==6330== Memcheck, a memory error detector. ==6330== Copyright (C) 2002-2005, and GNU GPL'd, by Julian Seward et al. ==6330== Using LibVEX rev 1575, a library for dynamic binary translation. ==6330== Copyright (C) 2004-2005, and GNU GPL'd, by OpenWorks LLP. ==6330== Using valgrind-3.1.1, a dynamic binary instrumentation framework. ==6330== Copyright (C) 2000-2005, and GNU GPL'd, by Julian Seward et al. ==6330== For more details, rerun with: -v ==6330== # command:# Seed set to 1158528429 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # trans (non-proline) backbone unit: # CA= -2.2088 1.0126 -0.0031 # O= -0.1499 2.2440 0.0017 # C= -0.6889 1.1368 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2099 1.0634 -0.0014 # O= -0.1233 2.2459 0.0075 # C= -0.6871 1.1518 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading monomeric-50pc.atoms have 448 chains in training database # Count of chains,residues,atoms: 448,112605,876684 # 109826 residues have no bad marker # 665 residues lack atoms needed to compute omega # 322 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 6 # HAS_OXT 325 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 523 # HAS_UNKNOWN_ATOMS 2 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 208 # NON_PLANAR_PEPTIDE 143 # BAD_PEPTIDE 1959 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-1332.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 493.895 sec, elapsed time= 499.727 sec) # command:# Reading spots from monomeric-50pc-dry-5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-5.hist # created burial cost function dry5 with radius 5 with spots at monomeric-50pc-dry-5.spot # command:# Reading spots from monomeric-50pc-wet-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 with spots at monomeric-50pc-wet-6.5.spot # command:# Reading spots from monomeric-50pc-dry-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 with spots at monomeric-50pc-dry-6.5.spot # command:# Reading spots from monomeric-50pc-generic-6.5.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 with spots at monomeric-50pc-generic-6.5.spot # command:# Reading spots from near-backbone-center.spot # reading histogram from smoothed-near-backbone-2spot.hist # Reading spots from near-backbone-count.spot # created burial cost function near_backbone with radius 9.65 with spots at near-backbone-center.spot counting only near-backbone-count.spot # command:# Reading spots from way-back-center.spot # reading histogram from smoothed-way-back-2spot.hist # Reading spots from way-back-count.spot # created burial cost function way_back with radius 8.9 with spots at way-back-center.spot counting only way-back-count.spot # command:# Reading spots from monomeric-50pc-dry-8.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 with spots at monomeric-50pc-dry-8.spot # command:# Reading spots from monomeric-50pc-dry-10.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 with spots at monomeric-50pc-dry-10.spot # command:# Reading spots from monomeric-50pc-dry-12.spot Read prototypes from /projects/compbio/experiments/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 with spots at monomeric-50pc-dry-12.spot # command:# reading histogram from dunbrack-2191-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # command:# reading histogram from dunbrack-2191-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins # command:# Prefix for input files set to /projects/compbio/lib/alphabet/ # command:# Read 3 alphabets from alpha.alphabet # command:CPU_time= 500.124 sec, elapsed time= 505.982 sec) # command:# Prefix for input files set to # command:# Making conformation for sequence T0346 numbered 1 through 172 Created new target T0346 from T0346.a2m # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:2he9A expands to /projects/compbio/data/pdb/2he9.pdb.gz 2he9A:==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x81171FB: JacobiRot(double (*) [4], double (*) [4], int, int) (Superpose.cc:124) ==6330== by 0x8117651: eigen4(double (*) [4], double*) (Superpose.cc:196) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== ==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x81171FB: JacobiRot(double (*) [4], double (*) [4], int, int) (Superpose.cc:124) ==6330== by 0x811766B: eigen4(double (*) [4], double*) (Superpose.cc:197) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== ==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x81171FB: JacobiRot(double (*) [4], double (*) [4], int, int) (Superpose.cc:124) ==6330== by 0x8117685: eigen4(double (*) [4], double*) (Superpose.cc:198) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== ==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x81171FB: JacobiRot(double (*) [4], double (*) [4], int, int) (Superpose.cc:124) ==6330== by 0x811769F: eigen4(double (*) [4], double*) (Superpose.cc:199) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== ==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x81171FB: JacobiRot(double (*) [4], double (*) [4], int, int) (Superpose.cc:124) ==6330== by 0x81176B9: eigen4(double (*) [4], double*) (Superpose.cc:200) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== ==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x81171FB: JacobiRot(double (*) [4], double (*) [4], int, int) (Superpose.cc:124) ==6330== by 0x81176D3: eigen4(double (*) [4], double*) (Superpose.cc:201) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== ==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x81177BA: eigen4(double (*) [4], double*) (Superpose.cc:205) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) ==6330== ==6330== Conditional jump or move depends on uninitialised value(s) ==6330== at 0x811785C: eigen4(double (*) [4], double*) (Superpose.cc:217) ==6330== by 0x811799F: Optimal_rotation(Pointlist const&, Pointlist const&, float const*) (Superpose.cc:262) ==6330== by 0x81140D1: Transform::optimal_transform(Pointlist const&, Pointlist const&, float const*, int, int, int) (Transform.cc:341) ==6330== by 0x8113B12: Transform::Transform(double const (*) [3]) (Transform.cc:251) ==6330== by 0x806C329: ChainsResiduesAndAtoms::add_chain_from_pdb(char const*, void*, std::vector >, char, int) (ChainsResiduesAndAtoms.cc:1191) ==6330== by 0x80BFA17: ReadPDBToCRA(ChainsResiduesAndAtoms*, char const*) (stl_uninitialized.h:109) ==6330== by 0x8074AAA: AddChainToTmpChain(NamedObject const*) (ReadPDBCommands.cc:204) ==6330== by 0x810E38E: NameToPtr::apply_all(void (*)(NamedObject const*)) const (NameToPtr.cc:162) ==6330== by 0x8073E71: ReadPDBFromIds(std::istream&, Command*, std::ostream&, NameToPtr*) (ReadPDBCommands.cc:239) ==6330== by 0x8075F0F: ReadConformPDBids(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:503) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) Skipped atom 196, because occupancy 5.0000000e-01 <= existing 0.500 in 2he9A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 210, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 212, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 2he9A Skipped atom 222, because occupancy 0.500 <= existing 0.500 in 2he9A Read 172 residues and 1335 atoms. # choosing archetypes in rotamer library # Found a chain break before 163 # copying to AlignedFragments data structure # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 140 * real_hbond + 1000 * knot + 100 * clens + 0 * rmsd + 35 * log_rmsd + 0 * rmsd_ca + 30 * log_rmsd_ca + 1 * GDT + 1 * smooth_GDT + 0.1 * missing_atoms ) # command:# SetCost created cost = # ) # command:CPU_time= 786.589 sec, elapsed time= 793.456 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -98.2558 # GDT_score(maxd=8,maxw=2.9)= -99.4933 # GDT_score(maxd=8,maxw=3.2)= -98.8317 # GDT_score(maxd=8,maxw=3.5)= -97.7784 # GDT_score(maxd=10,maxw=3.8)= -98.0477 # GDT_score(maxd=10,maxw=4)= -97.2248 # GDT_score(maxd=10,maxw=4.2)= -96.3005 # GDT_score(maxd=12,maxw=4.3)= -97.2385 # GDT_score(maxd=12,maxw=4.5)= -96.3504 # GDT_score(maxd=12,maxw=4.7)= -95.2871 # GDT_score(maxd=14,maxw=5.2)= -93.907 # GDT_score(maxd=14,maxw=5.5)= -91.7674 # command:# request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_641847783.pdb -s /var/tmp/to_scwrl_641847783.seq -o /var/tmp/from_scwrl_641847783.pdb > /var/tmp/scwrl_641847783.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_641847783.pdb # conformation set from SCWRL output # command:# naming current conformation model1-scwrl # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 2023.000 rmsd (weighted)= 1.216 (unweighted)= 1.427 superimposing iter= 1 total_weight= 7730.459 rmsd (weighted)= 0.446 (unweighted)= 1.429 superimposing iter= 2 total_weight= 2613.729 rmsd (weighted)= 0.315 (unweighted)= 1.430 superimposing iter= 3 total_weight= 1544.924 rmsd (weighted)= 0.292 (unweighted)= 1.430 superimposing iter= 4 total_weight= 1376.175 rmsd (weighted)= 0.286 (unweighted)= 1.430 superimposing iter= 5 total_weight= 1342.498 rmsd (weighted)= 0.285 (unweighted)= 1.431 # command:# Prefix for output files set to decoys/ # command:# ReadConformPDB reading from PDB file model2.ts-submitted looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -98.1105 # GDT_score(maxd=8,maxw=2.9)= -99.4192 # GDT_score(maxd=8,maxw=3.2)= -98.6966 # GDT_score(maxd=8,maxw=3.5)= -97.5758 # GDT_score(maxd=10,maxw=3.8)= -97.8684 # GDT_score(maxd=10,maxw=4)= -97.016 # GDT_score(maxd=10,maxw=4.2)= -96.0857 # GDT_score(maxd=12,maxw=4.3)= -97.0465 # GDT_score(maxd=12,maxw=4.5)= -96.1357 # GDT_score(maxd=12,maxw=4.7)= -95.0929 # GDT_score(maxd=14,maxw=5.2)= -93.6607 # GDT_score(maxd=14,maxw=5.5)= -91.6266 # command:# request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1333625676.pdb -s /var/tmp/to_scwrl_1333625676.seq -o /var/tmp/from_scwrl_1333625676.pdb > /var/tmp/scwrl_1333625676.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1333625676.pdb # conformation set from SCWRL output # command:# naming current conformation model2-scwrl # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -98.2558 # GDT_score(maxd=8,maxw=2.9)= -99.4938 # GDT_score(maxd=8,maxw=3.2)= -98.7993 # GDT_score(maxd=8,maxw=3.5)= -97.7182 # GDT_score(maxd=10,maxw=3.8)= -97.9938 # GDT_score(maxd=10,maxw=4)= -97.1861 # GDT_score(maxd=10,maxw=4.2)= -96.2808 # GDT_score(maxd=12,maxw=4.3)= -97.2039 # GDT_score(maxd=12,maxw=4.5)= -96.3273 # GDT_score(maxd=12,maxw=4.7)= -95.3237 # GDT_score(maxd=14,maxw=5.2)= -93.9322 # GDT_score(maxd=14,maxw=5.5)= -91.8485 # command:# request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1998121059.pdb -s /var/tmp/to_scwrl_1998121059.seq -o /var/tmp/from_scwrl_1998121059.pdb > /var/tmp/scwrl_1998121059.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1998121059.pdb # conformation set from SCWRL output # command:# naming current conformation model3-scwrl # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -98.1105 # GDT_score(maxd=8,maxw=2.9)= -99.5442 # GDT_score(maxd=8,maxw=3.2)= -98.7853 # GDT_score(maxd=8,maxw=3.5)= -97.6731 # GDT_score(maxd=10,maxw=3.8)= -97.9534 # GDT_score(maxd=10,maxw=4)= -97.1281 # GDT_score(maxd=10,maxw=4.2)= -96.2132 # GDT_score(maxd=12,maxw=4.3)= -97.1504 # GDT_score(maxd=12,maxw=4.5)= -96.2651 # GDT_score(maxd=12,maxw=4.7)= -95.2744 # GDT_score(maxd=14,maxw=5.2)= -93.9179 # GDT_score(maxd=14,maxw=5.5)= -91.8383 # command:# request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1524740048.pdb -s /var/tmp/to_scwrl_1524740048.seq -o /var/tmp/from_scwrl_1524740048.pdb > /var/tmp/scwrl_1524740048.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1524740048.pdb # conformation set from SCWRL output # command:# naming current conformation model4-scwrl # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # command:# fraction of real conformation used = 0.94186 # GDT_score = -88.9535 # GDT_score(maxd=8,maxw=2.9)= -90.065 # GDT_score(maxd=8,maxw=3.2)= -89.0403 # GDT_score(maxd=8,maxw=3.5)= -87.687 # GDT_score(maxd=10,maxw=3.8)= -88.3309 # GDT_score(maxd=10,maxw=4)= -87.4136 # GDT_score(maxd=10,maxw=4.2)= -86.4 # GDT_score(maxd=12,maxw=4.3)= -87.6624 # GDT_score(maxd=12,maxw=4.5)= -86.6577 # GDT_score(maxd=12,maxw=4.7)= -85.3677 # GDT_score(maxd=14,maxw=5.2)= -83.5532 # GDT_score(maxd=14,maxw=5.5)= -80.635 # command:# request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1494741487.pdb -s /var/tmp/to_scwrl_1494741487.seq -o /var/tmp/from_scwrl_1494741487.pdb > /var/tmp/scwrl_1494741487.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1494741487.pdb # conformation set from SCWRL output # command:# naming current conformation model5-scwrl # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0346.try1-opt2.pdb looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -98.1105 # GDT_score(maxd=8,maxw=2.9)= -99.5437 # GDT_score(maxd=8,maxw=3.2)= -98.7851 # GDT_score(maxd=8,maxw=3.5)= -97.6733 # GDT_score(maxd=10,maxw=3.8)= -97.9534 # GDT_score(maxd=10,maxw=4)= -97.1286 # GDT_score(maxd=10,maxw=4.2)= -96.2136 # GDT_score(maxd=12,maxw=4.3)= -97.1508 # GDT_score(maxd=12,maxw=4.5)= -96.2654 # GDT_score(maxd=12,maxw=4.7)= -95.2748 # GDT_score(maxd=14,maxw=5.2)= -93.918 # GDT_score(maxd=14,maxw=5.5)= -91.8383 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 2023.000 rmsd (weighted)= 1.172 (unweighted)= 1.377 superimposing iter= 1 total_weight= 7726.698 rmsd (weighted)= 0.428 (unweighted)= 1.380 superimposing iter= 2 total_weight= 2724.153 rmsd (weighted)= 0.295 (unweighted)= 1.382 superimposing iter= 3 total_weight= 1575.095 rmsd (weighted)= 0.270 (unweighted)= 1.383 superimposing iter= 4 total_weight= 1396.734 rmsd (weighted)= 0.263 (unweighted)= 1.383 superimposing iter= 5 total_weight= 1351.044 rmsd (weighted)= 0.260 (unweighted)= 1.384 # command:# Prefix for output files set to decoys/ # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0346.undertaker-align.pdb looking for model 1 WARNING: atoms too close: (T0346)G45.C and (T0346)C53.C only 0.000 apart, marking (T0346)C53.C as missing WARNING: atoms too close: (T0346)K46.N and (T0346)Y54.N only 0.000 apart, marking (T0346)K46.N as missing WARNING: atoms too close: (T0346)K46.CA and (T0346)Y54.CA only 0.000 apart, marking (T0346)K46.CA as missing WARNING: atoms too close: (T0346)K152.C and (T0346)T153.C only 0.000 apart, marking (T0346)T153.C as missing WARNING: atoms too close: (T0346)T153.N and (T0346)D154.N only 0.000 apart, marking (T0346)T153.N as missing WARNING: atoms too close: (T0346)T153.CA and (T0346)D154.CA only 0.000 apart, marking (T0346)T153.CA as missing # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.947674 # GDT_score = -89.2442 # GDT_score(maxd=8,maxw=2.9)= -90.3311 # GDT_score(maxd=8,maxw=3.2)= -89.2726 # GDT_score(maxd=8,maxw=3.5)= -87.8971 # GDT_score(maxd=10,maxw=3.8)= -88.5737 # GDT_score(maxd=10,maxw=4)= -87.6448 # GDT_score(maxd=10,maxw=4.2)= -86.6189 # GDT_score(maxd=12,maxw=4.3)= -87.9132 # GDT_score(maxd=12,maxw=4.5)= -86.8963 # GDT_score(maxd=12,maxw=4.7)= -85.5957 # GDT_score(maxd=14,maxw=5.2)= -83.7814 # GDT_score(maxd=14,maxw=5.5)= -80.8628 # command:# ReadConformPDB reading from PDB file T0346.undertaker-align.pdb looking for model 2 WARNING: atoms too close: (T0346)E41.C and (T0346)K42.C only 0.000 apart, marking (T0346)K42.C as missing WARNING: atoms too close: (T0346)K42.N and (T0346)G43.N only 0.000 apart, marking (T0346)K42.N as missing WARNING: atoms too close: (T0346)K42.CA and (T0346)G43.CA only 0.000 apart, marking (T0346)K42.CA as missing WARNING: atoms too close: (T0346)L151.C and (T0346)K152.C only 0.000 apart, marking (T0346)K152.C as missing WARNING: atoms too close: (T0346)K152.N and (T0346)T153.N only 0.000 apart, marking (T0346)K152.N as missing WARNING: atoms too close: (T0346)K152.CA and (T0346)T153.CA only 0.000 apart, marking (T0346)K152.CA as missing # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.947674 # GDT_score = -89.5349 # GDT_score(maxd=8,maxw=2.9)= -90.6215 # GDT_score(maxd=8,maxw=3.2)= -89.6567 # GDT_score(maxd=8,maxw=3.5)= -88.2518 # GDT_score(maxd=10,maxw=3.8)= -88.9004 # GDT_score(maxd=10,maxw=4)= -87.8545 # GDT_score(maxd=10,maxw=4.2)= -86.4569 # GDT_score(maxd=12,maxw=4.3)= -88.0625 # GDT_score(maxd=12,maxw=4.5)= -86.6654 # GDT_score(maxd=12,maxw=4.7)= -84.8719 # GDT_score(maxd=14,maxw=5.2)= -82.6244 # GDT_score(maxd=14,maxw=5.5)= -79.3543 # command:# ReadConformPDB reading from PDB file T0346.undertaker-align.pdb looking for model 3 WARNING: atoms too close: (T0346)G45.C and (T0346)C53.C only 0.000 apart, marking (T0346)C53.C as missing WARNING: atoms too close: (T0346)K46.N and (T0346)Y54.N only 0.000 apart, marking (T0346)K46.N as missing WARNING: atoms too close: (T0346)K46.CA and (T0346)Y54.CA only 0.000 apart, marking (T0346)K46.CA as missing WARNING: atoms too close: (T0346)K152.C and (T0346)T153.C only 0.000 apart, marking (T0346)T153.C as missing WARNING: atoms too close: (T0346)T153.N and (T0346)D154.N only 0.000 apart, marking (T0346)T153.N as missing WARNING: atoms too close: (T0346)T153.CA and (T0346)D154.CA only 0.000 apart, marking (T0346)T153.CA as missing # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # command:# naming current conformation align3 # command:# ReadConformPDB reading from PDB file T0346.undertaker-align.pdb looking for model 4 WARNING: atoms too close: (T0346)A156.C and (T0346)S157.C only 0.000 apart, marking (T0346)S157.C as missing WARNING: atoms too close: (T0346)S157.N and (T0346)R158.N only 0.000 apart, marking (T0346)S157.N as missing WARNING: atoms too close: (T0346)S157.CA and (T0346)R158.CA only 0.000 apart, marking (T0346)S157.CA as missing # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # command:# naming current conformation align4 # command:# ReadConformPDB reading from PDB file T0346.undertaker-align.pdb looking for model 5 WARNING: atoms too close: (T0346)G45.C and (T0346)C53.C only 0.000 apart, marking (T0346)C53.C as missing WARNING: atoms too close: (T0346)K46.N and (T0346)Y54.N only 0.000 apart, marking (T0346)K46.N as missing WARNING: atoms too close: (T0346)K46.CA and (T0346)Y54.CA only 0.000 apart, marking (T0346)K46.CA as missing WARNING: atoms too close: (T0346)H98.C and (T0346)D99.C only 0.000 apart, marking (T0346)D99.C as missing WARNING: atoms too close: (T0346)D99.N and (T0346)R100.N only 0.000 apart, marking (T0346)D99.N as missing WARNING: atoms too close: (T0346)D99.CA and (T0346)R100.CA only 0.000 apart, marking (T0346)D99.CA as missing # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # command:# naming current conformation align5 # command:# Prefix for input files set to decoys/ # command:# reading script from file read-pdb+servers.under # ReadConformPDB reading from PDB file T0346.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try1-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try1-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try2-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try2-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try3-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try3-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try4-opt2.gromacs0.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try4-opt2.gromacs0.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0346.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_458640242.pdb -s /var/tmp/to_scwrl_458640242.seq -o /var/tmp/from_scwrl_458640242.pdb > /var/tmp/scwrl_458640242.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_458640242.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1408012018.pdb -s /var/tmp/to_scwrl_1408012018.seq -o /var/tmp/from_scwrl_1408012018.pdb > /var/tmp/scwrl_1408012018.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1408012018.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_8957998.pdb -s /var/tmp/to_scwrl_8957998.seq -o /var/tmp/from_scwrl_8957998.pdb > /var/tmp/scwrl_8957998.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_8957998.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1509472034.pdb -s /var/tmp/to_scwrl_1509472034.seq -o /var/tmp/from_scwrl_1509472034.pdb > /var/tmp/scwrl_1509472034.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1509472034.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 ==6330== ==6330== Invalid write of size 8 ==6330== at 0x80A59C8: record_clash(int, XYZpoint const&, int, XYZpoint const&, double) (Clash.cc:189) ==6330== by 0x8119ABC: XYZbins::apply_to_points_near(void (*)(int, XYZpoint const&, int, XYZpoint const&, double), XYZpoint const&, double, int) (XYZbins.cc:317) ==6330== by 0x8119B55: XYZbins::apply_to_points_near(void (*)(int, XYZpoint const&, int, XYZpoint const&, double), Pointlist const*, double, int, int) (XYZbins.cc:341) ==6330== by 0x80A5035: ComputeClashes(ChainsResiduesAndAtoms const*, Pointlist const&, bool const*, int, int) (Clash.cc:294) ==6330== by 0x80A53F5: GetClashes(Conformation**, int) (Conformation.h:117) ==6330== by 0x8074DE4: AlignAndSetConformation(ChainsResiduesAndAtoms*, std::ostream&) (Conformation.h:217) ==6330== by 0x8077EBE: ReadXPDB(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:682) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) ==6330== by 0x8057B9D: EstInclude(std::istream&, Command*, std::ostream&) (Command.h:82) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) ==6330== Address 0x4FC6B70 is 16 bytes before a block of size 12 free'd ==6330== at 0x400518E: operator delete(void*) (vg_replace_malloc.c:246) ==6330== by 0x8050F52: AlignedFragments::make_spanning_tree() (XYZbins.h:135) ==6330== by 0x8052015: AlignedFragments::find_breaks() (AlignedFragments.cc:418) ==6330== by 0x80527ED: AlignedFragments::AlignedFragments(Conformation const&) (AlignedFragments.cc:441) ==6330== by 0x8075D44: AlignAndSetConformation(ChainsResiduesAndAtoms*, std::ostream&) (ReadPDBCommands.cc:424) ==6330== by 0x8077EBE: ReadXPDB(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:682) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) ==6330== by 0x8057B9D: EstInclude(std::istream&, Command*, std::ostream&) (Command.h:82) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) ==6330== by 0x804B843: main (Command.h:82) # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_271405110.pdb -s /var/tmp/to_scwrl_271405110.seq -o /var/tmp/from_scwrl_271405110.pdb > /var/tmp/scwrl_271405110.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_271405110.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_POPULUS_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1469868223.pdb -s /var/tmp/to_scwrl_1469868223.seq -o /var/tmp/from_scwrl_1469868223.pdb > /var/tmp/scwrl_1469868223.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1469868223.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1763194999.pdb -s /var/tmp/to_scwrl_1763194999.seq -o /var/tmp/from_scwrl_1763194999.pdb > /var/tmp/scwrl_1763194999.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1763194999.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_549062293.pdb -s /var/tmp/to_scwrl_549062293.seq -o /var/tmp/from_scwrl_549062293.pdb > /var/tmp/scwrl_549062293.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_549062293.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1959853809.pdb -s /var/tmp/to_scwrl_1959853809.seq -o /var/tmp/from_scwrl_1959853809.pdb > /var/tmp/scwrl_1959853809.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1959853809.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_796465963.pdb -s /var/tmp/to_scwrl_796465963.seq -o /var/tmp/from_scwrl_796465963.pdb > /var/tmp/scwrl_796465963.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_796465963.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_RECOM_TS5-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_635334029.pdb -s /var/tmp/to_scwrl_635334029.seq -o /var/tmp/from_scwrl_635334029.pdb > /var/tmp/scwrl_635334029.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_635334029.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS1-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_74628037.pdb -s /var/tmp/to_scwrl_74628037.seq -o /var/tmp/from_scwrl_74628037.pdb > /var/tmp/scwrl_74628037.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_74628037.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS2-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_727866368.pdb -s /var/tmp/to_scwrl_727866368.seq -o /var/tmp/from_scwrl_727866368.pdb > /var/tmp/scwrl_727866368.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_727866368.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS3-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_635069460.pdb -s /var/tmp/to_scwrl_635069460.seq -o /var/tmp/from_scwrl_635069460.pdb > /var/tmp/scwrl_635069460.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_635069460.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS4-scwrl # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1982981316.pdb -s /var/tmp/to_scwrl_1982981316.seq -o /var/tmp/from_scwrl_1982981316.pdb > /var/tmp/scwrl_1982981316.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1982981316.pdb # conformation set from SCWRL output # naming current conformation 3D-JIGSAW_TS5-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_749822881.pdb -s /var/tmp/to_scwrl_749822881.seq -o /var/tmp/from_scwrl_749822881.pdb > /var/tmp/scwrl_749822881.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_749822881.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1336859397.pdb -s /var/tmp/to_scwrl_1336859397.seq -o /var/tmp/from_scwrl_1336859397.pdb > /var/tmp/scwrl_1336859397.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1336859397.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_673418757.pdb -s /var/tmp/to_scwrl_673418757.seq -o /var/tmp/from_scwrl_673418757.pdb > /var/tmp/scwrl_673418757.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_673418757.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1013405909.pdb -s /var/tmp/to_scwrl_1013405909.seq -o /var/tmp/from_scwrl_1013405909.pdb > /var/tmp/scwrl_1013405909.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1013405909.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1198759278.pdb -s /var/tmp/to_scwrl_1198759278.seq -o /var/tmp/from_scwrl_1198759278.pdb > /var/tmp/scwrl_1198759278.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1198759278.pdb # conformation set from SCWRL output # naming current conformation 3Dpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1483278170.pdb -s /var/tmp/to_scwrl_1483278170.seq -o /var/tmp/from_scwrl_1483278170.pdb > /var/tmp/scwrl_1483278170.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1483278170.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_721402894.pdb -s /var/tmp/to_scwrl_721402894.seq -o /var/tmp/from_scwrl_721402894.pdb > /var/tmp/scwrl_721402894.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_721402894.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 165 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_925598360.pdb -s /var/tmp/to_scwrl_925598360.seq -o /var/tmp/from_scwrl_925598360.pdb > /var/tmp/scwrl_925598360.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_925598360.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1002993057.pdb -s /var/tmp/to_scwrl_1002993057.seq -o /var/tmp/from_scwrl_1002993057.pdb > /var/tmp/scwrl_1002993057.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1002993057.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1686934716.pdb -s /var/tmp/to_scwrl_1686934716.seq -o /var/tmp/from_scwrl_1686934716.pdb > /var/tmp/scwrl_1686934716.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1686934716.pdb # conformation set from SCWRL output # naming current conformation ABIpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1368949477.pdb -s /var/tmp/to_scwrl_1368949477.seq -o /var/tmp/from_scwrl_1368949477.pdb > /var/tmp/scwrl_1368949477.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1368949477.pdb # conformation set from SCWRL output # naming current conformation BayesHH_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1644840839.pdb -s /var/tmp/to_scwrl_1644840839.seq -o /var/tmp/from_scwrl_1644840839.pdb > /var/tmp/scwrl_1644840839.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1644840839.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_873076747.pdb -s /var/tmp/to_scwrl_873076747.seq -o /var/tmp/from_scwrl_873076747.pdb > /var/tmp/scwrl_873076747.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_873076747.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1219586890.pdb -s /var/tmp/to_scwrl_1219586890.seq -o /var/tmp/from_scwrl_1219586890.pdb > /var/tmp/scwrl_1219586890.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1219586890.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1022097241.pdb -s /var/tmp/to_scwrl_1022097241.seq -o /var/tmp/from_scwrl_1022097241.pdb > /var/tmp/scwrl_1022097241.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1022097241.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_220334587.pdb -s /var/tmp/to_scwrl_220334587.seq -o /var/tmp/from_scwrl_220334587.pdb > /var/tmp/scwrl_220334587.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_220334587.pdb # conformation set from SCWRL output # naming current conformation Bilab-ENABLE_TS5-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1678227132.pdb -s /var/tmp/to_scwrl_1678227132.seq -o /var/tmp/from_scwrl_1678227132.pdb > /var/tmp/scwrl_1678227132.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1678227132.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS1-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_282625612.pdb -s /var/tmp/to_scwrl_282625612.seq -o /var/tmp/from_scwrl_282625612.pdb > /var/tmp/scwrl_282625612.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_282625612.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS2-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_229292585.pdb -s /var/tmp/to_scwrl_229292585.seq -o /var/tmp/from_scwrl_229292585.pdb > /var/tmp/scwrl_229292585.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_229292585.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS3-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1040215520.pdb -s /var/tmp/to_scwrl_1040215520.seq -o /var/tmp/from_scwrl_1040215520.pdb > /var/tmp/scwrl_1040215520.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1040215520.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS4-scwrl # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_554030722.pdb -s /var/tmp/to_scwrl_554030722.seq -o /var/tmp/from_scwrl_554030722.pdb > /var/tmp/scwrl_554030722.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_554030722.pdb # conformation set from SCWRL output # naming current conformation CIRCLE_TS5-scwrl # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CPHmodels_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1699160808.pdb -s /var/tmp/to_scwrl_1699160808.seq -o /var/tmp/from_scwrl_1699160808.pdb > /var/tmp/scwrl_1699160808.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1699160808.pdb # conformation set from SCWRL output # naming current conformation CPHmodels_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # naming current conformation CaspIta-FOX_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_655926872.pdb -s /var/tmp/to_scwrl_655926872.seq -o /var/tmp/from_scwrl_655926872.pdb > /var/tmp/scwrl_655926872.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_655926872.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS1-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1103093014.pdb -s /var/tmp/to_scwrl_1103093014.seq -o /var/tmp/from_scwrl_1103093014.pdb > /var/tmp/scwrl_1103093014.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1103093014.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS2-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1511530970.pdb -s /var/tmp/to_scwrl_1511530970.seq -o /var/tmp/from_scwrl_1511530970.pdb > /var/tmp/scwrl_1511530970.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1511530970.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS3-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1452392834.pdb -s /var/tmp/to_scwrl_1452392834.seq -o /var/tmp/from_scwrl_1452392834.pdb > /var/tmp/scwrl_1452392834.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1452392834.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS4-scwrl # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1738427043.pdb -s /var/tmp/to_scwrl_1738427043.seq -o /var/tmp/from_scwrl_1738427043.pdb > /var/tmp/scwrl_1738427043.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1738427043.pdb # conformation set from SCWRL output # naming current conformation CaspIta-FOX_TS5-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1586159008.pdb -s /var/tmp/to_scwrl_1586159008.seq -o /var/tmp/from_scwrl_1586159008.pdb > /var/tmp/scwrl_1586159008.log Error: Couldn't open file /var/tmp/from_scwrl_1586159008.pdb or /var/tmp/from_scwrl_1586159008.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1586159008_b.pdb or decoys//var/tmp/from_scwrl_1586159008_b.pdb.gz for input Trying /var/tmp/from_scwrl_1586159008_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1586159008_b.pdb or /var/tmp/from_scwrl_1586159008_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1586159008_a.pdb or decoys//var/tmp/from_scwrl_1586159008_a.pdb.gz for input Trying /var/tmp/from_scwrl_1586159008_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1586159008_a.pdb or /var/tmp/from_scwrl_1586159008_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1586159008.pdb or /var/tmp/from_scwrl_1586159008_b.pdb or /var/tmp/from_scwrl_1586159008_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS1-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_32775556.pdb -s /var/tmp/to_scwrl_32775556.seq -o /var/tmp/from_scwrl_32775556.pdb > /var/tmp/scwrl_32775556.log Error: Couldn't open file /var/tmp/from_scwrl_32775556.pdb or /var/tmp/from_scwrl_32775556.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_32775556_b.pdb or decoys//var/tmp/from_scwrl_32775556_b.pdb.gz for input Trying /var/tmp/from_scwrl_32775556_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_32775556_b.pdb or /var/tmp/from_scwrl_32775556_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_32775556_a.pdb or decoys//var/tmp/from_scwrl_32775556_a.pdb.gz for input Trying /var/tmp/from_scwrl_32775556_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_32775556_a.pdb or /var/tmp/from_scwrl_32775556_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_32775556.pdb or /var/tmp/from_scwrl_32775556_b.pdb or /var/tmp/from_scwrl_32775556_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS2-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_226012856.pdb -s /var/tmp/to_scwrl_226012856.seq -o /var/tmp/from_scwrl_226012856.pdb > /var/tmp/scwrl_226012856.log Error: Couldn't open file /var/tmp/from_scwrl_226012856.pdb or /var/tmp/from_scwrl_226012856.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_226012856_b.pdb or decoys//var/tmp/from_scwrl_226012856_b.pdb.gz for input Trying /var/tmp/from_scwrl_226012856_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_226012856_b.pdb or /var/tmp/from_scwrl_226012856_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_226012856_a.pdb or decoys//var/tmp/from_scwrl_226012856_a.pdb.gz for input Trying /var/tmp/from_scwrl_226012856_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_226012856_a.pdb or /var/tmp/from_scwrl_226012856_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_226012856.pdb or /var/tmp/from_scwrl_226012856_b.pdb or /var/tmp/from_scwrl_226012856_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS3-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1421656677.pdb -s /var/tmp/to_scwrl_1421656677.seq -o /var/tmp/from_scwrl_1421656677.pdb > /var/tmp/scwrl_1421656677.log Error: Couldn't open file /var/tmp/from_scwrl_1421656677.pdb or /var/tmp/from_scwrl_1421656677.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1421656677_b.pdb or decoys//var/tmp/from_scwrl_1421656677_b.pdb.gz for input Trying /var/tmp/from_scwrl_1421656677_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_1421656677_b.pdb or /var/tmp/from_scwrl_1421656677_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_1421656677_a.pdb or decoys//var/tmp/from_scwrl_1421656677_a.pdb.gz for input Trying /var/tmp/from_scwrl_1421656677_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_1421656677_a.pdb or /var/tmp/from_scwrl_1421656677_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_1421656677.pdb or /var/tmp/from_scwrl_1421656677_b.pdb or /var/tmp/from_scwrl_1421656677_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS4-scwrl # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_782598437.pdb -s /var/tmp/to_scwrl_782598437.seq -o /var/tmp/from_scwrl_782598437.pdb > /var/tmp/scwrl_782598437.log Error: Couldn't open file /var/tmp/from_scwrl_782598437.pdb or /var/tmp/from_scwrl_782598437.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_782598437_b.pdb or decoys//var/tmp/from_scwrl_782598437_b.pdb.gz for input Trying /var/tmp/from_scwrl_782598437_b.pdb Error: Couldn't open file /var/tmp/from_scwrl_782598437_b.pdb or /var/tmp/from_scwrl_782598437_b.pdb.gz for input Warning: Couldn't open file decoys//var/tmp/from_scwrl_782598437_a.pdb or decoys//var/tmp/from_scwrl_782598437_a.pdb.gz for input Trying /var/tmp/from_scwrl_782598437_a.pdb Error: Couldn't open file /var/tmp/from_scwrl_782598437_a.pdb or /var/tmp/from_scwrl_782598437_a.pdb.gz for input Error: can't open any of /var/tmp/from_scwrl_782598437.pdb or /var/tmp/from_scwrl_782598437_b.pdb or /var/tmp/from_scwrl_782598437_a.pdb Error: no new SCWRL conformation added # naming current conformation Distill_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1562872253.pdb -s /var/tmp/to_scwrl_1562872253.seq -o /var/tmp/from_scwrl_1562872253.pdb > /var/tmp/scwrl_1562872253.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1562872253.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2095075434.pdb -s /var/tmp/to_scwrl_2095075434.seq -o /var/tmp/from_scwrl_2095075434.pdb > /var/tmp/scwrl_2095075434.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2095075434.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1796004345.pdb -s /var/tmp/to_scwrl_1796004345.seq -o /var/tmp/from_scwrl_1796004345.pdb > /var/tmp/scwrl_1796004345.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1796004345.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_614147885.pdb -s /var/tmp/to_scwrl_614147885.seq -o /var/tmp/from_scwrl_614147885.pdb > /var/tmp/scwrl_614147885.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_614147885.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1430869957.pdb -s /var/tmp/to_scwrl_1430869957.seq -o /var/tmp/from_scwrl_1430869957.pdb > /var/tmp/scwrl_1430869957.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1430869957.pdb # conformation set from SCWRL output # naming current conformation FAMSD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_369923593.pdb -s /var/tmp/to_scwrl_369923593.seq -o /var/tmp/from_scwrl_369923593.pdb > /var/tmp/scwrl_369923593.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_369923593.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS1-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1539746245.pdb -s /var/tmp/to_scwrl_1539746245.seq -o /var/tmp/from_scwrl_1539746245.pdb > /var/tmp/scwrl_1539746245.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1539746245.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS2-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_286379367.pdb -s /var/tmp/to_scwrl_286379367.seq -o /var/tmp/from_scwrl_286379367.pdb > /var/tmp/scwrl_286379367.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_286379367.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS3-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2056858309.pdb -s /var/tmp/to_scwrl_2056858309.seq -o /var/tmp/from_scwrl_2056858309.pdb > /var/tmp/scwrl_2056858309.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2056858309.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS4-scwrl # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_761212076.pdb -s /var/tmp/to_scwrl_761212076.seq -o /var/tmp/from_scwrl_761212076.pdb > /var/tmp/scwrl_761212076.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_761212076.pdb # conformation set from SCWRL output # naming current conformation FAMS_TS5-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1931220206.pdb -s /var/tmp/to_scwrl_1931220206.seq -o /var/tmp/from_scwrl_1931220206.pdb > /var/tmp/scwrl_1931220206.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1931220206.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS1-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_782451409.pdb -s /var/tmp/to_scwrl_782451409.seq -o /var/tmp/from_scwrl_782451409.pdb > /var/tmp/scwrl_782451409.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_782451409.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS2-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1980798966.pdb -s /var/tmp/to_scwrl_1980798966.seq -o /var/tmp/from_scwrl_1980798966.pdb > /var/tmp/scwrl_1980798966.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1980798966.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS3-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_805833800.pdb -s /var/tmp/to_scwrl_805833800.seq -o /var/tmp/from_scwrl_805833800.pdb > /var/tmp/scwrl_805833800.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_805833800.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS4-scwrl # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1002785996.pdb -s /var/tmp/to_scwrl_1002785996.seq -o /var/tmp/from_scwrl_1002785996.pdb > /var/tmp/scwrl_1002785996.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1002785996.pdb # conformation set from SCWRL output # naming current conformation FOLDpro_TS5-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1511542451.pdb -s /var/tmp/to_scwrl_1511542451.seq -o /var/tmp/from_scwrl_1511542451.pdb > /var/tmp/scwrl_1511542451.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1511542451.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1088459411.pdb -s /var/tmp/to_scwrl_1088459411.seq -o /var/tmp/from_scwrl_1088459411.pdb > /var/tmp/scwrl_1088459411.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1088459411.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1232078581.pdb -s /var/tmp/to_scwrl_1232078581.seq -o /var/tmp/from_scwrl_1232078581.pdb > /var/tmp/scwrl_1232078581.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1232078581.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_404274325.pdb -s /var/tmp/to_scwrl_404274325.seq -o /var/tmp/from_scwrl_404274325.pdb > /var/tmp/scwrl_404274325.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_404274325.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1642490133.pdb -s /var/tmp/to_scwrl_1642490133.seq -o /var/tmp/from_scwrl_1642490133.pdb > /var/tmp/scwrl_1642490133.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1642490133.pdb # conformation set from SCWRL output # naming current conformation FORTE1_AL5-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_783755743.pdb -s /var/tmp/to_scwrl_783755743.seq -o /var/tmp/from_scwrl_783755743.pdb > /var/tmp/scwrl_783755743.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_783755743.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL1-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1060201197.pdb -s /var/tmp/to_scwrl_1060201197.seq -o /var/tmp/from_scwrl_1060201197.pdb > /var/tmp/scwrl_1060201197.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1060201197.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL2-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_598099501.pdb -s /var/tmp/to_scwrl_598099501.seq -o /var/tmp/from_scwrl_598099501.pdb > /var/tmp/scwrl_598099501.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_598099501.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL3-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_147803067.pdb -s /var/tmp/to_scwrl_147803067.seq -o /var/tmp/from_scwrl_147803067.pdb > /var/tmp/scwrl_147803067.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_147803067.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL4-scwrl # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_365110385.pdb -s /var/tmp/to_scwrl_365110385.seq -o /var/tmp/from_scwrl_365110385.pdb > /var/tmp/scwrl_365110385.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_365110385.pdb # conformation set from SCWRL output # naming current conformation FORTE2_AL5-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_189042897.pdb -s /var/tmp/to_scwrl_189042897.seq -o /var/tmp/from_scwrl_189042897.pdb > /var/tmp/scwrl_189042897.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_189042897.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS1-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1733962075.pdb -s /var/tmp/to_scwrl_1733962075.seq -o /var/tmp/from_scwrl_1733962075.pdb > /var/tmp/scwrl_1733962075.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1733962075.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS2-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_397885941.pdb -s /var/tmp/to_scwrl_397885941.seq -o /var/tmp/from_scwrl_397885941.pdb > /var/tmp/scwrl_397885941.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_397885941.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS3-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_415055753.pdb -s /var/tmp/to_scwrl_415055753.seq -o /var/tmp/from_scwrl_415055753.pdb > /var/tmp/scwrl_415055753.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_415055753.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS4-scwrl # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1008135106.pdb -s /var/tmp/to_scwrl_1008135106.seq -o /var/tmp/from_scwrl_1008135106.pdb > /var/tmp/scwrl_1008135106.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1008135106.pdb # conformation set from SCWRL output # naming current conformation FPSOLVER-SERVER_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 112 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1180484377.pdb -s /var/tmp/to_scwrl_1180484377.seq -o /var/tmp/from_scwrl_1180484377.pdb > /var/tmp/scwrl_1180484377.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1180484377.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1977928007.pdb -s /var/tmp/to_scwrl_1977928007.seq -o /var/tmp/from_scwrl_1977928007.pdb > /var/tmp/scwrl_1977928007.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1977928007.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_955726893.pdb -s /var/tmp/to_scwrl_955726893.seq -o /var/tmp/from_scwrl_955726893.pdb > /var/tmp/scwrl_955726893.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_955726893.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_829005077.pdb -s /var/tmp/to_scwrl_829005077.seq -o /var/tmp/from_scwrl_829005077.pdb > /var/tmp/scwrl_829005077.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_829005077.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_444592245.pdb -s /var/tmp/to_scwrl_444592245.seq -o /var/tmp/from_scwrl_444592245.pdb > /var/tmp/scwrl_444592245.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_444592245.pdb # conformation set from SCWRL output # naming current conformation FUGMOD_TS5-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_239113203.pdb -s /var/tmp/to_scwrl_239113203.seq -o /var/tmp/from_scwrl_239113203.pdb > /var/tmp/scwrl_239113203.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_239113203.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL1-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1198928669.pdb -s /var/tmp/to_scwrl_1198928669.seq -o /var/tmp/from_scwrl_1198928669.pdb > /var/tmp/scwrl_1198928669.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1198928669.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL2-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1984338490.pdb -s /var/tmp/to_scwrl_1984338490.seq -o /var/tmp/from_scwrl_1984338490.pdb > /var/tmp/scwrl_1984338490.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1984338490.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL3-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_525492570.pdb -s /var/tmp/to_scwrl_525492570.seq -o /var/tmp/from_scwrl_525492570.pdb > /var/tmp/scwrl_525492570.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_525492570.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL4-scwrl # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1108303331.pdb -s /var/tmp/to_scwrl_1108303331.seq -o /var/tmp/from_scwrl_1108303331.pdb > /var/tmp/scwrl_1108303331.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1108303331.pdb # conformation set from SCWRL output # naming current conformation FUGUE_AL5-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_598066920.pdb -s /var/tmp/to_scwrl_598066920.seq -o /var/tmp/from_scwrl_598066920.pdb > /var/tmp/scwrl_598066920.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_598066920.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS1-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_309229129.pdb -s /var/tmp/to_scwrl_309229129.seq -o /var/tmp/from_scwrl_309229129.pdb > /var/tmp/scwrl_309229129.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_309229129.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS2-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1890754741.pdb -s /var/tmp/to_scwrl_1890754741.seq -o /var/tmp/from_scwrl_1890754741.pdb > /var/tmp/scwrl_1890754741.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1890754741.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS3-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 160 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_431382239.pdb -s /var/tmp/to_scwrl_431382239.seq -o /var/tmp/from_scwrl_431382239.pdb > /var/tmp/scwrl_431382239.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_431382239.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS4-scwrl # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 170 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1115062928.pdb -s /var/tmp/to_scwrl_1115062928.seq -o /var/tmp/from_scwrl_1115062928.pdb > /var/tmp/scwrl_1115062928.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1115062928.pdb # conformation set from SCWRL output # naming current conformation FUNCTION_TS5-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 99 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_746057090.pdb -s /var/tmp/to_scwrl_746057090.seq -o /var/tmp/from_scwrl_746057090.pdb > /var/tmp/scwrl_746057090.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_746057090.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS1-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1942924691.pdb -s /var/tmp/to_scwrl_1942924691.seq -o /var/tmp/from_scwrl_1942924691.pdb > /var/tmp/scwrl_1942924691.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1942924691.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS2-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_56038693.pdb -s /var/tmp/to_scwrl_56038693.seq -o /var/tmp/from_scwrl_56038693.pdb > /var/tmp/scwrl_56038693.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_56038693.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS3-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1978135671.pdb -s /var/tmp/to_scwrl_1978135671.seq -o /var/tmp/from_scwrl_1978135671.pdb > /var/tmp/scwrl_1978135671.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1978135671.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS4-scwrl # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_199715369.pdb -s /var/tmp/to_scwrl_199715369.seq -o /var/tmp/from_scwrl_199715369.pdb > /var/tmp/scwrl_199715369.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_199715369.pdb # conformation set from SCWRL output # naming current conformation GeneSilicoMetaServer_TS5-scwrl # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1698528826.pdb -s /var/tmp/to_scwrl_1698528826.seq -o /var/tmp/from_scwrl_1698528826.pdb > /var/tmp/scwrl_1698528826.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1698528826.pdb # conformation set from SCWRL output # naming current conformation HHpred1_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_614407768.pdb -s /var/tmp/to_scwrl_614407768.seq -o /var/tmp/from_scwrl_614407768.pdb > /var/tmp/scwrl_614407768.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_614407768.pdb # conformation set from SCWRL output # naming current conformation HHpred2_TS1-scwrl # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1259916565.pdb -s /var/tmp/to_scwrl_1259916565.seq -o /var/tmp/from_scwrl_1259916565.pdb > /var/tmp/scwrl_1259916565.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1259916565.pdb # conformation set from SCWRL output # naming current conformation HHpred3_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_149144680.pdb -s /var/tmp/to_scwrl_149144680.seq -o /var/tmp/from_scwrl_149144680.pdb > /var/tmp/scwrl_149144680.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_149144680.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_762210835.pdb -s /var/tmp/to_scwrl_762210835.seq -o /var/tmp/from_scwrl_762210835.pdb > /var/tmp/scwrl_762210835.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_762210835.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1625026950.pdb -s /var/tmp/to_scwrl_1625026950.seq -o /var/tmp/from_scwrl_1625026950.pdb > /var/tmp/scwrl_1625026950.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1625026950.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_338187577.pdb -s /var/tmp/to_scwrl_338187577.seq -o /var/tmp/from_scwrl_338187577.pdb > /var/tmp/scwrl_338187577.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_338187577.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_348689263.pdb -s /var/tmp/to_scwrl_348689263.seq -o /var/tmp/from_scwrl_348689263.pdb > /var/tmp/scwrl_348689263.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_348689263.pdb # conformation set from SCWRL output # naming current conformation Huber-Torda-Server_TS5-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2022912891.pdb -s /var/tmp/to_scwrl_2022912891.seq -o /var/tmp/from_scwrl_2022912891.pdb > /var/tmp/scwrl_2022912891.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2022912891.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS1-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_753243330.pdb -s /var/tmp/to_scwrl_753243330.seq -o /var/tmp/from_scwrl_753243330.pdb > /var/tmp/scwrl_753243330.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_753243330.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS2-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1356824368.pdb -s /var/tmp/to_scwrl_1356824368.seq -o /var/tmp/from_scwrl_1356824368.pdb > /var/tmp/scwrl_1356824368.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1356824368.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS3-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1055913623.pdb -s /var/tmp/to_scwrl_1055913623.seq -o /var/tmp/from_scwrl_1055913623.pdb > /var/tmp/scwrl_1055913623.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1055913623.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS4-scwrl # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_583687690.pdb -s /var/tmp/to_scwrl_583687690.seq -o /var/tmp/from_scwrl_583687690.pdb > /var/tmp/scwrl_583687690.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_583687690.pdb # conformation set from SCWRL output # naming current conformation LOOPP_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_165067614.pdb -s /var/tmp/to_scwrl_165067614.seq -o /var/tmp/from_scwrl_165067614.pdb > /var/tmp/scwrl_165067614.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_165067614.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1884918699.pdb -s /var/tmp/to_scwrl_1884918699.seq -o /var/tmp/from_scwrl_1884918699.pdb > /var/tmp/scwrl_1884918699.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1884918699.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1028279936.pdb -s /var/tmp/to_scwrl_1028279936.seq -o /var/tmp/from_scwrl_1028279936.pdb > /var/tmp/scwrl_1028279936.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1028279936.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_404180817.pdb -s /var/tmp/to_scwrl_404180817.seq -o /var/tmp/from_scwrl_404180817.pdb > /var/tmp/scwrl_404180817.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_404180817.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_936363722.pdb -s /var/tmp/to_scwrl_936363722.seq -o /var/tmp/from_scwrl_936363722.pdb > /var/tmp/scwrl_936363722.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_936363722.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_865134779.pdb -s /var/tmp/to_scwrl_865134779.seq -o /var/tmp/from_scwrl_865134779.pdb > /var/tmp/scwrl_865134779.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_865134779.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS1-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_929673387.pdb -s /var/tmp/to_scwrl_929673387.seq -o /var/tmp/from_scwrl_929673387.pdb > /var/tmp/scwrl_929673387.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_929673387.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS2-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2044667053.pdb -s /var/tmp/to_scwrl_2044667053.seq -o /var/tmp/from_scwrl_2044667053.pdb > /var/tmp/scwrl_2044667053.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2044667053.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS3-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1463201698.pdb -s /var/tmp/to_scwrl_1463201698.seq -o /var/tmp/from_scwrl_1463201698.pdb > /var/tmp/scwrl_1463201698.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1463201698.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS4-scwrl # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1238902515.pdb -s /var/tmp/to_scwrl_1238902515.seq -o /var/tmp/from_scwrl_1238902515.pdb > /var/tmp/scwrl_1238902515.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1238902515.pdb # conformation set from SCWRL output # naming current conformation Ma-OPUS-server_TS5-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1787938147.pdb -s /var/tmp/to_scwrl_1787938147.seq -o /var/tmp/from_scwrl_1787938147.pdb > /var/tmp/scwrl_1787938147.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1787938147.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS1-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1894583938.pdb -s /var/tmp/to_scwrl_1894583938.seq -o /var/tmp/from_scwrl_1894583938.pdb > /var/tmp/scwrl_1894583938.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1894583938.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS2-scwrl # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_206481797.pdb -s /var/tmp/to_scwrl_206481797.seq -o /var/tmp/from_scwrl_206481797.pdb > /var/tmp/scwrl_206481797.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_206481797.pdb # conformation set from SCWRL output # naming current conformation MetaTasser_TS3-scwrl # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_386511591.pdb -s /var/tmp/to_scwrl_386511591.seq -o /var/tmp/from_scwrl_386511591.pdb > /var/tmp/scwrl_386511591.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_386511591.pdb # conformation set from SCWRL output # naming current conformation NN_PUT_lab_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1690024982.pdb -s /var/tmp/to_scwrl_1690024982.seq -o /var/tmp/from_scwrl_1690024982.pdb > /var/tmp/scwrl_1690024982.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1690024982.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_262520490.pdb -s /var/tmp/to_scwrl_262520490.seq -o /var/tmp/from_scwrl_262520490.pdb > /var/tmp/scwrl_262520490.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_262520490.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_217163615.pdb -s /var/tmp/to_scwrl_217163615.seq -o /var/tmp/from_scwrl_217163615.pdb > /var/tmp/scwrl_217163615.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_217163615.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1889740351.pdb -s /var/tmp/to_scwrl_1889740351.seq -o /var/tmp/from_scwrl_1889740351.pdb > /var/tmp/scwrl_1889740351.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1889740351.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1961049316.pdb -s /var/tmp/to_scwrl_1961049316.seq -o /var/tmp/from_scwrl_1961049316.pdb > /var/tmp/scwrl_1961049316.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1961049316.pdb # conformation set from SCWRL output # naming current conformation PROTINFO-AB_TS5-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_831571383.pdb -s /var/tmp/to_scwrl_831571383.seq -o /var/tmp/from_scwrl_831571383.pdb > /var/tmp/scwrl_831571383.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_831571383.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS1-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1002173270.pdb -s /var/tmp/to_scwrl_1002173270.seq -o /var/tmp/from_scwrl_1002173270.pdb > /var/tmp/scwrl_1002173270.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1002173270.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS2-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2110193996.pdb -s /var/tmp/to_scwrl_2110193996.seq -o /var/tmp/from_scwrl_2110193996.pdb > /var/tmp/scwrl_2110193996.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2110193996.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS3-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1593782217.pdb -s /var/tmp/to_scwrl_1593782217.seq -o /var/tmp/from_scwrl_1593782217.pdb > /var/tmp/scwrl_1593782217.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1593782217.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS4-scwrl # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_479716574.pdb -s /var/tmp/to_scwrl_479716574.seq -o /var/tmp/from_scwrl_479716574.pdb > /var/tmp/scwrl_479716574.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_479716574.pdb # conformation set from SCWRL output # naming current conformation PROTINFO_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # Found a chain break before 111 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_300897926.pdb -s /var/tmp/to_scwrl_300897926.seq -o /var/tmp/from_scwrl_300897926.pdb > /var/tmp/scwrl_300897926.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_300897926.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1942471480.pdb -s /var/tmp/to_scwrl_1942471480.seq -o /var/tmp/from_scwrl_1942471480.pdb > /var/tmp/scwrl_1942471480.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1942471480.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_355145818.pdb -s /var/tmp/to_scwrl_355145818.seq -o /var/tmp/from_scwrl_355145818.pdb > /var/tmp/scwrl_355145818.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_355145818.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1054141256.pdb -s /var/tmp/to_scwrl_1054141256.seq -o /var/tmp/from_scwrl_1054141256.pdb > /var/tmp/scwrl_1054141256.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1054141256.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1151812201.pdb -s /var/tmp/to_scwrl_1151812201.seq -o /var/tmp/from_scwrl_1151812201.pdb > /var/tmp/scwrl_1151812201.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1151812201.pdb # conformation set from SCWRL output # naming current conformation Pcons6_TS5-scwrl # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1411059440.pdb -s /var/tmp/to_scwrl_1411059440.seq -o /var/tmp/from_scwrl_1411059440.pdb > /var/tmp/scwrl_1411059440.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1411059440.pdb # conformation set from SCWRL output # naming current conformation Phyre-1_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1637828946.pdb -s /var/tmp/to_scwrl_1637828946.seq -o /var/tmp/from_scwrl_1637828946.pdb > /var/tmp/scwrl_1637828946.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1637828946.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS1-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1316879815.pdb -s /var/tmp/to_scwrl_1316879815.seq -o /var/tmp/from_scwrl_1316879815.pdb > /var/tmp/scwrl_1316879815.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1316879815.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS2-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1148494492.pdb -s /var/tmp/to_scwrl_1148494492.seq -o /var/tmp/from_scwrl_1148494492.pdb > /var/tmp/scwrl_1148494492.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1148494492.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS3-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_518625235.pdb -s /var/tmp/to_scwrl_518625235.seq -o /var/tmp/from_scwrl_518625235.pdb > /var/tmp/scwrl_518625235.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_518625235.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS4-scwrl # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1721060632.pdb -s /var/tmp/to_scwrl_1721060632.seq -o /var/tmp/from_scwrl_1721060632.pdb > /var/tmp/scwrl_1721060632.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1721060632.pdb # conformation set from SCWRL output # naming current conformation Phyre-2_TS5-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2084858214.pdb -s /var/tmp/to_scwrl_2084858214.seq -o /var/tmp/from_scwrl_2084858214.pdb > /var/tmp/scwrl_2084858214.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2084858214.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS1-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1383760013.pdb -s /var/tmp/to_scwrl_1383760013.seq -o /var/tmp/from_scwrl_1383760013.pdb > /var/tmp/scwrl_1383760013.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1383760013.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS2-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_503250372.pdb -s /var/tmp/to_scwrl_503250372.seq -o /var/tmp/from_scwrl_503250372.pdb > /var/tmp/scwrl_503250372.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_503250372.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS3-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1982041621.pdb -s /var/tmp/to_scwrl_1982041621.seq -o /var/tmp/from_scwrl_1982041621.pdb > /var/tmp/scwrl_1982041621.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1982041621.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS4-scwrl # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0346 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_699478066.pdb -s /var/tmp/to_scwrl_699478066.seq -o /var/tmp/from_scwrl_699478066.pdb > /var/tmp/scwrl_699478066.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_699478066.pdb # conformation set from SCWRL output # naming current conformation Pmodeller6_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1742152887.pdb -s /var/tmp/to_scwrl_1742152887.seq -o /var/tmp/from_scwrl_1742152887.pdb > /var/tmp/scwrl_1742152887.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1742152887.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1622496121.pdb -s /var/tmp/to_scwrl_1622496121.seq -o /var/tmp/from_scwrl_1622496121.pdb > /var/tmp/scwrl_1622496121.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1622496121.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_446578357.pdb -s /var/tmp/to_scwrl_446578357.seq -o /var/tmp/from_scwrl_446578357.pdb > /var/tmp/scwrl_446578357.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_446578357.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS3-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_1948634684.pdb -s /var/tmp/to_scwrl_1948634684.seq -o /var/tmp/from_scwrl_1948634684.pdb > /var/tmp/scwrl_1948634684.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1948634684.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS4-scwrl # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 163 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2009007712.pdb -s /var/tmp/to_scwrl_2009007712.seq -o /var/tmp/from_scwrl_2009007712.pdb > /var/tmp/scwrl_2009007712.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2009007712.pdb # conformation set from SCWRL output # naming current conformation RAPTOR-ACE_TS5-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_2136603339.pdb -s /var/tmp/to_scwrl_2136603339.seq -o /var/tmp/from_scwrl_2136603339.pdb > /var/tmp/scwrl_2136603339.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2136603339.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS1-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 158 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # request to SCWRL produces command: ulimit -t 155 ; scwrl -i /var/tmp/to_scwrl_63671527.pdb -s /var/tmp/to_scwrl_63671527.seq -o /var/tmp/from_scwrl_63671527.pdb > /var/tmp/scwrl_63671527.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_63671527.pdb # conformation set from SCWRL output # naming current conformation RAPTORESS_TS2-scwrl # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 valgrind: m_mallocfree.c:186 (get_bszB_as_is): Assertion 'bszB_lo == bszB_hi' failed. valgrind: Heap block lo/hi size mismatch: lo = 88, hi = 1074811879. Probably caused by overrunning/underrunning a heap block's bounds. ==6330== at 0xB000E029: report_and_quit (m_libcassert.c:122) ==6330== by 0xB000E1C2: vgPlain_assert_fail (m_libcassert.c:185) ==6330== by 0xB0016395: vgPlain_arena_free (m_mallocfree.c:183) ==6330== by 0xB002B8AF: vgPlain_cli_free (replacemalloc_core.c:108) ==6330== by 0xB000155C: die_and_free_mem (mac_malloc_wrappers.c:120) ==6330== by 0xB002D06E: do_client_request (scheduler.c:987) ==6330== by 0xB002CADF: vgPlain_scheduler (scheduler.c:721) ==6330== by 0xB003C1AA: thread_wrapper (syswrap-linux.c:87) ==6330== by 0xB003C270: run_a_thread_NORETURN (syswrap-linux.c:120) sched status: running_tid=1 Thread 1: status = VgTs_Runnable ==6330== at 0x40054A6: operator delete[](void*) (vg_replace_malloc.c:256) ==6330== by 0x81112F8: Pointlist::~Pointlist() (Pointlist.cc:39) ==6330== by 0x8079122: ChainsResiduesAndAtoms::~ChainsResiduesAndAtoms() (ChainsResiduesAndAtoms.h:264) ==6330== by 0x8077F22: ReadXPDB(std::istream&, Command*, std::ostream&) (ReadPDBCommands.cc:683) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) ==6330== by 0x8057B9D: EstInclude(std::istream&, Command*, std::ostream&) (Command.h:82) ==6330== by 0x810A6FB: Command::execute(std::istream&, std::ostream&) (Command.h:75) ==6330== by 0x810A5F8: Command::read_command(std::istream&, std::ostream&) (Command.cc:27) ==6330== by 0x804B843: main (Command.h:82) Note: see also the FAQ.txt in the source distribution. It contains workarounds to several common problems. If that doesn't help, please report this bug to: www.valgrind.org In the bug report, send all the above text, the valgrind version, and what Linux distro you are using. Thanks.