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/T0282/ -e s/REAL_PDB/1xfkA/ \ -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 1123189134 # 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= 7.67083 sec, elapsed time= 51.1567 sec) # command:# Prefix for input files set to # command:# ReadTargetPDB reading from PDB file T0282.blank.pdb looking for model 1 Warning: all-zero PDB file read in ReadTargetPDB, so making up random conformation Read PDB file T0282.blank.pdb model 1 as target. Have 332 residues and 2600 atoms. # command:# command:# No conformations to remove in PopConform # command:# cleared Id set # command:# command:1xfkA expands to /projects/compbio/data/pdb/1xfk.pdb.gz 1xfkA: Read 324 residues and 2533 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= 9.11061 sec, elapsed time= 60.7193 sec) # command:# Prefix for input files set to # command:# ReadConformPDB reading from PDB file T0282.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 Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged 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 = 0.869969 # GDT_score = -60.5263 # GDT_score(maxd=8,maxw=2.9)= -63.1884 # GDT_score(maxd=8,maxw=3.2)= -60.2331 # GDT_score(maxd=8,maxw=3.5)= -57.163 # GDT_score(maxd=10,maxw=3.8)= -59.5686 # GDT_score(maxd=10,maxw=4)= -57.6388 # GDT_score(maxd=10,maxw=4.2)= -55.7875 # GDT_score(maxd=12,maxw=4.3)= -59.0097 # GDT_score(maxd=12,maxw=4.5)= -57.2036 # GDT_score(maxd=12,maxw=4.7)= -55.4506 # GDT_score(maxd=14,maxw=5.2)= -54.4007 # GDT_score(maxd=14,maxw=5.5)= -51.8133 # command:# ReadConformPDB reading from PDB file T0282.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 Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged 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 = 0.820433 # GDT_score = -60.9907 # GDT_score(maxd=8,maxw=2.9)= -64.0183 # GDT_score(maxd=8,maxw=3.2)= -61.2466 # GDT_score(maxd=8,maxw=3.5)= -58.1179 # GDT_score(maxd=10,maxw=3.8)= -60.2007 # GDT_score(maxd=10,maxw=4)= -58.2824 # GDT_score(maxd=10,maxw=4.2)= -56.4193 # GDT_score(maxd=12,maxw=4.3)= -59.3785 # GDT_score(maxd=12,maxw=4.5)= -57.5545 # GDT_score(maxd=12,maxw=4.7)= -55.7104 # GDT_score(maxd=14,maxw=5.2)= -54.4487 # GDT_score(maxd=14,maxw=5.5)= -51.9173 # command:# ReadConformPDB reading from PDB file T0282.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 Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged Warning: eigen4 may not have converged 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 = 0.842105 # GDT_score = -57.4303 # GDT_score(maxd=8,maxw=2.9)= -59.485 # GDT_score(maxd=8,maxw=3.2)= -56.697 # GDT_score(maxd=8,maxw=3.5)= -53.7191 # GDT_score(maxd=10,maxw=3.8)= -56.3098 # GDT_score(maxd=10,maxw=4)= -54.3247 # GDT_score(maxd=10,maxw=4.2)= -52.3961 # GDT_score(maxd=12,maxw=4.3)= -55.6838 # GDT_score(maxd=12,maxw=4.5)= -53.807 # GDT_score(maxd=12,maxw=4.7)= -51.9687 # GDT_score(maxd=14,maxw=5.2)= -50.9185 # GDT_score(maxd=14,maxw=5.5)= -48.3775 # 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 325 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -51.548 # GDT_score(maxd=8,maxw=2.9)= -54.3925 # GDT_score(maxd=8,maxw=3.2)= -50.7228 # GDT_score(maxd=8,maxw=3.5)= -47.3162 # GDT_score(maxd=10,maxw=3.8)= -50.3934 # GDT_score(maxd=10,maxw=4)= -48.3302 # GDT_score(maxd=10,maxw=4.2)= -46.3854 # GDT_score(maxd=12,maxw=4.3)= -50.2519 # GDT_score(maxd=12,maxw=4.5)= -48.3368 # GDT_score(maxd=12,maxw=4.7)= -46.5566 # GDT_score(maxd=14,maxw=5.2)= -46.1226 # GDT_score(maxd=14,maxw=5.5)= -43.8288 # command:# Prefix for output files set to # command:superimposing iter= 0 total_weight= 3.8170000e+03 rmsd (weighted)= 1.2891002e+01 (unweighted)= 1.8355086e+01 superimposing iter= 1 total_weight= 1.3660232e+04 rmsd (weighted)= 3.9657449e+00 (unweighted)= 1.9281503e+01 superimposing iter= 2 total_weight= 8.6441498e+03 rmsd (weighted)= 1.9513169e+00 (unweighted)= 1.9502204e+01 superimposing iter= 3 total_weight= 4.6464629e+03 rmsd (weighted)= 1.4036478e+00 (unweighted)= 1.9573336e+01 superimposing iter= 4 total_weight= 3.1520079e+03 rmsd (weighted)= 1.2438687e+00 (unweighted)= 1.9607540e+01 superimposing iter= 5 total_weight= 2.7307877e+03 rmsd (weighted)= 1.1884112e+00 (unweighted)= 1.9625810e+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 325 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -52.1672 # GDT_score(maxd=8,maxw=2.9)= -54.9964 # GDT_score(maxd=8,maxw=3.2)= -51.3338 # GDT_score(maxd=8,maxw=3.5)= -47.8889 # GDT_score(maxd=10,maxw=3.8)= -50.9184 # GDT_score(maxd=10,maxw=4)= -48.8141 # GDT_score(maxd=10,maxw=4.2)= -46.8681 # GDT_score(maxd=12,maxw=4.3)= -50.7021 # GDT_score(maxd=12,maxw=4.5)= -48.7911 # GDT_score(maxd=12,maxw=4.7)= -46.9809 # GDT_score(maxd=14,maxw=5.2)= -46.4823 # GDT_score(maxd=14,maxw=5.5)= -44.1616 # command:# ReadConformPDB reading from PDB file model3.ts-submitted looking for model 1 # Found a chain break before 327 # 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 = -54.5666 # GDT_score(maxd=8,maxw=2.9)= -57.1563 # GDT_score(maxd=8,maxw=3.2)= -53.6536 # GDT_score(maxd=8,maxw=3.5)= -50.2997 # GDT_score(maxd=10,maxw=3.8)= -53.1446 # GDT_score(maxd=10,maxw=4)= -51.0771 # GDT_score(maxd=10,maxw=4.2)= -49.0947 # GDT_score(maxd=12,maxw=4.3)= -52.7886 # GDT_score(maxd=12,maxw=4.5)= -50.8521 # GDT_score(maxd=12,maxw=4.7)= -49.0389 # GDT_score(maxd=14,maxw=5.2)= -48.3906 # GDT_score(maxd=14,maxw=5.5)= -45.9406 # command:# ReadConformPDB reading from PDB file model4.ts-submitted looking for model 1 # 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 # fraction of real conformation used = 0.863777 # GDT_score = -61.3003 # GDT_score(maxd=8,maxw=2.9)= -63.2864 # GDT_score(maxd=8,maxw=3.2)= -60.5698 # GDT_score(maxd=8,maxw=3.5)= -57.7057 # GDT_score(maxd=10,maxw=3.8)= -60.0244 # GDT_score(maxd=10,maxw=4)= -58.1483 # GDT_score(maxd=10,maxw=4.2)= -56.3166 # GDT_score(maxd=12,maxw=4.3)= -59.4567 # GDT_score(maxd=12,maxw=4.5)= -57.6613 # GDT_score(maxd=12,maxw=4.7)= -55.8897 # GDT_score(maxd=14,maxw=5.2)= -54.784 # GDT_score(maxd=14,maxw=5.5)= -52.1775 # command:# ReadConformPDB reading from PDB file model5.ts-submitted looking for model 1 # command:# fraction of real conformation used = 0.817337 # GDT_score = -60.9907 # GDT_score(maxd=8,maxw=2.9)= -64.1143 # GDT_score(maxd=8,maxw=3.2)= -61.335 # GDT_score(maxd=8,maxw=3.5)= -58.1984 # GDT_score(maxd=10,maxw=3.8)= -60.2494 # GDT_score(maxd=10,maxw=4)= -58.3281 # GDT_score(maxd=10,maxw=4.2)= -56.463 # GDT_score(maxd=12,maxw=4.3)= -59.4022 # GDT_score(maxd=12,maxw=4.5)= -57.5772 # GDT_score(maxd=12,maxw=4.7)= -55.7322 # GDT_score(maxd=14,maxw=5.2)= -54.455 # GDT_score(maxd=14,maxw=5.5)= -51.9228 # command:# Prefix for input files set to decoys/ # command:# ReadConformPDB reading from PDB file T0282.try1-opt2.pdb looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -54.5666 # GDT_score(maxd=8,maxw=2.9)= -57.1524 # GDT_score(maxd=8,maxw=3.2)= -53.6494 # GDT_score(maxd=8,maxw=3.5)= -50.2967 # GDT_score(maxd=10,maxw=3.8)= -53.1416 # GDT_score(maxd=10,maxw=4)= -51.0744 # GDT_score(maxd=10,maxw=4.2)= -49.0927 # GDT_score(maxd=12,maxw=4.3)= -52.7859 # GDT_score(maxd=12,maxw=4.5)= -50.8501 # GDT_score(maxd=12,maxw=4.7)= -49.0381 # GDT_score(maxd=14,maxw=5.2)= -48.389 # GDT_score(maxd=14,maxw=5.5)= -45.9389 # command:# Removing conformation named T0282.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 285 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model2.pdb.gz looking for model 1 # Found a chain break before 286 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model3.pdb.gz looking for model 1 # Found a chain break before 293 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model4.pdb.gz looking for model 1 # Found a chain break before 285 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file robetta-model5.pdb.gz looking for model 1 # Found a chain break before 292 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try1-opt1.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try1-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try1-opt2.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try1-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try2-opt1.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try2-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try2-opt2.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try2-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try3-opt1.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try3-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 327 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try3-opt2.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try3-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try4-opt1.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try4-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try4-opt2.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try4-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try5-opt1.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try5-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try5-opt2.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try5-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try6-opt1.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try6-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try6-opt2.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try6-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try7-opt1.pdb.gz looking for model 1 # Found a chain break before 298 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try7-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 298 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try7-opt2.pdb.gz looking for model 1 # Found a chain break before 304 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try7-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 304 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try8-opt1.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try8-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try8-opt2.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try8-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try9-opt1.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try9-opt1-scwrl.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try9-opt2.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file T0282.try9-opt2.repack-nonPC.pdb.gz looking for model 1 # Found a chain break before 325 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file try8-patched.pdb.gz looking for model 1 # Found a chain break before 324 # copying to AlignedFragments data structure # command:CPU_time= 95.1025 sec, elapsed time= 320.106 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 try8-patched.pdb.gz costs 0 real_cost = 0.457338 T0282.try9-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.476355 T0282.try9-opt2.pdb.gz costs 0 real_cost = 0.476502 T0282.try9-opt1-scwrl.pdb.gz costs 0 real_cost = 0.474589 T0282.try9-opt1.pdb.gz costs 0 real_cost = 0.474751 T0282.try8-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.468738 T0282.try8-opt2.pdb.gz costs 0 real_cost = 0.469238 T0282.try8-opt1-scwrl.pdb.gz costs 0 real_cost = 0.476997 T0282.try8-opt1.pdb.gz costs 0 real_cost = 0.476902 T0282.try7-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.656687 T0282.try7-opt2.pdb.gz costs 0 real_cost = 0.656421 T0282.try7-opt1-scwrl.pdb.gz costs 0 real_cost = 0.658833 T0282.try7-opt1.pdb.gz costs 0 real_cost = 0.658877 T0282.try6-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.468881 T0282.try6-opt2.pdb.gz costs 0 real_cost = 0.468871 T0282.try6-opt1-scwrl.pdb.gz costs 0 real_cost = 0.466596 T0282.try6-opt1.pdb.gz costs 0 real_cost = 0.466649 T0282.try5-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.481317 T0282.try5-opt2.pdb.gz costs 0 real_cost = 0.481695 T0282.try5-opt1-scwrl.pdb.gz costs 0 real_cost = 0.484234 T0282.try5-opt1.pdb.gz costs 0 real_cost = 0.484512 T0282.try4-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.467872 T0282.try4-opt2.pdb.gz costs 0 real_cost = 0.46811 T0282.try4-opt1-scwrl.pdb.gz costs 0 real_cost = 0.471989 T0282.try4-opt1.pdb.gz costs 0 real_cost = 0.471876 T0282.try3-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.466009 T0282.try3-opt2.pdb.gz costs 0 real_cost = 0.466076 T0282.try3-opt1-scwrl.pdb.gz costs 0 real_cost = 0.466435 T0282.try3-opt1.pdb.gz costs 0 real_cost = 0.466516 T0282.try2-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.465324 T0282.try2-opt2.pdb.gz costs 0 real_cost = 0.465103 T0282.try2-opt1-scwrl.pdb.gz costs 0 real_cost = 0.461645 T0282.try2-opt1.pdb.gz costs 0 real_cost = 0.461702 T0282.try1-opt2.repack-nonPC.pdb.gz costs 0 real_cost = 0.440922 T0282.try1-opt2.pdb.gz costs 0 real_cost = 0.44133 T0282.try1-opt1-scwrl.pdb.gz costs 0 real_cost = 0.452684 T0282.try1-opt1.pdb.gz costs 0 real_cost = 0.453142 robetta-model5.pdb.gz costs 0 real_cost = 0.298277 robetta-model4.pdb.gz costs 0 real_cost = 0.345689 robetta-model3.pdb.gz costs 0 real_cost = 0.231627 robetta-model2.pdb.gz costs 0 real_cost = 0.283578 robetta-model1.pdb.gz costs 0 real_cost = 0.375383 model5.ts-submitted costs 0 real_cost = 0.083817 model4.ts-submitted costs 0 real_cost = 0.118031 model3.ts-submitted costs 0 real_cost = 0.441327 model2.ts-submitted costs 0 real_cost = 0.468778 model1.ts-submitted costs 0 real_cost = 0.476569 align3 costs 0 real_cost = 0.119843 align2 costs 0 real_cost = -0.00582124 align1 costs 0 real_cost = 0.127553 1xfkA costs 0 real_cost = -2.82 # command:CPU_time= 1142 sec, elapsed time= 1623.78 sec) # command:# ReadConformPDB reading from PDB file robetta-model1.pdb looking for model 1 # Found a chain break before 285 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -55.7276 # GDT_score(maxd=8,maxw=2.9)= -57.5241 # GDT_score(maxd=8,maxw=3.2)= -53.8777 # GDT_score(maxd=8,maxw=3.5)= -50.4756 # GDT_score(maxd=10,maxw=3.8)= -53.9968 # GDT_score(maxd=10,maxw=4)= -51.7827 # GDT_score(maxd=10,maxw=4.2)= -49.6806 # GDT_score(maxd=12,maxw=4.3)= -53.8375 # GDT_score(maxd=12,maxw=4.5)= -51.7754 # GDT_score(maxd=12,maxw=4.7)= -49.8208 # GDT_score(maxd=14,maxw=5.2)= -49.2039 # GDT_score(maxd=14,maxw=5.5)= -46.6948 # 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 286 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -59.6749 # GDT_score(maxd=8,maxw=2.9)= -61.6388 # GDT_score(maxd=8,maxw=3.2)= -58.1398 # GDT_score(maxd=8,maxw=3.5)= -54.8062 # GDT_score(maxd=10,maxw=3.8)= -58.0821 # GDT_score(maxd=10,maxw=4)= -55.9586 # GDT_score(maxd=10,maxw=4.2)= -53.8987 # GDT_score(maxd=12,maxw=4.3)= -57.8317 # GDT_score(maxd=12,maxw=4.5)= -55.804 # GDT_score(maxd=12,maxw=4.7)= -53.8156 # GDT_score(maxd=14,maxw=5.2)= -53.0049 # GDT_score(maxd=14,maxw=5.5)= -50.3974 # 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 293 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -56.9659 # GDT_score(maxd=8,maxw=2.9)= -58.4119 # GDT_score(maxd=8,maxw=3.2)= -55.1109 # GDT_score(maxd=8,maxw=3.5)= -52.0577 # GDT_score(maxd=10,maxw=3.8)= -55.3416 # GDT_score(maxd=10,maxw=4)= -53.4016 # GDT_score(maxd=10,maxw=4.2)= -51.4689 # GDT_score(maxd=12,maxw=4.3)= -55.4097 # GDT_score(maxd=12,maxw=4.5)= -53.4897 # GDT_score(maxd=12,maxw=4.7)= -51.6007 # GDT_score(maxd=14,maxw=5.2)= -51.051 # GDT_score(maxd=14,maxw=5.5)= -48.55 # 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 285 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -54.5666 # GDT_score(maxd=8,maxw=2.9)= -56.3284 # GDT_score(maxd=8,maxw=3.2)= -52.7086 # GDT_score(maxd=8,maxw=3.5)= -49.3484 # GDT_score(maxd=10,maxw=3.8)= -52.8359 # GDT_score(maxd=10,maxw=4)= -50.6511 # GDT_score(maxd=10,maxw=4.2)= -48.5747 # GDT_score(maxd=12,maxw=4.3)= -52.7352 # GDT_score(maxd=12,maxw=4.5)= -50.6984 # GDT_score(maxd=12,maxw=4.7)= -48.7764 # GDT_score(maxd=14,maxw=5.2)= -48.237 # GDT_score(maxd=14,maxw=5.5)= -45.7764 # 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 292 # copying to AlignedFragments data structure # command:# fraction of real conformation used = 1 # GDT_score = -52.8638 # GDT_score(maxd=8,maxw=2.9)= -55.6263 # GDT_score(maxd=8,maxw=3.2)= -52.0308 # GDT_score(maxd=8,maxw=3.5)= -48.7076 # GDT_score(maxd=10,maxw=3.8)= -52.0344 # GDT_score(maxd=10,maxw=4)= -49.9126 # GDT_score(maxd=10,maxw=4.2)= -47.8957 # GDT_score(maxd=12,maxw=4.3)= -51.9761 # GDT_score(maxd=12,maxw=4.5)= -49.9932 # GDT_score(maxd=12,maxw=4.7)= -48.1109 # GDT_score(maxd=14,maxw=5.2)= -47.7023 # GDT_score(maxd=14,maxw=5.5)= -45.2709 # command:# Removing conformation named robetta-model5.pdb # command:CPU_time= 1197.33 sec, elapsed time= 1699.19 sec) # command:rm -f sort.tmp /projects/compbio/bin/sorttbl smooth_GDT < decoys/evaluate.rdb > sort.tmp mv -f sort.tmp decoys/evaluate.rdb