mkdir tmp mkdir und /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a3lL.0.4.a2m \ -target T0110 -template 1a3lL \ -out T0110-1a3lL.0.4 -outdir und partial PDB gets fragment 206 through 215 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values MET 1 11 ARG 3 32 GLU 4 13 PHE 5 3 ARG 7 28 SER 8 2 ASP 9 5 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists gmake: [und/T0110-1a3lL.0.5.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists gmake: [und/T0110-1a3lL.0.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a3lL.0.5.a2m \ -target T0110 -template 1a3lL \ -out T0110-1a3lL.0.5 -outdir und partial PDB gets fragment 204 through 216 extending start Debugging on ! Reading sequence file Reading input structure 14 residues read Measuring phi and psi Getting chi values MET 1 9 ARG 3 32 GLU 4 13 PHE 5 4 LYS 6 26 ARG 7 27 SER 8 3 ASP 9 5 ARG 10 32 VAL 11 2 GLN 13 8 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists gmake: [und/T0110-1a3lL.2.5.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists gmake: [und/T0110-1a3lL.2.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a3lL.2.5.a2m \ -target T0110 -template 1a3lL \ -out T0110-1a3lL.2.5 -outdir und partial PDB gets fragment 204 through 215 extending start extending end Debugging on ! Reading sequence file Reading input structure 14 residues read Measuring phi and psi Getting chi values ARG 1 24 GLU 2 13 PHE 3 4 LYS 4 27 ARG 5 32 SER 6 2 ASP 7 5 ARG 8 30 VAL 9 1 GLN 11 13 GLU 12 15 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists gmake: [und/T0110-1a3lL.4.4.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists gmake: [und/T0110-1a3lL.4.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a3lL.4.4.a2m \ -target T0110 -template 1a3lL \ -out T0110-1a3lL.4.4 -outdir und partial PDB gets fragment 204 through 215 extending start extending end Debugging on ! Reading sequence file Reading input structure 14 residues read Measuring phi and psi Getting chi values PHE 1 3 LYS 2 26 ARG 3 32 ASP 5 5 ARG 6 27 GLN 9 14 GLU 10 15 ILE 11 3 GLN 12 15 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists gmake: [und/T0110-1a3lL.6.2.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists gmake: [und/T0110-1a3lL.6.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a3lL.6.2.a2m \ -target T0110 -template 1a3lL \ -out T0110-1a3lL.6.2 -outdir und partial PDB gets fragment 204 through 213 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ARG 1 24 ASP 3 5 ARG 4 28 VAL 5 3 GLN 7 13 GLU 8 14 ILE 9 2 GLN 10 16 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists gmake: [und/T0110-1a3lL.7.4.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists gmake: [und/T0110-1a3lL.7.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a3lL.7.4.a2m \ -target T0110 -template 1a3lL \ -out T0110-1a3lL.7.4 -outdir und partial PDB gets fragment 203 through 212 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values SER 1 2 ASP 2 4 ARG 3 27 VAL 4 3 GLN 6 15 GLU 7 13 ILE 8 3 GLN 9 14 LYS 10 28 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists gmake: [und/T0110-1a3lL.8.5.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists gmake: [und/T0110-1a3lL.8.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a3lL.8.5.a2m \ -target T0110 -template 1a3lL \ -out T0110-1a3lL.8.5 -outdir und partial PDB gets fragment 202 through 211 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASP 1 8 ARG 2 32 VAL 3 2 GLN 5 15 GLU 6 13 ILE 7 5 GLN 8 12 LYS 9 27 GLU 10 14 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 1.90566 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists gmake: [und/T0110-1a48.112.5.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists gmake: [und/T0110-1a48.112.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m fragments/T0110-1a48.112.5.a2m \ -target T0110 -template 1a48 \ -out T0110-1a48.112.5 -outdir und Skipped atom 121, because occupancy 0.5 <= existing 0.500001 Skipped atom 123, because occupancy 0.5 <= existing 0.500001 Skipped atom 125, because occupancy 0.5 <= existing 0.500001 Skipped atom 127, because occupancy 0.5 <= existing 0.500001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1a48-orig.a2m Writing a2m file: tmp/1a48-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192/tmp -alignfile tmp/1a48-orig.a2m \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp/1a48-orig.a2m (1 sequences, 306 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192/tmp.a2m (1 sequences, 306 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192/tmp.mod tmp/1a48-align.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14192