make -k 1a4mA.indexes \ 1aj8A.indexes \ 1sig.indexes \ 1quuA.indexes \ 2spcA.indexes \ 1cunA.indexes \ 1ncx.indexes \ 1elrA.indexes \ 1qsdA.indexes \ 1pbwA.indexes \ 1bpwA.indexes \ 1qsdA.indexes \ 1dgfA.indexes make[1]: Entering directory `/export/projects/compbio/experiments/casp4/t97' make -k und/T0097-1a4mA-local.index und/1a4mA-T0097-local.index \ und/1a4mA-T0097-fssp-global.index make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97' mkdir tmp mkdir und /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1a4mA/T0097-1a4mA-local.pw.a2m.gz \ -target T0097 -template 1a4mA \ -out T0097-1a4mA-local -outdir und partial PDB gets fragment 277 through 325 extending start extending end partial PDB gets fragment 328 through 342 extending start extending end Debugging on ! Reading sequence file Reading input structure 68 residues read Measuring phi and psi Getting chi values ILE 1 2 LEU 2 3 LYS 3 26 GLN 4 11 GLN 6 10 ASP 7 4 LEU 9 3 SER 10 3 VAL 12 1 LYS 13 29 GLU 14 13 THR 15 2 LYS 17 31 LYS 18 25 TRP 19 7 SER 21 3 GLN 22 13 TYR 23 2 LYS 25 26 ILE 26 2 MET 27 10 LYS 29 24 ILE 30 3 LEU 31 3 ASP 32 6 GLN 33 11 GLU 35 13 ASP 36 4 PRO 38 2 SER 40 3 LEU 42 3 ILE 45 4 SER 46 2 LYS 47 30 LEU 48 3 ILE 49 3 GLU 52 13 ASN 53 6 LYS 54 24 MET 55 9 SER 56 2 LYS 59 30 GLU 61 13 GLN 64 15 ARG 65 27 SER 66 3 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: keepclash 5 38 58.3579 keepclash 15 18 61.9769 keepclash 32 36 20.0000 keepclash 54 56 12.0835 turnclash 36 3 2 0 32.6184 Cluster 1 = 2 5 32 36 38 Cluster 2 = 15 18 Cluster 3 = 54 56 9 clashing residues after turn Residue clashes: 5-38 15-18 32-36 36-38 36-2 54-56 cluster 1 has 5 members and 0.000e+00 combinations: 2 38 32 5 36 Energy 82.1109 Searching cluster 2 Combinations for 5 members in cluster 1 OK: 0.000e+00 - Sending to search 58.357929 < 82.110939: keeping 48.302742 < 63.766193: keeping 22.857204 < 53.730423: keeping 2.857203 < 25.271297: keeping 0.000000 < 6.926544: keeping Solved cluster 1: residual clashing 2.00 cluster 2 has 2 members and 4.400e+01 combinations: 15 18 Energy 61.9769 Searching cluster 15 Combinations for 2 members in cluster 2 OK: 4.400e+01 - Sending to search 0.000000 < 61.976856: keeping Solved cluster 2: residual clashing 1.21 cluster 3 has 2 members and 1.200e+01 combinations: 54 56 Energy 14.7344 Searching cluster 54 Combinations for 2 members in cluster 3 OK: 1.200e+01 - Sending to search 0.054130 < 14.734430: keeping Solved cluster 3: residual clashing 3.68 Still clashes at these sidechain pairs: Residual clashes = 27.85226 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1a4mA-T0097-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1a4mA-T0097-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1a4mA/1a4mA-T0097-local.pw.a2m.gz \ -target T0097 -template 1a4mA \ -out 1a4mA-T0097-local -outdir und Sequence named T0097 has all gap columns. It will be included anyway. /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1a4mA-T0097-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1a4mA-T0097-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1a4mA/1a4mA-T0097-fssp-global.pw.a2m.gz \ -target T0097 -template 1a4mA \ -out 1a4mA-T0097-fssp-global -outdir und partial PDB gets fragment 8 through 10 extending start extending end partial PDB gets fragment 12 through 15 extending start extending end partial PDB gets fragment 95 through 103 extending start extending end partial PDB gets fragment 124 through 138 extending start extending end partial PDB gets fragment 143 through 148 extending start extending end partial PDB gets fragment 152 through 170 extending start extending end partial PDB gets fragment 186 through 190 extending start extending end partial PDB gets fragment 193 through 200 extending start extending end partial PDB gets fragment 210 through 210 extending start extending end partial PDB gets fragment 238 through 249 extending start extending end partial PDB gets fragment 251 through 258 extending start extending end partial PDB gets fragment 275 through 279 extending start extending end partial PDB gets fragment 299 through 299 extending start extending end Debugging on ! Reading sequence file Reading input structure 122 residues read Measuring phi and psi Getting chi values CYS 2 2 PRO 6 2 TYR 8 2 LEU 13 3 GLN 16 12 PHE 17 4 ILE 18 3 GLU 19 15 SER 23 3 SER 24 3 ARG 25 26 GLU 26 12 ARG 28 27 GLN 29 11 ILE 31 3 LYS 33 29 GLN 34 14 GLN 36 11 ASP 37 4 LYS 42 24 GLU 43 13 THR 44 2 ASP 45 5 LYS 48 29 LYS 49 21 TRP 50 3 GLN 53 16 TYR 54 3 LYS 56 23 ILE 57 3 MET 58 10 LYS 60 26 ILE 61 3 LEU 62 3 ASP 63 4 GLN 64 9 GLU 66 12 PHE 69 2 PRO 70 2 SER 72 2 GLU 73 15 LEU 76 3 ARG 78 27 ILE 79 2 SER 80 3 LYS 81 26 LEU 82 3 ILE 83 3 GLU 86 13 ASN 89 4 LYS 90 30 MET 91 11 SER 92 2 LYS 95 26 LYS 96 24 GLU 97 15 GLU 98 12 GLN 100 13 ARG 103 20 SER 104 2 LEU 105 3 ASN 106 5 ILE 107 2 LEU 108 3 THR 109 2 PHE 113 3 ARG 114 32 LYS 115 25 LYS 116 26 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 7 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 3 rotamers of residue Y 55 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue P 71 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 2 rotamers of residue I 80 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 3 7 11.5477 keepclash 18 19 12.0720 keepclash 18 61 44.8005 keepclash 26 65 37.6734 keepclash 30 65 11.2830 keepclash 55 80 144.8427 keepclash 59 80 21.4053 keepclash 59 84 30.0000 keepclash 91 114 88.8481 turnclash 19 2 54 0 28.1540 turnclash 26 10 46 0 22.6573 turnclash 26 20 44 5 54.4217 turnclash 91 2 97 0 60.9603 turnclash 91 6 117 0 29.6213 Cluster 1 = 3 7 Cluster 2 = 18 19 26 30 44 46 54 61 65 Cluster 3 = 55 59 80 84 Cluster 4 = 91 97 114 117 19 clashing residues after turn Residue clashes: 3-7 18-19 18-26 18-61 19-54 26-61 26-65 26-46 26-44 30-65 55-80 59-80 59-84 61-46 91-114 91-97 91-117 97-117 cluster 1 has 2 members and 4.000e+00 combinations: 7 3 Energy 59.3154 Searching cluster 3 Combinations for 2 members in cluster 1 OK: 4.000e+00 - Sending to search 0.000000 < 59.315411: keeping 2.712080 < 48.013866: keeping 0.000000 < 38.076332: keeping Solved cluster 1: residual clashing 35.61 cluster 2 has 9 members and 3.293e+06 combinations: 46 44 54 18 19 65 30 61 26 Energy 114.6928 Searching cluster 18 Combinations for 9 members in cluster 2 OK: 3.293e+06 - Sending to search 107.712219 < 114.692802: keeping 92.739693 < 113.033752: keeping 76.427986 < 98.492943: keeping 68.725258 < 85.199409: keeping 66.898438 < 75.045990: keeping 51.925911 < 73.444130: keeping 36.270973 < 58.903313: keeping 27.911478 < 46.266548: keeping 23.924767 < 35.456367: keeping 22.415182 < 32.256893: keeping 16.628490 < 30.802036: keeping 12.641779 < 24.278519: keeping 12.641779 < 21.079044: keeping 12.071997 < 20.089178: keeping 3.986711 < 19.633862: keeping 0.000000 < 14.753447: keeping 0.000000 < 11.553975: keeping Solved cluster 2: residual clashing 10.56 cluster 3 has 4 members and 1.200e+01 combinations: 55 80 59 84 Energy 453.7517 Searching cluster 55 Combinations for 4 members in cluster 3 OK: 1.200e+01 - Sending to search 186.456970 < 453.751740: keeping 177.037247 < 445.257172: keeping 167.246292 < 438.992249: keeping 65.959290 < 430.497681: keeping 56.168335 < 157.855591: keeping 51.405281 < 149.361008: keeping 41.614319 < 147.752792: keeping Solved cluster 3: residual clashing 139.26 cluster 4 has 4 members and 1.152e+04 combinations: 97 117 114 91 Energy 91.4374 Searching cluster 91 Combinations for 4 members in cluster 4 OK: 1.152e+04 - Sending to search 88.848083 < 91.437447: keeping 60.960327 < 91.437439: keeping 12.781628 < 64.074165: keeping 6.659330 < 16.138918: keeping 4.163329 < 11.295465: keeping 0.000000 < 7.871834: keeping 0.000000 < 6.131609: keeping 0.000000 < 5.352426: keeping Solved cluster 4: residual clashing 5.02 Still clashes at these sidechain pairs: ires= 55 irot= 2 jres= 77 jrot= 1 103.9178 ires= 59 irot= 10 jres= 80 jrot= 2 21.4053 ires= 59 irot= 10 jres= 84 jrot= 2 20.2090 Residual clashes = 165.98705 Printing make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97' make -k und/T0097-1aj8A-local.index und/1aj8A-T0097-local.index \ und/1aj8A-T0097-fssp-global.index make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0097-1aj8A-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0097-1aj8A-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1aj8A/T0097-1aj8A-local.pw.a2m.gz \ -target T0097 -template 1aj8A \ -out T0097-1aj8A-local -outdir und partial PDB gets fragment 220 through 262 extending start extending end partial PDB gets fragment 266 through 275 extending start extending end partial PDB gets fragment 277 through 298 extending start extending end Debugging on ! Reading sequence file Reading input structure 81 residues read Measuring phi and psi Getting chi values TYR 2 3 ASP 3 4 LEU 5 3 ILE 10 4 SER 13 3 ARG 15 31 ARG 18 25 GLN 19 12 ILE 21 3 LEU 22 3 LYS 23 30 GLN 24 12 GLN 26 11 ASP 27 4 LEU 29 2 SER 30 3 VAL 32 1 LYS 33 27 GLU 34 12 THR 35 3 ASP 36 6 LYS 37 26 LYS 38 26 TRP 39 5 SER 41 2 GLN 42 13 LEU 46 3 LYS 47 24 MET 49 10 ILE 52 4 LEU 53 3 ASP 54 4 GLN 55 13 GLU 59 13 ASP 60 4 PHE 61 2 PRO 62 2 SER 64 3 GLU 65 12 LEU 66 3 ILE 69 4 SER 70 3 LYS 71 26 ILE 73 2 ASN 75 6 LYS 76 26 MET 77 10 GLU 79 13 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 3 rotamers of residue L 6 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 25 rotamers of residue R 19 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. All 3 rotamers of residue L 23 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 6 35 56.7690 keepclash 10 67 24.3772 keepclash 16 69 12.8377 keepclash 19 69 53.6664 keepclash 19 70 10.4584 keepclash 60 63 17.6549 turnclash 16 19 17 0 40.9081 Cluster 1 = 6 10 35 67 Cluster 2 = 16 17 19 69 70 Cluster 3 = 60 63 11 clashing residues after turn Residue clashes: 6-10 6-35 10-67 16-69 16-17 19-69 19-70 60-63 cluster 1 has 4 members and 0.000e+00 combinations: 10 67 6 35 Energy 115.5461 Searching cluster 6 Combinations for 4 members in cluster 1 OK: 0.000e+00 - Sending to search 73.883957 < 115.546097: keeping 64.595787 < 108.415894: keeping 53.379196 < 99.298050: keeping 54.936096 < 88.417175: keeping 44.377243 < 71.751129: keeping Solved cluster 1: residual clashing 61.53 cluster 2 has 5 members and 0.000e+00 combinations: 17 69 19 70 16 Energy 211.9447 Searching cluster 16 Combinations for 5 members in cluster 2 OK: 0.000e+00 - Sending to search 76.502571 < 211.944717: keeping 64.972900 < 211.929108: keeping 50.226871 < 202.627945: keeping 49.766975 < 120.735260: keeping 38.237301 < 120.719650: keeping 33.601944 < 111.418472: keeping 33.142044 < 59.408665: keeping 21.612373 < 59.393055: keeping 26.266218 < 50.091881: keeping 20.848120 < 40.809074: keeping Solved cluster 2: residual clashing 37.24 cluster 3 has 2 members and 1.300e+01 combinations: 63 60 Energy 22.1079 Searching cluster 60 Combinations for 2 members in cluster 3 OK: 1.300e+01 - Sending to search 0.000000 < 22.107920: keeping Solved cluster 3: residual clashing 5.14 Still clashes at these sidechain pairs: ires= 6 irot= 3 jres= 10 jrot= 1 20.0000 ires= 9 irot= 1 jres= 35 jrot= 11 10.8427 ires= 10 irot= 1 jres= 67 jrot= 2 24.3772 ires= 19 irot= 21 jres= 70 jrot= 2 20.0000 Residual clashes = 78.74986 Printing mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1aj8A-T0097-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1aj8A-T0097-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1aj8A/1aj8A-T0097-local.pw.a2m.gz \ -target T0097 -template 1aj8A \ -out 1aj8A-T0097-local -outdir und Sequence named T0097 has all gap columns. It will be included anyway. /projects/kestrel/users/karplus/burial/slicer/slicer: no segments found mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/1aj8A-T0097-fssp-global.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/1aj8A-T0097-fssp-global.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1aj8A/1aj8A-T0097-fssp-global.pw.a2m.gz \ -target T0097 -template 1aj8A \ -out 1aj8A-T0097-fssp-global -outdir und partial PDB gets fragment 0 through 12 extending end partial PDB gets fragment 39 through 40 extending start extending end partial PDB gets fragment 91 through 100 extending start extending end partial PDB gets fragment 137 through 144 extending start extending end partial PDB gets fragment 163 through 170 extending start extending end partial PDB gets fragment 201 through 206 extending start extending end partial PDB gets fragment 242 through 252 extending start extending end partial PDB gets fragment 278 through 281 extending start extending end partial PDB gets fragment 286 through 300 extending start extending end partial PDB gets fragment 336 through 359 extending start Debugging on ! Reading sequence file Reading input structure 119 residues read Measuring phi and psi Getting chi values TYR 1 3 ASP 2 4 GLN 7 12 PHE 8 3 GLU 10 16 SER 12 3 SER 15 3 ARG 16 26 GLU 19 12 GLN 22 15 LEU 25 3 LYS 26 26 GLN 27 12 GLN 31 15 ASP 32 4 SER 35 3 LYS 38 32 THR 42 2 ASP 43 6 LYS 45 28 SER 48 3 GLN 51 12 LEU 53 3 LYS 54 25 MET 56 10 ILE 61 4 ASP 63 5 GLU 66 14 ASP 67 5 PHE 68 2 PRO 69 2 SER 73 3 GLU 74 12 ILE 80 4 SER 81 3 LYS 82 26 ILE 84 2 ASN 86 6 LYS 87 26 MET 88 10 GLU 90 13 LYS 92 21 LYS 95 26 GLU 96 12 GLU 97 12 GLN 99 13 ARG 100 26 SER 101 3 LEU 102 2 ASN 103 4 ILE 104 3 LEU 105 3 THR 106 2 PHE 108 3 LYS 110 26 LYS 111 28 GLU 114 13 LYS 115 26 GLU 116 15 LEU 118 3 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: keepclash 10 11 10.0787 keepclash 20 32 33.4860 keepclash 26 57 32.4375 keepclash 65 67 16.2509 keepclash 69 81 20.3255 keepclash 69 85 16.2492 Cluster 1 = 10 11 Cluster 2 = 20 32 Cluster 3 = 26 57 Cluster 4 = 65 67 Cluster 5 = 69 81 85 11 clashing residues after turn Residue clashes: 10-11 20-32 26-57 65-67 69-81 69-85 cluster 1 has 2 members and 0.000e+00 combinations: 10 11 Energy 10.0787 Searching cluster 10 Combinations for 2 members in cluster 1 OK: 0.000e+00 - Sending to search 0.000000 < 10.078718: keeping Solved cluster 1: residual clashing 0.39 cluster 2 has 2 members and 1.800e+02 combinations: 20 32 Energy 33.4860 Searching cluster 20 Combinations for 2 members in cluster 2 OK: 1.800e+02 - Sending to search 17.693058 < 33.485954: keeping 0.000000 < 17.747784: keeping Solved cluster 2: residual clashing 0.11 cluster 3 has 2 members and 9.000e+00 combinations: 26 57 Energy 32.4375 Searching cluster 26 Combinations for 2 members in cluster 3 OK: 9.000e+00 - Sending to search 10.081428 < 32.437527: keeping 0.000000 < 12.182400: keeping Solved cluster 3: residual clashing 1.81 cluster 4 has 2 members and 0.000e+00 combinations: 65 67 Energy 16.2509 Searching cluster 65 Combinations for 2 members in cluster 4 OK: 0.000e+00 - Sending to search 0.000000 < 16.250875: keeping Solved cluster 4: residual clashing 0.17 cluster 5 has 3 members and 8.000e+00 combinations: 69 85 81 Energy 36.5747 Searching cluster 69 Combinations for 3 members in cluster 5 OK: 8.000e+00 - Sending to search 20.325535 < 36.574745: keeping 0.000000 < 21.621908: keeping Solved cluster 5: residual clashing 1.47 Still clashes at these sidechain pairs: Residual clashes = 33.28457 Printing make[2]: Leaving directory `/export/projects/compbio/experiments/casp4/t97' make -k und/T0097-1sig-local.index und/1sig-T0097-local.index \ und/1sig-T0097-fssp-global.index make[2]: Entering directory `/export/projects/compbio/experiments/casp4/t97' mkdir tmp mkdir: cannot create tmp. tmp: File exists make[2]: [und/T0097-1sig-local.index] Error 2 (ignored) mkdir und mkdir: cannot create und. und: File exists make[2]: [und/T0097-1sig-local.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m 1sig/T0097-1sig-local.pw.a2m.gz \ -target T0097 -template 1sig \ -out T0097-1sig-local -outdir und PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1sig-orig.a2m Writing a2m file: tmp/1sig-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-beta-2694 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-beta-2694/tmp -alignfile tmp/1sig-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/1sig-orig.a2m (1 sequences, 339 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-beta-2694/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-beta-2694/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-beta-2694/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-beta-2694/tmp.a2m (1 sequences, 339 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-beta-2694/tmp.mod tmp/1sig-align.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-beta-2694