/projects/compbio/experiments/protein-predict/casp8/starter-directory/Make.main:53: DOMAINS are 'D1' /projects/compbio/experiments/protein-predict/casp8/starter-directory/Make.main:255: job running on peep.cse.ucsc.edu SAM: checkseq v3.5 (July 15, 2005) compiled 05/31/06_11:54:08 Done with sequence reading /projects/compbio/experiments/protein-predict/casp8/starter-directory/Make.main:287: LENGTH= 145 SAM: checkseq v3.5 (July 15, 2005) compiled 05/31/06_11:54:08 Done with sequence reading /projects/compbio/experiments/protein-predict/casp8/starter-directory/Make.main:3246: DIMER_BREAK_BEFORE='S146' if [ ! -e decoys/read-servers.under ]; then false; fi # this file should be built from the target level (not the domain level) and so is not listed as a dependency rm -f D1/decoys/servers-real_cost.rdb sed -e s/XXX0000/T0514/ -e s/START_COL/1/ -e 's/ReadConformPDBids/ReadConformPDB\tT0514_D1.pdb\nNameConform\tT0514_D1/' -e 's|OutFilePrefix decoys|OutFilePrefix D1/decoys|' -e 's|EVALDIR|/projects/compbio/experiments/protein-predict/casp8/T0514/decoys/SAM_T08/|' -e s/evaluate_domain.COSTFCN/servers-real_cost/ -e s/_domain// -e 's|include COSTFCN.costfcn||' -e s/read-pdb/read-servers/ -e s/REAL_PDB/3dtdA/ -e 's/ReadConformPDB .*//' -e 's/[pP]rintConformPDB .*//' -e 's/PrintConformGDT .*//' -e 's/SCWRLConform.*//' -e 's/NameConform .*//' < /projects/compbio/experiments/protein-predict/casp8/starter-directory/scripts/evaluate.under | nice -2 /projects/compbio/programs/undertaker/undertaker # command:# Seed set to 1240641294 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading monomeric-50pc.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 8101 examples # computed average cis backbone unit from 20 examples # trans (non-proline) backbone unit: # CA= -2.2101 1.0129 -0.0033 # O= -0.1508 2.2440 0.0016 # C= -0.6897 1.1364 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4583 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1438 2.4522 0.0007 # O= -2.0283 0.9702 0.0005 # C= -0.8017 1.0759 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4664 -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 # 105973 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 8 # BAD_PEPTIDE 5792 # HIGH_B_FACTOR 0 # 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-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 5.419 sec, elapsed time= 8.683 sec. # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp8/T0514/decoys/SAM_T08// # command:# Making conformation for sequence T0514 numbered 1 through 145 undertaker: ConformCommands.cc:348: Conformation* RandomConformation(const ChainsResiduesAndAtoms*, bool): Assertion `frag>=0' failed. /bin/sh: line 1: 4695 Done sed -e s/XXX0000/T0514/ -e s/START_COL/1/ -e 's/ReadConformPDBids/ReadConformPDB\tT0514_D1.pdb\nNameConform\tT0514_D1/' -e 's|OutFilePrefix decoys|OutFilePrefix D1/decoys|' -e 's|EVALDIR|/projects/compbio/experiments/protein-predict/casp8/T0514/decoys/SAM_T08/|' -e s/evaluate_domain.COSTFCN/servers-real_cost/ -e s/_domain// -e 's|include COSTFCN.costfcn||' -e s/read-pdb/read-servers/ -e s/REAL_PDB/3dtdA/ -e 's/ReadConformPDB .*//' -e 's/[pP]rintConformPDB .*//' -e 's/PrintConformGDT .*//' -e 's/SCWRLConform.*//' -e 's/NameConform .*//'