYD core.conformation.Conformation: (8) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (8) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (8) Slave Node 8: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 8 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 8 protocols.jd2.MPIWorkPoolJobDistributor: (8) Slave Node 8: Received job id 0 from master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 4 slaves to finish jobs protocols.jd2.JobDistributor: (8) no more batches to process... protocols.jd2.JobDistributor: (8) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (8) no jobs were attempted, did you forget to pass -overwrite? core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (5) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (5) current variant for 22 CYS core.conformation.Conformation: (5) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (5) current variant for 22 CYD core.conformation.Conformation: (5) current variant for 97 CYD core.conformation.Conformation: (5) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (5) current variant for 253 CYS core.conformation.Conformation: (5) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (5) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (5) current variant for 281 CYD core.conformation.Conformation: (5) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (5) current variant for 143 CYS core.conformation.Conformation: (5) current variant for 208 CYS core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (5) current variant for 143 CYD core.conformation.Conformation: (5) current variant for 208 CYD core.conformation.Conformation: (5) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD core.conformation.Conformation: (5) current variant for 269 CYS core.conformation.Conformation: (5) current variant for 295 CYS core.conformation.Conformation: (5) current variant for 269 CYD core.conformation.Conformation: (5) current variant for 295 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (1) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 1 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 3 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received job id 0 from master. protocols.evaluation.ChiWellRmsdEvaluatorCreator: (5) Evaluation Creator active ... protocols.jd2.MPIWorkPoolJobDistributor: (5) Slave Node 5: Requesting new job id from master protocols.jd2.JobDistributor: (1) no more batches to process... protocols.jd2.JobDistributor: (1) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (1) no jobs were attempted, did you forget to pass -overwrite? protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 5 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 5 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 2 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (5) Slave Node 5: Received job id 0 from master. protocols.jd2.JobDistributor: (5) no more batches to process... protocols.jd2.JobDistributor: (5) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (5) no jobs were attempted, did you forget to pass -overwrite? core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD protocols.antibody.SnugDockProtocol: (3) Beginning apply function of SnugDockProtocol. protocols.antibody.SnugDockProtocol: (3) Setting up data for SnugDockProtocol. basic.io.database: (3) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt core.conformation.Conformation: (6) Found disulfide between residues 22 97 core.conformation.Conformation: (6) current variant for 22 CYS core.conformation.Conformation: (6) current variant for 97 CYS core.conformation.Conformation: (6) current variant for 22 CYD core.conformation.Conformation: (6) current variant for 97 CYD core.conformation.Conformation: (6) Found disulfide between residues 253 281 protocols.antibody.AntibodyNumberingParser: (3) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (3) Antibody CDR definition read successfully core.conformation.Conformation: (6) current variant for 253 CYS core.conformation.Conformation: (6) current variant for 281 CYS antibody.AntibodyInfo: (3) Successfully finished the CDR definition antibody.AntibodyInfo: (3) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (3) ARMGSDYDVWFDYW antibody.AntibodyInfo: (3) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (3) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (3) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 9 Omega: TTTTTTCTT core.conformation.Conformation: (6) current variant for 253 CYD core.conformation.Conformation: (6) current variant for 281 CYD core.conformation.Conformation: (6) Found disulfide between residues 143 208 core.conformation.Conformation: (6) current variant for 143 CYS core.conformation.Conformation: (6) current variant for 208 CYS core.conformation.Conformation: (6) current variant for 143 CYD core.conformation.Conformation: (6) current variant for 208 CYD core.conformation.Conformation: (6) Found disulfide between residues 269 295 core.conformation.Conformation: (6) current variant for 269 CYS core.conformation.Conformation: (6) current variant for 295 CYS core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.conformation.Conformation: (6) current variant for 269 CYD core.conformation.Conformation: (6) current variant for 295 CYD core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD protocols.evaluation.ChiWellRmsdEvaluatorCreator: (6) Evaluation Creator active ... core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 protocols.jd2.MPIWorkPoolJobDistributor: (6) Slave Node 6: Requesting new job id from master core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 6 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 6 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 2 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (6) Slave Node 6: Received job id 0 from master. protocols.jd2.JobDistributor: (6) no more batches to process... protocols.jd2.JobDistributor: (6) 2 jobs considered, 0 jobs attempted in 0 seconds protocols.jd2.JobDistributor: (6) no jobs were attempted, did you forget to pass -overwrite? core.conformation.Conformation: (3) Found disulfide between residues 23 88 core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 88 CYD core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 88 CYD core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD core.conformation.Conformation: (3) Found disulfide between residues 23 51 core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 51 CYD core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 51 CYD core.conformation.Conformation: (3) Found disulfide between residues 39 65 core.conformation.Conformation: (3) current variant for 39 CYD core.conformation.Conformation: (3) current variant for 65 CYD core.conformation.Conformation: (3) current variant for 39 CYD core.conformation.Conformation: (3) current variant for 65 CYD core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (3) Found disulfide between residues 23 88 core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 88 CYD core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 88 CYD core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (3) Found disulfide between residues 23 51 core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 51 CYD core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 51 CYD core.conformation.Conformation: (3) Found disulfide between residues 39 65 core.conformation.Conformation: (3) current variant for 39 CYD core.conformation.Conformation: (3) current variant for 65 CYD core.conformation.Conformation: (3) current variant for 39 CYD core.conformation.Conformation: (3) current variant for 65 CYD core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (3) Found disulfide between residues 23 88 core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 88 CYD core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 88 CYD core.kinematics.FoldTree: (3) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (3) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (3) Found disulfide between residues 23 51 core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 51 CYD core.conformation.Conformation: (3) current variant for 23 CYD core.conformation.Conformation: (3) current variant for 51 CYD core.conformation.Conformation: (3) Found disulfide between residues 39 65 core.conformation.Conformation: (3) current variant for 39 CYD core.conformation.Conformation: (3) current variant for 65 CYD core.conformation.Conformation: (3) current variant for 39 CYD core.conformation.Conformation: (3) current variant for 65 CYD basic.io.database: (3) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: (3) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (3) Antibody CDR definition read successfully antibody.AntibodyInfo: (3) Successfully finished the CDR definition antibody.AntibodyInfo: (3) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (3) ARMGSDYDVWFDYW antibody.AntibodyInfo: (3) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (3) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (3) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (3) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (3) Length: 9 Omega: TTTTTTCTT protocols.antibody.SnugDockProtocol: (3) Is my new SnugDock fold tree ok? 1 basic.io.database: (3) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: (3) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (3) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (3) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS basic.io.database: (3) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS basic.io.database: (3) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 basic.io.database: (3) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD basic.io.database: (3) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv core.conformation.Conformation: (4) Found disulfide between residues 269 295 basic.io.database: (3) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.scoring.ramachandran: (3) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: (3) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD protocols.antibody.SnugDockProtocol: (4) Beginning apply function of SnugDockProtocol. protocols.antibody.SnugDockProtocol: (4) Setting up data for SnugDockProtocol. basic.io.database: (4) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: (4) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (4) Antibody CDR definition read successfully antibody.AntibodyInfo: (4) Successfully finished the CDR definition antibody.AntibodyInfo: (4) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (4) ARMGSDYDVWFDYW antibody.AntibodyInfo: (4) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (4) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (4) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 9 Omega: TTTTTTCTT core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 23 88 core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 88 CYD core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 88 CYD core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 23 51 core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 51 CYD core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 51 CYD core.conformation.Conformation: (4) Found disulfide between residues 39 65 core.conformation.Conformation: (4) current variant for 39 CYD core.conformation.Conformation: (4) current variant for 65 CYD core.conformation.Conformation: (4) current variant for 39 CYD core.conformation.Conformation: (4) current variant for 65 CYD core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 23 88 core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 88 CYD core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 88 CYD core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 23 51 core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 51 CYD core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 51 CYD core.conformation.Conformation: (4) Found disulfide between residues 39 65 core.conformation.Conformation: (4) current variant for 39 CYD core.conformation.Conformation: (4) current variant for 65 CYD core.conformation.Conformation: (4) current variant for 39 CYD core.conformation.Conformation: (4) current variant for 65 CYD core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 23 88 core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 88 CYD core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 88 CYD core.kinematics.FoldTree: (4) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (4) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (4) Found disulfide between residues 23 51 core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 51 CYD core.conformation.Conformation: (4) current variant for 23 CYD core.conformation.Conformation: (4) current variant for 51 CYD core.conformation.Conformation: (4) Found disulfide between residues 39 65 core.conformation.Conformation: (4) current variant for 39 CYD core.conformation.Conformation: (4) current variant for 65 CYD core.conformation.Conformation: (4) current variant for 39 CYD core.conformation.Conformation: (4) current variant for 65 CYD basic.io.database: (4) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: (4) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (4) Antibody CDR definition read successfully antibody.AntibodyInfo: (4) Successfully finished the CDR definition antibody.AntibodyInfo: (4) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (4) ARMGSDYDVWFDYW antibody.AntibodyInfo: (4) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (4) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (4) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (4) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (4) Length: 9 Omega: TTTTTTCTT protocols.antibody.SnugDockProtocol: (4) Is my new SnugDock fold tree ok? 1 basic.io.database: (4) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: (4) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (4) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (4) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: (4) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (4) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (4) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (4) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (4) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.scoring.ramachandran: (4) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: (4) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD protocols.antibody.SnugDockProtocol: (1) Beginning apply function of SnugDockProtocol. protocols.antibody.SnugDockProtocol: (1) Setting up data for SnugDockProtocol. basic.io.database: (1) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: (1) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (1) Antibody CDR definition read successfully antibody.AntibodyInfo: (1) Successfully finished the CDR definition antibody.AntibodyInfo: (1) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (1) ARMGSDYDVWFDYW antibody.AntibodyInfo: (1) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (1) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (1) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 9 Omega: TTTTTTCTT core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 23 88 core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 88 CYD core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 88 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 23 51 core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 51 CYD core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 51 CYD core.conformation.Conformation: (1) Found disulfide between residues 39 65 core.conformation.Conformation: (1) current variant for 39 CYD core.conformation.Conformation: (1) current variant for 65 CYD core.conformation.Conformation: (1) current variant for 39 CYD core.conformation.Conformation: (1) current variant for 65 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 23 88 core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 88 CYD core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 88 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 23 51 core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 51 CYD core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 51 CYD core.conformation.Conformation: (1) Found disulfide between residues 39 65 core.conformation.Conformation: (1) current variant for 39 CYD core.conformation.Conformation: (1) current variant for 65 CYD core.conformation.Conformation: (1) current variant for 39 CYD core.conformation.Conformation: (1) current variant for 65 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 23 88 core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 88 CYD core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 88 CYD core.kinematics.FoldTree: (1) delete_jump_seqpos: deleting jump 1 core.kinematics.FoldTree: (1) delete_jump_seqpos: renumbering jump 2 to 1 core.conformation.Conformation: (1) Found disulfide between residues 23 51 core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 51 CYD core.conformation.Conformation: (1) current variant for 23 CYD core.conformation.Conformation: (1) current variant for 51 CYD core.conformation.Conformation: (1) Found disulfide between residues 39 65 core.conformation.Conformation: (1) current variant for 39 CYD core.conformation.Conformation: (1) current variant for 65 CYD core.conformation.Conformation: (1) current variant for 39 CYD core.conformation.Conformation: (1) current variant for 65 CYD basic.io.database: (1) Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: (1) Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: (1) Antibody CDR definition read successfully antibody.AntibodyInfo: (1) Successfully finished the CDR definition antibody.AntibodyInfo: (1) AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: (1) ARMGSDYDVWFDYW antibody.AntibodyInfo: (1) AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: (1) AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: (1) Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 15 Omega: TTTTTTTTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 9 Omega: TTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: (1) Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: (1) Length: 9 Omega: TTTTTTCTT protocols.antibody.SnugDockProtocol: (1) Is my new SnugDock fold tree ok? 1 basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (1) Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.scoring.ramachandran: (1) shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: (1) Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.scoring.etable: (9) Starting energy table calculation core.scoring.etable: (9) smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (9) smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (9) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.scoring.etable: (9) Finished calculating energy tables. basic.io.database: (9) Database file opened: scoring/score_functions/rama/fd/all.ramaProb core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.etable: (1) Starting energy table calculation core.scoring.etable: (1) smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (1) smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (1) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.etable: (3) Starting energy table calculation core.scoring.etable: (3) smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (3) smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (3) smooth_etable: spline smoothing solvation etables (max_dis = 6) basic.io.database: (9) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb core.scoring.etable: (1) Finished calculating energy tables. basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/all.ramaProb core.scoring.etable: (3) Finished calculating energy tables. basic.io.database: (3) Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: (9) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (9) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (9) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (9) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (9) Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (9) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (9) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (9) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB basic.io.database: (1) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB basic.io.database: (3) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: (3) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (3) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (3) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (3) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (3) Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (3) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (3) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (3) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (1) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (1) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (1) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.import_pose.import_pose: (9) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (4) SCOREFUNCTION: ref2015 core.scoring.etable: (4) Starting energy table calculation core.scoring.etable: (4) smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (4) smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (4) smooth_etable: spline smoothing solvation etables (max_dis = 6) core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.import_pose.import_pose: (3) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (9) Found disulfide between residues 22 97 core.conformation.Conformation: (9) current variant for 22 CYS core.conformation.Conformation: (9) current variant for 97 CYS core.conformation.Conformation: (9) current variant for 22 CYD core.conformation.Conformation: (9) current variant for 97 CYD core.conformation.Conformation: (9) Found disulfide between residues 253 281 core.conformation.Conformation: (9) current variant for 253 CYS core.conformation.Conformation: (9) current variant for 281 CYS core.conformation.Conformation: (9) current variant for 253 CYD core.conformation.Conformation: (9) current variant for 281 CYD core.conformation.Conformation: (9) Found disulfide between residues 143 208 core.conformation.Conformation: (9) current variant for 143 CYS core.conformation.Conformation: (9) current variant for 208 CYS core.conformation.Conformation: (9) current variant for 143 CYD core.conformation.Conformation: (9) current variant for 208 CYD core.conformation.Conformation: (9) Found disulfide between residues 269 295 core.conformation.Conformation: (9) current variant for 269 CYS core.conformation.Conformation: (9) current variant for 295 CYS core.conformation.Conformation: (3) Found disulfide between residues 22 97 core.conformation.Conformation: (3) current variant for 22 CYS core.conformation.Conformation: (3) current variant for 97 CYS core.conformation.Conformation: (3) current variant for 22 CYD core.conformation.Conformation: (3) current variant for 97 CYD core.conformation.Conformation: (3) Found disulfide between residues 253 281 core.conformation.Conformation: (3) current variant for 253 CYS core.conformation.Conformation: (3) current variant for 281 CYS core.conformation.Conformation: (3) current variant for 253 CYD core.conformation.Conformation: (3) current variant for 281 CYD core.conformation.Conformation: (3) Found disulfide between residues 143 208 core.conformation.Conformation: (3) current variant for 143 CYS core.conformation.Conformation: (3) current variant for 208 CYS core.conformation.Conformation: (3) current variant for 143 CYD core.conformation.Conformation: (3) current variant for 208 CYD core.conformation.Conformation: (3) Found disulfide between residues 269 295 core.conformation.Conformation: (3) current variant for 269 CYS core.conformation.Conformation: (3) current variant for 295 CYS core.conformation.Conformation: (3) current variant for 269 CYD core.conformation.Conformation: (3) current variant for 295 CYD core.conformation.Conformation: (9) current variant for 269 CYD core.conformation.Conformation: (9) current variant for 295 CYD basic.io.database: (3) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: (3) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (3) Reading options... core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (3) SCOREFUNCTION: ref2015 protocols.antibody.SnugDockProtocol: (3) SnugDockProtocol has been configured to operate on an Antibody-Antigen complex with the following information: protocols.antibody.SnugDockProtocol: (3) //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: (3) /// Rosetta Antibody Info /// protocols.antibody.SnugDockProtocol: (3) /// /// protocols.antibody.SnugDockProtocol: (3) /// Antibody Type: Regular Antibody protocols.antibody.SnugDockProtocol: (3) /// Light Chain Type: unknown protocols.antibody.SnugDockProtocol: (3) /// Predict H3 Cterminus Base: KINKED protocols.antibody.SnugDockProtocol: (3) /// protocols.antibody.SnugDockProtocol: (3) /// H1 info: protocols.antibody.SnugDockProtocol: (3) /// length: 12 protocols.antibody.SnugDockProtocol: (3) /// sequence: GFSLSTYGMGVG protocols.antibody.SnugDockProtocol: (3) /// north_cluster: H1-15-1 protocols.antibody.SnugDockProtocol: (3) /// loop_info: LOOP start: 26 stop: 37 cut: 32 size: 12 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (3) protocols.antibody.SnugDockProtocol: (3) /// H2 info: protocols.antibody.SnugDockProtocol: (3) /// length: 16 protocols.antibody.SnugDockProtocol: (3) /// sequence: HIWWDDVKRYNPALKS protocols.antibody.SnugDockProtocol: (3) /// north_cluster: H2-9-1 protocols.antibody.SnugDockProtocol: (3) /// loop_info: LOOP start: 52 stop: 67 cut: 60 size: 16 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (3) protocols.antibody.SnugDockProtocol: (3) /// H3 info: protocols.antibody.SnugDockProtocol: (3) /// length: 11 protocols.antibody.SnugDockProtocol: (3) /// sequence: MGSDYDVWFDY protocols.antibody.SnugDockProtocol: (3) /// north_cluster: H3-13-2 protocols.antibody.SnugDockProtocol: (3) /// loop_info: LOOP start: 100 stop: 110 cut: 101 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (3) protocols.antibody.SnugDockProtocol: (3) /// L1 info: protocols.antibody.SnugDockProtocol: (3) /// length: 11 protocols.antibody.SnugDockProtocol: (3) /// sequence: RASKSISKYLA protocols.antibody.SnugDockProtocol: (3) /// north_cluster: L1-11-1 protocols.antibody.SnugDockProtocol: (3) /// loop_info: LOOP start: 144 stop: 154 cut: 149 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (3) protocols.antibody.SnugDockProtocol: (3) /// L2 info: protocols.antibody.SnugDockProtocol: (3) /// length: 7 protocols.antibody.SnugDockProtocol: (3) /// sequence: SGSTLQS protocols.antibody.SnugDockProtocol: (3) /// north_cluster: L2-8-1 protocols.antibody.SnugDockProtocol: (3) /// loop_info: LOOP start: 170 stop: 176 cut: 173 size: 7 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (3) protocols.antibody.SnugDockProtocol: (3) /// L3 info: protocols.antibody.SnugDockProtocol: (3) /// length: 9 protocols.antibody.SnugDockProtocol: (3) /// sequence: QQHNEYPYT protocols.antibody.SnugDockProtocol: (3) /// north_cluster: L3-9-cis7-1 protocols.antibody.SnugDockProtocol: (3) /// loop_info: LOOP start: 209 stop: 217 cut: 213 size: 9 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (3) protocols.antibody.SnugDockProtocol: (3) //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: (3) protocols.antibody.SnugDockProtocol: (3) Using universal FoldTree. antibody.util: (3) Automatically setting kink constraint! protocols.antibody.SnugDockProtocol: (3) Beginning application of DockingProtocol. protocols.docking.DockingProtocol: (3) //////////////////////////////////////////////////////////////////////////////// basic.io.database: (9) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: (9) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (9) Reading options... protocols.docking.DockingProtocol: (3) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (3) /// /// protocols.docking.DockingProtocol: (3) /// Dockable Jumps: 1 /// core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 protocols.docking.DockingProtocol: (3) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (3) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (3) /// Low Resolution Filter: off /// protocols.docking.DockingProtocol: (3) /// High Resolution Filter: off /// protocols.docking.DockingProtocol: (3) //////////////////////////////////////////////////////////////////////////////// core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (9) SCOREFUNCTION: ref2015 protocols.antibody.SnugDockProtocol: (9) SnugDockProtocol has been configured to operate on an Antibody-Antigen complex with the following information: protocols.antibody.SnugDockProtocol: (9) //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: (9) /// Rosetta Antibody Info /// protocols.antibody.SnugDockProtocol: (9) /// /// protocols.antibody.SnugDockProtocol: (9) /// Antibody Type: Regular Antibody protocols.antibody.SnugDockProtocol: (9) /// Light Chain Type: unknown protocols.antibody.SnugDockProtocol: (9) /// Predict H3 Cterminus Base: KINKED protocols.antibody.SnugDockProtocol: (9) /// protocols.antibody.SnugDockProtocol: (9) /// H1 info: protocols.antibody.SnugDockProtocol: (9) /// length: 12 protocols.antibody.SnugDockProtocol: (9) /// sequence: GFSLSTYGMGVG protocols.antibody.SnugDockProtocol: (9) /// north_cluster: H1-15-1 protocols.antibody.SnugDockProtocol: (9) /// loop_info: LOOP start: 26 stop: 37 cut: 32 size: 12 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (9) protocols.antibody.SnugDockProtocol: (9) /// H2 info: protocols.antibody.SnugDockProtocol: (9) /// length: 16 protocols.antibody.SnugDockProtocol: (9) /// sequence: HIWWDDVKRYNPALKS protocols.antibody.SnugDockProtocol: (9) /// north_cluster: H2-9-1 protocols.antibody.SnugDockProtocol: (9) /// loop_info: LOOP start: 52 stop: 67 cut: 60 size: 16 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (9) protocols.antibody.SnugDockProtocol: (9) /// H3 info: protocols.antibody.SnugDockProtocol: (9) /// length: 11 protocols.antibody.SnugDockProtocol: (9) /// sequence: MGSDYDVWFDY protocols.antibody.SnugDockProtocol: (9) /// north_cluster: H3-13-2 protocols.antibody.SnugDockProtocol: (9) /// loop_info: LOOP start: 100 stop: 110 cut: 101 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (9) protocols.antibody.SnugDockProtocol: (9) /// L1 info: protocols.antibody.SnugDockProtocol: (9) /// length: 11 protocols.antibody.SnugDockProtocol: (9) /// sequence: RASKSISKYLA protocols.antibody.SnugDockProtocol: (9) /// north_cluster: L1-11-1 protocols.antibody.SnugDockProtocol: (9) /// loop_info: LOOP start: 144 stop: 154 cut: 149 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (9) protocols.antibody.SnugDockProtocol: (9) /// L2 info: protocols.antibody.SnugDockProtocol: (9) /// length: 7 protocols.antibody.SnugDockProtocol: (9) /// sequence: SGSTLQS protocols.antibody.SnugDockProtocol: (9) /// north_cluster: L2-8-1 protocols.antibody.SnugDockProtocol: (9) /// loop_info: LOOP start: 170 stop: 176 cut: 173 size: 7 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (9) protocols.antibody.SnugDockProtocol: (9) /// L3 info: protocols.antibody.SnugDockProtocol: (9) /// length: 9 protocols.antibody.SnugDockProtocol: (9) /// sequence: QQHNEYPYT protocols.antibody.SnugDockProtocol: (9) /// north_cluster: L3-9-cis7-1 protocols.antibody.SnugDockProtocol: (9) /// loop_info: LOOP start: 209 stop: 217 cut: 213 size: 9 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (9) protocols.antibody.SnugDockProtocol: (9) //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: (9) protocols.antibody.SnugDockProtocol: (9) Using universal FoldTree. antibody.util: (9) Automatically setting kink constraint! protocols.antibody.SnugDockProtocol: (9) Beginning application of DockingProtocol. protocols.docking.DockingProtocol: (9) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (9) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (9) /// /// protocols.docking.DockingProtocol: (9) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (9) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (9) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (9) /// Low Resolution Filter: off /// protocols.docking.DockingProtocol: (9) /// High Resolution Filter: off /// protocols.docking.DockingProtocol: (9) //////////////////////////////////////////////////////////////////////////////// core.chemical.GlobalResidueTypeSet: (3) Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: (3) Total time to initialize 0.034949 seconds. core.chemical.GlobalResidueTypeSet: (9) Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: (9) Total time to initialize 0.029768 seconds. core.scoring.etable: (4) Finished calculating energy tables. basic.io.database: (4) Database file opened: scoring/score_functions/rama/fd/all.ramaProb protocols.docking.DockingProtocol: (3) FOLD_TREE EDGE 1 2 1 EDGE 1 3 2 EDGE 3 4 3 EDGE 2 5 4 EDGE 3 6 5 EDGE 4 126 6 EDGE 5 236 7 EDGE 236 339 -1 EDGE 6 28 -1 EDGE 28 35 -1 EDGE 28 42 8 EDGE 42 36 -1 EDGE 42 57 -1 EDGE 57 61 -1 EDGE 57 65 9 EDGE 65 62 -1 EDGE 65 103 -1 EDGE 103 109 -1 EDGE 103 115 10 EDGE 115 125 -1 EDGE 115 110 -1 EDGE 126 149 -1 EDGE 149 154 -1 EDGE 149 159 11 EDGE 159 155 -1 EDGE 159 174 -1 EDGE 174 178 -1 EDGE 174 181 12 EDGE 181 179 -1 EDGE 181 214 -1 EDGE 214 218 -1 EDGE 214 222 13 EDGE 222 235 -1 EDGE 222 219 -1 protocols.docking.DockingInitialPerturbation: (3) dock_pert: true protocols.docking.DockingInitialPerturbation: (3) option[ docking::dock_pert ]()0 1 protocols.docking.DockingInitialPerturbation: (3) sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: (3) sliding into contact protocols.docking.DockingInitialPerturbation: (3) Moving away protocols.docking.DockingInitialPerturbation: (3) Moving together protocols.moves.RigidBodyMover: (3) Translate: Jump (before): RT -0.323734 0.0861665 -0.942216 0.765791 -0.560986 -0.314419 -0.555662 -0.823329 0.115625 -5.65417 28.1013 21.4289 protocols.moves.RigidBodyMover: (3) Translate: Jump (after): RT -0.323734 0.0861665 -0.942216 0.765791 -0.560986 -0.314419 -0.555662 -0.823329 0.115625 -5.39563 27.2122 21.051 protocols.moves.RigidBodyMover: (3) Translate: Jump (before): RT -0.323734 0.0861665 -0.942216 0.765791 -0.560986 -0.314419 -0.555662 -0.823329 0.115625 -5.39563 27.2122 21.051 protocols.moves.RigidBodyMover: (3) Translate: Jump (after): RT -0.323734 0.0861665 -0.942216 0.765791 -0.560986 -0.314419 -0.555662 -0.823329 0.115625 -5.65417 28.1013 21.4289 protocols.docking.DockingProtocol: (3) finished initial perturbation ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose. ERROR:: Exit from: src/core/conformation/Conformation.hh line: 510 protocols.jd2.JobDistributor: (3) [ ERROR ] [ERROR] Exception caught by JobDistributor for job snug_input_0001 [ ERROR ]: Caught exception: File: src/core/conformation/Conformation.hh:510 [ ERROR ] UtilityExitException ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose. AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. protocols.jd2.JobDistributor: (3) [ WARNING ] snug_input_0001 reported failure and will NOT retry protocols.jd2.MPIWorkPoolJobDistributor: (3) Job 1 failed! Slave process 3 transmitting failure to master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 3 with tag 40 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master node: Received job failure message for job id 1 from node 3. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 1 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 1 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 2 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (3) Slave Node 3: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 3 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 3 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 1 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (3) Slave Node 3: Received job id 0 from master. protocols.jd2.JobDistributor: (3) no more batches to process... protocols.jd2.JobDistributor: (3) 2 jobs considered, 1 jobs attempted in 87 seconds --------------------------------------------------------------- [ ERROR ]: Error(s) were encountered when running jobs. 1 jobs failed; Check the output further up for additional error messages. --------------------------------------------------------------- -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[62701,1],3] Exit code: 255 -------------------------------------------------------------------------- core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB basic.io.database: (4) Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: (4) Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (4) Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (4) Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (4) Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (4) Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (4) Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (4) shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (4) Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.import_pose.import_pose: (1) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (4) Found disulfide between residues 22 97 core.conformation.Conformation: (4) current variant for 22 CYS core.conformation.Conformation: (4) current variant for 97 CYS core.conformation.Conformation: (4) current variant for 22 CYD core.conformation.Conformation: (4) current variant for 97 CYD core.conformation.Conformation: (4) Found disulfide between residues 253 281 core.conformation.Conformation: (4) current variant for 253 CYS core.conformation.Conformation: (4) current variant for 281 CYS core.conformation.Conformation: (4) current variant for 253 CYD core.conformation.Conformation: (4) current variant for 281 CYD core.conformation.Conformation: (4) Found disulfide between residues 143 208 core.conformation.Conformation: (4) current variant for 143 CYS core.conformation.Conformation: (4) current variant for 208 CYS core.conformation.Conformation: (4) current variant for 143 CYD core.conformation.Conformation: (4) current variant for 208 CYD core.conformation.Conformation: (4) Found disulfide between residues 269 295 core.conformation.Conformation: (4) current variant for 269 CYS core.conformation.Conformation: (4) current variant for 295 CYS core.conformation.Conformation: (4) current variant for 269 CYD core.conformation.Conformation: (4) current variant for 295 CYD core.scoring.ScoreFunctionFactory: (4) SCOREFUNCTION: ref2015 core.import_pose.import_pose: (4) File 'native_input.pdb' automatically determined to be of type PDB core.conformation.Conformation: (1) Found disulfide between residues 22 97 core.conformation.Conformation: (1) current variant for 22 CYS core.conformation.Conformation: (1) current variant for 97 CYS core.conformation.Conformation: (1) current variant for 22 CYD core.conformation.Conformation: (1) current variant for 97 CYD core.conformation.Conformation: (1) Found disulfide between residues 253 281 core.conformation.Conformation: (1) current variant for 253 CYS core.conformation.Conformation: (1) current variant for 281 CYS core.conformation.Conformation: (1) current variant for 253 CYD core.conformation.Conformation: (1) current variant for 281 CYD core.conformation.Conformation: (1) Found disulfide between residues 143 208 core.conformation.Conformation: (1) current variant for 143 CYS core.conformation.Conformation: (1) current variant for 208 CYS core.conformation.Conformation: (1) current variant for 143 CYD core.conformation.Conformation: (1) current variant for 208 CYD core.conformation.Conformation: (1) Found disulfide between residues 269 295 core.conformation.Conformation: (1) current variant for 269 CYS core.conformation.Conformation: (1) current variant for 295 CYS core.conformation.Conformation: (1) current variant for 269 CYD core.conformation.Conformation: (1) current variant for 295 CYD basic.io.database: (1) Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: (1) Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 protocols.docking.DockingInitialPerturbation: (1) Reading options... core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: (1) SCOREFUNCTION: ref2015 protocols.antibody.SnugDockProtocol: (1) SnugDockProtocol has been configured to operate on an Antibody-Antigen complex with the following information: protocols.antibody.SnugDockProtocol: (1) //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: (1) /// Rosetta Antibody Info /// protocols.antibody.SnugDockProtocol: (1) /// /// protocols.antibody.SnugDockProtocol: (1) /// Antibody Type: Regular Antibody protocols.antibody.SnugDockProtocol: (1) /// Light Chain Type: unknown protocols.antibody.SnugDockProtocol: (1) /// Predict H3 Cterminus Base: KINKED protocols.antibody.SnugDockProtocol: (1) /// protocols.antibody.SnugDockProtocol: (1) /// H1 info: protocols.antibody.SnugDockProtocol: (1) /// length: 12 protocols.antibody.SnugDockProtocol: (1) /// sequence: GFSLSTYGMGVG protocols.antibody.SnugDockProtocol: (1) /// north_cluster: H1-15-1 protocols.antibody.SnugDockProtocol: (1) /// loop_info: LOOP start: 26 stop: 37 cut: 32 size: 12 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (1) protocols.antibody.SnugDockProtocol: (1) /// H2 info: protocols.antibody.SnugDockProtocol: (1) /// length: 16 protocols.antibody.SnugDockProtocol: (1) /// sequence: HIWWDDVKRYNPALKS protocols.antibody.SnugDockProtocol: (1) /// north_cluster: H2-9-1 protocols.antibody.SnugDockProtocol: (1) /// loop_info: LOOP start: 52 stop: 67 cut: 60 size: 16 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (1) protocols.antibody.SnugDockProtocol: (1) /// H3 info: protocols.antibody.SnugDockProtocol: (1) /// length: 11 protocols.antibody.SnugDockProtocol: (1) /// sequence: MGSDYDVWFDY protocols.antibody.SnugDockProtocol: (1) /// north_cluster: H3-13-2 protocols.antibody.SnugDockProtocol: (1) /// loop_info: LOOP start: 100 stop: 110 cut: 101 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (1) protocols.antibody.SnugDockProtocol: (1) /// L1 info: protocols.antibody.SnugDockProtocol: (1) /// length: 11 protocols.antibody.SnugDockProtocol: (1) /// sequence: RASKSISKYLA protocols.antibody.SnugDockProtocol: (1) /// north_cluster: L1-11-1 protocols.antibody.SnugDockProtocol: (1) /// loop_info: LOOP start: 144 stop: 154 cut: 149 size: 11 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (1) protocols.antibody.SnugDockProtocol: (1) /// L2 info: protocols.antibody.SnugDockProtocol: (1) /// length: 7 protocols.antibody.SnugDockProtocol: (1) /// sequence: SGSTLQS protocols.antibody.SnugDockProtocol: (1) /// north_cluster: L2-8-1 protocols.antibody.SnugDockProtocol: (1) /// loop_info: LOOP start: 170 stop: 176 cut: 173 size: 7 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (1) protocols.antibody.SnugDockProtocol: (1) /// L3 info: protocols.antibody.SnugDockProtocol: (1) /// length: 9 protocols.antibody.SnugDockProtocol: (1) /// sequence: QQHNEYPYT protocols.antibody.SnugDockProtocol: (1) /// north_cluster: L3-9-cis7-1 protocols.antibody.SnugDockProtocol: (1) /// loop_info: LOOP start: 209 stop: 217 cut: 213 size: 9 skip rate: 0 extended?: False protocols.antibody.SnugDockProtocol: (1) protocols.antibody.SnugDockProtocol: (1) //////////////////////////////////////////////////////////////////////////////// protocols.antibody.SnugDockProtocol: (1) protocols.antibody.SnugDockProtocol: (1) Using universal FoldTree. antibody.util: (1) Automatically setting kink constraint! protocols.antibody.SnugDockProtocol: (1) Beginning application of DockingProtocol. protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// protocols.docking.DockingProtocol: (1) /// Rosetta 3 Docking Protocol /// protocols.docking.DockingProtocol: (1) /// /// protocols.docking.DockingProtocol: (1) /// Dockable Jumps: 1 /// protocols.docking.DockingProtocol: (1) /// Low Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// High Resolution Docking Protocol: on /// protocols.docking.DockingProtocol: (1) /// Low Resolution Filter: off /// protocols.docking.DockingProtocol: (1) /// High Resolution Filter: off /// protocols.docking.DockingProtocol: (1) //////////////////////////////////////////////////////////////////////////////// core.chemical.GlobalResidueTypeSet: (1) Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: (1) Total time to initialize 0.03003 seconds. protocols.docking.DockingProtocol: (1) FOLD_TREE EDGE 1 2 1 EDGE 1 3 2 EDGE 3 4 3 EDGE 2 5 4 EDGE 3 6 5 EDGE 4 126 6 EDGE 5 236 7 EDGE 236 339 -1 EDGE 6 28 -1 EDGE 28 35 -1 EDGE 28 42 8 EDGE 42 36 -1 EDGE 42 57 -1 EDGE 57 61 -1 EDGE 57 65 9 EDGE 65 62 -1 EDGE 65 103 -1 EDGE 103 109 -1 EDGE 103 115 10 EDGE 115 125 -1 EDGE 115 110 -1 EDGE 126 149 -1 EDGE 149 154 -1 EDGE 149 159 11 EDGE 159 155 -1 EDGE 159 174 -1 EDGE 174 178 -1 EDGE 174 181 12 EDGE 181 179 -1 EDGE 181 214 -1 EDGE 214 218 -1 EDGE 214 222 13 EDGE 222 235 -1 EDGE 222 219 -1 protocols.docking.DockingInitialPerturbation: (1) dock_pert: true protocols.docking.DockingInitialPerturbation: (1) option[ docking::dock_pert ]()0 1 protocols.docking.DockingInitialPerturbation: (1) sliding into contact for centroid mode protocols.docking.DockingInitialPerturbation: (1) sliding into contact protocols.docking.DockingInitialPerturbation: (1) Moving away protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.17207 23.2816 20.2162 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.37326 24.091 20.7679 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.37326 24.091 20.7679 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.57445 24.9004 21.3197 protocols.docking.DockingInitialPerturbation: (1) Moving together protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.57445 24.9004 21.3197 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.37326 24.091 20.7679 protocols.moves.RigidBodyMover: (1) Translate: Jump (before): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.37326 24.091 20.7679 protocols.moves.RigidBodyMover: (1) Translate: Jump (after): RT 0.801372 0.273185 0.532141 -0.116208 -0.801568 0.586502 0.58677 -0.531845 -0.610607 -7.57445 24.9004 21.3197 protocols.docking.DockingProtocol: (1) finished initial perturbation ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose. ERROR:: Exit from: src/core/conformation/Conformation.hh line: 510 protocols.jd2.JobDistributor: (1) [ ERROR ] [ERROR] Exception caught by JobDistributor for job snug_input_0002 [ ERROR ]: Caught exception: File: src/core/conformation/Conformation.hh:510 [ ERROR ] UtilityExitException ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose. AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. protocols.jd2.JobDistributor: (1) [ WARNING ] snug_input_0002 reported failure and will NOT retry protocols.jd2.MPIWorkPoolJobDistributor: (1) Job 2 failed! Slave process 1 transmitting failure to master. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 40 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master node: Received job failure message for job id 2 from node 1. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 2 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master set job 2 as failed/deletable. protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 2 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Requesting new job id from master protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Received message from 1 with tag 10 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Sending spin down signal to node 1 protocols.jd2.MPIWorkPoolJobDistributor: (0) Master Node: Waiting for 1 slaves to finish jobs protocols.jd2.MPIWorkPoolJobDistributor: (1) Slave Node 1: Received job id 0 from master. protocols.jd2.JobDistributor: (1) no more batches to process... protocols.jd2.JobDistributor: (1) 2 jobs considered, 1 jobs attempted in 111 seconds --------------------------------------------------------------- [ ERROR ]: Error(s) were encountered when running jobs. 1 jobs failed; Check the output further up for additional error messages. --------------------------------------------------------------- -------------------------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code. Per user-direction, the job has been aborted. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was: Process name: [[62704,1],1] Exit code: 255 -------------------------------------------------------------------------- [1] + 83158 done ./job_prep6_snug_v4.sh HL_A 2