core.init: Mini-Rosetta version Split from developer trunk at 53488 from http://www.rosettacommons.org core.init: command: /mnt/people/lulab/rosetta/rosetta3.5/rosetta_source/bin/match.linuxgccrelease @femoco.flags -database /mnt/people/lulab/rosetta/rosetta3.5/rosetta_database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=803719025 seed_offset=0 real_seed=803719025 core.init.random: RandomGenerator:init: Normal mode, seed=803719025 RG_type=mt19937 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6243 residue types core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 7 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 37 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 37 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 37 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 37 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 85 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 85 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 85 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 85 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 100 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 100 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 100 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 100 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 7 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 37 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 85 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 100 because of missing atom number 6 atom name CG core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN6_mem_env_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 core.pack.dunbrack: Dunbrack library took 7.41 seconds to load from ASCII core.pack.dunbrack: Opening file /tmp/105659.1.ge2/dun02jTbv2P for output. core.pack.dunbrack: Moving temporary file to /mnt/people/lulab/rosetta/rosetta3.5/rosetta_database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 94 rotamers at 4 positions. core.pack.pack_rotamers: IG: 4152 bytes apps.public.match.match: Selecting orientation atoms: C1 FE3 FE8 protocols.match.MatcherTask: WARNING WARNING WARNING: no grid file specified for option -grid_boundary. The bounding grid will be generated from the dimensions of the pose. This is experimental at the moment. protocols.match.MatcherTask: Bounding box lower corner set to (-25.362,-24.6118,-29.0816), upper corner set to to (7.39727,12.7639,2.898). protocols.toolbox.match_enzdes_util.EnzConstraintIO: read enzyme constraints from femococonstraints.cst ... done, 2 cst blocks were read. protocols.toolbox.match_enzdes_util.AllowedSeqposForGeomCst: Reading match::scaffold_active_stie_residues femoco.pos: 7 15 31 32 33 34 35 36 37 38 39 40 41 42 51 52 53 54 55 56 57 58 59 60 61 62 72 73 74 75 76 77 78 79 80 81 protocols.BumpGrid: Atom type CNH2 with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type COO with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type CH1 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type CH2 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type CH3 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type aroC with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Ntrp with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Nhis with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type NH2O with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Nlys with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Narg with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Npro with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type OH with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type ONH2 with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type OOC with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Oaro with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type S with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Nbb with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type CAbb with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type CObb with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type OCbb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Phos with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Pbb with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Hpol with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Hapo with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Haro with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type HNbb with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type HOH with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type F with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cl with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Br with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type I with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Zn2p with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type Fe2p with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type Fe3p with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type Mg2p with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Ca2p with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Pha with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type OPha with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type OHha with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Hha with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type CO3 with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type OC3 with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Si with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type OSi with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Oice with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Hice with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Na1p with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type K1p with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type SUCK with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type REPL with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type REPLS with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type HREPS with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type VIRT with ProbeRadius 0 = 0 protocols.match.Matcher: Set occupied space bounding box: Lower (-25.362, -24.6118, -29.0816) Upper (7.39727, 12.7639, 2.898) protocols.match.Matcher: Matcher::initialize_from_file: n geometric constraints: 2 protocols.match.Matcher: Begin constraint1 protocols.match.Matcher: Upstream residue type CYD for geometric constraint #1 protocols.match.Matcher: Did not locate ALGORITHM_INFO:: match for constraint 1 protocols.match.Matcher: CYD ICS protocols.match.Matcher: U3: CA U2: CB U1: SG D1: FE1 D2: S1 D3: C1 protocols.match.Matcher: Adding Classical Match Algorithm with geometry samples: protocols.match.Matcher: tor_U3D1: 350 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 protocols.match.Matcher: ang_U2D1: 97 102 107 112 117 protocols.match.Matcher: dis_U1D1: 2.15 2.25 2.35 protocols.match.Matcher: tor_U2D2: 357.82 7.82 17.82 57.82 67.82 77.82 117.82 127.82 137.82 177.82 187.82 197.82 237.82 247.82 257.82 297.82 307.82 317.82 protocols.match.Matcher: ang_U1D2: 105 110 115 protocols.match.Matcher: tor_U1D3: 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 protocols.match.downstream.LigandConformerBuilder: Initializing from residue ICS protocols.match.downstream.LigandConformerBuilder: No ligand rotamer library found, matching with geometry specified form .params file. protocols.match.downstream.LigandConformerBuilder: Ligand conformers were split up into 1 match-redundant groups. protocols.match.Matcher: Begin constraint2 protocols.match.Matcher: Upstream residue type HIS for geometric constraint #2 protocols.match.Matcher: HIS ICS protocols.match.Matcher: U3: CD2 U2: CG U1: ND1 D1: FE2 D2: S2 D3: C1 protocols.match.Matcher: Upstream residue type HIS_D for geometric constraint #2 protocols.match.Matcher: HIS_D ICS protocols.match.Matcher: U3: ND1 U2: CE1 U1: NE2 D1: FE2 D2: S2 D3: C1 Created UpstreamCollisionFilter Created UpstreamDownstreamCollisionFilter protocols.match.Matcher: Initializing BumpGrids... protocols.match.Matcher: ...done protocols.match.Matcher: TIMING: Bump grids took 5.17 seconds to compute protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 7 and found 18742 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 15 and found 28561 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 31 and found 587 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 32 and found 5053 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 33 and found 25093 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 34 and found 2169 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 35 and found 2216 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 36 and found 639 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 37 and found 16501 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 38 and found 15195 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 39 and found 82436 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 40 and found 6443 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 41 and found 75124 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 42 and found 1536 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 51 and found 5175 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 52 and found 68227 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 53 and found 11583 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 54 and found 35840 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 55 and found 54 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 56 and found 29111 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 57 and found 9622 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 58 and found 18590 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 59 and found 19764 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 60 and found 14509 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 61 and found 61660 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 62 and found 22289 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 72 and found 10355 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 73 and found 2713 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 74 and found 0 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 75 and found 20641 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 76 and found 432 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 77 and found 41098 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 78 and found 22591 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 79 and found 108359 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 9447840 downstream conformations at residue 80 and found 0 hits. protocols.match.upstream.ProteinUpstreamBuilder: Considered 6298560 downstream conformations at residue 81 and found 1848 hits. protocols.match.downstream.ClassicMatchAlgorithm: Finished round 1 with 784756 hits. protocols.match.downstream.SecondaryMatcherToUpstreamResidue: Preparing for hit generation ERROR: olditer != target_restype_index_map_.end() ERROR:: Exit from: src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.cc line: 677