core.init: Rosetta version unknown:exported from http://www.rosettacommons.org core.init: command: /mnt/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/bin/match.linuxgccrelease @femoco.flags -database /mnt/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-1020922883 seed_offset=0 real_seed=-1020922883 core.init.random: RandomGenerator:init: Normal mode, seed=-1020922883 RG_type=mt19937 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 415 residue types core.chemical.ResidueTypeSet: Total time to initialize 1.05 seconds. core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue THR:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OG1 on residue THR:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue THR:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD1 on residue LEU 3 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG2 on residue VAL 9 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 11 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 16 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 16 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 16 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 16 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 20 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 31 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 31 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 31 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 31 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 37 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 37 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 73 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 73 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 73 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 73 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 89 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 89 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 89 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU 92 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 96 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 96 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 96 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 96 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 119 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 119 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 182 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 182 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 182 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 182 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 209 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 209 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 211 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 218 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 225 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 225 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 225 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 225 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 242 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 242 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 242 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 248 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 248 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 263 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 263 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 263 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 277 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 277 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 277 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 277 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASP 278 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD2 on residue ASP 278 core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 7 atom name CD1 core.pack.pack_missing_sidechains: packing residue number 9 because of missing atom number 7 atom name CG2 core.pack.pack_missing_sidechains: packing residue number 11 because of missing atom number 9 atom name NZ core.pack.pack_missing_sidechains: packing residue number 16 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 20 because of missing atom number 9 atom name NZ core.pack.pack_missing_sidechains: packing residue number 31 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 37 because of missing atom number 7 atom name OD1 core.pack.pack_missing_sidechains: packing residue number 73 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 89 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 92 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 96 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 119 because of missing atom number 8 atom name OE1 core.pack.pack_missing_sidechains: packing residue number 182 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 209 because of missing atom number 7 atom name OD1 core.pack.pack_missing_sidechains: packing residue number 211 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 218 because of missing atom number 7 atom name OD1 core.pack.pack_missing_sidechains: packing residue number 225 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 242 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 248 because of missing atom number 8 atom name CE core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 9 atom name NZ core.pack.pack_missing_sidechains: packing residue number 263 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 277 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 278 because of missing atom number 7 atom name OD1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 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 core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/mnt/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.17 seconds to load from binary core.pack.pack_rotamers: built 412 rotamers at 25 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 26268 bytes apps.public.match.match: Selecting orientation atoms: FE3 O5 O4 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 (-7.50626,70.942,32.208), upper corner set to to (48.204,108.788,82.1497). 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 OEC-small.pos: 171 172 173 174 175 176 177 179 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 Oet2 with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Oet3 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 Bsp2 with ProbeRadius 6 = 1.75 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 Co2p with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Cu2p 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 He with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Li with ProbeRadius 1 = 1 protocols.BumpGrid: Atom type Be with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ne with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Al with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ar with ProbeRadius 5 = 1.65 protocols.BumpGrid: Atom type Sc with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Ti with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type V with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Cr with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Mn with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ni with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ga with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ge with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type As with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Se with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Kr with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Rb with ProbeRadius 6 = 1.75 protocols.BumpGrid: Atom type Sr with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Y with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Zr with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Nb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Mo with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Tc with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ru with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Rh with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Pd with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ag with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cd with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type In with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Sn with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Sb with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Te with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Xe with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Cs with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ba with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type La with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Ce with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Pr with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Nd with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Pm with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Sm with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Eu with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Gd with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Tb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Dy with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Ho with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Er with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Tm with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Yb with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Lu with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Hf with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ta with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type W with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Re with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Os with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Ir with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Pt with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Au with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Hg with ProbeRadius 2 = 1.17 protocols.BumpGrid: Atom type Tl with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Pb with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Bi with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Po with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type At with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Rn with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Fr with ProbeRadius 7 = 1.85 protocols.BumpGrid: Atom type Ra with ProbeRadius 4 = 1.55 protocols.BumpGrid: Atom type Ac with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Th with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Pa with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type U with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Np with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Pu with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Am with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cm with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Bk with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Cf with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Es with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Fm with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Md with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type No with ProbeRadius 3 = 1.4 protocols.BumpGrid: Atom type Lr with ProbeRadius 3 = 1.4 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.BumpGrid: Atom type MPct with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type MPnm with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type MPdp with ProbeRadius 0 = 0 protocols.BumpGrid: Atom type MPtk with ProbeRadius 0 = 0 protocols.match.Matcher: Set occupied space bounding box: Lower (-7.50626, 70.942, 32.208) Upper (48.204, 108.788, 82.1497) protocols.match.Matcher: Matcher::initialize_from_file: n geometric constraints: 2 protocols.match.Matcher: Begin constraint1 protocols.match.Matcher:  Upstream residue type LG1 for geometric constraint #1 protocols.match.Matcher:  Did not locate ALGORITHM_INFO:: match for constraint 1 protocols.match.Matcher:  LG1 ASP protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE3 D1: OD1 D2: CG D3: CB protocols.match.Matcher:  Adding Classical Match Algorithm with geometry samples: protocols.match.Matcher:  tor_U3D1: 73.6 78.6 83.6 88.6 93.6 98.6 103.6 108.6 113.6 protocols.match.Matcher:  ang_U2D1: 78.98 83.98 88.98 93.98 98.98 103.98 108.98 protocols.match.Matcher:  dis_U1D1: 2 protocols.match.Matcher:  tor_U2D2: 28.49 33.49 38.49 43.49 48.49 53.49 58.49 63.49 68.49 protocols.match.Matcher:  ang_U1D2: 113.98 118.98 123.98 128.98 133.98 138.98 143.98 protocols.match.Matcher:  tor_U1D3: 157.49 162.49 167.49 172.49 177.49 182.49 187.49 192.49 197.49 protocols.match.downstream.LigandConformerBuilder: Initializing from residue LG1 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:  LG1 ASP protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE3 D1: OD2 D2: CG D3: CB protocols.match.Matcher:  Adding Classical Match Algorithm with geometry samples: protocols.match.Matcher:  tor_U3D1: 73.6 78.6 83.6 88.6 93.6 98.6 103.6 108.6 113.6 protocols.match.Matcher:  ang_U2D1: 78.98 83.98 88.98 93.98 98.98 103.98 108.98 protocols.match.Matcher:  dis_U1D1: 2 protocols.match.Matcher:  tor_U2D2: 28.49 33.49 38.49 43.49 48.49 53.49 58.49 63.49 68.49 protocols.match.Matcher:  ang_U1D2: 113.98 118.98 123.98 128.98 133.98 138.98 143.98 protocols.match.Matcher:  tor_U1D3: 157.49 162.49 167.49 172.49 177.49 182.49 187.49 192.49 197.49 protocols.match.downstream.LigandConformerBuilder: Initializing from residue LG1 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:  LG1 GLU protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE3 D1: OE1 D2: CD D3: CG protocols.match.Matcher:  Adding Classical Match Algorithm with geometry samples: protocols.match.Matcher:  tor_U3D1: 73.6 78.6 83.6 88.6 93.6 98.6 103.6 108.6 113.6 protocols.match.Matcher:  ang_U2D1: 78.98 83.98 88.98 93.98 98.98 103.98 108.98 protocols.match.Matcher:  dis_U1D1: 2 protocols.match.Matcher:  tor_U2D2: 28.49 33.49 38.49 43.49 48.49 53.49 58.49 63.49 68.49 protocols.match.Matcher:  ang_U1D2: 113.98 118.98 123.98 128.98 133.98 138.98 143.98 protocols.match.Matcher:  tor_U1D3: 157.49 162.49 167.49 172.49 177.49 182.49 187.49 192.49 197.49 protocols.match.downstream.LigandConformerBuilder: Initializing from residue LG1 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:  LG1 GLU protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE3 D1: OE2 D2: CD D3: CG protocols.match.Matcher:  Adding Classical Match Algorithm with geometry samples: protocols.match.Matcher:  tor_U3D1: 73.6 78.6 83.6 88.6 93.6 98.6 103.6 108.6 113.6 protocols.match.Matcher:  ang_U2D1: 78.98 83.98 88.98 93.98 98.98 103.98 108.98 protocols.match.Matcher:  dis_U1D1: 2 protocols.match.Matcher:  tor_U2D2: 28.49 33.49 38.49 43.49 48.49 53.49 58.49 63.49 68.49 protocols.match.Matcher:  ang_U1D2: 113.98 118.98 123.98 128.98 133.98 138.98 143.98 protocols.match.Matcher:  tor_U1D3: 157.49 162.49 167.49 172.49 177.49 182.49 187.49 192.49 197.49 protocols.match.downstream.LigandConformerBuilder: Initializing from residue LG1 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 LG1 for geometric constraint #2 protocols.match.Matcher:  LG1 ASP protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE4 D1: OD1 D2: CG D3: CB protocols.match.Matcher:  LG1 ASP protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE4 D1: OD2 D2: CG D3: CB protocols.match.Matcher:  LG1 GLU protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE4 D1: OE1 D2: CD D3: CG protocols.match.Matcher:  LG1 GLU protocols.match.Matcher:  U3: FE1 U2: O5 U1: FE4 D1: OE2 D2: CD D3: CG Created UpstreamCollisionFilter Created UpstreamDownstreamCollisionFilter protocols.match.Matcher: Initializing BumpGrids... protocols.match.Matcher: ...done protocols.match.Matcher:  TIMING: Bump grids took 8.13 seconds to compute  ERROR: build_sets_[ build_set_id ].restype().has( "1HA" ) ERROR:: Exit from: src/protocols/match/upstream/ProteinUpstreamBuilder.cc line: 1203 /scs/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x341) [0x2affb281f891] /scs/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libprotocols.6.so(protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(unsigned long, core::conformation::Residue&, protocols::match::upstream::ScaffoldBuildPoint const&) const+0x6ea) [0x2affa655ceea] /scs/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libprotocols.6.so(protocols::match::upstream::ProteinUpstreamBuilder::build(protocols::match::upstream::ScaffoldBuildPoint const&) const+0x2f1) [0x2affa6562e51] /scs/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libprotocols.6.so(protocols::match::downstream::DownstreamAlgorithm::default_build_hits_at_all_positions(protocols::match::Matcher const&) const+0xc1) [0x2affa665eee1] /scs/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libprotocols.6.so(protocols::match::downstream::ClassicMatchAlgorithm::build_hits_at_all_positions(protocols::match::Matcher&)+0x176) [0x2affa66577a6] /scs/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libprotocols.6.so(protocols::match::Matcher::generate_hits_for_constraint(unsigned long)+0x35) [0x2affa6b5cf85] /scs/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/build/src/release/linux/2.6/64/x86/gcc/4.4/default/libprotocols.6.so(protocols::match::Matcher::generate_hits()+0x43) [0x2affa6b666b3] /mnt/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/bin/match.linuxgccrelease() [0x405715] /mnt/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/bin/match.linuxgccrelease() [0x406438] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3caac1ed5d] /mnt/people/lulab/rosetta/rosetta_src_2016.29.58808_bundle/main/source/bin/match.linuxgccrelease() [0x4046d9] caught exception [ERROR] EXCN_utility_exit has been thrown from: src/protocols/match/upstream/ProteinUpstreamBuilder.cc line: 1203 ERROR: build_sets_[ build_set_id ].restype().has( "1HA" )