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 rm -f decoys/evaluate.rdb sed -e s/XXX0000/T0281/ -e s/REAL_PDB/1whzA/ \ -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 1122886708 # 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= 7.61484 sec, elapsed time= 45.7096 sec) # command:# Prefix for input files set to # command:# ReadTargetPDB reading from PDB file T0281.blank.pdb looking for model 1 Warning: all-zero PDB file read in ReadTargetPDB, so making up random conformation Read PDB file T0281.blank.pdb model 1 as target. Have 70 residues and 575 atoms. # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:1whzA expands to /projects/compbio/data/pdb/1whz.pdb.gz 1whzA: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 70 residues and 576 atoms. # choosing archetypes in rotamer library # Found a chain break before 48 # copying to AlignedFragments data structure # 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= 10.5984 sec, elapsed time= 64.1931 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0281.t2k.undertaker-align.pdb looking for model 1 # command:# naming current conformation align1 # command:# fraction of real conformation used = 0.828571 # GDT_score = -32.5 # GDT_score(maxd=8,maxw=2.9)= -31.0248 # GDT_score(maxd=8,maxw=3.2)= -30.3615 # GDT_score(maxd=8,maxw=3.5)= -29.543 # GDT_score(maxd=10,maxw=3.8)= -31.1714 # GDT_score(maxd=10,maxw=4)= -30.6128 # GDT_score(maxd=10,maxw=4.2)= -30.0648 # GDT_score(maxd=12,maxw=4.3)= -32.0491 # GDT_score(maxd=12,maxw=4.5)= -31.4503 # GDT_score(maxd=12,maxw=4.7)= -30.8415 # GDT_score(maxd=14,maxw=5.2)= -31.3858 # GDT_score(maxd=14,maxw=5.5)= -30.5244 # command:# ReadConformPDB reading from PDB file T0281.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 # fraction of real conformation used = 0.314286 # GDT_score = -27.8571 # GDT_score(maxd=8,maxw=2.9)= -28.4309 # GDT_score(maxd=8,maxw=3.2)= -27.7841 # GDT_score(maxd=8,maxw=3.5)= -27.2009 # GDT_score(maxd=10,maxw=3.8)= -27.6006 # GDT_score(maxd=10,maxw=4)= -27.2206 # GDT_score(maxd=10,maxw=4.2)= -26.8282 # GDT_score(maxd=12,maxw=4.3)= -27.4159 # GDT_score(maxd=12,maxw=4.5)= -27.0175 # GDT_score(maxd=12,maxw=4.7)= -26.5865 # GDT_score(maxd=14,maxw=5.2)= -26.1487 # GDT_score(maxd=14,maxw=5.5)= -25.4602 # command:# ReadConformPDB reading from PDB file T0281.t2k.undertaker-align.pdb looking for model 3 # command:# naming current conformation align3 # command:# fraction of real conformation used = 0.771429 # GDT_score = -40.3571 # GDT_score(maxd=8,maxw=2.9)= -37.994 # GDT_score(maxd=8,maxw=3.2)= -36.3071 # GDT_score(maxd=8,maxw=3.5)= -34.9093 # GDT_score(maxd=10,maxw=3.8)= -38.1653 # GDT_score(maxd=10,maxw=4)= -37.2571 # GDT_score(maxd=10,maxw=4.2)= -36.4353 # GDT_score(maxd=12,maxw=4.3)= -39.496 # GDT_score(maxd=12,maxw=4.5)= -38.6295 # GDT_score(maxd=12,maxw=4.7)= -37.8368 # GDT_score(maxd=14,maxw=5.2)= -38.5 # GDT_score(maxd=14,maxw=5.5)= -37.413 # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file model1.ts-submitted looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -55.3571 # GDT_score(maxd=8,maxw=2.9)= -53.7752 # GDT_score(maxd=8,maxw=3.2)= -50.8162 # GDT_score(maxd=8,maxw=3.5)= -48.1748 # GDT_score(maxd=10,maxw=3.8)= -52.1228 # GDT_score(maxd=10,maxw=4)= -50.4172 # GDT_score(maxd=10,maxw=4.2)= -48.783 # GDT_score(maxd=12,maxw=4.3)= -52.8416 # GDT_score(maxd=12,maxw=4.5)= -51.1968 # GDT_score(maxd=12,maxw=4.7)= -49.6267 # GDT_score(maxd=14,maxw=5.2)= -49.6489 # GDT_score(maxd=14,maxw=5.5)= -47.6421 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 8.5500000e+02 rmsd (weighted)= 7.3264481e+00 (unweighted)= 7.5867687e+00 superimposing iter= 1 total_weight= 2.3972643e+03 rmsd (weighted)= 3.3452034e+00 (unweighted)= 7.7090078e+00 superimposing iter= 2 total_weight= 7.3783412e+02 rmsd (weighted)= 2.8737361e+00 (unweighted)= 7.8687368e+00 superimposing iter= 3 total_weight= 6.8627472e+02 rmsd (weighted)= 2.5859328e+00 (unweighted)= 8.0100516e+00 superimposing iter= 4 total_weight= 6.6137992e+02 rmsd (weighted)= 2.3844949e+00 (unweighted)= 8.1142447e+00 superimposing iter= 5 total_weight= 6.3987183e+02 rmsd (weighted)= 2.2427966e+00 (unweighted)= 8.1838581e+00 # 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 69 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -50 # GDT_score(maxd=8,maxw=2.9)= -44.1782 # GDT_score(maxd=8,maxw=3.2)= -42.5373 # GDT_score(maxd=8,maxw=3.5)= -41.0954 # GDT_score(maxd=10,maxw=3.8)= -45.66 # GDT_score(maxd=10,maxw=4)= -44.6594 # GDT_score(maxd=10,maxw=4.2)= -43.6892 # GDT_score(maxd=12,maxw=4.3)= -47.6955 # GDT_score(maxd=12,maxw=4.5)= -46.655 # GDT_score(maxd=12,maxw=4.7)= -45.663 # GDT_score(maxd=14,maxw=5.2)= -46.6377 # GDT_score(maxd=14,maxw=5.5)= -45.0295 # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -45.3571 # GDT_score(maxd=8,maxw=2.9)= -42.8705 # GDT_score(maxd=8,maxw=3.2)= -40.3246 # GDT_score(maxd=8,maxw=3.5)= -38.1367 # GDT_score(maxd=10,maxw=3.8)= -42.5971 # GDT_score(maxd=10,maxw=4)= -41.1658 # GDT_score(maxd=10,maxw=4.2)= -39.8178 # GDT_score(maxd=12,maxw=4.3)= -44.2026 # GDT_score(maxd=12,maxw=4.5)= -42.8095 # GDT_score(maxd=12,maxw=4.7)= -41.4926 # GDT_score(maxd=14,maxw=5.2)= -42.2664 # GDT_score(maxd=14,maxw=5.5)= -40.5065 # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -48.9286 # GDT_score(maxd=8,maxw=2.9)= -46.5957 # GDT_score(maxd=8,maxw=3.2)= -44.174 # GDT_score(maxd=8,maxw=3.5)= -42.102 # GDT_score(maxd=10,maxw=3.8)= -46.2439 # GDT_score(maxd=10,maxw=4)= -44.8762 # GDT_score(maxd=10,maxw=4.2)= -43.4537 # GDT_score(maxd=12,maxw=4.3)= -47.7171 # GDT_score(maxd=12,maxw=4.5)= -46.2398 # GDT_score(maxd=12,maxw=4.7)= -44.88 # GDT_score(maxd=14,maxw=5.2)= -45.4132 # GDT_score(maxd=14,maxw=5.5)= -43.4816 # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -35.7143 # GDT_score(maxd=8,maxw=2.9)= -34.9789 # GDT_score(maxd=8,maxw=3.2)= -33.8425 # GDT_score(maxd=8,maxw=3.5)= -32.7059 # GDT_score(maxd=10,maxw=3.8)= -34.5551 # GDT_score(maxd=10,maxw=4)= -33.7653 # GDT_score(maxd=10,maxw=4.2)= -32.9959 # GDT_score(maxd=12,maxw=4.3)= -35.4157 # GDT_score(maxd=12,maxw=4.5)= -34.6125 # GDT_score(maxd=12,maxw=4.7)= -33.8372 # GDT_score(maxd=14,maxw=5.2)= -34.2364 # GDT_score(maxd=14,maxw=5.5)= -33.131 # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0281.try1-opt2.pdb looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -35.7143 # GDT_score(maxd=8,maxw=2.9)= -34.9789 # GDT_score(maxd=8,maxw=3.2)= -33.8424 # GDT_score(maxd=8,maxw=3.5)= -32.7049 # GDT_score(maxd=10,maxw=3.8)= -34.5544 # GDT_score(maxd=10,maxw=4)= -33.7651 # GDT_score(maxd=10,maxw=4.2)= -32.996 # GDT_score(maxd=12,maxw=4.3)= -35.4156 # GDT_score(maxd=12,maxw=4.5)= -34.6127 # GDT_score(maxd=12,maxw=4.7)= -33.8363 # GDT_score(maxd=14,maxw=5.2)= -34.2355 # GDT_score(maxd=14,maxw=5.5)= -33.1306 # command:# Removing conformation named T0281.try1-opt2.pdb # command:# reading script from file read-pdb.under # ReadConformPDB reading from PDB file robetta-model10.pdb.gz looking for model 1 # Found a chain break before 19 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model1.pdb.gz looking for model 1 # Found a chain break before 42 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # Found a chain break before 32 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model6.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model7.pdb.gz looking for model 1 # Found a chain break before 41 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model8.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file robetta-model9.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try10-opt1.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try10-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try10-opt2.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try10-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try11-opt1.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try11-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try11-opt2.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try11-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try12-opt1.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try12-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try12-opt2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try12-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try13-opt1.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try13-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try13-opt2.force-repack.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try13-opt2.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try13-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try14-opt1.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try14-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try14-opt2.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try14-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try15-opt1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try15-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try15-opt2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try15-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try16-opt1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try16-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try16-opt2.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try16-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try17-opt1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try17-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try17-opt2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try17-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try18-opt1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try18-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try18-opt2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try18-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try19-opt1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try19-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try19-opt2.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try19-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try20-opt1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try20-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try20-opt2.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try20-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try21-opt1.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try21-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try21-opt2.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try21-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 69 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try22-opt1.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try22-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try22-opt2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try22-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try23-opt1.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try23-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try23-opt2.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try23-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try24-opt1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try24-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try24-opt2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try24-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 44 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0281.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file try15-try14-chimera.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # command:CPU_time= 14.0949 sec, elapsed time= 86.1712 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 try15-try14-chimera.pdb.gz costs 0 real_cost = 0.462578 T0281.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.431353 T0281.try9-opt2.pdb.gz costs 0 real_cost = 0.430588 T0281.try9-opt1-scwrl.pdb.gz costs 0 real_cost = 0.430592 T0281.try9-opt1.pdb.gz costs 0 real_cost = 0.428894 T0281.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.377887 T0281.try8-opt2.pdb.gz costs 0 real_cost = 0.374733 T0281.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 0.376833 T0281.try8-opt1.pdb.gz costs 0 real_cost = 0.372848 T0281.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.368767 T0281.try7-opt2.pdb.gz costs 0 real_cost = 0.367216 T0281.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 0.36984 T0281.try7-opt1.pdb.gz costs 0 real_cost = 0.368606 T0281.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.386929 T0281.try6-opt2.pdb.gz costs 0 real_cost = 0.382472 T0281.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 0.385667 T0281.try6-opt1.pdb.gz costs 0 real_cost = 0.380911 T0281.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.386277 T0281.try5-opt2.pdb.gz costs 0 real_cost = 0.381241 T0281.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 0.391237 T0281.try5-opt1.pdb.gz costs 0 real_cost = 0.388169 T0281.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.591621 T0281.try4-opt2.pdb.gz costs 0 real_cost = 0.590038 T0281.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 0.597073 T0281.try4-opt1.pdb.gz costs 0 real_cost = 0.597398 T0281.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.600471 T0281.try3-opt2.pdb.gz costs 0 real_cost = 0.601282 T0281.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 0.597918 T0281.try3-opt1.pdb.gz costs 0 real_cost = 0.598241 T0281.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.506135 T0281.try2-opt2.pdb.gz costs 0 real_cost = 0.506431 T0281.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 0.5114 T0281.try2-opt1.pdb.gz costs 0 real_cost = 0.511837 T0281.try24-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.356496 T0281.try24-opt2.pdb.gz costs 0 real_cost = 0.35123 T0281.try24-opt1-scwrl.pdb.gz costs 0 real_cost = 0.366202 T0281.try24-opt1.pdb.gz costs 0 real_cost = 0.361327 T0281.try23-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.587714 T0281.try23-opt2.pdb.gz costs 0 real_cost = 0.58711 T0281.try23-opt1-scwrl.pdb.gz costs 0 real_cost = 0.577003 T0281.try23-opt1.pdb.gz costs 0 real_cost = 0.576854 T0281.try22-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.381567 T0281.try22-opt2.pdb.gz costs 0 real_cost = 0.380395 T0281.try22-opt1-scwrl.pdb.gz costs 0 real_cost = 0.394864 T0281.try22-opt1.pdb.gz costs 0 real_cost = 0.395403 T0281.try21-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.37557 T0281.try21-opt2.pdb.gz costs 0 real_cost = 0.372723 T0281.try21-opt1-scwrl.pdb.gz costs 0 real_cost = 0.376656 T0281.try21-opt1.pdb.gz costs 0 real_cost = 0.372958 T0281.try20-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.463451 T0281.try20-opt2.pdb.gz costs 0 real_cost = 0.46257 T0281.try20-opt1-scwrl.pdb.gz costs 0 real_cost = 0.464817 T0281.try20-opt1.pdb.gz costs 0 real_cost = 0.461857 T0281.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.710329 T0281.try1-opt2.pdb.gz costs 0 real_cost = 0.708664 T0281.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 0.70713 T0281.try1-opt1.pdb.gz costs 0 real_cost = 0.706937 T0281.try19-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.419601 T0281.try19-opt2.pdb.gz costs 0 real_cost = 0.418722 T0281.try19-opt1-scwrl.pdb.gz costs 0 real_cost = 0.420317 T0281.try19-opt1.pdb.gz costs 0 real_cost = 0.418326 T0281.try18-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.463649 T0281.try18-opt2.pdb.gz costs 0 real_cost = 0.462406 T0281.try18-opt1-scwrl.pdb.gz costs 0 real_cost = 0.471197 T0281.try18-opt1.pdb.gz costs 0 real_cost = 0.468258 T0281.try17-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.471635 T0281.try17-opt2.pdb.gz costs 0 real_cost = 0.47071 T0281.try17-opt1-scwrl.pdb.gz costs 0 real_cost = 0.471584 T0281.try17-opt1.pdb.gz costs 0 real_cost = 0.468166 T0281.try16-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.471049 T0281.try16-opt2.pdb.gz costs 0 real_cost = 0.469007 T0281.try16-opt1-scwrl.pdb.gz costs 0 real_cost = 0.47464 T0281.try16-opt1.pdb.gz costs 0 real_cost = 0.471159 T0281.try15-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.422964 T0281.try15-opt2.pdb.gz costs 0 real_cost = 0.421951 T0281.try15-opt1-scwrl.pdb.gz costs 0 real_cost = 0.42476 T0281.try15-opt1.pdb.gz costs 0 real_cost = 0.421484 T0281.try14-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.3761 T0281.try14-opt2.pdb.gz costs 0 real_cost = 0.373218 T0281.try14-opt1-scwrl.pdb.gz costs 0 real_cost = 0.376037 T0281.try14-opt1.pdb.gz costs 0 real_cost = 0.371658 T0281.try13-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.377934 T0281.try13-opt2.pdb.gz costs 0 real_cost = 0.373469 T0281.try13-opt2.force-repack.pdb.gz costs 0 real_cost = 0.378518 T0281.try13-opt1-scwrl.pdb.gz costs 0 real_cost = 0.377991 T0281.try13-opt1.pdb.gz costs 0 real_cost = 0.3732 T0281.try12-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.423119 T0281.try12-opt2.pdb.gz costs 0 real_cost = 0.422173 T0281.try12-opt1-scwrl.pdb.gz costs 0 real_cost = 0.426824 T0281.try12-opt1.pdb.gz costs 0 real_cost = 0.423277 T0281.try11-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.433172 T0281.try11-opt2.pdb.gz costs 0 real_cost = 0.432089 T0281.try11-opt1-scwrl.pdb.gz costs 0 real_cost = 0.43413 T0281.try11-opt1.pdb.gz costs 0 real_cost = 0.431753 T0281.try10-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.37852 T0281.try10-opt2.pdb.gz costs 0 real_cost = 0.374298 T0281.try10-opt1-scwrl.pdb.gz costs 0 real_cost = 0.378849 T0281.try10-opt1.pdb.gz costs 0 real_cost = 0.373836 robetta-model9.pdb.gz costs 0 real_cost = 0.789601 robetta-model8.pdb.gz costs 0 real_cost = 0.270967 robetta-model7.pdb.gz costs 0 real_cost = 0.63092 robetta-model6.pdb.gz costs 0 real_cost = 0.347187 robetta-model5.pdb.gz costs 0 real_cost = 0.706294 robetta-model4.pdb.gz costs 0 real_cost = 0.342176 robetta-model3.pdb.gz costs 0 real_cost = 0.825068 robetta-model2.pdb.gz costs 0 real_cost = 0.366762 robetta-model1.pdb.gz costs 0 real_cost = 0.812477 robetta-model10.pdb.gz costs 0 real_cost = 0.259972 model5.ts-submitted costs 0 real_cost = 0.708669 model4.ts-submitted costs 0 real_cost = 0.416949 model3.ts-submitted costs 0 real_cost = 0.463445 model2.ts-submitted costs 0 real_cost = 0.372717 model1.ts-submitted costs 0 real_cost = 0.351214 align3 costs 0 real_cost = 0.508942 align2 costs 0 real_cost = 0.395652 align1 costs 0 real_cost = 0.792436 1whzA costs 0 real_cost = -2.82 # command:CPU_time= 45.845 sec, elapsed time= 190.498 sec) # command:# ReadConformPDB reading from PDB file robetta-model1.pdb looking for model 1 # Found a chain break before 42 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -26.0714 # GDT_score(maxd=8,maxw=2.9)= -24.6413 # GDT_score(maxd=8,maxw=3.2)= -23.8257 # GDT_score(maxd=8,maxw=3.5)= -22.8856 # GDT_score(maxd=10,maxw=3.8)= -25.3318 # GDT_score(maxd=10,maxw=4)= -24.6781 # GDT_score(maxd=10,maxw=4.2)= -23.9872 # GDT_score(maxd=12,maxw=4.3)= -26.995 # GDT_score(maxd=12,maxw=4.5)= -26.2397 # GDT_score(maxd=12,maxw=4.7)= -25.5486 # GDT_score(maxd=14,maxw=5.2)= -26.8382 # GDT_score(maxd=14,maxw=5.5)= -25.8418 # command:# Removing conformation named robetta-model1.pdb # command:# ReadConformPDB reading from PDB file robetta-model2.pdb looking for model 1 # command:# fraction of real conformation used = 1 # GDT_score = -46.4286 # GDT_score(maxd=8,maxw=2.9)= -43.0545 # GDT_score(maxd=8,maxw=3.2)= -40.5814 # GDT_score(maxd=8,maxw=3.5)= -38.331 # GDT_score(maxd=10,maxw=3.8)= -43.3209 # GDT_score(maxd=10,maxw=4)= -41.8202 # GDT_score(maxd=10,maxw=4.2)= -40.4249 # GDT_score(maxd=12,maxw=4.3)= -45.0431 # GDT_score(maxd=12,maxw=4.5)= -43.5859 # GDT_score(maxd=12,maxw=4.7)= -42.1964 # GDT_score(maxd=14,maxw=5.2)= -42.9497 # GDT_score(maxd=14,maxw=5.5)= -41.0512 # 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 36 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -29.6429 # GDT_score(maxd=8,maxw=2.9)= -31.2201 # GDT_score(maxd=8,maxw=3.2)= -29.7877 # GDT_score(maxd=8,maxw=3.5)= -28.3365 # GDT_score(maxd=10,maxw=3.8)= -29.6544 # GDT_score(maxd=10,maxw=4)= -28.7845 # GDT_score(maxd=10,maxw=4.2)= -27.8981 # GDT_score(maxd=12,maxw=4.3)= -29.7359 # GDT_score(maxd=12,maxw=4.5)= -28.8587 # GDT_score(maxd=12,maxw=4.7)= -28.0562 # GDT_score(maxd=14,maxw=5.2)= -28.1463 # GDT_score(maxd=14,maxw=5.5)= -27.0312 # 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 49 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -47.5 # GDT_score(maxd=8,maxw=2.9)= -43.3776 # GDT_score(maxd=8,maxw=3.2)= -41.3822 # GDT_score(maxd=8,maxw=3.5)= -39.2652 # GDT_score(maxd=10,maxw=3.8)= -43.8472 # GDT_score(maxd=10,maxw=4)= -42.3691 # GDT_score(maxd=10,maxw=4.2)= -40.9848 # GDT_score(maxd=12,maxw=4.3)= -45.3713 # GDT_score(maxd=12,maxw=4.5)= -43.9341 # GDT_score(maxd=12,maxw=4.7)= -42.6117 # GDT_score(maxd=14,maxw=5.2)= -43.385 # GDT_score(maxd=14,maxw=5.5)= -41.6341 # 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 32 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -32.5 # GDT_score(maxd=8,maxw=2.9)= -29.6694 # GDT_score(maxd=8,maxw=3.2)= -28.3824 # GDT_score(maxd=8,maxw=3.5)= -27.0517 # GDT_score(maxd=10,maxw=3.8)= -30.0678 # GDT_score(maxd=10,maxw=4)= -29.1773 # GDT_score(maxd=10,maxw=4.2)= -28.2721 # GDT_score(maxd=12,maxw=4.3)= -31.4877 # GDT_score(maxd=12,maxw=4.5)= -30.5327 # GDT_score(maxd=12,maxw=4.7)= -29.659 # GDT_score(maxd=14,maxw=5.2)= -30.8057 # GDT_score(maxd=14,maxw=5.5)= -29.5455 # command:# Removing conformation named robetta-model5.pdb # command:CPU_time= 46.6309 sec, elapsed time= 196.4 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl smooth_GDT < decoys/evaluate.rdb > sort.tmp mv -f sort.tmp decoys/evaluate.rdb