# command:# Seed set to 1027746169 # command:# Prefix for input files set to # command:# reading script from file define-score.script # Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/ # reading monomeric-50pc.atoms # After reading monomeric-50pc.atoms have 448 chains in training database # 111547 residues have no bad marker # 670 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 28 # Note: may sum to more than number of residues, # because one residue may have multiple problems # Reading rotamer library from monomeric-50pc.rot # Prefix for input files set to /projects/kestrel/users/karplus/burial/undertaker/spots/ # ReadAtomType pdb-name.types Read AtomType pdb-name with 37 types. # ReadClashTable pdb-atom-name.clash # Read ClashTable pdb-atom-name Reading spots from monomeric-50pc-wet-6.5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-wet-6.5.hist # created burial cost function wet6.5 with radius 6.5 Reading spots from monomeric-50pc-dry-6.5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-6.5.hist # created burial cost function dry6.5 with radius 6.5 Reading spots from monomeric-50pc-generic-6.5.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-generic-6.5.hist # created burial cost function gen6.5 with radius 6.5 Reading spots from monomeric-50pc-dry-8.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-8.hist # created burial cost function dry8 with radius 8 Reading spots from monomeric-50pc-dry-10.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-10.hist # created burial cost function dry10 with radius 10 Reading spots from monomeric-50pc-dry-12.spot. Read prototypes from /projects/kestrel/users/karplus/burial/undertaker/spots/../normalize_prototypes/prototypes # reading histogram from smoothed-monomeric-50pc-dry-12.hist # created burial cost function dry12 with radius 12 # reading histogram from monomeric-smoothed-alpha.hist # created alpha cost function alpha with offset 0 and 360 bins # reading histogram from monomeric-smoothed-alpha-1.hist # created alpha cost function alpha_prev with offset -1 and 360 bins CPU_time= 5580 msec, elapsed time= 6084.21 msec) # Prefix for input files set to # Reading target chain from PDB file T0132.blank.pdb Read PDB file T0132.blank.pdb as target. Have 154 residues and 1170 atoms. # No conformations to remove in PopConform # SetCost created cost = # ( 0.2 * gen6.5(6.5) + 0.2 * wet6.5(6.5, /log(length)) + 1 * dry6.5(6.5) + 1 * dry8(8) + 1 * dry12(12) + 0 * radius_norm + 0.2 * radius_fit + 0.2 * sidechain + 1 * clashes + -0.2 * sidechain_clashes + 0.5 * backbone_clashes + 5 * break + 0.01 * constraints + 1 * alpha + 1 * alpha_prev + 1 * contact_order ) # command:CPU_time= 5590 msec, elapsed time= 6233.7 msec) # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 407 20 (100%) # n-terminus 2 408 196 (49%) # middle 1 109496 20 (100%) # middle 2 108592 400 (100%) # middle 3 107719 7822 (97.775%) # middle 4 106865 64233 (40.1456%) # c-terminus 1 408 20 (100%) # c-terminus 2 406 227 (56.75%) # ss-bonds 409 # command:CPU_time= 8700 msec, elapsed time= 9346.66 msec) # command:# Prefix for output files set to decoys/ # command:# created conformation for T0132 from sequence in target chain replacing old conformation. # command:# naming current conformation T0132-rand # command:CPU_time= 8700 msec, elapsed time= 9349.09 msec) # command:# Prefix for input files set to # command:# reading script from file T0132-undertaker-align.script # Reading fragments from alignment file Couldn't open file /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-global-adpstyle5.pw.a2m.gz or /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-global-adpstyle5.pw.a2m.gz.gz for input Trying /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-global-adpstyle5.pw.a2m.gz Couldn't open file /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-global-adpstyle5.pw.a2m.gz or /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-global-adpstyle5.pw.a2m.gz.gz for input sh: 19923052: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: ref: command not found sh: NP: command not found sh: 16272768: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: 13626231: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: NP: command not found sh: 15614865: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: 15613361: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: ref: command not found sh: 15602193: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: ref: command not found sh: NP: command not found sh: 15805310: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: P49851: command not found sh: sp: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: NP: command not found sh: ref: command not found sh: 16122425: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: 16760145: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: ref: command not found sh: 15924868: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: 15927452: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: ref: command not found sh: NP: command not found sh: 15835436: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: ref: command not found sh: NP: command not found sh: 13541468: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: ref: command not found sh: 16803985: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: ref: command not found sh: NP: command not found sh: 15801479: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: NP: command not found sh: ref: command not found sh: 15676820: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: NP: command not found sh: 15794068: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: NP: command not found sh: ref: command not found sh: 15605264: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: NP: command not found sh: 15601694: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: ref: command not found sh: 9790025: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: NP: command not found sh: 12331400: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: 17485787: command not found sh: XP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: XP: command not found sh: ref: command not found sh: 14768741: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: sp: command not found sh: Q9R0X4: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: ref: command not found sh: NP: command not found sh: 15790012: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: ref: command not found sh: 13472339: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: 15791208: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: 15965651: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: NP: command not found sh: ref: command not found sh: 17937565: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: emb: command not found sh: CAB46201: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: NP: command not found sh: ref: command not found sh: 15889285: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: NP: command not found sh: ref: command not found sh: 17986786: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: ref: command not found sh: 13626231: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 19923052: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: ref: command not found sh: 17545196: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: emb: command not found sh: 5327040: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: NP: command not found sh: ref: command not found sh: 15792244: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 15891126: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: NP: command not found sh: ref: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: XP: command not found sh: ref: command not found sh: 20535287: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: ref: command not found sh: 18314041: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: ref: command not found sh: 15595646: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-fssp-global-adpstyle5.pw.a2m.gz # adding 1bvqA to template set 1bvqA:# found chain 1bvqA in template set T0132 15 :GVLLLRTLAMPSDTNANGDIFGGWIMSQMDMG 1bvqA 3 :RSITMQQRIEFGDCDPAGIVWYPNYHRWLDAA Fragment has 10 clashes (null) has 10 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 34 residues other bump:1.06866 Ang OD1(109) at 48.8094 14.2136 4.54363 in (null):N-9999 (15) and OD1(122) at 49.0324 13.5826 5.37683 in (null):N-9999 (17) other bump:1.65531 Ang CG(107) at 49.7114 14.9997 4.85634 in (null):N-9999 (15) and OD1(122) at 49.0324 13.5826 5.37683 in (null):N-9999 (17) other bump:2.03682 Ang ND2(108) at 50.1337 15.1341 6.10413 in (null):N-9999 (15) and OD1(122) at 49.0324 13.5826 5.37683 in (null):N-9999 (17) other bump:2.51554 Ang ND2(108) at 50.1337 15.1341 6.10413 in (null):N-9999 (15) and ND2(121) at 49.5326 13.1147 7.47842 in (null):N-9999 (17) other bump:2.28812 Ang OD1(109) at 48.8094 14.2136 4.54363 in (null):N-9999 (15) and CG(120) at 49.588 12.8049 6.1699 in (null):N-9999 (17) other bump:2.56088 Ang CG(107) at 49.7114 14.9997 4.85634 in (null):N-9999 (15) and CG(120) at 49.588 12.8049 6.1699 in (null):N-9999 (17) other bump:2.39319 Ang ND2(108) at 50.1337 15.1341 6.10413 in (null):N-9999 (15) and CG(120) at 49.588 12.8049 6.1699 in (null):N-9999 (17) neighbor-bump: 2.8095 Ang C(47) at 33.161 26.368 5.632 in (null):R-9999 (6) and CG2(51) at 35.6701 27.5535 5.1937 in (null):T-9999 (7) other bump:2.80932 Ang CD2(34) at 34.7011 29.2303 7.22879 in (null):L-9999 (5) and CG2(51) at 35.6701 27.5535 5.1937 in (null):T-9999 (7) neighbor-bump: 2.24129 Ang O(46) at 33.452 27.36 4.937 in (null):R-9999 (6) and CG2(51) at 35.6701 27.5535 5.1937 in (null):T-9999 (7) T0132 47 :G 1bvqA 46 :P Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues T0132 48 :AILAKEIAHGRVVTVA 1bvqA 50 :TVVERGIVGTPIVSCN Fragment has 14 clashes (null) has 14 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 18 residues neighbor-bump: 2.89821 Ang C(104) at 48.712 33.977 19.642 in (null):T-9999 (14) and CG2(109) at 47.8467 32.676 17.201 in (null):V-9999 (15) neighbor-bump: 2.45655 Ang O(96) at 51.704 36.71 19.582 in (null):V-9999 (13) and CG2(101) at 51.1229 35.9908 21.8579 in (null):T-9999 (14) neighbor-bump: 2.90601 Ang C(97) at 50.593 36.998 19.184 in (null):V-9999 (13) and CG2(101) at 51.1229 35.9908 21.8579 in (null):T-9999 (14) neighbor-bump: 2.14692 Ang O(57) at 44.73 45.499 7.772 in (null):A-9999 (8) and CE1(65) at 45.4381 44.5496 5.98137 in (null):H-9999 (9) neighbor-bump: 1.14495 Ang O(57) at 44.73 45.499 7.772 in (null):A-9999 (8) and ND1(64) at 45.5486 44.8947 7.24701 in (null):H-9999 (9) neighbor-bump: 3.13871 Ang CA(55) at 45.01 47.785 8.346 in (null):A-9999 (8) and ND1(64) at 45.5486 44.8947 7.24701 in (null):H-9999 (9) neighbor-bump: 2.25322 Ang C(58) at 44.528 46.375 8.605 in (null):A-9999 (8) and ND1(64) at 45.5486 44.8947 7.24701 in (null):H-9999 (9) neighbor-bump: 2.59043 Ang O(57) at 44.73 45.499 7.772 in (null):A-9999 (8) and CD2(63) at 44.4362 43.0009 7.15273 in (null):H-9999 (9) neighbor-bump: 1.61556 Ang O(57) at 44.73 45.499 7.772 in (null):A-9999 (8) and CG(62) at 44.9101 43.9132 8.02267 in (null):H-9999 (9) neighbor-bump: 2.55844 Ang C(58) at 44.528 46.375 8.605 in (null):A-9999 (8) and CG(62) at 44.9101 43.9132 8.02267 in (null):H-9999 (9) neighbor-bump: 2.59212 Ang C(58) at 44.528 46.375 8.605 in (null):A-9999 (8) and CB(61) at 44.8299 43.9755 9.53795 in (null):H-9999 (9) other bump:2.69154 Ang CG2(11) at 43.1798 49.2299 5.69424 in (null):I-9999 (2) and O(52) at 42.582 49.114 8.316 in (null):I-9999 (7) other bump:2.35382 Ang CE(33) at 38.4254 52.3416 12.8621 in (null):K-9999 (5) and CD1(51) at 40.263 50.871 12.896 in (null):I-9999 (7) other bump:2.21539 Ang NZ(34) at 38.0534 50.8641 12.7357 in (null):K-9999 (5) and CD1(51) at 40.263 50.871 12.896 in (null):I-9999 (7) T0132 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWVKK 1bvqA 66 :ASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTT Fragment has 17 clashes (null) has 17 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 39 residues other bump:2.47461 Ang CG2(57) at 39.4598 17.0837 10.1056 in (null):I-9999 (7) and CG2(269) at 37.3619 17.7592 11.2308 in (null):V-9999 (35) other bump:2.96772 Ang CD(239) at 33.735 23.5616 19.5704 in (null):E-9999 (32) and NE1(259) at 32.8819 21.3733 17.7562 in (null):W-9999 (34) other bump:2.87911 Ang CG1(96) at 36.2935 23.038 9.8441 in (null):V-9999 (13) and CG1(247) at 37.76 22.734 12.303 in (null):V-9999 (33) other bump:2.79408 Ang CD1(147) at 38.4449 32.1579 23.994 in (null):L-9999 (20) and CE(224) at 37.0158 29.757 23.99 in (null):K-9999 (30) other bump:2.75518 Ang CD2(148) at 35.9297 32.2884 23.929 in (null):L-9999 (20) and CE(224) at 37.0158 29.757 23.99 in (null):K-9999 (30) other bump:2.91844 Ang CD2(148) at 35.9297 32.2884 23.929 in (null):L-9999 (20) and CD(223) at 36.2404 29.6502 22.7204 in (null):K-9999 (30) other bump:2.97508 Ang CG(146) at 37.2344 33.0588 23.7394 in (null):L-9999 (20) and CB(221) at 37.4249 31.3892 21.2844 in (null):K-9999 (30) other bump:2.9956 Ang CD1(147) at 38.4449 32.1579 23.994 in (null):L-9999 (20) and CB(221) at 37.4249 31.3892 21.2844 in (null):K-9999 (30) other bump:3.16828 Ang CD2(148) at 35.9297 32.2884 23.929 in (null):L-9999 (20) and CB(221) at 37.4249 31.3892 21.2844 in (null):K-9999 (30) other bump:2.49971 Ang CE(156) at 41.9954 36.4564 28.0745 in (null):K-9999 (21) and NZ(208) at 42.8232 34.4442 26.8439 in (null):K-9999 (28) other bump:2.39776 Ang CE1(118) at 31.1197 29.7953 19.3178 in (null):Y-9999 (16) and OE1(133) at 32.5151 30.453 21.1534 in (null):Q-9999 (18) other bump:2.61851 Ang OD1(15) at 43.2464 19.4805 21.4415 in (null):N-9999 (2) and CG1(32) at 41.4972 17.7757 20.4975 in (null):I-9999 (4) other bump:2.4847 Ang SD(6) at 47.1918 25.1912 15.2821 in (null):M-9999 (1) and CZ(26) at 47.064 22.784 14.68 in (null):F-9999 (3) other bump:1.59807 Ang CE(7) at 46.0323 23.9742 14.95 in (null):M-9999 (1) and CZ(26) at 47.064 22.784 14.68 in (null):F-9999 (3) other bump:1.98043 Ang CE(7) at 46.0323 23.9742 14.95 in (null):M-9999 (1) and CE2(25) at 45.968 22.236 14.003 in (null):F-9999 (3) other bump:3.1178 Ang SD(6) at 47.1918 25.1912 15.2821 in (null):M-9999 (1) and CE1(24) at 47.577 22.142 15.806 in (null):F-9999 (3) other bump:2.54476 Ang CE(7) at 46.0323 23.9742 14.95 in (null):M-9999 (1) and CE1(24) at 47.577 22.142 15.806 in (null):F-9999 (3) T0132 108 :PIG 1bvqA 103 :PGG Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 5 residues neighbor-bump: 2.95475 Ang C(8) at 30.502 10.487 5.408 in (null):P-9999 (1) and CG1(12) at 29.8684 7.67224 4.77072 in (null):I-9999 (2) neighbor-bump: 2.35293 Ang C(8) at 30.502 10.487 5.408 in (null):P-9999 (1) and CB(11) at 29.8796 8.3474 6.16363 in (null):I-9999 (2) neighbor-bump: 1.88714 Ang O(7) at 31.153 9.74 6.145 in (null):P-9999 (1) and CB(11) at 29.8796 8.3474 6.16363 in (null):I-9999 (2) T0132 113 :YCVTDAVFTFVAVDNNG 1bvqA 108 :QLVMRADEIRVFAMNDG Fragment has 3 clashes (null) has 3 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 19 residues other bump:2.77153 Ang CB(56) at 44.0152 33.5989 17.2862 in (null):F-9999 (8) and CE2(79) at 42.7394 35.8479 16.2885 in (null):F-9999 (10) neighbor-bump: 2.85668 Ang C(26) at 39.965 19.422 15.603 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) neighbor-bump: 2.42254 Ang O(25) at 41.092 18.965 15.737 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) Number of specific fragments= 6 total=6 Number of alignments=1 # Reading fragments from alignment file Couldn't open file /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle1.pw.a2m.gz or /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle1.pw.a2m.gz.gz for input Trying /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle1.pw.a2m.gz Couldn't open file /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle1.pw.a2m.gz or /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle1.pw.a2m.gz.gz for input # Reading fragments from alignment file Couldn't open file /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle5.pw.a2m.gz or /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle5.pw.a2m.gz.gz for input Trying /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle5.pw.a2m.gz Couldn't open file /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle5.pw.a2m.gz or /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-2track-local-adpstyle5.pw.a2m.gz.gz for input sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: NP: command not found sh: 16272768: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: 13626231: command not found sh: XP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 15614865: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: NP: command not found sh: 15613361: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: 15602193: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: NP: command not found sh: 15805310: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: P49851: command not found sh: sp: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: NP: command not found sh: ref: command not found sh: 16122425: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: NP: command not found sh: ref: command not found sh: 16760145: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: NP: command not found sh: ref: command not found sh: 15924868: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: ref: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: ref: command not found sh: 15835436: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: NP: command not found sh: ref: command not found sh: 13541468: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: 16803985: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: NP: command not found sh: ref: command not found sh: 15801479: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: 15676820: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: ref: command not found sh: NP: command not found sh: 15794068: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: 15605264: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: NP: command not found sh: 15601694: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: 9790025: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: NP: command not found sh: 12331400: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: 17485787: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: 14768741: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: 15790012: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: NP: command not found sh: ref: command not found sh: 13472339: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: NP: command not found sh: ref: command not found sh: 15791208: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: NP: command not found sh: ref: command not found sh: 15965651: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: NP: command not found sh: ref: command not found sh: 17937565: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: dbj: command not found sh: BAA89437: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: ref: command not found sh: NP: command not found sh: 15889285: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: NP: command not found sh: ref: command not found sh: 17986786: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: XP: command not found sh: ref: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 5327041: command not found sh: emb: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: 17545196: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: emb: command not found sh: 5327040: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: ref: command not found sh: 15792244: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: dbj: command not found sh: BAA89437: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: ref: command not found sh: NP: command not found sh: 15891126: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: ref: command not found sh: NP: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: 20535287: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: 18314041: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: NP: command not found sh: ref: command not found sh: 15595646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle1.pw.a2m.gz # found chain 1bvqA in template set T0132 39 :IMSQMDMGGAILAKEIAHGRVVTVAVESMNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWVKKVA 1bvqA 38 :YFIKCGLPPWRQTVVERGIVGTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG Fragment has 30 clashes (null) has 30 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 69 residues neighbor-bump: 1.84427 Ang O(495) at 31.153 9.74 6.145 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 2.31772 Ang C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 3.14282 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and CA(498) at 28.582 9.428 6.203 in (null):A-9999 (67) neighbor-bump: 1.95103 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and N(497) at 29.194 10.425 5.355 in (null):A-9999 (67) self-bump: 2.3527 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 2.20723 Ang CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 1.25472 Ang CA(491) at 31.187 11.533 4.553 in (null):V-9999 (66) and CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) other bump:2.47461 Ang CG2(257) at 39.4598 17.0837 10.1056 in (null):I-9999 (35) and CG2(469) at 37.3619 17.7592 11.2308 in (null):V-9999 (63) other bump:2.96772 Ang CD(439) at 33.735 23.5616 19.5704 in (null):E-9999 (60) and NE1(459) at 32.8819 21.3733 17.7562 in (null):W-9999 (62) other bump:2.87911 Ang CG1(296) at 36.2935 23.038 9.8441 in (null):V-9999 (41) and CG1(447) at 37.76 22.734 12.303 in (null):V-9999 (61) other bump:2.79408 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.75518 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.91844 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CD(423) at 36.2404 29.6502 22.7204 in (null):K-9999 (58) other bump:2.97508 Ang CG(346) at 37.2344 33.0588 23.7394 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.9956 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:3.16828 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.49971 Ang CE(356) at 41.9954 36.4564 28.0745 in (null):K-9999 (49) and NZ(408) at 42.8232 34.4442 26.8439 in (null):K-9999 (56) other bump:2.39776 Ang CE1(318) at 31.1197 29.7953 19.3178 in (null):Y-9999 (44) and OE1(333) at 32.5151 30.453 21.1534 in (null):Q-9999 (46) other bump:2.61852 Ang OD1(215) at 43.2464 19.4805 21.4415 in (null):N-9999 (30) and CG1(232) at 41.4972 17.7757 20.4975 in (null):I-9999 (32) other bump:2.4847 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.59807 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.98044 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE2(225) at 45.968 22.236 14.003 in (null):F-9999 (31) other bump:3.1178 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) other bump:2.54477 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) neighbor-bump: 3.16621 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and CA(155) at 44.107 42.553 13.08 in (null):V-9999 (22) neighbor-bump: 2.16426 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and N(154) at 43.818 43.1 11.758 in (null):V-9999 (22) neighbor-bump: 1.52039 Ang O(145) at 44.73 45.499 7.772 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.33105 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.60525 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CB(149) at 45.0756 44.0982 9.74666 in (null):V-9999 (21) other bump:2.39785 Ang O(68) at 40.772 48.514 4.996 in (null):A-9999 (10) and CG(94) at 43.0269 49.187 5.45686 in (null):K-9999 (14) T0132 110 :G 1bvqA 105 :G Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues T0132 113 :YCVTDAVFTFVAV 1bvqA 108 :QLVMRADEIRVFA Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.92416 Ang CG2(87) at 47.542 44.032 17.247 in (null):V-9999 (11) and CG1(98) at 47.9279 45.7692 14.9267 in (null):V-9999 (13) other bump:2.77153 Ang CB(56) at 44.0152 33.5989 17.2862 in (null):F-9999 (8) and CE2(79) at 42.7394 35.8479 16.2885 in (null):F-9999 (10) neighbor-bump: 2.42254 Ang O(25) at 41.092 18.965 15.737 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) neighbor-bump: 2.85668 Ang C(26) at 39.965 19.422 15.603 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) T0132 126 :DNNGRSRTIPRE 1bvqA 124 :GERLRAIEVPAD Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues self-bump: 1.38808 Ang CA(11) at 58.067 51.967 9.609 in (null):N-9999 (2) and CB(12) at 59.3677 51.684 10.0027 in (null):N-9999 (2) self-bump: 1.33771 Ang CA(3) at 55.65 54.923 9.872 in (null):D-9999 (1) and CB(4) at 56.643 55.7765 10.1457 in (null):D-9999 (1) Number of specific fragments= 4 total=10 Number of alignments=2 sh: ref: command not found sh: 19923052: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: ref: command not found sh: NP: command not found sh: 16272768: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: XP: command not found sh: 13626231: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: 15614865: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: NP: command not found sh: ref: command not found sh: 15613361: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: NP: command not found sh: ref: command not found sh: 15602193: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: NP: command not found sh: ref: command not found sh: 15805310: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: sp: command not found sh: P49851: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: ref: command not found sh: 16122425: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: 16760145: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: 15924868: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: ref: command not found sh: 15927452: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: NP: command not found sh: 15835436: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: NP: command not found sh: 13541468: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: ref: command not found sh: NP: command not found sh: 16803985: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: 15801479: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: NP: command not found sh: 15676820: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: NP: command not found sh: 15794068: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: 15605264: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: ref: command not found sh: 15601694: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: ref: command not found sh: 9790025: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: NP: command not found sh: ref: command not found sh: 12331400: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: ref: command not found sh: 17485787: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: XP: command not found sh: ref: command not found sh: 14768741: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: 15790012: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: NP: command not found sh: 13472339: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: NP: command not found sh: 15791208: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: NP: command not found sh: ref: command not found sh: 15965651: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: 17937565: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: NP: command not found sh: 15889285: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: ref: command not found sh: 17986786: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: ref: command not found sh: 13626231: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: NP: command not found sh: ref: command not found sh: 19923052: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 5327041: command not found sh: emb: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: ref: command not found sh: 17545196: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: 5327040: command not found sh: CAB46202: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: NP: command not found sh: ref: command not found sh: 15792244: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: ref: command not found sh: NP: command not found sh: 15891126: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: NP: command not found sh: ref: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: ref: command not found sh: 20535287: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: ref: command not found sh: 18314041: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: ref: command not found sh: NP: command not found sh: 15595646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-local-adpstyle5.pw.a2m.gz # found chain 1bvqA in template set T0132 39 :IMSQMDMGGAILAKEIAHGRVVTVAVESMNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWVKKVA 1bvqA 38 :YFIKCGLPPWRQTVVERGIVGTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG Fragment has 30 clashes (null) has 30 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 69 residues neighbor-bump: 1.84427 Ang O(495) at 31.153 9.74 6.145 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 2.31772 Ang C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 3.14282 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and CA(498) at 28.582 9.428 6.203 in (null):A-9999 (67) neighbor-bump: 1.95103 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and N(497) at 29.194 10.425 5.355 in (null):A-9999 (67) self-bump: 2.3527 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 2.20723 Ang CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 1.25472 Ang CA(491) at 31.187 11.533 4.553 in (null):V-9999 (66) and CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) other bump:2.47461 Ang CG2(257) at 39.4598 17.0837 10.1056 in (null):I-9999 (35) and CG2(469) at 37.3619 17.7592 11.2308 in (null):V-9999 (63) other bump:2.96772 Ang CD(439) at 33.735 23.5616 19.5704 in (null):E-9999 (60) and NE1(459) at 32.8819 21.3733 17.7562 in (null):W-9999 (62) other bump:2.87911 Ang CG1(296) at 36.2935 23.038 9.8441 in (null):V-9999 (41) and CG1(447) at 37.76 22.734 12.303 in (null):V-9999 (61) other bump:2.79408 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.75518 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.91844 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CD(423) at 36.2404 29.6502 22.7204 in (null):K-9999 (58) other bump:2.97508 Ang CG(346) at 37.2344 33.0588 23.7394 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.9956 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:3.16828 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.49971 Ang CE(356) at 41.9954 36.4564 28.0745 in (null):K-9999 (49) and NZ(408) at 42.8232 34.4442 26.8439 in (null):K-9999 (56) other bump:2.39776 Ang CE1(318) at 31.1197 29.7953 19.3178 in (null):Y-9999 (44) and OE1(333) at 32.5151 30.453 21.1534 in (null):Q-9999 (46) other bump:2.61852 Ang OD1(215) at 43.2464 19.4805 21.4415 in (null):N-9999 (30) and CG1(232) at 41.4972 17.7757 20.4975 in (null):I-9999 (32) other bump:2.4847 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.59807 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.98044 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE2(225) at 45.968 22.236 14.003 in (null):F-9999 (31) other bump:3.1178 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) other bump:2.54477 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) neighbor-bump: 3.16621 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and CA(155) at 44.107 42.553 13.08 in (null):V-9999 (22) neighbor-bump: 2.16426 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and N(154) at 43.818 43.1 11.758 in (null):V-9999 (22) neighbor-bump: 1.52039 Ang O(145) at 44.73 45.499 7.772 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.33105 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.60525 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CB(149) at 45.0756 44.0982 9.74666 in (null):V-9999 (21) other bump:2.39785 Ang O(68) at 40.772 48.514 4.996 in (null):A-9999 (10) and CG(94) at 43.0269 49.187 5.45686 in (null):K-9999 (14) T0132 110 :G 1bvqA 105 :G Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues T0132 113 :YCVTDAVFTFVAV 1bvqA 108 :QLVMRADEIRVFA Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.92416 Ang CG2(87) at 47.542 44.032 17.247 in (null):V-9999 (11) and CG1(98) at 47.9279 45.7692 14.9267 in (null):V-9999 (13) other bump:2.77153 Ang CB(56) at 44.0152 33.5989 17.2862 in (null):F-9999 (8) and CE2(79) at 42.7394 35.8479 16.2885 in (null):F-9999 (10) neighbor-bump: 2.42254 Ang O(25) at 41.092 18.965 15.737 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) neighbor-bump: 2.85668 Ang C(26) at 39.965 19.422 15.603 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) T0132 126 :DNNGRSRTIPRE 1bvqA 124 :GERLRAIEVPAD Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues self-bump: 1.38808 Ang CA(11) at 58.067 51.967 9.609 in (null):N-9999 (2) and CB(12) at 59.3677 51.684 10.0027 in (null):N-9999 (2) self-bump: 1.33771 Ang CA(3) at 55.65 54.923 9.872 in (null):D-9999 (1) and CB(4) at 56.643 55.7765 10.1457 in (null):D-9999 (1) Number of specific fragments= 4 total=14 Number of alignments=3 sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: ref: command not found sh: 16272768: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: XP: command not found sh: 13626231: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: 15614865: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: NP: command not found sh: 15613361: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: NP: command not found sh: 15602193: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: NP: command not found sh: 15805310: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: sp: command not found sh: P49851: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: ref: command not found sh: 16122425: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: ref: command not found sh: 16760145: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: ref: command not found sh: NP: command not found sh: 15924868: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: 15927452: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: NP: command not found sh: 15835436: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: 13541468: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: ref: command not found sh: NP: command not found sh: 16803985: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: NP: command not found sh: ref: command not found sh: 15801479: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: ref: command not found sh: NP: command not found sh: 15676820: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: ref: command not found sh: NP: command not found sh: 15794068: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: NP: command not found sh: ref: command not found sh: 15605264: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: ref: command not found sh: 15601694: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: ref: command not found sh: 9790025: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: ref: command not found sh: NP: command not found sh: 12331400: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: 17485787: command not found sh: XP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: 14768741: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: 15790012: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: NP: command not found sh: ref: command not found sh: 13472339: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: NP: command not found sh: ref: command not found sh: 15791208: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: 15965651: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: NP: command not found sh: 17937565: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: ref: command not found sh: NP: command not found sh: 15889285: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: ref: command not found sh: 17986786: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: ref: command not found sh: XP: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: NP: command not found sh: ref: command not found sh: 19923052: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 17545196: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: 5327040: command not found sh: CAB46202: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: 15792244: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: NP: command not found sh: ref: command not found sh: 15891126: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: NP: command not found sh: ref: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: 20535287: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: 18314041: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: ref: command not found sh: 15595646: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle5.pw.a2m.gz # found chain 1bvqA in template set T0132 39 :IMSQMDMGGAILAKEIAHGRVVTVAVESMNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWVKKVA 1bvqA 38 :YFIKCGLPPWRQTVVERGIVGTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG Fragment has 30 clashes (null) has 30 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 69 residues neighbor-bump: 1.84427 Ang O(495) at 31.153 9.74 6.145 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 2.31772 Ang C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 3.14282 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and CA(498) at 28.582 9.428 6.203 in (null):A-9999 (67) neighbor-bump: 1.95103 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and N(497) at 29.194 10.425 5.355 in (null):A-9999 (67) self-bump: 2.3527 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 2.20723 Ang CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 1.25472 Ang CA(491) at 31.187 11.533 4.553 in (null):V-9999 (66) and CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) other bump:2.47461 Ang CG2(257) at 39.4598 17.0837 10.1056 in (null):I-9999 (35) and CG2(469) at 37.3619 17.7592 11.2308 in (null):V-9999 (63) other bump:2.96772 Ang CD(439) at 33.735 23.5616 19.5704 in (null):E-9999 (60) and NE1(459) at 32.8819 21.3733 17.7562 in (null):W-9999 (62) other bump:2.87911 Ang CG1(296) at 36.2935 23.038 9.8441 in (null):V-9999 (41) and CG1(447) at 37.76 22.734 12.303 in (null):V-9999 (61) other bump:2.79408 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.75518 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.91844 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CD(423) at 36.2404 29.6502 22.7204 in (null):K-9999 (58) other bump:2.97508 Ang CG(346) at 37.2344 33.0588 23.7394 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.9956 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:3.16828 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.49971 Ang CE(356) at 41.9954 36.4564 28.0745 in (null):K-9999 (49) and NZ(408) at 42.8232 34.4442 26.8439 in (null):K-9999 (56) other bump:2.39776 Ang CE1(318) at 31.1197 29.7953 19.3178 in (null):Y-9999 (44) and OE1(333) at 32.5151 30.453 21.1534 in (null):Q-9999 (46) other bump:2.61852 Ang OD1(215) at 43.2464 19.4805 21.4415 in (null):N-9999 (30) and CG1(232) at 41.4972 17.7757 20.4975 in (null):I-9999 (32) other bump:2.4847 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.59807 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.98044 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE2(225) at 45.968 22.236 14.003 in (null):F-9999 (31) other bump:3.1178 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) other bump:2.54477 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) neighbor-bump: 3.16621 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and CA(155) at 44.107 42.553 13.08 in (null):V-9999 (22) neighbor-bump: 2.16426 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and N(154) at 43.818 43.1 11.758 in (null):V-9999 (22) neighbor-bump: 1.52039 Ang O(145) at 44.73 45.499 7.772 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.33105 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.60525 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CB(149) at 45.0756 44.0982 9.74666 in (null):V-9999 (21) other bump:2.39785 Ang O(68) at 40.772 48.514 4.996 in (null):A-9999 (10) and CG(94) at 43.0269 49.187 5.45686 in (null):K-9999 (14) T0132 110 :G 1bvqA 105 :G Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues T0132 113 :YCVTDAVFTFVAV 1bvqA 108 :QLVMRADEIRVFA Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.92416 Ang CG2(87) at 47.542 44.032 17.247 in (null):V-9999 (11) and CG1(98) at 47.9279 45.7692 14.9267 in (null):V-9999 (13) other bump:2.77153 Ang CB(56) at 44.0152 33.5989 17.2862 in (null):F-9999 (8) and CE2(79) at 42.7394 35.8479 16.2885 in (null):F-9999 (10) neighbor-bump: 2.42254 Ang O(25) at 41.092 18.965 15.737 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) neighbor-bump: 2.85668 Ang C(26) at 39.965 19.422 15.603 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) T0132 126 :DNNGRSRTIPRE 1bvqA 124 :GERLRAIEVPAD Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues self-bump: 1.38808 Ang CA(11) at 58.067 51.967 9.609 in (null):N-9999 (2) and CB(12) at 59.3677 51.684 10.0027 in (null):N-9999 (2) self-bump: 1.33771 Ang CA(3) at 55.65 54.923 9.872 in (null):D-9999 (1) and CB(4) at 56.643 55.7765 10.1457 in (null):D-9999 (1) Number of specific fragments= 4 total=18 Number of alignments=4 sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: NP: command not found sh: 16272768: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: XP: command not found sh: 13626231: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: 15614865: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: NP: command not found sh: ref: command not found sh: 15613361: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: NP: command not found sh: ref: command not found sh: 15602193: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: 15805310: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: P49851: command not found sh: sp: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: 16122425: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: NP: command not found sh: ref: command not found sh: 16760145: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: NP: command not found sh: ref: command not found sh: 15924868: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: ref: command not found sh: NP: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: NP: command not found sh: 15835436: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: ref: command not found sh: NP: command not found sh: 13541468: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: NP: command not found sh: 16803985: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: NP: command not found sh: 15801479: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: ref: command not found sh: 15676820: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: ref: command not found sh: 15794068: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: 15605264: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: ref: command not found sh: NP: command not found sh: 15601694: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: ref: command not found sh: 9790025: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: 12331400: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: ref: command not found sh: 17485787: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: XP: command not found sh: ref: command not found sh: 14768741: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: NP: command not found sh: ref: command not found sh: 15790012: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: NP: command not found sh: ref: command not found sh: 13472339: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: NP: command not found sh: 15791208: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: NP: command not found sh: ref: command not found sh: 15965651: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: NP: command not found sh: ref: command not found sh: 17937565: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: NP: command not found sh: 15889285: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: ref: command not found sh: 17986786: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: ref: command not found sh: XP: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: pir: command not found sh: 7514038: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 17545196: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: 5327040: command not found sh: emb: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: NP: command not found sh: ref: command not found sh: 15792244: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: dbj: command not found sh: BAA89437: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: NP: command not found sh: ref: command not found sh: 15891126: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: NP: command not found sh: ref: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: ref: command not found sh: 20535287: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: 18314041: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: NP: command not found sh: 15595646: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/1bvqA-T0132-vit-adpstyle1.pw.a2m.gz # found chain 1bvqA in template set T0132 39 :IMSQMDMGGAILAKEIAHGRVVTVAVESMNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWVKKVA 1bvqA 38 :YFIKCGLPPWRQTVVERGIVGTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSRTTPG Fragment has 30 clashes (null) has 30 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 69 residues neighbor-bump: 1.84427 Ang O(495) at 31.153 9.74 6.145 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 2.31772 Ang C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) and CB(499) at 29.8757 8.41235 6.22983 in (null):A-9999 (67) neighbor-bump: 3.14282 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and CA(498) at 28.582 9.428 6.203 in (null):A-9999 (67) neighbor-bump: 1.95103 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and N(497) at 29.194 10.425 5.355 in (null):A-9999 (67) self-bump: 2.3527 Ang CG1(493) at 29.2521 10.7516 3.43238 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 2.20723 Ang CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) and C(496) at 30.502 10.487 5.408 in (null):V-9999 (66) self-bump: 1.25472 Ang CA(491) at 31.187 11.533 4.553 in (null):V-9999 (66) and CB(492) at 30.438 11.6903 3.55873 in (null):V-9999 (66) other bump:2.47461 Ang CG2(257) at 39.4598 17.0837 10.1056 in (null):I-9999 (35) and CG2(469) at 37.3619 17.7592 11.2308 in (null):V-9999 (63) other bump:2.96772 Ang CD(439) at 33.735 23.5616 19.5704 in (null):E-9999 (60) and NE1(459) at 32.8819 21.3733 17.7562 in (null):W-9999 (62) other bump:2.87911 Ang CG1(296) at 36.2935 23.038 9.8441 in (null):V-9999 (41) and CG1(447) at 37.76 22.734 12.303 in (null):V-9999 (61) other bump:2.79408 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.75518 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CE(424) at 37.0158 29.757 23.99 in (null):K-9999 (58) other bump:2.91844 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CD(423) at 36.2404 29.6502 22.7204 in (null):K-9999 (58) other bump:2.97508 Ang CG(346) at 37.2344 33.0588 23.7394 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.9956 Ang CD1(347) at 38.4449 32.1579 23.994 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:3.16828 Ang CD2(348) at 35.9297 32.2884 23.929 in (null):L-9999 (48) and CB(421) at 37.4249 31.3892 21.2844 in (null):K-9999 (58) other bump:2.49971 Ang CE(356) at 41.9954 36.4564 28.0745 in (null):K-9999 (49) and NZ(408) at 42.8232 34.4442 26.8439 in (null):K-9999 (56) other bump:2.39776 Ang CE1(318) at 31.1197 29.7953 19.3178 in (null):Y-9999 (44) and OE1(333) at 32.5151 30.453 21.1534 in (null):Q-9999 (46) other bump:2.61852 Ang OD1(215) at 43.2464 19.4805 21.4415 in (null):N-9999 (30) and CG1(232) at 41.4972 17.7757 20.4975 in (null):I-9999 (32) other bump:2.4847 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.59807 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CZ(226) at 47.064 22.784 14.68 in (null):F-9999 (31) other bump:1.98044 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE2(225) at 45.968 22.236 14.003 in (null):F-9999 (31) other bump:3.1178 Ang SD(206) at 47.1918 25.1912 15.2821 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) other bump:2.54477 Ang CE(207) at 46.0323 23.9742 14.95 in (null):M-9999 (29) and CE1(224) at 47.577 22.142 15.806 in (null):F-9999 (31) neighbor-bump: 3.16621 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and CA(155) at 44.107 42.553 13.08 in (null):V-9999 (22) neighbor-bump: 2.16426 Ang CG1(150) at 45.0672 42.5986 10.0632 in (null):V-9999 (21) and N(154) at 43.818 43.1 11.758 in (null):V-9999 (22) neighbor-bump: 1.52039 Ang O(145) at 44.73 45.499 7.772 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.33105 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CG2(151) at 45.4541 44.2611 8.27689 in (null):V-9999 (21) neighbor-bump: 2.60525 Ang C(146) at 44.528 46.375 8.605 in (null):R-9999 (20) and CB(149) at 45.0756 44.0982 9.74666 in (null):V-9999 (21) other bump:2.39785 Ang O(68) at 40.772 48.514 4.996 in (null):A-9999 (10) and CG(94) at 43.0269 49.187 5.45686 in (null):K-9999 (14) T0132 110 :G 1bvqA 105 :G Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 3 residues T0132 113 :YCVTDAVFTFVAV 1bvqA 108 :QLVMRADEIRVFA Fragment has 4 clashes (null) has 4 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 15 residues other bump:2.92416 Ang CG2(87) at 47.542 44.032 17.247 in (null):V-9999 (11) and CG1(98) at 47.9279 45.7692 14.9267 in (null):V-9999 (13) other bump:2.77153 Ang CB(56) at 44.0152 33.5989 17.2862 in (null):F-9999 (8) and CE2(79) at 42.7394 35.8479 16.2885 in (null):F-9999 (10) neighbor-bump: 2.42254 Ang O(25) at 41.092 18.965 15.737 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) neighbor-bump: 2.85668 Ang C(26) at 39.965 19.422 15.603 in (null):V-9999 (3) and CG2(30) at 42.3156 20.8436 14.8193 in (null):T-9999 (4) T0132 126 :DNNGRSRTIPRE 1bvqA 124 :GERLRAIEVPAD Fragment has 2 clashes (null) has 2 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 14 residues self-bump: 1.38808 Ang CA(11) at 58.067 51.967 9.609 in (null):N-9999 (2) and CB(12) at 59.3677 51.684 10.0027 in (null):N-9999 (2) self-bump: 1.33771 Ang CA(3) at 55.65 54.923 9.872 in (null):D-9999 (1) and CB(4) at 56.643 55.7765 10.1457 in (null):D-9999 (1) Number of specific fragments= 4 total=22 Number of alignments=5 sh: ref: command not found sh: 19923052: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: 16272768: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: 13626231: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: NP: command not found sh: 15614865: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: ref: command not found sh: 15613361: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: ref: command not found sh: NP: command not found sh: 15602193: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: NP: command not found sh: 15805310: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: sp: command not found sh: P49851: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: NP: command not found sh: ref: command not found sh: 16122425: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: NP: command not found sh: ref: command not found sh: 16760145: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: NP: command not found sh: 15924868: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: ref: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: 15835436: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: 13541468: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: ref: command not found sh: NP: command not found sh: 16803985: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: NP: command not found sh: ref: command not found sh: 15801479: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: NP: command not found sh: ref: command not found sh: 15676820: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: NP: command not found sh: ref: command not found sh: 15794068: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: ref: command not found sh: 15605264: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: ref: command not found sh: NP: command not found sh: 15601694: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: ref: command not found sh: 9790025: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: ref: command not found sh: NP: command not found sh: 12331400: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: 17485787: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: 14768741: command not found sh: XP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: NP: command not found sh: ref: command not found sh: 15790012: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: 13472339: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: NP: command not found sh: ref: command not found sh: 15791208: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: 15965651: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: 17937565: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: dbj: command not found sh: BAA89437: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: emb: command not found sh: CAB46201: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: ref: command not found sh: 15889285: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: ref: command not found sh: 17986786: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: 13626231: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: NP: command not found sh: ref: command not found sh: 19923052: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 17545196: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: emb: command not found sh: 5327040: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: 15792244: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: dbj: command not found sh: BAA89437: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: NP: command not found sh: ref: command not found sh: 15891126: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: NP: command not found sh: 14600646: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: 20535287: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: 18314041: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: NP: command not found sh: 15595646: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle5.pw.a2m.gz # found chain 1bvqA in template set T0132 59 :VVTVA 1bvqA 60 :PIVSC Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues T0132 66 :SMNFIKPISVGDVVCCYGQCLKVGRSSI 1bvqA 65 :NASFVCTASYDDVLTIETCIKEWRRKSF Fragment has 8 clashes (null) has 8 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 30 residues other bump:2.79706 Ang SG(146) at 36.4004 39.4286 21.7249 in (null):C-9999 (20) and CG2(204) at 39.0497 39.9589 21.001 in (null):I-9999 (28) other bump:2.39776 Ang CE1(124) at 31.1197 29.7953 19.3178 in (null):Y-9999 (17) and OE1(139) at 32.5151 30.453 21.1534 in (null):Q-9999 (19) other bump:2.61852 Ang OD1(21) at 43.2464 19.4805 21.4415 in (null):N-9999 (3) and CG1(38) at 41.4972 17.7757 20.4975 in (null):I-9999 (5) other bump:2.48469 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.59807 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.98043 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE2(31) at 45.968 22.236 14.003 in (null):F-9999 (4) other bump:3.1178 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) other bump:2.54476 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) Number of specific fragments= 2 total=24 Number of alignments=6 sh: 19923052: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: dbj: command not found sh: BAB27086: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: 16272768: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: 13626231: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: 15614865: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: ref: command not found sh: 15613361: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: NP: command not found sh: ref: command not found sh: 15602193: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: 15805310: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: sp: command not found sh: P49851: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: 16122425: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: ref: command not found sh: 16760145: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: ref: command not found sh: 15924868: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: ref: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: 15835436: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: ref: command not found sh: NP: command not found sh: 13541468: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: NP: command not found sh: ref: command not found sh: 16803985: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: ref: command not found sh: 15801479: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: 15676820: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: NP: command not found sh: ref: command not found sh: 15794068: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: ref: command not found sh: 15605264: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: NP: command not found sh: 15601694: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: ref: command not found sh: 9790025: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: 12331400: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: ref: command not found sh: 17485787: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: ref: command not found sh: 14768741: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: 15790012: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: NP: command not found sh: 13472339: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: NP: command not found sh: ref: command not found sh: 15791208: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: ref: command not found sh: NP: command not found sh: 15965651: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: 17937565: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: NP: command not found sh: ref: command not found sh: 15889285: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: ref: command not found sh: NP: command not found sh: 17986786: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: ref: command not found sh: XP: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 5327041: command not found sh: emb: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: 17545196: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: emb: command not found sh: 5327040: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: ref: command not found sh: 15792244: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: ref: command not found sh: 15891126: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: ref: command not found sh: NP: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: XP: command not found sh: ref: command not found sh: 20535287: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: ref: command not found sh: 18314041: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: NP: command not found sh: ref: command not found sh: 15595646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-local-adpstyle1.pw.a2m.gz # found chain 1bvqA in template set T0132 66 :SMNFIKPISVGDVVCCYGQCLKVGRSS 1bvqA 65 :NASFVCTASYDDVLTIETCIKEWRRKS Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 29 residues other bump:2.39776 Ang CE1(124) at 31.1197 29.7953 19.3178 in (null):Y-9999 (17) and OE1(139) at 32.5151 30.453 21.1534 in (null):Q-9999 (19) other bump:2.61852 Ang OD1(21) at 43.2464 19.4805 21.4415 in (null):N-9999 (3) and CG1(38) at 41.4972 17.7757 20.4975 in (null):I-9999 (5) other bump:2.48469 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.59807 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.98043 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE2(31) at 45.968 22.236 14.003 in (null):F-9999 (4) other bump:3.1178 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) other bump:2.54476 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) Number of specific fragments= 1 total=25 Number of alignments=7 sh: 19923052: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: dbj: command not found sh: BAB27086: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: 16272768: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: ref: command not found sh: XP: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: 15614865: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: ref: command not found sh: NP: command not found sh: 15613361: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: 15602193: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: ref: command not found sh: 15805310: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: sp: command not found sh: P49851: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: NP: command not found sh: 16122425: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: ref: command not found sh: NP: command not found sh: 16760145: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: NP: command not found sh: 15924868: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: ref: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: NP: command not found sh: 15835436: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: 13541468: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: NP: command not found sh: ref: command not found sh: 16803985: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: ref: command not found sh: 15801479: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: 15676820: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: ref: command not found sh: 15794068: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: NP: command not found sh: 15605264: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: NP: command not found sh: ref: command not found sh: 15601694: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: 9790025: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: ref: command not found sh: NP: command not found sh: 12331400: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: ref: command not found sh: 17485787: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: ref: command not found sh: XP: command not found sh: 14768741: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: NP: command not found sh: 15790012: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: 13472339: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: 15791208: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: NP: command not found sh: ref: command not found sh: 15965651: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: NP: command not found sh: 17937565: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: NP: command not found sh: ref: command not found sh: 15889285: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: NP: command not found sh: ref: command not found sh: 17986786: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: ref: command not found sh: XP: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: ref: command not found sh: NP: command not found sh: 19923052: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: ref: command not found sh: 17545196: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: 5327040: command not found sh: emb: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: 15792244: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: dbj: command not found sh: BAA89437: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: ref: command not found sh: NP: command not found sh: 15891126: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: 14600646: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: ref: command not found sh: 20535287: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: ref: command not found sh: 18314041: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: ref: command not found sh: NP: command not found sh: 15595646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle1.pw.a2m.gz # found chain 1bvqA in template set T0132 66 :SMNFIKPISVGDVVCCYGQCLKVGRSS 1bvqA 65 :NASFVCTASYDDVLTIETCIKEWRRKS Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 29 residues other bump:2.39776 Ang CE1(124) at 31.1197 29.7953 19.3178 in (null):Y-9999 (17) and OE1(139) at 32.5151 30.453 21.1534 in (null):Q-9999 (19) other bump:2.61852 Ang OD1(21) at 43.2464 19.4805 21.4415 in (null):N-9999 (3) and CG1(38) at 41.4972 17.7757 20.4975 in (null):I-9999 (5) other bump:2.48469 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.59807 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.98043 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE2(31) at 45.968 22.236 14.003 in (null):F-9999 (4) other bump:3.1178 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) other bump:2.54476 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) Number of specific fragments= 1 total=26 Number of alignments=8 sh: ref: command not found sh: 19923052: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: dbj: command not found sh: BAB27086: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: NP: command not found sh: ref: command not found sh: 16272768: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: XP: command not found sh: ref: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: 15614865: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: 15613361: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: NP: command not found sh: 15602193: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: NP: command not found sh: 15805310: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: P49851: command not found sh: sp: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: NP: command not found sh: 16122425: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: ref: command not found sh: NP: command not found sh: 16760145: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: NP: command not found sh: ref: command not found sh: 15924868: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: ref: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: ref: command not found sh: NP: command not found sh: 15835436: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: NP: command not found sh: ref: command not found sh: 13541468: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: NP: command not found sh: 16803985: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: 15801479: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: ref: command not found sh: NP: command not found sh: 15676820: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: 15794068: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: NP: command not found sh: ref: command not found sh: 15605264: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: 15601694: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: 9790025: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: NP: command not found sh: ref: command not found sh: 12331400: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: ref: command not found sh: 17485787: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: ref: command not found sh: 14768741: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: sp: command not found sh: Q9R0X4: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: NP: command not found sh: ref: command not found sh: 15790012: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: NP: command not found sh: ref: command not found sh: 13472339: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: ref: command not found sh: NP: command not found sh: 15791208: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: NP: command not found sh: ref: command not found sh: 15965651: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: NP: command not found sh: 17937565: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: dbj: command not found sh: BAA89437: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: emb: command not found sh: CAB46201: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: 15889285: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: NP: command not found sh: 17986786: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: XP: command not found sh: ref: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: NP: command not found sh: ref: command not found sh: 19923052: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 17545196: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: 5327040: command not found sh: emb: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: ref: command not found sh: NP: command not found sh: 15792244: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: NP: command not found sh: 15891126: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: ref: command not found sh: NP: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: ref: command not found sh: 20535287: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: 18314041: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: 15595646: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-vit-adpstyle5.pw.a2m.gz # found chain 1bvqA in template set T0132 59 :VVTVA 1bvqA 60 :PIVSC Fragment has 0 clashes (null) has 0 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 7 residues T0132 66 :SMNFIKPISVGDVVCCYGQCLKVGRSSI 1bvqA 65 :NASFVCTASYDDVLTIETCIKEWRRKSF Fragment has 8 clashes (null) has 8 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 30 residues other bump:2.79706 Ang SG(146) at 36.4004 39.4286 21.7249 in (null):C-9999 (20) and CG2(204) at 39.0497 39.9589 21.001 in (null):I-9999 (28) other bump:2.39776 Ang CE1(124) at 31.1197 29.7953 19.3178 in (null):Y-9999 (17) and OE1(139) at 32.5151 30.453 21.1534 in (null):Q-9999 (19) other bump:2.61852 Ang OD1(21) at 43.2464 19.4805 21.4415 in (null):N-9999 (3) and CG1(38) at 41.4972 17.7757 20.4975 in (null):I-9999 (5) other bump:2.48469 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.59807 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CZ(32) at 47.064 22.784 14.68 in (null):F-9999 (4) other bump:1.98043 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE2(31) at 45.968 22.236 14.003 in (null):F-9999 (4) other bump:3.1178 Ang SD(12) at 47.1918 25.1912 15.2821 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) other bump:2.54476 Ang CE(13) at 46.0323 23.9742 14.95 in (null):M-9999 (2) and CE1(30) at 47.577 22.142 15.806 in (null):F-9999 (4) Number of specific fragments= 2 total=28 Number of alignments=9 sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: dbj: command not found sh: BAB27086: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: NP: command not found sh: ref: command not found sh: 16272768: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: XP: command not found sh: ref: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 15614865: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: ref: command not found sh: NP: command not found sh: 15613361: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: 15602193: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: ref: command not found sh: NP: command not found sh: 15805310: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: P49851: command not found sh: sp: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: ref: command not found sh: NP: command not found sh: 16122425: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: 16760145: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: ref: command not found sh: 15924868: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: ref: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: 15835436: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: NP: command not found sh: 13541468: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: NP: command not found sh: ref: command not found sh: 16803985: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: NP: command not found sh: 15801479: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: ref: command not found sh: 15676820: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: ref: command not found sh: 15794068: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: NP: command not found sh: 15605264: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: ref: command not found sh: 15601694: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: ref: command not found sh: 9790025: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: ref: command not found sh: 12331400: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: 17485787: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: XP: command not found sh: ref: command not found sh: 14768741: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: sp: command not found sh: Q9R0X4: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: NP: command not found sh: ref: command not found sh: 15790012: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: ref: command not found sh: NP: command not found sh: 13472339: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: ref: command not found sh: NP: command not found sh: 15791208: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: 15965651: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: 17937565: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: ref: command not found sh: NP: command not found sh: 15889285: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: 17986786: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: XP: command not found sh: 13626231: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: ref: command not found sh: 19923052: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 17545196: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: emb: command not found sh: 5327040: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: ref: command not found sh: NP: command not found sh: 15792244: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 15891126: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: ref: command not found sh: 14600646: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: 20535287: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: 18314041: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: NP: command not found sh: ref: command not found sh: 15595646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle1.pw.a2m.gz # found chain 1bvqA in template set T0132 26 :SDTNANGDIF 1bvqA 14 :GDCDPAGIVW Fragment has 7 clashes (null) has 7 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 12 residues other bump:1.06866 Ang OD1(28) at 48.8094 14.2136 4.54363 in (null):N-9999 (4) and OD1(41) at 49.0324 13.5826 5.37683 in (null):N-9999 (6) other bump:1.65531 Ang CG(26) at 49.7114 14.9997 4.85634 in (null):N-9999 (4) and OD1(41) at 49.0324 13.5826 5.37683 in (null):N-9999 (6) other bump:2.03682 Ang ND2(27) at 50.1337 15.1341 6.10413 in (null):N-9999 (4) and OD1(41) at 49.0324 13.5826 5.37683 in (null):N-9999 (6) other bump:2.51554 Ang ND2(27) at 50.1337 15.1341 6.10413 in (null):N-9999 (4) and ND2(40) at 49.5326 13.1147 7.47842 in (null):N-9999 (6) other bump:2.28812 Ang OD1(28) at 48.8094 14.2136 4.54363 in (null):N-9999 (4) and CG(39) at 49.588 12.8049 6.1699 in (null):N-9999 (6) other bump:2.56088 Ang CG(26) at 49.7114 14.9997 4.85634 in (null):N-9999 (4) and CG(39) at 49.588 12.8049 6.1699 in (null):N-9999 (6) other bump:2.39319 Ang ND2(27) at 50.1337 15.1341 6.10413 in (null):N-9999 (4) and CG(39) at 49.588 12.8049 6.1699 in (null):N-9999 (6) Number of specific fragments= 1 total=29 sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: NP: command not found sh: ref: command not found sh: 16272768: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: XP: command not found sh: ref: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: 15614865: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: 15613361: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: NP: command not found sh: ref: command not found sh: 15602193: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: 15805310: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: sp: command not found sh: P49851: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: NP: command not found sh: ref: command not found sh: 16122425: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: 16760145: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: ref: command not found sh: NP: command not found sh: 15924868: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: 15927452: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: 15835436: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: NP: command not found sh: 13541468: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: 16803985: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: NP: command not found sh: ref: command not found sh: 15801479: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: NP: command not found sh: 15676820: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: 15794068: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: NP: command not found sh: 15605264: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: NP: command not found sh: 15601694: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: NP: command not found sh: 9790025: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: ref: command not found sh: 12331400: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: XP: command not found sh: ref: command not found sh: 17485787: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: XP: command not found sh: 14768741: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: ref: command not found sh: 15790012: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: NP: command not found sh: 13472339: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: ref: command not found sh: NP: command not found sh: 15791208: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: ref: command not found sh: 15965651: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: ref: command not found sh: NP: command not found sh: 17937565: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: NP: command not found sh: 15889285: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: NP: command not found sh: ref: command not found sh: 17986786: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: XP: command not found sh: ref: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: NP: command not found sh: ref: command not found sh: 19923052: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: 17545196: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: emb: command not found sh: 5327040: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: NP: command not found sh: ref: command not found sh: 15792244: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: NP: command not found sh: ref: command not found sh: 15891126: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: NP: command not found sh: ref: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: ref: command not found sh: 20535287: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: 18314041: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: NP: command not found sh: ref: command not found sh: 15595646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1bvqA read from /projects/compbio/experiments/casp5/t0132/selected/1bvqA/T0132-1bvqA-simpleSW-adpstyle5.pw.a2m.gz # found chain 1bvqA in template set Number of specific fragments= 0 total=29 sh: NP: command not found sh: ref: command not found sh: 19923052: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: BAB27086: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: NP: command not found sh: ref: command not found sh: 16272768: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: XP: command not found sh: 13626231: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|13626231|ref|XP_001296.2|_170:319 or gi|13626231|ref|XP, so skipping it. # gi|7514038|pir||JC5416_176:324 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: ref: command not found sh: 15614865: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_176:324 or gi|7514038|pir||JC5416, so skipping it. # gi|15614865|ref|NP_243168.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15614865|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP or /projects/compbio/bin/pdb-get gi|15614865|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15614865|ref|NP for chain gi|15614865|ref|NP sh: NP: command not found sh: ref: command not found sh: 15613361: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15614865|ref|NP_243168.1|_7:143 or gi|15614865|ref|NP, so skipping it. # gi|15613361|ref|NP_241664.1|_7:143 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15613361|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP or /projects/compbio/bin/pdb-get gi|15613361|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15613361|ref|NP for chain gi|15613361|ref|NP sh: NP: command not found sh: ref: command not found sh: 15602193: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15613361|ref|NP_241664.1|_7:143 or gi|15613361|ref|NP, so skipping it. # gi|15602193|ref|NP_245265.1|_7:141 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15602193|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP or /projects/compbio/bin/pdb-get gi|15602193|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15602193|ref|NP for chain gi|15602193|ref|NP sh: NP: command not found sh: ref: command not found sh: 15805310: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15602193|ref|NP_245265.1|_7:141 or gi|15602193|ref|NP, so skipping it. # gi|15805310|ref|NP_294002.1|_76:215 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15805310|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP or /projects/compbio/bin/pdb-get gi|15805310|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15805310|ref|NP for chain gi|15805310|ref|NP sh: 1730265: command not found sh: sp: command not found sh: P49851: command not found sh: YKHA: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15805310|ref|NP_294002.1|_76:215 or gi|15805310|ref|NP, so skipping it. # gi|1730265|sp|P49851|YKHA_BACSU_4:141 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|1730265|sp|P49851|YKHA to template set Couldn't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA or /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|1730265|sp|P49851|YKHA for chain gi|1730265|sp|P49851|YKHA sh: NP: command not found sh: ref: command not found sh: 16122425: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|1730265|sp|P49851|YKHA_BACSU_4:141 or gi|1730265|sp|P49851|YKHA, so skipping it. # gi|16122425|ref|NP_405738.1|_5:137 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16122425|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP or /projects/compbio/bin/pdb-get gi|16122425|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16122425|ref|NP for chain gi|16122425|ref|NP sh: NP: command not found sh: 16760145: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16122425|ref|NP_405738.1|_5:137 or gi|16122425|ref|NP, so skipping it. # gi|16760145|ref|NP_455762.1|_6:130 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16760145|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP or /projects/compbio/bin/pdb-get gi|16760145|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16760145|ref|NP for chain gi|16760145|ref|NP sh: NP: command not found sh: ref: command not found sh: 15924868: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16760145|ref|NP_455762.1|_6:130 or gi|16760145|ref|NP, so skipping it. # gi|15924868|ref|NP_372402.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15924868|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP or /projects/compbio/bin/pdb-get gi|15924868|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15924868|ref|NP for chain gi|15924868|ref|NP sh: NP: command not found sh: ref: command not found sh: 15927452: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15924868|ref|NP_372402.1|_5:147 or gi|15924868|ref|NP, so skipping it. # gi|15927452|ref|NP_374985.1|_5:147 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15927452|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP or /projects/compbio/bin/pdb-get gi|15927452|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15927452|ref|NP for chain gi|15927452|ref|NP sh: ref: command not found sh: NP: command not found sh: 15835436: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15927452|ref|NP_374985.1|_5:147 or gi|15927452|ref|NP, so skipping it. # gi|15835436|ref|NP_297195.1|_22:149 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15835436|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP or /projects/compbio/bin/pdb-get gi|15835436|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15835436|ref|NP for chain gi|15835436|ref|NP sh: 13541468: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15835436|ref|NP_297195.1|_22:149 or gi|15835436|ref|NP, so skipping it. # gi|13541468|ref|NP_111156.1|_5:143 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13541468|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP or /projects/compbio/bin/pdb-get gi|13541468|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13541468|ref|NP for chain gi|13541468|ref|NP sh: NP: command not found sh: 16803985: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13541468|ref|NP_111156.1|_5:143 or gi|13541468|ref|NP, so skipping it. # gi|16803985|ref|NP_465470.1|_9:145 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|16803985|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP or /projects/compbio/bin/pdb-get gi|16803985|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16803985|ref|NP for chain gi|16803985|ref|NP sh: NP: command not found sh: ref: command not found sh: 15801479: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16803985|ref|NP_465470.1|_9:145 or gi|16803985|ref|NP, so skipping it. # gi|15801479|ref|NP_287496.1|_6:129 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15801479|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP or /projects/compbio/bin/pdb-get gi|15801479|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15801479|ref|NP for chain gi|15801479|ref|NP sh: ref: command not found sh: 15676820: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15801479|ref|NP_287496.1|_6:129 or gi|15801479|ref|NP, so skipping it. # gi|15676820|ref|NP_273965.1|_7:138 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15676820|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP or /projects/compbio/bin/pdb-get gi|15676820|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15676820|ref|NP for chain gi|15676820|ref|NP sh: ref: command not found sh: NP: command not found sh: 15794068: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15676820|ref|NP_273965.1|_7:138 or gi|15676820|ref|NP, so skipping it. # gi|15794068|ref|NP_283890.1|_7:137 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15794068|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP or /projects/compbio/bin/pdb-get gi|15794068|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15794068|ref|NP for chain gi|15794068|ref|NP sh: NP: command not found sh: ref: command not found sh: 15605264: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15794068|ref|NP_283890.1|_7:137 or gi|15794068|ref|NP, so skipping it. # gi|15605264|ref|NP_220050.1|_23:150 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15605264|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP or /projects/compbio/bin/pdb-get gi|15605264|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15605264|ref|NP for chain gi|15605264|ref|NP sh: NP: command not found sh: ref: command not found sh: 15601694: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15605264|ref|NP_220050.1|_23:150 or gi|15605264|ref|NP, so skipping it. # gi|15601694|ref|NP_233325.1|_4:135 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15601694|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP or /projects/compbio/bin/pdb-get gi|15601694|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15601694|ref|NP for chain gi|15601694|ref|NP sh: ref: command not found sh: NP: command not found sh: 9790025: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15601694|ref|NP_233325.1|_4:135 or gi|15601694|ref|NP, so skipping it. # gi|9790025|ref|NP_062710.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|9790025|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP or /projects/compbio/bin/pdb-get gi|9790025|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|9790025|ref|NP for chain gi|9790025|ref|NP sh: 12331400: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|9790025|ref|NP_062710.1|_277:407 or gi|9790025|ref|NP, so skipping it. # gi|12331400|ref|NP_073727.1|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|12331400|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP or /projects/compbio/bin/pdb-get gi|12331400|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12331400|ref|NP for chain gi|12331400|ref|NP sh: 17485787: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12331400|ref|NP_073727.1|_277:407 or gi|12331400|ref|NP, so skipping it. # gi|17485787|ref|XP_011984.3|_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17485787|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP or /projects/compbio/bin/pdb-get gi|17485787|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17485787|ref|XP for chain gi|17485787|ref|XP sh: ref: command not found sh: 14768741: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17485787|ref|XP_011984.3|_277:407 or gi|17485787|ref|XP, so skipping it. # gi|14768741|ref|XP_041442.1|_27:157 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|14768741|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP or /projects/compbio/bin/pdb-get gi|14768741|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14768741|ref|XP for chain gi|14768741|ref|XP sh: 12643842: command not found sh: Q9R0X4: command not found sh: sp: command not found sh: AC48: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14768741|ref|XP_041442.1|_27:157 or gi|14768741|ref|XP, so skipping it. # gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|12643842|sp|Q9R0X4|AC48 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 or /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12643842|sp|Q9R0X4|AC48 for chain gi|12643842|sp|Q9R0X4|AC48 sh: ref: command not found sh: NP: command not found sh: 15790012: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12643842|sp|Q9R0X4|AC48_MOUSE_277:407 or gi|12643842|sp|Q9R0X4|AC48, so skipping it. # gi|15790012|ref|NP_279836.1|_6:136 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15790012|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP or /projects/compbio/bin/pdb-get gi|15790012|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15790012|ref|NP for chain gi|15790012|ref|NP sh: 13472339: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15790012|ref|NP_279836.1|_6:136 or gi|15790012|ref|NP, so skipping it. # gi|13472339|ref|NP_103906.1|_12:128 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13472339|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP or /projects/compbio/bin/pdb-get gi|13472339|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13472339|ref|NP for chain gi|13472339|ref|NP sh: NP: command not found sh: 15791208: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13472339|ref|NP_103906.1|_12:128 or gi|13472339|ref|NP, so skipping it. # gi|15791208|ref|NP_281032.1|_3:125 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15791208|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP or /projects/compbio/bin/pdb-get gi|15791208|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15791208|ref|NP for chain gi|15791208|ref|NP sh: NP: command not found sh: 15965651: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15791208|ref|NP_281032.1|_3:125 or gi|15791208|ref|NP, so skipping it. # gi|15965651|ref|NP_386004.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15965651|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP or /projects/compbio/bin/pdb-get gi|15965651|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15965651|ref|NP for chain gi|15965651|ref|NP sh: 17937565: command not found sh: ref: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15965651|ref|NP_386004.1|_6:126 or gi|15965651|ref|NP, so skipping it. # gi|17937565|ref|NP_534354.1|_6:126 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17937565|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP or /projects/compbio/bin/pdb-get gi|17937565|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17937565|ref|NP for chain gi|17937565|ref|NP sh: 6705946: command not found sh: BAA89437: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17937565|ref|NP_534354.1|_6:126 or gi|17937565|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_189:327 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: 5327039: command not found sh: CAB46201: command not found sh: emb: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_189:327 or gi|6705946|dbj|BAA89437, so skipping it. # gi|5327039|emb|CAB46201.1|_40:189 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|5327039|emb|CAB46201 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 or /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327039|emb|CAB46201 for chain gi|5327039|emb|CAB46201 sh: ref: command not found sh: 15889285: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327039|emb|CAB46201.1|_40:189 or gi|5327039|emb|CAB46201, so skipping it. # gi|15889285|ref|NP_354966.1|_8:127 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15889285|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP or /projects/compbio/bin/pdb-get gi|15889285|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15889285|ref|NP for chain gi|15889285|ref|NP sh: ref: command not found sh: NP: command not found sh: 17986786: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15889285|ref|NP_354966.1|_8:127 or gi|15889285|ref|NP, so skipping it. # gi|17986786|ref|NP_539420.1|_9:129 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17986786|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP or /projects/compbio/bin/pdb-get gi|17986786|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17986786|ref|NP for chain gi|17986786|ref|NP sh: XP: command not found sh: ref: command not found sh: 13626231: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17986786|ref|NP_539420.1|_9:129 or gi|17986786|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_9:147 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: ref: command not found sh: 19923052: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|13626231|ref|XP_001296.2|_9:147 or gi|13626231|ref|XP, so skipping it. # gi|19923052|ref|NP_579926.1|_11:147 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: emb: command not found sh: 5327041: command not found sh: CAB46203: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_11:147 or gi|19923052|ref|NP, so skipping it. # gi|5327041|emb|CAB46203.1|_5:138 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|5327041|emb|CAB46203 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 or /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327041|emb|CAB46203 for chain gi|5327041|emb|CAB46203 sh: 7514038: command not found sh: pir: command not found PDB file download failed: Can't locate PDB file for gi sh: JC5416: command not found Error: can't find template for gi|5327041|emb|CAB46203.1|_5:138 or gi|5327041|emb|CAB46203, so skipping it. # gi|7514038|pir||JC5416_12:152 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|7514038|pir||JC5416 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 or /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|7514038|pir||JC5416 for chain gi|7514038|pir||JC5416 sh: NP: command not found sh: ref: command not found sh: 17545196: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|7514038|pir||JC5416_12:152 or gi|7514038|pir||JC5416, so skipping it. # gi|17545196|ref|NP_518598.1|_20:137 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|17545196|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP or /projects/compbio/bin/pdb-get gi|17545196|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|17545196|ref|NP for chain gi|17545196|ref|NP sh: emb: command not found sh: 5327040: command not found sh: CAB46202: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|17545196|ref|NP_518598.1|_20:137 or gi|17545196|ref|NP, so skipping it. # gi|5327040|emb|CAB46202.1|_29:159 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|5327040|emb|CAB46202 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 or /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|5327040|emb|CAB46202 for chain gi|5327040|emb|CAB46202 sh: ref: command not found sh: NP: command not found sh: 15792244: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|5327040|emb|CAB46202.1|_29:159 or gi|5327040|emb|CAB46202, so skipping it. # gi|15792244|ref|NP_282067.1|_7:124 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15792244|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP or /projects/compbio/bin/pdb-get gi|15792244|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15792244|ref|NP for chain gi|15792244|ref|NP sh: BAA89437: command not found sh: 6705946: command not found sh: dbj: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15792244|ref|NP_282067.1|_7:124 or gi|15792244|ref|NP, so skipping it. # gi|6705946|dbj|BAA89437.1|_27:168 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|6705946|dbj|BAA89437 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 or /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|6705946|dbj|BAA89437 for chain gi|6705946|dbj|BAA89437 sh: NP: command not found sh: 15891126: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|6705946|dbj|BAA89437.1|_27:168 or gi|6705946|dbj|BAA89437, so skipping it. # gi|15891126|ref|NP_356798.1|_12:124 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15891126|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP or /projects/compbio/bin/pdb-get gi|15891126|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15891126|ref|NP for chain gi|15891126|ref|NP sh: ref: command not found sh: NP: command not found sh: 14600646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|15891126|ref|NP_356798.1|_12:124 or gi|15891126|ref|NP, so skipping it. # gi|14600646|ref|NP_147163.1|_190:331 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|14600646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP or /projects/compbio/bin/pdb-get gi|14600646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|14600646|ref|NP for chain gi|14600646|ref|NP sh: 20535287: command not found sh: ref: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|14600646|ref|NP_147163.1|_190:331 or gi|14600646|ref|NP, so skipping it. # gi|20535287|ref|XP_068105.4|_134:245 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|20535287|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP or /projects/compbio/bin/pdb-get gi|20535287|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|20535287|ref|XP for chain gi|20535287|ref|XP sh: NP: command not found sh: ref: command not found sh: 18314041: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|20535287|ref|XP_068105.4|_134:245 or gi|20535287|ref|XP, so skipping it. # gi|18314041|ref|NP_560708.1|_158:272 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|18314041|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP or /projects/compbio/bin/pdb-get gi|18314041|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|18314041|ref|NP for chain gi|18314041|ref|NP sh: ref: command not found sh: NP: command not found sh: 15595646: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|18314041|ref|NP_560708.1|_158:272 or gi|18314041|ref|NP, so skipping it. # gi|15595646|ref|NP_249140.1|_51:161 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding gi|15595646|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP or /projects/compbio/bin/pdb-get gi|15595646|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|15595646|ref|NP for chain gi|15595646|ref|NP Error: can't find template for gi|15595646|ref|NP_249140.1|_51:161 or gi|15595646|ref|NP, so skipping it. # 1krs read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle5.pw.a2m.gz # adding 1krs to template set 1krs:# found chain 1krs in template set T0132 33 :DIFGGWIMSQMDMGGAILAKEIAHGRVVTVAVES 1krs 68 :VAVAGRMMTRRIMGKASFVTLQDVGGRIQLYVAR Fragment has 27 clashes (null) has 27 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 36 residues other bump:3.01867 Ang CG1(122) at -7.5969 -7.05142 -1.2487 in (null):I-9999 (17) and CB(231) at -5.298 -5.812 0.265 in (null):V-9999 (32) neighbor-bump: 2.50644 Ang CG2(221) at -1.59271 -2.66612 -1.32995 in (null):V-9999 (30) and N(224) at -0.815 -4.842 -2.301 in (null):A-9999 (31) other bump:3.01549 Ang C(139) at -4.732 -3.11 -5.786 in (null):A-9999 (19) and CG1(220) at -3.20716 -2.4761 -3.26286 in (null):V-9999 (30) other bump:2.97864 Ang CB(137) at -5.983 -3.496 -3.619 in (null):A-9999 (19) and CG1(220) at -3.20716 -2.4761 -3.26286 in (null):V-9999 (30) other bump:2.92956 Ang CE(145) at -3.42042 -1.54827 -11.4309 in (null):K-9999 (20) and CG2(213) at -1.25668 -1.9138 -9.49003 in (null):T-9999 (29) other bump:2.32459 Ang CD1(22) at -1.45183 2.85787 -3.23544 in (null):F-9999 (3) and CG1(206) at -0.333 2.533 -5.247 in (null):V-9999 (28) other bump:1.33847 Ang CE1(24) at -0.556191 2.11035 -3.99678 in (null):F-9999 (3) and CG1(206) at -0.333 2.533 -5.247 in (null):V-9999 (28) other bump:2.40432 Ang CZ(26) at 0.0107155 0.957152 -3.46394 in (null):F-9999 (3) and CG1(206) at -0.333 2.533 -5.247 in (null):V-9999 (28) other bump:2.84242 Ang CE1(24) at -0.556191 2.11035 -3.99678 in (null):F-9999 (3) and CB(205) at 0.481 2.921 -6.516 in (null):V-9999 (28) other bump:2.64016 Ang CG2(162) at -6.56622 5.26241 -9.92991 in (null):I-9999 (22) and CG1(199) at -4.35316 4.20276 -10.9046 in (null):V-9999 (27) other bump:2.24616 Ang O(49) at -8.626 5.882 -6.198 in (null):W-9999 (6) and CG1(161) at -7.82391 6.54559 -8.18836 in (null):I-9999 (22) other bump:2.50483 Ang CG2(55) at -7.23617 3.15883 -5.68333 in (null):I-9999 (7) and N(158) at -5.794 4.735 -6.991 in (null):I-9999 (22) other bump:2.63342 Ang CG2(55) at -7.23617 3.15883 -5.68333 in (null):I-9999 (7) and C(157) at -5.073 3.643 -7.105 in (null):E-9999 (21) other bump:2.01527 Ang CB(20) at -2.73892 3.28607 -1.11453 in (null):F-9999 (3) and OE2(155) at -4.48661 3.36436 -2.11491 in (null):E-9999 (21) other bump:2.84595 Ang CG(21) at -1.79228 2.4641 -1.94301 in (null):F-9999 (3) and OE2(155) at -4.48661 3.36436 -2.11491 in (null):E-9999 (21) other bump:2.73394 Ang CB(20) at -2.73892 3.28607 -1.11453 in (null):F-9999 (3) and CD(153) at -4.94427 2.22184 -2.33036 in (null):E-9999 (21) other bump:2.89389 Ang CG2(55) at -7.23617 3.15883 -5.68333 in (null):I-9999 (7) and CG(152) at -5.53561 1.92239 -3.69489 in (null):E-9999 (21) other bump:2.50124 Ang CD1(56) at -7.68265 0.653976 -3.88862 in (null):I-9999 (7) and CG(152) at -5.53561 1.92239 -3.69489 in (null):E-9999 (21) other bump:2.42094 Ang CG2(55) at -7.23617 3.15883 -5.68333 in (null):I-9999 (7) and CB(151) at -5.01089 2.84786 -4.78204 in (null):E-9999 (21) other bump:3.09853 Ang CB(53) at -8.5519 2.37645 -5.6061 in (null):I-9999 (7) and CA(150) at -5.525 2.488 -6.259 in (null):E-9999 (21) other bump:1.92601 Ang CG2(55) at -7.23617 3.15883 -5.68333 in (null):I-9999 (7) and CA(150) at -5.525 2.488 -6.259 in (null):E-9999 (21) other bump:2.39166 Ang OD1(94) at -11.2739 -8.72966 -2.60547 in (null):D-9999 (12) and CG2(123) at -9.12714 -9.01523 -1.5906 in (null):I-9999 (17) self-bump: 1.34693 Ang CA(115) at -6.564 -10.877 1.569 in (null):A-9999 (16) and CB(116) at -5.527 -11.648 1.949 in (null):A-9999 (16) self-bump: 2.36213 Ang N(29) at -3.152 6.526 -0.483 in (null):G-9999 (4) and O(31) at -4.509 7.147 -2.314 in (null):G-9999 (4) neighbor-bump: 2.06895 Ang CA(11) at 0.898 3.921 1.015 in (null):I-9999 (2) and N(18) at -1.009 4.293 0.304 in (null):F-9999 (3) neighbor-bump: 2.48962 Ang CB(12) at 0.597444 5.38644 1.86025 in (null):I-9999 (2) and N(18) at -1.009 4.293 0.304 in (null):F-9999 (3) neighbor-bump: 2.05962 Ang CA(3) at 4.193 3.108 1.697 in (null):D-9999 (1) and N(10) at 2.265 3.699 1.278 in (null):I-9999 (2) T0132 67 :MN 1krs 109 :YN Fragment has 5 clashes (null) has 5 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 4 residues neighbor-bump: 2.8394 Ang CG(5) at -9.4628 -6.37989 2.7189 in (null):M-9999 (1) and CB(12) at -9.906 -5.661 0.008 in (null):N-9999 (2) neighbor-bump: 2.90794 Ang CG(5) at -9.4628 -6.37989 2.7189 in (null):M-9999 (1) and CA(11) at -9.994 -4.328 0.728 in (null):N-9999 (2) neighbor-bump: 2.34451 Ang CB(4) at -9.85909 -5.67482 4.02281 in (null):M-9999 (1) and N(10) at -9.398 -4.48 2.059 in (null):N-9999 (2) neighbor-bump: 2.01227 Ang CG(5) at -9.4628 -6.37989 2.7189 in (null):M-9999 (1) and N(10) at -9.398 -4.48 2.059 in (null):N-9999 (2) self-bump: 2.21996 Ang CB(4) at -9.85909 -5.67482 4.02281 in (null):M-9999 (1) and C(9) at -9.57 -3.696 3.059 in (null):M-9999 (1) T0132 69 :FIKPISVGDVVCCYGQCLKVGRSSIKIKVEV 1krs 112 :QFKKWDLGDILGAKGKLFKTKTGELSIHCTE Fragment has 26 clashes (null) has 26 clashes, 0 disulphide bonds, and 0 hydrogen bonds in 33 residues other bump:3.17254 Ang CA(109) at 1.976 -1.088 3.003 in (null):G-9999 (15) and C(211) at 1.305 -3.992 1.916 in (null):K-9999 (28) other bump:1.64842 Ang CG1(147) at 4.8808 -7.11558 -8.46051 in (null):V-9999 (20) and NZ(192) at 3.41825 -7.85226 -8.27195 in (null):K-9999 (26) other bump:1.25811 Ang CG1(147) at 4.8808 -7.11558 -8.46051 in (null):V-9999 (20) and CE(191) at 3.85349 -6.39676 -8.35662 in (null):K-9999 (26) other bump:2.2384 Ang CB(146) at 5.87824 -6.62109 -7.42899 in (null):V-9999 (20) and CE(191) at 3.85349 -6.39676 -8.35662 in (null):K-9999 (26) other bump:2.52912 Ang CG2(148) at 5.13544 -6.07536 -6.2003 in (null):V-9999 (20) and CE(191) at 3.85349 -6.39676 -8.35662 in (null):K-9999 (26) other bump:2.24968 Ang CG1(147) at 4.8808 -7.11558 -8.46051 in (null):V-9999 (20) and CD(190) at 3.83784 -5.89156 -6.88727 in (null):K-9999 (26) other bump:2.23359 Ang CB(146) at 5.87824 -6.62109 -7.42899 in (null):V-9999 (20) and CD(190) at 3.83784 -5.89156 -6.88727 in (null):K-9999 (26) other bump:1.47969 Ang CG2(148) at 5.13544 -6.07536 -6.2003 in (null):V-9999 (20) and CD(190) at 3.83784 -5.89156 -6.88727 in (null):K-9999 (26) other bump:2.76882 Ang CB(146) at 5.87824 -6.62109 -7.42899 in (null):V-9999 (20) and CG(189) at 4.28935 -4.45662 -6.75306 in (null):K-9999 (26) other bump:1.90833 Ang CG2(148) at 5.13544 -6.07536 -6.2003 in (null):V-9999 (20) and CG(189) at 4.28935 -4.45662 -6.75306 in (null):K-9999 (26) other bump:2.42868 Ang CG2(148) at 5.13544 -6.07536 -6.2003 in (null):V-9999 (20) and CB(188) at 4.20895 -4.02872 -5.2776 in (null):K-9999 (26) self-bump: 2.20547 Ang CB(174) at 11.5407 -1.90927 -5.26203 in (null):S-9999 (24) and C(177) at 9.533 -2.817 -5.166 in (null):S-9999 (24) other bump:2.37443 Ang O(133) at 7.512 -5.315 -4.053 in (null):L-9999 (18) and O(176) at 8.887 -3.4 -4.336 in (null):S-9999 (24) other bump:2.7123 Ang C(134) at 8.235 -5.76 -3.169 in (null):L-9999 (18) and O(176) at 8.887 -3.4 -4.336 in (null):S-9999 (24) self-bump: 1.29947 Ang CA(173) at 10.995 -3.076 -5.434 in (null):S-9999 (24) and CB(174) at 11.5407 -1.90927 -5.26203 in (null):S-9999 (24) other bump:2.47445 Ang CE(140) at 13.055 -10.228 -6.096 in (null):K-9999 (19) and OG(169) at 14.2448 -8.06132 -6.20851 in (null):S-9999 (23) other bump:2.32104 Ang NZ(141) at 14.526 -10.343 -5.889 in (null):K-9999 (19) and OG(169) at 14.2448 -8.06132 -6.20851 in (null):S-9999 (23) neighbor-bump: 2.2112 Ang O(164) at 14.018 -7.076 -8.175 in (null):R-9999 (22) and OG(169) at 14.2448 -8.06132 -6.20851 in (null):S-9999 (23) self-bump: 1.38798 Ang CA(85) at -3.895 7.585 4.082 in (null):C-9999 (12) and CB(86) at -3.79639 8.60807 5.01479 in (null):C-9999 (12) other bump:2.75131 Ang CD1(42) at -9.7795 4.22083 1.44058 in (null):I-9999 (5) and CG2(81) at -7.861 5.83889 0.313212 in (null):V-9999 (11) neighbor-bump: 2.46027 Ang CG1(54) at -14.2513 12.3952 -5.75017 in (null):V-9999 (7) and N(58) at -13.894 12.494 -3.318 in (null):G-9999 (8) self-bump: 1.38927 Ang CA(52) at -14.182 10.426 -4.323 in (null):V-9999 (7) and CB(53) at -14.9632 11.1759 -5.19326 in (null):V-9999 (7) other bump:2.71358 Ang O(11) at -13.113 0.956 2.034 in (null):F-9999 (1) and CB(32) at -15.651 1.84 2.409 in (null):P-9999 (4) other bump:3.01111 Ang C(1) at -13.571 -2.199 2.49 in (null):G-9999 (0) and N(21) at -13.126 -0.852 -0.166 in (null):K-9999 (3) neighbor-bump: 2.57024 Ang C(1) at -13.571 -2.199 2.49 in (null):G-9999 (0) and C(12) at -12.402 0.09 2.482 in (null):F-9999 (1) self-bump: 1.39005 Ang CA(3) at -12.622 -0.51 3.858 in (null):F-9999 (1) and CB(4) at -11.638 -0.165638 4.77742 in (null):F-9999 (1) Number of specific fragments= 3 total=32 Number of alignments=10 sh: 19923052: command not found sh: NP: command not found sh: ref: command not found PDB file download failed: Can't locate PDB file for gi # Reading fragments from alignment file # T0132 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle1.pw.a2m.gz # gi|19923052|ref|NP_579926.1|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle1.pw.a2m.gz # adding gi|19923052|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP or /projects/compbio/bin/pdb-get gi|19923052|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|19923052|ref|NP for chain gi|19923052|ref|NP sh: 12846238: command not found sh: dbj: command not found sh: BAB27086: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|19923052|ref|NP_579926.1|_170:319 or gi|19923052|ref|NP, so skipping it. # gi|12846238|dbj|BAB27086.1|_11:160 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle1.pw.a2m.gz # adding gi|12846238|dbj|BAB27086 to template set Couldn't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 or /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|12846238|dbj|BAB27086 for chain gi|12846238|dbj|BAB27086 sh: ref: command not found sh: 16272768: command not found sh: NP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|12846238|dbj|BAB27086.1|_11:160 or gi|12846238|dbj|BAB27086, so skipping it. # gi|16272768|ref|NP_438987.1|_2:152 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle1.pw.a2m.gz # adding gi|16272768|ref|NP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP or /projects/compbio/bin/pdb-get gi|16272768|ref|NP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|16272768|ref|NP for chain gi|16272768|ref|NP sh: ref: command not found sh: 13626231: command not found sh: XP: command not found PDB file download failed: Can't locate PDB file for gi Error: can't find template for gi|16272768|ref|NP_438987.1|_2:152 or gi|16272768|ref|NP, so skipping it. # gi|13626231|ref|XP_001296.2|_170:319 read from /projects/compbio/experiments/casp5/t0132/selected/1krs/1krs-T0132-local-adpstyle1.pw.a2m.gz # adding gi|13626231|ref|XP to template set Couldn't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP or /projects/compbio/bin/pdb-get gi|13626231|ref|XP.gz for input Error: can't open file /projects/compbio/bin/pdb-get gi|13626231|ref|XP for chain gi|13626231|ref|XP sh: 7514038: command not found sh: pir: command not found