mkdir -p decoys cd decoys; /projects/compbio/experiments/undertaker/scripts/make-read-decoys.csh > read-pdb.under chgrp protein decoys/read-pdb.under chmod g+w decoys/read-pdb.under chmod: changing permissions of `decoys/read-pdb.under': Operation not permitted make: [decoys/read-pdb.under] Error 1 (ignored) rm -f decoys/evaluate_1.rdb sed -e s/XXX0000/T0262/ -e s/_domain/_1/ \ -e "s/# DO READ/ReadConformPDB T0262_1.real.pdb/" \ < /projects/compbio/experiments/protein-predict/casp6/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1123450635 # 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-1332-2symm.clash # Read ClashTable exp-pdb-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 7.79382 sec, elapsed time= 47.8797 sec) # command:# Prefix for input files set to # command:# ReadTargetPDB reading from PDB file T0262.blank.pdb looking for model 1 Warning: all-zero PDB file read in ReadTargetPDB, so making up random conformation Read PDB file T0262.blank.pdb model 1 as target. Have 256 residues and 2011 atoms. # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:# ReadConformPDB reading from PDB file T0262_1.real.pdb looking for model 1 # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 0.1 * knot + 0.5 * clens + 0 * rmsd + 0.13 * log_rmsd + 0 * rmsd_ca + 0.13 * log_rmsd_ca + 0.005 * GDT + 0.005 * smooth_GDT ) # command:# SetCost created cost = # ( 0 * missing_atoms ) # command:CPU_time= 9.1926 sec, elapsed time= 53.5104 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 1 # command:# naming current conformation align1 # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 0.819444 # GDT_score = -31.25 # GDT_score(maxd=8,maxw=2.9)= -29.0801 # GDT_score(maxd=8,maxw=3.2)= -27.9878 # GDT_score(maxd=8,maxw=3.5)= -26.8984 # GDT_score(maxd=10,maxw=3.8)= -29.3038 # GDT_score(maxd=10,maxw=4)= -28.5619 # GDT_score(maxd=10,maxw=4.2)= -27.8632 # GDT_score(maxd=12,maxw=4.3)= -30.087 # GDT_score(maxd=12,maxw=4.5)= -29.3622 # GDT_score(maxd=12,maxw=4.7)= -28.6128 # GDT_score(maxd=14,maxw=5.2)= -28.8356 # GDT_score(maxd=14,maxw=5.5)= -27.8311 # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 2 # command:# naming current conformation align2 # command:# fraction of real conformation used = 0.75 # GDT_score = -39.5833 # GDT_score(maxd=8,maxw=2.9)= -41.1371 # GDT_score(maxd=8,maxw=3.2)= -38.9203 # GDT_score(maxd=8,maxw=3.5)= -36.7322 # GDT_score(maxd=10,maxw=3.8)= -39.2457 # GDT_score(maxd=10,maxw=4)= -37.9084 # GDT_score(maxd=10,maxw=4.2)= -36.6697 # GDT_score(maxd=12,maxw=4.3)= -39.7088 # GDT_score(maxd=12,maxw=4.5)= -38.4612 # GDT_score(maxd=12,maxw=4.7)= -37.2474 # GDT_score(maxd=14,maxw=5.2)= -37.3386 # GDT_score(maxd=14,maxw=5.5)= -35.7565 # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 3 # command:# naming current conformation align3 # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 0.819444 # GDT_score = -30.2083 # GDT_score(maxd=8,maxw=2.9)= -30.0147 # GDT_score(maxd=8,maxw=3.2)= -28.6641 # GDT_score(maxd=8,maxw=3.5)= -27.5167 # GDT_score(maxd=10,maxw=3.8)= -29.547 # GDT_score(maxd=10,maxw=4)= -28.8335 # GDT_score(maxd=10,maxw=4.2)= -28.1312 # GDT_score(maxd=12,maxw=4.3)= -30.1476 # GDT_score(maxd=12,maxw=4.5)= -29.425 # GDT_score(maxd=12,maxw=4.7)= -28.7428 # GDT_score(maxd=14,maxw=5.2)= -29.0455 # GDT_score(maxd=14,maxw=5.5)= -28.02 # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 254 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -23.6111 # GDT_score(maxd=8,maxw=2.9)= -22.3905 # GDT_score(maxd=8,maxw=3.2)= -21.7931 # GDT_score(maxd=8,maxw=3.5)= -21.1525 # GDT_score(maxd=10,maxw=3.8)= -23.5388 # GDT_score(maxd=10,maxw=4)= -23.0563 # GDT_score(maxd=10,maxw=4.2)= -22.6198 # GDT_score(maxd=12,maxw=4.3)= -25.1656 # GDT_score(maxd=12,maxw=4.5)= -24.6644 # GDT_score(maxd=12,maxw=4.7)= -24.2059 # GDT_score(maxd=14,maxw=5.2)= -25.4148 # GDT_score(maxd=14,maxw=5.5)= -24.5316 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 8.7800000e+02 rmsd (weighted)= 1.2991525e+01 (unweighted)= 8.4215233e+01 superimposing iter= 1 total_weight= 1.6085513e+03 rmsd (weighted)= 7.4659811e+00 (unweighted)= 8.5966471e+01 superimposing iter= 2 total_weight= 8.7684058e+02 rmsd (weighted)= 6.0103941e+00 (unweighted)= 8.7162004e+01 superimposing iter= 3 total_weight= 6.9241668e+02 rmsd (weighted)= 5.4851254e+00 (unweighted)= 8.7953118e+01 superimposing iter= 4 total_weight= 6.3240295e+02 rmsd (weighted)= 5.2497417e+00 (unweighted)= 8.8471890e+01 superimposing iter= 5 total_weight= 6.1208191e+02 rmsd (weighted)= 5.1132730e+00 (unweighted)= 8.8792351e+01 # 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 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -26.0417 # GDT_score(maxd=8,maxw=2.9)= -23.9492 # GDT_score(maxd=8,maxw=3.2)= -23.1363 # GDT_score(maxd=8,maxw=3.5)= -22.3651 # GDT_score(maxd=10,maxw=3.8)= -24.7018 # GDT_score(maxd=10,maxw=4)= -24.1284 # GDT_score(maxd=10,maxw=4.2)= -23.5747 # GDT_score(maxd=12,maxw=4.3)= -26.8223 # GDT_score(maxd=12,maxw=4.5)= -26.1858 # GDT_score(maxd=12,maxw=4.7)= -25.5963 # GDT_score(maxd=14,maxw=5.2)= -27.468 # GDT_score(maxd=14,maxw=5.5)= -26.4707 # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -35.7639 # GDT_score(maxd=8,maxw=2.9)= -33.01 # GDT_score(maxd=8,maxw=3.2)= -31.4778 # GDT_score(maxd=8,maxw=3.5)= -30.2063 # GDT_score(maxd=10,maxw=3.8)= -33.609 # GDT_score(maxd=10,maxw=4)= -32.6983 # GDT_score(maxd=10,maxw=4.2)= -31.8111 # GDT_score(maxd=12,maxw=4.3)= -35.4607 # GDT_score(maxd=12,maxw=4.5)= -34.5019 # GDT_score(maxd=12,maxw=4.7)= -33.6174 # GDT_score(maxd=14,maxw=5.2)= -34.7925 # GDT_score(maxd=14,maxw=5.5)= -33.3706 # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -34.7222 # GDT_score(maxd=8,maxw=2.9)= -33.2059 # GDT_score(maxd=8,maxw=3.2)= -31.5361 # GDT_score(maxd=8,maxw=3.5)= -29.9625 # GDT_score(maxd=10,maxw=3.8)= -33.3022 # GDT_score(maxd=10,maxw=4)= -32.2334 # GDT_score(maxd=10,maxw=4.2)= -31.2275 # GDT_score(maxd=12,maxw=4.3)= -34.8969 # GDT_score(maxd=12,maxw=4.5)= -33.8397 # GDT_score(maxd=12,maxw=4.7)= -32.8725 # GDT_score(maxd=14,maxw=5.2)= -34.0232 # GDT_score(maxd=14,maxw=5.5)= -32.6053 # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -32.9861 # GDT_score(maxd=8,maxw=2.9)= -31.6435 # GDT_score(maxd=8,maxw=3.2)= -30.1281 # GDT_score(maxd=8,maxw=3.5)= -28.7362 # GDT_score(maxd=10,maxw=3.8)= -32.2692 # GDT_score(maxd=10,maxw=4)= -31.3502 # GDT_score(maxd=10,maxw=4.2)= -30.5042 # GDT_score(maxd=12,maxw=4.3)= -34.0842 # GDT_score(maxd=12,maxw=4.5)= -33.1616 # GDT_score(maxd=12,maxw=4.7)= -32.2824 # GDT_score(maxd=14,maxw=5.2)= -33.392 # GDT_score(maxd=14,maxw=5.5)= -32.1009 # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0262.try1-opt2.pdb looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -32.9861 # GDT_score(maxd=8,maxw=2.9)= -31.1713 # GDT_score(maxd=8,maxw=3.2)= -29.7014 # GDT_score(maxd=8,maxw=3.5)= -28.346 # GDT_score(maxd=10,maxw=3.8)= -31.888 # GDT_score(maxd=10,maxw=4)= -30.988 # GDT_score(maxd=10,maxw=4.2)= -30.1597 # GDT_score(maxd=12,maxw=4.3)= -33.6827 # GDT_score(maxd=12,maxw=4.5)= -32.7784 # GDT_score(maxd=12,maxw=4.7)= -31.9155 # GDT_score(maxd=14,maxw=5.2)= -32.987 # GDT_score(maxd=14,maxw=5.5)= -31.718 # command:# Removing conformation named T0262.try1-opt2.pdb # command:# reading script from file read-pdb.under # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv1.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv2.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv3.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # command:CPU_time= 18.5052 sec, elapsed time= 86.8483 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate_1.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged T0262.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.886535 T0262.try8-opt2.pdb.gz costs 0 real_cost = 0.883287 T0262.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 0.893561 T0262.try8-opt1.pdb.gz costs 0 real_cost = 0.893444 T0262.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.782338 T0262.try7-opt2.pdb.gz costs 0 real_cost = 0.782461 T0262.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 0.792409 T0262.try7-opt1.pdb.gz costs 0 real_cost = 0.792957 T0262.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.647996 T0262.try6-opt2.pdb.gz costs 0 real_cost = 0.648111 T0262.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 0.648053 T0262.try6-opt1.pdb.gz costs 0 real_cost = 0.65089 T0262.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.673737 T0262.try5-opt2.pdb.gz costs 0 real_cost = 0.673194 T0262.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 0.681705 T0262.try5-opt1.pdb.gz costs 0 real_cost = 0.68041 T0262.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.651122 T0262.try4-opt2.pdb.gz costs 0 real_cost = 0.650558 T0262.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 0.702134 T0262.try4-opt1.pdb.gz costs 0 real_cost = 0.704053 T0262.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.786373 T0262.try3-opt2.pdb.gz costs 0 real_cost = 0.786396 T0262.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 0.798563 T0262.try3-opt1.pdb.gz costs 0 real_cost = 0.798788 T0262.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.831272 T0262.try2-opt2.pdb.gz costs 0 real_cost = 0.831675 T0262.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 0.832621 T0262.try2-opt1.pdb.gz costs 0 real_cost = 0.83217 T0262.try1-opt2.pdb.gz costs 0 real_cost = 0.681016 T0262.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 0.679041 T0262.try1-opt1.pdb.gz costs 0 real_cost = 0.678917 T0262.chimer.dv3.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 0.667859 T0262.chimer.dv2.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 0.667859 T0262.chimer.dv1.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 0.667859 T0262.chimer.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 0.667859 robetta-model5.pdb.gz costs 0 real_cost = 0.940279 robetta-model4.pdb.gz costs 0 real_cost = 0.987402 robetta-model3.pdb.gz costs 0 real_cost = 0.970022 robetta-model2.pdb.gz costs 0 real_cost = 0.969015 robetta-model1.pdb.gz costs 0 real_cost = 0.880083 model5.ts-submitted costs 0 real_cost = 0.681039 model4.ts-submitted costs 0 real_cost = 0.651337 model3.ts-submitted costs 0 real_cost = 0.648103 model2.ts-submitted costs 0 real_cost = 0.782616 model1.ts-submitted costs 0 real_cost = 0.881683 Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged align3 costs 0 real_cost = 0.814297 align2 costs 0 real_cost = 0.596607 align1 costs 0 real_cost = 0.931485 T0262_1.real.pdb costs 0 real_cost = -2.82 # command:CPU_time= 33.218 sec, elapsed time= 141.82 sec) # command:# ReadConformPDB reading from PDB file robetta-model1.pdb looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -26.3889 # GDT_score(maxd=8,maxw=2.9)= -23.7086 # GDT_score(maxd=8,maxw=3.2)= -22.9134 # GDT_score(maxd=8,maxw=3.5)= -22.1399 # GDT_score(maxd=10,maxw=3.8)= -24.8213 # GDT_score(maxd=10,maxw=4)= -24.2681 # GDT_score(maxd=10,maxw=4.2)= -23.7042 # GDT_score(maxd=12,maxw=4.3)= -26.5521 # GDT_score(maxd=12,maxw=4.5)= -25.9128 # GDT_score(maxd=12,maxw=4.7)= -25.283 # GDT_score(maxd=14,maxw=5.2)= -26.4125 # GDT_score(maxd=14,maxw=5.5)= -25.4898 # command:# Removing conformation named robetta-model1.pdb # command:# ReadConformPDB reading from PDB file robetta-model2.pdb looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -18.4028 # GDT_score(maxd=8,maxw=2.9)= -17.5393 # GDT_score(maxd=8,maxw=3.2)= -17.0108 # GDT_score(maxd=8,maxw=3.5)= -16.5051 # GDT_score(maxd=10,maxw=3.8)= -17.6989 # GDT_score(maxd=10,maxw=4)= -17.3695 # GDT_score(maxd=10,maxw=4.2)= -17.0397 # GDT_score(maxd=12,maxw=4.3)= -18.932 # GDT_score(maxd=12,maxw=4.5)= -18.5434 # GDT_score(maxd=12,maxw=4.7)= -18.168 # GDT_score(maxd=14,maxw=5.2)= -19.5566 # GDT_score(maxd=14,maxw=5.5)= -18.9444 # command:# Removing conformation named robetta-model2.pdb # command:# ReadConformPDB reading from PDB file robetta-model3.pdb looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -20.8333 # GDT_score(maxd=8,maxw=2.9)= -19.7797 # GDT_score(maxd=8,maxw=3.2)= -19.5962 # GDT_score(maxd=8,maxw=3.5)= -19.3234 # GDT_score(maxd=10,maxw=3.8)= -20.7884 # GDT_score(maxd=10,maxw=4)= -20.3865 # GDT_score(maxd=10,maxw=4.2)= -19.9448 # GDT_score(maxd=12,maxw=4.3)= -21.9729 # GDT_score(maxd=12,maxw=4.5)= -21.4814 # GDT_score(maxd=12,maxw=4.7)= -20.981 # GDT_score(maxd=14,maxw=5.2)= -21.835 # GDT_score(maxd=14,maxw=5.5)= -21.0985 # command:# Removing conformation named robetta-model3.pdb # command:# ReadConformPDB reading from PDB file robetta-model4.pdb looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -20.8333 # GDT_score(maxd=8,maxw=2.9)= -19.2823 # GDT_score(maxd=8,maxw=3.2)= -19.0153 # GDT_score(maxd=8,maxw=3.5)= -18.6325 # GDT_score(maxd=10,maxw=3.8)= -20.1945 # GDT_score(maxd=10,maxw=4)= -19.7506 # GDT_score(maxd=10,maxw=4.2)= -19.3392 # GDT_score(maxd=12,maxw=4.3)= -20.954 # GDT_score(maxd=12,maxw=4.5)= -20.5165 # GDT_score(maxd=12,maxw=4.7)= -20.1163 # GDT_score(maxd=14,maxw=5.2)= -20.6754 # GDT_score(maxd=14,maxw=5.5)= -19.9755 # command:# Removing conformation named robetta-model4.pdb # command:# ReadConformPDB reading from PDB file robetta-model5.pdb looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -19.7917 # GDT_score(maxd=8,maxw=2.9)= -18.5594 # GDT_score(maxd=8,maxw=3.2)= -17.9276 # GDT_score(maxd=8,maxw=3.5)= -17.2841 # GDT_score(maxd=10,maxw=3.8)= -19.1162 # GDT_score(maxd=10,maxw=4)= -18.5877 # GDT_score(maxd=10,maxw=4.2)= -18.0738 # GDT_score(maxd=12,maxw=4.3)= -20.8702 # GDT_score(maxd=12,maxw=4.5)= -20.2777 # GDT_score(maxd=12,maxw=4.7)= -19.7104 # GDT_score(maxd=14,maxw=5.2)= -21.1674 # GDT_score(maxd=14,maxw=5.5)= -20.3238 # command:# Removing conformation named robetta-model5.pdb # command:CPU_time= 35.0537 sec, elapsed time= 149.085 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate_1.rdb > sort.tmp mv -f sort.tmp decoys/evaluate_1.rdb rm -f decoys/evaluate_2.rdb sed -e s/XXX0000/T0262/ -e s/_domain/_2/ \ -e "s/# DO READ/ReadConformPDB T0262_2.real.pdb/" \ < /projects/compbio/experiments/protein-predict/casp6/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1123403943 # 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-1332-2symm.clash # Read ClashTable exp-pdb-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 7.71483 sec, elapsed time= 27.7508 sec) # command:# Prefix for input files set to # command:# ReadTargetPDB reading from PDB file T0262.blank.pdb looking for model 1 Warning: all-zero PDB file read in ReadTargetPDB, so making up random conformation Read PDB file T0262.blank.pdb model 1 as target. Have 256 residues and 2011 atoms. # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:# ReadConformPDB reading from PDB file T0262_2.real.pdb looking for model 1 # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 0.1 * knot + 0.5 * clens + 0 * rmsd + 0.13 * log_rmsd + 0 * rmsd_ca + 0.13 * log_rmsd_ca + 0.005 * GDT + 0.005 * smooth_GDT ) # command:# SetCost created cost = # ( 0 * missing_atoms ) # command:CPU_time= 9.11061 sec, elapsed time= 31.7329 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 1 # command:# naming current conformation align1 # command:Error: conformation and real conformation have <3 CA atoms in common # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 2 # command:# naming current conformation align2 # command:Error: conformation and real conformation have <3 CA atoms in common # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 3 # command:# naming current conformation align3 # command:Error: conformation and real conformation have <3 CA atoms in common # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 254 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -19.0722 # GDT_score(maxd=8,maxw=2.9)= -17.7823 # GDT_score(maxd=8,maxw=3.2)= -16.9261 # GDT_score(maxd=8,maxw=3.5)= -16.1822 # GDT_score(maxd=10,maxw=3.8)= -18.0718 # GDT_score(maxd=10,maxw=4)= -17.575 # GDT_score(maxd=10,maxw=4.2)= -17.0817 # GDT_score(maxd=12,maxw=4.3)= -19.005 # GDT_score(maxd=12,maxw=4.5)= -18.4811 # GDT_score(maxd=12,maxw=4.7)= -17.9734 # GDT_score(maxd=14,maxw=5.2)= -18.6534 # GDT_score(maxd=14,maxw=5.5)= -17.8609 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 1.1540000e+03 rmsd (weighted)= 1.4616917e+01 (unweighted)= 6.3699659e+01 superimposing iter= 1 total_weight= 1.7764360e+03 rmsd (weighted)= 9.2205340e+00 (unweighted)= 6.3968861e+01 superimposing iter= 2 total_weight= 1.1511412e+03 rmsd (weighted)= 7.3594015e+00 (unweighted)= 6.3743746e+01 superimposing iter= 3 total_weight= 9.3885058e+02 rmsd (weighted)= 6.5411705e+00 (unweighted)= 6.3558155e+01 superimposing iter= 4 total_weight= 8.3700161e+02 rmsd (weighted)= 6.1642559e+00 (unweighted)= 6.3453118e+01 superimposing iter= 5 total_weight= 7.9145568e+02 rmsd (weighted)= 5.9742505e+00 (unweighted)= 6.3407383e+01 # 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 253 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -15.4639 # GDT_score(maxd=8,maxw=2.9)= -14.0759 # GDT_score(maxd=8,maxw=3.2)= -13.4138 # GDT_score(maxd=8,maxw=3.5)= -12.7942 # GDT_score(maxd=10,maxw=3.8)= -14.3527 # GDT_score(maxd=10,maxw=4)= -13.9009 # GDT_score(maxd=10,maxw=4.2)= -13.4844 # GDT_score(maxd=12,maxw=4.3)= -15.2414 # GDT_score(maxd=12,maxw=4.5)= -14.7931 # GDT_score(maxd=12,maxw=4.7)= -14.383 # GDT_score(maxd=14,maxw=5.2)= -15.1866 # GDT_score(maxd=14,maxw=5.5)= -14.6394 # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -17.7835 # GDT_score(maxd=8,maxw=2.9)= -16.718 # GDT_score(maxd=8,maxw=3.2)= -16.1756 # GDT_score(maxd=8,maxw=3.5)= -15.5845 # GDT_score(maxd=10,maxw=3.8)= -17.2069 # GDT_score(maxd=10,maxw=4)= -16.8105 # GDT_score(maxd=10,maxw=4.2)= -16.4518 # GDT_score(maxd=12,maxw=4.3)= -18.2921 # GDT_score(maxd=12,maxw=4.5)= -17.8868 # GDT_score(maxd=12,maxw=4.7)= -17.4602 # GDT_score(maxd=14,maxw=5.2)= -18.2301 # GDT_score(maxd=14,maxw=5.5)= -17.5731 # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -18.8144 # GDT_score(maxd=8,maxw=2.9)= -16.2108 # GDT_score(maxd=8,maxw=3.2)= -15.6762 # GDT_score(maxd=8,maxw=3.5)= -15.0546 # GDT_score(maxd=10,maxw=3.8)= -17.5394 # GDT_score(maxd=10,maxw=4)= -17.0748 # GDT_score(maxd=10,maxw=4.2)= -16.6544 # GDT_score(maxd=12,maxw=4.3)= -19.1604 # GDT_score(maxd=12,maxw=4.5)= -18.6708 # GDT_score(maxd=12,maxw=4.7)= -18.1834 # GDT_score(maxd=14,maxw=5.2)= -19.2812 # GDT_score(maxd=14,maxw=5.5)= -18.5107 # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -14.6907 # GDT_score(maxd=8,maxw=2.9)= -13.5782 # GDT_score(maxd=8,maxw=3.2)= -13.3128 # GDT_score(maxd=8,maxw=3.5)= -12.9557 # GDT_score(maxd=10,maxw=3.8)= -14.1699 # GDT_score(maxd=10,maxw=4)= -13.8738 # GDT_score(maxd=10,maxw=4.2)= -13.573 # GDT_score(maxd=12,maxw=4.3)= -15.1593 # GDT_score(maxd=12,maxw=4.5)= -14.8129 # GDT_score(maxd=12,maxw=4.7)= -14.4897 # GDT_score(maxd=14,maxw=5.2)= -15.2938 # GDT_score(maxd=14,maxw=5.5)= -14.7497 # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0262.try1-opt2.pdb looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -15.4639 # GDT_score(maxd=8,maxw=2.9)= -13.921 # GDT_score(maxd=8,maxw=3.2)= -13.6238 # GDT_score(maxd=8,maxw=3.5)= -13.2397 # GDT_score(maxd=10,maxw=3.8)= -14.4978 # GDT_score(maxd=10,maxw=4)= -14.1853 # GDT_score(maxd=10,maxw=4.2)= -13.8698 # GDT_score(maxd=12,maxw=4.3)= -15.3666 # GDT_score(maxd=12,maxw=4.5)= -15.0112 # GDT_score(maxd=12,maxw=4.7)= -14.6795 # GDT_score(maxd=14,maxw=5.2)= -15.4038 # GDT_score(maxd=14,maxw=5.5)= -14.8537 # command:# Removing conformation named T0262.try1-opt2.pdb # command:# reading script from file read-pdb.under # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv1.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv2.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv3.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # command:CPU_time= 19.0261 sec, elapsed time= 59.4557 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate_2.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged T0262.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.995222 T0262.try8-opt2.pdb.gz costs 0 real_cost = 0.997986 T0262.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 0.999141 T0262.try8-opt1.pdb.gz costs 0 real_cost = 0.998566 T0262.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.06808 T0262.try7-opt2.pdb.gz costs 0 real_cost = 1.06794 T0262.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 1.07428 T0262.try7-opt1.pdb.gz costs 0 real_cost = 1.07398 T0262.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.05009 T0262.try6-opt2.pdb.gz costs 0 real_cost = 1.05034 T0262.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 1.05337 T0262.try6-opt1.pdb.gz costs 0 real_cost = 1.05369 T0262.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.08411 T0262.try5-opt2.pdb.gz costs 0 real_cost = 1.08399 T0262.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 1.08827 T0262.try5-opt1.pdb.gz costs 0 real_cost = 1.08866 T0262.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.983158 T0262.try4-opt2.pdb.gz costs 0 real_cost = 0.982792 T0262.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 0.973988 T0262.try4-opt1.pdb.gz costs 0 real_cost = 0.973863 T0262.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.01922 T0262.try3-opt2.pdb.gz costs 0 real_cost = 1.01891 T0262.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 1.02188 T0262.try3-opt1.pdb.gz costs 0 real_cost = 1.02189 T0262.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.02675 T0262.try2-opt2.pdb.gz costs 0 real_cost = 1.02575 T0262.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 1.03336 T0262.try2-opt1.pdb.gz costs 0 real_cost = 1.03302 T0262.try1-opt2.pdb.gz costs 0 real_cost = 1.05843 T0262.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 1.06207 T0262.try1-opt1.pdb.gz costs 0 real_cost = 1.06197 T0262.chimer.dv3.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 1.00609 T0262.chimer.dv2.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 0.97733 T0262.chimer.dv1.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 1.0516 T0262.chimer.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 0.970232 robetta-model5.pdb.gz costs 0 real_cost = 0.538047 robetta-model4.pdb.gz costs 0 real_cost = 0.543548 robetta-model3.pdb.gz costs 0 real_cost = 0.560472 robetta-model2.pdb.gz costs 0 real_cost = 0.929896 robetta-model1.pdb.gz costs 0 real_cost = 0.556467 model5.ts-submitted costs 0 real_cost = 1.05804 model4.ts-submitted costs 0 real_cost = 0.983169 model3.ts-submitted costs 0 real_cost = 1.05033 model2.ts-submitted costs 0 real_cost = 1.06794 model1.ts-submitted costs 0 real_cost = 0.997923 align3 costs 0 real_cost = -1.32 align2 costs 0 real_cost = -1.32 align1 costs 0 real_cost = -1.32 T0262_2.real.pdb costs 0 real_cost = -2.82 # command:CPU_time= 48.4836 sec, elapsed time= 113.422 sec) # command:# ReadConformPDB reading from PDB file robetta-model1.pdb looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -41.2371 # GDT_score(maxd=8,maxw=2.9)= -39.2998 # GDT_score(maxd=8,maxw=3.2)= -37.385 # GDT_score(maxd=8,maxw=3.5)= -35.4552 # GDT_score(maxd=10,maxw=3.8)= -39.6066 # GDT_score(maxd=10,maxw=4)= -38.2324 # GDT_score(maxd=10,maxw=4.2)= -36.8751 # GDT_score(maxd=12,maxw=4.3)= -41.2786 # GDT_score(maxd=12,maxw=4.5)= -39.8596 # GDT_score(maxd=12,maxw=4.7)= -38.542 # GDT_score(maxd=14,maxw=5.2)= -39.3031 # GDT_score(maxd=14,maxw=5.5)= -37.4967 # command:# Removing conformation named robetta-model1.pdb # command:# ReadConformPDB reading from PDB file robetta-model2.pdb looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -23.1959 # GDT_score(maxd=8,maxw=2.9)= -21.2764 # GDT_score(maxd=8,maxw=3.2)= -20.5923 # GDT_score(maxd=8,maxw=3.5)= -19.9302 # GDT_score(maxd=10,maxw=3.8)= -21.9106 # GDT_score(maxd=10,maxw=4)= -21.3852 # GDT_score(maxd=10,maxw=4.2)= -20.8301 # GDT_score(maxd=12,maxw=4.3)= -22.9766 # GDT_score(maxd=12,maxw=4.5)= -22.3711 # GDT_score(maxd=12,maxw=4.7)= -21.7976 # GDT_score(maxd=14,maxw=5.2)= -22.6451 # GDT_score(maxd=14,maxw=5.5)= -21.7473 # command:# Removing conformation named robetta-model2.pdb # command:# ReadConformPDB reading from PDB file robetta-model3.pdb looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -41.4948 # GDT_score(maxd=8,maxw=2.9)= -41.0629 # GDT_score(maxd=8,maxw=3.2)= -39.0104 # GDT_score(maxd=8,maxw=3.5)= -36.9606 # GDT_score(maxd=10,maxw=3.8)= -40.8865 # GDT_score(maxd=10,maxw=4)= -39.4618 # GDT_score(maxd=10,maxw=4.2)= -38.0459 # GDT_score(maxd=12,maxw=4.3)= -42.227 # GDT_score(maxd=12,maxw=4.5)= -40.766 # GDT_score(maxd=12,maxw=4.7)= -39.4097 # GDT_score(maxd=14,maxw=5.2)= -40.043 # GDT_score(maxd=14,maxw=5.5)= -38.1963 # command:# Removing conformation named robetta-model3.pdb # command:# ReadConformPDB reading from PDB file robetta-model4.pdb looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -43.5567 # GDT_score(maxd=8,maxw=2.9)= -41.6616 # GDT_score(maxd=8,maxw=3.2)= -39.5254 # GDT_score(maxd=8,maxw=3.5)= -37.4307 # GDT_score(maxd=10,maxw=3.8)= -41.3883 # GDT_score(maxd=10,maxw=4)= -39.93 # GDT_score(maxd=10,maxw=4.2)= -38.4919 # GDT_score(maxd=12,maxw=4.3)= -42.6206 # GDT_score(maxd=12,maxw=4.5)= -41.142 # GDT_score(maxd=12,maxw=4.7)= -39.7698 # GDT_score(maxd=14,maxw=5.2)= -40.3331 # GDT_score(maxd=14,maxw=5.5)= -38.4705 # command:# Removing conformation named robetta-model4.pdb # command:# ReadConformPDB reading from PDB file robetta-model5.pdb looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -42.5258 # GDT_score(maxd=8,maxw=2.9)= -39.8964 # GDT_score(maxd=8,maxw=3.2)= -37.9506 # GDT_score(maxd=8,maxw=3.5)= -35.9722 # GDT_score(maxd=10,maxw=3.8)= -39.9838 # GDT_score(maxd=10,maxw=4)= -38.5908 # GDT_score(maxd=10,maxw=4.2)= -37.2164 # GDT_score(maxd=12,maxw=4.3)= -41.602 # GDT_score(maxd=12,maxw=4.5)= -40.1687 # GDT_score(maxd=12,maxw=4.7)= -38.8379 # GDT_score(maxd=14,maxw=5.2)= -39.5767 # GDT_score(maxd=14,maxw=5.5)= -37.7554 # command:# Removing conformation named robetta-model5.pdb # command:CPU_time= 51.3452 sec, elapsed time= 154.08 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl real_cost < decoys/evaluate_2.rdb > sort.tmp mv -f sort.tmp decoys/evaluate_2.rdb rm -f decoys/evaluate.rdb sed -e s/XXX0000/T0262/ -e s/REAL_PDB/1wfxA/ \ -e "s/_domain//" \ -e "s/# DO READ/ReadConformPDBids/" \ < /projects/compbio/experiments/protein-predict/casp6/starter-directory/evaluate.under \ | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1122906682 # 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-1332-2symm.clash # Read ClashTable exp-pdb-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 7.74882 sec, elapsed time= 21.746 sec) # command:# Prefix for input files set to # command:# ReadTargetPDB reading from PDB file T0262.blank.pdb looking for model 1 Warning: all-zero PDB file read in ReadTargetPDB, so making up random conformation Read PDB file T0262.blank.pdb model 1 as target. Have 256 residues and 2011 atoms. # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:1wfxA expands to /projects/compbio/data/pdb/1wfx.pdb.gz 1wfxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Read 180 residues and 1442 atoms. # command:# Saving current conformation as real # command:# Prefix for output files set to decoys/ # command:# SetRealCost created real_cost = # ( 0.1 * knot + 0.5 * clens + 0 * rmsd + 0.13 * log_rmsd + 0 * rmsd_ca + 0.13 * log_rmsd_ca + 0.005 * GDT + 0.005 * smooth_GDT ) # command:# SetCost created cost = # ( 0 * missing_atoms ) # command:CPU_time= 9.1856 sec, elapsed time= 24.8381 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 1 # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.327778 # GDT_score = -12.5 # GDT_score(maxd=8,maxw=2.9)= -11.5418 # GDT_score(maxd=8,maxw=3.2)= -11.1105 # GDT_score(maxd=8,maxw=3.5)= -10.682 # GDT_score(maxd=10,maxw=3.8)= -11.6434 # GDT_score(maxd=10,maxw=4)= -11.3638 # GDT_score(maxd=10,maxw=4.2)= -11.0872 # GDT_score(maxd=12,maxw=4.3)= -11.9781 # GDT_score(maxd=12,maxw=4.5)= -11.6926 # GDT_score(maxd=12,maxw=4.7)= -11.414 # GDT_score(maxd=14,maxw=5.2)= -11.5097 # GDT_score(maxd=14,maxw=5.5)= -11.1243 # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 2 # command:# naming current conformation align2 # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 0.3 # GDT_score = -16.1111 # GDT_score(maxd=8,maxw=2.9)= -16.5717 # GDT_score(maxd=8,maxw=3.2)= -15.6471 # GDT_score(maxd=8,maxw=3.5)= -14.7764 # GDT_score(maxd=10,maxw=3.8)= -15.7837 # GDT_score(maxd=10,maxw=4)= -15.2445 # GDT_score(maxd=10,maxw=4.2)= -14.7305 # GDT_score(maxd=12,maxw=4.3)= -15.9633 # GDT_score(maxd=12,maxw=4.5)= -15.4514 # GDT_score(maxd=12,maxw=4.7)= -14.9795 # GDT_score(maxd=14,maxw=5.2)= -15.0284 # GDT_score(maxd=14,maxw=5.5)= -14.3982 # command:# ReadConformPDB reading from PDB file T0262.t2k.undertaker-align.pdb looking for model 3 # command:# naming current conformation align3 # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 0.327778 # GDT_score = -12.0833 # GDT_score(maxd=8,maxw=2.9)= -11.9704 # GDT_score(maxd=8,maxw=3.2)= -11.4254 # GDT_score(maxd=8,maxw=3.5)= -10.9699 # GDT_score(maxd=10,maxw=3.8)= -11.765 # GDT_score(maxd=10,maxw=4)= -11.4773 # GDT_score(maxd=10,maxw=4.2)= -11.1954 # GDT_score(maxd=12,maxw=4.3)= -11.9985 # GDT_score(maxd=12,maxw=4.5)= -11.7121 # GDT_score(maxd=12,maxw=4.7)= -11.442 # GDT_score(maxd=14,maxw=5.2)= -11.5687 # GDT_score(maxd=14,maxw=5.5)= -11.1736 # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # choosing archetypes in rotamer library # Found a chain break before 254 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -10.5556 # GDT_score(maxd=8,maxw=2.9)= -8.90405 # GDT_score(maxd=8,maxw=3.2)= -8.74638 # GDT_score(maxd=8,maxw=3.5)= -8.51206 # GDT_score(maxd=10,maxw=3.8)= -9.70735 # GDT_score(maxd=10,maxw=4)= -9.49976 # GDT_score(maxd=10,maxw=4.2)= -9.31194 # GDT_score(maxd=12,maxw=4.3)= -10.9548 # GDT_score(maxd=12,maxw=4.5)= -10.7148 # GDT_score(maxd=12,maxw=4.7)= -10.4953 # GDT_score(maxd=14,maxw=5.2)= -11.7195 # GDT_score(maxd=14,maxw=5.5)= -11.3206 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 2.1620000e+03 rmsd (weighted)= 1.7397164e+01 (unweighted)= 5.3609010e+01 superimposing iter= 1 total_weight= 3.4999705e+03 rmsd (weighted)= 1.0924942e+01 (unweighted)= 5.3165561e+01 superimposing iter= 2 total_weight= 1.7763167e+03 rmsd (weighted)= 9.7832508e+00 (unweighted)= 5.3006920e+01 superimposing iter= 3 total_weight= 1.5094511e+03 rmsd (weighted)= 9.5265253e+00 (unweighted)= 5.2941887e+01 superimposing iter= 4 total_weight= 1.4499830e+03 rmsd (weighted)= 9.4687188e+00 (unweighted)= 5.2903233e+01 superimposing iter= 5 total_weight= 1.4357576e+03 rmsd (weighted)= 9.4587267e+00 (unweighted)= 5.2873795e+01 # 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 253 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -11.6667 # GDT_score(maxd=8,maxw=2.9)= -10.1782 # GDT_score(maxd=8,maxw=3.2)= -9.79688 # GDT_score(maxd=8,maxw=3.5)= -9.46138 # GDT_score(maxd=10,maxw=3.8)= -10.9365 # GDT_score(maxd=10,maxw=4)= -10.6674 # GDT_score(maxd=10,maxw=4.2)= -10.397 # GDT_score(maxd=12,maxw=4.3)= -12.3037 # GDT_score(maxd=12,maxw=4.5)= -11.9695 # GDT_score(maxd=12,maxw=4.7)= -11.6493 # GDT_score(maxd=14,maxw=5.2)= -12.8088 # GDT_score(maxd=14,maxw=5.5)= -12.2871 # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -14.8611 # GDT_score(maxd=8,maxw=2.9)= -13.1846 # GDT_score(maxd=8,maxw=3.2)= -12.5735 # GDT_score(maxd=8,maxw=3.5)= -12.0479 # GDT_score(maxd=10,maxw=3.8)= -13.9187 # GDT_score(maxd=10,maxw=4)= -13.5032 # GDT_score(maxd=10,maxw=4.2)= -13.1247 # GDT_score(maxd=12,maxw=4.3)= -15.2077 # GDT_score(maxd=12,maxw=4.5)= -14.7787 # GDT_score(maxd=12,maxw=4.7)= -14.3862 # GDT_score(maxd=14,maxw=5.2)= -15.5492 # GDT_score(maxd=14,maxw=5.5)= -14.926 # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -13.75 # GDT_score(maxd=8,maxw=2.9)= -13.1685 # GDT_score(maxd=8,maxw=3.2)= -12.5371 # GDT_score(maxd=8,maxw=3.5)= -11.9355 # GDT_score(maxd=10,maxw=3.8)= -13.2069 # GDT_score(maxd=10,maxw=4)= -12.7835 # GDT_score(maxd=10,maxw=4.2)= -12.3864 # GDT_score(maxd=12,maxw=4.3)= -13.8147 # GDT_score(maxd=12,maxw=4.5)= -13.3982 # GDT_score(maxd=12,maxw=4.7)= -13.006 # GDT_score(maxd=14,maxw=5.2)= -13.6385 # GDT_score(maxd=14,maxw=5.5)= -13.0759 # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -12.9167 # GDT_score(maxd=8,maxw=2.9)= -11.9208 # GDT_score(maxd=8,maxw=3.2)= -11.3349 # GDT_score(maxd=8,maxw=3.5)= -10.8395 # GDT_score(maxd=10,maxw=3.8)= -12.246 # GDT_score(maxd=10,maxw=4)= -11.9115 # GDT_score(maxd=10,maxw=4.2)= -11.6088 # GDT_score(maxd=12,maxw=4.3)= -13.016 # GDT_score(maxd=12,maxw=4.5)= -12.6844 # GDT_score(maxd=12,maxw=4.7)= -12.3676 # GDT_score(maxd=14,maxw=5.2)= -13.1194 # GDT_score(maxd=14,maxw=5.5)= -12.6401 # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0262.try1-opt2.pdb looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -12.9167 # GDT_score(maxd=8,maxw=2.9)= -11.9223 # GDT_score(maxd=8,maxw=3.2)= -11.3364 # GDT_score(maxd=8,maxw=3.5)= -10.8409 # GDT_score(maxd=10,maxw=3.8)= -12.2474 # GDT_score(maxd=10,maxw=4)= -11.9128 # GDT_score(maxd=10,maxw=4.2)= -11.61 # GDT_score(maxd=12,maxw=4.3)= -13.0295 # GDT_score(maxd=12,maxw=4.5)= -12.6973 # GDT_score(maxd=12,maxw=4.7)= -12.3798 # GDT_score(maxd=14,maxw=5.2)= -13.3237 # GDT_score(maxd=14,maxw=5.5)= -12.8327 # command:# Removing conformation named T0262.try1-opt2.pdb # command:# reading script from file read-pdb.under # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv1.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv2.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.chimer.dv3.d2-try3.d1-try2.d3-try2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 251 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 235 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 237 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 238 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 234 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 253 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 252 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0262.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # command:CPU_time= 30.9593 sec, elapsed time= 77.064 sec) # command:# Prefix for output files set to decoys/ # command:# Will now start reporting costs to decoys/evaluate.rdb # command:# CostConform Warning: Couldn't open file decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot or decoys//projects/compbio/experiments/undertaker/spots/near-backbone-center.spot.gz for input Trying /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot # Reading spots from /projects/compbio/experiments/undertaker/spots/near-backbone-center.spot Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged T0262.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.10586 T0262.try8-opt2.pdb.gz costs 0 real_cost = 1.10489 T0262.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 1.10831 T0262.try8-opt1.pdb.gz costs 0 real_cost = 1.10741 T0262.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.08716 T0262.try7-opt2.pdb.gz costs 0 real_cost = 1.08791 T0262.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 1.09212 T0262.try7-opt1.pdb.gz costs 0 real_cost = 1.09215 T0262.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.04768 T0262.try6-opt2.pdb.gz costs 0 real_cost = 1.0481 T0262.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 1.04777 T0262.try6-opt1.pdb.gz costs 0 real_cost = 1.04824 T0262.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.06679 T0262.try5-opt2.pdb.gz costs 0 real_cost = 1.06691 T0262.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 1.07934 T0262.try5-opt1.pdb.gz costs 0 real_cost = 1.07919 T0262.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.05684 T0262.try4-opt2.pdb.gz costs 0 real_cost = 1.05845 T0262.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 1.06943 T0262.try4-opt1.pdb.gz costs 0 real_cost = 1.07128 T0262.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.07116 T0262.try3-opt2.pdb.gz costs 0 real_cost = 1.07059 T0262.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 1.07167 T0262.try3-opt1.pdb.gz costs 0 real_cost = 1.07186 T0262.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 1.12299 T0262.try2-opt2.pdb.gz costs 0 real_cost = 1.12333 T0262.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 1.12544 T0262.try2-opt1.pdb.gz costs 0 real_cost = 1.12512 T0262.try1-opt2.pdb.gz costs 0 real_cost = 1.08982 T0262.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 1.09169 T0262.try1-opt1.pdb.gz costs 0 real_cost = 1.09179 T0262.chimer.dv3.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 1.03344 T0262.chimer.dv2.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 1.02799 T0262.chimer.dv1.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 1.06217 T0262.chimer.d2-try3.d1-try2.d3-try2.pdb.gz costs 0 real_cost = 1.0536 robetta-model5.pdb.gz costs 0 real_cost = 1.01765 robetta-model4.pdb.gz costs 0 real_cost = 0.999883 robetta-model3.pdb.gz costs 0 real_cost = 0.998682 robetta-model2.pdb.gz costs 0 real_cost = 1.10876 robetta-model1.pdb.gz costs 0 real_cost = 0.941707 model5.ts-submitted costs 0 real_cost = 1.08907 model4.ts-submitted costs 0 real_cost = 1.05829 model3.ts-submitted costs 0 real_cost = 1.04814 model2.ts-submitted costs 0 real_cost = 1.08653 model1.ts-submitted costs 0 real_cost = 1.10491 Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged align3 costs 0 real_cost = 1.0469 align2 costs 0 real_cost = 0.913752 align1 costs 0 real_cost = 1.07057 1wfxA costs 0 real_cost = -2.82 # command:CPU_time= 197.944 sec, elapsed time= 420.993 sec) # command:# ReadConformPDB reading from PDB file robetta-model1.pdb looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -21.6667 # GDT_score(maxd=8,maxw=2.9)= -20.8612 # GDT_score(maxd=8,maxw=3.2)= -19.7089 # GDT_score(maxd=8,maxw=3.5)= -18.5964 # GDT_score(maxd=10,maxw=3.8)= -21.0158 # GDT_score(maxd=10,maxw=4)= -20.2512 # GDT_score(maxd=10,maxw=4.2)= -19.5144 # GDT_score(maxd=12,maxw=4.3)= -22.3158 # GDT_score(maxd=12,maxw=4.5)= -21.5318 # GDT_score(maxd=12,maxw=4.7)= -20.8046 # GDT_score(maxd=14,maxw=5.2)= -21.7081 # GDT_score(maxd=14,maxw=5.5)= -20.7273 # command:# Removing conformation named robetta-model1.pdb # command:# ReadConformPDB reading from PDB file robetta-model2.pdb looking for model 1 # Found a chain break before 255 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -11.6667 # GDT_score(maxd=8,maxw=2.9)= -11.0565 # GDT_score(maxd=8,maxw=3.2)= -10.7246 # GDT_score(maxd=8,maxw=3.5)= -10.354 # GDT_score(maxd=10,maxw=3.8)= -11.1827 # GDT_score(maxd=10,maxw=4)= -10.9069 # GDT_score(maxd=10,maxw=4.2)= -10.6151 # GDT_score(maxd=12,maxw=4.3)= -11.7954 # GDT_score(maxd=12,maxw=4.5)= -11.4789 # GDT_score(maxd=12,maxw=4.7)= -11.174 # GDT_score(maxd=14,maxw=5.2)= -11.7169 # GDT_score(maxd=14,maxw=5.5)= -11.253 # command:# Removing conformation named robetta-model2.pdb # command:# ReadConformPDB reading from PDB file robetta-model3.pdb looking for model 1 # Found a chain break before 254 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -21.9444 # GDT_score(maxd=8,maxw=2.9)= -21.87 # GDT_score(maxd=8,maxw=3.2)= -20.5843 # GDT_score(maxd=8,maxw=3.5)= -19.3828 # GDT_score(maxd=10,maxw=3.8)= -21.5273 # GDT_score(maxd=10,maxw=4)= -20.7343 # GDT_score(maxd=10,maxw=4.2)= -19.9744 # GDT_score(maxd=12,maxw=4.3)= -22.3783 # GDT_score(maxd=12,maxw=4.5)= -21.5915 # GDT_score(maxd=12,maxw=4.7)= -20.8563 # GDT_score(maxd=14,maxw=5.2)= -21.4819 # GDT_score(maxd=14,maxw=5.5)= -20.5134 # command:# Removing conformation named robetta-model3.pdb # command:# ReadConformPDB reading from PDB file robetta-model4.pdb looking for model 1 # Found a chain break before 248 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -22.2222 # GDT_score(maxd=8,maxw=2.9)= -21.4285 # GDT_score(maxd=8,maxw=3.2)= -20.2012 # GDT_score(maxd=8,maxw=3.5)= -19.0234 # GDT_score(maxd=10,maxw=3.8)= -21.2211 # GDT_score(maxd=10,maxw=4)= -20.4434 # GDT_score(maxd=10,maxw=4.2)= -19.6974 # GDT_score(maxd=12,maxw=4.3)= -21.9897 # GDT_score(maxd=12,maxw=4.5)= -21.2201 # GDT_score(maxd=12,maxw=4.7)= -20.5063 # GDT_score(maxd=14,maxw=5.2)= -20.9956 # GDT_score(maxd=14,maxw=5.5)= -20.0634 # command:# Removing conformation named robetta-model4.pdb # command:# ReadConformPDB reading from PDB file robetta-model5.pdb looking for model 1 # Found a chain break before 250 # copying to AlignedFragments data structure # command:Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged # fraction of real conformation used = 1 # GDT_score = -21.8056 # GDT_score(maxd=8,maxw=2.9)= -20.8967 # GDT_score(maxd=8,maxw=3.2)= -19.7192 # GDT_score(maxd=8,maxw=3.5)= -18.5855 # GDT_score(maxd=10,maxw=3.8)= -20.7989 # GDT_score(maxd=10,maxw=4)= -20.0424 # GDT_score(maxd=10,maxw=4.2)= -19.3155 # GDT_score(maxd=12,maxw=4.3)= -21.732 # GDT_score(maxd=12,maxw=4.5)= -20.9739 # GDT_score(maxd=12,maxw=4.7)= -20.265 # GDT_score(maxd=14,maxw=5.2)= -20.8812 # GDT_score(maxd=14,maxw=5.5)= -19.9455 # command:# Removing conformation named robetta-model5.pdb # command:CPU_time= 209.346 sec, elapsed time= 467.865 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl smooth_GDT < decoys/evaluate.rdb > sort.tmp mv -f sort.tmp decoys/evaluate.rdb