high resolution protein docking doesn’t work

This topic has 17 replies, 2 voices, and was last updated 13 years, 11 months ago by Anonymous.

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- December 2, 2010 at 10:36 am #707
  Anonymous
  Hi
  I am using rosetta docking_protocol.linuxiccrelease @flags > docking.log for initial protein docking. 10000 initial pose(only backbone) were generated by this. Then I clustered top200 pose by cluster.linuxiccrelease @flags >& cluster.log &
  The best scoring one from the largest cluster were submitted for rosetta refinement(add sidechain and hydrogens) :relax.linuxgccrelease @flags > log
  
  I try to use the refined protein complex for high resolution docking, but it doesn’t work. All the pose generated by high resolution protein-protein docking are the same with my initial refined protein complex.
  
  Does anybody have any suggestions?
  
  Thank you very much
- December 2, 2010 at 3:07 pm #4685
  Anonymous
  I’m not sure what the problem is.
  
  You did centroid docking, picked a good model, and relaxed it.
  
  Then you did fullatom docking refinement on THAT model, and it returned the result that you already had a good answer, because it declined to move it far from the starting structure.
  
  What’s wrong?
- December 4, 2010 at 7:46 am #4692
  Anonymous
  yes, my workflow is something like this.
  I don’t know why it declined to move it.Does it mean the docking results is already good enough?
  when I did low resolution docking and don’t relax it, then I submitted for full atom hight resolution docking(initial model from low resolution has no sidechain), it works but don’t work well: the scoring are all positive and in the best score pose two protein partner separated with each other.
- December 6, 2010 at 3:26 pm #4695
  Anonymous
  I guess an important question is, does it not move it AT ALL, (every atom in the same place), or does it just move it very little? Very little movement means Rosetta thinks it’s already good. (I assume the scores are negative).
  
  The second situation you describe is due to poor packing or unrelaxed issues in the crystal structure; this is expected behavior.
- December 6, 2010 at 6:16 pm #4697
  Anonymous
  it doesn’t move at all. All the pose have the same scoring function. Both of my undocked protein are high resolution: 1.7 and 2.1 A resolution. Do you have any suguestion for this?
  
  Thank you very much
- December 7, 2010 at 3:04 pm #4700
  Anonymous
  If it doesn’t move at all, every atom is identical, then something is wrong such that it is not doing any modeling. Can you try posting the log file so I can look for a likely error?
- December 10, 2010 at 7:54 am #4715
  Anonymous
  Thank you very much. Here is the log:
  
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-547989175 seed_offset=0 real_seed=-547989175
  core.init.random: RandomGenerator:init: Normal mode, seed=-547989175 RG_type=mt19937
  core.io.database: Database file opened: /soft/rosetta3.1/database/env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cbeta_den.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/pair_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cenpack_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_pair_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.io.database: Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
  core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-61886964 seed_offset=0 real_seed=-61886964
  core.init.random: RandomGenerator:init: Normal mode, seed=-61886964 RG_type=mt19937
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 relax.pdb 1
  protocols.jobdist.JobDistributors: Looking for an available job: 2 1 relax.pdb 2
  protocols.jobdist.JobDistributors: Looking for an available job: 3 1 relax.pdb 3
  protocols.jobdist.JobDistributors: Looking for an available job: 4 1 relax.pdb 4
  protocols.jobdist.main: Starting relax_0004 …
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Dunbrack library took 4 seconds to load from ASCII
  Warning: Unable to locate database file Dunbrack02.lib.bin
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Opening file /tmp/dun021AKknu for output.
  core.scoring.dunbrack: Moving temporary file to /soft/rosetta3.1/database/Dunbrack02.lib.bin
  protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Pcore.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=850133497 seed_offset=0 real_seed=850133497
  core.init.random: RandomGenerator:init: Normal mode, seed=850133497 RG_type=mt19937
  core.io.database: Database file opened: /soft/rosetta3.1/database/env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cbeta_den.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/pair_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cenpack_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_pair_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.io.database: Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
  core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=2024095980 seed_offset=0 real_seed=2024095980
  core.init.random: RandomGenerator:init: Normal mode, seed=2024095980 RG_type=mt19937
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 relax.pdb 1
  protocols.jobdist.JobDistributors: Looking for an available job: 2 1 relax.pdb 2
  protocols.jobdist.main: Starting relax_0002 …
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Dunbrack library took 3.97 seconds to load from ASCII
  Warning: Unable to locate database file Dunbrack02.lib.bin
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Opening file /tmp/dun02QSCd6r for output.
  core.scoring.dunbrack: Moving temporary file to /soft/rosetta3.1/database/Dunbrack02.lib.bin
  protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command lcore.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=2074012388 seed_offset=0 real_seed=2074012388
  core.init.random: RandomGenerator:init: Normal mode, seed=2074012388 RG_type=mt19937
  core.io.database: Database file opened: /soft/rosetta3.1/database/env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cbeta_den.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/pair_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cenpack_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_pair_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.io.database: Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
  core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-98731217 seed_offset=0 real_seed=-98731217
  core.init.random: RandomGenerator:init: Normal mode, seed=-98731217 RG_type=mt19937
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 relax.pdb 1
  protocols.jobdist.JobDistributors: Looking for an available job: 2 1 relax.pdb 2
  protocols.jobdist.JobDistributors: Looking for an available job: 3 1 relax.pdb 3
  protocols.jobdist.JobDistributors: Looking for an available job: 4 1 relax.pdb 4
  protocols.jobdist.JobDistributors: Looking for an available job: 5 1 relax.pdb 5
  protocols.jobdist.main: Starting relax_0005 …
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Dunbrack library took 5.96 seconds to load from ASCII
  Warning: Unable to locate database file Dunbrack02.lib.bin
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Opening file /tmp/dun02AST7Et for output.
  core.scoring.dunbrack: Moving temporary file to /soft/rosetta3.1/database/Dunbrack02.lib.bin
  protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command licore.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-449616428 seed_offset=0 real_seed=-449616428
  core.init.random: RandomGenerator:init: Normal mode, seed=-449616428 RG_type=mt19937
  core.io.database: Database file opened: /soft/rosetta3.1/database/env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cbeta_den.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/pair_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cenpack_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_pair_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.io.database: Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
  core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1409266343 seed_offset=0 real_seed=-1409266343
  core.init.random: RandomGenerator:init: Normal mode, seed=-1409266343 RG_type=mt19937
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 relax.pdb 1
  protocols.jobdist.JobDistributors: Looking for an available job: 2 1 relax.pdb 2
  protocols.jobdist.JobDistributors: Looking for an available job: 3 1 relax.pdb 3
  protocols.jobdist.JobDistributors: Looking for an available job: 4 1 relax.pdb 4
  protocols.jobdist.JobDistributors: Looking for an available job: 5 1 relax.pdb 5
  protocols.jobdist.JobDistributors: Looking for an available job: 6 1 relax.pdb 6
  protocols.jobdist.main: Starting relax_0006 …
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Dunbrack library took 7.09 seconds to load from ASCII
  Warning: Unable to locate database file Dunbrack02.lib.bin
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Opening file /tmp/dun02Xtx3RE for output.
  core.scoring.dunbrack: Moving temporary file to /soft/rosetta3.1/database/Dunbrack02.lib.bin
  protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=1685200335 seed_offset=0 real_seed=1685200335
  core.init.random: RandomGenerator:init: Normal mode, seed=1685200335 RG_type=mt19937
  core.io.database: Database file opened: /soft/rosetta3.1/database/env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cbeta_den.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/pair_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cenpack_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_pair_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.io.database: Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
  core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-98971307 seed_offset=0 real_seed=-98971307
  core.init.random: RandomGenerator:init: Normal mode, seed=-98971307 RG_type=mt19937
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 relax.pdb 1
  protocols.jobdist.JobDistributors: Looking for an available job: 2 1 relax.pdb 2
  protocols.jobdist.JobDistributors: Looking for an available job: 3 1 relax.pdb 3
  protocols.jobdist.main: Starting relax_0003 …
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Dunbrack library took 7.07 seconds to load from ASCII
  Warning: Unable to locate database file Dunbrack02.lib.bin
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Opening file /tmp/dun02EsL6B5 for output.
  core.scoring.dunbrack: Moving temporary file to /soft/rosetta3.1/database/Dunbrack02.lib.bin
  protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initicore.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=2084526778 seed_offset=0 real_seed=2084526778
  core.init.random: RandomGenerator:init: Normal mode, seed=2084526778 RG_type=mt19937
  core.io.database: Database file opened: /soft/rosetta3.1/database/env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cbeta_den.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/pair_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cenpack_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_pair_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.io.database: Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
  core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-117393692 seed_offset=0 real_seed=-117393692
  core.init.random: RandomGenerator:init: Normal mode, seed=-117393692 RG_type=mt19937
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 relax.pdb 1
  protocols.jobdist.main: Starting relax_0001 …
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Dunbrack library took 7.22 seconds to load from ASCII
  Warning: Unable to locate database file Dunbrack02.lib.bin
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Opening file /tmp/dun02RdsiAw for output.
  core.scoring.dunbrack: Moving temporary file to /soft/rosetta3.1/database/Dunbrack02.lib.bin
  protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating Deine()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298acker task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209456 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209012 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209012 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209012 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209012 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.8968ne()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199752 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.movinitialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 431 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 208800 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 431 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 208800 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 431 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 208800 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0alize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 428 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 207876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 428 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 207876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 202660 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 202660 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0003 in 55 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 4 1 relax.pdb 4
  protocols.jobdist.JobDistributors: Looking for an available job: 5 1 relax.pdb 5
  protocols.jobdist.JobDistributors: Looking for an available job: 6 1 relax.pdb 6
  protocols.jobdist.JobDistributors: Looking for an available job: 7 1 relax.pdb 7
  protocols.jobdist.JobDistributors: Looking for an available job: 8 1 relax.pdb 8
  protocols.jobdist.JobDistributors: Looking for an available job: 9 1 relax.pdb 9
  protocols.jobdist.JobDistributors: Looking for an available job: 10 1 relax.pdb 10
  protocols.jobdist.main: Finished all 1 structures in 55 seconds.
  Done!
  
  nsePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0001 in 60 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 2 1 relax.pdb 2
  protocols.jobdist.JobDistributors: Looking for an available job: 3 1 relax.pdb 3
  protocols.jobdist.JobDistributors: Looking for an available job: 4 1 relax.pdb 4
  protocols.jobdist.JobDistributors: Looking for an available job: 5 1 relax.pdb 5
  protocols.jobdist.JobDistributors: Looking for an available job: 6 1 relax.pdb 6
  protocols.jobdist.JobDistributors: Looking for an available job: 7 1 relax.pdb 7
  protocols.jobdist.JobDistributors: Looking for an available job: 8 1 relax.pdb 8
  protocols.jobdist.JobDistributors: Looking for an available job: 9 1 relax.pdb 9
  protocols.jobdist.JobDistributors: Looking for an available job: 10 1 relax.pdb 10
  protocols.jobdist.main: Finished all 1 structures in 60 seconds.
  Done!
  
  -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0002 in 41 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 3 1 relax.pdb 3
  protocols.jobdist.JobDistributors: Looking for an available job: 4 1 relax.pdb 4
  protocols.jobdist.JobDistributors: Looking for an available job: 5 1 relax.pdb 5
  protocols.jobdist.JobDistributors: Looking for an available job: 6 1 relax.pdb 6
  protocols.jobdist.JobDistributors: Looking for an available job: 7 1 relax.pdb 7
  protocols.jobdist.main: Starting relax_0007 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating De92 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0004 in 46 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 5 1 relax.pdb 5
  protocols.jobdist.JobDistributors: Looking for an available job: 6 1 relax.pdb 6
  protocols.jobdist.JobDistributors: Looking for an available job: 7 1 relax.pdb 7
  protocols.jobdist.JobDistributors: Looking for an available job: 8 1 relax.pdb 8
  protocols.jobdist.main: Starting relax_0008 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 426 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 200028 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command l.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0006 in 54 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 7 1 relax.pdb 7
  protocols.jobdist.JobDistributors: Looking for an available job: 8 1 relax.pdb 8
  protocols.jobdist.JobDistributors: Looking for an available job: 9 1 relax.pdb 9
  protocols.jobdist.JobDistributors: Looking for an available job: 10 1 relax.pdb 10
  protocols.jobdist.main: Starting relax_0010 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  cores.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0005 in 49 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 6 1 relax.pdb 6
  protocols.jobdist.JobDistributors: Looking for an available job: 7 1 relax.pdb 7
  protocols.jobdist.JobDistributors: Looking for an available job: 8 1 relax.pdb 8
  protocols.jobdist.JobDistributors: Looking for an available job: 9 1 relax.pdb 9
  protocols.jobdist.main: Starting relax_0009 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210892 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: inmpiexec_dream (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null
  mpiexec_dream (handle_stdin_input 1090): e.g.: mpiexec -n 4 a.out < /dev/null &
  nsePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0007 in 36 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 8 1 relax.pdb 8
  protocols.jobdist.JobDistributors: Looking for an available job: 9 1 relax.pdb 9
  protocols.jobdist.JobDistributors: Looking for an available job: 10 1 relax.pdb 10
  protocols.jobdist.main: Finished all 2 structures in 78 seconds.
  Done!
  
  ine()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 426 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 200028 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 426 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 200028 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 211256 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0008 in 32 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 9 1 relax.pdb 9
  protocols.jobdist.JobDistributors: Looking for an available job: 10 1 relax.pdb 10
  protocols.jobdist.main: Finished all 2 structures in 78 seconds.
  Done!
  
  itialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210892 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210892 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210892 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0009 in 35 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 10 1 relax.pdb 10
  protocols.jobdist.main: Finished all 2 structures in 84 seconds.
  Done!
  
  e.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209444 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209444 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 433 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209860 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0010 in 30 seconds.
  protocols.jobdist.main: Finished all 2 structures in 84 seconds.
  Done!
- December 10, 2010 at 2:58 pm #4722
  Anonymous
  The log is sort of jumbled – is this being run in MPI? The docking MPI executeable requires that you pre-create specifically named output directories (the names escape me, I’ll look it up if necessary). It may be that it’s not writing the outputs you need because those directories aren’t present, and when you try to look at the output you’re comparing input to input instead.
- December 12, 2010 at 8:36 am #4737
  Anonymous
  Thank you very much for your so kind reply. I do use the command ” mpirun -np 6 docking_protocol.linuxgccrelease @flags2 > docking2.log&” for this job so that it would be finished much faster. Could you please give me some advices how to enable the option “specify named output directories”? I would be very appreciated for your kind helps.
  
  Here is my output section in flags2:
  
  -out
  -nstruct 10
  # this should be set to a large number for effective sampling
  -mute core.util.prof
  # reduces copious output, without overdoing as with -mute all
  -file
  -o dock_output2
  # scorefile will be named dock_output2.sc (or .fasc for fullatom)
  -fullatom
- December 12, 2010 at 8:39 am #4738
  Anonymous
  BTW, even I use one CPU to run(command: docking_protocol.linuxgccrelease @flags2 > docking2.log&), it still doesn’t work. all atoms positions are the same. Here is the log:
  
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1273310667 seed_offset=0 real_seed=-1273310667
  core.init.random: RandomGenerator:init: Normal mode, seed=-1273310667 RG_type=mt19937
  core.io.database: Database file opened: /soft/rosetta3.1/database/env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cbeta_den.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/pair_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/cenpack_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_env_log.txt
  core.io.database: Database file opened: /soft/rosetta3.1/database/interchain_pair_log.txt
  core.scoring.etable: Starting energy table calculation
  core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
  core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
  core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
  core.scoring.etable: Finished calculating energy tables.
  core.io.database: Database file opened: /soft/rosetta3.1/database/pdb_pair_stats_fine
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_n
  core.io.database: Database file opened: /soft/rosetta3.1/database/P_AA_pp
  core.options: option[ out::file::fullatom ]() re-interpreted as setting option[ out::file::residue_type_set ]() to fa_standard
  core.init: command: docking_protocol.linuxgccrelease @flags2
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=455037431 seed_offset=0 real_seed=455037431
  core.init.random: RandomGenerator:init: Normal mode, seed=455037431 RG_type=mt19937
  protocols.jobdist.JobDistributors: Looking for an available job: 1 1 relax.pdb 1
  protocols.jobdist.main: Starting relax_0001 …
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Dunbrack library took 2.63 seconds to load from ASCII
  Warning: Unable to locate database file Dunbrack02.lib.bin
  Warning: Unable to locate database file Dunbrack02.lib.bin
  core.scoring.dunbrack: Opening file /tmp/dun02GOfmrM for output.
  core.scoring.dunbrack: Moving temporary file to /soft/rosetta3.1/database/Dunbrack02.lib.bin
  protocols.docking.DockingHighRes: ::::::::::::::::::DOCK_MCM:::::::::::::::::::
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210980 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210980 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209004 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209004 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0001 in 26 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 2 1 relax.pdb 2
  protocols.jobdist.main: Starting relax_0002 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199752 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199752 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199752 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 433 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 208748 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 433 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 208748 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0002 in 21 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 3 1 relax.pdb 3
  protocols.jobdist.main: Starting relax_0003 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0003 in 20 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 4 1 relax.pdb 4
  protocols.jobdist.main: Starting relax_0004 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199752 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199752 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 407 rotamers at 45 positions.
  core.pack.pack_rotamers: IG: 179016 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 431 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 431 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209876 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0004 in 22 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 5 1 relax.pdb 5
  protocols.jobdist.main: Starting relax_0005 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0005 in 19 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 6 1 relax.pdb 6
  protocols.jobdist.main: Starting relax_0006 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 211256 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 211256 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 211256 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 211256 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 211256 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0006 in 22 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 7 1 relax.pdb 7
  protocols.jobdist.main: Starting relax_0007 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210852 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210852 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210852 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 426 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 200184 bytes
  core.pack.task: Packer task: initialize from command line()
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  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0007 in 21 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 8 1 relax.pdb 8
  protocols.jobdist.main: Starting relax_0008 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199624 bytes
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199624 bytes
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199624 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199624 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199624 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.pack_rotamers: built 425 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 199624 bytes
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0008 in 19 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 9 1 relax.pdb 9
  protocols.jobdist.main: Starting relax_0009 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
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  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210952 bytes
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 434 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 210832 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 438 rotamers at 52 positions.
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  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 211256 bytes
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  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0009 in 21 seconds.
  protocols.jobdist.JobDistributors: Looking for an available job: 10 1 relax.pdb 10
  protocols.jobdist.main: Starting relax_0010 …
  protocols.docking.DockingProtocol: Setting docking foldtree
  protocols.docking.DockingProtocol: old fold tree: FOLD_TREE EDGE 1 228 -1 EDGE 1 229 1 EDGE 229 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingProtocol: new fold tree: FOLD_TREE EDGE 1 85 -1 EDGE 85 228 -1 EDGE 85 360 1 EDGE 360 229 -1 EDGE 360 402 -1
  protocols.docking.DockingProtocol:
  protocols.docking.DockingHighRes: in DockingHighRes.apply
  core.pack.task: Packer task: initialize from command line()
  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 405 rotamers at 47 positions.
  core.pack.pack_rotamers: IG: 189636 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 424 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 197440 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 424 rotamers at 50 positions.
  core.pack.pack_rotamers: IG: 197440 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209456 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209456 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209456 bytes
  core.pack.task: Packer task: initialize from command line()
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  core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
  core.pack.pack_rotamers: built 435 rotamers at 51 positions.
  core.pack.pack_rotamers: IG: 209456 bytes
  core.pack.task: Packer task: initialize from command line()
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  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 31.1896 4.39459 17.4186
  protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.0542331 0.444298 -0.894236 0.896892 -0.371974 -0.239208 -0.438912 -0.815006 -0.378314 894.449 145.051 502.186
  protocols.jobdist.main: Finished relax_0010 in 20 seconds.
  protocols.jobdist.main: Finished all 10 structures in 213 seconds.
  Done!
- December 12, 2010 at 6:19 pm #4740
  Anonymous
  When you say it still fails on one processor – is that still the MPI compiled executeable? Or did you recompile it without MPI?
  - December 13, 2010 at 3:21 am #4741
    Anonymous
    I compile the whole rosetta suite using the command “scons bin mode=release -j8”. When I run the job, I didn’t change anything on program itself.
    I use one CPU, I mean I use the command: “docking_protocol.linuxgccrelease @flags2 > docking2.log&”; while I also try to use multiple CPU to run the job using the command: “mpirun -np 6 docking_protocol.linuxgccrelease @flags2 > docking2.log&”. I’ve installed MPICH2 and intel ICC and Ifort in my linux computer.
- December 13, 2010 at 7:30 pm #4746
  Anonymous
  From that compiling command line, we haven’t actually activated the MPI compilation. This is consistent with the log file (I examined it further and it’s missing some of the MPI only output). MPI compilation is triggered by adding “extras=mpi” to the command line.
  
  If you use mpirun on a non-MPI Rosetta executeable (which I think you did), you’ll still get the jumbled log file you got.
  
  So, one thing to try is to recompile with extras=mpi. This will not overwrite your non-mpi binaries, but it may change the symlinks in the bin/ directory. Explore the build/ directory instead to find the mpi vs. non-mpi files.
  
  None of this addresses the root issue, that your inputs are not changing when they are output. I’m still not sure what’s causing that, but the log files sure look like Rosetta thinks it is working correctly.
  
  Try going to (rosetta_source)/test/integration and running the docking integration test with “python integration.py docking -d (path to database)”. See if the result is different from the input protein. Try putting your own protein in the input folder tests/docking/input and changing the flags file and seeing if that works.
  - December 14, 2010 at 2:56 am #4750
    Anonymous
    it seems to work for the test and I found the new generated docking result is different from input structure. However, when I don’t know why use the high resolution protocol, it still doesn’t work.
    
    here is the command in terminal
    
    test/integration> python integration.py docking -d /soft/rosetta3.1/database
    Running docking on localhost …
    Finished docking in 18 seconds
    
    Just generated ‘ref’ results; run again after making changes.
    test/integration> python integration.py docking -d /soft/rosetta3.1/database
    Running docking on localhost …
    Finished docking in 31 seconds
    
    FAIL docking
    Files ref/docking/1brs_0001.pdb and new/docking/1brs_0001.pdb differ
    Files ref/docking/1brs.fasc and new/docking/1brs.fasc differ
    Files ref/docking/flags and new/docking/flags differ
    Only in new/docking/input: relax.pdb
    Files ref/docking/log and new/docking/log differ
    Only in new/docking: relax_0001.pdb
    
    1 test(s) failed. Use ‘diff’ to compare results.
    
    Here is my flag for high resolution:
    
    -in
    -file
    -s 08.pdb
    # the input file should have two single, complete chains A and B
    # for Ab molecules (with L+H chains) use -docking::partners flag below
    -path
    -database /soft/rosetta3.1/database
    # customize this to point to your installation directory
    -docking
    # very small perturbations occur in the absence of any docking flags
    -docking_local_refine
    -dock_pert 3 8
    # do a small perturbation with partner2: -dock_pert DEGREES ANGSTROMS
    #-spin
    # rotate partner2 about the intermolecular axis
    -dock_min
    # Minimize the final fullatom structures. default=’false’
    #-partners
    # defines the docking partners by ChainID; see manual
    -out
    -nstruct 10
    # this should be set to a large number for effective sampling
    -mute core.util.prof
    # reduces copious output, without overdoing as with -mute all
    -file
    -o dock_output2
    # scorefile will be named dock_output2.sc (or .fasc for fullatom)
    -fullatom
- December 14, 2010 at 6:33 am #4751
  Anonymous
  I found the major difference between my structure and the example is that: mine is full atom or only backbone structures; the example input structure contains backbone and hydrogens.
- December 14, 2010 at 3:39 pm #4754
  Anonymous
  I believe dock_min is your problem. Try taking it out and using the default dock_mcm instead.
  
  Looking at the code, dock_min does nothing but a minimization of the docking pose. Since your starting pose was created by Rosetta’s relax mode, which would have minimized it before output, then it has nothing to do – it’s already minimized according to the scorefunction. That’s why you get no change.
  
  dock_mcm is an actual docking sampling protocol (you don’t need to pass a flag for it, it’s the default).
  - December 17, 2010 at 2:01 am #4760
    Anonymous
    Thank you very much. It works now.
- December 19, 2010 at 7:49 am #4763
  Anonymous
  Enclosed this thread, please find a part of the PDB file.
  Thank you very much
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