# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0334/ # command:# Making conformation for sequence T0334 numbered 1 through 530 Created new target T0334 from T0334.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0334/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334//projects/compbio/experiments/protein-predict/casp7/T0334/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0334//projects/compbio/experiments/protein-predict/casp7/T0334/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0334/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0334/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)L36.CB) [> 4.0612 = 6.7687 < 8.7993] w=1.0000 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)L37.CB) [> 3.2646 = 5.4410 < 7.0733] w=1.0000 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)L37.CB) [> 4.3044 = 7.1740 < 9.3263] w=1.0000 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)L36.CB) [> 2.9193 = 4.8655 < 6.3252] w=1.0000 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)L37.CB) [> 4.0765 = 6.7942 < 8.8325] w=1.0000 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)L36.CB) [> 4.0412 = 6.7354 < 8.7559] w=0.9941 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)L37.CB) [> 3.8219 = 6.3699 < 8.2809] w=0.9941 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)Q38.CB) [> 2.9324 = 4.8873 < 6.3534] w=0.9941 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)L36.CB) [> 3.5028 = 5.8380 < 7.5894] w=0.9941 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)Q38.CB) [> 2.6346 = 4.3909 < 5.7082] w=0.9941 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)D33.CB) [> 2.9265 = 4.8775 < 6.3408] w=0.9882 to align # Constraint # added constraint: constraint((T0334)A21.CB, (T0334)L36.CB) [> 2.9792 = 4.9654 < 6.4550] w=0.9882 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)A21.CB) [> 3.1606 = 5.2677 < 6.8480] w=0.9882 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)A20.CB) [> 3.2701 = 5.4501 < 7.0852] w=0.9882 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)L24.CB) [> 3.3379 = 5.5631 < 7.2320] w=0.9882 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)I34.CB) [> 2.9465 = 4.9108 < 6.3840] w=0.9823 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)T35.CB) [> 3.1344 = 5.2239 < 6.7911] w=0.9823 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)I34.CB) [> 3.8785 = 6.4642 < 8.4035] w=0.9823 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)T35.CB) [> 4.2952 = 7.1587 < 9.3063] w=0.9823 to align # Constraint # added constraint: constraint((T0334)L24.CB, (T0334)I34.CB) [> 3.0056 = 5.0093 < 6.5121] w=0.9823 to align # Constraint # added constraint: constraint((T0334)G25.CA, (T0334)I34.CB) [> 3.4036 = 5.6726 < 7.3744] w=0.9823 to align # Constraint # added constraint: constraint((T0334)A21.CB, (T0334)I34.CB) [> 3.1899 = 5.3165 < 6.9115] w=0.9704 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)F224.CB) [> 3.8978 = 6.4963 < 8.4453] w=0.9409 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)L36.CB) [> 4.3391 = 7.2318 < 9.4013] w=0.9350 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)D33.CB) [> 4.3638 = 7.2730 < 9.4549] w=0.9231 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)I34.CB) [> 4.5194 = 7.5324 < 9.7921] w=0.9221 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)Q38.CB) [> 4.4394 = 7.3990 < 9.6187] w=0.9057 to align # Constraint # added constraint: constraint((T0334)E198.CB, (T0334)R212.CB) [> 3.2385 = 5.3975 < 7.0167] w=0.9036 to align # Constraint # added constraint: constraint((T0334)R196.CB, (T0334)T213.CB) [> 3.7895 = 6.3159 < 8.2107] w=0.8878 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)I34.CB) [> 4.2427 = 7.0712 < 9.1926] w=0.8817 to align # Constraint # added constraint: constraint((T0334)H199.CB, (T0334)V211.CB) [> 4.3229 = 7.2048 < 9.3663] w=0.8624 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)A221.CB) [> 3.7392 = 6.2320 < 8.1016] w=0.8581 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)V211.CB) [> 3.3306 = 5.5510 < 7.2163] w=0.8563 to align # Constraint # added constraint: constraint((T0334)H199.CB, (T0334)R212.CB) [> 2.6416 = 4.4028 < 5.7236] w=0.8387 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)D220.CB) [> 4.1315 = 6.8858 < 8.9516] w=0.8345 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)V211.CB) [> 3.3937 = 5.6562 < 7.3530] w=0.8328 to align # Constraint # added constraint: constraint((T0334)S210.CB, (T0334)F219.CB) [> 3.9051 = 6.5084 < 8.4610] w=0.8312 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)R212.CB) [> 4.3363 = 7.2272 < 9.3954] w=0.8275 to align # Constraint # added constraint: constraint((T0334)V211.CB, (T0334)F224.CB) [> 3.8484 = 6.4141 < 8.3383] w=0.8269 to align # Constraint # added constraint: constraint((T0334)E198.CB, (T0334)T213.CB) [> 3.7254 = 6.2090 < 8.0717] w=0.8050 to align # Constraint # added constraint: constraint((T0334)R196.CB, (T0334)A214.CB) [> 3.1707 = 5.2845 < 6.8698] w=0.7991 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)T213.CB) [> 3.4405 = 5.7341 < 7.4544] w=0.7991 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)T35.CB) [> 4.4462 = 7.4103 < 9.6334] w=0.7972 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)A39.CB) [> 4.4249 = 7.3749 < 9.5874] w=0.7928 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)S210.CB) [> 4.4264 = 7.3774 < 9.5906] w=0.7896 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)A221.CB) [> 3.5653 = 5.9422 < 7.7248] w=0.7835 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)D222.CB) [> 3.0982 = 5.1636 < 6.7127] w=0.7835 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)A221.CB) [> 3.6300 = 6.0500 < 7.8650] w=0.7835 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)L223.CB) [> 2.8321 = 4.7201 < 6.1361] w=0.7835 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)F224.CB) [> 4.3873 = 7.3121 < 9.5057] w=0.7835 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)V225.CB) [> 3.8594 = 6.4323 < 8.3620] w=0.7835 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)A221.CB) [> 2.5700 = 4.2833 < 5.5683] w=0.7835 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)L223.CB) [> 4.4368 = 7.3946 < 9.6130] w=0.7835 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)F224.CB) [> 3.0066 = 5.0110 < 6.5143] w=0.7835 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)V225.CB) [> 4.3035 = 7.1726 < 9.3243] w=0.7835 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)V225.CB) [> 2.6682 = 4.4471 < 5.7812] w=0.7835 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)F224.CB) [> 4.0844 = 6.8074 < 8.8496] w=0.7835 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)V225.CB) [> 4.1242 = 6.8736 < 8.9357] w=0.7835 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)D226.CB) [> 3.1531 = 5.2552 < 6.8317] w=0.7835 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)V225.CB) [> 4.1388 = 6.8980 < 8.9674] w=0.7835 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)V225.CB) [> 3.2221 = 5.3702 < 6.9812] w=0.7835 to align # Constraint # added constraint: constraint((T0334)Q201.CB, (T0334)S210.CB) [> 2.8032 = 4.6720 < 6.0736] w=0.7779 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)C227.CB) [> 3.7211 = 6.2018 < 8.0623] w=0.7776 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)C227.CB) [> 2.2521 = 3.7535 < 4.8796] w=0.7776 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)C227.CB) [> 2.6075 = 4.3458 < 5.6496] w=0.7776 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)C227.CB) [> 3.6252 = 6.0420 < 7.8546] w=0.7776 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)C227.CB) [> 3.4654 = 5.7756 < 7.5083] w=0.7776 to align # Constraint # added constraint: constraint((T0334)L36.CB, (T0334)H192.CB) [> 3.3925 = 5.6542 < 7.3505] w=0.7776 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)C227.CB) [> 2.8453 = 4.7422 < 6.1648] w=0.7717 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)C227.CB) [> 3.9854 = 6.6424 < 8.6351] w=0.7717 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)C227.CB) [> 4.0580 = 6.7633 < 8.7923] w=0.7717 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)S228.CB) [> 3.2614 = 5.4356 < 7.0663] w=0.7717 to align # Constraint # added constraint: constraint((T0334)Q38.CB, (T0334)H192.CB) [> 4.2589 = 7.0981 < 9.2276] w=0.7717 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)S228.CB) [> 3.2810 = 5.4683 < 7.1088] w=0.7658 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)L223.CB) [> 4.2156 = 7.0259 < 9.1337] w=0.7599 to align # Constraint # added constraint: constraint((T0334)Q38.CB, (T0334)V193.CB) [> 4.0591 = 6.7651 < 8.7947] w=0.7540 to align # Constraint # added constraint: constraint((T0334)L24.CB, (T0334)V372.CB) [> 3.3017 = 5.5028 < 7.1536] w=0.7498 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)V364.CB) [> 2.5776 = 4.2960 < 5.5848] w=0.7498 to align # Constraint # added constraint: constraint((T0334)V211.CB, (T0334)A221.CB) [> 3.9729 = 6.6216 < 8.6081] w=0.7441 to align # Constraint # added constraint: constraint((T0334)S210.CB, (T0334)D220.CB) [> 3.1847 = 5.3079 < 6.9003] w=0.7425 to align # Constraint # added constraint: constraint((T0334)A39.CB, (T0334)R196.CB) [> 2.7472 = 4.5786 < 5.9522] w=0.7421 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)F219.CB) [> 3.4524 = 5.7539 < 7.4801] w=0.7421 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)V364.CB) [> 3.2400 = 5.4000 < 7.0200] w=0.7379 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)L368.CB) [> 2.6448 = 4.4079 < 5.7303] w=0.7379 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)A367.CB) [> 2.7244 = 4.5407 < 5.9029] w=0.7338 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)L368.CB) [> 2.8648 = 4.7747 < 6.2071] w=0.7320 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)Y365.CB) [> 3.2650 = 5.4417 < 7.0742] w=0.7320 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)D222.CB) [> 4.0298 = 6.7163 < 8.7312] w=0.7303 to align # Constraint # added constraint: constraint((T0334)Y23.CB, (T0334)L368.CB) [> 3.4508 = 5.7513 < 7.4766] w=0.7261 to align # Constraint # added constraint: constraint((T0334)T35.CB, (T0334)F219.CB) [> 3.8672 = 6.4454 < 8.3790] w=0.7244 to align # Constraint # added constraint: constraint((T0334)A39.CB, (T0334)D195.CB) [> 4.1244 = 6.8740 < 8.9362] w=0.7244 to align # Constraint # added constraint: constraint((T0334)Q38.CB, (T0334)E194.CB) [> 3.7891 = 6.3151 < 8.2097] w=0.7151 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)I361.CB) [> 3.3651 = 5.6086 < 7.2911] w=0.7108 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)L371.CB) [> 3.1901 = 5.3169 < 6.9119] w=0.7101 to align # Constraint # added constraint: constraint((T0334)Y23.CB, (T0334)Y369.CB) [> 3.6018 = 6.0030 < 7.8038] w=0.7084 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)V364.CB) [> 3.4875 = 5.8125 < 7.5563] w=0.7084 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)F224.CB) [> 4.5885 = 7.6475 < 9.9417] w=0.7083 to align # Constraint # added constraint: constraint((T0334)S22.CB, (T0334)A184.CB) [> 3.4936 = 5.8227 < 7.5695] w=0.7067 to align # Constraint # added constraint: constraint((T0334)L36.CB, (T0334)R191.CB) [> 3.6002 = 6.0002 < 7.8003] w=0.7007 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)L24.CB) [> 4.4666 = 7.4444 < 9.6777] w=0.6948 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)V364.CB) [> 3.6324 = 6.0539 < 7.8701] w=0.6924 to align # Constraint # added constraint: constraint((T0334)G347.CA, (T0334)V364.CB) [> 2.8282 = 4.7136 < 6.1277] w=0.6924 to align # Constraint # added constraint: constraint((T0334)P40.CB, (T0334)E194.CB) [> 4.1446 = 6.9077 < 8.9800] w=0.6889 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)A184.CB) [> 3.7685 = 6.2809 < 8.1652] w=0.6889 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)L180.CB) [> 2.5325 = 4.2208 < 5.4870] w=0.6795 to align # Constraint # added constraint: constraint((T0334)Q201.CB, (T0334)R212.CB) [> 4.0604 = 6.7674 < 8.7976] w=0.6732 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)V197.CB) [> 3.5465 = 5.9109 < 7.6841] w=0.6712 to align # Constraint # added constraint: constraint((T0334)A21.CB, (T0334)A184.CB) [> 3.3510 = 5.5851 < 7.2606] w=0.6712 to align # Constraint # added constraint: constraint((T0334)G347.CA, (T0334)F363.CB) [> 3.4825 = 5.8041 < 7.5453] w=0.6687 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)V197.CB) [> 2.9806 = 4.9677 < 6.4580] w=0.6653 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)G229.CA) [> 4.4274 = 7.3790 < 9.5927] w=0.6653 to align # Constraint # added constraint: constraint((T0334)T35.CB, (T0334)A221.CB) [> 4.4831 = 7.4719 < 9.7134] w=0.6593 to align # Constraint # added constraint: constraint((T0334)S22.CB, (T0334)F183.CB) [> 3.4095 = 5.6825 < 7.3872] w=0.6575 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)A367.CB) [> 3.9683 = 6.6139 < 8.5980] w=0.6551 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)G229.CA) [> 4.5315 = 7.5525 < 9.8182] w=0.6499 to align # Constraint # added constraint: constraint((T0334)Q38.CB, (T0334)D195.CB) [> 4.4059 = 7.3432 < 9.5462] w=0.6475 to align # Constraint # added constraint: constraint((T0334)E198.CB, (T0334)A214.CB) [> 3.3922 = 5.6537 < 7.3499] w=0.6450 to align # Constraint # added constraint: constraint((T0334)L36.CB, (T0334)V190.CB) [> 4.0029 = 6.6715 < 8.6729] w=0.6416 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)V211.CB) [> 3.3371 = 5.5618 < 7.2304] w=0.6399 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)A32.CB) [> 3.4188 = 5.6981 < 7.4075] w=0.6387 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)L371.CB) [> 3.5425 = 5.9042 < 7.6755] w=0.6374 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)V344.CB) [> 3.9938 = 6.6563 < 8.6532] w=0.6280 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)V344.CB) [> 4.2117 = 7.0196 < 9.1254] w=0.6280 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)L371.CB) [> 3.6345 = 6.0574 < 7.8747] w=0.6280 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)A32.CB) [> 3.2573 = 5.4288 < 7.0574] w=0.6269 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)I346.CB) [> 3.9445 = 6.5741 < 8.5464] w=0.6197 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)I346.CB) [> 2.6037 = 4.3395 < 5.6413] w=0.6197 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)T213.CB) [> 3.8943 = 6.4905 < 8.4377] w=0.6180 to align # Constraint # added constraint: constraint((T0334)I34.CB, (T0334)V190.CB) [> 3.7924 = 6.3207 < 8.2169] w=0.6180 to align # Constraint # added constraint: constraint((T0334)S22.CB, (T0334)L180.CB) [> 3.5764 = 5.9606 < 7.7488] w=0.6162 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)G347.CA) [> 2.4657 = 4.1094 < 5.3422] w=0.6137 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)I346.CB) [> 3.6266 = 6.0444 < 7.8577] w=0.6078 to align # Constraint # added constraint: constraint((T0334)T35.CB, (T0334)H192.CB) [> 4.2818 = 7.1364 < 9.2773] w=0.6065 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)I346.CB) [> 4.1260 = 6.8767 < 8.9398] w=0.6043 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)S345.CB) [> 2.8436 = 4.7394 < 6.1612] w=0.6043 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)L371.CB) [> 3.2744 = 5.4573 < 7.0945] w=0.6037 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)L36.CB) [> 4.6720 = 7.7867 < 10.1227] w=0.6028 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)C343.CB) [> 3.1580 = 5.2634 < 6.8424] w=0.5984 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)A177.CB) [> 3.8401 = 6.4002 < 8.3203] w=0.5984 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)L180.CB) [> 3.8551 = 6.4251 < 8.3526] w=0.5984 to align # Constraint # added constraint: constraint((T0334)G347.CA, (T0334)A367.CB) [> 3.4810 = 5.8017 < 7.5423] w=0.5978 to align # Constraint # added constraint: constraint((T0334)Y23.CB, (T0334)V372.CB) [> 2.4984 = 4.1640 < 5.4132] w=0.5960 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)I346.CB) [> 3.5655 = 5.9425 < 7.7253] w=0.5925 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)F375.CB) [> 3.7594 = 6.2657 < 8.1454] w=0.5901 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)R212.CB) [> 4.4772 = 7.4621 < 9.7007] w=0.5899 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)V211.CB) [> 4.2706 = 7.1176 < 9.2529] w=0.5848 to align # Constraint # added constraint: constraint((T0334)D222.CB, (T0334)N342.CB) [> 3.9381 = 6.5634 < 8.5324] w=0.5807 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)R181.CB) [> 3.7258 = 6.2096 < 8.0725] w=0.5807 to align # Constraint # added constraint: constraint((T0334)T35.CB, (T0334)R191.CB) [> 3.5398 = 5.8998 < 7.6697] w=0.5768 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)V344.CB) [> 4.0964 = 6.8273 < 8.8755] w=0.5748 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)V344.CB) [> 2.8920 = 4.8200 < 6.2660] w=0.5748 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)G347.CA) [> 3.7847 = 6.3079 < 8.2003] w=0.5748 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)A177.CB) [> 3.7277 = 6.2128 < 8.0767] w=0.5748 to align # Constraint # added constraint: constraint((T0334)Q201.CB, (T0334)V211.CB) [> 4.1874 = 6.9791 < 9.0728] w=0.5730 to align # Constraint # added constraint: constraint((T0334)G347.CA, (T0334)G360.CA) [> 4.0642 = 6.7736 < 8.8057] w=0.5723 to align # Constraint # added constraint: constraint((T0334)D6.CB, (T0334)D33.CB) [> 3.3225 = 5.5374 < 7.1987] w=0.5721 to align # Constraint # added constraint: constraint((T0334)D41.CB, (T0334)E194.CB) [> 3.5163 = 5.8605 < 7.6187] w=0.5706 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)C343.CB) [> 4.0317 = 6.7195 < 8.7353] w=0.5689 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)N342.CB) [> 3.8183 = 6.3639 < 8.2730] w=0.5689 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)N342.CB) [> 2.9231 = 4.8718 < 6.3334] w=0.5689 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)E209.CB) [> 3.9043 = 6.5071 < 8.4593] w=0.5673 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)F375.CB) [> 3.4031 = 5.6718 < 7.3733] w=0.5629 to align # Constraint # added constraint: constraint((T0334)S210.CB, (T0334)A221.CB) [> 3.8586 = 6.4310 < 8.3603] w=0.5581 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)I346.CB) [> 2.9050 = 4.8417 < 6.2942] w=0.5511 to align # Constraint # added constraint: constraint((T0334)S350.CB, (T0334)A367.CB) [> 4.2054 = 7.0091 < 9.1118] w=0.5505 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)L368.CB) [> 3.1762 = 5.2936 < 6.8817] w=0.5505 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)V211.CB) [> 4.1656 = 6.9427 < 9.0255] w=0.5475 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)C343.CB) [> 4.5181 = 7.5302 < 9.7893] w=0.5452 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)A177.CB) [> 3.6548 = 6.0913 < 7.9187] w=0.5452 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)L368.CB) [> 3.0067 = 5.0112 < 6.5146] w=0.5428 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)V372.CB) [> 3.0947 = 5.1578 < 6.7052] w=0.5369 to align # Constraint # added constraint: constraint((T0334)F230.CB, (T0334)T348.CB) [> 3.1574 = 5.2623 < 6.8410] w=0.5323 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)T348.CB) [> 4.2311 = 7.0518 < 9.1674] w=0.5306 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)L368.CB) [> 3.6740 = 6.1233 < 7.9602] w=0.5191 to align # Constraint # added constraint: constraint((T0334)G25.CA, (T0334)L188.CB) [> 3.6596 = 6.0993 < 7.9290] w=0.5171 to align # Constraint # added constraint: constraint((T0334)G229.CA, (T0334)G347.CA) [> 3.8672 = 6.4453 < 8.3788] w=0.5156 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)F224.CB) [> 3.3943 = 5.6572 < 7.3544] w=0.5105 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)L180.CB) [> 4.1318 = 6.8863 < 8.9522] w=0.5097 to align # Constraint # added constraint: constraint((T0334)D195.CB, (T0334)T215.CB) [> 3.7755 = 6.2926 < 8.1804] w=0.5060 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)A221.CB) [> 4.0222 = 6.7037 < 8.7148] w=0.5053 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)V193.CB) [> 3.2647 = 5.4411 < 7.0734] w=0.5053 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)C343.CB) [> 4.1190 = 6.8650 < 8.9244] w=0.4920 to align # Constraint # added constraint: constraint((T0334)L24.CB, (T0334)F375.CB) [> 3.8370 = 6.3951 < 8.3136] w=0.4896 to align # Constraint # added constraint: constraint((T0334)G347.CA, (T0334)L368.CB) [> 4.3026 = 7.1709 < 9.3222] w=0.4855 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)D222.CB) [> 4.3609 = 7.2681 < 9.4486] w=0.4811 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)A173.CB) [> 4.1397 = 6.8996 < 8.9694] w=0.4802 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)H192.CB) [> 3.6277 = 6.0461 < 7.8599] w=0.4689 to align # Constraint # added constraint: constraint((T0334)L36.CB, (T0334)V193.CB) [> 4.2202 = 7.0337 < 9.1438] w=0.4620 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)F219.CB) [> 4.3641 = 7.2734 < 9.4555] w=0.4588 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)S345.CB) [> 4.4006 = 7.3343 < 9.5346] w=0.4565 to align # Constraint # added constraint: constraint((T0334)D6.CB, (T0334)F219.CB) [> 3.9523 = 6.5872 < 8.5634] w=0.4565 to align # Constraint # added constraint: constraint((T0334)G229.CA, (T0334)S349.CB) [> 2.8796 = 4.7994 < 6.2392] w=0.4561 to align # Constraint # added constraint: constraint((T0334)T348.CB, (T0334)V364.CB) [> 3.9556 = 6.5927 < 8.5705] w=0.4554 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)G229.CA) [> 4.5640 = 7.6067 < 9.8888] w=0.4549 to align # Constraint # added constraint: constraint((T0334)D6.CB, (T0334)D220.CB) [> 4.0268 = 6.7113 < 8.7247] w=0.4506 to align # Constraint # added constraint: constraint((T0334)A39.CB, (T0334)V197.CB) [> 4.4318 = 7.3863 < 9.6022] w=0.4506 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)L37.CB) [> 4.6315 = 7.7192 < 10.0350] w=0.4489 to align # Constraint # added constraint: constraint((T0334)G229.CA, (T0334)T348.CB) [> 2.4404 = 4.0673 < 5.2875] w=0.4384 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)F224.CB) [> 3.1822 = 5.3036 < 6.8947] w=0.4345 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)S349.CB) [> 3.7823 = 6.3038 < 8.1950] w=0.4325 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)Y365.CB) [> 3.6444 = 6.0740 < 7.8962] w=0.4304 to align # Constraint # added constraint: constraint((T0334)I34.CB, (T0334)G189.CA) [> 3.8195 = 6.3658 < 8.2755] w=0.4280 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)N342.CB) [> 3.9228 = 6.5380 < 8.4994] w=0.4269 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)S349.CB) [> 3.2018 = 5.3364 < 6.9373] w=0.4266 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)R196.CB) [> 4.5122 = 7.5204 < 9.7765] w=0.4252 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)S349.CB) [> 4.4442 = 7.4070 < 9.6291] w=0.4241 to align # Constraint # added constraint: constraint((T0334)R181.CB, (T0334)H192.CB) [> 3.8297 = 6.3829 < 8.2977] w=0.4234 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)S345.CB) [> 4.5483 = 7.5805 < 9.8547] w=0.4151 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)V364.CB) [> 3.8642 = 6.4404 < 8.3725] w=0.4151 to align # Constraint # added constraint: constraint((T0334)A275.CB, (T0334)W284.CB) [> 3.6017 = 6.0028 < 7.8036] w=0.4114 to align # Constraint # added constraint: constraint((T0334)D6.CB, (T0334)T35.CB) [> 2.9745 = 4.9575 < 6.4448] w=0.4110 to align # Constraint # added constraint: constraint((T0334)S228.CB, (T0334)S349.CB) [> 3.0468 = 5.0779 < 6.6013] w=0.4088 to align # Constraint # added constraint: constraint((T0334)D6.CB, (T0334)A221.CB) [> 3.3265 = 5.5442 < 7.2074] w=0.4088 to align # Constraint # added constraint: constraint((T0334)T348.CB, (T0334)G360.CA) [> 4.1536 = 6.9226 < 8.9994] w=0.4064 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)L24.CB) [> 4.5170 = 7.5284 < 9.7869] w=0.4060 to align # Constraint # added constraint: constraint((T0334)P40.CB, (T0334)D195.CB) [> 4.3277 = 7.2129 < 9.3767] w=0.4029 to align # Constraint # added constraint: constraint((T0334)A21.CB, (T0334)V190.CB) [> 3.2876 = 5.4794 < 7.1231] w=0.3852 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)I42.CB) [> 3.5397 = 5.8995 < 7.6693] w=0.3846 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)Y365.CB) [> 4.3180 = 7.1966 < 9.3556] w=0.3831 to align # Constraint # added constraint: constraint((T0334)A173.CB, (T0334)I361.CB) [> 3.7988 = 6.3313 < 8.2307] w=0.3796 to align # Constraint # added constraint: constraint((T0334)G25.CA, (T0334)V190.CB) [> 3.8448 = 6.4080 < 8.3304] w=0.3792 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)G347.CA) [> 4.6004 = 7.6674 < 9.9676] w=0.3772 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)P40.CB) [> 4.4561 = 7.4269 < 9.6550] w=0.3755 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)T44.CB) [> 3.0289 = 5.0481 < 6.5626] w=0.3742 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)S228.CB) [> 4.5328 = 7.5546 < 9.8209] w=0.3737 to align # Constraint # added constraint: constraint((T0334)F230.CB, (T0334)S349.CB) [> 4.1869 = 6.9782 < 9.0717] w=0.3733 to align # Constraint # added constraint: constraint((T0334)V193.CB, (T0334)T213.CB) [> 4.4117 = 7.3528 < 9.5586] w=0.3724 to align # Constraint # added constraint: constraint((T0334)E198.CB, (T0334)V211.CB) [> 4.1691 = 6.9484 < 9.0330] w=0.3718 to align # Constraint # added constraint: constraint((T0334)S274.CB, (T0334)W284.CB) [> 3.9213 = 6.5355 < 8.4961] w=0.3700 to align # Constraint # added constraint: constraint((T0334)D6.CB, (T0334)I34.CB) [> 3.8924 = 6.4873 < 8.4335] w=0.3692 to align # Constraint # added constraint: constraint((T0334)I42.CB, (T0334)R181.CB) [> 3.6612 = 6.1020 < 7.9325] w=0.3629 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)V364.CB) [> 4.2446 = 7.0743 < 9.1966] w=0.3625 to align # Constraint # added constraint: constraint((T0334)G206.CA, (T0334)A221.CB) [> 4.0352 = 6.7253 < 8.7429] w=0.3615 to align # Constraint # added constraint: constraint((T0334)D195.CB, (T0334)T213.CB) [> 3.0987 = 5.1645 < 6.7139] w=0.3571 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)L223.CB) [> 4.3029 = 7.1715 < 9.3230] w=0.3570 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)Y369.CB) [> 3.3709 = 5.6182 < 7.3036] w=0.3535 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)P43.CB) [> 3.6046 = 6.0077 < 7.8100] w=0.3530 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)L223.CB) [> 4.0897 = 6.8162 < 8.8611] w=0.3517 to align # Constraint # added constraint: constraint((T0334)I34.CB, (T0334)R191.CB) [> 4.3222 = 7.2037 < 9.3648] w=0.3497 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)L45.CB) [> 3.8593 = 6.4322 < 8.3619] w=0.3474 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)D222.CB) [> 4.1525 = 6.9208 < 8.9971] w=0.3458 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)V197.CB) [> 4.6552 = 7.7587 < 10.0863] w=0.3441 to align # Constraint # added constraint: constraint((T0334)I5.CB, (T0334)F219.CB) [> 4.3745 = 7.2908 < 9.4780] w=0.3441 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)A214.CB) [> 4.2045 = 7.0075 < 9.1098] w=0.3427 to align # Constraint # added constraint: constraint((T0334)I5.CB, (T0334)A221.CB) [> 4.3884 = 7.3140 < 9.5081] w=0.3421 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)D195.CB) [> 2.9153 = 4.8588 < 6.3164] w=0.3393 to align # Constraint # added constraint: constraint((T0334)A32.CB, (T0334)F375.CB) [> 4.1632 = 6.9387 < 9.0203] w=0.3378 to align # Constraint # added constraint: constraint((T0334)C351.CB, (T0334)F363.CB) [> 3.9010 = 6.5016 < 8.4521] w=0.3375 to align # Constraint # added constraint: constraint((T0334)V353.CB, (T0334)F363.CB) [> 3.6964 = 6.1607 < 8.0089] w=0.3362 to align # Constraint # added constraint: constraint((T0334)K285.CB, (T0334)G295.CA) [> 3.8318 = 6.3863 < 8.3022] w=0.3354 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)Q38.CB) [> 4.5392 = 7.5654 < 9.8350] w=0.3341 to align # Constraint # added constraint: constraint((T0334)A21.CB, (T0334)H192.CB) [> 4.6276 = 7.7126 < 10.0265] w=0.3321 to align # Constraint # added constraint: constraint((T0334)S345.CB, (T0334)A367.CB) [> 4.3710 = 7.2849 < 9.4704] w=0.3308 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)V47.CB) [> 3.6428 = 6.0713 < 7.8926] w=0.3278 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)I42.CB) [> 3.9855 = 6.6425 < 8.6352] w=0.3255 to align # Constraint # added constraint: constraint((T0334)T273.CB, (T0334)K285.CB) [> 3.6783 = 6.1305 < 7.9696] w=0.3227 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)T31.CB) [> 3.4313 = 5.7188 < 7.4345] w=0.3215 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)Y296.CB) [> 3.6250 = 6.0416 < 7.8541] w=0.3176 to align # Constraint # added constraint: constraint((T0334)S22.CB, (T0334)K187.CB) [> 4.0499 = 6.7498 < 8.7747] w=0.3172 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)F363.CB) [> 3.9536 = 6.5893 < 8.5660] w=0.3146 to align # Constraint # added constraint: constraint((T0334)K285.CB, (T0334)T294.CB) [> 3.5051 = 5.8418 < 7.5944] w=0.3118 to align # Constraint # added constraint: constraint((T0334)W284.CB, (T0334)G295.CA) [> 3.3882 = 5.6470 < 7.3411] w=0.3118 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)E209.CB) [> 4.1135 = 6.8558 < 8.9126] w=0.3109 to align # Constraint # added constraint: constraint((T0334)S274.CB, (T0334)K285.CB) [> 3.3860 = 5.6433 < 7.3363] w=0.3109 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)F183.CB) [> 4.4728 = 7.4546 < 9.6910] w=0.3087 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)V297.CB) [> 3.8641 = 6.4401 < 8.3722] w=0.3058 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)H374.CB) [> 4.1825 = 6.9708 < 9.0620] w=0.3038 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)T31.CB) [> 3.0891 = 5.1485 < 6.6931] w=0.3038 to align # Constraint # added constraint: constraint((T0334)L24.CB, (T0334)V225.CB) [> 4.6474 = 7.7456 < 10.0693] w=0.3027 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)F375.CB) [> 3.7392 = 6.2321 < 8.1017] w=0.3022 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)N342.CB) [> 2.5801 = 4.3002 < 5.5903] w=0.3010 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)I346.CB) [> 4.5717 = 7.6195 < 9.9053] w=0.3003 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)A367.CB) [> 3.6967 = 6.1611 < 8.0094] w=0.2957 to align # Constraint # added constraint: constraint((T0334)T273.CB, (T0334)W284.CB) [> 4.0732 = 6.7886 < 8.8252] w=0.2932 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)I42.CB) [> 4.0408 = 6.7346 < 8.7550] w=0.2901 to align # Constraint # added constraint: constraint((T0334)P40.CB, (T0334)V193.CB) [> 4.1818 = 6.9697 < 9.0606] w=0.2860 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)H192.CB) [> 4.4353 = 7.3922 < 9.6099] w=0.2850 to align # Constraint # added constraint: constraint((T0334)A21.CB, (T0334)L180.CB) [> 4.2026 = 7.0043 < 9.1056] w=0.2839 to align # Constraint # added constraint: constraint((T0334)N207.CB, (T0334)N342.CB) [> 3.2019 = 5.3365 < 6.9374] w=0.2832 to align # Constraint # added constraint: constraint((T0334)W284.CB, (T0334)Y296.CB) [> 3.5499 = 5.9165 < 7.6915] w=0.2821 to align # Constraint # added constraint: constraint((T0334)G232.CA, (T0334)S349.CB) [> 3.2970 = 5.4949 < 7.1434] w=0.2813 to align # Constraint # added constraint: constraint((T0334)G30.CA, (T0334)P376.CB) [> 3.8603 = 6.4338 < 8.3639] w=0.2788 to align # Constraint # added constraint: constraint((T0334)G48.CA, (T0334)A173.CB) [> 3.2849 = 5.4748 < 7.1172] w=0.2787 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)G360.CA) [> 3.6661 = 6.1101 < 7.9431] w=0.2779 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)V364.CB) [> 4.3627 = 7.2711 < 9.4525] w=0.2767 to align # Constraint # added constraint: constraint((T0334)D41.CB, (T0334)D195.CB) [> 3.5472 = 5.9120 < 7.6857] w=0.2728 to align # Constraint # added constraint: constraint((T0334)G46.CA, (T0334)A173.CB) [> 3.6254 = 6.0423 < 7.8549] w=0.2724 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)M315.CB) [> 2.8881 = 4.8135 < 6.2576] w=0.2720 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)V372.CB) [> 4.0985 = 6.8308 < 8.8801] w=0.2707 to align # Constraint # added constraint: constraint((T0334)Y23.CB, (T0334)K373.CB) [> 3.5238 = 5.8730 < 7.6349] w=0.2707 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)L36.CB) [> 4.7126 = 7.8542 < 10.2105] w=0.2696 to align # Constraint # added constraint: constraint((T0334)S345.CB, (T0334)L371.CB) [> 4.4278 = 7.3797 < 9.5936] w=0.2683 to align # Constraint # added constraint: constraint((T0334)A32.CB, (T0334)V372.CB) [> 4.4057 = 7.3429 < 9.5457] w=0.2669 to align # Constraint # added constraint: constraint((T0334)Y23.CB, (T0334)L371.CB) [> 4.5669 = 7.6115 < 9.8949] w=0.2648 to align # Constraint # added constraint: constraint((T0334)Y23.CB, (T0334)Y365.CB) [> 3.2540 = 5.4233 < 7.0503] w=0.2602 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)C343.CB) [> 3.2223 = 5.3704 < 6.9816] w=0.2596 to align # Constraint # added constraint: constraint((T0334)N207.CB, (T0334)D222.CB) [> 3.9145 = 6.5242 < 8.4815] w=0.2589 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)A20.CB) [> 4.6811 = 7.8019 < 10.1424] w=0.2586 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)Y298.CB) [> 3.3019 = 5.5032 < 7.1542] w=0.2585 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)D226.CB) [> 4.6037 = 7.6728 < 9.9746] w=0.2561 to align # Constraint # added constraint: constraint((T0334)R202.CB, (T0334)V340.CB) [> 4.2035 = 7.0058 < 9.1075] w=0.2557 to align # Constraint # added constraint: constraint((T0334)S350.CB, (T0334)F363.CB) [> 3.5711 = 5.9518 < 7.7374] w=0.2547 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)S350.CB) [> 4.5530 = 7.5884 < 9.8649] w=0.2543 to align # Constraint # added constraint: constraint((T0334)F272.CB, (T0334)P287.CB) [> 3.8066 = 6.3444 < 8.2477] w=0.2542 to align # Constraint # added constraint: constraint((T0334)W284.CB, (T0334)T294.CB) [> 4.2286 = 7.0476 < 9.1620] w=0.2527 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)V297.CB) [> 3.4298 = 5.7164 < 7.4313] w=0.2527 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)T35.CB) [> 4.3644 = 7.2740 < 9.4562] w=0.2501 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)G46.CA) [> 3.8926 = 6.4878 < 8.4341] w=0.2501 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)F375.CB) [> 4.2407 = 7.0678 < 9.1882] w=0.2495 to align # Constraint # added constraint: constraint((T0334)G295.CA, (T0334)F312.CB) [> 4.0817 = 6.8028 < 8.8436] w=0.2471 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)G295.CA) [> 3.9636 = 6.6061 < 8.5879] w=0.2468 to align # Constraint # added constraint: constraint((T0334)L9.CB, (T0334)S210.CB) [> 4.4381 = 7.3968 < 9.6159] w=0.2436 to align # Constraint # added constraint: constraint((T0334)E49.CB, (T0334)A173.CB) [> 3.3812 = 5.6354 < 7.3260] w=0.2432 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)C343.CB) [> 4.6904 = 7.8173 < 10.1625] w=0.2425 to align # Constraint # added constraint: constraint((T0334)D172.CB, (T0334)M288.CB) [> 3.6865 = 6.1441 < 7.9873] w=0.2425 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)I235.CB) [> 3.6323 = 6.0538 < 7.8700] w=0.2424 to align # Constraint # added constraint: constraint((T0334)I286.CB, (T0334)G295.CA) [> 3.8596 = 6.4327 < 8.3625] w=0.2424 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)A238.CB) [> 3.0565 = 5.0942 < 6.6224] w=0.2424 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)V297.CB) [> 3.8121 = 6.3534 < 8.2595] w=0.2409 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)Q370.CB) [> 4.3248 = 7.2080 < 9.3705] w=0.2388 to align # Constraint # added constraint: constraint((T0334)L36.CB, (T0334)G189.CA) [> 4.0983 = 6.8304 < 8.8796] w=0.2387 to align # Constraint # added constraint: constraint((T0334)M239.CB, (T0334)C343.CB) [> 3.9769 = 6.6282 < 8.6167] w=0.2375 to align # Constraint # added constraint: constraint((T0334)G232.CA, (T0334)H249.CB) [> 3.7299 = 6.2165 < 8.0814] w=0.2359 to align # Constraint # added constraint: constraint((T0334)F272.CB, (T0334)I286.CB) [> 3.7569 = 6.2615 < 8.1400] w=0.2345 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)T294.CB) [> 3.9230 = 6.5384 < 8.4999] w=0.2306 to align # Constraint # added constraint: constraint((T0334)A257.CB, (T0334)T294.CB) [> 3.8024 = 6.3374 < 8.2386] w=0.2306 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)Y298.CB) [> 3.7183 = 6.1972 < 8.0564] w=0.2306 to align # Constraint # added constraint: constraint((T0334)T31.CB, (T0334)P376.CB) [> 3.7693 = 6.2822 < 8.1669] w=0.2291 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)Y296.CB) [> 4.2887 = 7.1478 < 9.2921] w=0.2290 to align # Constraint # added constraint: constraint((T0334)P271.CB, (T0334)P287.CB) [> 3.9647 = 6.6079 < 8.5903] w=0.2281 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)L180.CB) [> 4.5318 = 7.5530 < 9.8189] w=0.2265 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)V372.CB) [> 4.3754 = 7.2924 < 9.4801] w=0.2259 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)G360.CA) [> 3.0525 = 5.0875 < 6.6137] w=0.2247 to align # Constraint # added constraint: constraint((T0334)D253.CB, (T0334)Y298.CB) [> 3.8033 = 6.3388 < 8.2404] w=0.2247 to align # Constraint # added constraint: constraint((T0334)H199.CB, (T0334)S210.CB) [> 3.9257 = 6.5428 < 8.5057] w=0.2246 to align # Constraint # added constraint: constraint((T0334)E354.CB, (T0334)F363.CB) [> 4.2466 = 7.0776 < 9.2009] w=0.2239 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)Y369.CB) [> 4.1316 = 6.8860 < 8.9518] w=0.2234 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)G48.CA) [> 3.8791 = 6.4652 < 8.4047] w=0.2214 to align # Constraint # added constraint: constraint((T0334)V47.CB, (T0334)A173.CB) [> 3.1332 = 5.2220 < 6.7886] w=0.2192 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)I361.CB) [> 3.0004 = 5.0007 < 6.5009] w=0.2188 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)V364.CB) [> 4.3379 = 7.2298 < 9.3988] w=0.2188 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)G347.CA) [> 4.5398 = 7.5662 < 9.8361] w=0.2188 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)G293.CA) [> 3.6495 = 6.0825 < 7.9072] w=0.2188 to align # Constraint # added constraint: constraint((T0334)A257.CB, (T0334)G293.CA) [> 3.7142 = 6.1903 < 8.0474] w=0.2188 to align # Constraint # added constraint: constraint((T0334)F230.CB, (T0334)F352.CB) [> 3.6770 = 6.1283 < 7.9668] w=0.2188 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)L371.CB) [> 4.4448 = 7.4081 < 9.6305] w=0.2175 to align # Constraint # added constraint: constraint((T0334)T348.CB, (T0334)F363.CB) [> 4.4219 = 7.3699 < 9.5809] w=0.2137 to align # Constraint # added constraint: constraint((T0334)N335.CB, (T0334)C351.CB) [> 3.9795 = 6.6325 < 8.6222] w=0.2134 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)I361.CB) [> 3.9046 = 6.5077 < 8.4600] w=0.2129 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)D226.CB) [> 4.6561 = 7.7602 < 10.0883] w=0.2129 to align # Constraint # added constraint: constraint((T0334)L55.CB, (T0334)I361.CB) [> 3.7798 = 6.2996 < 8.1895] w=0.2129 to align # Constraint # added constraint: constraint((T0334)A257.CB, (T0334)G295.CA) [> 3.5345 = 5.8908 < 7.6580] w=0.2129 to align # Constraint # added constraint: constraint((T0334)S274.CB, (T0334)T283.CB) [> 4.3854 = 7.3090 < 9.5017] w=0.2129 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)M315.CB) [> 3.6516 = 6.0860 < 7.9118] w=0.2129 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)F312.CB) [> 3.8238 = 6.3729 < 8.2848] w=0.2128 to align # Constraint # added constraint: constraint((T0334)T273.CB, (T0334)P287.CB) [> 4.4451 = 7.4085 < 9.6310] w=0.2128 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)G341.CA) [> 3.9298 = 6.5497 < 8.5146] w=0.2123 to align # Constraint # added constraint: constraint((T0334)N207.CB, (T0334)D220.CB) [> 3.5062 = 5.8437 < 7.5968] w=0.2115 to align # Constraint # added constraint: constraint((T0334)A20.CB, (T0334)V344.CB) [> 4.6086 = 7.6810 < 9.9854] w=0.2081 to align # Constraint # added constraint: constraint((T0334)M239.CB, (T0334)V340.CB) [> 3.2553 = 5.4255 < 7.0532] w=0.2079 to align # Constraint # added constraint: constraint((T0334)R202.CB, (T0334)C343.CB) [> 3.9113 = 6.5188 < 8.4744] w=0.2070 to align # Constraint # added constraint: constraint((T0334)Q259.CB, (T0334)F292.CB) [> 3.9390 = 6.5650 < 8.5345] w=0.2070 to align # Constraint # added constraint: constraint((T0334)V260.CB, (T0334)F292.CB) [> 3.5199 = 5.8664 < 7.6264] w=0.2070 to align # Constraint # added constraint: constraint((T0334)A255.CB, (T0334)V297.CB) [> 3.9190 = 6.5317 < 8.4913] w=0.2069 to align # Constraint # added constraint: constraint((T0334)D253.CB, (T0334)S299.CB) [> 3.7418 = 6.2363 < 8.1072] w=0.2069 to align # Constraint # added constraint: constraint((T0334)N207.CB, (T0334)G341.CA) [> 3.0770 = 5.1284 < 6.6669] w=0.2063 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)V47.CB) [> 3.8449 = 6.4081 < 8.3305] w=0.2053 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)F312.CB) [> 3.7441 = 6.2402 < 8.1123] w=0.2011 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)L325.CB) [> 3.2545 = 5.4241 < 7.0513] w=0.2011 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)M239.CB) [> 3.6150 = 6.0250 < 7.8325] w=0.2010 to align # Constraint # added constraint: constraint((T0334)Y296.CB, (T0334)F312.CB) [> 3.4295 = 5.7158 < 7.4306] w=0.2010 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)Y298.CB) [> 3.1113 = 5.1855 < 6.7411] w=0.2010 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)L234.CB) [> 3.5777 = 5.9628 < 7.7516] w=0.1994 to align # Constraint # added constraint: constraint((T0334)K4.CB, (T0334)F219.CB) [> 3.4222 = 5.7037 < 7.4148] w=0.1964 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)V332.CB) [> 4.1431 = 6.9051 < 8.9767] w=0.1959 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)T44.CB) [> 4.1368 = 6.8946 < 8.9630] w=0.1954 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)V297.CB) [> 3.8373 = 6.3955 < 8.3141] w=0.1952 to align # Constraint # added constraint: constraint((T0334)A338.CB, (T0334)S350.CB) [> 3.0776 = 5.1293 < 6.6681] w=0.1951 to align # Constraint # added constraint: constraint((T0334)G232.CA, (T0334)D248.CB) [> 3.4327 = 5.7212 < 7.4376] w=0.1945 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)F219.CB) [> 3.6052 = 6.0086 < 7.8112] w=0.1936 to align # Constraint # added constraint: constraint((T0334)S210.CB, (T0334)F224.CB) [> 4.4425 = 7.4041 < 9.6253] w=0.1907 to align # Constraint # added constraint: constraint((T0334)C351.CB, (T0334)G360.CA) [> 4.2245 = 7.0408 < 9.1531] w=0.1896 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)F363.CB) [> 3.2243 = 5.3738 < 6.9860] w=0.1892 to align # Constraint # added constraint: constraint((T0334)L55.CB, (T0334)Y362.CB) [> 3.3631 = 5.6051 < 7.2867] w=0.1892 to align # Constraint # added constraint: constraint((T0334)L45.CB, (T0334)A173.CB) [> 4.1242 = 6.8737 < 8.9358] w=0.1892 to align # Constraint # added constraint: constraint((T0334)A255.CB, (T0334)Y296.CB) [> 3.5246 = 5.8743 < 7.6366] w=0.1892 to align # Constraint # added constraint: constraint((T0334)A255.CB, (T0334)F330.CB) [> 4.0283 = 6.7138 < 8.7280] w=0.1892 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)F330.CB) [> 4.1235 = 6.8726 < 8.9343] w=0.1892 to align # Constraint # added constraint: constraint((T0334)I276.CB, (T0334)K285.CB) [> 4.2232 = 7.0386 < 9.1502] w=0.1892 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)L325.CB) [> 3.6862 = 6.1437 < 7.9868] w=0.1892 to align # Constraint # added constraint: constraint((T0334)S280.CB, (T0334)M315.CB) [> 3.2685 = 5.4475 < 7.0817] w=0.1892 to align # Constraint # added constraint: constraint((T0334)H374.CB, (T0334)L384.CB) [> 3.2973 = 5.4954 < 7.1441] w=0.1892 to align # Constraint # added constraint: constraint((T0334)N335.CB, (T0334)S345.CB) [> 4.0789 = 6.7982 < 8.8377] w=0.1892 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)A308.CB) [> 3.6060 = 6.0100 < 7.8130] w=0.1892 to align # Constraint # added constraint: constraint((T0334)A275.CB, (T0334)K285.CB) [> 4.1417 = 6.9028 < 8.9736] w=0.1867 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)V47.CB) [> 3.4365 = 5.7276 < 7.4459] w=0.1847 to align # Constraint # added constraint: constraint((T0334)T51.CB, (T0334)F171.CB) [> 3.5440 = 5.9067 < 7.6787] w=0.1837 to align # Constraint # added constraint: constraint((T0334)F59.CB, (T0334)V176.CB) [> 4.1808 = 6.9679 < 9.0583] w=0.1837 to align # Constraint # added constraint: constraint((T0334)T294.CB, (T0334)F312.CB) [> 3.6639 = 6.1065 < 7.9384] w=0.1833 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)G295.CA) [> 3.6496 = 6.0827 < 7.9075] w=0.1833 to align # Constraint # added constraint: constraint((T0334)A255.CB, (T0334)G295.CA) [> 3.6029 = 6.0048 < 7.8062] w=0.1833 to align # Constraint # added constraint: constraint((T0334)A257.CB, (T0334)I328.CB) [> 3.6963 = 6.1605 < 8.0087] w=0.1833 to align # Constraint # added constraint: constraint((T0334)Q259.CB, (T0334)G293.CA) [> 3.5889 = 5.9815 < 7.7760] w=0.1833 to align # Constraint # added constraint: constraint((T0334)M278.CB, (T0334)M315.CB) [> 3.1928 = 5.3213 < 6.9177] w=0.1833 to align # Constraint # added constraint: constraint((T0334)N335.CB, (T0334)S350.CB) [> 3.3472 = 5.5787 < 7.2523] w=0.1833 to align # Constraint # added constraint: constraint((T0334)W284.CB, (T0334)V297.CB) [> 3.9404 = 6.5674 < 8.5376] w=0.1832 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)N236.CB) [> 4.1269 = 6.8782 < 8.9417] w=0.1832 to align # Constraint # added constraint: constraint((T0334)I208.CB, (T0334)V340.CB) [> 4.0882 = 6.8136 < 8.8576] w=0.1827 to align # Constraint # added constraint: constraint((T0334)K285.CB, (T0334)Y296.CB) [> 4.1156 = 6.8593 < 8.9171] w=0.1816 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)G46.CA) [> 4.1387 = 6.8979 < 8.9673] w=0.1787 to align # Constraint # added constraint: constraint((T0334)A50.CB, (T0334)A173.CB) [> 2.9597 = 4.9329 < 6.4127] w=0.1782 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)L233.CB) [> 4.0476 = 6.7460 < 8.7698] w=0.1774 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)R327.CB) [> 3.6814 = 6.1357 < 7.9765] w=0.1774 to align # Constraint # added constraint: constraint((T0334)A257.CB, (T0334)R327.CB) [> 4.3240 = 7.2067 < 9.3687] w=0.1774 to align # Constraint # added constraint: constraint((T0334)Q370.CB, (T0334)F388.CB) [> 3.7346 = 6.2243 < 8.0916] w=0.1774 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)R327.CB) [> 3.4716 = 5.7859 < 7.5217] w=0.1774 to align # Constraint # added constraint: constraint((T0334)S280.CB, (T0334)E311.CB) [> 4.0976 = 6.8293 < 8.8781] w=0.1774 to align # Constraint # added constraint: constraint((T0334)E270.CB, (T0334)P287.CB) [> 3.6124 = 6.0207 < 7.8270] w=0.1774 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)S350.CB) [> 4.3920 = 7.3200 < 9.5160] w=0.1774 to align # Constraint # added constraint: constraint((T0334)I5.CB, (T0334)D33.CB) [> 4.1373 = 6.8955 < 8.9641] w=0.1773 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)G295.CA) [> 3.8427 = 6.4045 < 8.3258] w=0.1773 to align # Constraint # added constraint: constraint((T0334)D33.CB, (T0334)G189.CA) [> 4.2714 = 7.1191 < 9.2548] w=0.1758 to align # Constraint # added constraint: constraint((T0334)E209.CB, (T0334)V218.CB) [> 3.8495 = 6.4159 < 8.3406] w=0.1748 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)D220.CB) [> 3.8386 = 6.3976 < 8.3169] w=0.1733 to align # Constraint # added constraint: constraint((T0334)V47.CB, (T0334)I361.CB) [> 4.1377 = 6.8961 < 8.9649] w=0.1719 to align # Constraint # added constraint: constraint((T0334)I52.CB, (T0334)S358.CB) [> 3.5154 = 5.8591 < 7.6168] w=0.1719 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)G360.CA) [> 4.1772 = 6.9619 < 9.0505] w=0.1715 to align # Constraint # added constraint: constraint((T0334)L234.CB, (T0334)S345.CB) [> 3.6688 = 6.1146 < 7.9490] w=0.1715 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)W316.CB) [> 3.8851 = 6.4751 < 8.4176] w=0.1715 to align # Constraint # added constraint: constraint((T0334)A255.CB, (T0334)R327.CB) [> 3.9742 = 6.6237 < 8.6108] w=0.1715 to align # Constraint # added constraint: constraint((T0334)A257.CB, (T0334)L325.CB) [> 3.8849 = 6.4749 < 8.4173] w=0.1715 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)Y298.CB) [> 4.0165 = 6.6942 < 8.7025] w=0.1714 to align # Constraint # added constraint: constraint((T0334)V297.CB, (T0334)A308.CB) [> 3.6165 = 6.0275 < 7.8358] w=0.1703 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)A50.CB) [> 4.0640 = 6.7733 < 8.8053] w=0.1678 to align # Constraint # added constraint: constraint((T0334)I34.CB, (T0334)L188.CB) [> 4.2240 = 7.0399 < 9.1519] w=0.1674 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)V372.CB) [> 4.0929 = 6.8215 < 8.8680] w=0.1667 to align # Constraint # added constraint: constraint((T0334)V309.CB, (T0334)L325.CB) [> 4.0256 = 6.7093 < 8.7221] w=0.1661 to align # Constraint # added constraint: constraint((T0334)V297.CB, (T0334)F312.CB) [> 3.7373 = 6.2288 < 8.0975] w=0.1660 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)Q370.CB) [> 3.5417 = 5.9029 < 7.6738] w=0.1656 to align # Constraint # added constraint: constraint((T0334)Q259.CB, (T0334)L325.CB) [> 3.5119 = 5.8532 < 7.6092] w=0.1656 to align # Constraint # added constraint: constraint((T0334)F330.CB, (T0334)E354.CB) [> 2.8974 = 4.8290 < 6.2777] w=0.1656 to align # Constraint # added constraint: constraint((T0334)D253.CB, (T0334)F330.CB) [> 3.7258 = 6.2096 < 8.0725] w=0.1656 to align # Constraint # added constraint: constraint((T0334)A257.CB, (T0334)Y296.CB) [> 4.0611 = 6.7684 < 8.7990] w=0.1655 to align # Constraint # added constraint: constraint((T0334)H199.CB, (T0334)A238.CB) [> 4.0458 = 6.7430 < 8.7659] w=0.1655 to align # Constraint # added constraint: constraint((T0334)A308.CB, (T0334)L325.CB) [> 4.2449 = 7.0748 < 9.1972] w=0.1640 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)S299.CB) [> 3.6895 = 6.1491 < 7.9939] w=0.1639 to align # Constraint # added constraint: constraint((T0334)D172.CB, (T0334)I361.CB) [> 3.7895 = 6.3158 < 8.2105] w=0.1608 to align # Constraint # added constraint: constraint((T0334)D253.CB, (T0334)R334.CB) [> 4.0815 = 6.8025 < 8.8432] w=0.1601 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)S299.CB) [> 3.9135 = 6.5224 < 8.4792] w=0.1597 to align # Constraint # added constraint: constraint((T0334)Q259.CB, (T0334)R291.CB) [> 3.4157 = 5.6928 < 7.4007] w=0.1597 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)A308.CB) [> 3.6898 = 6.1497 < 7.9946] w=0.1597 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)L234.CB) [> 4.0544 = 6.7573 < 8.7844] w=0.1597 to align # Constraint # added constraint: constraint((T0334)H170.CB, (T0334)I286.CB) [> 4.0167 = 6.6945 < 8.7028] w=0.1597 to align # Constraint # added constraint: constraint((T0334)F363.CB, (T0334)M395.CB) [> 3.9550 = 6.5918 < 8.5693] w=0.1597 to align # Constraint # added constraint: constraint((T0334)C351.CB, (T0334)F396.CB) [> 3.3565 = 5.5942 < 7.2724] w=0.1597 to align # Constraint # added constraint: constraint((T0334)S350.CB, (T0334)I392.CB) [> 4.3963 = 7.3272 < 9.5254] w=0.1597 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)C351.CB) [> 2.8886 = 4.8143 < 6.2586] w=0.1597 to align # Constraint # added constraint: constraint((T0334)G333.CA, (T0334)F352.CB) [> 2.8037 = 4.6729 < 6.0747] w=0.1597 to align # Constraint # added constraint: constraint((T0334)V332.CB, (T0334)E354.CB) [> 3.9293 = 6.5488 < 8.5134] w=0.1597 to align # Constraint # added constraint: constraint((T0334)T51.CB, (T0334)I361.CB) [> 4.2381 = 7.0635 < 9.1825] w=0.1597 to align # Constraint # added constraint: constraint((T0334)V260.CB, (T0334)G293.CA) [> 3.5773 = 5.9622 < 7.7508] w=0.1596 to align # Constraint # added constraint: constraint((T0334)A255.CB, (T0334)Y298.CB) [> 3.8755 = 6.4592 < 8.3970] w=0.1596 to align # Constraint # added constraint: constraint((T0334)I286.CB, (T0334)Y296.CB) [> 4.1822 = 6.9703 < 9.0614] w=0.1596 to align # Constraint # added constraint: constraint((T0334)H192.CB, (T0334)T213.CB) [> 4.2931 = 7.1552 < 9.3018] w=0.1578 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)E49.CB) [> 2.9172 = 4.8619 < 6.3205] w=0.1560 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)I235.CB) [> 4.1343 = 6.8905 < 8.9577] w=0.1547 to align # Constraint # added constraint: constraint((T0334)T51.CB, (T0334)A173.CB) [> 3.5997 = 5.9994 < 7.7993] w=0.1545 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)F292.CB) [> 3.7418 = 6.2363 < 8.1072] w=0.1538 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)V200.CB) [> 4.6175 = 7.6958 < 10.0045] w=0.1538 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)F388.CB) [> 3.6540 = 6.0900 < 7.9170] w=0.1538 to align # Constraint # added constraint: constraint((T0334)L63.CB, (T0334)F183.CB) [> 4.0758 = 6.7929 < 8.8308] w=0.1538 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)I328.CB) [> 3.8268 = 6.3780 < 8.2915] w=0.1538 to align # Constraint # added constraint: constraint((T0334)L234.CB, (T0334)C343.CB) [> 3.8588 = 6.4313 < 8.3607] w=0.1538 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)L234.CB) [> 4.2449 = 7.0748 < 9.1973] w=0.1538 to align # Constraint # added constraint: constraint((T0334)A58.CB, (T0334)Y365.CB) [> 3.6188 = 6.0314 < 7.8408] w=0.1538 to align # Constraint # added constraint: constraint((T0334)R202.CB, (T0334)N342.CB) [> 3.7111 = 6.1851 < 8.0407] w=0.1538 to align # Constraint # added constraint: constraint((T0334)L55.CB, (T0334)Y365.CB) [> 3.1018 = 5.1696 < 6.7205] w=0.1538 to align # Constraint # added constraint: constraint((T0334)K285.CB, (T0334)W316.CB) [> 4.1038 = 6.8397 < 8.8916] w=0.1538 to align # Constraint # added constraint: constraint((T0334)I52.CB, (T0334)Y362.CB) [> 2.8667 = 4.7778 < 6.2112] w=0.1538 to align # Constraint # added constraint: constraint((T0334)I65.CB, (T0334)F179.CB) [> 3.4897 = 5.8162 < 7.5611] w=0.1538 to align # Constraint # added constraint: constraint((T0334)G347.CA, (T0334)T359.CB) [> 4.4436 = 7.4061 < 9.6279] w=0.1538 to align # Constraint # added constraint: constraint((T0334)D253.CB, (T0334)R329.CB) [> 3.5552 = 5.9253 < 7.7028] w=0.1538 to align # Constraint # added constraint: constraint((T0334)G333.CA, (T0334)C351.CB) [> 3.4403 = 5.7338 < 7.4540] w=0.1538 to align # Constraint # added constraint: constraint((T0334)G333.CA, (T0334)V353.CB) [> 4.4749 = 7.4581 < 9.6955] w=0.1538 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)F396.CB) [> 3.4841 = 5.8069 < 7.5490] w=0.1538 to align # Constraint # added constraint: constraint((T0334)W339.CB, (T0334)T385.CB) [> 4.0317 = 6.7195 < 8.7354] w=0.1538 to align # Constraint # added constraint: constraint((T0334)V353.CB, (T0334)T399.CB) [> 3.3910 = 5.6517 < 7.3472] w=0.1538 to align # Constraint # added constraint: constraint((T0334)T359.CB, (T0334)T399.CB) [> 2.9971 = 4.9951 < 6.4936] w=0.1538 to align # Constraint # added constraint: constraint((T0334)M246.CB, (T0334)G333.CA) [> 4.1219 = 6.8698 < 8.9308] w=0.1535 to align # Constraint # added constraint: constraint((T0334)E241.CB, (T0334)L250.CB) [> 3.6211 = 6.0352 < 7.8458] w=0.1531 to align # Constraint # added constraint: constraint((T0334)F230.CB, (T0334)R334.CB) [> 2.9622 = 4.9370 < 6.4181] w=0.1483 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)E49.CB) [> 3.6126 = 6.0209 < 7.8272] w=0.1482 to align # Constraint # added constraint: constraint((T0334)F230.CB, (T0334)R336.CB) [> 3.0504 = 5.0839 < 6.6091] w=0.1481 to align # Constraint # added constraint: constraint((T0334)L356.CB, (T0334)H406.CB) [> 3.0963 = 5.1604 < 6.7086] w=0.1478 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)G360.CA) [> 4.2963 = 7.1605 < 9.3086] w=0.1478 to align # Constraint # added constraint: constraint((T0334)V260.CB, (T0334)R291.CB) [> 3.9867 = 6.6446 < 8.6379] w=0.1478 to align # Constraint # added constraint: constraint((T0334)D253.CB, (T0334)V297.CB) [> 3.7644 = 6.2740 < 8.1561] w=0.1478 to align # Constraint # added constraint: constraint((T0334)G46.CA, (T0334)D172.CB) [> 3.6190 = 6.0316 < 7.8411] w=0.1478 to align # Constraint # added constraint: constraint((T0334)L234.CB, (T0334)S349.CB) [> 3.4894 = 5.8156 < 7.5603] w=0.1478 to align # Constraint # added constraint: constraint((T0334)T51.CB, (T0334)H170.CB) [> 4.3481 = 7.2469 < 9.4210] w=0.1478 to align # Constraint # added constraint: constraint((T0334)I328.CB, (T0334)P355.CB) [> 4.0792 = 6.7986 < 8.8382] w=0.1478 to align # Constraint # added constraint: constraint((T0334)A338.CB, (T0334)F388.CB) [> 3.8203 = 6.3672 < 8.2774] w=0.1478 to align # Constraint # added constraint: constraint((T0334)A338.CB, (T0334)N389.CB) [> 2.9976 = 4.9961 < 6.4949] w=0.1478 to align # Constraint # added constraint: constraint((T0334)V332.CB, (T0334)V353.CB) [> 3.7806 = 6.3010 < 8.1912] w=0.1478 to align # Constraint # added constraint: constraint((T0334)L244.CB, (T0334)R336.CB) [> 4.0125 = 6.6875 < 8.6938] w=0.1477 to align # Constraint # added constraint: constraint((T0334)E240.CB, (T0334)V340.CB) [> 4.2142 = 7.0236 < 9.1307] w=0.1429 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)L45.CB) [> 3.6426 = 6.0711 < 7.8924] w=0.1427 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)T294.CB) [> 3.7297 = 6.2162 < 8.0811] w=0.1419 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)E357.CB) [> 2.9691 = 4.9485 < 6.4330] w=0.1419 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)Y296.CB) [> 4.0257 = 6.7095 < 8.7223] w=0.1419 to align # Constraint # added constraint: constraint((T0334)E357.CB, (T0334)F402.CB) [> 3.3814 = 5.6357 < 7.3264] w=0.1419 to align # Constraint # added constraint: constraint((T0334)L356.CB, (T0334)I403.CB) [> 3.2525 = 5.4208 < 7.0471] w=0.1419 to align # Constraint # added constraint: constraint((T0334)E354.CB, (T0334)I403.CB) [> 3.1419 = 5.2365 < 6.8074] w=0.1419 to align # Constraint # added constraint: constraint((T0334)Q259.CB, (T0334)T294.CB) [> 4.0028 = 6.6714 < 8.6728] w=0.1419 to align # Constraint # added constraint: constraint((T0334)T51.CB, (T0334)Y362.CB) [> 4.0766 = 6.7944 < 8.8327] w=0.1419 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)F352.CB) [> 4.6052 = 7.6753 < 9.9779] w=0.1419 to align # Constraint # added constraint: constraint((T0334)D203.CB, (T0334)N342.CB) [> 3.9722 = 6.6203 < 8.6064] w=0.1419 to align # Constraint # added constraint: constraint((T0334)R337.CB, (T0334)N389.CB) [> 3.2036 = 5.3394 < 6.9412] w=0.1419 to align # Constraint # added constraint: constraint((T0334)V332.CB, (T0334)F352.CB) [> 3.8011 = 6.3352 < 8.2357] w=0.1419 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)R331.CB) [> 3.9024 = 6.5039 < 8.4551] w=0.1419 to align # Constraint # added constraint: constraint((T0334)Y23.CB, (T0334)Q370.CB) [> 4.6024 = 7.6707 < 9.9719] w=0.1406 to align # Constraint # added constraint: constraint((T0334)F352.CB, (T0334)F363.CB) [> 3.7234 = 6.2057 < 8.0674] w=0.1403 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)L45.CB) [> 4.5016 = 7.5027 < 9.7535] w=0.1395 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)D226.CB) [> 4.6871 = 7.8118 < 10.1553] w=0.1394 to align # Constraint # added constraint: constraint((T0334)E49.CB, (T0334)F171.CB) [> 4.1731 = 6.9551 < 9.0417] w=0.1364 to align # Constraint # added constraint: constraint((T0334)M246.CB, (T0334)R334.CB) [> 3.5760 = 5.9600 < 7.7480] w=0.1364 to align # Constraint # added constraint: constraint((T0334)S130.CB, (T0334)F139.CB) [> 3.8158 = 6.3596 < 8.2675] w=0.1363 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)Y362.CB) [> 3.9890 = 6.6484 < 8.6429] w=0.1360 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)G293.CA) [> 4.0086 = 6.6810 < 8.6853] w=0.1360 to align # Constraint # added constraint: constraint((T0334)L251.CB, (T0334)S300.CB) [> 3.8946 = 6.4910 < 8.4383] w=0.1360 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)T322.CB) [> 3.4954 = 5.8257 < 7.5735] w=0.1360 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)V332.CB) [> 4.0783 = 6.7972 < 8.8364] w=0.1360 to align # Constraint # added constraint: constraint((T0334)R331.CB, (T0334)F352.CB) [> 3.3695 = 5.6158 < 7.3005] w=0.1360 to align # Constraint # added constraint: constraint((T0334)F243.CB, (T0334)V340.CB) [> 3.8195 = 6.3658 < 8.2755] w=0.1360 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)S299.CB) [> 3.8134 = 6.3557 < 8.2624] w=0.1359 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)Y298.CB) [> 3.9922 = 6.6536 < 8.6497] w=0.1359 to align # Constraint # added constraint: constraint((T0334)V260.CB, (T0334)T294.CB) [> 3.9740 = 6.6234 < 8.6103] w=0.1359 to align # Constraint # added constraint: constraint((T0334)G232.CA, (T0334)T348.CB) [> 4.3046 = 7.1743 < 9.3265] w=0.1336 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)I52.CB) [> 3.9700 = 6.6167 < 8.6017] w=0.1331 to align # Constraint # added constraint: constraint((T0334)V193.CB, (T0334)R217.CB) [> 4.4359 = 7.3932 < 9.6111] w=0.1312 to align # Constraint # added constraint: constraint((T0334)F312.CB, (T0334)L325.CB) [> 3.9029 = 6.5048 < 8.4562] w=0.1306 to align # Constraint # added constraint: constraint((T0334)V297.CB, (T0334)E311.CB) [> 3.8551 = 6.4252 < 8.3528] w=0.1306 to align # Constraint # added constraint: constraint((T0334)T31.CB, (T0334)V372.CB) [> 4.4298 = 7.3830 < 9.5979] w=0.1305 to align # Constraint # added constraint: constraint((T0334)V260.CB, (T0334)L325.CB) [> 3.4625 = 5.7708 < 7.5020] w=0.1301 to align # Constraint # added constraint: constraint((T0334)Q259.CB, (T0334)I328.CB) [> 3.7119 = 6.1865 < 8.0425] w=0.1301 to align # Constraint # added constraint: constraint((T0334)A58.CB, (T0334)Y369.CB) [> 3.3951 = 5.6586 < 7.3561] w=0.1301 to align # Constraint # added constraint: constraint((T0334)T51.CB, (T0334)W169.CB) [> 3.0275 = 5.0458 < 6.5595] w=0.1301 to align # Constraint # added constraint: constraint((T0334)I65.CB, (T0334)F183.CB) [> 3.1620 = 5.2699 < 6.8509] w=0.1301 to align # Constraint # added constraint: constraint((T0334)E357.CB, (T0334)I403.CB) [> 3.2146 = 5.3577 < 6.9650] w=0.1301 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)I328.CB) [> 3.5286 = 5.8810 < 7.6453] w=0.1301 to align # Constraint # added constraint: constraint((T0334)E357.CB, (T0334)T399.CB) [> 3.7293 = 6.2154 < 8.0801] w=0.1301 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)R329.CB) [> 4.4460 = 7.4100 < 9.6330] w=0.1301 to align # Constraint # added constraint: constraint((T0334)S274.CB, (T0334)I286.CB) [> 3.6892 = 6.1486 < 7.9932] w=0.1277 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)D226.CB) [> 4.6232 = 7.7054 < 10.0170] w=0.1253 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)V372.CB) [> 4.2597 = 7.0994 < 9.2292] w=0.1253 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)G333.CA) [> 3.7638 = 6.2730 < 8.1549] w=0.1249 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)G48.CA) [> 4.3733 = 7.2888 < 9.4755] w=0.1246 to align # Constraint # added constraint: constraint((T0334)E49.CB, (T0334)I361.CB) [> 4.1663 = 6.9438 < 9.0269] w=0.1246 to align # Constraint # added constraint: constraint((T0334)I52.CB, (T0334)A173.CB) [> 2.6756 = 4.4594 < 5.7972] w=0.1246 to align # Constraint # added constraint: constraint((T0334)A50.CB, (T0334)I361.CB) [> 3.6121 = 6.0202 < 7.8263] w=0.1246 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)R334.CB) [> 3.6921 = 6.1535 < 7.9995] w=0.1246 to align # Constraint # added constraint: constraint((T0334)I346.CB, (T0334)A366.CB) [> 4.4901 = 7.4836 < 9.7286] w=0.1242 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)F330.CB) [> 3.5127 = 5.8545 < 7.6108] w=0.1242 to align # Constraint # added constraint: constraint((T0334)I235.CB, (T0334)S345.CB) [> 3.4278 = 5.7130 < 7.4269] w=0.1242 to align # Constraint # added constraint: constraint((T0334)E49.CB, (T0334)I286.CB) [> 3.8438 = 6.4063 < 8.3281] w=0.1242 to align # Constraint # added constraint: constraint((T0334)G48.CA, (T0334)I361.CB) [> 3.8203 = 6.3671 < 8.2772] w=0.1242 to align # Constraint # added constraint: constraint((T0334)G48.CA, (T0334)S358.CB) [> 4.2615 = 7.1025 < 9.2332] w=0.1242 to align # Constraint # added constraint: constraint((T0334)L244.CB, (T0334)N335.CB) [> 3.8187 = 6.3645 < 8.2739] w=0.1242 to align # Constraint # added constraint: constraint((T0334)T51.CB, (T0334)A168.CB) [> 3.6378 = 6.0630 < 7.8819] w=0.1242 to align # Constraint # added constraint: constraint((T0334)I52.CB, (T0334)A168.CB) [> 3.6225 = 6.0374 < 7.8486] w=0.1242 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)F330.CB) [> 3.0725 = 5.1209 < 6.6571] w=0.1242 to align # Constraint # added constraint: constraint((T0334)L244.CB, (T0334)V340.CB) [> 3.4948 = 5.8247 < 7.5721] w=0.1242 to align # Constraint # added constraint: constraint((T0334)N236.CB, (T0334)S345.CB) [> 4.0769 = 6.7948 < 8.8332] w=0.1241 to align # Constraint # added constraint: constraint((T0334)Q38.CB, (T0334)V47.CB) [> 3.5691 = 5.9485 < 7.7331] w=0.1231 to align # Constraint # added constraint: constraint((T0334)T294.CB, (T0334)W316.CB) [> 3.7594 = 6.2657 < 8.1455] w=0.1226 to align # Constraint # added constraint: constraint((T0334)E241.CB, (T0334)V340.CB) [> 3.5745 = 5.9574 < 7.7447] w=0.1192 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)G333.CA) [> 3.1419 = 5.2365 < 6.8075] w=0.1190 to align # Constraint # added constraint: constraint((T0334)I52.CB, (T0334)D172.CB) [> 3.6159 = 6.0266 < 7.8345] w=0.1190 to align # Constraint # added constraint: constraint((T0334)W126.CB, (T0334)V176.CB) [> 4.0554 = 6.7589 < 8.7866] w=0.1187 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)Y298.CB) [> 3.7698 = 6.2830 < 8.1679] w=0.1183 to align # Constraint # added constraint: constraint((T0334)L251.CB, (T0334)S299.CB) [> 3.7453 = 6.2422 < 8.1149] w=0.1183 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)V332.CB) [> 3.4832 = 5.8053 < 7.5469] w=0.1183 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)I328.CB) [> 4.2819 = 7.1365 < 9.2775] w=0.1183 to align # Constraint # added constraint: constraint((T0334)P53.CB, (T0334)N166.CB) [> 3.4977 = 5.8295 < 7.5783] w=0.1183 to align # Constraint # added constraint: constraint((T0334)L356.CB, (T0334)F407.CB) [> 3.3126 = 5.5210 < 7.1774] w=0.1183 to align # Constraint # added constraint: constraint((T0334)P53.CB, (T0334)Y167.CB) [> 3.9618 = 6.6031 < 8.5840] w=0.1183 to align # Constraint # added constraint: constraint((T0334)F363.CB, (T0334)T399.CB) [> 3.5327 = 5.8879 < 7.6543] w=0.1183 to align # Constraint # added constraint: constraint((T0334)P53.CB, (T0334)A168.CB) [> 4.1482 = 6.9137 < 8.9878] w=0.1183 to align # Constraint # added constraint: constraint((T0334)A168.CB, (T0334)S358.CB) [> 4.2205 = 7.0341 < 9.1443] w=0.1183 to align # Constraint # added constraint: constraint((T0334)R331.CB, (T0334)E354.CB) [> 4.1198 = 6.8663 < 8.9262] w=0.1183 to align # Constraint # added constraint: constraint((T0334)V332.CB, (T0334)R400.CB) [> 3.5191 = 5.8651 < 7.6246] w=0.1183 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)Y296.CB) [> 4.1159 = 6.8599 < 8.9178] w=0.1182 to align # Constraint # added constraint: constraint((T0334)E198.CB, (T0334)S210.CB) [> 3.3226 = 5.5377 < 7.1991] w=0.1181 to align # Constraint # added constraint: constraint((T0334)G232.CA, (T0334)V269.CB) [> 3.3596 = 5.5994 < 7.2792] w=0.1171 to align # Constraint # added constraint: constraint((T0334)I120.CB, (T0334)V148.CB) [> 3.1922 = 5.3203 < 6.9163] w=0.1166 to align # Constraint # added constraint: constraint((T0334)I5.CB, (T0334)A32.CB) [> 3.6084 = 6.0140 < 7.8182] w=0.1158 to align # Constraint # added constraint: constraint((T0334)D33.CB, (T0334)V190.CB) [> 4.5729 = 7.6215 < 9.9080] w=0.1142 to align # Constraint # added constraint: constraint((T0334)R157.CB, (T0334)D172.CB) [> 3.0537 = 5.0895 < 6.6163] w=0.1141 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)G333.CA) [> 3.1479 = 5.2465 < 6.8205] w=0.1131 to align # Constraint # added constraint: constraint((T0334)A338.CB, (T0334)C351.CB) [> 4.4422 = 7.4037 < 9.6248] w=0.1127 to align # Constraint # added constraint: constraint((T0334)I52.CB, (T0334)I361.CB) [> 3.7480 = 6.2466 < 8.1206] w=0.1127 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)A338.CB) [> 3.3952 = 5.6587 < 7.3563] w=0.1124 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)S300.CB) [> 3.7335 = 6.2225 < 8.0892] w=0.1124 to align # Constraint # added constraint: constraint((T0334)A50.CB, (T0334)S358.CB) [> 2.4602 = 4.1004 < 5.3305] w=0.1124 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)V176.CB) [> 3.8634 = 6.4390 < 8.3707] w=0.1124 to align # Constraint # added constraint: constraint((T0334)A50.CB, (T0334)H170.CB) [> 3.3324 = 5.5540 < 7.2202] w=0.1124 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)G347.CA) [> 3.7910 = 6.3183 < 8.2138] w=0.1124 to align # Constraint # added constraint: constraint((T0334)A50.CB, (T0334)A168.CB) [> 3.6624 = 6.1040 < 7.9352] w=0.1124 to align # Constraint # added constraint: constraint((T0334)W339.CB, (T0334)F388.CB) [> 3.4218 = 5.7030 < 7.4139] w=0.1124 to align # Constraint # added constraint: constraint((T0334)F363.CB, (T0334)F396.CB) [> 3.8062 = 6.3436 < 8.2467] w=0.1124 to align # Constraint # added constraint: constraint((T0334)Q370.CB, (T0334)I392.CB) [> 3.4866 = 5.8111 < 7.5544] w=0.1124 to align # Constraint # added constraint: constraint((T0334)V353.CB, (T0334)I403.CB) [> 2.8421 = 4.7368 < 6.1579] w=0.1124 to align # Constraint # added constraint: constraint((T0334)F330.CB, (T0334)P355.CB) [> 4.1702 = 6.9503 < 9.0354] w=0.1124 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)I235.CB) [> 4.1686 = 6.9476 < 9.0319] w=0.1123 to align # Constraint # added constraint: constraint((T0334)V11.CB, (T0334)G232.CA) [> 4.4287 = 7.3812 < 9.5955] w=0.1123 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)S299.CB) [> 3.9092 = 6.5153 < 8.4698] w=0.1107 to align # Constraint # added constraint: constraint((T0334)S123.CB, (T0334)F224.CB) [> 4.0062 = 6.6769 < 8.6800] w=0.1107 to align # Constraint # added constraint: constraint((T0334)S123.CB, (T0334)V225.CB) [> 4.0940 = 6.8234 < 8.8704] w=0.1107 to align # Constraint # added constraint: constraint((T0334)S123.CB, (T0334)D226.CB) [> 3.1197 = 5.1996 < 6.7594] w=0.1107 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)G46.CA) [> 3.7752 = 6.2919 < 8.1795] w=0.1103 to align # Constraint # added constraint: constraint((T0334)L234.CB, (T0334)F243.CB) [> 3.7136 = 6.1893 < 8.0461] w=0.1103 to align # Constraint # added constraint: constraint((T0334)L28.CB, (T0334)V372.CB) [> 3.8689 = 6.4482 < 8.3827] w=0.1099 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)T51.CB) [> 3.7445 = 6.2409 < 8.1131] w=0.1091 to align # Constraint # added constraint: constraint((T0334)P40.CB, (T0334)E49.CB) [> 3.6342 = 6.0570 < 7.8741] w=0.1083 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)G48.CA) [> 3.6875 = 6.1458 < 7.9895] w=0.1083 to align # Constraint # added constraint: constraint((T0334)V148.CB, (T0334)V190.CB) [> 2.9984 = 4.9973 < 6.4964] w=0.1082 to align # Constraint # added constraint: constraint((T0334)I149.CB, (T0334)V193.CB) [> 3.8389 = 6.3982 < 8.3177] w=0.1082 to align # Constraint # added constraint: constraint((T0334)D151.CB, (T0334)V193.CB) [> 3.0023 = 5.0038 < 6.5049] w=0.1082 to align # Constraint # added constraint: constraint((T0334)D151.CB, (T0334)T213.CB) [> 3.9248 = 6.5413 < 8.5036] w=0.1082 to align # Constraint # added constraint: constraint((T0334)A152.CB, (T0334)D195.CB) [> 4.1652 = 6.9421 < 9.0247] w=0.1082 to align # Constraint # added constraint: constraint((T0334)N153.CB, (T0334)D195.CB) [> 4.2717 = 7.1196 < 9.2554] w=0.1082 to align # Constraint # added constraint: constraint((T0334)I34.CB, (T0334)V372.CB) [> 4.5931 = 7.6551 < 9.9516] w=0.1076 to align # Constraint # added constraint: constraint((T0334)V47.CB, (T0334)V176.CB) [> 4.2127 = 7.0212 < 9.1276] w=0.1068 to align # Constraint # added constraint: constraint((T0334)F59.CB, (T0334)I361.CB) [> 3.5796 = 5.9660 < 7.7558] w=0.1068 to align # Constraint # added constraint: constraint((T0334)I52.CB, (T0334)E357.CB) [> 3.8977 = 6.4961 < 8.4449] w=0.1068 to align # Constraint # added constraint: constraint((T0334)W126.CB, (T0334)F179.CB) [> 3.7682 = 6.2804 < 8.1645] w=0.1068 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)R331.CB) [> 4.1011 = 6.8351 < 8.8857] w=0.1065 to align # Constraint # added constraint: constraint((T0334)A50.CB, (T0334)I286.CB) [> 4.0654 = 6.7756 < 8.8083] w=0.1065 to align # Constraint # added constraint: constraint((T0334)G48.CA, (T0334)D172.CB) [> 3.8425 = 6.4042 < 8.3254] w=0.1064 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)F330.CB) [> 3.5928 = 5.9881 < 7.7845] w=0.1064 to align # Constraint # added constraint: constraint((T0334)A27.CB, (T0334)V372.CB) [> 2.9211 = 4.8685 < 6.3291] w=0.1064 to align # Constraint # added constraint: constraint((T0334)H262.CB, (T0334)G290.CA) [> 3.9766 = 6.6276 < 8.6159] w=0.1064 to align # Constraint # added constraint: constraint((T0334)A50.CB, (T0334)W169.CB) [> 4.2772 = 7.1287 < 9.2674] w=0.1064 to align # Constraint # added constraint: constraint((T0334)D265.CB, (T0334)F292.CB) [> 3.8867 = 6.4778 < 8.4211] w=0.1064 to align # Constraint # added constraint: constraint((T0334)E49.CB, (T0334)H170.CB) [> 3.4465 = 5.7442 < 7.4675] w=0.1064 to align # Constraint # added constraint: constraint((T0334)Q56.CB, (T0334)W169.CB) [> 3.4004 = 5.6673 < 7.3674] w=0.1064 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)E354.CB) [> 3.9085 = 6.5142 < 8.4684] w=0.1064 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)R329.CB) [> 3.4670 = 5.7783 < 7.5118] w=0.1064 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)A58.CB) [> 4.1177 = 6.8629 < 8.9218] w=0.1064 to align # Constraint # added constraint: constraint((T0334)V269.CB, (T0334)P287.CB) [> 3.6498 = 6.0830 < 7.9080] w=0.1064 to align # Constraint # added constraint: constraint((T0334)A39.CB, (T0334)S228.CB) [> 4.6477 = 7.7462 < 10.0700] w=0.1064 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)V309.CB) [> 3.7611 = 6.2685 < 8.1490] w=0.1064 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)S210.CB) [> 3.9785 = 6.6309 < 8.6202] w=0.1063 to align # Constraint # added constraint: constraint((T0334)W284.CB, (T0334)G293.CA) [> 4.4864 = 7.4774 < 9.7206] w=0.1048 to align # Constraint # added constraint: constraint((T0334)I120.CB, (T0334)P147.CB) [> 4.2785 = 7.1308 < 9.2701] w=0.1047 to align # Constraint # added constraint: constraint((T0334)I120.CB, (T0334)L223.CB) [> 2.9768 = 4.9614 < 6.4498] w=0.1047 to align # Constraint # added constraint: constraint((T0334)H124.CB, (T0334)D226.CB) [> 4.1529 = 6.9214 < 8.9979] w=0.1047 to align # Constraint # added constraint: constraint((T0334)P121.CB, (T0334)I149.CB) [> 2.8499 = 4.7499 < 6.1749] w=0.1047 to align # Constraint # added constraint: constraint((T0334)I120.CB, (T0334)F224.CB) [> 4.4617 = 7.4362 < 9.6670] w=0.1047 to align # Constraint # added constraint: constraint((T0334)L122.CB, (T0334)V225.CB) [> 3.0189 = 5.0315 < 6.5409] w=0.1047 to align # Constraint # added constraint: constraint((T0334)G133.CA, (T0334)L150.CB) [> 3.8526 = 6.4209 < 8.3472] w=0.1047 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)V200.CB) [> 3.8038 = 6.3396 < 8.2415] w=0.1047 to align # Constraint # added constraint: constraint((T0334)T348.CB, (T0334)T359.CB) [> 3.6791 = 6.1318 < 7.9714] w=0.1040 to align # Constraint # added constraint: constraint((T0334)L233.CB, (T0334)F243.CB) [> 3.7003 = 6.1672 < 8.0173] w=0.1039 to align # Constraint # added constraint: constraint((T0334)I149.CB, (T0334)F219.CB) [> 3.6679 = 6.1132 < 7.9471] w=0.1023 to align # Constraint # added constraint: constraint((T0334)L251.CB, (T0334)G333.CA) [> 3.6956 = 6.1593 < 8.0071] w=0.1013 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)A366.CB) [> 2.9295 = 4.8825 < 6.3473] w=0.1009 to align # Constraint # added constraint: constraint((T0334)S350.CB, (T0334)T359.CB) [> 3.3512 = 5.5854 < 7.2610] w=0.1009 to align # Constraint # added constraint: constraint((T0334)P156.CB, (T0334)N166.CB) [> 4.1196 = 6.8661 < 8.9259] w=0.1009 to align # Constraint # added constraint: constraint((T0334)E357.CB, (T0334)H406.CB) [> 3.3453 = 5.5755 < 7.2482] w=0.1005 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)S274.CB) [> 4.1464 = 6.9106 < 8.9838] w=0.1005 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)G295.CA) [> 3.8658 = 6.4429 < 8.3758] w=0.1005 to align # Constraint # added constraint: constraint((T0334)H262.CB, (T0334)F292.CB) [> 3.3044 = 5.5073 < 7.1595] w=0.1005 to align # Constraint # added constraint: constraint((T0334)I235.CB, (T0334)S349.CB) [> 3.2200 = 5.3667 < 6.9767] w=0.1005 to align # Constraint # added constraint: constraint((T0334)E270.CB, (T0334)K285.CB) [> 3.7627 = 6.2711 < 8.1525] w=0.1005 to align # Constraint # added constraint: constraint((T0334)S274.CB, (T0334)W316.CB) [> 4.5518 = 7.5863 < 9.8622] w=0.1005 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)R329.CB) [> 4.3604 = 7.2674 < 9.4476] w=0.1005 to align # Constraint # added constraint: constraint((T0334)T359.CB, (T0334)I403.CB) [> 3.4671 = 5.7784 < 7.5120] w=0.1005 to align # Constraint # added constraint: constraint((T0334)A39.CB, (T0334)E198.CB) [> 4.1299 = 6.8832 < 8.9482] w=0.1005 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)R331.CB) [> 3.3212 = 5.5353 < 7.1959] w=0.1005 to align # Constraint # added constraint: constraint((T0334)P271.CB, (T0334)K285.CB) [> 4.0062 = 6.6771 < 8.6802] w=0.1005 to align # Constraint # added constraint: constraint((T0334)A366.CB, (T0334)M395.CB) [> 3.4281 = 5.7136 < 7.4276] w=0.1005 to align # Constraint # added constraint: constraint((T0334)Y131.CB, (T0334)D140.CB) [> 3.8224 = 6.3707 < 8.2819] w=0.1004 to align # Constraint # added constraint: constraint((T0334)L63.CB, (T0334)V176.CB) [> 4.2129 = 7.0215 < 9.1279] w=0.1003 to align # Constraint # added constraint: constraint((T0334)L159.CB, (T0334)D172.CB) [> 3.5692 = 5.9487 < 7.7333] w=0.0988 to align # Constraint # added constraint: constraint((T0334)H124.CB, (T0334)G229.CA) [> 4.0527 = 6.7546 < 8.7809] w=0.0988 to align # Constraint # added constraint: constraint((T0334)Q119.CB, (T0334)P147.CB) [> 2.9401 = 4.9002 < 6.3703] w=0.0988 to align # Constraint # added constraint: constraint((T0334)Q119.CB, (T0334)D222.CB) [> 3.3203 = 5.5338 < 7.1940] w=0.0988 to align # Constraint # added constraint: constraint((T0334)I120.CB, (T0334)I149.CB) [> 4.3614 = 7.2690 < 9.4497] w=0.0988 to align # Constraint # added constraint: constraint((T0334)P121.CB, (T0334)V211.CB) [> 3.3242 = 5.5403 < 7.2024] w=0.0988 to align # Constraint # added constraint: constraint((T0334)P121.CB, (T0334)L223.CB) [> 4.3241 = 7.2069 < 9.3690] w=0.0988 to align # Constraint # added constraint: constraint((T0334)L122.CB, (T0334)R132.CB) [> 3.6243 = 6.0406 < 7.8527] w=0.0988 to align # Constraint # added constraint: constraint((T0334)L122.CB, (T0334)V148.CB) [> 3.9003 = 6.5004 < 8.4506] w=0.0988 to align # Constraint # added constraint: constraint((T0334)S130.CB, (T0334)L150.CB) [> 4.3325 = 7.2208 < 9.3870] w=0.0988 to align # Constraint # added constraint: constraint((T0334)R129.CB, (T0334)C227.CB) [> 2.4257 = 4.0428 < 5.2556] w=0.0988 to align # Constraint # added constraint: constraint((T0334)A97.CB, (T0334)D226.CB) [> 3.7662 = 6.2770 < 8.1601] w=0.0988 to align # Constraint # added constraint: constraint((T0334)F139.CB, (T0334)V190.CB) [> 4.2539 = 7.0898 < 9.2167] w=0.0988 to align # Constraint # added constraint: constraint((T0334)G133.CA, (T0334)V190.CB) [> 3.8833 = 6.4722 < 8.4138] w=0.0988 to align # Constraint # added constraint: constraint((T0334)R129.CB, (T0334)L150.CB) [> 3.7697 = 6.2829 < 8.1677] w=0.0988 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)V47.CB) [> 4.0234 = 6.7056 < 8.7173] w=0.0981 to align # Constraint # added constraint: constraint((T0334)E198.CB, (T0334)G216.CA) [> 4.5842 = 7.6404 < 9.9325] w=0.0957 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)S350.CB) [> 3.6295 = 6.0491 < 7.8639] w=0.0957 to align # Constraint # added constraint: constraint((T0334)L251.CB, (T0334)R334.CB) [> 2.8555 = 4.7592 < 6.1869] w=0.0950 to align # Constraint # added constraint: constraint((T0334)I5.CB, (T0334)V218.CB) [> 4.0964 = 6.8274 < 8.8756] w=0.0950 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)S358.CB) [> 3.6325 = 6.0542 < 7.8704] w=0.0946 to align # Constraint # added constraint: constraint((T0334)E354.CB, (T0334)H406.CB) [> 4.5875 = 7.6459 < 9.9396] w=0.0946 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)G341.CA) [> 4.7629 = 7.9381 < 10.3196] w=0.0946 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)R329.CB) [> 4.1208 = 6.8680 < 8.9284] w=0.0946 to align # Constraint # added constraint: constraint((T0334)I235.CB, (T0334)S350.CB) [> 4.2983 = 7.1638 < 9.3130] w=0.0946 to align # Constraint # added constraint: constraint((T0334)M71.CB, (T0334)F179.CB) [> 3.9749 = 6.6249 < 8.6123] w=0.0946 to align # Constraint # added constraint: constraint((T0334)M278.CB, (T0334)W316.CB) [> 4.6467 = 7.7445 < 10.0679] w=0.0946 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)S410.CB) [> 3.3350 = 5.5584 < 7.2259] w=0.0946 to align # Constraint # added constraint: constraint((T0334)S350.CB, (T0334)F396.CB) [> 4.2852 = 7.1420 < 9.2846] w=0.0946 to align # Constraint # added constraint: constraint((T0334)C351.CB, (T0334)R400.CB) [> 4.1738 = 6.9563 < 9.0432] w=0.0946 to align # Constraint # added constraint: constraint((T0334)E198.CB, (T0334)S228.CB) [> 4.6429 = 7.7382 < 10.0596] w=0.0946 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)E198.CB) [> 3.4935 = 5.8225 < 7.5692] w=0.0946 to align # Constraint # added constraint: constraint((T0334)D195.CB, (T0334)R212.CB) [> 3.8310 = 6.3849 < 8.3004] w=0.0945 to align # Constraint # added constraint: constraint((T0334)L63.CB, (T0334)S358.CB) [> 3.9120 = 6.5200 < 8.4761] w=0.0944 to align # Constraint # added constraint: constraint((T0334)L63.CB, (T0334)D172.CB) [> 3.3506 = 5.5843 < 7.2596] w=0.0944 to align # Constraint # added constraint: constraint((T0334)S300.CB, (T0334)L325.CB) [> 3.5272 = 5.8787 < 7.6423] w=0.0930 to align # Constraint # added constraint: constraint((T0334)Y125.CB, (T0334)P156.CB) [> 3.0143 = 5.0238 < 6.5310] w=0.0929 to align # Constraint # added constraint: constraint((T0334)Y125.CB, (T0334)R157.CB) [> 3.8870 = 6.4784 < 8.4219] w=0.0929 to align # Constraint # added constraint: constraint((T0334)Y108.CB, (T0334)F224.CB) [> 4.1372 = 6.8954 < 8.9640] w=0.0929 to align # Constraint # added constraint: constraint((T0334)L122.CB, (T0334)C227.CB) [> 3.6471 = 6.0785 < 7.9021] w=0.0929 to align # Constraint # added constraint: constraint((T0334)H124.CB, (T0334)C227.CB) [> 2.5296 = 4.2160 < 5.4809] w=0.0929 to align # Constraint # added constraint: constraint((T0334)Y108.CB, (T0334)V225.CB) [> 3.1474 = 5.2457 < 6.8194] w=0.0929 to align # Constraint # added constraint: constraint((T0334)Y108.CB, (T0334)D226.CB) [> 4.2447 = 7.0744 < 9.1967] w=0.0929 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)C351.CB) [> 2.8019 = 4.6698 < 6.0707] w=0.0898 to align # Constraint # added constraint: constraint((T0334)L113.CB, (T0334)L356.CB) [> 3.9526 = 6.5877 < 8.5641] w=0.0895 to align # Constraint # added constraint: constraint((T0334)P156.CB, (T0334)T165.CB) [> 3.3539 = 5.5898 < 7.2667] w=0.0891 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)A173.CB) [> 4.5880 = 7.6467 < 9.9406] w=0.0887 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)S350.CB) [> 4.1414 = 6.9024 < 8.9732] w=0.0887 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)F407.CB) [> 3.7995 = 6.3325 < 8.2322] w=0.0887 to align # Constraint # added constraint: constraint((T0334)F330.CB, (T0334)F407.CB) [> 3.6674 = 6.1123 < 7.9459] w=0.0887 to align # Constraint # added constraint: constraint((T0334)P261.CB, (T0334)R291.CB) [> 3.5388 = 5.8980 < 7.6675] w=0.0887 to align # Constraint # added constraint: constraint((T0334)V309.CB, (T0334)R327.CB) [> 3.9042 = 6.5070 < 8.4591] w=0.0887 to align # Constraint # added constraint: constraint((T0334)Q259.CB, (T0334)T322.CB) [> 3.8712 = 6.4520 < 8.3876] w=0.0887 to align # Constraint # added constraint: constraint((T0334)I235.CB, (T0334)N335.CB) [> 3.8609 = 6.4349 < 8.3654] w=0.0887 to align # Constraint # added constraint: constraint((T0334)K83.CB, (T0334)S274.CB) [> 3.4378 = 5.7297 < 7.4486] w=0.0887 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)I276.CB) [> 3.9455 = 6.5759 < 8.5486] w=0.0887 to align # Constraint # added constraint: constraint((T0334)L251.CB, (T0334)R329.CB) [> 3.9883 = 6.6471 < 8.6412] w=0.0887 to align # Constraint # added constraint: constraint((T0334)G12.CA, (T0334)P40.CB) [> 4.6888 = 7.8147 < 10.1591] w=0.0887 to align # Constraint # added constraint: constraint((T0334)V332.CB, (T0334)I403.CB) [> 4.1498 = 6.9163 < 8.9912] w=0.0887 to align # Constraint # added constraint: constraint((T0334)F59.CB, (T0334)F179.CB) [> 4.5019 = 7.5031 < 9.7541] w=0.0887 to align # Constraint # added constraint: constraint((T0334)H199.CB, (T0334)T213.CB) [> 4.5403 = 7.5671 < 9.8372] w=0.0887 to align # Constraint # added constraint: constraint((T0334)L55.CB, (T0334)A366.CB) [> 4.1167 = 6.8612 < 8.9196] w=0.0887 to align # Constraint # added constraint: constraint((T0334)V260.CB, (T0334)N326.CB) [> 3.3645 = 5.6075 < 7.2898] w=0.0887 to align # Constraint # added constraint: constraint((T0334)T258.CB, (T0334)V309.CB) [> 4.1433 = 6.9056 < 8.9772] w=0.0886 to align # Constraint # added constraint: constraint((T0334)D195.CB, (T0334)V211.CB) [> 3.2494 = 5.4156 < 7.0403] w=0.0886 to align # Constraint # added constraint: constraint((T0334)A142.CB, (T0334)V190.CB) [> 3.2046 = 5.3410 < 6.9433] w=0.0886 to align # Constraint # added constraint: constraint((T0334)W126.CB, (T0334)G229.CA) [> 3.8371 = 6.3951 < 8.3137] w=0.0870 to align # Constraint # added constraint: constraint((T0334)S130.CB, (T0334)A184.CB) [> 4.2048 = 7.0080 < 9.1104] w=0.0870 to align # Constraint # added constraint: constraint((T0334)H124.CB, (T0334)S228.CB) [> 2.6719 = 4.4532 < 5.7891] w=0.0870 to align # Constraint # added constraint: constraint((T0334)W126.CB, (T0334)C227.CB) [> 3.7281 = 6.2136 < 8.0776] w=0.0870 to align # Constraint # added constraint: constraint((T0334)S130.CB, (T0334)P156.CB) [> 3.7819 = 6.3032 < 8.1941] w=0.0870 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)F224.CB) [> 2.8268 = 4.7113 < 6.1247] w=0.0870 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)D226.CB) [> 3.5938 = 5.9896 < 7.7865] w=0.0870 to align # Constraint # added constraint: constraint((T0334)Y108.CB, (T0334)L223.CB) [> 3.9493 = 6.5822 < 8.5569] w=0.0870 to align # Constraint # added constraint: constraint((T0334)H109.CB, (T0334)V225.CB) [> 4.3556 = 7.2594 < 9.4372] w=0.0870 to align # Constraint # added constraint: constraint((T0334)H109.CB, (T0334)D226.CB) [> 3.4502 = 5.7503 < 7.4755] w=0.0870 to align # Constraint # added constraint: constraint((T0334)R129.CB, (T0334)V225.CB) [> 4.3385 = 7.2309 < 9.4002] w=0.0870 to align # Constraint # added constraint: constraint((T0334)S110.CB, (T0334)D128.CB) [> 3.4266 = 5.7110 < 7.4243] w=0.0870 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)A366.CB) [> 4.5542 = 7.5904 < 9.8675] w=0.0863 to align # Constraint # added constraint: constraint((T0334)F139.CB, (T0334)L188.CB) [> 4.2439 = 7.0732 < 9.1951] w=0.0846 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)F224.CB) [> 4.6311 = 7.7185 < 10.0340] w=0.0843 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)S349.CB) [> 3.8684 = 6.4473 < 8.3815] w=0.0839 to align # Constraint # added constraint: constraint((T0334)N153.CB, (T0334)D172.CB) [> 3.9816 = 6.6359 < 8.6267] w=0.0835 to align # Constraint # added constraint: constraint((T0334)A81.CB, (T0334)Y362.CB) [> 3.5296 = 5.8827 < 7.6475] w=0.0832 to align # Constraint # added constraint: constraint((T0334)V80.CB, (T0334)A366.CB) [> 3.2699 = 5.4498 < 7.0847] w=0.0832 to align # Constraint # added constraint: constraint((T0334)G48.CA, (T0334)V176.CB) [> 4.6059 = 7.6764 < 9.9793] w=0.0832 to align # Constraint # added constraint: constraint((T0334)E146.CB, (T0334)F179.CB) [> 3.5544 = 5.9240 < 7.7012] w=0.0832 to align # Constraint # added constraint: constraint((T0334)E146.CB, (T0334)V176.CB) [> 3.8549 = 6.4248 < 8.3522] w=0.0832 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)G293.CA) [> 3.2569 = 5.4282 < 7.0566] w=0.0832 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)F363.CB) [> 4.3190 = 7.1982 < 9.3577] w=0.0828 to align # Constraint # added constraint: constraint((T0334)E354.CB, (T0334)F407.CB) [> 2.6880 = 4.4800 < 5.8240] w=0.0828 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)F59.CB) [> 4.3938 = 7.3230 < 9.5199] w=0.0828 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)V353.CB) [> 3.3585 = 5.5975 < 7.2768] w=0.0828 to align # Constraint # added constraint: constraint((T0334)Y108.CB, (T0334)S274.CB) [> 3.3054 = 5.5089 < 7.1616] w=0.0828 to align # Constraint # added constraint: constraint((T0334)H106.CB, (T0334)F272.CB) [> 2.8822 = 4.8036 < 6.2447] w=0.0828 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)T348.CB) [> 3.7933 = 6.3221 < 8.2187] w=0.0828 to align # Constraint # added constraint: constraint((T0334)F230.CB, (T0334)P355.CB) [> 4.5041 = 7.5068 < 9.7589] w=0.0828 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)F302.CB) [> 4.2245 = 7.0408 < 9.1531] w=0.0828 to align # Constraint # added constraint: constraint((T0334)Q370.CB, (T0334)L384.CB) [> 3.8745 = 6.4575 < 8.3947] w=0.0828 to align # Constraint # added constraint: constraint((T0334)W70.CB, (T0334)F179.CB) [> 3.4959 = 5.8265 < 7.5745] w=0.0828 to align # Constraint # added constraint: constraint((T0334)A76.CB, (T0334)F179.CB) [> 3.1624 = 5.2706 < 6.8518] w=0.0828 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)V364.CB) [> 4.7118 = 7.8530 < 10.2088] w=0.0828 to align # Constraint # added constraint: constraint((T0334)I10.CB, (T0334)I346.CB) [> 4.4793 = 7.4654 < 9.7051] w=0.0828 to align # Constraint # added constraint: constraint((T0334)A58.CB, (T0334)I361.CB) [> 3.7608 = 6.2680 < 8.1484] w=0.0828 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)P411.CB) [> 3.3123 = 5.5205 < 7.1767] w=0.0828 to align # Constraint # added constraint: constraint((T0334)L356.CB, (T0334)S410.CB) [> 3.5187 = 5.8644 < 7.6238] w=0.0828 to align # Constraint # added constraint: constraint((T0334)T359.CB, (T0334)F402.CB) [> 4.3076 = 7.1793 < 9.3330] w=0.0828 to align # Constraint # added constraint: constraint((T0334)V332.CB, (T0334)Q404.CB) [> 3.6054 = 6.0090 < 7.8116] w=0.0828 to align # Constraint # added constraint: constraint((T0334)A266.CB, (T0334)R291.CB) [> 4.3536 = 7.2560 < 9.4328] w=0.0828 to align # Constraint # added constraint: constraint((T0334)F243.CB, (T0334)R337.CB) [> 4.2250 = 7.0416 < 9.1541] w=0.0828 to align # Constraint # added constraint: constraint((T0334)S300.CB, (T0334)R327.CB) [> 3.2928 = 5.4880 < 7.1345] w=0.0828 to align # Constraint # added constraint: constraint((T0334)A266.CB, (T0334)F292.CB) [> 3.7634 = 6.2723 < 8.1541] w=0.0828 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)T385.CB) [> 4.4998 = 7.4996 < 9.7495] w=0.0828 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)S300.CB) [> 3.8014 = 6.3356 < 8.2363] w=0.0827 to align # Constraint # added constraint: constraint((T0334)F139.CB, (T0334)A184.CB) [> 4.1188 = 6.8646 < 8.9240] w=0.0827 to align # Constraint # added constraint: constraint((T0334)F62.CB, (T0334)S358.CB) [> 3.1602 = 5.2670 < 6.8471] w=0.0826 to align # Constraint # added constraint: constraint((T0334)I8.CB, (T0334)L28.CB) [> 4.2469 = 7.0782 < 9.2016] w=0.0812 to align # Constraint # added constraint: constraint((T0334)W126.CB, (T0334)R157.CB) [> 4.0236 = 6.7060 < 8.7178] w=0.0811 to align # Constraint # added constraint: constraint((T0334)H124.CB, (T0334)L150.CB) [> 4.5908 = 7.6513 < 9.9467] w=0.0811 to align # Constraint # added constraint: constraint((T0334)Y125.CB, (T0334)L150.CB) [> 3.7391 = 6.2318 < 8.1013] w=0.0811 to align # Constraint # added constraint: constraint((T0334)S110.CB, (T0334)V225.CB) [> 4.1419 = 6.9031 < 8.9741] w=0.0811 to align # Constraint # added constraint: constraint((T0334)H192.CB, (T0334)R217.CB) [> 4.3298 = 7.2164 < 9.3813] w=0.0804 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)V372.CB) [> 4.7496 = 7.9160 < 10.2908] w=0.0783 to align # Constraint # added constraint: constraint((T0334)A81.CB, (T0334)F363.CB) [> 3.6426 = 6.0709 < 7.8922] w=0.0773 to align # Constraint # added constraint: constraint((T0334)A81.CB, (T0334)A366.CB) [> 3.8497 = 6.4162 < 8.3411] w=0.0773 to align # Constraint # added constraint: constraint((T0334)F59.CB, (T0334)D172.CB) [> 3.5273 = 5.8788 < 7.6424] w=0.0773 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)C351.CB) [> 4.0411 = 6.7351 < 8.7556] w=0.0769 to align # Constraint # added constraint: constraint((T0334)S280.CB, (T0334)S299.CB) [> 3.7181 = 6.1967 < 8.0558] w=0.0769 to align # Constraint # added constraint: constraint((T0334)R231.CB, (T0334)S247.CB) [> 4.1399 = 6.8999 < 8.9698] w=0.0769 to align # Constraint # added constraint: constraint((T0334)V47.CB, (T0334)D172.CB) [> 4.1244 = 6.8739 < 8.9361] w=0.0769 to align # Constraint # added constraint: constraint((T0334)F230.CB, (T0334)H249.CB) [> 3.7000 = 6.1666 < 8.0166] w=0.0769 to align # Constraint # added constraint: constraint((T0334)D105.CB, (T0334)F272.CB) [> 3.9207 = 6.5346 < 8.4950] w=0.0769 to align # Constraint # added constraint: constraint((T0334)G229.CA, (T0334)E354.CB) [> 3.1436 = 5.2393 < 6.8111] w=0.0769 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)R334.CB) [> 4.1438 = 6.9064 < 8.9783] w=0.0769 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)A275.CB) [> 3.6066 = 6.0110 < 7.8143] w=0.0769 to align # Constraint # added constraint: constraint((T0334)L55.CB, (T0334)S358.CB) [> 2.9618 = 4.9363 < 6.4171] w=0.0769 to align # Constraint # added constraint: constraint((T0334)A277.CB, (T0334)F409.CB) [> 4.1958 = 6.9929 < 9.0908] w=0.0769 to align # Constraint # added constraint: constraint((T0334)A366.CB, (T0334)I392.CB) [> 4.3682 = 7.2804 < 9.4645] w=0.0769 to align # Constraint # added constraint: constraint((T0334)V260.CB, (T0334)G295.CA) [> 4.1204 = 6.8673 < 8.9275] w=0.0768 to align # Constraint # added constraint: constraint((T0334)Y116.CB, (T0334)Y144.CB) [> 3.4473 = 5.7455 < 7.4691] w=0.0768 to align # Constraint # added constraint: constraint((T0334)H199.CB, (T0334)M239.CB) [> 4.1024 = 6.8374 < 8.8886] w=0.0768 to align # Constraint # added constraint: constraint((T0334)A142.CB, (T0334)L188.CB) [> 3.5424 = 5.9041 < 7.6753] w=0.0768 to align # Constraint # added constraint: constraint((T0334)Q38.CB, (T0334)G48.CA) [> 3.9805 = 6.6342 < 8.6245] w=0.0753 to align # Constraint # added constraint: constraint((T0334)H106.CB, (T0334)F224.CB) [> 3.8272 = 6.3786 < 8.2922] w=0.0752 to align # Constraint # added constraint: constraint((T0334)S110.CB, (T0334)C227.CB) [> 3.5657 = 5.9428 < 7.7256] w=0.0752 to align # Constraint # added constraint: constraint((T0334)H117.CB, (T0334)L223.CB) [> 2.6650 = 4.4416 < 5.7741] w=0.0752 to align # Constraint # added constraint: constraint((T0334)H117.CB, (T0334)D222.CB) [> 2.5715 = 4.2858 < 5.5715] w=0.0752 to align # Constraint # added constraint: constraint((T0334)L234.CB, (T0334)H249.CB) [> 4.3922 = 7.3204 < 9.5165] w=0.0742 to align # Constraint # added constraint: constraint((T0334)W87.CB, (T0334)A366.CB) [> 3.8031 = 6.3384 < 8.2399] w=0.0714 to align # Constraint # added constraint: constraint((T0334)P104.CB, (T0334)Y116.CB) [> 3.9280 = 6.5467 < 8.5107] w=0.0713 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)E354.CB) [> 4.2959 = 7.1599 < 9.3079] w=0.0713 to align # Constraint # added constraint: constraint((T0334)G64.CA, (T0334)Y362.CB) [> 3.3248 = 5.5414 < 7.2038] w=0.0713 to align # Constraint # added constraint: constraint((T0334)W18.CB, (T0334)I361.CB) [> 4.3477 = 7.2462 < 9.4200] w=0.0710 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)V353.CB) [> 3.1494 = 5.2490 < 6.8236] w=0.0710 to align # Constraint # added constraint: constraint((T0334)N86.CB, (T0334)I276.CB) [> 3.7538 = 6.2564 < 8.1334] w=0.0710 to align # Constraint # added constraint: constraint((T0334)H106.CB, (T0334)T273.CB) [> 4.0114 = 6.6858 < 8.6915] w=0.0710 to align # Constraint # added constraint: constraint((T0334)I82.CB, (T0334)S274.CB) [> 4.0356 = 6.7261 < 8.7439] w=0.0710 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)E354.CB) [> 3.9378 = 6.5630 < 8.5318] w=0.0710 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)E354.CB) [> 3.9548 = 6.5913 < 8.5687] w=0.0710 to align # Constraint # added constraint: constraint((T0334)V136.CB, (T0334)W169.CB) [> 4.0119 = 6.6864 < 8.6924] w=0.0710 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)A277.CB) [> 3.3642 = 5.6071 < 7.2892] w=0.0710 to align # Constraint # added constraint: constraint((T0334)K83.CB, (T0334)A275.CB) [> 3.8954 = 6.4924 < 8.4401] w=0.0710 to align # Constraint # added constraint: constraint((T0334)Y131.CB, (T0334)F171.CB) [> 4.0320 = 6.7200 < 8.7359] w=0.0710 to align # Constraint # added constraint: constraint((T0334)V80.CB, (T0334)R158.CB) [> 4.0483 = 6.7471 < 8.7712] w=0.0710 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)S274.CB) [> 3.6913 = 6.1521 < 7.9977] w=0.0710 to align # Constraint # added constraint: constraint((T0334)I85.CB, (T0334)I276.CB) [> 3.8200 = 6.3666 < 8.2766] w=0.0710 to align # Constraint # added constraint: constraint((T0334)A76.CB, (T0334)F171.CB) [> 3.6433 = 6.0722 < 7.8939] w=0.0710 to align # Constraint # added constraint: constraint((T0334)V269.CB, (T0334)F292.CB) [> 4.1918 = 6.9864 < 9.0823] w=0.0710 to align # Constraint # added constraint: constraint((T0334)K285.CB, (T0334)L318.CB) [> 3.8017 = 6.3362 < 8.2371] w=0.0710 to align # Constraint # added constraint: constraint((T0334)S155.CB, (T0334)Y167.CB) [> 3.8963 = 6.4938 < 8.4419] w=0.0710 to align # Constraint # added constraint: constraint((T0334)Y78.CB, (T0334)H170.CB) [> 3.8600 = 6.4333 < 8.3632] w=0.0710 to align # Constraint # added constraint: constraint((T0334)L36.CB, (T0334)M71.CB) [> 4.1216 = 6.8693 < 8.9301] w=0.0710 to align # Constraint # added constraint: constraint((T0334)M278.CB, (T0334)R412.CB) [> 4.5813 = 7.6354 < 9.9261] w=0.0710 to align # Constraint # added constraint: constraint((T0334)K279.CB, (T0334)R412.CB) [> 4.2306 = 7.0510 < 9.1663] w=0.0710 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)P411.CB) [> 4.2113 = 7.0189 < 9.1245] w=0.0710 to align # Constraint # added constraint: constraint((T0334)G281.CA, (T0334)R412.CB) [> 2.7001 = 4.5001 < 5.8502] w=0.0710 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)R412.CB) [> 4.1586 = 6.9310 < 9.0102] w=0.0710 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)T385.CB) [> 4.6781 = 7.7969 < 10.1359] w=0.0710 to align # Constraint # added constraint: constraint((T0334)L159.CB, (T0334)A168.CB) [> 3.8542 = 6.4236 < 8.3507] w=0.0710 to align # Constraint # added constraint: constraint((T0334)C313.CB, (T0334)L325.CB) [> 3.3974 = 5.6623 < 7.3609] w=0.0710 to align # Constraint # added constraint: constraint((T0334)A97.CB, (T0334)S228.CB) [> 3.9005 = 6.5008 < 8.4510] w=0.0709 to align # Constraint # added constraint: constraint((T0334)H109.CB, (T0334)C227.CB) [> 4.3790 = 7.2983 < 9.4878] w=0.0693 to align # Constraint # added constraint: constraint((T0334)L113.CB, (T0334)V225.CB) [> 3.4903 = 5.8172 < 7.5623] w=0.0693 to align # Constraint # added constraint: constraint((T0334)F127.CB, (T0334)R157.CB) [> 4.1650 = 6.9416 < 9.0241] w=0.0693 to align # Constraint # added constraint: constraint((T0334)F127.CB, (T0334)V136.CB) [> 3.6594 = 6.0989 < 7.9286] w=0.0685 to align # Constraint # added constraint: constraint((T0334)A97.CB, (T0334)S123.CB) [> 4.1323 = 6.8871 < 8.9532] w=0.0685 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)S349.CB) [> 3.5441 = 5.9069 < 7.6790] w=0.0661 to align # Constraint # added constraint: constraint((T0334)M239.CB, (T0334)T283.CB) [> 2.9626 = 4.9376 < 6.4189] w=0.0659 to align # Constraint # added constraint: constraint((T0334)R129.CB, (T0334)F179.CB) [> 3.2095 = 5.3492 < 6.9539] w=0.0654 to align # Constraint # added constraint: constraint((T0334)L122.CB, (T0334)F352.CB) [> 3.8975 = 6.4958 < 8.4446] w=0.0654 to align # Constraint # added constraint: constraint((T0334)P138.CB, (T0334)A366.CB) [> 2.8977 = 4.8294 < 6.2783] w=0.0654 to align # Constraint # added constraint: constraint((T0334)V80.CB, (T0334)Q370.CB) [> 4.4607 = 7.4345 < 9.6649] w=0.0654 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)R334.CB) [> 3.2067 = 5.3445 < 6.9479] w=0.0654 to align # Constraint # added constraint: constraint((T0334)I65.CB, (T0334)Y362.CB) [> 3.7473 = 6.2456 < 8.1193] w=0.0654 to align # Constraint # added constraint: constraint((T0334)H106.CB, (T0334)H117.CB) [> 3.7373 = 6.2288 < 8.0974] w=0.0654 to align # Constraint # added constraint: constraint((T0334)Q56.CB, (T0334)A168.CB) [> 3.9348 = 6.5580 < 8.5254] w=0.0651 to align # Constraint # added constraint: constraint((T0334)W339.CB, (T0334)P355.CB) [> 3.2021 = 5.3368 < 6.9378] w=0.0651 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)V353.CB) [> 4.2765 = 7.1275 < 9.2657] w=0.0651 to align # Constraint # added constraint: constraint((T0334)N205.CB, (T0334)G341.CA) [> 4.2135 = 7.0225 < 9.1293] w=0.0651 to align # Constraint # added constraint: constraint((T0334)F352.CB, (T0334)V364.CB) [> 4.0868 = 6.8114 < 8.8548] w=0.0651 to align # Constraint # added constraint: constraint((T0334)G48.CA, (T0334)P355.CB) [> 4.5141 = 7.5234 < 9.7805] w=0.0651 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)L356.CB) [> 4.4961 = 7.4935 < 9.7416] w=0.0651 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)V353.CB) [> 4.3596 = 7.2660 < 9.4458] w=0.0651 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)V353.CB) [> 3.8735 = 6.4558 < 8.3926] w=0.0651 to align # Constraint # added constraint: constraint((T0334)H106.CB, (T0334)S274.CB) [> 3.1579 = 5.2631 < 6.8421] w=0.0651 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)L356.CB) [> 3.9983 = 6.6638 < 8.6629] w=0.0651 to align # Constraint # added constraint: constraint((T0334)F272.CB, (T0334)W284.CB) [> 4.2311 = 7.0518 < 9.1673] w=0.0651 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)S345.CB) [> 3.8291 = 6.3819 < 8.2964] w=0.0651 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)S345.CB) [> 3.6539 = 6.0898 < 7.9168] w=0.0651 to align # Constraint # added constraint: constraint((T0334)P261.CB, (T0334)F292.CB) [> 3.8918 = 6.4863 < 8.4321] w=0.0651 to align # Constraint # added constraint: constraint((T0334)W126.CB, (T0334)L175.CB) [> 4.4176 = 7.3626 < 9.5714] w=0.0650 to align # Constraint # added constraint: constraint((T0334)V353.CB, (T0334)F396.CB) [> 3.7280 = 6.2133 < 8.0773] w=0.0650 to align # Constraint # added constraint: constraint((T0334)L513.CB, (T0334)F523.CB) [> 3.5493 = 5.9155 < 7.6901] w=0.0650 to align # Constraint # added constraint: constraint((T0334)F352.CB, (T0334)Y362.CB) [> 3.9035 = 6.5059 < 8.4576] w=0.0650 to align # Constraint # added constraint: constraint((T0334)S345.CB, (T0334)F363.CB) [> 4.4409 = 7.4015 < 9.6219] w=0.0650 to align # Constraint # added constraint: constraint((T0334)L55.CB, (T0334)E357.CB) [> 3.5573 = 5.9288 < 7.7074] w=0.0650 to align # Constraint # added constraint: constraint((T0334)S77.CB, (T0334)W169.CB) [> 3.7411 = 6.2352 < 8.1058] w=0.0650 to align # Constraint # added constraint: constraint((T0334)E99.CB, (T0334)V200.CB) [> 3.8214 = 6.3691 < 8.2798] w=0.0650 to align # Constraint # added constraint: constraint((T0334)I34.CB, (T0334)A76.CB) [> 3.0435 = 5.0726 < 6.5943] w=0.0650 to align # Constraint # added constraint: constraint((T0334)T35.CB, (T0334)S77.CB) [> 2.8360 = 4.7267 < 6.1447] w=0.0650 to align # Constraint # added constraint: constraint((T0334)L36.CB, (T0334)A76.CB) [> 3.3438 = 5.5730 < 7.2448] w=0.0650 to align # Constraint # added constraint: constraint((T0334)P261.CB, (T0334)L325.CB) [> 3.6464 = 6.0773 < 7.9005] w=0.0650 to align # Constraint # added constraint: constraint((T0334)L100.CB, (T0334)V200.CB) [> 3.7851 = 6.3084 < 8.2010] w=0.0650 to align # Constraint # added constraint: constraint((T0334)A97.CB, (T0334)V197.CB) [> 4.0548 = 6.7580 < 8.7854] w=0.0650 to align # Constraint # added constraint: constraint((T0334)Y116.CB, (T0334)K145.CB) [> 3.6709 = 6.1182 < 7.9536] w=0.0650 to align # Constraint # added constraint: constraint((T0334)S350.CB, (T0334)G360.CA) [> 3.7638 = 6.2730 < 8.1549] w=0.0650 to align # Constraint # added constraint: constraint((T0334)F62.CB, (T0334)I361.CB) [> 4.0076 = 6.6793 < 8.6831] w=0.0648 to align # Constraint # added constraint: constraint((T0334)W126.CB, (T0334)S228.CB) [> 4.4538 = 7.4231 < 9.6500] w=0.0634 to align # Constraint # added constraint: constraint((T0334)Y125.CB, (T0334)S155.CB) [> 4.3872 = 7.3120 < 9.5056] w=0.0634 to align # Constraint # added constraint: constraint((T0334)F171.CB, (T0334)L289.CB) [> 4.0830 = 6.8050 < 8.8464] w=0.0626 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)S345.CB) [> 2.7679 = 4.6131 < 5.9971] w=0.0602 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)S350.CB) [> 3.2245 = 5.3742 < 6.9865] w=0.0602 to align # Constraint # added constraint: constraint((T0334)G229.CA, (T0334)R334.CB) [> 4.6157 = 7.6929 < 10.0008] w=0.0596 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)T348.CB) [> 3.7771 = 6.2951 < 8.1837] w=0.0596 to align # Constraint # added constraint: constraint((T0334)I85.CB, (T0334)Y362.CB) [> 3.6252 = 6.0421 < 7.8547] w=0.0596 to align # Constraint # added constraint: constraint((T0334)L113.CB, (T0334)K163.CB) [> 3.6373 = 6.0621 < 7.8808] w=0.0595 to align # Constraint # added constraint: constraint((T0334)G293.CA, (T0334)I328.CB) [> 4.3878 = 7.3130 < 9.5068] w=0.0595 to align # Constraint # added constraint: constraint((T0334)G46.CA, (T0334)S254.CB) [> 3.4873 = 5.8121 < 7.5558] w=0.0595 to align # Constraint # added constraint: constraint((T0334)I149.CB, (T0334)F179.CB) [> 3.3774 = 5.6290 < 7.3177] w=0.0595 to align # Constraint # added constraint: constraint((T0334)N86.CB, (T0334)L356.CB) [> 3.9948 = 6.6580 < 8.6554] w=0.0595 to align # Constraint # added constraint: constraint((T0334)W284.CB, (T0334)P355.CB) [> 3.3811 = 5.6352 < 7.3258] w=0.0595 to align # Constraint # added constraint: constraint((T0334)A97.CB, (T0334)F179.CB) [> 3.8188 = 6.3647 < 8.2741] w=0.0595 to align # Constraint # added constraint: constraint((T0334)L100.CB, (T0334)F179.CB) [> 3.1470 = 5.2449 < 6.8184] w=0.0595 to align # Constraint # added constraint: constraint((T0334)R231.CB, (T0334)V269.CB) [> 4.1065 = 6.8442 < 8.8974] w=0.0595 to align # Constraint # added constraint: constraint((T0334)T165.CB, (T0334)L175.CB) [> 3.2599 = 5.4331 < 7.0630] w=0.0595 to align # Constraint # added constraint: constraint((T0334)S123.CB, (T0334)F352.CB) [> 2.3078 = 3.8463 < 5.0002] w=0.0595 to align # Constraint # added constraint: constraint((T0334)F139.CB, (T0334)Y362.CB) [> 3.1610 = 5.2684 < 6.8489] w=0.0595 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)R334.CB) [> 4.2487 = 7.0811 < 9.2055] w=0.0595 to align # Constraint # added constraint: constraint((T0334)C74.CB, (T0334)T359.CB) [> 3.8405 = 6.4008 < 8.3210] w=0.0595 to align # Constraint # added constraint: constraint((T0334)V197.CB, (T0334)L234.CB) [> 4.2835 = 7.1392 < 9.2809] w=0.0591 to align # Constraint # added constraint: constraint((T0334)T15.CB, (T0334)Y362.CB) [> 3.9945 = 6.6575 < 8.6548] w=0.0591 to align # Constraint # added constraint: constraint((T0334)S110.CB, (T0334)A277.CB) [> 3.9495 = 6.5825 < 8.5572] w=0.0591 to align # Constraint # added constraint: constraint((T0334)Y108.CB, (T0334)A275.CB) [> 3.9484 = 6.5806 < 8.5548] w=0.0591 to align # Constraint # added constraint: constraint((T0334)A277.CB, (T0334)R412.CB) [> 4.4525 = 7.4208 < 9.6471] w=0.0591 to align # Constraint # added constraint: constraint((T0334)E357.CB, (T0334)F407.CB) [> 4.5470 = 7.5783 < 9.8518] w=0.0591 to align # Constraint # added constraint: constraint((T0334)H109.CB, (T0334)I276.CB) [> 3.8861 = 6.4768 < 8.4199] w=0.0591 to align # Constraint # added constraint: constraint((T0334)D226.CB, (T0334)T348.CB) [> 3.7485 = 6.2474 < 8.1216] w=0.0591 to align # Constraint # added constraint: constraint((T0334)L251.CB, (T0334)R301.CB) [> 3.9587 = 6.5978 < 8.5772] w=0.0591 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)E354.CB) [> 4.3261 = 7.2102 < 9.3733] w=0.0591 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)I346.CB) [> 3.7918 = 6.3197 < 8.2156] w=0.0591 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)I346.CB) [> 4.3383 = 7.2305 < 9.3997] w=0.0591 to align # Constraint # added constraint: constraint((T0334)P104.CB, (T0334)F272.CB) [> 3.2178 = 5.3630 < 6.9719] w=0.0591 to align # Constraint # added constraint: constraint((T0334)V136.CB, (T0334)A168.CB) [> 3.4573 = 5.7622 < 7.4909] w=0.0591 to align # Constraint # added constraint: constraint((T0334)Y125.CB, (T0334)F179.CB) [> 3.4941 = 5.8234 < 7.5705] w=0.0591 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)L325.CB) [> 4.1936 = 6.9894 < 9.0863] w=0.0591 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)I392.CB) [> 3.9061 = 6.5101 < 8.4632] w=0.0591 to align # Constraint # added constraint: constraint((T0334)V80.CB, (T0334)F272.CB) [> 3.4232 = 5.7053 < 7.4170] w=0.0591 to align # Constraint # added constraint: constraint((T0334)S349.CB, (T0334)F363.CB) [> 2.6017 = 4.3361 < 5.6370] w=0.0591 to align # Constraint # added constraint: constraint((T0334)P156.CB, (T0334)Y167.CB) [> 3.1698 = 5.2830 < 6.8679] w=0.0591 to align # Constraint # added constraint: constraint((T0334)A275.CB, (T0334)S410.CB) [> 3.3886 = 5.6476 < 7.3419] w=0.0591 to align # Constraint # added constraint: constraint((T0334)E99.CB, (T0334)E198.CB) [> 3.8539 = 6.4232 < 8.3501] w=0.0591 to align # Constraint # added constraint: constraint((T0334)H117.CB, (T0334)Y141.CB) [> 3.8453 = 6.4089 < 8.3315] w=0.0590 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)Y362.CB) [> 3.5769 = 5.9615 < 7.7500] w=0.0590 to align # Constraint # added constraint: constraint((T0334)F62.CB, (T0334)E357.CB) [> 4.0913 = 6.8189 < 8.8645] w=0.0589 to align # Constraint # added constraint: constraint((T0334)F62.CB, (T0334)D172.CB) [> 3.5743 = 5.9571 < 7.7442] w=0.0589 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)G295.CA) [> 4.6738 = 7.7896 < 10.1265] w=0.0575 to align # Constraint # added constraint: constraint((T0334)G14.CA, (T0334)N267.CB) [> 4.5022 = 7.5036 < 9.7547] w=0.0574 to align # Constraint # added constraint: constraint((T0334)A16.CB, (T0334)A266.CB) [> 2.5589 = 4.2649 < 5.5443] w=0.0574 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)A266.CB) [> 3.4453 = 5.7422 < 7.4648] w=0.0574 to align # Constraint # added constraint: constraint((T0334)F139.CB, (T0334)V148.CB) [> 4.2640 = 7.1067 < 9.2387] w=0.0574 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)S350.CB) [> 3.0231 = 5.0385 < 6.5501] w=0.0567 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)S345.CB) [> 3.1355 = 5.2259 < 6.7937] w=0.0567 to align # Constraint # added constraint: constraint((T0334)L251.CB, (T0334)W339.CB) [> 3.6618 = 6.1029 < 7.9338] w=0.0543 to align # Constraint # added constraint: constraint((T0334)L250.CB, (T0334)W339.CB) [> 4.0506 = 6.7510 < 8.7763] w=0.0543 to align # Constraint # added constraint: constraint((T0334)W284.CB, (T0334)E354.CB) [> 4.1474 = 6.9123 < 8.9860] w=0.0542 to align # Constraint # added constraint: constraint((T0334)K115.CB, (T0334)F127.CB) [> 3.7672 = 6.2786 < 8.1622] w=0.0536 to align # Constraint # added constraint: constraint((T0334)L114.CB, (T0334)F127.CB) [> 3.1120 = 5.1866 < 6.7426] w=0.0536 to align # Constraint # added constraint: constraint((T0334)W87.CB, (T0334)T359.CB) [> 3.6399 = 6.0665 < 7.8864] w=0.0536 to align # Constraint # added constraint: constraint((T0334)W87.CB, (T0334)L356.CB) [> 3.6187 = 6.0312 < 7.8406] w=0.0536 to align # Constraint # added constraint: constraint((T0334)S110.CB, (T0334)L356.CB) [> 4.0826 = 6.8043 < 8.8456] w=0.0536 to align # Constraint # added constraint: constraint((T0334)N86.CB, (T0334)L113.CB) [> 3.2392 = 5.3987 < 7.0183] w=0.0536 to align # Constraint # added constraint: constraint((T0334)Y125.CB, (T0334)Y365.CB) [> 4.2730 = 7.1216 < 9.2581] w=0.0536 to align # Constraint # added constraint: constraint((T0334)Y131.CB, (T0334)F179.CB) [> 2.7868 = 4.6447 < 6.0381] w=0.0536 to align # Constraint # added constraint: constraint((T0334)S130.CB, (T0334)F179.CB) [> 3.2131 = 5.3552 < 6.9618] w=0.0536 to align # Constraint # added constraint: constraint((T0334)G112.CA, (T0334)L356.CB) [> 3.7277 = 6.2128 < 8.0766] w=0.0536 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)P355.CB) [> 3.9996 = 6.6661 < 8.6659] w=0.0536 to align # Constraint # added constraint: constraint((T0334)Y144.CB, (T0334)V164.CB) [> 4.0672 = 6.7787 < 8.8123] w=0.0536 to align # Constraint # added constraint: constraint((T0334)R231.CB, (T0334)E270.CB) [> 3.8823 = 6.4705 < 8.4116] w=0.0536 to align # Constraint # added constraint: constraint((T0334)Y125.CB, (T0334)Y369.CB) [> 4.0555 = 6.7591 < 8.7868] w=0.0536 to align # Constraint # added constraint: constraint((T0334)C74.CB, (T0334)L356.CB) [> 3.5089 = 5.8481 < 7.6025] w=0.0536 to align # Constraint # added constraint: constraint((T0334)A39.CB, (T0334)G268.CA) [> 4.3621 = 7.2701 < 9.4511] w=0.0536 to align # Constraint # added constraint: constraint((T0334)F127.CB, (T0334)V353.CB) [> 3.8080 = 6.3467 < 8.2507] w=0.0536 to align # Constraint # added constraint: constraint((T0334)C74.CB, (T0334)F179.CB) [> 3.2136 = 5.3560 < 6.9628] w=0.0532 to align # Constraint # added constraint: constraint((T0334)G17.CA, (T0334)Q38.CB) [> 4.5688 = 7.6147 < 9.8991] w=0.0532 to align # Constraint # added constraint: constraint((T0334)V225.CB, (T0334)S350.CB) [> 4.5386 = 7.5643 < 9.8336] w=0.0532 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)F363.CB) [> 3.3350 = 5.5583 < 7.2258] w=0.0532 to align # Constraint # added constraint: constraint((T0334)K83.CB, (T0334)A366.CB) [> 3.4232 = 5.7053 < 7.4169] w=0.0532 to align # Constraint # added constraint: constraint((T0334)R231.CB, (T0334)H249.CB) [> 4.1694 = 6.9491 < 9.0338] w=0.0532 to align # Constraint # added constraint: constraint((T0334)D264.CB, (T0334)T294.CB) [> 4.2303 = 7.0504 < 9.1656] w=0.0532 to align # Constraint # added constraint: constraint((T0334)P40.CB, (T0334)A50.CB) [> 3.7859 = 6.3099 < 8.2029] w=0.0532 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)C313.CB) [> 3.9463 = 6.5771 < 8.5503] w=0.0532 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)T273.CB) [> 3.2566 = 5.4276 < 7.0559] w=0.0532 to align # Constraint # added constraint: constraint((T0334)H109.CB, (T0334)S274.CB) [> 3.8104 = 6.3507 < 8.2559] w=0.0532 to align # Constraint # added constraint: constraint((T0334)I82.CB, (T0334)T273.CB) [> 3.3462 = 5.5770 < 7.2501] w=0.0532 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)F272.CB) [> 3.7637 = 6.2728 < 8.1546] w=0.0532 to align # Constraint # added constraint: constraint((T0334)K83.CB, (T0334)T273.CB) [> 3.8696 = 6.4493 < 8.3841] w=0.0532 to align # Constraint # added constraint: constraint((T0334)T283.CB, (T0334)L318.CB) [> 3.9433 = 6.5722 < 8.5438] w=0.0532 to align # Constraint # added constraint: constraint((T0334)F292.CB, (T0334)L325.CB) [> 4.2688 = 7.1147 < 9.2492] w=0.0532 to align # Constraint # added constraint: constraint((T0334)D222.CB, (T0334)V344.CB) [> 3.7737 = 6.2896 < 8.1764] w=0.0532 to align # Constraint # added constraint: constraint((T0334)Y144.CB, (T0334)F179.CB) [> 2.9350 = 4.8917 < 6.3592] w=0.0532 to align # Constraint # added constraint: constraint((T0334)F127.CB, (T0334)Y141.CB) [> 3.6545 = 6.0909 < 7.9181] w=0.0532 to align # Constraint # added constraint: constraint((T0334)I85.CB, (T0334)A277.CB) [> 3.7287 = 6.2144 < 8.0788] w=0.0532 to align # Constraint # added constraint: constraint((T0334)Q56.CB, (T0334)P66.CB) [> 4.2757 = 7.1261 < 9.2639] w=0.0532 to align # Constraint # added constraint: constraint((T0334)Q370.CB, (T0334)R387.CB) [> 3.3605 = 5.6008 < 7.2810] w=0.0532 to align # Constraint # added constraint: constraint((T0334)W70.CB, (T0334)Y369.CB) [> 3.4957 = 5.8262 < 7.5741] w=0.0532 to align # Constraint # added constraint: constraint((T0334)A266.CB, (T0334)G293.CA) [> 3.9059 = 6.5099 < 8.4628] w=0.0532 to align # Constraint # added constraint: constraint((T0334)M19.CB, (T0334)W70.CB) [> 4.3098 = 7.1830 < 9.3379] w=0.0532 to align # Constraint # added constraint: constraint((T0334)W70.CB, (T0334)Y365.CB) [> 3.2645 = 5.4408 < 7.0730] w=0.0532 to align # Constraint # added constraint: constraint((T0334)H262.CB, (T0334)K285.CB) [> 4.1585 = 6.9309 < 9.0101] w=0.0532 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)F407.CB) [> 3.1386 = 5.2311 < 6.8004] w=0.0532 to align # Constraint # added constraint: constraint((T0334)A277.CB, (T0334)V506.CB) [> 4.6501 = 7.7501 < 10.0751] w=0.0532 to align # Constraint # added constraint: constraint((T0334)A173.CB, (T0334)E357.CB) [> 4.1192 = 6.8654 < 8.9250] w=0.0532 to align # Constraint # added constraint: constraint((T0334)E49.CB, (T0334)G293.CA) [> 4.2811 = 7.1351 < 9.2756] w=0.0532 to align # Constraint # added constraint: constraint((T0334)Y78.CB, (T0334)A168.CB) [> 3.7560 = 6.2599 < 8.1379] w=0.0532 to align # Constraint # added constraint: constraint((T0334)K83.CB, (T0334)G93.CA) [> 3.6998 = 6.1663 < 8.0161] w=0.0532 to align # Constraint # added constraint: constraint((T0334)D263.CB, (T0334)K285.CB) [> 3.4828 = 5.8046 < 7.5460] w=0.0532 to align # Constraint # added constraint: constraint((T0334)A39.CB, (T0334)A81.CB) [> 3.9056 = 6.5093 < 8.4621] w=0.0532 to align # Constraint # added constraint: constraint((T0334)Q38.CB, (T0334)V80.CB) [> 3.8513 = 6.4189 < 8.3445] w=0.0532 to align # Constraint # added constraint: constraint((T0334)S349.CB, (T0334)A366.CB) [> 4.3187 = 7.1978 < 9.3571] w=0.0532 to align # Constraint # added constraint: constraint((T0334)R327.CB, (T0334)S350.CB) [> 3.5850 = 5.9750 < 7.7675] w=0.0532 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)Q370.CB) [> 3.0972 = 5.1619 < 6.7105] w=0.0532 to align # Constraint # added constraint: constraint((T0334)F62.CB, (T0334)Y108.CB) [> 3.5876 = 5.9794 < 7.7732] w=0.0530 to align # Constraint # added constraint: constraint((T0334)S123.CB, (T0334)Y144.CB) [> 3.4573 = 5.7621 < 7.4907] w=0.0520 to align # Constraint # added constraint: constraint((T0334)H106.CB, (T0334)V200.CB) [> 3.5384 = 5.8974 < 7.6666] w=0.0516 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)V225.CB) [> 4.3544 = 7.2573 < 9.4345] w=0.0515 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)V344.CB) [> 4.4372 = 7.3954 < 9.6140] w=0.0508 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)V344.CB) [> 3.0100 = 5.0167 < 6.5217] w=0.0508 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)S345.CB) [> 3.8496 = 6.4161 < 8.3409] w=0.0508 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)S345.CB) [> 4.4423 = 7.4039 < 9.6251] w=0.0484 to align # Constraint # added constraint: constraint((T0334)T57.CB, (T0334)A173.CB) [> 3.3096 = 5.5160 < 7.1708] w=0.0478 to align # Constraint # added constraint: constraint((T0334)A152.CB, (T0334)S358.CB) [> 3.2181 = 5.3635 < 6.9726] w=0.0477 to align # Constraint # added constraint: constraint((T0334)E67.CB, (T0334)I82.CB) [> 2.7551 = 4.5919 < 5.9694] w=0.0477 to align # Constraint # added constraint: constraint((T0334)M71.CB, (T0334)I82.CB) [> 2.5425 = 4.2375 < 5.5087] w=0.0477 to align # Constraint # added constraint: constraint((T0334)L150.CB, (T0334)F179.CB) [> 3.0876 = 5.1459 < 6.6897] w=0.0477 to align # Constraint # added constraint: constraint((T0334)I82.CB, (T0334)L114.CB) [> 3.2249 = 5.3749 < 6.9873] w=0.0477 to align # Constraint # added constraint: constraint((T0334)S274.CB, (T0334)R334.CB) [> 3.3428 = 5.5713 < 7.2427] w=0.0477 to align # Constraint # added constraint: constraint((T0334)I276.CB, (T0334)R334.CB) [> 3.4933 = 5.8222 < 7.5689] w=0.0477 to align # Constraint # added constraint: constraint((T0334)S110.CB, (T0334)S358.CB) [> 2.8471 = 4.7452 < 6.1687] w=0.0477 to align # Constraint # added constraint: constraint((T0334)L113.CB, (T0334)S358.CB) [> 4.1576 = 6.9293 < 9.0081] w=0.0477 to align # Constraint # added constraint: constraint((T0334)D61.CB, (T0334)S110.CB) [> 3.5593 = 5.9321 < 7.7117] w=0.0477 to align # Constraint # added constraint: constraint((T0334)Y131.CB, (T0334)T165.CB) [> 4.5765 = 7.6275 < 9.9158] w=0.0477 to align # Constraint # added constraint: constraint((T0334)F60.CB, (T0334)A173.CB) [> 3.6713 = 6.1189 < 7.9545] w=0.0477 to align # Constraint # added constraint: constraint((T0334)Y116.CB, (T0334)D172.CB) [> 4.0576 = 6.7626 < 8.7914] w=0.0477 to align # Constraint # added constraint: constraint((T0334)R129.CB, (T0334)P138.CB) [> 3.0809 = 5.1349 < 6.6753] w=0.0477 to align # Constraint # added constraint: constraint((T0334)P138.CB, (T0334)Q370.CB) [> 4.4341 = 7.3901 < 9.6071] w=0.0477 to align # Constraint # added constraint: constraint((T0334)F139.CB, (T0334)A366.CB) [> 3.9695 = 6.6158 < 8.6006] w=0.0477 to align # Constraint # added constraint: constraint((T0334)A58.CB, (T0334)Y144.CB) [> 3.4910 = 5.8184 < 7.5639] w=0.0477 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)F363.CB) [> 4.2577 = 7.0962 < 9.2250] w=0.0473 to align # Constraint # added constraint: constraint((T0334)C343.CB, (T0334)F388.CB) [> 3.6549 = 6.0915 < 7.9190] w=0.0473 to align # Constraint # added constraint: constraint((T0334)R231.CB, (T0334)S349.CB) [> 4.1210 = 6.8684 < 8.9289] w=0.0473 to align # Constraint # added constraint: constraint((T0334)N86.CB, (T0334)A277.CB) [> 3.4500 = 5.7501 < 7.4751] w=0.0473 to align # Constraint # added constraint: constraint((T0334)F59.CB, (T0334)Y78.CB) [> 3.9092 = 6.5153 < 8.4699] w=0.0473 to align # Constraint # added constraint: constraint((T0334)A27.CB, (T0334)Y369.CB) [> 3.2293 = 5.3821 < 6.9967] w=0.0473 to align # Constraint # added constraint: constraint((T0334)S345.CB, (T0334)P355.CB) [> 3.1033 = 5.1722 < 6.7238] w=0.0473 to align # Constraint # added constraint: constraint((T0334)S345.CB, (T0334)E354.CB) [> 3.1047 = 5.1745 < 6.7268] w=0.0473 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)P355.CB) [> 3.2364 = 5.3941 < 7.0123] w=0.0473 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)E354.CB) [> 4.2334 = 7.0557 < 9.1725] w=0.0473 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)S350.CB) [> 2.8616 = 4.7694 < 6.2002] w=0.0473 to align # Constraint # added constraint: constraint((T0334)F224.CB, (T0334)S349.CB) [> 4.0273 = 6.7121 < 8.7257] w=0.0473 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)S350.CB) [> 4.3213 = 7.2021 < 9.3628] w=0.0473 to align # Constraint # added constraint: constraint((T0334)L223.CB, (T0334)S349.CB) [> 2.9981 = 4.9969 < 6.4959] w=0.0473 to align # Constraint # added constraint: constraint((T0334)D222.CB, (T0334)S349.CB) [> 3.8484 = 6.4140 < 8.3382] w=0.0473 to align # Constraint # added constraint: constraint((T0334)V200.CB, (T0334)S350.CB) [> 4.3878 = 7.3131 < 9.5070] w=0.0473 to align # Constraint # added constraint: constraint((T0334)R212.CB, (T0334)T385.CB) [> 3.9731 = 6.6217 < 8.6083] w=0.0473 to align # Constraint # added constraint: constraint((T0334)G13.CA, (T0334)A39.CB) [> 4.6413 = 7.7355 < 10.0561] w=0.0473 to align # Constraint # added constraint: constraint((T0334)I82.CB, (T0334)A275.CB) [> 3.3761 = 5.6269 < 7.3149] w=0.0473 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)D160.CB) [> 3.0746 = 5.1243 < 6.6616] w=0.0473 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)W282.CB) [> 4.6020 = 7.6700 < 9.9710] w=0.0473 to align # Constraint # added constraint: constraint((T0334)E357.CB, (T0334)A405.CB) [> 4.6660 = 7.7767 < 10.1097] w=0.0473 to align # Constraint # added constraint: constraint((T0334)H109.CB, (T0334)A275.CB) [> 3.2781 = 5.4635 < 7.1026] w=0.0473 to align # Constraint # added constraint: constraint((T0334)T57.CB, (T0334)D172.CB) [> 3.4067 = 5.6779 < 7.3813] w=0.0473 to align # Constraint # added constraint: constraint((T0334)N86.CB, (T0334)M278.CB) [> 3.3410 = 5.5683 < 7.2387] w=0.0473 to align # Constraint # added constraint: constraint((T0334)H262.CB, (T0334)L325.CB) [> 3.6181 = 6.0301 < 7.8391] w=0.0473 to align # Constraint # added constraint: constraint((T0334)I85.CB, (T0334)A275.CB) [> 4.2145 = 7.0242 < 9.1315] w=0.0473 to align # Constraint # added constraint: constraint((T0334)T294.CB, (T0334)C313.CB) [> 4.2636 = 7.1059 < 9.2377] w=0.0473 to align # Constraint # added constraint: constraint((T0334)D222.CB, (T0334)C343.CB) [> 3.6026 = 6.0044 < 7.8057] w=0.0473 to align # Constraint # added constraint: constraint((T0334)S274.CB, (T0334)M288.CB) [> 3.6438 = 6.0730 < 7.8948] w=0.0473 to align # Constraint # added constraint: constraint((T0334)L514.CB, (T0334)F523.CB) [> 4.3630 = 7.2716 < 9.4531] w=0.0473 to align # Constraint # added constraint: constraint((T0334)S254.CB, (T0334)T294.CB) [> 3.2173 = 5.3622 < 6.9708] w=0.0473 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)F409.CB) [> 3.7856 = 6.3093 < 8.2021] w=0.0473 to align # Constraint # added constraint: constraint((T0334)V269.CB, (T0334)L318.CB) [> 4.0062 = 6.6770 < 8.6801] w=0.0473 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)T294.CB) [> 4.0755 = 6.7925 < 8.8302] w=0.0473 to align # Constraint # added constraint: constraint((T0334)S350.CB, (T0334)Y362.CB) [> 3.0827 = 5.1378 < 6.6791] w=0.0473 to align # Constraint # added constraint: constraint((T0334)F84.CB, (T0334)G93.CA) [> 3.3860 = 5.6433 < 7.3363] w=0.0473 to align # Constraint # added constraint: constraint((T0334)L37.CB, (T0334)I82.CB) [> 3.5691 = 5.9485 < 7.7330] w=0.0473 to align # Constraint # added constraint: constraint((T0334)H106.CB, (T0334)L223.CB) [> 3.1296 = 5.2160 < 6.7808] w=0.0473 to align # Constraint # added constraint: constraint((T0334)H262.CB, (T0334)I286.CB) [> 4.4778 = 7.4630 < 9.7019] w=0.0472 to align # Constraint # added constraint: constraint((T0334)F107.CB, (T0334)L223.CB) [> 4.6713 = 7.7855 < 10.1212] w=0.0472 to align # Constraint # added constraint: constraint((T0334)W87.CB, (T0334)Y365.CB) [> 2.8335 = 4.7225 < 6.1392] w=0.0472 to align # Constraint # added constraint: constraint((T0334)L100.CB, (T0334)D226.CB) [> 3.9492 = 6.5820 < 8.5566] w=0.0456 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)Q370.CB) [> 3.8510 = 6.4183 < 8.3438] w=0.0449 to align # Constraint # added constraint: constraint((T0334)V256.CB, (T0334)I346.CB) [> 3.5975 = 5.9957 < 7.7945] w=0.0449 to align # Constraint # added constraint: constraint((T0334)W87.CB, (T0334)E354.CB) [> 4.6151 = 7.6918 < 9.9993] w=0.0418 to align # Constraint # added constraint: constraint((T0334)A97.CB, (T0334)Y365.CB) [> 3.8193 = 6.3656 < 8.2752] w=0.0418 to align # Constraint # added constraint: constraint((T0334)E67.CB, (T0334)K83.CB) [> 3.2090 = 5.3484 < 6.9529] w=0.0418 to align # Constraint # added constraint: constraint((T0334)F60.CB, (T0334)D172.CB) [> 4.0206 = 6.7010 < 8.7114] w=0.0418 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)I286.CB) [> 3.4625 = 5.7709 < 7.5021] w=0.0418 to align # Constraint # added constraint: constraint((T0334)H249.CB, (T0334)K285.CB) [> 4.0526 = 6.7543 < 8.7806] w=0.0418 to align # Constraint # added constraint: constraint((T0334)K279.CB, (T0334)S349.CB) [> 3.7344 = 6.2240 < 8.0912] w=0.0418 to align # Constraint # added constraint: constraint((T0334)A277.CB, (T0334)T348.CB) [> 3.7359 = 6.2266 < 8.0945] w=0.0418 to align # Constraint # added constraint: constraint((T0334)H117.CB, (T0334)L356.CB) [> 2.7365 = 4.5608 < 5.9290] w=0.0418 to align # Constraint # added constraint: constraint((T0334)F111.CB, (T0334)E357.CB) [> 3.2846 = 5.4743 < 7.1166] w=0.0418 to align # Constraint # added constraint: constraint((T0334)R129.CB, (T0334)Q370.CB) [> 4.3861 = 7.3102 < 9.5033] w=0.0418 to align # Constraint # added constraint: constraint((T0334)R129.CB, (T0334)A366.CB) [> 3.9534 = 6.5890 < 8.5658] w=0.0418 to align # Constraint # added constraint: constraint((T0334)K7.CB, (T0334)L28.CB) [> 4.5774 = 7.6291 < 9.9178] w=0.0414 to align # Constraint # added constraint: constraint((T0334)Q370.CB, (T0334)T385.CB) [> 4.5285 = 7.5475 < 9.8118] w=0.0414 to align # Constraint # added constraint: constraint((T0334)C227.CB, (T0334)S350.CB) [> 3.7028 = 6.1713 < 8.0227] w=0.0414 to align # Constraint # added constraint: constraint((T0334)F62.CB, (T0334)Y369.CB) [> 4.1905 = 6.9841 < 9.0794] w=0.0414 to align # Constraint # added constraint: constraint((T0334)V344.CB, (T0334)L356.CB) [> 3.0845 = 5.1409 < 6.6831] w=0.0414 to align # Constraint # added constraint: constraint((T0334)A405.CB, (T0334)K433.CB) [> 4.3185 = 7.1976 < 9.3568] w=0.0414 to align # Constraint # added constraint: constraint((T0334)G3.CA, (T0334)F219.CB) [> 3.4397 = 5.7328 < 7.4527] w=0.0414 to align # Constraint # added constraint: constraint((T0334)G341.CA, (T0334)H374.CB) [> 4.1778 = 6.9630 < 9.0519] w=0.0414 to align # Constraint # added constraint: constraint((T0334)E354.CB, (T0334)F402.CB) [> 4.6282 = 7.7137 < 10.0278] w=0.0414 to align # Constraint # added constraint: constraint((T0334)L356.CB, (T0334)F402.CB) [> 2.6816 = 4.4693 < 5.8101] w=0.0414 to align # Constraint # added constraint: constraint((T0334)S110.CB, (T0334)Y167.CB) [> 3.7704 = 6.2840 < 8.1693] w=0.0414 to align # Constraint # added constraint: constraint((T0334)I82.CB, (T0334)E96.CB) [> 3.9432 = 6.5720 < 8.5436] w=0.0414 to align # Constraint # added constraint: constraint((T0334)C143.CB, (T0334)N166.CB) [> 4.0939 = 6.8232 < 8.8701] w=0.0414 to align # Constraint # added constraint: constraint((T0334)V136.CB, (T0334)Y167.CB) [> 3.8186 = 6.3643 < 8.2737] w=0.0414 to align # Constraint # added constraint: constraint((T0334)W282.CB, (T0334)Y408.CB) [> 4.1229 = 6.8716 < 8.9330] w=0.0414 to align # Constraint # added constraint: constraint((T0334)N252.CB, (T0334)G295.CA) [> 3.1855 = 5.3091 < 6.9019] w=0.0414 to align # Constraint # added constraint: constraint((T0334)P53.CB, (T0334)T165.CB) [> 3.2918 = 5.4863 < 7.1321] w=0.0414 to align # Constraint # added constraint: constraint((T0334)Y78.CB, (T0334)Y167.CB) [> 3.5151 = 5.8584 < 7.6160] w=0.0414 to align # Constraint # added constraint: constraint((T0334)R334.CB, (T0334)V344.CB) [> 3.4823 = 5.8038 < 7.5450] w=0.0414 to align # Constraint # added constraint: constraint((T0334)L234.CB, (T0334)L250.CB) [> 3.3306 = 5.5511 < 7.2164] w=0.0414 to align # Constraint # added constraint: constraint((T0334)L100.CB, (T0334)V197.CB) [> 4.1577 = 6.9295 < 9.0083] w=0.0397 to align # Constraint # added constraint: constraint((T0334)R157.CB, (T0334)S358.CB) [> 4.5076 = 7.5127 < 9.7665] w=0.0361 to align # Constraint # added constraint: constraint((T0334)R231.CB, (T0334)R334.CB) [> 2.8881 = 4.8135 < 6.2576] w=0.0361 to align # Constraint # added constraint: constraint((T0334)I85.CB, (T0334)A366.CB) [> 4.0311 = 6.7185 < 8.7340] w=0.0360 to align # Constraint # added constraint: constraint((T0334)F111.CB, (T0334)F127.CB) [> 3.3419 = 5.5699 < 7.2409] w=0.0360 to align # Constraint # added constraint: constraint((T0334)H117.CB, (T0334)T359.CB) [> 4.7219 = 7.8699 < 10.2309] w=0.0359 to align # Constraint # added constraint: constraint((T0334)1nhs expands to /projects/compbio/data/pdb/1nhs.pdb.gz 1nhs:Warning: there is no chain 1nhs will retry with 1nhsA # T0334 read from 1nhs/merged-good-all-a2m # 1nhs read from 1nhs/merged-good-all-a2m # adding 1nhs to template set # found chain 1nhs in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1nhs)M1 Warning: unaligning (T0334)L159 because of BadResidue code BAD_PEPTIDE in next template residue (1nhs)K123 Warning: unaligning (T0334)D160 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)K123 Warning: unaligning (T0334)G161 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)D124 Warning: unaligning (T0334)S162 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nhs)L125 T0334 7 :KILIVGGGTAGWMAASYLGKA 1nhs 2 :KVIVLGSSHGGYEAVEELLNL T0334 29 :QGTADITLLQAPDIPTL 1nhs 23 :HPDAEIQWYEKGDFISF T0334 46 :GVG 1nhs 41 :CCG T0334 55 :LQTAF 1nhs 44 :MQLYL T0334 123 :SHYWFDRS 1nhs 63 :GEKMESRG T0334 136 :VEPFDYACYKEPVILD 1nhs 71 :VNVFSNTEITAIQPKE T0334 152 :ANRSPRR 1nhs 115 :PFELDIP T0334 166 :NYAW 1nhs 126 :DNIY T0334 170 :HFD 1nhs 188 :YLD T0334 174 :HLVADFLRRFA 1nhs 191 :KEFTDVLTEEM T0334 186 :EKLGVRHVED 1nhs 202 :EANNITIATG T0334 196 :RVEHVQ 1nhs 213 :TVERYE T0334 204 :ANGNIESVRTATG 1nhs 219 :GDGRVQKVVTDKN T0334 218 :VFDADLFVDCSGFRGLL 1nhs 232 :AYDADLVVVAVGVRPNT T0334 236 :NKAMEE 1nhs 249 :AWLKGT T0334 242 :PFLD 1nhs 256 :ELHP T0334 247 :SDHLLNDSAVAT 1nhs 260 :NGLIKTDEYMRT T0334 263 :DDD 1nhs 272 :SEP T0334 268 :GVE 1nhs 319 :PFP T0334 271 :PFTSAIAMKSGWTWKIPM 1nhs 324 :QGSSGLAVFDYKFASTGI T0334 310 :REFCEMWHL 1nhs 343 :EVMAQKLGK T0334 324 :PLNRIRFRVGRNRRAWVG 1nhs 352 :ETKAVTVVEDYLMDFNPD Number of specific fragments extracted= 22 number of extra gaps= 1 total=1361 Number of alignments=58 # 1nhs read from 1nhs/merged-good-all-a2m # found chain 1nhs in template set Warning: unaligning (T0334)D101 because of BadResidue code BAD_PEPTIDE in next template residue (1nhs)K123 Warning: unaligning (T0334)G102 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)K123 Warning: unaligning (T0334)G103 because of BadResidue code BAD_PEPTIDE at template residue (1nhs)D124 Warning: unaligning (T0334)P104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1nhs)L125 T0334 7 :KILIVGGGTAGWMAASYLGK 1nhs 2 :KVIVLGSSHGGYEAVEELLN T0334 28 :L 1nhs 22 :L T0334 29 :QGT 1nhs 24 :PDA T0334 33 :DITLLQAPD 1nhs 27 :EIQWYEKGD T0334 42 :IPTLGVG 1nhs 37 :ISFLCCG T0334 57 :TAFFDFLGIPED 1nhs 44 :MQLYLEGKVKDV T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1nhs 64 :EKMESRGVNVFSNTEITAIQPKEHQVT T0334 96 :EAREL 1nhs 117 :ELDIP T0334 105 :DHFYHSFGLL 1nhs 126 :DNIYLMRGRQ T0334 115 :KYHEQIPLSHYWFDRSYRG 1nhs 147 :PEVNNVVVIGSGYIGIEAA T0334 139 :FDYACYKEPVILD 1nhs 166 :EAFAKAGKKVTVI T0334 152 :ANRSPRRLD 1nhs 180 :ILDRPLGVY T0334 172 :DAHLVADFLRRFA 1nhs 189 :LDKEFTDVLTEEM T0334 186 :EKLGVRHVED 1nhs 202 :EANNITIATG T0334 196 :RVEHV 1nhs 213 :TVERY T0334 203 :DANGNIESVRTATG 1nhs 218 :EGDGRVQKVVTDKN T0334 218 :VFDADLFVDCSGFRG 1nhs 232 :AYDADLVVVAVGVRP T0334 233 :LLINKAMEEPF 1nhs 249 :AWLKGTLELHP T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1nhs 260 :NGLIKTDEYMRTSEPDVFAVGDA T0334 270 :EPF 1nhs 323 :VQG T0334 275 :AIAMKSGWTWKIPML 1nhs 328 :GLAVFDYKFASTGIN T0334 306 :DEAVREF 1nhs 343 :EVMAQKL T0334 322 :TQPLNRIRFRVGRNRRAWVG 1nhs 350 :GKETKAVTVVEDYLMDFNPD T0334 342 :NCVSIG 1nhs 388 :GAQLMS T0334 378 :KSLNPVLTARFNREIE 1nhs 394 :KADLTANINAISLAIQ T0334 414 :DTPFWRANKELRL 1nhs 410 :AKMTIEDLAYADF Number of specific fragments extracted= 26 number of extra gaps= 1 total=1387 Number of alignments=59 # 1nhs read from 1nhs/merged-good-all-a2m # found chain 1nhs in template set T0334 2 :SGKIDKILIVGGGTAGWMAASYLGK 1nhs 146 :DPEVNNVVVIGSGYIGIEAAEAFAK T0334 30 :GTADITLLQAPDIP 1nhs 171 :AGKKVTVIDILDRP T0334 63 :LGI 1nhs 185 :LGV T0334 101 :D 1nhs 188 :Y T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQ 1nhs 189 :LDKEFTDVLTEEMEANNITIATGETVERYE T0334 204 :ANGNIESVRT 1nhs 219 :GDGRVQKVVT T0334 215 :TGRVFDADLFVDCSGFR 1nhs 229 :DKNAYDADLVVVAVGVR T0334 258 :TQVPH 1nhs 246 :PNTAW T0334 316 :WHLDPETQPLNRIRFRVGR 1nhs 251 :LKGTLELHPNGLIKTDEYM T0334 337 :RAWVGNCVSIGTSS 1nhs 270 :RTSEPDVFAVGDAT T0334 361 :IYFVYAALYQLVKHFPDK 1nhs 299 :ATNARKQGRFAVKNLEEP Number of specific fragments extracted= 11 number of extra gaps= 0 total=1398 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pxc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1pxc/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1pxc/merged-good-all-a2m.gz for input Trying 1pxc/merged-good-all-a2m Error: Couldn't open file 1pxc/merged-good-all-a2m or 1pxc/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w4xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w4xA expands to /projects/compbio/data/pdb/1w4x.pdb.gz 1w4xA:Skipped atom 2639, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2641, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2643, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2645, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2647, because occupancy 0.500 <= existing 0.500 in 1w4xA Skipped atom 2649, because occupancy 0.500 <= existing 0.500 in 1w4xA # T0334 read from 1w4xA/merged-good-all-a2m # 1w4xA read from 1w4xA/merged-good-all-a2m # adding 1w4xA to template set # found chain 1w4xA in template set T0334 3 :GKIDKILIVGGGTAGWMAASYLGKA 1w4xA 14 :PEEVDVLVVGAGFSGLYALYRLREL T0334 31 :TADITLLQAP 1w4xA 39 :GRSVHVIETA T0334 41 :DIPT 1w4xA 50 :DVGG T0334 57 :TAF 1w4xA 54 :VWY T0334 128 :DRSYR 1w4xA 57 :WNRYP T0334 141 :YACYKEPVILD 1w4xA 62 :GARCDIESIEY T0334 152 :ANRSPRRLDGSKVTNY 1w4xA 74 :YSFSEEVLQEWNWTER T0334 169 :W 1w4xA 90 :Y T0334 171 :FDAHLVADFLRRFA 1w4xA 91 :ASQPEILRYINFVA T0334 186 :EKLG 1w4xA 105 :DKFD T0334 192 :HVED 1w4xA 113 :ITFH T0334 196 :RVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRG 1w4xA 118 :TVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLS T0334 243 :FLDMSDH 1w4xA 155 :VPQLPNF T0334 264 :DDANGVEPFTSAIA 1w4xA 162 :PGLKDFAGNLYHTG T0334 278 :MKS 1w4xA 177 :WPH T0334 333 :GRNR 1w4xA 180 :EPVD T0334 338 :AWVGNCVSIG 1w4xA 184 :FSGQRVGVIG T0334 362 :YFVYAALYQLVKHFPD 1w4xA 196 :SSGIQVSPQIAKQAAE T0334 378 :KSLNPVLTARFNREIETMFDDTRD 1w4xA 228 :APLDPEFLADLKKRYAEFREESRN T0334 440 :GM 1w4xA 252 :TP T0334 478 :LGLVPDAPSPRLAHMPQ 1w4xA 254 :GGTHRYQGPKSALEVSD T0334 497 :ESVDEVFGAVKDR 1w4xA 271 :EELVETLERYWQE Number of specific fragments extracted= 22 number of extra gaps= 0 total=1420 Number of alignments=61 # 1w4xA read from 1w4xA/merged-good-all-a2m # found chain 1w4xA in template set T0334 3 :GKI 1w4xA 13 :PPE T0334 7 :KILIVGGGTAGWMAASYLGK 1w4xA 18 :DVLVVGAGFSGLYALYRLRE T0334 29 :QGT 1w4xA 38 :LGR T0334 33 :DITLLQAPD 1w4xA 41 :SVHVIETAG T0334 46 :GVGEATIP 1w4xA 50 :DVGGVWYW T0334 57 :TAF 1w4xA 58 :NRY T0334 61 :DFLGIPED 1w4xA 61 :PGARCDIE T0334 103 :GPDHFYHSFGLL 1w4xA 70 :IEYCYSFSEEVL T0334 116 :YHE 1w4xA 83 :EWN T0334 152 :ANRSPR 1w4xA 86 :WTERYA T0334 172 :DAHLVADFLRRFA 1w4xA 92 :SQPEILRYINFVA T0334 186 :EKLGVR 1w4xA 105 :DKFDLR T0334 192 :HVED 1w4xA 113 :ITFH T0334 196 :RVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRG 1w4xA 118 :TVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLS T0334 233 :LLI 1w4xA 156 :PQL T0334 261 :PHDDDANGVEPFTS 1w4xA 159 :PNFPGLKDFAGNLY T0334 275 :AIAMKSGWTW 1w4xA 175 :GNWPHEPVDF T0334 289 :LGR 1w4xA 185 :SGQ T0334 292 :FGTGYVYSSRFATE 1w4xA 219 :PHFAVPARNAPLDP T0334 306 :DEAVREFCEM 1w4xA 271 :EELVETLERY T0334 316 :WHLDP 1w4xA 282 :QEGGP T0334 321 :ETQPLNRIRFRVGRNR 1w4xA 349 :NRDNVHLVDTLSAPIE T0334 337 :RAWVGNCVSI 1w4xA 425 :TAGFPNLFFI T0334 350 :SCFVEPLESTGIYFVYAA 1w4xA 435 :AGPGSPSALSNMLVSIEQ T0334 395 :MFDDTRDFIQAHFY 1w4xA 453 :HVEWVTDHIAYMFK T0334 422 :KEL 1w4xA 467 :NGL T0334 427 :ADGMQEKIDMYRAGM 1w4xA 476 :LEKEDEWVEHVNEIA T0334 442 :AINAPASDDAQLYYGNFE 1w4xA 500 :SWYTGANVPGKPRVFMLY T0334 489 :L 1w4xA 518 :V T0334 497 :ESVD 1w4xA 519 :GGFH T0334 505 :AVKDRQRNLLE 1w4xA 523 :RYRQICDEVAA Number of specific fragments extracted= 31 number of extra gaps= 0 total=1451 Number of alignments=62 # 1w4xA read from 1w4xA/merged-good-all-a2m # found chain 1w4xA in template set T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1w4xA 14 :PEEVDVLVVGAGFSGLYALYRLRE T0334 30 :GTADITLLQ 1w4xA 38 :LGRSVHVIE T0334 39 :APDIPT 1w4xA 48 :AGDVGG T0334 57 :TAF 1w4xA 54 :VWY T0334 64 :GI 1w4xA 57 :WN T0334 78 :YKVAIK 1w4xA 59 :RYPGAR T0334 103 :GPDHFY 1w4xA 65 :CDIESI T0334 130 :S 1w4xA 71 :E T0334 149 :ILDANRSPRRLDGSKVTNY 1w4xA 72 :YCYSFSEEVLQEWNWTERY T0334 171 :FDAHLVADFLRRFATEKLGV 1w4xA 91 :ASQPEILRYINFVADKFDLR T0334 191 :RHVEDRVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRG 1w4xA 113 :ITFHTTVTAAAFDEATNTWTVDTNHGDRIRARYLIMASGQLS T0334 240 :EEPFLDMSDHLLNDSAVATQ 1w4xA 155 :VPQLPNFPGLKDFAGNLYHT T0334 262 :HDDDANGVE 1w4xA 175 :GNWPHEPVD T0334 271 :PF 1w4xA 186 :GQ T0334 342 :NCVSIG 1w4xA 188 :RVGVIG T0334 356 :LESTGIYFVYAALYQL 1w4xA 194 :TGSSGIQVSPQIAKQA T0334 378 :KSLNPVLTARFNREIETMFDDTR 1w4xA 228 :APLDPEFLADLKKRYAEFREESR T0334 410 :SPRTDTP 1w4xA 256 :THRYQGP T0334 424 :LR 1w4xA 263 :KS T0334 426 :LADGMQEKIDMYRAGMAI 1w4xA 269 :SDEELVETLERYWQEGGP T0334 471 :YYCVLAGLGLVPDAPSPR 1w4xA 287 :DILAAYRDILRDRDANER T0334 492 :MPQATESVDEVFGAVKDRQRNL 1w4xA 305 :VAEFIRNKIRNTVRDPEVAERL Number of specific fragments extracted= 22 number of extra gaps= 0 total=1473 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbwA expands to /projects/compbio/data/pdb/2fbw.pdb.gz 2fbwA:# T0334 read from 2fbwA/merged-good-all-a2m # 2fbwA read from 2fbwA/merged-good-all-a2m # adding 2fbwA to template set # found chain 2fbwA in template set Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE in next template residue (2fbwA)S402 Warning: unaligning (T0334)S349 because of BadResidue code BAD_PEPTIDE at template residue (2fbwA)S402 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 2fbwA 17 :HEFDAVVVGAGGAGLRAAFGLSE T0334 30 :GTADITLLQAPDIPTLGVGEATI 2fbwA 40 :AGFNTACVTKLFPTRSHTVAAQG T0334 53 :PNLQTAFFDFLGI 2fbwA 78 :WHFYDTVKGSDWL T0334 71 :MRECNASYKVAIKF 2fbwA 93 :QDAIHYMTEQAPAA T0334 123 :SHYWFDRSYR 2fbwA 107 :VIELENYGMP T0334 136 :VEPFDYACYKEPVILD 2fbwA 117 :FSRTEEGKIYQRAFGG T0334 155 :SPR 2fbwA 135 :LQF T0334 160 :DGSKVTNYAWHF 2fbwA 138 :GKGGQAHRCCCV T0334 172 :DAHLVADFLRRFA 2fbwA 153 :TGHSLLHTLYGRS T0334 186 :EKLGVRHVED 2fbwA 166 :LRYDTSYFVE T0334 196 :RVEHVQR 2fbwA 177 :FALDLLM T0334 204 :ANGNIESVR 2fbwA 184 :ENGECRGVI T0334 213 :TATG 2fbwA 196 :IEDG T0334 217 :RVFDADLFVDCSGFR 2fbwA 202 :HRFRAKNTVIATGGY T0334 236 :NKA 2fbwA 217 :GRT T0334 239 :MEEPFLDMSDHLLNDSAV 2fbwA 240 :AGLPCQDLEFVQFHPTGI T0334 264 :DD 2fbwA 258 :YG T0334 267 :NGVEPF 2fbwA 310 :EGRGCG T0334 279 :KSGWTWKIPML 2fbwA 316 :PEKDHVYLQLH T0334 302 :FATE 2fbwA 327 :HLPP T0334 306 :DEAVREFCEMWHLDPETQ 2fbwA 338 :PGISETAMIFAGVDVTKE T0334 327 :RIRFRVG 2fbwA 356 :PIPVLPT T0334 339 :WVGNCVSIG 2fbwA 388 :VVPGLYACG T0334 350 :SCFVEPLESTGIYFVYAALYQLVKHFPD 2fbwA 403 :VHGANRLGANSLLDLVVFGRACALTIAE T0334 378 :KSLNPVLTARFNREIE 2fbwA 443 :PNAGEESVANLDKLRF T0334 394 :TMFDDTRDFIQAHFYFS 2fbwA 467 :EARLNMQKTMQSHAAVF T0334 445 :AP 2fbwA 484 :RT T0334 496 :TESVDEVFGAVKDRQR 2fbwA 486 :GSILQEGCEKLSQIYR Number of specific fragments extracted= 28 number of extra gaps= 1 total=1501 Number of alignments=64 # 2fbwA read from 2fbwA/merged-good-all-a2m # found chain 2fbwA in template set Warning: unaligning (T0334)F352 because of BadResidue code BAD_PEPTIDE in next template residue (2fbwA)S402 T0334 7 :KILIVGGGTAGWMAASYLGK 2fbwA 20 :DAVVVGAGGAGLRAAFGLSE T0334 29 :QGT 2fbwA 40 :AGF T0334 33 :DITLLQAP 2fbwA 43 :NTACVTKL T0334 46 :GVGEATIPNLQTAFFDFLGIPED 2fbwA 51 :FPTRSHTVAAQGGINAALGNMED T0334 76 :ASYKVAIKFINW 2fbwA 74 :DNWRWHFYDTVK T0334 103 :GPDHFYHSFGLL 2fbwA 86 :GSDWLGDQDAIH T0334 115 :KYHEQI 2fbwA 102 :QAPAAV T0334 139 :FDYACYKEP 2fbwA 108 :IELENYGMP T0334 148 :VILD 2fbwA 125 :IYQR T0334 152 :ANRSPRRLDGSKVTNYAWHF 2fbwA 130 :FGGQSLQFGKGGQAHRCCCV T0334 172 :DAHLVADFLRRFA 2fbwA 153 :TGHSLLHTLYGRS T0334 186 :EKLGVRHVED 2fbwA 166 :LRYDTSYFVE T0334 196 :RVEHVQRDAN 2fbwA 177 :FALDLLMENG T0334 207 :NIESVRTA 2fbwA 187 :ECRGVIAL T0334 215 :TGR 2fbwA 198 :DGT T0334 218 :VFDADLFVDCSGF 2fbwA 203 :RFRAKNTVIATGG T0334 233 :LLINKAMEEPFL 2fbwA 234 :TAMVTRAGLPCQ T0334 271 :PFTSAIAMK 2fbwA 246 :DLEFVQFHP T0334 280 :SGWTWKIPMLGR 2fbwA 271 :EGGILINSQGER T0334 292 :FGTGYVYSSRFATE 2fbwA 317 :EKDHVYLQLHHLPP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 2fbwA 338 :PGISETAMIFAGVDVTKEPIPVLPTVHYNMG T0334 337 :RAWVGNCVSIGTSSC 2fbwA 386 :DKVVPGLYACGEAAS T0334 353 :VEP 2fbwA 403 :VHG T0334 356 :LESTGIYFVYAALYQLVKHFP 2fbwA 409 :LGANSLLDLVVFGRACALTIA T0334 377 :DKSLNPVLTARFNREI 2fbwA 442 :KPNAGEESVANLDKLR T0334 393 :ETMFDDTRDFIQAHFYFSPR 2fbwA 466 :SEARLNMQKTMQSHAAVFRT T0334 496 :TESVDEVFGAVKDRQRNLLE 2fbwA 486 :GSILQEGCEKLSQIYRDLAH T0334 516 :TLPSLHEFLR 2fbwA 512 :GIVWNTDLVE Number of specific fragments extracted= 28 number of extra gaps= 1 total=1529 Number of alignments=65 # 2fbwA read from 2fbwA/merged-good-all-a2m # found chain 2fbwA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 2fbwA 20 :DAVVVGAGGAGLRAAFGLSE T0334 30 :GTADITLLQAPDIPTLGV 2fbwA 40 :AGFNTACVTKLFPTRSHT T0334 77 :SYKVAIKFI 2fbwA 58 :VAAQGGINA T0334 97 :ARELDGGPDHFYHSFGLLKYHEQIPLSHYWFD 2fbwA 67 :ALGNMEDDNWRWHFYDTVKGSDWLGDQDAIHY T0334 138 :PFDYACYKEPVILDANRSPRRLDGSKVTNYAWH 2fbwA 99 :MTEQAPAAVIELENYGMPFSRTEEGKIYQRAFG T0334 171 :F 2fbwA 149 :V T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGN 2fbwA 153 :TGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGEC T0334 208 :IESVRTATGR 2fbwA 191 :VIALCIEDGT T0334 218 :VFDADLFVDCSGFRG 2fbwA 203 :RFRAKNTVIATGGYG T0334 247 :SDHLLNDS 2fbwA 218 :RTYFSCTS T0334 307 :EAVREFCEMWHLDPETQ 2fbwA 335 :TRLPGISETAMIFAGVD T0334 336 :RRAWVGNCVSIGTSS 2fbwA 385 :EDKVVPGLYACGEAA T0334 351 :CFVEPLESTGIYFVYAALYQLVKHFP 2fbwA 404 :HGANRLGANSLLDLVVFGRACALTIA T0334 377 :DKSLNPVLTARFNREI 2fbwA 442 :KPNAGEESVANLDKLR T0334 422 :K 2fbwA 460 :D T0334 423 :ELRLADGMQEKIDMYRAGMAI 2fbwA 462 :TIRTSEARLNMQKTMQSHAAV T0334 479 :GLVPDAPSPRLAHMPQATE 2fbwA 483 :FRTGSILQEGCEKLSQIYR Number of specific fragments extracted= 17 number of extra gaps= 0 total=1546 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zovA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1zovA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1zovA/merged-good-all-a2m.gz for input Trying 1zovA/merged-good-all-a2m Error: Couldn't open file 1zovA/merged-good-all-a2m or 1zovA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cj3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cj3A expands to /projects/compbio/data/pdb/1cj3.pdb.gz 1cj3A:# T0334 read from 1cj3A/merged-good-all-a2m # 1cj3A read from 1cj3A/merged-good-all-a2m # adding 1cj3A to template set # found chain 1cj3A in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1cj3A)M1 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1cj3A 2 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1cj3A 24 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1cj3A 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1cj3A 57 :REAGV T0334 123 :SHYWFDRSYR 1cj3A 62 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVILD 1cj3A 72 :HEGVEIAFAGQRRRID T0334 155 :SPRRLDG 1cj3A 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1cj3A 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1cj3A 114 :EASGATTVYQ T0334 196 :RVEHVQR 1cj3A 125 :AEVRLHD T0334 203 :DANG 1cj3A 133 :QGER T0334 209 :ESVRTA 1cj3A 137 :PYVTFE T0334 215 :TG 1cj3A 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1cj3A 148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEPFL 1cj3A 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1cj3A 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1cj3A 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1cj3A 219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1cj3A 232 :EDWSDERFWTELKARL T0334 318 :L 1cj3A 254 :K T0334 322 :TQ 1cj3A 255 :LV T0334 324 :PLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1cj3A 262 :EKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFY 1cj3A 318 :REGRGELLERYSAICLRRIWKAERFSWWMTS T0334 409 :FSPRTDTPFWR 1cj3A 351 :HRFPDTDAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFL 1cj3A 362 :RIQQTELEYYLGSEAGLATIA Number of specific fragments extracted= 25 number of extra gaps= 0 total=1571 Number of alignments=67 # 1cj3A read from 1cj3A/merged-good-all-a2m # found chain 1cj3A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1cj3A)M1 T0334 6 :D 1cj3A 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1cj3A 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1cj3A 24 :AGI T0334 33 :DITLLQAPD 1cj3A 27 :DNVILERQT T0334 52 :IPNLQ 1cj3A 36 :PDEVL T0334 61 :DFLGIPED 1cj3A 41 :GRIRAGVL T0334 69 :EWMRECNASYKVAIKFINW 1cj3A 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1cj3A 73 :EGVEIAFAGQRR T0334 115 :KYHE 1cj3A 87 :DLKR T0334 152 :ANRSPRRLD 1cj3A 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1cj3A 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1cj3A 114 :EASGATTVYQ T0334 196 :RVEHVQRDANGNIE 1cj3A 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1cj3A 139 :VTFE T0334 215 :TGR 1cj3A 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1cj3A 149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1cj3A 167 :QSIPAERLKV T0334 247 :SDHLLND 1cj3A 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1cj3A 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1cj3A 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1cj3A 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEM 1cj3A 223 :VQVPLTEKVEDWSDERFWTELKAR T0334 317 :HLDP 1cj3A 248 :PAEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1cj3A 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1cj3A 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWR 1cj3A 359 :FSQ T0334 508 :DRQRNLLETLPSLHEFLRQ 1cj3A 362 :RIQQTELEYYLGSEAGLAT Number of specific fragments extracted= 27 number of extra gaps= 0 total=1598 Number of alignments=68 # 1cj3A read from 1cj3A/merged-good-all-a2m # found chain 1cj3A in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1cj3A 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1cj3A 24 :AGIDNVILERQT T0334 43 :PTLGVGE 1cj3A 41 :GRIRAGV T0334 51 :TIPNLQTAF 1cj3A 48 :LEQGMVDLL T0334 61 :DFLGIP 1cj3A 57 :REAGVD T0334 68 :D 1cj3A 63 :R T0334 70 :WMRECNASY 1cj3A 64 :RMARDGLVH T0334 79 :KVAIKFINWRT 1cj3A 74 :GVEIAFAGQRR T0334 95 :SE 1cj3A 85 :RI T0334 157 :RRLDGSKVT 1cj3A 87 :DLKRLSGGK T0334 167 :YAWHFDAHLVADFLRRFATEKLGVRHVE 1cj3A 96 :TVTVYGQTEVTRDLMEAREASGATTVYQ T0334 197 :VEHVQRD 1cj3A 124 :AAEVRLH T0334 204 :ANGNIESVRTATGR 1cj3A 134 :GERPYVTFERDGER T0334 218 :VFDADLFVDCSGFRGLLINK 1cj3A 149 :RLDCDYIAGCDGFHGISRQS T0334 244 :LDMSDH 1cj3A 169 :IPAERL T0334 250 :LLNDSAVATQV 1cj3A 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1cj3A 191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1cj3A 231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1cj3A 256 :VTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPR 1cj3A 321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 481 :VPDAPS 1cj3A 357 :DAFSQR T0334 505 :AVKDRQRNLLETLPSLHEFLRQQ 1cj3A 363 :IQQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 22 number of extra gaps= 0 total=1620 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dob/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1dob/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1dob/merged-good-all-a2m.gz for input Trying 1dob/merged-good-all-a2m Error: Couldn't open file 1dob/merged-good-all-a2m or 1dob/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mo9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 1mo9A/merged-good-all-a2m # 1mo9A read from 1mo9A/merged-good-all-a2m # found chain 1mo9A in training set Warning: unaligning (T0334)T413 because of BadResidue code BAD_PEPTIDE in next template residue (1mo9A)L502 Warning: unaligning (T0334)D414 because of BadResidue code BAD_PEPTIDE at template residue (1mo9A)L502 T0334 2 :SGKIDKILIVGGGTAGWMAASYLGK 1mo9A 40 :DPREYDAIFIGGGAAGRFGSAYLRA T0334 30 :GTADITLLQAPDIPTLGVGEA 1mo9A 65 :MGGRQLIVDRWPFLGGSCPHN T0334 52 :IPNLQTAFFDFL 1mo9A 86 :ACVPHHLFSDCA T0334 78 :YKVAIKFINWRTAGEGTS 1mo9A 98 :AELMLARTFSGQYWFPDM T0334 113 :LLKYHEQIPLSHYWFDR 1mo9A 116 :TEKVVGIKEVVDLFRAG T0334 170 :HFDAHLVADFLRRFA 1mo9A 251 :LIKDNETRAYVLDRM T0334 186 :EKLGVRHVED 1mo9A 266 :KEQGMEIISG T0334 196 :RVEHVQRDANGNIESVR 1mo9A 277 :NVTRIEEDANGRVQAVV T0334 213 :TATG 1mo9A 296 :TPNG T0334 217 :RVFDADLFVDCSG 1mo9A 301 :MRIETDFVFLGLG T0334 230 :FRGLLINKAMEEPFLD 1mo9A 316 :PRSAELAKILGLDLGP T0334 247 :SDHLLNDSAVATQV 1mo9A 332 :KGEVLVNEYLQTSV T0334 264 :D 1mo9A 346 :P T0334 266 :ANGVE 1mo9A 376 :MGEKI T0334 271 :PFTSAIAMKSGWTWKIPML 1mo9A 385 :KNYPDFLHTHYEVSFLGMG T0334 290 :GRFGTGYVYSSRFATE 1mo9A 411 :GHEIVTIKMPPDTENG T0334 318 :LDPETQPLNRIR 1mo9A 442 :FGKGTAHMSGFQ T0334 330 :FRVGRNR 1mo9A 457 :IDAKTRK T0334 338 :AW 1mo9A 464 :VL T0334 342 :NCVSIGTSS 1mo9A 466 :GAHHVGYGA T0334 382 :PVLTARFNREIETMF 1mo9A 475 :KDAFQYLNVLIKQGL T0334 403 :IQAHFYFSPR 1mo9A 491 :VDELGDMDEL T0334 415 :TP 1mo9A 503 :NP T0334 519 :SLHEFLRQQHG 1mo9A 506 :HFIQLSRLRAG Number of specific fragments extracted= 24 number of extra gaps= 1 total=1644 Number of alignments=70 # 1mo9A read from 1mo9A/merged-good-all-a2m # found chain 1mo9A in training set T0334 2 :SGKID 1mo9A 39 :NDPRE T0334 7 :KILIVGGGTAGWMAASYLGK 1mo9A 45 :DAIFIGGGAAGRFGSAYLRA T0334 29 :QGT 1mo9A 65 :MGG T0334 33 :DITLLQAPD 1mo9A 68 :RQLIVDRWP T0334 42 :IPTL 1mo9A 78 :LGGS T0334 46 :GVGEATIP 1mo9A 106 :FSGQYWFP T0334 61 :DFLGIPED 1mo9A 114 :DMTEKVVG T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1mo9A 124 :EVVDLFRAGRNGPHGIMNFQSKEQLNL T0334 96 :EARELDGGPDHFYHSFGLL 1mo9A 188 :TLDVPGVNAKGVFDHATLV T0334 115 :KYHEQIPLSHYWFDRSYRG 1mo9A 212 :EPGSTVVVVGGSKTAVEYG T0334 139 :FDYACYKEPVILD 1mo9A 231 :CFFNATGRRTVML T0334 152 :ANRSPRRL 1mo9A 245 :RTEPLKLI T0334 172 :DAHLVADFLRRFA 1mo9A 253 :KDNETRAYVLDRM T0334 186 :EKLGVRHVED 1mo9A 266 :KEQGMEIISG T0334 196 :RVEHVQRDANGNIESVRTA 1mo9A 277 :NVTRIEEDANGRVQAVVAM T0334 215 :TGR 1mo9A 298 :NGE T0334 218 :VFDADLFVDCSGFRG 1mo9A 302 :RIETDFVFLGLGEQP T0334 233 :LLINKAMEEPFLD 1mo9A 319 :AELAKILGLDLGP T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1mo9A 332 :KGEVLVNEYLQTSVPNVYAVGDL T0334 270 :EPFTS 1mo9A 410 :AGHEI T0334 275 :AIAMK 1mo9A 416 :TIKMP T0334 280 :SGWTWKIPMLGRFGTGYVYSSRFATE 1mo9A 451 :GFQKIVIDAKTRKVLGAHHVGYGAKD T0334 306 :DEAVREFCE 1mo9A 479 :QYLNVLIKQ T0334 378 :KSLNPVL 1mo9A 488 :GLTVDEL Number of specific fragments extracted= 24 number of extra gaps= 0 total=1668 Number of alignments=71 # 1mo9A read from 1mo9A/merged-good-all-a2m # found chain 1mo9A in training set T0334 5 :IDKILIVGGGTAGWMAASYLGK 1mo9A 214 :GSTVVVVGGSKTAVEYGCFFNA T0334 30 :GTADITLLQAPDI 1mo9A 236 :TGRRTVMLVRTEP T0334 62 :FLGIPEDE 1mo9A 249 :LKLIKDNE T0334 176 :VADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVR 1mo9A 257 :TRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVV T0334 213 :TATGR 1mo9A 296 :TPNGE T0334 218 :VFDADLFVDCSGF 1mo9A 302 :RIETDFVFLGLGE T0334 231 :RG 1mo9A 317 :RS T0334 310 :REFCEMWHLDPETQPLNRIRFR 1mo9A 319 :AELAKILGLDLGPKGEVLVNEY T0334 336 :RRAWVGNCVSIGTSSCFVE 1mo9A 341 :LQTSVPNVYAVGDLIGGPM T0334 361 :IYFVYAALYQLVKHFPDKS 1mo9A 361 :MFKARKSGCYAARNVMGEK Number of specific fragments extracted= 10 number of extra gaps= 0 total=1678 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ykjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ykjA expands to /projects/compbio/data/pdb/1ykj.pdb.gz 1ykjA:# T0334 read from 1ykjA/merged-good-all-a2m # 1ykjA read from 1ykjA/merged-good-all-a2m # adding 1ykjA to template set # found chain 1ykjA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1ykjA)M1001 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ykjA 1002 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1ykjA 1024 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1ykjA 1040 :LGRIRGGVLEQGMVDLL T0334 61 :DFLGI 1ykjA 1057 :REAGV T0334 123 :SHYWFDRSYR 1ykjA 1062 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVIL 1ykjA 1072 :HEGVEIAFAGQRRRI T0334 154 :RSPRRLDG 1ykjA 1087 :DLKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1ykjA 1095 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1ykjA 1114 :EACGATTVYQ T0334 196 :RVEHVQR 1ykjA 1125 :AEVRLHD T0334 203 :DANG 1ykjA 1133 :QGER T0334 209 :ESVRTA 1ykjA 1137 :PYVTFE T0334 215 :TG 1ykjA 1144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1ykjA 1148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEP 1ykjA 1166 :RQSIPAE T0334 243 :FLDMSDHLLNDSAVAT 1ykjA 1174 :LKVFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1ykjA 1190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1ykjA 1219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1ykjA 1232 :EDWSDERFWTELKARL T0334 319 :DPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1ykjA 1257 :TGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTD 1ykjA 1318 :REGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFP T0334 415 :TPFWR 1ykjA 1357 :DAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLRQQH 1ykjA 1362 :RIQQTELEYYLGSEAGLATIAENYV Number of specific fragments extracted= 23 number of extra gaps= 0 total=1701 Number of alignments=73 # 1ykjA read from 1ykjA/merged-good-all-a2m # found chain 1ykjA in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1ykjA)M1001 T0334 6 :D 1ykjA 1002 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1ykjA 1004 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1ykjA 1024 :AGI T0334 33 :DITLLQAPD 1ykjA 1027 :DNVILERQT T0334 52 :IPNLQTAF 1ykjA 1036 :PDYVLGRI T0334 61 :DFLG 1ykjA 1044 :RGGV T0334 69 :EWMRECNASYKVAIKFINW 1ykjA 1054 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1ykjA 1073 :EGVEIAFAGQRR T0334 115 :KYHE 1ykjA 1087 :DLKR T0334 152 :ANRSPRRLD 1ykjA 1092 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1ykjA 1101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1ykjA 1114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1ykjA 1125 :AEVRLHDLQGERPY T0334 211 :VRTA 1ykjA 1139 :VTFE T0334 215 :TGR 1ykjA 1144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1ykjA 1149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1ykjA 1167 :QSIPAERLKV T0334 247 :SDHLLND 1ykjA 1178 :ERVYPFG T0334 254 :SAVATQVPHDD 1ykjA 1186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1ykjA 1197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1ykjA 1216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1ykjA 1223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1ykjA 1259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1ykjA 1317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWR 1ykjA 1359 :FSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLRQ 1ykjA 1362 :RIQQTELEYYLGSEAGLATIAEN Number of specific fragments extracted= 26 number of extra gaps= 0 total=1727 Number of alignments=74 # 1ykjA read from 1ykjA/merged-good-all-a2m # found chain 1ykjA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1ykjA 1004 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1ykjA 1024 :AGIDNVILERQT T0334 43 :PTL 1ykjA 1041 :GRI T0334 47 :VGEATIPNLQTAF 1ykjA 1044 :RGGVLEQGMVDLL T0334 61 :DFLGIP 1ykjA 1057 :REAGVD T0334 69 :EWMRE 1ykjA 1063 :RRMAR T0334 75 :NASYKVAIKFINWRTAGE 1ykjA 1068 :DGLVHEGVEIAFAGQRRR T0334 95 :SE 1ykjA 1086 :ID T0334 158 :RLDGS 1ykjA 1088 :LKRLS T0334 164 :VTNYAWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRD 1ykjA 1093 :GGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDL T0334 204 :ANGNIESVRTATGR 1ykjA 1134 :GERPYVTFERDGER T0334 218 :VFDADLFVDCSGFRG 1ykjA 1149 :RLDCDYIAGCDGFHG T0334 241 :EPFLDMSDH 1ykjA 1166 :RQSIPAERL T0334 250 :LLNDSAVATQV 1ykjA 1180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1ykjA 1191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1ykjA 1231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1ykjA 1256 :VTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1ykjA 1321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTD T0334 486 :SPRLAHMPQATESVDEVFGAVKDRQRNLL 1ykjA 1358 :AFSQRIQQTELEYYLGSEAGLATIAENYV Number of specific fragments extracted= 19 number of extra gaps= 0 total=1746 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iut/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1iut/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1iut/merged-good-all-a2m.gz for input Trying 1iut/merged-good-all-a2m Error: Couldn't open file 1iut/merged-good-all-a2m or 1iut/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kdgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 1kdgA/merged-good-all-a2m # 1kdgA read from 1kdgA/merged-good-all-a2m # found chain 1kdgA in training set Warning: unaligning (T0334)K4 because first residue in template chain is (1kdgA)T215 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1kdgA 216 :PYDYIIVGAGPGGIIAADRLSE T0334 30 :GTADITLLQAPDI 1kdgA 238 :AGKKVLLLERGGP T0334 46 :GVGEATIPNL 1kdgA 255 :TGGTYVAPWA T0334 61 :DFLGI 1kdgA 265 :TSSGL T0334 87 :WRTAGEGTSEARELDGGP 1kdgA 270 :TKFDIPGLFESLFTDSNP T0334 106 :HFYHSFG 1kdgA 293 :DITVFAG T0334 129 :RSY 1kdgA 302 :VGG T0334 141 :YACYKEPVILD 1kdgA 305 :GTSVNGALYWY T0334 154 :RSPRR 1kdgA 316 :PNDGD T0334 159 :LDGSKVTNYAW 1kdgA 322 :SSSVGWPSSWT T0334 170 :HFDAHLVADFLRRFA 1kdgA 401 :GKRAGPVATYLQTAL T0334 186 :EKLGVRHVED 1kdgA 416 :ARPNFTFKTN T0334 196 :RVEHVQR 1kdgA 427 :MVSNVVR T0334 204 :ANGNIESVRTA 1kdgA 434 :NGSQILGVQTN T0334 215 :T 1kdgA 447 :T T0334 217 :RVFDAD 1kdgA 452 :GFIPVT T0334 223 :LFVDCSGFRGLL 1kdgA 461 :RVILSAGAFGTS T0334 236 :NKA 1kdgA 473 :RIL T0334 243 :FLDMSDH 1kdgA 499 :LPPQNQW T0334 250 :LLN 1kdgA 508 :LPV T0334 253 :DSAVATQVPHDDD 1kdgA 519 :SINLVFTHPSIDA T0334 266 :ANGVE 1kdgA 539 :WSNPR T0334 271 :PFTSAIAMKSGWTW 1kdgA 555 :SGVFAGASPKLNFW T0334 285 :KIPMLGR 1kdgA 570 :AYSGSDG T0334 292 :FGTGYVYSSRFATE 1kdgA 579 :RYAQGTVRPGAASV T0334 306 :DEAVREFCEMW 1kdgA 639 :PVDKTVLLQAL T0334 317 :HLDPETQ 1kdgA 657 :GSIPGLT T0334 324 :PLNRIRFRVGRNRRAWVGNC 1kdgA 690 :WVSSTTIGSSPQSAVVDSNV T0334 344 :VSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1kdgA 717 :LFIVDAGIIPHLPTGNPQGTLMSAAEQAAAKILA T0334 378 :KSL 1kdgA 752 :AGG Number of specific fragments extracted= 30 number of extra gaps= 0 total=1776 Number of alignments=76 # 1kdgA read from 1kdgA/merged-good-all-a2m # found chain 1kdgA in training set Warning: unaligning (T0334)I5 because first residue in template chain is (1kdgA)T215 Warning: unaligning (T0334)L380 because last residue in template chain is (1kdgA)P755 T0334 6 :D 1kdgA 216 :P T0334 7 :KILIVGGGTAGWMAASYLGK 1kdgA 218 :DYIIVGAGPGGIIAADRLSE T0334 29 :QGT 1kdgA 238 :AGK T0334 33 :DITLLQAPDIPTLGVGEATIP 1kdgA 241 :KVLLLERGGPSTKQTGGTYVA T0334 57 :TAFFDFLGIPED 1kdgA 262 :PWATSSGLTKFD T0334 96 :EARELDG 1kdgA 274 :IPGLFES T0334 103 :GPDHFYHSFGLLKYHEQIPLSHYWFDRSYRGKTVEP 1kdgA 284 :DSNPFWWCKDITVFAGCLVGGGTSVNGALYWYPNDG T0334 139 :FDYACYKEP 1kdgA 368 :QLLKGQGYN T0334 172 :DAHLVADFLRRFA 1kdgA 403 :RAGPVATYLQTAL T0334 186 :EKLGVRHVED 1kdgA 416 :ARPNFTFKTN T0334 196 :RVEHVQRDAN 1kdgA 427 :MVSNVVRNGS T0334 207 :NIESVRTAT 1kdgA 437 :QILGVQTND T0334 218 :VFDA 1kdgA 453 :FIPV T0334 222 :DLFVDCSGFRG 1kdgA 460 :GRVILSAGAFG T0334 233 :LLINKAMEEPFLDM 1kdgA 472 :SRILFQSGIGPTDM T0334 254 :SAVATQVPHDDDANGVEPFTSAIAMK 1kdgA 502 :QNQWINLPVGMNAQDNPSINLVFTHP T0334 280 :SGWTWKIPM 1kdgA 563 :PKLNFWRAY T0334 289 :LGR 1kdgA 575 :DGF T0334 294 :TGYVYSSRFATE 1kdgA 581 :AQGTVRPGAASV T0334 306 :DEAVREFCEM 1kdgA 639 :PVDKTVLLQA T0334 316 :WHLDP 1kdgA 650 :HDVVS T0334 321 :ETQPLNRIRF 1kdgA 658 :SIPGLTMITP T0334 342 :NCVSIGTSSCFVEPL 1kdgA 716 :NLFIVDAGIIPHLPT T0334 358 :STGIYFVYAALYQLVKHFP 1kdgA 731 :GNPQGTLMSAAEQAAAKIL T0334 377 :DKS 1kdgA 752 :AGG Number of specific fragments extracted= 25 number of extra gaps= 0 total=1801 Number of alignments=77 # 1kdgA read from 1kdgA/merged-good-all-a2m # found chain 1kdgA in training set Warning: unaligning (T0334)K4 because first residue in template chain is (1kdgA)T215 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1kdgA 216 :PYDYIIVGAGPGGIIAADRLSE T0334 30 :GTADITLLQAPDIPTLGVGEATIPNLQ 1kdgA 238 :AGKKVLLLERGGPSTKQTGGTYVAPWA T0334 61 :DFLGI 1kdgA 265 :TSSGL T0334 76 :ASYKVAIKFINWRTAGEGTSEAREL 1kdgA 270 :TKFDIPGLFESLFTDSNPFWWCKDI T0334 101 :DGGPDHFYHSFGLLKYHEQIPLSHYWFD 1kdgA 325 :VGWPSSWTNHAPYTSKLSSRLPSTDHPS T0334 130 :SYRGKTVEPFDYACYKEPVILDANRSPRRLDGSKVTNY 1kdgA 353 :TDGQRYLEQSFNVVSQLLKGQGYNQATINDNPNYKDHV T0334 168 :AWHF 1kdgA 395 :AFDF T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1kdgA 403 :RAGPVATYLQTALARPNFTFKTNVMVSNVVRNGSQ T0334 208 :IESVRTATGR 1kdgA 438 :ILGVQTNDPT T0334 218 :VFDAD 1kdgA 453 :FIPVT T0334 223 :LFVDCSGFRG 1kdgA 461 :RVILSAGAFG T0334 233 :LLINKAMEEP 1kdgA 484 :DMIQTVQSNP T0334 293 :GTGYVYSSRFAT 1kdgA 519 :SINLVFTHPSID T0334 307 :EAVREFCEMWHLDPETQ 1kdgA 671 :QTLEEYVDAYDPATMNS T0334 338 :AWVGNCVSI 1kdgA 712 :FGTNNLFIV T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDK 1kdgA 721 :DAGIIPHLPTGNPQGTLMSAAEQAAAKILAL Number of specific fragments extracted= 16 number of extra gaps= 0 total=1817 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fcdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fcdA expands to /projects/compbio/data/pdb/1fcd.pdb.gz 1fcdA:# T0334 read from 1fcdA/merged-good-all-a2m # 1fcdA read from 1fcdA/merged-good-all-a2m # adding 1fcdA to template set # found chain 1fcdA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)T37 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)T37 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)L44 Warning: unaligning (T0334)N54 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)L44 Warning: unaligning (T0334)T273 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)K129 Warning: unaligning (T0334)S274 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)K129 Warning: unaligning (T0334)K279 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)E132 Warning: unaligning (T0334)S280 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)E132 Warning: unaligning (T0334)Y298 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fcdA)P155 Warning: unaligning (T0334)S299 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P155 Warning: unaligning (T0334)T304 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)C161 Warning: unaligning (T0334)E305 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)C161 Warning: unaligning (T0334)T322 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)N214 Warning: unaligning (T0334)Q323 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)N214 Warning: unaligning (T0334)I328 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)P275 Warning: unaligning (T0334)R329 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)P275 Warning: unaligning (T0334)I346 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)G293 Warning: unaligning (T0334)G347 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)G293 Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)D294 Warning: unaligning (T0334)V353 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fcdA)P300 Warning: unaligning (T0334)E354 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P300 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1fcdA 2 :GRKVVVVGGGTGGATAAKYIKL T0334 28 :LQGTADITLLQA 1fcdA 24 :ADPSIEVTLIEP T0334 42 :IPTLG 1fcdA 38 :DYYTC T0334 55 :LQTAF 1fcdA 45 :SNEVI T0334 141 :YACYKEPVI 1fcdA 50 :GGDRKLESI T0334 166 :NYAW 1fcdA 59 :KHGY T0334 182 :RFA 1fcdA 63 :DGL T0334 186 :EKLGVRHVEDRVEHV 1fcdA 66 :RAHGIQVVHDSATGI T0334 203 :DANG 1fcdA 81 :DPDK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fcdA 85 :KLVKTAGGAEFGYDRCVVAPGI T0334 244 :L 1fcdA 107 :E T0334 245 :DMSDH 1fcdA 109 :IYDKI T0334 253 :DS 1fcdA 114 :EG T0334 261 :PHDDDANGVEPF 1fcdA 116 :YSEEAAAKLPHA T0334 275 :A 1fcdA 130 :A T0334 288 :MLGRFGTGYV 1fcdA 144 :MADGGTVVIA T0334 300 :SRFA 1fcdA 156 :AAPF T0334 306 :DEAVREFCEMWHL 1fcdA 198 :SQFSKGWERLYGF T0334 320 :PE 1fcdA 211 :GT T0334 324 :PLNR 1fcdA 270 :DAGW T0334 330 :FRVGRNRRAWVGNCVS 1fcdA 276 :VDIKTFESSIHKGIHV T0334 349 :SSCF 1fcdA 295 :ASIA T0334 355 :PLESTGIYF 1fcdA 302 :PKSGYSANS T0334 364 :VYAALYQLVKHFPD 1fcdA 312 :GKVAAAAVVVLLKG T0334 409 :FSPRTDTP 1fcdA 371 :VTPVDAPD T0334 497 :ESVDEVFGAVKDRQRNLLETL 1fcdA 379 :WVLEREVQYAYSWYNNIVHDT Number of specific fragments extracted= 26 number of extra gaps= 10 total=1843 Number of alignments=79 # 1fcdA read from 1fcdA/merged-good-all-a2m # found chain 1fcdA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)T37 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)T37 Warning: unaligning (T0334)I52 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)L44 Warning: unaligning (T0334)P53 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)L44 Warning: unaligning (T0334)L250 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)P275 Warning: unaligning (T0334)L251 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)P275 Warning: unaligning (T0334)I346 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)G293 Warning: unaligning (T0334)G347 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)G293 Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)D294 Warning: unaligning (T0334)V353 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P300 T0334 7 :KILIVGGGTAGWMAASYLGK 1fcdA 4 :KVVVVGGGTGGATAAKYIKL T0334 28 :L 1fcdA 24 :A T0334 29 :QGT 1fcdA 26 :PSI T0334 33 :DITLLQA 1fcdA 29 :EVTLIEP T0334 46 :GVG 1fcdA 38 :DYY T0334 50 :AT 1fcdA 41 :TC T0334 54 :N 1fcdA 45 :S T0334 57 :TAF 1fcdA 46 :NEV T0334 61 :DFLGIPED 1fcdA 49 :IGGDRKLE T0334 69 :EWM 1fcdA 63 :DGL T0334 186 :EKLGVRHVEDRVEHV 1fcdA 66 :RAHGIQVVHDSATGI T0334 203 :DANG 1fcdA 81 :DPDK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fcdA 85 :KLVKTAGGAEFGYDRCVVAPGI T0334 231 :RGLLINKAMEEPFL 1fcdA 257 :RAGKIAQIAGLTND T0334 247 :SDH 1fcdA 271 :AGW T0334 252 :ND 1fcdA 276 :VD T0334 254 :SAVAT 1fcdA 279 :KTFES T0334 338 :AWVGNCVS 1fcdA 284 :SIHKGIHV T0334 349 :SSCF 1fcdA 295 :ASIA T0334 354 :EPLESTGIYFVYAALYQLV 1fcdA 301 :MPKSGYSANSQGKVAAAAV T0334 418 :WRANKELRL 1fcdA 320 :VVLLKGEEP T0334 427 :AD 1fcdA 377 :PD T0334 497 :ESVDEVFGAVKDRQRNLLETL 1fcdA 379 :WVLEREVQYAYSWYNNIVHDT Number of specific fragments extracted= 23 number of extra gaps= 5 total=1866 Number of alignments=80 # 1fcdA read from 1fcdA/merged-good-all-a2m # found chain 1fcdA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)T37 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)T37 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)L44 Warning: unaligning (T0334)N54 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)L44 Warning: unaligning (T0334)I328 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)P275 Warning: unaligning (T0334)R329 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)P275 Warning: unaligning (T0334)I346 because of BadResidue code BAD_PEPTIDE in next template residue (1fcdA)G293 Warning: unaligning (T0334)G347 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)G293 Warning: unaligning (T0334)T348 because of BadResidue code BAD_PEPTIDE at template residue (1fcdA)D294 Warning: unaligning (T0334)C351 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1fcdA)P300 Warning: unaligning (T0334)F352 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1fcdA)P300 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1fcdA 2 :GRKVVVVGGGTGGATAAKYIKL T0334 28 :LQGTADITLLQA 1fcdA 24 :ADPSIEVTLIEP T0334 42 :IPTLG 1fcdA 38 :DYYTC T0334 55 :LQTA 1fcdA 45 :SNEV T0334 148 :VILDANRSPRRLDGSK 1fcdA 49 :IGGDRKLESIKHGYDG T0334 184 :ATEKLGVRHVE 1fcdA 65 :LRAHGIQVVHD T0334 196 :RVEHVQ 1fcdA 76 :SATGID T0334 204 :ANG 1fcdA 82 :PDK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fcdA 85 :KLVKTAGGAEFGYDRCVVAPGI T0334 258 :TQVPHD 1fcdA 107 :ELIYDK T0334 300 :SRFATED 1fcdA 113 :IEGYSEE T0334 322 :TQPLNR 1fcdA 268 :TNDAGW T0334 330 :FRVGRNRRAWVGNCVS 1fcdA 276 :VDIKTFESSIHKGIHV T0334 349 :S 1fcdA 295 :A T0334 350 :S 1fcdA 298 :A T0334 353 :VEPLESTGIYFVYAALYQLVKHFPDKSLN 1fcdA 301 :MPKSGYSANSQGKVAAAAVVVLLKGEEPG T0334 407 :FYFSPRTDT 1fcdA 353 :YRPNADGSA T0334 467 :NNSNYYCVLAGLGLVPDAPSPRLAHMPQATESVDEV 1fcdA 363 :ESVPDSGGVTPVDAPDWVLEREVQYAYSWYNNIVHD Number of specific fragments extracted= 18 number of extra gaps= 5 total=1884 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 1c0pA/merged-good-all-a2m # 1c0pA read from 1c0pA/merged-good-all-a2m # found chain 1c0pA in training set Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)K1005 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)A1053 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)A1053 Warning: unaligning (T0334)Y116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0334)H117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)D1170 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1230 Warning: unaligning (T0334)R291 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1230 Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1236 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1236 Warning: unaligning (T0334)L318 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1271 Warning: unaligning (T0334)D319 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 T0334 1 :MSGK 1c0pA 1000 :MMHS T0334 7 :KILIVGGGTAGWMAASYLGK 1c0pA 1006 :RVVVLGSGVIGLSSALILAR T0334 30 :GTADITLLQAPDI 1c0pA 1026 :KGYSVHILARDLP T0334 43 :P 1c0pA 1049 :P T0334 46 :GV 1c0pA 1050 :WA T0334 50 :ATIPN 1c0pA 1054 :NWTPF T0334 60 :FDFLGI 1c0pA 1059 :MTLTDG T0334 75 :NASYKVAIKFINWRTAGE 1c0pA 1065 :PRQAKWEESTFKKWVELV T0334 101 :DGGP 1c0pA 1083 :PTGH T0334 105 :DHFYHSFGLLK 1c0pA 1092 :GTRRFAQNEDG T0334 141 :YACYKEPVILD 1c0pA 1105 :GHWYKDITPNY T0334 152 :ANRSPRRLDGSKVTN 1c0pA 1117 :PLPSSECPPGAIGVT T0334 170 :HFDAHLVADFLRRFA 1c0pA 1136 :SVHAPKYCQYLAREL T0334 186 :EKLGVRHVEDR 1c0pA 1151 :QKLGATFERRT T0334 199 :HVQRD 1c0pA 1164 :SLEQA T0334 206 :G 1c0pA 1171 :G T0334 221 :ADLFVDCSG 1c0pA 1172 :ADLVVNATG T0334 236 :NKAMEEPFLDMSDHLLN 1c0pA 1181 :LGAKSIAGIDDQAAEPI T0334 253 :DSAVATQVPH 1c0pA 1199 :GQTVLVKSPC T0334 270 :EPFTSAIAMKSGWTWKIPML 1c0pA 1209 :KRCTMDSSDPASPAYIIPRP T0334 292 :FGT 1c0pA 1232 :VIC T0334 297 :VYSSRFATE 1c0pA 1237 :TYGVGDWDL T0334 306 :DEAVREFCEMW 1c0pA 1249 :PETVQRILKHC T0334 317 :H 1c0pA 1269 :D T0334 320 :PETQ 1c0pA 1272 :IEGI T0334 324 :PLNRIRFRVG 1c0pA 1295 :EAERIVLPLD T0334 343 :CVSIG 1c0pA 1325 :VTLVH T0334 353 :VEPLESTGIYFVYAALYQLVKHFP 1c0pA 1330 :AYGFSSAGYQQSWGAAEDVAQLVD T0334 386 :ARFNR 1c0pA 1354 :EAFQR Number of specific fragments extracted= 29 number of extra gaps= 8 total=1913 Number of alignments=82 # 1c0pA read from 1c0pA/merged-good-all-a2m # found chain 1c0pA in training set Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0334)D61 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)A1053 Warning: unaligning (T0334)F62 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)A1053 Warning: unaligning (T0334)E99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0334)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0334)A204 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)D1170 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)D1170 Warning: unaligning (T0334)L289 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1230 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1230 Warning: unaligning (T0334)G295 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1236 Warning: unaligning (T0334)Y296 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1236 Warning: unaligning (T0334)E321 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 T0334 2 :SGKI 1c0pA 1000 :MMHS T0334 7 :KILIVGGGTAGWMAASYLGK 1c0pA 1006 :RVVVLGSGVIGLSSALILAR T0334 29 :QGT 1c0pA 1026 :KGY T0334 33 :DITLLQAP 1c0pA 1029 :SVHILARD T0334 46 :GVGEATIPNLQTAFF 1c0pA 1037 :LPEDVSSQTFASPWA T0334 63 :LGIPED 1c0pA 1054 :NWTPFM T0334 69 :EWMRECNASYKVAIK 1c0pA 1065 :PRQAKWEESTFKKWV T0334 96 :EAR 1c0pA 1100 :EDG T0334 101 :DG 1c0pA 1105 :GH T0334 109 :HSFGLLKYHE 1c0pA 1107 :WYKDITPNYR T0334 152 :ANRSPRRLDGSKVTNYAWHF 1c0pA 1117 :PLPSSECPPGAIGVTYDTLS T0334 172 :DAHLVADFLRRFA 1c0pA 1138 :HAPKYCQYLAREL T0334 186 :EKLGVRHVEDR 1c0pA 1151 :QKLGATFERRT T0334 199 :HVQRD 1c0pA 1164 :SLEQA T0334 206 :G 1c0pA 1171 :G T0334 221 :ADLFVDCSGFRGLLI 1c0pA 1172 :ADLVVNATGLGAKSI T0334 239 :MEEPF 1c0pA 1187 :AGIDD T0334 247 :SDHLLND 1c0pA 1192 :QAAEPIR T0334 254 :SAVATQVP 1c0pA 1200 :QTVLVKSP T0334 270 :EPFTSAIAMKSGWTWKIPM 1c0pA 1209 :KRCTMDSSDPASPAYIIPR T0334 291 :RFGT 1c0pA 1231 :EVIC T0334 297 :VYSSRFATE 1c0pA 1237 :TYGVGDWDL T0334 306 :DEAVREFCEM 1c0pA 1249 :PETVQRILKH T0334 316 :WHLDP 1c0pA 1260 :LRLDP T0334 322 :TQPLNRIRFRVGRNR 1c0pA 1272 :IEGIEVLRHNVGLRP T0334 337 :RAWVG 1c0pA 1298 :RIVLP T0334 342 :NCVS 1c0pA 1324 :EVTL T0334 351 :CFVEPLESTGIYFVYAALYQLVKHF 1c0pA 1328 :VHAYGFSSAGYQQSWGAAEDVAQLV T0334 389 :NREIET 1c0pA 1353 :DEAFQR Number of specific fragments extracted= 29 number of extra gaps= 8 total=1942 Number of alignments=83 # 1c0pA read from 1c0pA/merged-good-all-a2m # found chain 1c0pA in training set Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)K1005 Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)K1005 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)A1053 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)A1053 Warning: unaligning (T0334)T94 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1c0pA)L1104 Warning: unaligning (T0334)S95 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1c0pA)L1104 Warning: unaligning (T0334)V197 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1163 Warning: unaligning (T0334)E198 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1163 Warning: unaligning (T0334)A204 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)D1170 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)D1170 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1230 Warning: unaligning (T0334)R291 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)G1230 Warning: unaligning (T0334)Y298 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)G1236 Warning: unaligning (T0334)H317 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)T1271 Warning: unaligning (T0334)L318 because of BadResidue code BAD_PEPTIDE at template residue (1c0pA)T1271 Warning: unaligning (T0334)N342 because of BadResidue code BAD_PEPTIDE in next template residue (1c0pA)S1316 T0334 1 :MSGK 1c0pA 1000 :MMHS T0334 7 :KILIVGGGTAGWMAASYLGK 1c0pA 1006 :RVVVLGSGVIGLSSALILAR T0334 30 :GTADITLLQAP 1c0pA 1026 :KGYSVHILARD T0334 41 :DIPTLGV 1c0pA 1045 :TFASPWA T0334 50 :ATI 1c0pA 1054 :NWT T0334 53 :PNLQTAFFDF 1c0pA 1065 :PRQAKWEEST T0334 68 :DEWMREC 1c0pA 1075 :FKKWVEL T0334 75 :NASYKVAIKF 1c0pA 1087 :AMWLKGTRRF T0334 88 :RTAGEG 1c0pA 1097 :AQNEDG T0334 96 :EARELDGGP 1c0pA 1105 :GHWYKDITP T0334 149 :ILDANRSPRRLDGSKVTNY 1c0pA 1114 :NYRPLPSSECPPGAIGVTY T0334 168 :AWHFDAHLVADFLRRFATEKLGV 1c0pA 1134 :TLSVHAPKYCQYLARELQKLGAT T0334 192 :HVEDR 1c0pA 1157 :FERRT T0334 199 :HVQRD 1c0pA 1164 :SLEQA T0334 206 :G 1c0pA 1171 :G T0334 221 :ADLFVDCSGFRG 1c0pA 1172 :ADLVVNATGLGA T0334 239 :MEEPFLDMSDHLLNDSAVATQV 1c0pA 1184 :KSIAGIDDQAAEPIRGQTVLVK T0334 267 :NGVEPFTSAIAMKSGWTWKIPML 1c0pA 1206 :SPCKRCTMDSSDPASPAYIIPRP T0334 295 :GYV 1c0pA 1232 :VIC T0334 299 :SSRFATEDEAVREFCEMW 1c0pA 1242 :DWDLSVNPETVQRILKHC T0334 319 :DPET 1c0pA 1272 :IEGI T0334 324 :PLNRIRFRVGRNRRAWVG 1c0pA 1297 :ERIVLPLDRTKSPLSLGR T0334 343 :CVSIGTSSCFV 1c0pA 1324 :EVTLVHAYGFS T0334 358 :ST 1c0pA 1335 :SA T0334 364 :VYAALYQLVKH 1c0pA 1337 :GYQQSWGAAED T0334 388 :FNREIETMFDD 1c0pA 1348 :VAQLVDEAFQR Number of specific fragments extracted= 26 number of extra gaps= 9 total=1968 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xhcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xhcA expands to /projects/compbio/data/pdb/1xhc.pdb.gz 1xhcA:Skipped atom 303, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 305, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 307, because occupancy 0.350 <= existing 0.650 in 1xhcA Skipped atom 309, because occupancy 0.350 <= existing 0.650 in 1xhcA # T0334 read from 1xhcA/merged-good-all-a2m # 1xhcA read from 1xhcA/merged-good-all-a2m # adding 1xhcA to template set # found chain 1xhcA in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1xhcA)S1 Warning: unaligning (T0334)A142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)R82 Warning: unaligning (T0334)C143 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)R82 Warning: unaligning (T0334)P355 because of BadResidue code BAD_PEPTIDE in next template residue (1xhcA)I268 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE at template residue (1xhcA)I268 T0334 7 :KILIVGGGTAGW 1xhcA 2 :KVVIVGNGPGGF T0334 23 :YLGKALQGTADITLLQAPDIPTLG 1xhcA 14 :ELAKQLSQTYEVTVIDKEPVPYYS T0334 52 :IPNLQTAF 1xhcA 38 :KPMLSHYI T0334 63 :LGI 1xhcA 46 :AGF T0334 92 :EGTSEARELD 1xhcA 49 :IPRNRLFPYS T0334 123 :SHYWFDRSYRG 1xhcA 59 :LDWYRKRGIEI T0334 134 :KTVEPFDY 1xhcA 73 :EEAKLIDR T0334 145 :KEPVILD 1xhcA 89 :KGEVPYD T0334 152 :ANRSPRRLDG 1xhcA 105 :AREPQIKGKE T0334 167 :YAW 1xhcA 115 :YLL T0334 170 :HFD 1xhcA 172 :GLD T0334 174 :HLVADFLRRFA 1xhcA 175 :EELSNMIKDML T0334 186 :EKLGVRHVED 1xhcA 186 :EETGVKFFLN T0334 196 :RVEHV 1xhcA 197 :ELLEA T0334 204 :ANG 1xhcA 202 :NEE T0334 210 :SVRTATGR 1xhcA 205 :GVLTNSGF T0334 219 :FDADLFVDCSGFRGLL 1xhcA 213 :IEGKVKICAIGIVPNV T0334 235 :INKAMEEP 1xhcA 230 :LARRSGIH T0334 246 :MSDH 1xhcA 238 :TGRG T0334 258 :TQV 1xhcA 242 :ILI T0334 278 :MKSG 1xhcA 245 :DDNF T0334 287 :P 1xhcA 249 :R T0334 338 :AWVGNCVSIGTSSCFVE 1xhcA 250 :TSAKDVYAIGDCAEYSG T0334 357 :EST 1xhcA 269 :AGT T0334 361 :IYFVYAALYQLVKHFPDKSLN 1xhcA 272 :AKAAMEQARVLADILKGEPRR Number of specific fragments extracted= 25 number of extra gaps= 2 total=1993 Number of alignments=85 # 1xhcA read from 1xhcA/merged-good-all-a2m # found chain 1xhcA in template set Warning: unaligning (T0334)A90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)R82 Warning: unaligning (T0334)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)R82 Warning: unaligning (T0334)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)K83 Warning: unaligning (T0334)Y125 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)G144 Warning: unaligning (T0334)W126 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)G144 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE in next template residue (1xhcA)I268 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE at template residue (1xhcA)I268 T0334 7 :KILIVGGGTAGWMAASYLG 1xhcA 2 :KVVIVGNGPGGFELAKQLS T0334 29 :QGT 1xhcA 21 :QTY T0334 33 :DITLLQAPDIPTLGVG 1xhcA 24 :EVTVIDKEPVPYYSKP T0334 57 :TAFFDFLGIPED 1xhcA 40 :MLSHYIAGFIPR T0334 69 :EWMRECNASYKVAIKFINWRT 1xhcA 60 :DWYRKRGIEIRLAEEAKLIDR T0334 93 :GTS 1xhcA 84 :VVI T0334 96 :EARELDG 1xhcA 107 :EPQIKGK T0334 105 :DHFYHSFGLL 1xhcA 114 :EYLLTLRTIF T0334 115 :KYHEQIPLSH 1xhcA 133 :ENSGEAIIIG T0334 127 :FDRSYRG 1xhcA 145 :FIGLELA T0334 139 :FDYACYKEPVILD 1xhcA 152 :GNLAEAGYHVKLI T0334 152 :ANRSPRR 1xhcA 166 :RGAMFLG T0334 172 :DAHLVADFLRRFA 1xhcA 173 :LDEELSNMIKDML T0334 186 :EKLGVRHVED 1xhcA 186 :EETGVKFFLN T0334 196 :RVEHV 1xhcA 197 :ELLEA T0334 203 :DANG 1xhcA 202 :NEEG T0334 211 :VRTATG 1xhcA 206 :VLTNSG T0334 218 :VFDADLFVDCSGFRG 1xhcA 212 :FIEGKVKICAIGIVP T0334 233 :LLINKAMEEPF 1xhcA 228 :VDLARRSGIHT T0334 247 :SDHLLNDSAVA 1xhcA 239 :GRGILIDDNFR T0334 338 :AWVGNCVSIGTSSCF 1xhcA 250 :TSAKDVYAIGDCAEY T0334 354 :EP 1xhcA 265 :SG T0334 358 :STGIYFVYAALYQLVKHFPDKSLN 1xhcA 269 :AGTAKAAMEQARVLADILKGEPRR Number of specific fragments extracted= 23 number of extra gaps= 3 total=2016 Number of alignments=86 # 1xhcA read from 1xhcA/merged-good-all-a2m # found chain 1xhcA in template set Warning: unaligning (T0334)D6 because first residue in template chain is (1xhcA)S1 Warning: unaligning (T0334)A90 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xhcA)R82 Warning: unaligning (T0334)G91 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)R82 Warning: unaligning (T0334)E92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xhcA)K83 Warning: unaligning (T0334)L356 because of BadResidue code BAD_PEPTIDE in next template residue (1xhcA)I268 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE at template residue (1xhcA)I268 T0334 7 :KILIVGGGTAG 1xhcA 2 :KVVIVGNGPGG T0334 22 :SYLGKALQGTADITLLQAPDIPTLG 1xhcA 13 :FELAKQLSQTYEVTVIDKEPVPYYS T0334 52 :IPNLQTAF 1xhcA 38 :KPMLSHYI T0334 63 :LGI 1xhcA 46 :AGF T0334 66 :PE 1xhcA 50 :PR T0334 68 :DEWMRECNASYKVAIKFINWRT 1xhcA 59 :LDWYRKRGIEIRLAEEAKLIDR T0334 93 :GTSEAREL 1xhcA 84 :VVITEKGE T0334 101 :DGGPDH 1xhcA 106 :REPQIK T0334 119 :QIPLSHYWFDRSYRGKTVEPFD 1xhcA 112 :GKEYLLTLRTIFDADRIKESIE T0334 141 :YACYKEPVILDANRSPRRLDGSKVTNY 1xhcA 147 :GLELAGNLAEAGYHVKLIHRGAMFLGL T0334 173 :AHLVADFLRRFATEKLGVRHVEDRVEHVQ 1xhcA 174 :DEELSNMIKDMLEETGVKFFLNSELLEAN T0334 204 :ANG 1xhcA 203 :EEG T0334 211 :VRTAT 1xhcA 206 :VLTNS T0334 217 :RVFDADLFVDCSGF 1xhcA 211 :GFIEGKVKICAIGI T0334 258 :TQV 1xhcA 225 :VPN T0334 274 :SAIAMKSGW 1xhcA 228 :VDLARRSGI T0334 291 :RFGTGYVYSSRF 1xhcA 237 :HTGRGILIDDNF T0334 337 :RAWVGNCVSIGTSSCF 1xhcA 249 :RTSAKDVYAIGDCAEY T0334 355 :P 1xhcA 266 :G T0334 358 :STGIYFVYAALYQLVKHFPDKSL 1xhcA 269 :AGTAKAAMEQARVLADILKGEPR Number of specific fragments extracted= 20 number of extra gaps= 2 total=2036 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k0iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 1k0iA/merged-good-all-a2m # 1k0iA read from 1k0iA/merged-good-all-a2m # found chain 1k0iA in training set Warning: unaligning (T0334)K4 because first residue in template chain is (1k0iA)M1 T0334 5 :IDKILIVGGGTAGWMAASYLGKA 1k0iA 2 :KTQVAIIGAGPSGLLLGQLLHKA T0334 31 :TADITLLQAPDI 1k0iA 25 :GIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1k0iA 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1k0iA 57 :REAGV T0334 123 :SHYWFDRSYR 1k0iA 62 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVILD 1k0iA 72 :HEGVEIAFAGQRRRID T0334 155 :SPRRLDG 1k0iA 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1k0iA 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1k0iA 114 :EACGATTVYQ T0334 196 :RVEHVQR 1k0iA 125 :AEVRLHD T0334 203 :DANG 1k0iA 133 :QGER T0334 209 :ESVRTA 1k0iA 137 :PYVTFE T0334 215 :TG 1k0iA 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1k0iA 148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEPFL 1k0iA 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1k0iA 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1k0iA 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1k0iA 219 :SQYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1k0iA 232 :EDWSDERFWTELKARL T0334 324 :PLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1k0iA 262 :EKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFY 1k0iA 318 :REGRGELLERYSAICLRRIWKAERFSWWMTS T0334 409 :FSPRTDTPFWR 1k0iA 351 :HRFPDTDAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLR 1k0iA 362 :RIQQTELEYYLGSEAGLATIAE Number of specific fragments extracted= 23 number of extra gaps= 0 total=2059 Number of alignments=88 # 1k0iA read from 1k0iA/merged-good-all-a2m # found chain 1k0iA in training set Warning: unaligning (T0334)I5 because first residue in template chain is (1k0iA)M1 T0334 6 :D 1k0iA 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1k0iA 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1k0iA 24 :AGI T0334 33 :DITLLQAPD 1k0iA 27 :DNVILERQT T0334 52 :IPNLQTAF 1k0iA 36 :PDYVLGRI T0334 61 :DFLGIPED 1k0iA 44 :RAGVLEQG T0334 69 :EWMRECNASYKVAIKFINW 1k0iA 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1k0iA 73 :EGVEIAFAGQRR T0334 115 :KYHE 1k0iA 87 :DLKR T0334 152 :ANRSPRRLD 1k0iA 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1k0iA 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1k0iA 114 :EACGATTVYQ T0334 196 :RVEHVQRDANGNIE 1k0iA 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1k0iA 139 :VTFE T0334 215 :TGR 1k0iA 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1k0iA 149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1k0iA 167 :QSIPAERLKV T0334 247 :SDHLLND 1k0iA 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1k0iA 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1k0iA 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1k0iA 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1k0iA 223 :VQVPLSEKVEDWSDERFWTELKARLPSEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1k0iA 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1k0iA 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWR 1k0iA 359 :FSQ T0334 497 :ESVDEVFGAVKD 1k0iA 362 :RIQQTELEYYLG T0334 509 :RQRNLLE 1k0iA 377 :GLATIAE Number of specific fragments extracted= 27 number of extra gaps= 0 total=2086 Number of alignments=89 # 1k0iA read from 1k0iA/merged-good-all-a2m # found chain 1k0iA in training set T0334 7 :KILIVGGGTAGWMAASYLGK 1k0iA 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1k0iA 24 :AGIDNVILERQT T0334 42 :IPTLGV 1k0iA 42 :RIRAGV T0334 51 :TIPNLQTAF 1k0iA 48 :LEQGMVDLL T0334 61 :DFLGIP 1k0iA 57 :REAGVD T0334 68 :DEWMRECNASYKVAIKFINWRT 1k0iA 63 :RRMARDGLVHEGVEIAFAGQRR T0334 155 :SPRRLDGSKVT 1k0iA 85 :RIDLKRLSGGK T0334 167 :YAWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTATGR 1k0iA 96 :TVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGE T0334 218 :VFDADLFVDCSGFRG 1k0iA 149 :RLDCDYIAGCDGFHG T0334 241 :EPFLDMSDH 1k0iA 166 :RQSIPAERL T0334 250 :LLNDSAVATQV 1k0iA 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1k0iA 191 :DTPPVSHELIYANHPRGFALCSQRSATRSQYYVQV T0334 300 :SRFATEDEAVREFCEMWHLD 1k0iA 231 :VEDWSDERFWTELKARLPSE T0334 320 :PETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1k0iA 258 :GPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1k0iA 321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTD T0334 486 :SPRLAHMPQATESVDEVFGAVKDRQRNL 1k0iA 358 :AFSQRIQQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 16 number of extra gaps= 0 total=2102 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ladA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3ladA expands to /projects/compbio/data/pdb/3lad.pdb.gz 3ladA:# T0334 read from 3ladA/merged-good-all-a2m # 3ladA read from 3ladA/merged-good-all-a2m # adding 3ladA to template set # found chain 3ladA in template set Warning: unaligning (T0334)K4 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)Q2 Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)K3 Warning: unaligning (T0334)W70 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)I91 Warning: unaligning (T0334)M71 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)I91 Warning: unaligning (T0334)F219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)A268 Warning: unaligning (T0334)D220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)A268 Warning: unaligning (T0334)C227 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V276 Warning: unaligning (T0334)S228 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V276 Warning: unaligning (T0334)L234 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)T283 Warning: unaligning (T0334)N236 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)T283 Warning: unaligning (T0334)D253 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)P360 Warning: unaligning (T0334)S254 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)P360 Warning: unaligning (T0334)A255 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)E361 T0334 6 :DKILIVGGGTAGWMAASYLGKA 3ladA 4 :FDVIVIGAGPGGYVAAIKSAQL T0334 31 :TADITLLQA 3ladA 26 :GLKTALIEK T0334 40 :PDIPTLGVGEATIPNLQTAF 3ladA 40 :GKTALGGTCLNVGCIPSKAL T0334 66 :PEDE 3ladA 86 :DVPT T0334 72 :RECNASY 3ladA 92 :ARKDQIV T0334 79 :KVAIKFINWRTAGE 3ladA 100 :NLTGGVASLIKANG T0334 104 :P 3ladA 114 :V T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSYR 3ladA 126 :GKKVEVTAADGSSQVLDTENVILASGSK T0334 136 :VEPFDYACYKEPVILD 3ladA 154 :PVEIPPAPVDQDVIVD T0334 152 :ANRSPRRLDGSKVTN 3ladA 173 :ALDFQNVPGKLGVIG T0334 170 :HFD 3ladA 218 :AVD T0334 174 :HLVADFLRRFA 3ladA 221 :EQVAKEAQKIL T0334 186 :EKLGVRHVED 3ladA 232 :TKQGLKILLG T0334 196 :RVEHVQRDANGNIESVRTATG 3ladA 243 :RVTGTEVKNKQVTVKFVDAEG T0334 217 :RV 3ladA 265 :KS T0334 221 :ADLFVD 3ladA 269 :FDKLIV T0334 229 :GFRGL 3ladA 277 :GRRPV T0334 237 :KA 3ladA 284 :DL T0334 239 :MEEPFLDMSDHLLN 3ladA 345 :AQMNYDLIPAVIYT T0334 256 :VATQVPHDDDA 3ladA 362 :IAGVGKTEQAL T0334 267 :NGVEPFTSAIAMKS 3ladA 375 :EGVAINVGVFPFAA T0334 281 :GWTWKIPMLGR 3ladA 400 :GFVKVIADAKT T0334 292 :FGTGYVYSSRFA 3ladA 413 :VLGVHVIGPSAA T0334 307 :EAVREFCE 3ladA 425 :ELVQQGAI Number of specific fragments extracted= 24 number of extra gaps= 6 total=2126 Number of alignments=91 # 3ladA read from 3ladA/merged-good-all-a2m # found chain 3ladA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (3ladA)S1 Warning: unaligning (T0334)I5 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)Q2 Warning: unaligning (T0334)D6 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)K3 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V83 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V83 Warning: unaligning (T0334)E49 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3ladA)A84 Warning: unaligning (T0334)L55 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)I91 Warning: unaligning (T0334)Q56 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)I91 Warning: unaligning (T0334)F219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)A268 Warning: unaligning (T0334)D220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)A268 Warning: unaligning (T0334)C227 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V276 Warning: unaligning (T0334)S228 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V276 Warning: unaligning (T0334)K237 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)D289 Warning: unaligning (T0334)A238 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)D289 Warning: unaligning (T0334)M239 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)S290 T0334 7 :KILIVGGGTAGWMAASYLGK 3ladA 5 :DVIVIGAGPGGYVAAIKSAQ T0334 29 :QGT 3ladA 25 :LGL T0334 33 :DITLLQAPD 3ladA 28 :KTALIEKYK T0334 42 :IPTL 3ladA 38 :KEGK T0334 46 :G 3ladA 81 :G T0334 50 :ATIPN 3ladA 85 :IDVPT T0334 57 :TAFFDFLGI 3ladA 92 :ARKDQIVRN T0334 69 :EWMRECNASYKVAIKFI 3ladA 107 :SLIKANGVTLFEGHGKL T0334 96 :EARELDGGPDHFYHSFGLL 3ladA 156 :EIPPAPVDQDVIVDSTGAL T0334 115 :KYHEQIPLSHYWFDRSYRG 3ladA 178 :NVPGKLGVIGAGVIGLELG T0334 139 :FDYACYKEPVILD 3ladA 197 :SVWARLGAEVTVL T0334 152 :ANRSPRRL 3ladA 211 :AMDKFLPA T0334 172 :DAHLVADFLRRFA 3ladA 219 :VDEQVAKEAQKIL T0334 186 :EKLGVRHVED 3ladA 232 :TKQGLKILLG T0334 196 :RVEHVQRDAN 3ladA 243 :RVTGTEVKNK T0334 207 :NIE 3ladA 253 :QVT T0334 211 :VRTAT 3ladA 256 :VKFVD T0334 216 :GR 3ladA 263 :GE T0334 218 :V 3ladA 266 :S T0334 221 :ADLFVD 3ladA 269 :FDKLIV T0334 229 :GFRG 3ladA 277 :GRRP T0334 233 :LLIN 3ladA 284 :DLLA T0334 240 :EEPFLD 3ladA 291 :GVTLDE T0334 247 :SDHLLNDSAVATQVPHDDDANGV 3ladA 297 :RGFIYVDDYCATSVPGVYAIGDV T0334 270 :EPFTS 3ladA 375 :EGVAI T0334 275 :AIAMK 3ladA 381 :VGVFP T0334 280 :SGWTWKIPM 3ladA 400 :GFVKVIADA T0334 289 :LGRFGTGYVYSSR 3ladA 410 :TDRVLGVHVIGPS T0334 364 :VYAALYQLVKHFP 3ladA 423 :AAELVQQGAIAME T0334 377 :DKSLNPVLTARF 3ladA 449 :AHPALSEALHEA Number of specific fragments extracted= 30 number of extra gaps= 5 total=2156 Number of alignments=92 # 3ladA read from 3ladA/merged-good-all-a2m # found chain 3ladA in template set Warning: unaligning (T0334)F219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)A268 Warning: unaligning (T0334)D220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)A268 Warning: unaligning (T0334)C227 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)V276 Warning: unaligning (T0334)S228 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)V276 Warning: unaligning (T0334)H262 because of BadResidue code BAD_PEPTIDE in next template residue (3ladA)T283 Warning: unaligning (T0334)D263 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)T283 Warning: unaligning (T0334)G268 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (3ladA)D289 Warning: unaligning (T0334)V269 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (3ladA)D289 Warning: unaligning (T0334)E270 because of BadResidue code BAD_PEPTIDE at template residue (3ladA)S290 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 3ladA 178 :NVPGKLGVIGAGVIGLELGSVWAR T0334 30 :GTADITLLQAPDIPT 3ladA 202 :LGAEVTVLEAMDKFL T0334 63 :LGIP 3ladA 217 :PAVD T0334 174 :HLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTATGR 3ladA 221 :EQVAKEAQKILTKQGLKILLGARVTGTEVKNKQVTVKFVDAEGE T0334 218 :V 3ladA 266 :S T0334 221 :ADLFVD 3ladA 269 :FDKLIV T0334 229 :GF 3ladA 277 :GR T0334 258 :TQV 3ladA 279 :RPV T0334 264 :DDAN 3ladA 284 :DLLA T0334 271 :PFTS 3ladA 291 :GVTL T0334 292 :FGTGYVYSSRFAT 3ladA 295 :DERGFIYVDDYCA T0334 338 :AWVGNCVSIGTSSCFVE 3ladA 308 :TSVPGVYAIGDVVRGAM T0334 360 :GIYFVYAALYQLVKHFPDKSL 3ladA 325 :LAHKASEEGVVVAERIAGHKA Number of sp# WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 352 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 525 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 517 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 453 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 460 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 Skipped atom 762, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1386, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1388, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1390, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 1392, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 762, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 764, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 766, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 768, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1386, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1388, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1390, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 1392, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 522 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 520 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 513 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 521 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 524 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 446 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking fo1chuA expands to /projects/compbio/data/pdb/1chu.pdb.gz 1chuA:# T0334 read from 1chuA/merged-good-all-a2m # 1chuA read from 1chuA/merged-good-all-a2m # adding 1chuA to template set # found chain 1chuA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)P40 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)P40 Warning: unaligning (T0334)P43 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E43 Warning: unaligning (T0334)T44 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E43 Warning: unaligning (T0334)I65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)F57 Warning: unaligning (T0334)T89 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S92 Warning: unaligning (T0334)A90 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S92 Warning: unaligning (T0334)R132 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)T142 Warning: unaligning (T0334)V193 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E158 Warning: unaligning (T0334)E194 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E158 Warning: unaligning (T0334)G290 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)G274 Warning: unaligning (T0334)R291 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)G274 Warning: unaligning (T0334)S300 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)H315 Warning: unaligning (T0334)R301 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)H315 Warning: unaligning (T0334)A303 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)A318 Warning: unaligning (T0334)T304 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)A318 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S389 Warning: unaligning (T0334)S358 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S389 Warning: unaligning (T0334)T516 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1chuA)F481 Warning: unaligning (T0334)L517 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1chuA)F481 T0334 5 :IDKILIVGGGTAGWMAASYLG 1chuA 8 :SCDVLIIGSGAAGLSLALRLA T0334 30 :GTADITLLQA 1chuA 29 :DQHQVIVLSK T0334 42 :I 1chuA 41 :V T0334 66 :PEDE 1chuA 58 :DETD T0334 70 :WMRECNASYK 1chuA 63 :IDSHVEDTLI T0334 80 :VAIKFINWR 1chuA 82 :AVEFVASNA T0334 91 :G 1chuA 93 :C T0334 123 :SHYWFDRSY 1chuA 94 :VQWLIDQGV T0334 183 :FATEKLGVRH 1chuA 147 :KALNHPNIRV T0334 195 :D 1chuA 159 :R T0334 196 :RVEHVQR 1chuA 161 :NAVDLIV T0334 203 :DANGNIESVR 1chuA 174 :PGTRRVVGAW T0334 213 :TATG 1chuA 186 :NRNK T0334 217 :RVFDADLFVDCSGFRGLL 1chuA 193 :ETCHAKAVVLATGGASKV T0334 236 :NKA 1chuA 211 :YQY T0334 239 :MEEPFLDMSDHLLNDSAV 1chuA 231 :AGCRVANLEFNQFHPTAL T0334 261 :PHDDDANGVEPFTSA 1chuA 249 :YHPQARNFLLTEALR T0334 279 :KSG 1chuA 264 :GEG T0334 284 :WKIPML 1chuA 267 :AYLKRP T0334 292 :FGT 1chuA 276 :RFM T0334 295 :GYVYS 1chuA 309 :MFLDI T0334 302 :F 1chuA 316 :K T0334 305 :E 1chuA 319 :D T0334 306 :DEAVREFCEM 1chuA 326 :PMIYEKLLGL T0334 317 :HLDPETQPLNRIRFRVG 1chuA 336 :GIDLTQEPVPIVPAAHY T0334 339 :WVGNCVSIG 1chuA 366 :DVEGLYAIG T0334 348 :TSSCFVEPL 1chuA 379 :TGLHGANRM T0334 359 :TGIYFVYAALYQLVKHFPD 1chuA 390 :NSLLECLVYGWSAAEDITR T0334 378 :KSLNPVLTARFNREIETMFDDTRDF 1chuA 426 :RVENPDERVVIQHNWHELRLFMWDY T0334 442 :AINA 1chuA 452 :GIVR T0334 492 :MPQATESVDEVFGAVKDRQRNLLE 1chuA 456 :TTKRLERALRRITMLQQEIDEYYA T0334 518 :PSLHEFLRQQ 1chuA 482 :RVSNNLLELR Number of specific fragments extracted= 32 number of extra gaps= 9 total=2345 Number of alignments=100 # 1chuA read from 1chuA/merged-good-all-a2m # found chain 1chuA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1chuA)N2 Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)P40 Warning: unaligning (T0334)G46 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)P40 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E43 Warning: unaligning (T0334)E49 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E43 Warning: unaligning (T0334)L63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)F57 Warning: unaligning (T0334)E118 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S92 Warning: unaligning (T0334)Q119 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S92 Warning: unaligning (T0334)P147 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)T142 Warning: unaligning (T0334)D172 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)L144 Warning: unaligning (T0334)V193 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E158 Warning: unaligning (T0334)E194 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E158 Warning: unaligning (T0334)M288 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)G274 Warning: unaligning (T0334)L289 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)G274 Warning: unaligning (T0334)S300 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)H315 Warning: unaligning (T0334)R301 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)H315 Warning: unaligning (T0334)A303 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)A318 Warning: unaligning (T0334)T304 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)A318 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S389 Warning: unaligning (T0334)S358 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S389 Warning: unaligning (T0334)T516 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1chuA)F481 Warning: unaligning (T0334)L517 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1chuA)F481 T0334 3 :GKID 1chuA 3 :TLPE T0334 7 :KILIVGGGTAGWMAASYLG 1chuA 10 :DVLIIGSGAAGLSLALRLA T0334 29 :QGT 1chuA 29 :DQH T0334 33 :DITLLQA 1chuA 32 :QVIVLSK T0334 47 :V 1chuA 41 :V T0334 64 :GIPED 1chuA 58 :DETDS T0334 69 :EWMRECNAS 1chuA 65 :SHVEDTLIA T0334 104 :PDHFYHSFGLL 1chuA 74 :GAGICDRHAVE T0334 115 :KYH 1chuA 88 :SNA T0334 120 :IP 1chuA 93 :CV T0334 139 :FDYACYKE 1chuA 95 :QWLIDQGV T0334 173 :AHLVA 1chuA 145 :VSKAL T0334 186 :EKLGVRH 1chuA 150 :NHPNIRV T0334 195 :D 1chuA 159 :R T0334 196 :RVEHVQR 1chuA 161 :NAVDLIV T0334 203 :DANG 1chuA 173 :LPGT T0334 207 :NIESVRTA 1chuA 178 :RVVGAWVW T0334 216 :GR 1chuA 190 :ET T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1chuA 194 :TCHAKAVVLATGGASKVYQYTTNPDISSG T0334 247 :SDHLLNDSAV 1chuA 239 :EFNQFHPTAL T0334 264 :DDANG 1chuA 249 :YHPQA T0334 271 :PFTS 1chuA 254 :RNFL T0334 275 :AIAMKSGWTWKIP 1chuA 260 :EALRGEGAYLKRP T0334 290 :GR 1chuA 275 :TR T0334 292 :FGTGYVYS 1chuA 306 :ADCMFLDI T0334 302 :F 1chuA 316 :K T0334 305 :E 1chuA 319 :D T0334 306 :DEAVREFCEM 1chuA 326 :PMIYEKLLGL T0334 317 :HLDPETQPLNRIRFRVGRNR 1chuA 336 :GIDLTQEPVPIVPAAHYTCG T0334 337 :RAWVGNCVSIGTSSCF 1chuA 364 :RTDVEGLYAIGEVSYT T0334 353 :VEP 1chuA 381 :LHG T0334 356 :L 1chuA 387 :M T0334 359 :TGIYFVYAALYQLVKHFP 1chuA 390 :NSLLECLVYGWSAAEDIT T0334 377 :DKSLNPVLTARFNREIETMFDDTRDF 1chuA 425 :SRVENPDERVVIQHNWHELRLFMWDY T0334 478 :LG 1chuA 451 :VG T0334 489 :LAHMPQATESVDEVFGAVKDRQRNLLE 1chuA 453 :IVRTTKRLERALRRITMLQQEIDEYYA T0334 518 :PSLHEFLR 1chuA 482 :RVSNNLLE Number of specific fragments extracted= 37 number of extra gaps= 10 total=2382 Number of alignments=101 # 1chuA read from 1chuA/merged-good-all-a2m # found chain 1chuA in template set Warning: unaligning (T0334)P40 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)P40 Warning: unaligning (T0334)D41 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)P40 Warning: unaligning (T0334)P43 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E43 Warning: unaligning (T0334)T44 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E43 Warning: unaligning (T0334)I65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)F57 Warning: unaligning (T0334)D140 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S92 Warning: unaligning (T0334)Y141 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S92 Warning: unaligning (T0334)P156 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)T142 Warning: unaligning (T0334)H192 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)E158 Warning: unaligning (T0334)V193 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)E158 Warning: unaligning (T0334)I276 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)A228 Warning: unaligning (T0334)A277 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)A228 Warning: unaligning (T0334)E357 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S389 Warning: unaligning (T0334)S358 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S389 Warning: unaligning (T0334)S379 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1chuA)H414 Warning: unaligning (T0334)P411 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1chuA)H414 Warning: unaligning (T0334)T413 because of BadResidue code BAD_PEPTIDE in next template residue (1chuA)S417 Warning: unaligning (T0334)D414 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)S417 Warning: unaligning (T0334)T415 because of BadResidue code BAD_PEPTIDE at template residue (1chuA)T418 Warning: unaligning (T0334)T516 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1chuA)F481 T0334 5 :IDKILIVGGGTAGWMAASYLG 1chuA 8 :SCDVLIIGSGAAGLSLALRLA T0334 30 :GTADITLLQA 1chuA 29 :DQHQVIVLSK T0334 42 :I 1chuA 41 :V T0334 66 :PEDEWMREC 1chuA 58 :DETDSIDSH T0334 114 :LKYHEQIPLSHYWFDR 1chuA 68 :EDTLIAGAGICDRHAV T0334 133 :GKTVEPF 1chuA 84 :EFVASNA T0334 142 :ACYKEPVIL 1chuA 93 :CVQWLIDQG T0334 155 :S 1chuA 102 :V T0334 183 :FATEK 1chuA 147 :KALNH T0334 188 :LGVR 1chuA 153 :NIRV T0334 194 :EDRVEHVQRD 1chuA 159 :RTNAVDLIVS T0334 204 :ANGN 1chuA 175 :GTRR T0334 208 :IESVRTATGR 1chuA 181 :GAWVWNRNKE T0334 218 :VFDADLFVDCSGFRG 1chuA 194 :TCHAKAVVLATGGAS T0334 248 :DHL 1chuA 209 :KVY T0334 261 :PHDDDANGVEPFTSA 1chuA 212 :QYTTNPDISSGDGIA T0334 278 :MKSGWTWKIPMLGRFGTGYVYSSR 1chuA 229 :WRAGCRVANLEFNQFHPTALYHPQ T0334 302 :FATED 1chuA 257 :LLTEA T0334 307 :EAVREFCEMWHLDPETQ 1chuA 323 :QHFPMIYEKLLGLGIDL T0334 324 :PLNRIRFRVGRN 1chuA 342 :EPVPIVPAAHYT T0334 338 :AWV 1chuA 354 :CGG T0334 341 :GNCVSIGTSS 1chuA 368 :EGLYAIGEVS T0334 351 :CFVEPL 1chuA 382 :HGANRM T0334 359 :TGIYFVYAALYQLVKHFPDK 1chuA 390 :NSLLECLVYGWSAAEDITRR T0334 412 :R 1chuA 415 :D T0334 416 :PFWRANKELRLADGMQEKIDMYRA 1chuA 419 :LPPWDESRVENPDERVVIQHNWHE T0334 458 :FEEEFRNFWNNSNY 1chuA 443 :LRLFMWDYVGIVRT T0334 493 :PQATESVDEVFGAVKDRQRNLLE 1chuA 457 :TKRLERALRRITMLQQEIDEYYA Number of specific fragments extracted= 28 number of extra gaps= 8 total=2410 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bs3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bs3A expands to /projects/compbio/data/pdb/2bs3.pdb.gz 2bs3A:Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 51, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1074, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2077, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2079, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2081, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2083, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2085, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2087, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2089, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2091, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2093, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2095, because occupancy 0.500 <= existing 0.500 in 2bs3A Skipped atom 2097, because occupancy 0.500 <= existing 0.500 in 2bs3A # T0334 read from 2bs3A/merged-good-all-a2m # 2bs3A read from 2bs3A/merged-good-all-a2m # adding 2bs3A to template set # found chain 2bs3A in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 2bs3A 5 :YCDSLVIGGGLAGLRAAVATQQ T0334 30 :GTADITLLQAPDI 2bs3A 27 :KGLSTIVLSLIPV T0334 43 :PTLGVGEATIPN 2bs3A 47 :AQGGMQASLGNS T0334 60 :FDFLGIPEDEWMRECNAS 2bs3A 59 :KMSDGDNEDLHFMDTVKG T0334 78 :YKVAIKFINWRTAG 2bs3A 83 :QKVARMFVNTAPKA T0334 123 :SHYWFDRSYR 2bs3A 97 :IRELAAWGVP T0334 136 :VEPFDYACYKEPVILD 2bs3A 107 :WTRIHKGDRMAIINAQ T0334 152 :ANRSPRRLDGSKVTNYAW 2bs3A 126 :ITEEDFRHGLIHSRDFGG T0334 170 :HFDAHLVADFLRRFAT 2bs3A 154 :DATGHTMLFAVANECL T0334 187 :KLGVRHVED 2bs3A 170 :KLGVSIQDR T0334 196 :RVEHVQR 2bs3A 180 :EAIALIH T0334 204 :ANGNIESVR 2bs3A 187 :QDGKCYGAV T0334 213 :TATG 2bs3A 199 :LVTG T0334 217 :RVFDADLFVDCSGFRGLL 2bs3A 205 :IAYVAKGTLIATGGYGRI T0334 239 :M 2bs3A 241 :L T0334 246 :MSDH 2bs3A 242 :ETGI T0334 250 :LLNDSAVATQV 2bs3A 248 :LGNMEAVQFHP T0334 275 :AIAMKSGWTW 2bs3A 259 :TPLFPSGILL T0334 285 :KIPMLGRFGT 2bs3A 278 :ILRDVDGHRF T0334 295 :GYVYSSRFATE 2bs3A 325 :HLWLDISILGR T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNRRA 2bs3A 343 :RDVQEICEYFAGIDPAEKWAPVLPMQHYSMGGI T0334 339 :WVGNCVSIGTSS 2bs3A 384 :KLKGLFSAGEAA T0334 351 :CFVEPLESTGIYFVYAALYQLVKHFPD 2bs3A 400 :HGFNRLGGNSVSEAVVAGMIVGEYFAE T0334 378 :KSLNPVLTARFNREIETMFD 2bs3A 437 :TKTLEKFVKGQEAYMKSLVE T0334 410 :SPRT 2bs3A 457 :SKGT T0334 424 :LRLADGMQEKIDMYRAGMAINAP 2bs3A 461 :EDVFKIKNRMKDVMDDNVGIFRD T0334 448 :SDDAQLYYGNFEEEFRNFWN 2bs3A 484 :GPHLEKAVKELEELYKKSKN T0334 471 :YYCVLAG 2bs3A 530 :ALCVAKG T0334 478 :LGLVPDA 2bs3A 545 :GAHNRED T0334 488 :RLAHM 2bs3A 584 :DVNEM T0334 493 :PQ 2bs3A 600 :KG T0334 496 :TESVDEVFGAVKDRQRNLLETLPSLHEFLRQQHG 2bs3A 606 :NPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMP Number of specific fragments extracted= 32 number of extra gaps= 0 total=2442 Number of alignments=103 # 2bs3A read from 2bs3A/merged-good-all-a2m # found chain 2bs3A in template set Warning: unaligning (T0334)I5 because first residue in template chain is (2bs3A)M1 Warning: unaligning (T0334)F352 because of BadResidue code BAD_PEPTIDE in next template residue (2bs3A)D398 T0334 6 :D 2bs3A 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 2bs3A 7 :DSLVIGGGLAGLRAAVATQQ T0334 29 :QGT 2bs3A 27 :KGL T0334 33 :DITLLQAP 2bs3A 30 :STIVLSLI T0334 46 :GVGEATIPNLQTAFFDFLGIPED 2bs3A 38 :PVKRSHSAAAQGGMQASLGNSKM T0334 100 :LDG 2bs3A 61 :SDG T0334 115 :KYHE 2bs3A 65 :NEDL T0334 122 :LSHYWFDRSYRGKTV 2bs3A 69 :HFMDTVKGSDWGCDQ T0334 139 :FDYACYKEPVILD 2bs3A 98 :RELAAWGVPWTRI T0334 152 :ANRSPRRLDGSKVTNYAWHF 2bs3A 112 :KGDRMAIINAQKTTITEEDF T0334 172 :DAHLVADFLRRFA 2bs3A 156 :TGHTMLFAVANEC T0334 186 :EKLGVRHVED 2bs3A 169 :LKLGVSIQDR T0334 196 :RVEHVQRDAN 2bs3A 180 :EAIALIHQDG T0334 207 :NIESVRTAT 2bs3A 190 :KCYGAVVRD T0334 216 :GR 2bs3A 202 :GD T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 2bs3A 206 :AYVAKGTLIATGGYGRIYKNTTNAVVCEG T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSG 2bs3A 243 :TGIAQLGNMEAVQFHPTPLFPSGILLTEGCRGDGG T0334 285 :KIPM 2bs3A 278 :ILRD T0334 289 :LGR 2bs3A 283 :DGH T0334 292 :FGTGYVYSSRFATE 2bs3A 323 :GQHLWLDISILGRK T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNRRAWVG 2bs3A 343 :RDVQEICEYFAGIDPAEKWAPVLPMQHYSMGGIRTD T0334 342 :NCVSIGTSSC 2bs3A 387 :GLFSAGEAAC T0334 353 :VEP 2bs3A 399 :MHG T0334 356 :LESTGIYFVYAALYQLVKHFP 2bs3A 405 :LGGNSVSEAVVAGMIVGEYFA T0334 377 :DKSLNPVLTARFNREIETMF 2bs3A 436 :ETKTLEKFVKGQEAYMKSLV T0334 397 :DDTRDFIQAHFYFS 2bs3A 465 :KIKNRMKDVMDDNV T0334 411 :PRTDTP 2bs3A 480 :IFRDGP T0334 417 :FWRA 2bs3A 487 :LEKA T0334 427 :ADGMQEKIDMYRAG 2bs3A 491 :VKELEELYKKSKNV T0334 450 :DAQLYYGNFEEEFRNFWNNSNYYCVLAG 2bs3A 505 :GIKNKRLHANPELEEAYRVPMMLKVALC T0334 478 :LGL 2bs3A 583 :LDV T0334 481 :VPDAPSPRLAHMPQ 2bs3A 587 :EMEIAPGYRGYGAK T0334 495 :ATESVDEVFGAVKDRQRNLLETLPSLHEFLRQQHG 2bs3A 605 :ENPLSVKRQEEIDKIQSELEAAGKDRHAIQEALMP Number of specific fragments extracted= 33 number of extra gaps= 1 total=2475 Number of alignments=104 # 2bs3A read from 2bs3A/merged-good-all-a2m # found chain 2bs3A in template set Warning: unaligning (T0334)F352 because of BadResidue code BAD_PEPTIDE in next template residue (2bs3A)D398 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 2bs3A 4 :QYCDSLVIGGGLAGLRAAVATQQ T0334 30 :GTADITLLQAPDIPTLGVGEATI 2bs3A 27 :KGLSTIVLSLIPVKRSHSAAAQG T0334 53 :PNLQTAF 2bs3A 68 :LHFMDTV T0334 61 :DFLGIP 2bs3A 75 :KGSDWG T0334 68 :DEWMRECNAS 2bs3A 97 :IRELAAWGVP T0334 87 :WRTAGEGTSEARELDGGPD 2bs3A 107 :WTRIHKGDRMAIINAQKTT T0334 150 :LDANRSPRRLDGSKVTNYAWHF 2bs3A 130 :DFRHGLIHSRDFGGTKKWRTCY T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGN 2bs3A 156 :TGHTMLFAVANECLKLGVSIQDRKEAIALIHQDGKC T0334 208 :IESVRTATGR 2bs3A 194 :AVVRDLVTGD T0334 218 :VFDADLFVDCSGFRG 2bs3A 206 :AYVAKGTLIATGGYG T0334 248 :DHLLND 2bs3A 221 :RIYKNT T0334 264 :DDANGVEPFTSAIAMKSG 2bs3A 227 :TNAVVCEGTGTAIALETG T0334 307 :EAVREFCEMWHLDP 2bs3A 344 :DVQEICEYFAGIDP T0334 322 :TQPLNRIRF 2bs3A 358 :AEKWAPVLP T0334 331 :RVGRNRRAWVGNCVSIGTSSC 2bs3A 376 :RTDYRGEAKLKGLFSAGEAAC T0334 353 :VEPLESTGIYFVYAALYQLVKHFP 2bs3A 402 :FNRLGGNSVSEAVVAGMIVGEYFA T0334 377 :DKSLNPVLTARFNREIETMFD 2bs3A 436 :ETKTLEKFVKGQEAYMKSLVE T0334 410 :SPRTD 2bs3A 457 :SKGTE T0334 425 :RLADGMQEKIDMYRAGMAI 2bs3A 462 :DVFKIKNRMKDVMDDNVGI T0334 479 :GLVPDAPSPRLAHMPQATESV 2bs3A 481 :FRDGPHLEKAVKELEELYKKS Number of specific fragments extracted= 20 number of extra gaps= 1 total=2495 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b5qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b5qA expands to /projects/compbio/data/pdb/1b5q.pdb.gz 1b5qA:# T0334 read from 1b5qA/merged-good-all-a2m # 1b5qA read from 1b5qA/merged-good-all-a2m # adding 1b5qA to template set # found chain 1b5qA in template set Warning: unaligning (T0334)T185 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)Q215 Warning: unaligning (T0334)E186 because of BadResidue code BAD_PEPTIDE at template residue (1b5qA)Q215 Warning: unaligning (T0334)A238 because of BadResidue code BAD_PEPTIDE in next template residue (1b5qA)D274 Warning: unaligning (T0334)L380 because last residue in template chain is (1b5qA)C463 T0334 7 :KILIVGG# Found a chain break before 470 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 391 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 322 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 463 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 491 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 527 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 491 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 529 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 Skipped atom 111, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 113, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 115, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 117, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 119, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 121, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 123, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 125, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 127, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 129, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 131, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 133, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 135, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 139, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 141, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 143, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 145, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 147, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 464 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 456 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 412 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 519 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0334 can't currently be optimized by undertaker # copying to AlignedFragments data structure 1trb expands to /projects/compbio/data/pdb/1trb.pdb.gz 1trb:Warning: there is no chain 1trb will retry with 1trbA # T0334 read from 1trb/merged-good-all-a2m # 1trb read from 1trb/merged-good-all-a2m # adding 1trb to template set # found chain 1trb in template set Warning: unaligning (T0334)H317 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)D224 Warning: unaligning (T0334)L318 because of BadResidue code BAD_PEPTIDE at template residue (1trb)D224 Warning: unaligning (T0334)D319 because of BadResidue code BAD_PEPTIDE at template residue (1trb)T225 Warning: unaligning (T0334)P320 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N227 Warning: unaligning (T0334)E321 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N227 Warning: unaligning (T0334)Q323 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N230 Warning: unaligning (T0334)P324 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N230 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1trb 4 :KHSKLLILGSGPAGYTAAVYAAR T0334 30 :GTADITLLQAPDIPT 1trb 27 :ANLQPVLITGMEKGG T0334 53 :P 1trb 42 :Q T0334 141 :YACYKEPVI 1trb 43 :LTTTTEVEN T0334 155 :SPRRLDG 1trb 52 :WPGDPND T0334 171 :FDAHLVADFLRRFA 1trb 59 :LTGPLLMERMHEHA T0334 186 :EKLGVRHVEDRVEHVQRDANG 1trb 73 :TKFETEIIFDHINKVDLQNRP T0334 209 :ESVRTATGR 1trb 94 :FRLNGDNGE T0334 219 :FDADLFVDCSGFR 1trb 103 :YTCDALIIATGAS T0334 236 :NKAMEEP 1trb 116 :ARYLGLP T0334 245 :DMSDH 1trb 127 :FKGRG T0334 250 :LLN 1trb 133 :SAC T0334 272 :FTSA 1trb 140 :GFFY T0334 279 :KSGWTWKIPMLG 1trb 144 :RNQKVAVIGGGN T0334 291 :R 1trb 166 :N T0334 292 :FGTGYVYSSRFATE 1trb 169 :SEVHLIHRRDGFRA T0334 306 :DEAVREFCEMW 1trb 184 :KILIKRLMDKV T0334 322 :T 1trb 228 :S T0334 325 :LNRIRFRVG 1trb 231 :IESLDVAGL T0334 339 :WVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1trb 277 :SIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG Number of specific fragments extracted= 20 number of extra gaps= 2 total=2597 Number of alignments=109 # 1trb read from 1trb/merged-good-all-a2m # found chain 1trb in template set Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N198 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N198 Warning: unaligning (T0334)A214 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)D224 Warning: unaligning (T0334)T215 because of BadResidue code BAD_PEPTIDE in next template residue (1trb)N227 Warning: unaligning (T0334)G216 because of BadResidue code BAD_PEPTIDE at template residue (1trb)N227 Warning: unaligning (T0334)S379 because last residue in template chain is (1trb)L316 T0334 4 :KID 1trb 2 :TTK T0334 7 :KILIVGGGTAGWMAASYLGK 1trb 7 :KLLILGSGPAGYTAAVYAAR T0334 29 :QGT 1trb 27 :ANL T0334 33 :DITLLQAPD 1trb 30 :QPVLITGME T0334 47 :VGEATIPN 1trb 39 :KGGQLTTT T0334 57 :TAFFDFLGIPED 1trb 47 :TEVENWPGDPND T0334 69 :EWMRECNASYKVAIKFINWRTAGEGTS 1trb 70 :EHATKFETEIIFDHINKVDLQNRPFRL T0334 96 :EARELDGGPDHFYHSFGLLKYHEQIPLSHYWFDRSYRG 1trb 124 :EEAFKGRGVSACATSDGFFYRNQKVAVIGGGNTAVEEA T0334 139 :FDYACYKEPVILD 1trb 162 :LYLSNIASEVHLI T0334 152 :ANRSPR 1trb 176 :RRDGFR T0334 172 :DAHLVADFLRRFA 1trb 182 :AEKILIKRLMDKV T0334 186 :EK 1trb 195 :EN T0334 190 :VRHVED 1trb 199 :IILHTN T0334 196 :RVEHVQRDANG 1trb 206 :TLEEVTGDQMG T0334 208 :IESVRT 1trb 217 :VTGVRL T0334 217 :R 1trb 228 :S T0334 218 :VFDADLFVDCSGFRG 1trb 233 :SLDVAGLFVAIGHSP T0334 233 :LLINKAMEEP 1trb 250 :AIFEGQLELE T0334 247 :SDHLLND 1trb 260 :NGYIKVQ T0334 261 :PHDD 1trb 267 :SGIH T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1trb 271 :GNATQTSIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLD T0334 378 :K 1trb 315 :G Number of specific fragments extracted= 22 number of extra gaps= 3 total=2619 Number of alignments=110 # 1trb read from 1trb/merged-good-all-a2m # found chain 1trb in template set Warning: unaligning (T0334)K378 because last residue in template chain is (1trb)L316 T0334 6 :DKILIVGGGTAGWMAASYLGK 1trb 6 :SKLLILGSGPAGYTAAVYAAR T0334 30 :GTADITLLQAPDI 1trb 27 :ANLQPVLITGMEK T0334 48 :GEA 1trb 40 :GGQ T0334 78 :YKVAIKFINWRTAGEGT 1trb 43 :LTTTTEVENWPGDPNDL T0334 172 :DAHLVADFLRRFATEKLGVRHVE 1trb 60 :TGPLLMERMHEHATKFETEIIFD T0334 196 :RVEHVQRDANG 1trb 83 :HINKVDLQNRP T0334 209 :ESVRT 1trb 94 :FRLNG T0334 215 :TGRVFDADLFVDCSGF 1trb 99 :DNGEYTCDALIIATGA T0334 299 :SSRFATED 1trb 115 :SARYLGLP T0334 327 :RIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1trb 265 :VQSGIHGNATQTSIPGVFAAGDVMDHIYRQAITSAGTGCMAALDAERYLDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=2629 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bgj/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bgj expands to /projects/compbio/data/pdb/1bgj.pdb.gz 1bgj:Warning: there is no chain 1bgj will retry with 1bgjA # T0334 read from 1bgj/merged-good-all-a2m # 1bgj read from 1bgj/merged-good-all-a2m # adding 1bgj to template set # found chain 1bgj in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1bgj)M1 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1bgj 2 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1bgj 24 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1bgj 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1bgj 57 :REAGV T0334 123 :SHYWFDRSYR 1bgj 62 :DRRMARDGLV T0334 139 :FDYAC 1bgj 72 :HEGVE T0334 144 :YKEPVILD 1bgj 80 :AGQRRRID T0334 155 :SPRRLDG 1bgj 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1bgj 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1bgj 114 :EASGATTVYQ T0334 196 :RVEHVQR 1bgj 125 :AEVRLHD T0334 203 :DANG 1bgj 133 :QGER T0334 209 :ESVRTA 1bgj 137 :PYVTFE T0334 215 :TG 1bgj 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1bgj 148 :LRLDCDYIAGCDGFRGIS T0334 236 :NKAMEEPFL 1bgj 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1bgj 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1bgj 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1bgj 219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1bgj 232 :EDWSDERFWTELKARL T0334 317 :HL 1bgj 254 :KL T0334 323 :Q 1bgj 256 :V T0334 324 :PLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1bgj 262 :EKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTD 1bgj 318 :REGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFP T0334 415 :TPFWR 1bgj 357 :DAFSQ T0334 504 :GAVKDRQRNLLETLPSLHEFLRQQH 1bgj 362 :RIQQTELEYYLGSEAGLATIAENYV Number of specific fragments extracted= 26 number of extra gaps= 0 total=2655 Number of alignments=112 # 1bgj read from 1bgj/merged-good-all-a2m # found chain 1bgj in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1bgj)M1 T0334 6 :D 1bgj 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1bgj 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1bgj 24 :AGI T0334 33 :DITLLQAPD 1bgj 27 :DNVILERQT T0334 52 :IPNLQTAF 1bgj 36 :PDYVLGRI T0334 61 :DFLGIPED 1bgj 44 :RAGVLEQG T0334 69 :EWMRECNASYKVAIKFINW 1bgj 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1bgj 73 :EGVEIAFAGQRR T0334 115 :KYHE 1bgj 87 :DLKR T0334 152 :ANRSPRRLD 1bgj 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1bgj 101 :GQTEVTRDLMEAR T0334 186 :EKLGVRHVED 1bgj 114 :EASGATTVYQ T0334 196 :RVEHVQRDANGNIE 1bgj 125 :AEVRLHDLQGERPY T0334 211 :VRTA 1bgj 139 :VTFE T0334 215 :TGR 1bgj 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1bgj 149 :RLDCDYIAGCDGFRGISR T0334 237 :KAMEEPFLDM 1bgj 167 :QSIPAERLKV T0334 247 :SDHLLND 1bgj 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1bgj 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1bgj 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1bgj 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEM 1bgj 223 :VQVPLTEKVEDWSDERFWTELKAR T0334 317 :HLDP 1bgj 248 :PAEV T0334 321 :ETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1bgj 259 :PSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTP 1bgj 317 :YREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDT T0334 417 :FWRANKELRL 1bgj 359 :FSQRIQQTEL T0334 427 :ADGMQEKIDMY 1bgj 375 :EAGLATIAENY Number of specific fragments extracted= 27 number of extra gaps= 0 total=2682 Number of alignments=113 # 1bgj read from 1bgj/merged-good-all-a2m # found chain 1bgj in template set T0334 7 :KILIVGGGTAGWMAASYLGK 1bgj 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1bgj 24 :AGIDNVILERQT T0334 42 :IPTLGVGE 1bgj 40 :LGRIRAGV T0334 51 :TIPNLQTAF 1bgj 48 :LEQGMVDLL T0334 61 :DFLGIP 1bgj 57 :REAGVD T0334 68 :DEWMRECNASYKVAIKF 1bgj 63 :RRMARDGLVHEGVEIAF T0334 90 :AGEGTSEA 1bgj 80 :AGQRRRID T0334 158 :RLDGSKVTN 1bgj 88 :LKRLSGGKT T0334 168 :AWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQR 1bgj 97 :VTVYGQTEVTRDLMEAREASGATTVYQAAEVRLHD T0334 204 :ANGNIESVRTATGR 1bgj 134 :GERPYVTFERDGER T0334 218 :VFDADLFVDCSGFRGLLIN 1bgj 149 :RLDCDYIAGCDGFRGISRQ T0334 243 :FLDMSDH 1bgj 168 :SIPAERL T0334 250 :LLNDSAVATQV 1bgj 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1bgj 191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1bgj 231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1bgj 256 :VTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1bgj 321 :RGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTD T0334 486 :SPRLAH 1bgj 358 :AFSQRI T0334 506 :VKDRQRNLLETLPSLHEFLRQQ 1bgj 364 :QQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 19 number of extra gaps= 0 total=2701 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1el5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 1el5A/merged-good-all-a2m # 1el5A read from 1el5A/merged-good-all-a2m # found chain 1el5A in training set Warning: unaligning (T0334)G3 because first residue in template chain is (1el5A)S1 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1el5A 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDI 1el5A 25 :QGVKTLLVDAFDP T0334 43 :PTLGVGE 1el5A 53 :HAYGEGR T0334 57 :TAF 1el5A 60 :EYV T0334 79 :KVAIKFINWRTAGE 1el5A 63 :PLALRSQELWYELE T0334 96 :EARELDGGP 1el5A 77 :KETHHKIFT T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSYR 1el5A 87 :TGVLVFGPKGESAFVAETMEAAKEHSLT T0334 136 :VEPFDYACYKEPVI 1el5A 115 :VDLLEGDEINKRWP T0334 152 :ANRSPRRLDGSKVTNYAW 1el5A 129 :GITVPENYNAIFEPNSGV T0334 171 :FDAHLVADFLRRFA 1el5A 147 :LFSENCIRAYRELA T0334 186 :EKLGVRHVED 1el5A 161 :EARGAKVLTH T0334 196 :RVEHVQRDANG 1el5A 172 :RVEDFDISPDS T0334 209 :ESVRTATG 1el5A 183 :VKIETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDMSDH 1el5A 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPLQPYR T0334 253 :DSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGR 1el5A 223 :QVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGG T0334 292 :FGTGYVY 1el5A 264 :LKLGYHT T0334 299 :SSRFATE 1el5A 276 :DPDTINR T0334 306 :DEAVREFCEMW 1el5A 288 :PEDESNLRAFL T0334 317 :HLDPET 1el5A 300 :EYMPGA T0334 324 :PLNRIRFRVGRNR 1el5A 306 :NGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1el5A 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKSL 1el5A 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKT Number of specific fragments extracted= 22 number of extra gaps= 0 total=2723 Number of alignments=115 # 1el5A read from 1el5A/merged-good-all-a2m # found chain 1el5A in training set Warning: unaligning (T0334)K4 because first residue in template chain is (1el5A)S1 T0334 5 :ID 1el5A 2 :TH T0334 7 :KILIVGGGTAGWMAASYLGK 1el5A 5 :DVIVVGAGSMGMAAGYQLAK T0334 29 :QGT 1el5A 25 :QGV T0334 33 :DITLLQAPD 1el5A 28 :KTLLVDAFD T0334 42 :IPTL 1el5A 38 :PHTN T0334 46 :GVGEATIPNLQTAF 1el5A 49 :RIIRHAYGEGREYV T0334 64 :GI 1el5A 63 :PL T0334 69 :EWMRECNAS 1el5A 70 :ELWYELEKE T0334 103 :GPDHFYHSFGLL 1el5A 79 :THHKIFTKTGVL T0334 115 :KYHEQIPLSHYW 1el5A 94 :PKGESAFVAETM T0334 139 :FDYACYKEPVILDANRSPRRLDGSKVTNYAWHF 1el5A 106 :EAAKEHSLTVDLLEGDEINKRWPGITVPENYNA T0334 172 :DAHLVADFLRRFA 1el5A 148 :FSENCIRAYRELA T0334 186 :EKLGVRHVED 1el5A 161 :EARGAKVLTH T0334 196 :RVEHVQRDAN 1el5A 172 :RVEDFDISPD T0334 207 :NIE 1el5A 182 :SVK T0334 211 :VRTATG 1el5A 185 :IETANG T0334 218 :VFDADLFVDCSGFRGLLINKAMEEPFLDM 1el5A 191 :SYTADKLIVSMGAWNSKLLSKLNLDIPLQ T0334 252 :NDSAVATQVPHDDDANGV 1el5A 222 :RQVVGFFESDESKYSNDI T0334 271 :PFTS 1el5A 240 :DFPG T0334 275 :AIAMKSGWTWKIPM 1el5A 245 :MVEVPNGIYYGFPS T0334 289 :LGR 1el5A 260 :GGC T0334 292 :FGTGYVYSSRFATE 1el5A 264 :LKLGYHTFGQKIDP T0334 306 :DEAVREFCEMWHLDPETQPLNRIRFRVGRNR 1el5A 288 :PEDESNLRAFLEEYMPGANGELKRGAVCMYT T0334 338 :AWVGNCVSIG 1el5A 319 :KTLDEHFIID T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHFPDKS 1el5A 334 :SNVVIAAGFSGHGFKFSSGVGEVLSQLALTGK T0334 482 :PDAPSPRLAH 1el5A 366 :TEHDISIFSI Number of specific fragments extracted= 26 number of extra gaps= 0 total=2749 Number of alignments=116 # 1el5A read from 1el5A/merged-good-all-a2m # found chain 1el5A in training set Warning: unaligning (T0334)G3 because first residue in template chain is (1el5A)S1 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1el5A 2 :THFDVIVVGAGSMGMAAGYQLAK T0334 30 :GTADITLLQAPDIPT 1el5A 25 :QGVKTLLVDAFDPPH T0334 45 :LGVGEATIPNLQTAF 1el5A 55 :YGEGREYVPLALRSQ T0334 61 :DFL 1el5A 70 :ELW T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1el5A 73 :YELEKETHHKIFTKTGVLVFGPKGESAF T0334 110 :SFGLLKYHEQIPLSHYWFD 1el5A 101 :VAETMEAAKEHSLTVDLLE T0334 146 :EPVILDANRSPRRLDGSKV 1el5A 120 :GDEINKRWPGITVPENYNA T0334 168 :AWHFDAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1el5A 144 :SGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDS T0334 209 :ESVRTAT 1el5A 183 :VKIETAN T0334 217 :RVFDADLFVDCSGFRGL 1el5A 190 :GSYTADKLIVSMGAWNS T0334 237 :KA 1el5A 207 :KL T0334 246 :MSDH 1el5A 209 :LSKL T0334 250 :LLNDSAVATQVPHDDD 1el5A 218 :LQPYRQVVGFFESDES T0334 266 :ANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSS 1el5A 236 :SNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHT T0334 307 :EAVREFCEMWHLDPETQPLNRIRFRVGRNRRAW 1el5A 289 :EDESNLRAFLEEYMPGANGELKRGAVCMYTKTL T0334 340 :VGNCVSIGTSSCFVEP 1el5A 333 :HSNVVIAAGFSGHGFK T0334 357 :ESTG 1el5A 349 :FSSG T0334 367 :ALYQLVKHFPDKS 1el5A 353 :VGEVLSQLALTGK T0334 410 :SPRTDTPFWRANKELR 1el5A 366 :TEHDISIFSINRPALK Number of specific fragments extracted= 19 number of extra gaps= 0 total=2768 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3grs/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 3grs/merged-good-all-a2m # 3grs read from 3grs/merged-good-all-a2m # found chain 3grs in training set Warning: unaligning (T0334)P104 because of BadResidue code BAD_PEPTIDE in next template residue (3grs)G92 Warning: unaligning (T0334)D105 because of BadResidue code BAD_PEPTIDE at template residue (3grs)G92 Warning: unaligning (T0334)H106 because of BadResidue code BAD_PEPTIDE at template residue (3grs)K93 Warning: unaligning (T0334)R157 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3grs)Q167 Warning: unaligning (T0334)R158 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3grs)Q167 T0334 5 :IDKILIVGGGTAGWMAASYLGKA 3grs 20 :SYDYLVIGGGSGGLASARRAAEL T0334 31 :TADITLLQAPDIPTLGVGEATIPN 3grs 43 :GARAAVVESHKLGGTCVNVGCVPK T0334 57 :TAF 3grs 67 :KVM T0334 78 :YKVAIKFINWRTA 3grs 70 :WNTAVHSEFMHDH T0334 96 :EARELDGG 3grs 83 :ADYGFPSC T0334 107 :FYHSFGLLKYHEQIPLSHYWFDRSYRGKTVEPFD 3grs 94 :FNWRVIKEKRDAYVSRLNAIYQNNLTKSHIEIIR T0334 144 :YKEPVILD 3grs 128 :GHAAFTSD T0334 152 :ANRSP 3grs 161 :STPHE T0334 159 :LDGS 3grs 168 :IPGA T0334 166 :NYAW 3grs 172 :SLGI T0334 170 :HFD 3grs 225 :SFD T0334 174 :HLVADFLRRFA 3grs 228 :SMISTNCTEEL T0334 186 :EKLGVRHVED 3grs 239 :ENAGVEVLKF T0334 196 :RVEHVQRDANGNIESVRTA 3grs 250 :QVKEVKKTLSGLEVSMVTA T0334 215 :TG 3grs 270 :PG T0334 217 :RVFD 3grs 277 :TMIP T0334 221 :ADLFVDCSGFRGLL 3grs 282 :VDCLLWAIGRVPNT T0334 236 :NKA 3grs 296 :KDL T0334 239 :MEEPFLDMSDH 3grs 303 :LGIQTDDKGHI T0334 251 :LND 3grs 314 :IVD T0334 264 :DD 3grs 317 :EF T0334 266 :ANGVE 3grs 357 :KEDSK T0334 271 :PFTSAIAMKSGWTWKIPM 3grs 365 :NNIPTVVFSHPPIGTVGL T0334 309 :VREFCEMWH 3grs 384 :EDEAIHKYG T0334 320 :P 3grs 393 :I T0334 323 :QPLNRIRFRVGRNRRAWVGN 3grs 394 :ENVKTYSTSFTPMYHAVTKR T0334 343 :CVSIG 3grs 417 :CVMKM T0334 358 :STGIYF 3grs 430 :VVGIHM T0334 378 :KSLNPVLTARFNREIETMFD 3grs 437 :GLGCDEMLQGFAVAVKMGAT T0334 434 :IDMYRAGMAINAPASDDAQL 3grs 457 :KADFDNTVAIHPTSSEELVT Number of specific fragments extracted= 30 number of extra gaps= 2 total=2798 Number of alignments=118 # 3grs read from 3grs/merged-good-all-a2m # found chain 3grs in training set Warning: unaligning (T0334)F62 because of BadResidue code BAD_PEPTIDE in next template residue (3grs)G92 Warning: unaligning (T0334)L63 because of BadResidue code BAD_PEPTIDE at template residue (3grs)G92 Warning: unaligning (T0334)G64 because of BadResidue code BAD_PEPTIDE at template residue (3grs)K93 Warning: unaligning (T0334)L100 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3grs)Q167 Warning: unaligning (T0334)D101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3grs)Q167 T0334 5 :ID 3grs 19 :AS T0334 7 :KILIVGGGTAGWMAASYLGK 3grs 22 :DYLVIGGGSGGLASARRAAE T0334 29 :QGT 3grs 42 :LGA T0334 33 :DITLLQAPDIPTL 3grs 45 :RAAVVESHKLGGT T0334 46 :GVGEATIPN 3grs 81 :DHADYGFPS T0334 61 :D 3grs 90 :C T0334 65 :IPEDEWMRECNASYKVAIKFINWRTAGEGTS 3grs 94 :FNWRVIKEKRDAYVSRLNAIYQNNLTKSHIE T0334 96 :EARE 3grs 162 :TPHE T0334 102 :G 3grs 168 :I T0334 103 :GPDHFYHSFGLL 3grs 170 :GASLGITSDGFF T0334 115 :KYHEQIPLSHYWFDRSYRG 3grs 185 :ELPGRSVIVGAGYIAVEMA T0334 139 :FDYACYKEPVILD 3grs 204 :GILSALGSKTSLM T0334 152 :ANRSPRRL 3grs 218 :RHDKVLRS T0334 172 :DAHLVADFLRRFA 3grs 226 :FDSMISTNCTEEL T0334 186 :EKLGVRHVED 3grs 239 :ENAGVEVLKF T0334 196 :RVEHVQRDANG 3grs 250 :QVKEVKKTLSG T0334 209 :ESVRTA 3grs 261 :LEVSMV T0334 215 :TGR 3grs 270 :PGR T0334 218 :VF 3grs 278 :MI T0334 220 :DADLFVDCSGFRG 3grs 281 :DVDCLLWAIGRVP T0334 233 :LLI 3grs 298 :LSL T0334 237 :KAMEEPFLD 3grs 301 :NKLGIQTDD T0334 247 :SDHLLNDSAVATQV 3grs 310 :KGHIIVDEFQNTNV T0334 341 :GNCVSIGTSSCF 3grs 324 :KGIYAVGDVCGK T0334 358 :STGIYFVYAALYQLVKHFP 3grs 336 :ALLTPVAIAAGRKLAHRLF T0334 377 :DKSLN 3grs 357 :KEDSK Number of specific fragments extracted= 26 number of extra gaps= 2 total=2824 Number of alignments=119 # 3grs read from 3grs/merged-good-all-a2m # found chain 3grs in training set Warning: unaligning (T0334)G103 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (3grs)Q167 Warning: unaligning (T0334)P104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (3grs)Q167 T0334 5 :IDKILIVGGGTAGWMAASYLGK 3grs 20 :SYDYLVIGGGSGGLASARRAAE T0334 30 :GTADITLLQAPDIP 3grs 42 :LGARAAVVESHKLG T0334 51 :TIPNLQTAFFDFL 3grs 69 :MWNTAVHSEFMHD T0334 65 :IPE 3grs 94 :FNW T0334 68 :DEWMRECNASYKVA 3grs 115 :QNNLTKSHIEIIRG T0334 84 :FINWRTAGEGTS 3grs 129 :HAAFTSDPKPTI T0334 96 :EARELDG 3grs 159 :MPSTPHE T0334 105 :DHFYHSFGLLKYHEQIPLSHYWFDRSY 3grs 168 :IPGASLGITSDGFFQLEELPGRSVIVG T0334 135 :TVEPFDYACYKEPVILD 3grs 195 :AGYIAVEMAGILSALGS T0334 154 :RSPRRLDGSKVTN 3grs 212 :KTSLMIRHDKVLR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTA 3grs 226 :FDSMISTNCTEELENAGVEVLKFSQVKEVKKTLSGLEVSMVTA T0334 215 :TGR 3grs 270 :PGR T0334 218 :VF 3grs 278 :MI T0334 220 :DADLFVDCSGF 3grs 281 :DVDCLLWAIGR T0334 338 :AWVGNCVSIGTSSCFVEP 3grs 321 :TNVKGIYAVGDVCGKALL T0334 361 :IYFVYAALYQLVKHFP 3grs 339 :TPVAIAAGRKLAHRLF Number of specific fragments extracted= 16 number of extra gaps= 1 total=2840 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fecA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 1fecA/merged-good-all-a2m # 1fecA read from 1fecA/merged-good-all-a2m # found chain 1fecA in training set T0334 4 :KIDKILIVGGGTAGWMAASYLGKA 1fecA 2 :RAYDLVVIGAGSGGLEAGWNAASL T0334 30 :GTADITLLQAP 1fecA 26 :HKKRVAVIDLQ T0334 41 :DI 1fecA 38 :HH T0334 43 :PTLGVGEATIPNLQTAF 1fecA 41 :PPHYAALGGTCVNVGCV T0334 73 :ECNASYKVAIKFINWRTA 1fecA 58 :PKKLMVTGANYMDTIRES T0334 96 :EARELDGGPDHFYHSFGLL 1fecA 76 :AGFGWELDRESVRPNWKAL T0334 115 :KYHEQIPLSHYWFDR 1fecA 101 :AVSGINDSYEGMFAD T0334 159 :LDGSKVT 1fecA 116 :TEGLTFH T0334 166 :NYAW 1fecA 124 :GFGA T0334 170 :HFD 1fecA 228 :GFD T0334 174 :HLVADFLRRFA 1fecA 231 :SELRKQLTEQL T0334 186 :EKLGVRHVED 1fecA 242 :RANGINVRTH T0334 196 :RVEHVQRDANG 1fecA 253 :NPAKVTKNADG T0334 208 :IESVRTATGRVFDADLFVDCSGFRGL 1fecA 264 :TRHVVFESGAEADYDVVMLAIGRVPR T0334 234 :LIN 1fecA 292 :TLQ T0334 237 :KAMEEPFL 1fecA 296 :EKAGVEVA T0334 246 :MSDHLLNDSAV 1fecA 304 :KNGAIKVDAYS T0334 279 :KS 1fecA 406 :TY T0334 281 :GWTWKIPM 1fecA 410 :FMVRIVTN T0334 289 :LGR 1fecA 419 :ADG T0334 292 :FGTGYVYSSRFATE 1fecA 423 :VLGVHMLGDSSPEI T0334 306 :DEAVREFCEMW 1fecA 438 :QSVAICLKMGA T0334 323 :QPL 1fecA 461 :PTS Number of specific fragments extracted= 23 number of extra gaps= 0 total=2863 Number of alignments=121 # 1fecA read from 1fecA/merged-good-all-a2m # found chain 1fecA in training set T0334 5 :ID 1fecA 2 :RA T0334 7 :KILIVGGGTAGWMAASYLGK 1fecA 5 :DLVVIGAGSGGLEAGWNAAS T0334 28 :LQGT 1fecA 25 :LHKK T0334 33 :DITLLQAPD 1fecA 29 :RVAVIDLQK T0334 42 :IPTL 1fecA 39 :HGPP T0334 46 :GVGEATIPN 1fecA 75 :SAGFGWELD T0334 60 :FDFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1fecA 84 :RESVRPNWKALIAAKNKAVSGINDSYEGMFADTEGL T0334 96 :EARELDG 1fecA 162 :WPQHLGI T0334 103 :GPDHFYHSFGLL 1fecA 170 :GDDLCITSNEAF T0334 115 :KYHEQIPLSHYWFDRSYRGKTV 1fecA 185 :EAPKRALCVGGGYISIEFAGIF T0334 139 :FDYACYKEPVILD 1fecA 207 :NAYKARGGQVDLA T0334 152 :ANRSPRRL 1fecA 221 :RGDMILRG T0334 172 :DAHLVADFLRRFA 1fecA 229 :FDSELRKQLTEQL T0334 186 :EKLGVRHVED 1fecA 242 :RANGINVRTH T0334 196 :RVEHVQRDANGN 1fecA 253 :NPAKVTKNADGT T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fecA 265 :RHVVFESGAEADYDVVMLAIGR T0334 231 :RG 1fecA 289 :RS T0334 233 :LLI 1fecA 293 :LQL T0334 237 :KAMEEPFLD 1fecA 296 :EKAGVEVAK T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1fecA 305 :NGAIKVDAYSKTNVDNIYAIGDV T0334 281 :GWTWKIPM 1fecA 410 :FMVRIVTN T0334 289 :LGRFGTGYVYSSRFATE 1fecA 420 :DGEVLGVHMLGDSSPEI T0334 306 :DEAVREFCEMWHLDP 1fecA 438 :QSVAICLKMGAKISD T0334 321 :ETQPLNRIRFRVGRNR 1fecA 469 :SMRTPAYFYEKGKRVE Number of specific fragments extracted= 24 number of extra gaps= 0 total=2887 Number of alignments=122 # 1fecA read from 1fecA/merged-good-all-a2m # found chain 1fecA in training set T0334 5 :IDKILIVGGGTAGWMAASYLGKALQGTADITLLQAPDI 1fecA 187 :PKRALCVGGGYISIEFAGIFNAYKARGGQVDLAYRGDM T0334 51 :TI 1fecA 225 :IL T0334 63 :LGIP 1fecA 227 :RGFD T0334 174 :HLVADFLRRFATEKLGVRHVEDRVEHVQRDANGN 1fecA 231 :SELRKQLTEQLRANGINVRTHENPAKVTKNADGT T0334 209 :ESVRTATGRVFDADLFVDCSGF 1fecA 265 :RHVVFESGAEADYDVVMLAIGR T0334 244 :LDMSDHLLNDS 1fecA 287 :VPRSQTLQLEK T0334 321 :ETQPLNRIRFRVG 1fecA 301 :EVAKNGAIKVDAY T0334 336 :RRAWVGNCVSIGTSSCFVEPL 1fecA 314 :SKTNVDNIYAIGDVTDRVMLT T0334 362 :YFVYAALYQLVKHFP 1fecA 335 :PVAINEGAAFVDTVF Number of specific fragments extracted= 9 number of extra gaps= 0 total=2896 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aqjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aqjA expands to /projects/compbio/data/pdb/2aqj.pdb.gz 2aqjA:# T0334 read from 2aqjA/merged-good-all-a2m # 2aqjA read from 2aqjA/merged-good-all-a2m # adding 2aqjA to template set # found chain 2aqjA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (2aqjA)N2 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (2aqjA)G48 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (2aqjA)G48 Warning: unaligning (T0334)P376 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)D366 Warning: unaligning (T0334)D377 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)D366 Warning: unaligning (T0334)Q527 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)R517 Warning: unaligning (T0334)H528 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)R517 Warning: unaligning (T0334)G529 because last residue in template chain is (2aqjA)D518 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKALQGTADITLLQAPDIPTLG 2aqjA 3 :KPIKNIVIVGGGTAGWMAASYLVRALQQQANITLIESAAIPRIG T0334 49 :EATIPNLQTAFFDFLGIPEDEWM 2aqjA 49 :EATIPSLQKVFFDFLGIPEREWM T0334 96 :EARE 2aqjA 72 :PQVN T0334 100 :LDGGP 2aqjA 89 :KSPDP T0334 105 :DHFYHSFGLL 2aqjA 98 :HFYHLFGNVP T0334 120 :IPLSHYWFDRSYR 2aqjA 115 :THYWLRKREQGFQ T0334 142 :ACYKEPVILD 2aqjA 128 :QPMEYACYPQ T0334 152 :ANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFAT 2aqjA 143 :GKLAPCLSDGTRQMSHAWHFDAHLVADFLKRWAV T0334 187 :KLGVRHVEDRVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRGLLINKAMEEPFLDMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSSRFATEDEAVREFCEMWHLDPE 2aqjA 177 :ERGVNRVVDEVVDVRLNNRGYISNLLTKEGRTLEADLFIDCSGMRGLLINQALKEPFIDMSDYLLCDSAVASAVPNDDARDGVEPYTSSIAMNSGWTWKIPMLGRFGSGYVFSSHFTSRDQATADFLKLWGLSDN T0334 323 :QPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 2aqjA 312 :QPLNQIKFRVGRNKRAWVNNCVSIGLSSCFLEPLESTGIYFIYAALYQLVKHF T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTPFWRANK 2aqjA 367 :TSFDPRLSDAFNAEIVHMFDDCRDFVQAHYFTTSRDDTPFWLANR T0334 423 :ELRLADGMQEKIDMYRAGMAINAPASDDAQLY 2aqjA 413 :DLRLSDAIKEKVQRYKAGLPLTTTSFDDSTYY T0334 456 :GNFEEEFRNFWNNSNYYCVLAGLGLVPDAPSPRLAHMPQATESVDEVFGAVKDRQRNLLETLPSLHEFLRQ 2aqjA 445 :ETFDYEFKNFWLNGNYYCIFAGLGMLPDRSLPLLQHRPESIEKAEAMFASIRREAERLRTSLPTNYDYLRS Number of specific fragments extracted= 13 number of extra gaps= 3 total=2909 Number of alignments=124 # 2aqjA read from 2aqjA/merged-good-all-a2m # found chain 2aqjA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (2aqjA)N2 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (2aqjA)G48 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (2aqjA)G48 Warning: unaligning (T0334)A81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)I82 Warning: unaligning (T0334)I82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)I82 Warning: unaligning (T0334)P376 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)D366 Warning: unaligning (T0334)D377 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)D366 Warning: unaligning (T0334)Q527 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)R517 Warning: unaligning (T0334)H528 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)R517 Warning: unaligning (T0334)G529 because last residue in template chain is (2aqjA)D518 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKAL 2aqjA 3 :KPIKNIVIVGGGTAGWMAASYLVRAL T0334 29 :QGT 2aqjA 30 :QQA T0334 33 :DITLLQAPDIPTLG 2aqjA 33 :NITLIESAAIPRIG T0334 49 :EATIPNLQTAFFDFLGIPEDEWMRECNASYKV 2aqjA 49 :EATIPSLQKVFFDFLGIPEREWMPQVNGAFKA T0334 83 :KFINWRTAGEGT 2aqjA 83 :KFVNWRKSPDPS T0334 103 :GPDHFYHSFGLLKYHEQIPLSHYWFDRSYR 2aqjA 95 :RDDHFYHLFGNVPNCDGVPLTHYWLRKREQ T0334 152 :ANRSPRRLDGSKVTNYAWHF 2aqjA 125 :GFQQPMEYACYPQPGALDGK T0334 172 :DAHLVADFLRRFA 2aqjA 163 :DAHLVADFLKRWA T0334 186 :EKLGVRHVEDRVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRGLLINKAMEEPFLDMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSSRFATEDEAVREFCEMWHLDP 2aqjA 176 :VERGVNRVVDEVVDVRLNNRGYISNLLTKEGRTLEADLFIDCSGMRGLLINQALKEPFIDMSDYLLCDSAVASAVPNDDARDGVEPYTSSIAMNSGWTWKIPMLGRFGSGYVFSSHFTSRDQATADFLKLWGLSD T0334 322 :TQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 2aqjA 311 :NQPLNQIKFRVGRNKRAWVNNCVSIGLSSCFLEPLESTGIYFIYAALYQLVKHF T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTPFWRANK 2aqjA 367 :TSFDPRLSDAFNAEIVHMFDDCRDFVQAHYFTTSRDDTPFWLANR T0334 423 :ELRLADGMQEKIDMYRAGMAINAP 2aqjA 413 :DLRLSDAIKEKVQRYKAGLPLTTT T0334 448 :SDDAQLYYGNFEEEFRNFWNNSNYYCVLAGLGLVPDAPSPRLAHMPQATESVDEVFGAVKDRQRNLLETLPSLHEFLRQ 2aqjA 437 :SFDDSTYYETFDYEFKNFWLNGNYYCIFAGLGMLPDRSLPLLQHRPESIEKAEAMFASIRREAERLRTSLPTNYDYLRS Number of specific fragments extracted= 13 number of extra gaps= 4 total=2922 Number of alignments=125 # 2aqjA read from 2aqjA/merged-good-all-a2m # found chain 2aqjA in template set Warning: unaligning (T0334)S2 because first residue in template chain is (2aqjA)N2 Warning: unaligning (T0334)V47 because of BadResidue code BAD_PEPTIDE in next template residue (2aqjA)G48 Warning: unaligning (T0334)G48 because of BadResidue code BAD_PEPTIDE at template residue (2aqjA)G48 Warning: unaligning (T0334)A81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)I82 Warning: unaligning (T0334)I82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)I82 Warning: unaligning (T0334)P376 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)D366 Warning: unaligning (T0334)D377 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)D366 Warning: unaligning (T0334)L513 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2aqjA)R517 Warning: unaligning (T0334)L514 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2aqjA)R517 Warning: unaligning (T0334)E515 because last residue in template chain is (2aqjA)D518 T0334 3 :GKIDKILIVGGGTAGWMAASYLGKALQGTADITLLQAPDIPTLG 2aqjA 3 :KPIKNIVIVGGGTAGWMAASYLVRALQQQANITLIESAAIPRIG T0334 49 :EATIPNLQTAFFDFLGIPEDEWMRECNASYKV 2aqjA 49 :EATIPSLQKVFFDFLGIPEREWMPQVNGAFKA T0334 83 :KFINWRTAGEGTSEAREL 2aqjA 83 :KFVNWRKSPDPSRDDHFY T0334 101 :DGGPDHFYHSFGLLKYHEQIPLSHYWFDRSYRGKTV 2aqjA 105 :NVPNCDGVPLTHYWLRKREQGFQQPMEYACYPQPGA T0334 150 :LDANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFATEKLGVRHVE 2aqjA 141 :LDGKLAPCLSDGTRQMSHAWHFDAHLVADFLKRWAVERGVNRVVD T0334 196 :RVEHVQRDANGNIESVRTATGRVFDADLFVDCSGFRGLLINKAMEEPFLDMSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSSRFATEDEAVREFCEMWHLDP 2aqjA 186 :EVVDVRLNNRGYISNLLTKEGRTLEADLFIDCSGMRGLLINQALKEPFIDMSDYLLCDSAVASAVPNDDARDGVEPYTSSIAMNSGWTWKIPMLGRFGSGYVFSSHFTSRDQATADFLKLWGLSD T0334 322 :TQPLNRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 2aqjA 311 :NQPLNQIKFRVGRNKRAWVNNCVSIGLSSCFLEPLESTGIYFIYAALYQLVKHF T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTDTPFWRANK 2aqjA 367 :TSFDPRLSDAFNAEIVHMFDDCRDFVQAHYFTTSRDDTPFWLANR T0334 423 :ELRLADGMQEKIDMYRAGMAINAPASDDA 2aqjA 413 :DLRLSDAIKEKVQRYKAGLPLTTTSFDDS T0334 452 :QLYYGNFEEEFRNFWNNSNYYCVLAGLGLVP 2aqjA 453 :NFWLNGNYYCIFAGLGMLPDRSLPLLQHRPE T0334 483 :DAPSPRLAHMPQATESVDEVFGAVKDRQRN 2aqjA 486 :EKAEAMFASIRREAERLRTSLPTNYDYLRS Number of specific fragments extracted= 11 number of extra gaps= 4 total=2933 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l9cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1l9cA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1l9cA/merged-good-all-a2m.gz for input Trying 1l9cA/merged-good-all-a2m Error: Couldn't open file 1l9cA/merged-good-all-a2m or 1l9cA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p2hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p2hA expands to /projects/compbio/data/pdb/1p2h.pdb.gz 1p2hA:# T0334 read from 1p2hA/merged-good-all-a2m # 1p2hA read from 1p2hA/merged-good-all-a2m # adding 1p2hA to template set # found chain 1p2hA in template set Warning: unaligning (T0334)W87 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)S219 Warning: unaligning (T0334)R88 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)S219 Warning: unaligning (T0334)F127 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)A225 Warning: unaligning (T0334)D128 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)A225 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1p2hA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1p2hA 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1p2hA 178 :DQQ T0334 61 :DFLGI 1p2hA 181 :KAKKI T0334 66 :PEDEWMRECNA 1p2hA 188 :SPELMFEDTMK T0334 77 :SYKVAIKFIN 1p2hA 208 :LVKVLSSHSK T0334 123 :SHYW 1p2hA 220 :VDWM T0334 129 :RSYR 1p2hA 226 :MGAD T0334 144 :YKEPVI 1p2hA 230 :LTDVGM T0334 152 :ANRSPRRL 1p2hA 236 :MGGASVNR T0334 162 :SKVTNYAW 1p2hA 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1p2hA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1p2hA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1p2hA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1p2hA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1p2hA 302 :YWVKADAVILATGGFAK T0334 234 :L 1p2hA 323 :V T0334 236 :NKAM 1p2hA 324 :AKLD T0334 244 :LDMSDHLLNDS 1p2hA 328 :PSLKGFISTNQ T0334 267 :NGVE 1p2hA 339 :PGAV T0334 271 :PFTSAIAMKSGWTWKIPM 1p2hA 350 :ENAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1p2hA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1p2hA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1p2hA 459 :KALTETVARYN T0334 317 :HLDPETQ 1p2hA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1p2hA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1p2hA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1p2hA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 28 number of extra gaps= 2 total=2961 Number of alignments=127 # 1p2hA read from 1p2hA/merged-good-all-a2m # found chain 1p2hA in template set Warning: unaligning (T0334)P66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1p2hA)W176 Warning: unaligning (T0334)E67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1p2hA)W176 Warning: unaligning (T0334)R98 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)A225 Warning: unaligning (T0334)E99 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)A225 Warning: unaligning (T0334)R334 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)H504 Warning: unaligning (T0334)N335 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)H504 T0334 3 :GKID 1p2hA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1p2hA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1p2hA 148 :SGA T0334 33 :DITLLQAPD 1p2hA 151 :KVILIEKEP T0334 42 :IPTL 1p2hA 161 :IGGN T0334 57 :TAFFDFLGI 1p2hA 166 :KLAAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1p2hA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EA 1p2hA 222 :WM T0334 100 :LDGGPDHFYHSFGLL 1p2hA 226 :MGADLTDVGMMGGAS T0334 115 :KYHE 1p2hA 246 :RPTG T0334 152 :AN 1p2hA 251 :AG T0334 172 :DAHLVADFLRRFA 1p2hA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1p2hA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1p2hA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1p2hA 297 :M T0334 216 :GR 1p2hA 299 :KG T0334 218 :VFDADLFVDCSGFRG 1p2hA 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1p2hA 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1p2hA 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1p2hA 359 :MQYIQAHPT T0334 289 :LGR 1p2hA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1p2hA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1p2hA 462 :TETVARYNSL T0334 316 :WHLDP 1p2hA 473 :SSGKD T0334 321 :ETQPLNRIRF 1p2hA 490 :NEGNYYAIEV T0334 336 :R 1p2hA 505 :H T0334 337 :RAWVGNCVSIGTSSCFVEP 1p2hA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1p2hA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 28 number of extra gaps= 3 total=2989 Number of alignments=128 # 1p2hA read from 1p2hA/merged-good-all-a2m # found chain 1p2hA in template set Warning: unaligning (T0334)Y141 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)S219 Warning: unaligning (T0334)A142 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)S219 Warning: unaligning (T0334)P147 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)A225 Warning: unaligning (T0334)V148 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)A225 Warning: unaligning (T0334)R334 because of BadResidue code BAD_PEPTIDE in next template residue (1p2hA)H504 Warning: unaligning (T0334)N335 because of BadResidue code BAD_PEPTIDE at template residue (1p2hA)H504 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1p2hA 126 :TVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDI 1p2hA 148 :SGAKVILIEKEPV T0334 45 :LGVGEATI 1p2hA 161 :IGGNAKLA T0334 69 :EWMRECNASY 1p2hA 178 :DQQKAKKITD T0334 106 :HFYHSFGLLKYHEQIPLSHYWFDRSY 1p2hA 188 :SPELMFEDTMKGGQNINDPALVKVLS T0334 137 :EPFD 1p2hA 214 :SHSK T0334 143 :CYKE 1p2hA 220 :VDWM T0334 149 :ILDANRSPRRLDGSKVTN 1p2hA 226 :MGADLTDVGMMGGASVNR T0334 169 :WHF 1p2hA 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1p2hA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1p2hA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1p2hA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1p2hA 322 :RVAKL T0334 243 :FLDMSDHLLND 1p2hA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1p2hA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1p2hA 477 :DT T0334 324 :PLNRIRFRVG 1p2hA 493 :NYYAIEVTPG T0334 336 :RRA 1p2hA 505 :HTM T0334 339 :WVGNCVSIGTSSCFVEP 1p2hA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1p2hA 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 20 number of extra gaps= 3 total=3009 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ojt/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1ojt/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1ojt/merged-good-all-a2m.gz for input Trying 1ojt/merged-good-all-a2m Error: Couldn't open file 1ojt/merged-good-all-a2m or 1ojt/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fohA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fohA expands to /projects/compbio/data/pdb/1foh.pdb.gz 1fohA:# T0334 read from 1fohA/merged-good-all-a2m # 1fohA read from 1fohA/merged-good-all-a2m # adding 1fohA to template set # found chain 1fohA in template set Warning: unaligning (T0334)S300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fohA)F307 T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 1fohA 7 :YCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAP 1fohA 33 :KPDLKVRIIDKR T0334 41 :DIPTLGVGEATIPNLQTAF 1fohA 46 :TKVYNGQADGLQCRTLESL T0334 61 :DFLGI 1fohA 65 :KNLGL T0334 123 :SHYWFDRSYR 1fohA 70 :ADKILSEAND T0334 136 :VEPF 1fohA 80 :MSTI T0334 141 :YACYKEPVILD 1fohA 88 :PDENGHIRRTD T0334 154 :RSPRRLDGSKVTNYAW 1fohA 99 :RIPDTLPGISRYHQVV T0334 171 :FDAHLVADFLRRFATEKLG 1fohA 115 :LHQGRIERHILDSIAEISD T0334 190 :VRHVED 1fohA 136 :IKVERP T0334 196 :RVEHVQR 1fohA 143 :IPEKMEI T0334 203 :DANGNIESVRTA 1fohA 156 :DPEAYPVTMTLR T0334 216 :G 1fohA 211 :G T0334 217 :RVFDADLFVDCSGFRGLL 1fohA 214 :ETVHCKYVIGCDGGHSWV T0334 236 :NKAMEEPFL 1fohA 232 :RRTLGFEMI T0334 245 :DMSDH 1fohA 243 :QTDYI T0334 253 :DSAVATQVP 1fohA 248 :WGVLDAVPA T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1fohA 257 :SNFPDIRSRCAIHSAESGSIMIIPRENNLVRFYVQL T0334 306 :DEAVREFCEMWHL 1fohA 310 :EVVIANAKKIFHP T0334 322 :TQ 1fohA 323 :YT T0334 324 :PLNRIRFRVGRNRRAWVG 1fohA 332 :WFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 1fohA 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKL T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRT 1fohA 390 :GRAKRDILKTYEEERHAFAQALIDFDHQFSRLFSGR T0334 480 :LVPDAPSPRLAHMPQATESVDEVFGA 1fohA 426 :PAKDVADEMGVSMDVFKEAFVKGNEF Number of specific fragments extracted= 24 number of extra gaps= 0 total=3033 Number of alignments=130 # 1fohA read from 1fohA/merged-good-all-a2m # found chain 1fohA in template set Warning: unaligning (T0334)S300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fohA)F307 T0334 3 :GKID 1fohA 2 :KYSE T0334 7 :KILIVGGGTAGWMAASYLGK 1fohA 9 :DVLIVGAGPAGLMAARVLSE T0334 28 :L 1fohA 29 :Y T0334 29 :QGT 1fohA 34 :PDL T0334 33 :DITLLQAPD 1fohA 37 :KVRIIDKRS T0334 42 :IPTLGVGEATIPNLQTAF 1fohA 47 :KVYNGQADGLQCRTLESL T0334 61 :DFLGIPED 1fohA 65 :KNLGLADK T0334 103 :GPDHFYHSFGLL 1fohA 79 :DMSTIALYNPDE T0334 115 :KYHE 1fohA 92 :GHIR T0334 152 :ANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFATEKLG 1fohA 96 :RTDRIPDTLPGISRYHQVVLHQGRIERHILDSIAEISD T0334 190 :VRHVED 1fohA 136 :IKVERP T0334 196 :RVEHVQR 1fohA 143 :IPEKMEI T0334 203 :DANGNIESVRTA 1fohA 156 :DPEAYPVTMTLR T0334 216 :GR 1fohA 211 :GE T0334 218 :VFDADLFVDCSGFRGLLI 1fohA 215 :TVHCKYVIGCDGGHSWVR T0334 237 :KAMEEPFLDM 1fohA 233 :RTLGFEMIGE T0334 247 :SDHLLND 1fohA 245 :DYIWGVL T0334 254 :SAVATQVPHD 1fohA 253 :AVPASNFPDI T0334 270 :EPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1fohA 263 :RSRCAIHSAESGSIMIIPRENNLVRFYVQL T0334 306 :DEAVREFCEMWHLDP 1fohA 310 :EVVIANAKKIFHPYT T0334 321 :ETQPLNRIRFRVGRNRRAWVG 1fohA 329 :QLDWFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1fohA 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFS 1fohA 389 :TGRAKRDILKTYEEERHAFAQALIDFDHQFSRLF T0334 411 :PRT 1fohA 424 :GRP T0334 427 :ADGMQEKIDMYRAGMAINAP 1fohA 438 :MDVFKEAFVKGNEFASGTAI T0334 481 :VPD 1fohA 458 :NYD Number of specific fragments extracted= 26 number of extra gaps= 0 total=3059 Number of alignments=131 # 1fohA read from 1fohA/merged-good-all-a2m # found chain 1fohA in template set Warning: unaligning (T0334)S300 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1fohA)F307 T0334 4 :KIDKILIVGGGTAGWMAASYLGKAL 1fohA 6 :SYCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAPDIPTL 1fohA 33 :KPDLKVRIIDKRSTKVY T0334 46 :GVGEATIPNLQTAF 1fohA 51 :GQADGLQCRTLESL T0334 61 :DFLGI 1fohA 65 :KNLGL T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTSEARELDG 1fohA 70 :ADKILSEANDMSTIALYNPDENGHIRRTDRIPDTL T0334 161 :GSKVTNYAWHFDAHLVADFLRRFATEKL 1fohA 105 :PGISRYHQVVLHQGRIERHILDSIAEIS T0334 189 :GVRHVEDRVEHVQRDANGN 1fohA 136 :IKVERPLIPEKMEIDSSKA T0334 217 :R 1fohA 208 :K T0334 218 :VFDADLFVDCSGFRGLLIN 1fohA 215 :TVHCKYVIGCDGGHSWVRR T0334 238 :AMEEPFLDMSDHLLNDSAVATQV 1fohA 234 :TLGFEMIGEQTDYIWGVLDAVPA T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1fohA 257 :SNFPDIRSRCAIHSAESGSIMIIPRENNLVRFYVQL T0334 307 :EAVREFCEMWHLDP 1fohA 311 :VVIANAKKIFHPYT T0334 322 :T 1fohA 326 :D T0334 324 :PLNRIRFRVGRNRR 1fohA 332 :WFTAYHIGQRVTEK T0334 338 :AWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1fohA 347 :SKDERVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYF 1fohA 393 :KRDILKTYEEERHAFAQALIDFDHQFSRLFSGR T0334 443 :INAPASDDA 1fohA 426 :PAKDVADEM T0334 452 :QLYYGNFEEEFRNFWNNSNYYCV 1fohA 439 :DVFKEAFVKGNEFASGTAINYDE Number of specific fragments extracted= 18 number of extra gaps= 0 total=3077 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b3mA expands to Error: no filename for 1b3mA 1b3mA expands to Error: no filename for 1b3mA 1b3mA expands to Error: no filename for 1b3mA # T0334 read from 1b3mA/merged-good-all-a2m # 1b3mA read from 1b3mA/merged-good-all-a2m # adding 1b3mA to template set Error: can't find template for 1b3mA or 1b3mA, so skipping it. # 1b3mA read from 1b3mA/merged-good-all-a2m # adding 1b3mA to template set Error: can't find template for 1b3mA or 1b3mA, so skipping it. # 1b3mA read from 1b3mA/merged-good-all-a2m # adding 1b3mA to template set Error: can't find template for 1b3mA or 1b3mA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pbe/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pbe expands to /projects/compbio/data/pdb/1pbe.pdb.gz 1pbe:Warning: there is no chain 1pbe will retry with 1pbeA # T0334 read from 1pbe/merged-good-all-a2m # 1pbe read from 1pbe/merged-good-all-a2m # adding 1pbe to template set # found chain 1pbe in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1pbe)M1 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)G117 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)G117 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)E135 Warning: unaligning (T0334)G206 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)E135 Warning: unaligning (T0334)R331 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S270 Warning: unaligning (T0334)V332 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S270 Warning: unaligning (T0334)F402 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S343 Warning: unaligning (T0334)I403 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S343 Warning: unaligning (T0334)F417 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S360 Warning: unaligning (T0334)W418 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S360 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1pbe 2 :KTQVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPDI 1pbe 24 :AGIDNVILERQTP T0334 43 :PTLGVGEATIPNLQTAF 1pbe 40 :LGRIRAGVLEQGMVDLL T0334 61 :DFLGI 1pbe 57 :REAGV T0334 123 :SHYWFDRSYR 1pbe 62 :DRRMARDGLV T0334 136 :VEPFDYACYKEPVILD 1pbe 72 :HEGVEIAFAGQRRRID T0334 155 :SPRRLDG 1pbe 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFA 1pbe 95 :KTVTVYGQTEVTRDLMEAR T0334 186 :EK 1pbe 114 :EA T0334 190 :VRHVED 1pbe 118 :ATTVYQ T0334 196 :RVEHVQRDA 1pbe 125 :AEVRLHDLQ T0334 207 :N 1pbe 136 :R T0334 209 :ESVRTA 1pbe 137 :PYVTFE T0334 215 :TG 1pbe 144 :DG T0334 217 :RVFDADLFVDCSGFRGLL 1pbe 148 :LRLDCDYIAGCDGFHGIS T0334 236 :NKAMEEPFL 1pbe 166 :RQSIPAERL T0334 245 :DMSDHLLNDSAVAT 1pbe 176 :VFERVYPFGWLGLL T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGR 1pbe 190 :ADTPPVSHELIYANHPRGFALCSQRSAT T0334 292 :FGTGYVYSS 1pbe 219 :SRYYVQVPL T0334 301 :RFATEDEAVREFCEMW 1pbe 232 :EDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRF 1pbe 256 :VTGPSLEKSIAPL T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1pbe 271 :FVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLK T0334 378 :KSLNPVLTARFNREIETMFDDTRD 1pbe 318 :REGRGELLERYSAICLRRIWKAER T0334 404 :QAHFYFSPRTD 1pbe 344 :WWMTSVLHRFP T0334 415 :TP 1pbe 357 :DA T0334 419 :R 1pbe 361 :Q T0334 428 :DGMQEKIDMYR 1pbe 362 :RIQQTELEYYL Number of specific fragments extracted= 27 number of extra gaps= 5 total=3104 Number of alignments=133 # 1pbe read from 1pbe/merged-good-all-a2m # found chain 1pbe in template set Warning: unaligning (T0334)I5 because first residue in template chain is (1pbe)M1 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)G117 Warning: unaligning (T0334)G189 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)G117 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)E135 Warning: unaligning (T0334)G206 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)E135 Warning: unaligning (T0334)R331 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S270 Warning: unaligning (T0334)V332 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S270 Warning: unaligning (T0334)F402 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S343 Warning: unaligning (T0334)I403 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S343 Warning: unaligning (T0334)F417 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S360 Warning: unaligning (T0334)W418 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S360 T0334 6 :D 1pbe 2 :K T0334 7 :KILIVGGGTAGWMAASYLGK 1pbe 4 :QVAIIGAGPSGLLLGQLLHK T0334 29 :QGT 1pbe 24 :AGI T0334 33 :DITLLQAPD 1pbe 27 :DNVILERQT T0334 52 :I 1pbe 36 :P T0334 57 :TAFFDFLGIPE 1pbe 37 :DYVLGRIRAGV T0334 69 :EWMRECNASYKVAIKFINW 1pbe 54 :DLLREAGVDRRMARDGLVH T0334 103 :GPDHFYHSFGLL 1pbe 73 :EGVEIAFAGQRR T0334 115 :KYHE 1pbe 87 :DLKR T0334 152 :ANRSPRRLD 1pbe 92 :SGGKTVTVY T0334 172 :DAHLVADFLRRFA 1pbe 101 :GQTEVTRDLMEAR T0334 186 :EK 1pbe 114 :EA T0334 190 :VRHVED 1pbe 118 :ATTVYQ T0334 196 :RVEHVQRDA 1pbe 125 :AEVRLHDLQ T0334 207 :NIE 1pbe 136 :RPY T0334 211 :VRTA 1pbe 139 :VTFE T0334 215 :TGR 1pbe 144 :DGE T0334 218 :VFDADLFVDCSGFRGLLI 1pbe 149 :RLDCDYIAGCDGFHGISR T0334 237 :KAMEEPFLDM 1pbe 167 :QSIPAERLKV T0334 247 :SDHLLND 1pbe 178 :ERVYPFG T0334 254 :SAVATQVPHDD 1pbe 186 :LGLLADTPPVS T0334 271 :PFTSAIAMKSGWTWKIPM 1pbe 197 :HELIYANHPRGFALCSQR T0334 289 :LGR 1pbe 216 :ATR T0334 292 :FGTGYVYSSRFATEDEAVREFCEMWHLDP 1pbe 223 :VQVPLTEKVEDWSDERFWTELKARLPAEV T0334 321 :ETQPLNRIRF 1pbe 259 :PSLEKSIAPL T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pbe 271 :FVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFDDTRD 1pbe 317 :YREGRGELLERYSAICLRRIWKAER T0334 404 :QAHFYFSPRTDTP 1pbe 344 :WWMTSVLHRFPDT T0334 419 :R 1pbe 361 :Q T0334 508 :DRQRNLLETLPSLHEFLRQ 1pbe 362 :RIQQTELEYYLGSEAGLAT Number of specific fragments extracted= 30 number of extra gaps= 5 total=3134 Number of alignments=134 # 1pbe read from 1pbe/merged-good-all-a2m # found chain 1pbe in template set Warning: unaligning (T0334)K187 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)G117 Warning: unaligning (T0334)L188 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)G117 Warning: unaligning (T0334)A204 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)E135 Warning: unaligning (T0334)N205 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)E135 Warning: unaligning (T0334)R331 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S270 Warning: unaligning (T0334)V332 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S270 Warning: unaligning (T0334)D398 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S343 Warning: unaligning (T0334)T399 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S343 Warning: unaligning (T0334)G429 because of BadResidue code BAD_PEPTIDE in next template residue (1pbe)S360 Warning: unaligning (T0334)M430 because of BadResidue code BAD_PEPTIDE at template residue (1pbe)S360 T0334 7 :KILIVGGGTAGWMAASYLGK 1pbe 4 :QVAIIGAGPSGLLLGQLLHK T0334 30 :GTADITLLQAPD 1pbe 24 :AGIDNVILERQT T0334 43 :PTLGVGE 1pbe 41 :GRIRAGV T0334 51 :TIPNLQTAF 1pbe 48 :LEQGMVDLL T0334 61 :DFLGIP 1pbe 57 :REAGVD T0334 69 :EWMRECNASY 1pbe 63 :RRMARDGLVH T0334 79 :KVAIKF 1pbe 74 :GVEIAF T0334 90 :AGEGTSEA 1pbe 80 :AGQRRRID T0334 158 :RLDGSKV 1pbe 88 :LKRLSGG T0334 166 :NYAWHFDAHLVADFLRRFATE 1pbe 95 :KTVTVYGQTEVTRDLMEAREA T0334 189 :GVRHVEDRVEHVQRD 1pbe 118 :ATTVYQAAEVRLHDL T0334 206 :GNIESVRTATGR 1pbe 136 :RPYVTFERDGER T0334 218 :VFDADLFVDCSGFRGLLIN 1pbe 149 :RLDCDYIAGCDGFHGISRQ T0334 243 :FLDMSDH 1pbe 168 :SIPAERL T0334 250 :LLNDSAVATQV 1pbe 180 :VYPFGWLGLLA T0334 265 :DANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYS 1pbe 191 :DTPPVSHELIYANHPRGFALCSQRSATRSRYYVQV T0334 300 :SRFATEDEAVREFCEMW 1pbe 231 :VEDWSDERFWTELKARL T0334 318 :LDPETQPLNRIRF 1pbe 256 :VTGPSLEKSIAPL T0334 333 :GRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pbe 271 :FVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLL T0334 377 :DKSLNPVLTARFNREIETMFD 1pbe 321 :RGELLERYSAICLRRIWKAER T0334 400 :RDFIQAHFYFSPRT 1pbe 344 :WWMTSVLHRFPDTD T0334 428 :D 1pbe 358 :A T0334 431 :QE 1pbe 361 :QR T0334 505 :AVKDRQRNLLETLPSLHEFLRQQ 1pbe 363 :IQQTELEYYLGSEAGLATIAENY Number of specific fragments extracted= 24 number of extra gaps= 5 total=3158 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zk7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zk7A expands to /projects/compbio/data/pdb/1zk7.pdb.gz 1zk7A:# T0334 read from 1zk7A/merged-good-all-a2m # 1zk7A read from 1zk7A/merged-good-all-a2m # adding 1zk7A to template set # found chain 1zk7A in template set T0334 1 :MSG 1zk7A 1 :MEP T0334 5 :IDKILIVGGGTAGWMAASYLGK 1zk7A 4 :PVQVAVIGSGGAAMAAALKAVE T0334 30 :GTADITLLQAPDIPTLGVGEATIPN 1zk7A 26 :QGAQVTLIERGTIGGTCVNVGCVPS T0334 57 :TAF 1zk7A 51 :KIM T0334 78 :YKVAIKFINWRTAGE 1zk7A 54 :IRAAHIAHLRRESPF T0334 101 :DGGPDHFYHSFGLLKY 1zk7A 69 :DGGIAATVPTIDRSKL T0334 117 :HEQIPLSHYWFDRS 1zk7A 86 :AQQQARVDELRHAK T0334 155 :SPRRLDGS 1zk7A 100 :YEGILGGN T0334 166 :NYAW 1zk7A 108 :PAIT T0334 171 :FDAHLVADFLRRFA 1zk7A 213 :REDPAIGEAVTAAF T0334 186 :EKLGVRHVED 1zk7A 227 :RAEGIEVLEH T0334 196 :RVEHVQRDANG 1zk7A 238 :QASQVAHMDGE T0334 209 :ESVRTATG 1zk7A 249 :FVLTTTHG T0334 218 :VFDADLFVDCSGFRGLL 1zk7A 257 :ELRADKLLVATGRTPNT T0334 236 :NKA 1zk7A 274 :RSL T0334 239 :MEEPFLDMSDHLLNDSAVATQVPH 1zk7A 336 :AALDLTAMPAVVFTDPQVATVGYS T0334 264 :DD 1zk7A 360 :EA T0334 266 :ANGVEPFTSAIAMKS 1zk7A 365 :HDGIETDSRTLTLDN T0334 281 :GWT 1zk7A 391 :GFI T0334 284 :WKIPMLGR 1zk7A 395 :LVIEEGSH T0334 292 :FGTGYVYSSRF 1zk7A 404 :LIGVQAVAPEA T0334 306 :DEAVREFCEMW 1zk7A 415 :GELIQTAALAI T0334 317 :HLDPET 1zk7A 437 :QLFPYL Number of specific fragments extracted= 23 number of extra gaps= 0 total=3181 Number of alignments=136 # 1zk7A read from 1zk7A/merged-good-all-a2m # found chain 1zk7A in template set Warning: unaligning (T0334)G3 because first residue in template chain is (1zk7A)M1 T0334 4 :KID 1zk7A 2 :EPP T0334 7 :KILIVGGGTAGWMAASYLGK 1zk7A 6 :QVAVIGSGGAAMAAALKAVE T0334 29 :QGT 1zk7A 26 :QGA T0334 33 :DITLLQAPDIPTL 1zk7A 29 :QVTLIERGTIGGT T0334 46 :GVGEATIPN 1zk7A 66 :SPFDGGIAA T0334 61 :DFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1zk7A 75 :TVPTIDRSKLLAQQQARVDELRHAKYEGILGGNPA T0334 96 :EARELDGGPDHFYHSFGLL 1zk7A 152 :VPPIPGLKESPYWTSTEAL T0334 115 :KYHEQIPLSHYWFDRSYRG 1zk7A 174 :TIPERLAVIGSSVVALELA T0334 139 :FDYACYKEPVILDANRSPRRL 1zk7A 193 :QAFARLGSKVTVLARNTLFFR T0334 172 :DAHLVADFLRRFA 1zk7A 214 :EDPAIGEAVTAAF T0334 186 :EKLGVRHVED 1zk7A 227 :RAEGIEVLEH T0334 196 :RVEHVQRDANG 1zk7A 238 :QASQVAHMDGE T0334 209 :ESVRTATG 1zk7A 249 :FVLTTTHG T0334 218 :VFDADLFVDCSGFRG 1zk7A 257 :ELRADKLLVATGRTP T0334 233 :LLINKAMEEPFLD 1zk7A 275 :SLALDAAGVTVNA T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1zk7A 288 :QGAIVIDQGMRTSNPNIYAAGDC T0334 270 :EPFTS 1zk7A 366 :DGIET T0334 275 :AIAMK 1zk7A 372 :SRTLT T0334 280 :SGWTWKIPMLGRFGTGYVY 1zk7A 391 :GFIKLVIEEGSHRLIGVQA T0334 338 :AWVG 1zk7A 410 :VAPE T0334 364 :VYAALYQLVKHFPDKSLNPVLT 1zk7A 414 :AGELIQTAALAIRNRMTVQELA T0334 463 :RNFWNNS 1zk7A 436 :DQLFPYL T0334 470 :NYYCVLAGLG 1zk7A 447 :GLKLAAQTFN Number of specific fragments extracted= 23 number of extra gaps= 0 total=3204 Number of alignments=137 # 1zk7A read from 1zk7A/merged-good-all-a2m # found chain 1zk7A in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1zk7A)M1 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1zk7A 2 :EPPVQVAVIGSGGAAMAAALKAVE T0334 30 :GTADITLLQAPDIP 1zk7A 26 :QGAQVTLIERGTIG T0334 49 :E 1zk7A 40 :G T0334 51 :TIPNLQTAFF 1zk7A 53 :MIRAAHIAHL T0334 64 :GIPEDEWMREC 1zk7A 78 :TIDRSKLLAQQ T0334 75 :NASYKVAIKFINWRTAGEGTSEAREL 1zk7A 116 :EARFKDDQSLTVRLNEGGERVVMFDR T0334 101 :DGGPDHF 1zk7A 151 :AVPPIPG T0334 117 :HEQIPLSHYWFDRSYRGKT 1zk7A 158 :LKESPYWTSTEALASDTIP T0334 137 :EPFDYACYKEPVILDANR 1zk7A 184 :SSVVALELAQAFARLGSK T0334 155 :S 1zk7A 206 :A T0334 158 :RLDGSKV 1zk7A 207 :RNTLFFR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1zk7A 214 :EDPAIGEAVTAAFRAEGIEVLEHTQASQVAHMDGE T0334 209 :ESVRTAT 1zk7A 249 :FVLTTTH T0334 217 :RVFDADLFVDCSGF 1zk7A 256 :GELRADKLLVATGR T0334 240 :EEPFLDMSDH 1zk7A 272 :NTRSLALDAA T0334 321 :ETQPLNRIRFRVGR 1zk7A 284 :TVNAQGAIVIDQGM T0334 337 :RAWVGNCVSIGTSSCFVEP 1zk7A 298 :RTSNPNIYAAGDCTDQPQF T0334 361 :IYFVYAALYQLVKHFPDKSL 1zk7A 317 :VYVAAAAGTRAAINMTGGDA Number of specific fragments extracted= 18 number of extra gaps= 0 total=3222 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x31B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1x31B/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1x31B/merged-good-all-a2m.gz for input Trying 1x31B/merged-good-all-a2m Error: Couldn't open file 1x31B/merged-good-all-a2m or 1x31B/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cvjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cvjA expands to /projects/compbio/data/pdb/2cvj.pdb.gz 2cvjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0334 read from 2cvjA/merged-good-all-a2m # 2cvjA read from 2cvjA/merged-good-all-a2m # adding 2cvjA to template set # found chain 2cvjA in template set T0334 6 :DKILIVGGGTAGWMAASYLGK 2cvjA 2 :WDVIVVGGGPSGLSAALFLAR T0334 30 :GTADITLLQAPDIP 2cvjA 23 :AGLKVLVLDGGRSK T0334 62 :FLGI 2cvjA 37 :VKGV T0334 137 :EPFD 2cvjA 41 :SRVP T0334 154 :RSP 2cvjA 45 :NYP T0334 161 :GSKVT 2cvjA 48 :GLLDE T0334 171 :FDAHLVADFLRRFA 2cvjA 53 :PSGEELLRRLEAHA T0334 186 :EKLGVRHVEDRVEHVQRDANG 2cvjA 67 :RRYGAEVRPGVVKGVRDMGGV T0334 209 :ESVRTATG 2cvjA 88 :FEVETEEG T0334 218 :VFDADLFVDCSGFRGLL 2cvjA 96 :VEKAERLLLCTHKDPTL T0334 236 :NKAMEEPFLD 2cvjA 113 :PSLLGLTRRG T0334 249 :H 2cvjA 123 :A T0334 272 :FTSA 2cvjA 124 :YIDT T0334 279 :KSG 2cvjA 128 :DEG T0334 336 :RRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLN 2cvjA 131 :GRTSYPRVYAAGVARGKVPGHAIISAGDGAYVAVHLVSDLRGEPYK Number of specific fragments extracted= 15 number of extra gaps= 0 total=3237 Number of alignments=139 # 2cvjA read from 2cvjA/merged-good-all-a2m # found chain 2cvjA in template set Warning: unaligning (T0334)D6 because first residue in template chain is (2cvjA)M1 T0334 7 :KILIVGGGTAGWMAASYLGK 2cvjA 3 :DVIVVGGGPSGLSAALFLAR T0334 29 :QGT 2cvjA 23 :AGL T0334 33 :DITLLQAP 2cvjA 26 :KVLVLDGG T0334 96 :EARELDG 2cvjA 34 :RSKVKGV T0334 115 :KYHE 2cvjA 42 :RVPN T0334 152 :ANRSPRRL 2cvjA 46 :YPGLLDEP T0334 172 :DAHLVADFLRRFA 2cvjA 54 :SGEELLRRLEAHA T0334 186 :EKLGVRHVEDRVEHVQRDAN 2cvjA 67 :RRYGAEVRPGVVKGVRDMGG T0334 207 :N 2cvjA 87 :V T0334 209 :ESVRTATG 2cvjA 88 :FEVETEEG T0334 218 :VFDADLFVDCSG 2cvjA 96 :VEKAERLLLCTH T0334 231 :RGLLINKAMEEPFL 2cvjA 108 :KDPTLPSLLGLTRR T0334 247 :SDHLLNDSAVA 2cvjA 122 :GAYIDTDEGGR T0334 338 :AWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLN 2cvjA 133 :TSYPRVYAAGVARGKVPGHAIISAGDGAYVAVHLVSDLRGEPYK Number of specific fragments extracted= 14 number of extra gaps= 0 total=3251 Number of alignments=140 # 2cvjA read from 2cvjA/merged-good-all-a2m # found chain 2cvjA in template set T0334 7 :KILIVGGGTAGWMAASYLGK 2cvjA 3 :DVIVVGGGPSGLSAALFLAR T0334 30 :GTADITLLQAPDI 2cvjA 23 :AGLKVLVLDGGRS T0334 61 :DFLGIP 2cvjA 36 :KVKGVS T0334 154 :RSPRRLDGSKVTN 2cvjA 42 :RVPNYPGLLDEPS T0334 173 :AHLVADFLRRFATEKLGVRHVE 2cvjA 55 :GEELLRRLEAHARRYGAEVRPG T0334 196 :RVEHVQRDANG 2cvjA 77 :VVKGVRDMGGV T0334 209 :ESVRTAT 2cvjA 88 :FEVETEE T0334 217 :RVFDADLFVDCSGFRGLLIN 2cvjA 95 :GVEKAERLLLCTHKDPTLPS T0334 238 :AMEEPF 2cvjA 115 :LLGLTR T0334 326 :NRIRFRVGRNRRAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPDKSLN 2cvjA 121 :RGAYIDTDEGGRTSYPRVYAAGVARGKVPGHAIISAGDGAYVAVHLVSDLRGEPYK Number of specific fragments extracted= 10 number of extra gaps= 0 total=3261 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vdc expands to /projects/compbio/data/pdb/1vdc.pdb.gz 1vdc:Warning: there is no chain 1vdc will retry with 1vdcA # T0334 read from 1vdc/merged-good-all-a2m # 1vdc read from 1vdc/merged-good-all-a2m # adding 1vdc to template set # found chain 1vdc in template set Warning: unaligning (T0334)E321 because of BadResidue code BAD_PEPTIDE in next template residue (1vdc)D216 Warning: unaligning (T0334)T322 because of BadResidue code BAD_PEPTIDE at template residue (1vdc)D216 Warning: unaligning (T0334)V506 because last residue in template chain is (1vdc)I316 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1vdc 5 :NTRLCIVGSGPAAHTAAIYAAR T0334 30 :GTADITLLQAPDIPTLGVGEATIP 1vdc 27 :AELKPLLFEGWMANDIAPGGQLTT T0334 144 :YKEPVI 1vdc 46 :TTDVEN T0334 155 :SPRRLDG 1vdc 52 :FPGFPEG T0334 171 :FDAHLVADFLRRFA 1vdc 59 :ILGVELTDKFRKQS T0334 186 :EKLGVRHVEDRVEHVQR 1vdc 73 :ERFGTTIFTETVTKVDF T0334 204 :ANGN 1vdc 90 :SSKP T0334 209 :ESVRTATG 1vdc 94 :FKLFTDSK T0334 218 :VFDADLFVDCSGFR 1vdc 102 :AILADAVILAIGAV T0334 236 :NKAMEEPFLDMSDHLLNDSAV 1vdc 116 :AKRLSFVGSGEVLGGFWNRGI T0334 272 :FTSAIAMKSG 1vdc 133 :SACAVCDGAA T0334 287 :PM 1vdc 141B:PI T0334 289 :LGR 1vdc 144 :RNK T0334 292 :FGT 1vdc 148 :LAV T0334 295 :GYVYSSRFATE 1vdc 172 :YIIHRRDAFRA T0334 306 :DEAVREFCEMW 1vdc 184 :KIMQQRALSNP T0334 319 :DP 1vdc 213 :GE T0334 323 :Q 1vdc 217 :V T0334 324 :PLNRIRFRVG 1vdc 228 :TGDVSDLKVS T0334 339 :WVGNCVSIGTSSCFVEPL 1vdc 277 :SVPGVFAAGDVQDKKYRQ T0334 361 :IYFVYAALYQLV 1vdc 295 :AITAAGTGCMAA T0334 497 :ESVDEVFGA 1vdc 307 :LDAEHYLQE Number of specific fragments extracted= 22 number of extra gaps= 1 total=3283 Number of alignments=142 # 1vdc read from 1vdc/merged-good-all-a2m # found chain 1vdc in template set Warning: unaligning (T0334)G206 because of BadResidue code BAD_PEPTIDE in next template residue (1vdc)D216 Warning: unaligning (T0334)V506 because last residue in template chain is (1vdc)I316 T0334 5 :ID 1vdc 2 :ET T0334 7 :KILIVGGGTAGWMAASYLGK 1vdc 7 :RLCIVGSGPAAHTAAIYAAR T0334 29 :QGT 1vdc 27 :AEL T0334 33 :DITLLQAPDIPTLGVGEATIPN 1vdc 30 :KPLLFEGWMANDIAPGGQLTTT T0334 57 :TAFFDFLGIPED 1vdc 47 :TDVENFPGFPEG T0334 69 :EWMRECNAS 1vdc 70 :KQSERFGTT T0334 96 :EARELDG 1vdc 118 :RLSFVGS T0334 103 :GPDHFYHSFGLL 1vdc 126 :EVLGGFWNRGIS T0334 115 :KYHEQIPLSHYWFDRSYRG 1vdc 143 :FRNKPLAVIGGGDSAMEEA T0334 139 :FDYACYKEPVILD 1vdc 162 :NFLTKYGSKVYII T0334 152 :ANRSPRR 1vdc 176 :RRDAFRA T0334 172 :DAHL 1vdc 183 :SKIM T0334 181 :RRFATEKLGVRHVED 1vdc 187 :QQRALSNPKIDVIWN T0334 196 :RVEHVQRDAN 1vdc 203 :SVVEAYGDGE T0334 207 :NIESVRTAT 1vdc 217 :VLGGLKVKN T0334 216 :GR 1vdc 229 :GD T0334 218 :VFDADLFVDCSGFRG 1vdc 233 :DLKVSGLFFAIGHEP T0334 233 :LLI 1vdc 250 :KFL T0334 247 :SDHLLNDSAVATQVP 1vdc 253 :DGGVELDSDGYVVTK T0334 289 :LGRFG 1vdc 267 :PGTTQ T0334 338 :AWVGNCVSIGTSSCFVEP 1vdc 276 :TSVPGVFAAGDVQDKKYR T0334 360 :GIYFVYAALYQLV 1vdc 294 :QAITAAGTGCMAA T0334 497 :ESVDEVFGA 1vdc 307 :LDAEHYLQE Number of specific fragments extracted= 23 number of extra gaps= 1 total=3306 Number of alignments=143 # 1vdc read from 1vdc/merged-good-all-a2m # found chain 1vdc in template set Warning: unaligning (T0334)K378 because last residue in template chain is (1vdc)I316 T0334 7 :KILIVGGGTAGWMAASYLGK 1vdc 7 :RLCIVGSGPAAHTAAIYAAR T0334 30 :GTADITLLQAPDIPTLGVGEATI 1vdc 27 :AELKPLLFEGWMANDIAPGGQLT T0334 80 :VAIKFINWRTAGEGT 1vdc 45 :TTTDVENFPGFPEGI T0334 172 :DAHLVADFLRRFATEKLGVRHVE 1vdc 60 :LGVELTDKFRKQSERFGTTIFTE T0334 196 :RVEHVQRDANG 1vdc 83 :TVTKVDFSSKP T0334 209 :ESVRTAT 1vdc 94 :FKLFTDS T0334 217 :RVFDADLFVDCSGF 1vdc 101 :KAILADAVILAIGA T0334 256 :VATQVPHDDDANGVEPFTS 1vdc 115 :VAKRLSFVGSGEVLGGFWN T0334 329 :RFRVGRN 1vdc 264 :VTKPGTT T0334 337 :RAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFPD 1vdc 275 :QTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQE Number of specific fragments extracted= 10 number of extra gaps= 0 total=3316 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q1rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q1rA expands to /projects/compbio/data/pdb/1q1r.pdb.gz 1q1rA:# T0334 read from 1q1rA/merged-good-all-a2m # 1q1rA read from 1q1rA/merged-good-all-a2m # adding 1q1rA to template set # found chain 1q1rA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 1q1rA 4 :NDNVVIVGTGLAGVEVAFGLRA T0334 30 :GTA 1q1rA 26 :SGW T0334 33 :DITLLQAPDIPTLGVGEA 1q1rA 31 :NIRLVGDATVIPHHLPPL T0334 55 :LQ 1q1rA 49 :SK T0334 96 :EARELDGGPDHFYHSF 1q1rA 51 :AYLAGKATAESLYLRT T0334 123 :SHYWFDRS 1q1rA 67 :PDAYAAQN T0334 136 :VEPFDYACYKEPVILD 1q1rA 75 :IQLLGGTQVTAINRDR T0334 152 :ANRSPRRLDGSKVTNYAW 1q1rA 114 :PRPLPVASGAVGKANNFR T0334 170 :HFDAHLVADFLRRFA 1q1rA 187 :RVTAPPVSAFYEHLH T0334 186 :EKLGVRHVED 1q1rA 202 :REAGVDIRTG T0334 196 :RVEHVQRDANGN 1q1rA 213 :QVCGFEMSTDQQ T0334 208 :IESVRTATGRVFDADLFVDCSGFRGL 1q1rA 226 :VTAVLCEDGTRLPADLVIAGIGLIPN T0334 235 :INKAMEEPFLD 1q1rA 254 :LASAAGLQVDN T0334 246 :MSDHLLNDSAVATQVPH 1q1rA 276 :DPLIMAVGDCARFHSQL T0334 264 :DD 1q1rA 293 :YD T0334 266 :ANGVEPFTSAIAMKSGWTWKIPMLGR 1q1rA 321 :PRDEAAPWFWSDQYEIGLKMVGLSEG T0334 292 :FGTGYVYSSRFATE 1q1rA 348 :DRIIVRGSLAQPDF T0334 306 :DEAVREFCEMW 1q1rA 380 :PVEFNQSKQII T0334 317 :HLDP 1q1rA 392 :DRLP T0334 335 :NRR 1q1rA 396 :VEP T0334 373 :KHFPD 1q1rA 399 :NLLGD T0334 378 :KSLNPVLTARFNREIET 1q1rA 405 :SVPLKEIIAAAKAELSS Number of specific fragments extracted= 22 number of extra gaps= 0 total=3338 Number of alignments=145 # 1q1rA read from 1q1rA/merged-good-all-a2m # found chain 1q1rA in template set Warning: unaligning (T0334)K4 because first residue in template chain is (1q1rA)N2 T0334 5 :ID 1q1rA 3 :AN T0334 7 :KILIVGGGTAGWMAASYLGK 1q1rA 6 :NVVIVGTGLAGVEVAFGLRA T0334 29 :QGTA 1q1rA 26 :SGWE T0334 33 :DITLLQAPD 1q1rA 31 :NIRLVGDAT T0334 42 :IPTLGVGEATIPNLQTAFFDFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1q1rA 41 :IPHHLPPLSKAYLAGKATAESLYLRTPDAYAAQNIQLLGGTQVTAINRDRQQVI T0334 96 :EARELDG 1q1rA 116 :PLPVASG T0334 103 :GPDHFYHSFGLL 1q1rA 126 :KANNFRYLRTLE T0334 115 :KYHEQIPLSHYWFDRSYRG 1q1rA 147 :IADNRLVVIGGGYIGLEVA T0334 139 :FDYACYKEPVILD 1q1rA 166 :ATAIKANMHVTLL T0334 152 :ANRSPRRLD 1q1rA 180 :TAARVLERV T0334 172 :DAHLVADFLRRFA 1q1rA 189 :TAPPVSAFYEHLH T0334 186 :EKLGVRHVED 1q1rA 202 :REAGVDIRTG T0334 196 :RVEHVQRDANG 1q1rA 213 :QVCGFEMSTDQ T0334 207 :NIESVRTATGRVFDADLFVDCSGFRG 1q1rA 225 :KVTAVLCEDGTRLPADLVIAGIGLIP T0334 233 :LLINKAMEEPF 1q1rA 252 :CELASAAGLQV T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1q1rA 263 :DNGIVINEHMQTSDPLIMAVGDC T0334 270 :EPFTSAIAMKSGWTWKIPM 1q1rA 325 :AAPWFWSDQYEIGLKMVGL T0334 289 :LGRFGTGYVYSSRFATE 1q1rA 345 :EGYDRIIVRGSLAQPDF T0334 306 :DEAVREFCEM 1q1rA 380 :PVEFNQSKQI T0334 316 :WHLDP 1q1rA 391 :TDRLP T0334 321 :ETQP 1q1rA 404 :ESVP T0334 499 :VDEVFGAVKDRQRN 1q1rA 408 :LKEIIAAAKAELSS Number of specific fragments extracted= 22 number of extra gaps= 0 total=3360 Number of alignments=146 # 1q1rA read from 1q1rA/merged-good-all-a2m # found chain 1q1rA in template set T0334 6 :DKILIVGGGTAGWMAASYLGK 1q1rA 150 :NRLVVIGGGYIGLEVAATAIK T0334 30 :GTADITLLQAPDI 1q1rA 171 :ANMHVTLLDTAAR T0334 46 :GVGEATIPNLQTAF 1q1rA 184 :VLERVTAPPVSAFY T0334 181 :RRFATEKLGVRHVEDRVEHVQRDANGN 1q1rA 198 :EHLHREAGVDIRTGTQVCGFEMSTDQQ T0334 208 :IESVRTATGRVFDADLFVDCSGF 1q1rA 226 :VTAVLCEDGTRLPADLVIAGIGL T0334 231 :RGLLI 1q1rA 251 :NCELA T0334 237 :KAMEEP 1q1rA 256 :SAAGLQ T0334 292 :FGTGYVYSSRFA 1q1rA 262 :VDNGIVINEHMQ T0334 338 :AWVGNCVSIGTSSCFVEPLE 1q1rA 274 :TSDPLIMAVGDCARFHSQLY T0334 358 :STGIYFVYAALYQLVKHFPDKSLNPV 1q1rA 299 :IESVPNALEQARKIAAILCGKVPRDE T0334 405 :AHFYFSP 1q1rA 362 :SVFYLQG T0334 425 :RLADGMQEKIDMYRAGMAINAPASDDAQL 1q1rA 378 :NRPVEFNQSKQIITDRLPVEPNLLGDESV T0334 491 :HMPQATESVDEVFGA 1q1rA 407 :PLKEIIAAAKAELSS Number of specific fragments extracted= 13 number of extra gaps= 0 total=3373 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cj2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0334/1cj2A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0334/1cj2A/merged-good-all-a2m.gz for input Trying 1cj2A/merged-good-all-a2m Error: Couldn't open file 1cj2A/merged-good-all-a2m or 1cj2A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q9iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q9iA expands to /projects/compbio/data/pdb/1q9i.pdb.gz 1q9iA:# T0334 read from 1q9iA/merged-good-all-a2m # 1q9iA read from 1q9iA/merged-good-all-a2m # adding 1q9iA to template set # found chain 1q9iA in template set Warning: unaligning (T0334)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0334)T44 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1q9iA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDI 1q9iA 148 :SGAKVILIEKEPV T0334 45 :LGVGEATI 1q9iA 163 :GNAKLAAG T0334 57 :TAF 1q9iA 178 :DQQ T0334 61 :DFLGI 1q9iA 181 :KAKKI T0334 66 :PEDEWMRECNA 1q9iA 188 :SPELMFEDTMK T0334 77 :SYKVAIKFINWR 1q9iA 208 :LVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1q9iA 220 :VDWMTAMGAD T0334 141 :YACYKEPVI 1q9iA 230 :LTDVGMMGG T0334 155 :SPRRL 1q9iA 239 :ASVNR T0334 162 :SKVTNYAW 1q9iA 244 :AHRPTGGC T0334 171 :FDAHLVADFLRRFAT 1q9iA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1q9iA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1q9iA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1q9iA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1q9iA 302 :YWVKADAVILATGGFAK T0334 234 :L 1q9iA 323 :V T0334 236 :NKAM 1q9iA 324 :AKLD T0334 244 :LDMSDHLLNDS 1q9iA 328 :PSLKGFISTNQ T0334 267 :NGVE 1q9iA 339 :PGAV T0334 271 :PFTSAIAMKSGWTWKIPM 1q9iA 350 :ENAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1q9iA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1q9iA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1q9iA 459 :KALTETVARYN T0334 317 :HLDPETQ 1q9iA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1q9iA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1q9iA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1q9iA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 28 number of extra gaps= 1 total=3401 Number of alignments=148 # 1q9iA read from 1q9iA/merged-good-all-a2m # found chain 1q9iA in template set Warning: unaligning (T0334)I42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0334)P43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 Warning: unaligning (T0334)P66 because of BadResidue code BAD_PEPTIDE in next template residue (1q9iA)W176 Warning: unaligning (T0334)E67 because of BadResidue code BAD_PEPTIDE at template residue (1q9iA)W176 T0334 3 :GKID 1q9iA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1q9iA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1q9iA 148 :SGA T0334 33 :DITLLQAPD 1q9iA 151 :KVILIEKEP T0334 44 :TL 1q9iA 163 :GN T0334 59 :FFDFLGI 1q9iA 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1q9iA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1q9iA 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1q9iA 246 :RPTG T0334 152 :AN 1q9iA 251 :CG T0334 172 :DAHLVADFLRRFA 1q9iA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1q9iA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1q9iA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1q9iA 297 :M T0334 216 :GR 1q9iA 299 :KG T0334 218 :VFDADLFVDCSGFRG 1q9iA 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1q9iA 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1q9iA 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1q9iA 359 :MQYIQAHPT T0334 289 :LGR 1q9iA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1q9iA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1q9iA 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1q9iA 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1q9iA 503 :VHHTMG T0334 337 :RAWVGNCVSIGTSSCFVEP 1q9iA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1q9iA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 26 number of extra gaps= 2 total=3427 Number of alignments=149 # 1q9iA read from 1q9iA/merged-good-all-a2m # found chain 1q9iA in template set Warning: unaligning (T0334)L45 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q9iA)G162 Warning: unaligning (T0334)G46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q9iA)G162 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1q9iA 126 :TVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDI 1q9iA 148 :SGAKVILIEKEPV T0334 47 :VGEATI 1q9iA 163 :GNAKLA T0334 53 :P 1q9iA 178 :D T0334 58 :AF 1q9iA 179 :QQ T0334 61 :DFLGIPE 1q9iA 181 :KAKKITD T0334 68 :DEW 1q9iA 189 :PEL T0334 110 :SFGLLKYHEQIPLSHYWFDRSY 1q9iA 192 :MFEDTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVT 1q9iA 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVN T0334 168 :AWHF 1q9iA 243 :RAHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1q9iA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1q9iA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1q9iA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1q9iA 322 :RVAKL T0334 243 :FLDMSDHLLND 1q9iA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1q9iA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1q9iA 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1q9iA 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1q9iA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1q9iA 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 20 number of extra gaps= 1 total=3447 Number of alignments=150 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ebdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ebdA expands to /projects/compbio/data/pdb/1ebd.pdb.gz 1ebdA:# T0334 read from 1ebdA/merged-good-all-a2m # 1ebdA read from 1ebdA/merged-good-all-a2m # adding 1ebdA to template set # found chain 1ebdA in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGKA 1ebdA 8 :IETETLVVGAGPGGYVAAIRAAQL T0334 31 :TADITLLQAPDIPTLGVGEATIPN 1ebdA 32 :GQKVTIVEKGNLGGVCLNVGCIPS T0334 57 :TAF 1ebdA 56 :KAL T0334 66 :PE 1ebdA 84 :DF T0334 75 :NASYKVAIKFINWRTAGE 1ebdA 86 :AKVQEWKASVVKKLTGGV T0334 96 :EARELDGGP 1ebdA 104 :EGLLKGNKV T0334 105 :DHFYHSFGLL 1ebdA 125 :NTVRVVNGDS T0334 129 :RSYR 1ebdA 147 :TGSR T0334 136 :VEPFDYACYKEPVILD 1ebdA 151 :PIELPNFKFSNRILDS T0334 152 :ANRSPRRLDGSKVTNYAW 1ebdA 169 :ALNLGEVPKSLVVIGGGY T0334 170 :HFD 1ebdA 214 :GFE T0334 174 :HLVADFLRRFA 1ebdA 217 :KQMAAIIKKRL T0334 186 :EKLGVRHVED 1ebdA 228 :KKKGVEVVTN T0334 196 :RVEHVQRDANG 1ebdA 239 :LAKGAEEREDG T0334 209 :ESVRTA 1ebdA 250 :VTVTYE T0334 215 :TG 1ebdA 257 :NG T0334 217 :RVFDADLFVDCSGFRGLL 1ebdA 261 :KTIDADYVLVTVGRRPNT T0334 235 :IN 1ebdA 281 :LG T0334 237 :KAMEEPFLD 1ebdA 284 :EQIGIKMTN T0334 247 :SDHLLNDSAVATQV 1ebdA 293 :RGLIEVDQQCRTSV T0334 264 :DD 1ebdA 307 :PN T0334 266 :ANGVEPFTSAIAMKS 1ebdA 370 :DEGIDVIAAKFPFAA T0334 281 :GWTWKIPMLGRFGTGYVY 1ebdA 397 :FLKLVVRKEDGVIIGAQI T0334 299 :SSRFA 1ebdA 416 :GPNAS T0334 307 :EAVREFCEMW 1ebdA 421 :DMIAELGLAI T0334 317 :HL 1ebdA 433 :GM T0334 380 :L 1ebdA 435 :T Number of specific fragments extracted= 27 number of extra gaps= 0 total=3474 Number of alignments=151 # 1ebdA read from 1ebdA/merged-good-all-a2m # found chain 1ebdA in template set T0334 5 :ID 1ebdA 8 :IE T0334 7 :KILIVGGGTAGWMAASYLGK 1ebdA 11 :ETLVVGAGPGGYVAAIRAAQ T0334 29 :QGT 1ebdA 31 :LGQ T0334 33 :DITLLQAPDIPTLGVGEATIPN 1ebdA 34 :KVTIVEKGNLGGVCLNVGCIPS T0334 57 :TAF 1ebdA 56 :KAL T0334 82 :IKFINWRTAGEGTS 1ebdA 59 :ISASHRYEQAKHSE T0334 96 :EARELDG 1ebdA 151 :PIELPNF T0334 103 :GPDHFYHSFGLL 1ebdA 159 :FSNRILDSTGAL T0334 115 :KYHEQIPLSHYWFDRSYRG 1ebdA 174 :EVPKSLVVIGGGYIGIELG T0334 139 :FDYACYKEPVILD 1ebdA 193 :TAYANFGTKVTIL T0334 152 :ANRSPRRL 1ebdA 207 :GAGEILSG T0334 172 :DAHLVADFLRRFA 1ebdA 215 :FEKQMAAIIKKRL T0334 186 :EKLGVRHVED 1ebdA 228 :KKKGVEVVTN T0334 196 :RVEHVQRDANG 1ebdA 239 :LAKGAEEREDG T0334 209 :ESVRTA 1ebdA 250 :VTVTYE T0334 215 :TGR 1ebdA 257 :NGE T0334 218 :VFDADLFVDCSGFRG 1ebdA 262 :TIDADYVLVTVGRRP T0334 233 :LLINKAMEEPFLD 1ebdA 280 :ELGLEQIGIKMTN T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1ebdA 293 :RGLIEVDQQCRTSVPNIFAIGDI T0334 280 :SGWTWKIPM 1ebdA 395 :DGFLKLVVR T0334 289 :LGRFGTGYVY 1ebdA 405 :EDGVIIGAQI T0334 346 :IGTS 1ebdA 415 :IGPN T0334 364 :VYAALYQLVKHFPDKSLNPVLTA 1ebdA 419 :ASDMIAELGLAIEAGMTAEDIAL Number of specific fragments extracted= 23 number of extra gaps= 0 total=3497 Number of alignments=152 # 1ebdA read from 1ebdA/merged-good-all-a2m # found chain 1ebdA in template set T0334 5 :IDKILIVGGGTAGWMAASYLGK 1ebdA 176 :PKSLVVIGGGYIGIELGTAYAN T0334 30 :GTADITLLQAPDI 1ebdA 198 :FGTKVTILEGAGE T0334 45 :LG 1ebdA 211 :IL T0334 63 :LGIP 1ebdA 213 :SGFE T0334 174 :HLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRTATGR 1ebdA 217 :KQMAAIIKKRLKKKGVEVVTNALAKGAEEREDGVTVTYEANGET T0334 218 :VFDADLFVDCSGF 1ebdA 262 :TIDADYVLVTVGR T0334 260 :VPHDDDAN 1ebdA 275 :RPNTDELG T0334 316 :WHLDP 1ebdA 283 :LEQIG T0334 321 :ETQPLNRIRFRVGRN 1ebdA 289 :KMTNRGLIEVDQQCR T0334 338 :AWVGNCVSIGTSSCFV 1ebdA 304 :TSVPNIFAIGDIVPGP T0334 361 :IYFVYAALYQLVKHFPDKS 1ebdA 322 :AHKASYEGKVAAEAIAGHP Number of specific fragments extracted= 11 number of extra gaps= 0 total=3508 Number of alignments=153 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e39A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e39A expands to /projects/compbio/data/pdb/1e39.pdb.gz 1e39A:# T0334 read from 1e39A/merged-good-all-a2m # 1e39A read from 1e39A/merged-good-all-a2m # adding 1e39A to template set # found chain 1e39A in template set Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)V289 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1e39A 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1e39A 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1e39A 178 :DQQ T0334 61 :DFLGI 1e39A 181 :KAKKI T0334 66 :PEDEWMREC 1e39A 188 :SPELMFEDT T0334 75 :NASYKVAIKFINWR 1e39A 206 :PALVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1e39A 220 :VDWMTAMGAD T0334 144 :YKEPVI 1e39A 230 :LTDVGM T0334 152 :ANRSPRRL 1e39A 236 :MGGASVNR T0334 162 :SKVTNYAW 1e39A 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1e39A 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1e39A 267 :KRNIDLRMN T0334 196 :RVEHVQRDANG 1e39A 277 :RGIEVLKDDKG T0334 209 :ESVRTA 1e39A 290 :KGILVK T0334 215 :TG 1e39A 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1e39A 302 :YWVKADAVILATGGFAK T0334 234 :L 1e39A 323 :V T0334 236 :NKAM 1e39A 324 :AKLD T0334 244 :LDMSDHLLNDS 1e39A 328 :PSLKGFISTNQ T0334 267 :NGVE 1e39A 339 :PGAV T0334 273 :TSAIAMKSGWTWKIPM 1e39A 352 :AGGALKDMQYIQAAPT T0334 289 :LGRFGT 1e39A 371 :KGGVMV T0334 295 :GYVYSSRFATE 1e39A 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1e39A 462 :TETVARYNSLV T0334 317 :HLDPETQ 1e39A 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1e39A 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1e39A 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1e39A 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 28 number of extra gaps= 1 total=3536 Number of alignments=154 # 1e39A read from 1e39A/merged-good-all-a2m # found chain 1e39A in template set Warning: unaligning (T0334)P66 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)W176 Warning: unaligning (T0334)E67 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)W176 Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)V289 T0334 3 :GKID 1e39A 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1e39A 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1e39A 148 :SGA T0334 33 :DITLLQAPD 1e39A 151 :KVILIEKEP T0334 42 :IPTL 1e39A 161 :IGGN T0334 59 :FFDFLGI 1e39A 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1e39A 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1e39A 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1e39A 246 :RPTG T0334 152 :AN 1e39A 251 :AG T0334 172 :DAHLVADFLRRFA 1e39A 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1e39A 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANG 1e39A 277 :RGIEVLKDDKG T0334 209 :ESVRTA 1e39A 290 :KGILVK T0334 215 :T 1e39A 297 :M T0334 216 :GR 1e39A 299 :KG T0334 218 :VFDADLFVDCSGFRG 1e39A 303 :WVKADAVILATGGFA T0334 233 :LLINKAM 1e39A 321 :ERVAKLD T0334 264 :DDANGVEPFTSAIAMK 1e39A 328 :PSLKGFISTNQPGAVG T0334 280 :SGWTWKIPM 1e39A 359 :MQYIQAAPT T0334 289 :LGR 1e39A 371 :KGG T0334 292 :FGTGYVYSSRFATE 1e39A 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1e39A 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1e39A 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1e39A 503 :VHHTMG T0334 337 :RAWVGNCVSIGTSSCFVEP 1e39A 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1e39A 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 27 number of extra gaps= 2 total=3563 Number of alignments=155 # 1e39A read from 1e39A/merged-good-all-a2m # found chain 1e39A in template set Warning: unaligning (T0334)N207 because of BadResidue code BAD_PEPTIDE in next template residue (1e39A)V289 Warning: unaligning (T0334)I208 because of BadResidue code BAD_PEPTIDE at template residue (1e39A)V289 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1e39A 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPD 1e39A 148 :SGAKVILIEKEP T0334 44 :TLGVGEATI 1e39A 160 :VIGGNAKLA T0334 57 :TAF 1e39A 178 :DQQ T0334 61 :DFLGI 1e39A 181 :KAKKI T0334 66 :PEDE 1e39A 188 :SPEL T0334 110 :SFGLLKYHEQIPLSHYWFDRSY 1e39A 192 :MFEDTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVTN 1e39A 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVNR T0334 169 :WHF 1e39A 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANG 1e39A 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKG T0334 209 :ESVRT 1e39A 290 :KGILV T0334 214 :ATGR 1e39A 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1e39A 303 :WVKADAVILATGGFA T0334 233 :LLINK 1e39A 322 :RVAKL T0334 243 :FLDMSDHLLND 1e39A 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1e39A 463 :ETVARYNSLVSSGK T0334 322 :TQ 1e39A 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1e39A 493 :NYYAIEVTPGVHHTM T0334 339 :WVGNCVSIGTSSCFVEP 1e39A 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1e39A 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 20 number of extra gaps= 1 total=3583 Number of alignments=156 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gv4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gv4A expands to /projects/compbio/data/pdb/1gv4.pdb.gz 1gv4A:# T0334 read from 1gv4A/merged-good-all-a2m # 1gv4A read from 1gv4A/merged-good-all-a2m # adding 1gv4A to template set # found chain 1gv4A in template set T0334 2 :SGKIDKILIVGGGTAGWMAASYLGK 1gv4A 127 :APSHVPFLLIGGGTAAFAAARSIRA T0334 28 :LQGTADITLLQAPDIPTLGVGEATI 1gv4A 152 :RDPGARVLIVSEDPELPYMRPPLSK T0334 61 :DFLGIPEDEW 1gv4A 177 :ELWFSDDPNV T0334 127 :FDR 1gv4A 187 :TKT T0334 136 :VE 1gv4A 190 :LQ T0334 141 :YACYKEPVILDANRSPRR 1gv4A 192 :FRQWNGKERSIYFQPPSF T0334 159 :LDGSKVTNYAW 1gv4A 213 :AQDLPNIENGG T0334 170 :HFD 1gv4A 342 :ILP T0334 174 :HLVADFLRRFA 1gv4A 345 :QYLSNWTMEKV T0334 186 :EKLGVRHVED 1gv4A 356 :KREGVKVMPN T0334 196 :RVEHVQRDANG 1gv4A 367 :IVQSVGVSGGR T0334 209 :ESVRTATGRVFDADLFVDCSGFRGLL 1gv4A 378 :LLIKLKDGRKVETDHIVTAVGLEPNV T0334 235 :INKAMEEPFLDMSDH 1gv4A 405 :LAKTGGLEIDSDFGG T0334 250 :LLNDSAVAT 1gv4A 426 :LQARSNIWV T0334 266 :ANGVE 1gv4A 472 :AKPYW T0334 271 :PFTSAIA 1gv4A 478 :QSMFWSD T0334 278 :MKSGWTWKIPM 1gv4A 486 :GPDVGYEAIGL T0334 289 :LGR 1gv4A 499 :SSL T0334 292 :FGTGYVYSSRFATEDEAVREF 1gv4A 503 :TVGVFAKATAQDNPKSATEQS T0334 313 :CEMW 1gv4A 529 :SESE T0334 317 :HLDPETQPLNRIRFRVGRNRRAWV 1gv4A 550 :PQVPVEGEDYGKGVIFYLRDKVVV T0334 342 :NCVSIG 1gv4A 574 :GIVLWN T0334 361 :IYFVYAALYQ 1gv4A 584 :MPIARKIIKD Number of specific fragments extracted= 23 number of extra gaps= 0 total=3606 Number of alignments=157 # 1gv4A read from 1gv4A/merged-good-all-a2m # found chain 1gv4A in template set T0334 3 :GKID 1gv4A 127 :APSH T0334 7 :KILIVGGGTAGWMAASYLGK 1gv4A 132 :PFLLIGGGTAAFAAARSIRA T0334 28 :L 1gv4A 152 :R T0334 29 :QGT 1gv4A 154 :PGA T0334 33 :DITLLQAPD 1gv4A 157 :RVLIVSEDP T0334 42 :IPTLGVG 1gv4A 167 :LPYMRPP T0334 57 :TAF 1gv4A 174 :LSK T0334 61 :DFLGIPEDEWMRECNAS 1gv4A 177 :ELWFSDDPNVTKTLQFR T0334 78 :YKVAIKFINWRTAGEGTS 1gv4A 195 :WNGKERSIYFQPPSFYVS T0334 96 :EARELDG 1gv4A 215 :DLPNIEN T0334 123 :SHYWFDRSYRGKTVEP 1gv4A 222 :GGVAVLTGKKVVHLDV T0334 139 :FDYACYKEPVILD 1gv4A 320 :RKSQASGIEVIQL T0334 152 :ANRSPRRLD 1gv4A 334 :PEKGNMGKI T0334 172 :DAHLVADFLRRFA 1gv4A 343 :LPQYLSNWTMEKV T0334 186 :EKLGVRHVED 1gv4A 356 :KREGVKVMPN T0334 196 :RVEHVQRDAN 1gv4A 367 :IVQSVGVSGG T0334 207 :NIE 1gv4A 377 :RLL T0334 211 :VRTATGRVFDADLFVDCSGFRG 1gv4A 380 :IKLKDGRKVETDHIVTAVGLEP T0334 233 :LLINKAMEEPFLDMSDHLLNDSAV 1gv4A 403 :VELAKTGGLEIDSDFGGFRVNAEL T0334 338 :AWVGNCVSIGTSSCF 1gv4A 427 :QARSNIWVAGDAACF T0334 363 :FVYAALYQLVKHFPDKSLN 1gv4A 456 :HAVVSGRLAGENMTGAAKP Number of specific fragments extracted= 21 number of extra gaps= 0 total=3627 Number of alignments=158 # 1gv4A read from 1gv4A/merged-good-all-a2m # found chain 1gv4A in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGKAL 1gv4A 298 :EVKSITVIGGGFLGSELACALGRKS T0334 29 :QGTADITLLQAPDI 1gv4A 324 :ASGIEVIQLFPEKG T0334 46 :GVGEATIPNLQTAF 1gv4A 338 :NMGKILPQYLSNWT T0334 181 :RRFATEKLGVRHVEDRVEHVQRDANG 1gv4A 352 :MEKVKREGVKVMPNAIVQSVGVSGGR T0334 209 :ESVRTATGRVFDADLFVDCSGF 1gv4A 378 :LLIKLKDGRKVETDHIVTAVGL T0334 235 :INKAMEEPFLDMSDHLL 1gv4A 405 :LAKTGGLEIDSDFGGFR T0334 260 :V 1gv4A 422 :V T0334 300 :SRFA 1gv4A 423 :NAEL T0334 338 :AWVGNCVSIGTSSCFVE 1gv4A 427 :QARSNIWVAGDAACFYD T0334 358 :STGIYFVYAALYQLVKHFPDKSL 1gv4A 451 :VEHHDHAVVSGRLAGENMTGAAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=3637 Number of alignments=159 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f8rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f8rA expands to /projects/compbio/data/pdb/1f8r.pdb.gz 1f8rA:# T0334 read from 1f8rA/merged-good-all-a2m # 1f8rA read from 1f8rA/merged-good-all-a2m # adding 1f8rA to template set # found chain 1f8rA in template set T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1f8rA 31 :SNPKHVVIVGAGMAGLSAAYVLAG T0334 30 :GTADITLLQAP 1f8rA 55 :AGHQVTVLEAS T0334 41 :DI 1f8rA 67 :RP T0334 45 :LGVGEATIPNLQTAF 1f8rA 88 :PMRLPEKHRIVREYI T0334 61 :DFLGI 1f8rA 103 :RKFDL T0334 96 :EARELDGGPDHFYHSFG 1f8rA 108 :RLNEFSQENDNAWYFIK T0334 123 :SHYWFDR 1f8rA 130 :VGEVKKD T0334 141 :YACYKEPVI 1f8rA 137 :PGLLKYPVK T0334 152 :ANRS 1f8rA 146 :PSEA T0334 173 :AHLVADFLRRFA 1f8rA 240 :MDKLPTAMYRDI T0334 186 :EKL 1f8rA 252 :QDK T0334 192 :HVED 1f8rA 255 :VHFN T0334 196 :RVEHVQRDANG 1f8rA 260 :QVIKIQQNDQK T0334 209 :ESVRTA 1f8rA 271 :VTVVYE T0334 215 :TG 1f8rA 279 :SK T0334 217 :RVFDADLFVDCS 1f8rA 283 :PSVTADYVIVCT T0334 231 :RGLL 1f8rA 295 :TSRA T0334 236 :NKA 1f8rA 299 :VRL T0334 239 :MEEPFLDM 1f8rA 304 :FNPPLLPK T0334 250 :LLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPM 1f8rA 321 :YRSGTKIFLTCTTKFWEDDGIHGGKSTTDLPSRFIYYPN T0334 289 :LGR 1f8rA 363 :TNG T0334 292 :FGTGYVYSSRFATE 1f8rA 367 :GVIIAYGIGDDANF T0334 306 :DEAVREFCEMW 1f8rA 387 :KDCADIVFNDL T0334 317 :HLDPETQ 1f8rA 402 :QLPKKDI T0334 328 :IRFRVG 1f8rA 413 :YPSVIQ T0334 337 :RA 1f8rA 419 :KW T0334 339 :WVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKH 1f8rA 448 :SQGRIYFAGEYTAQAHGWIDSTIKSGLRAARDVNLA Number of specific fragments extracted= 27 number of extra gaps= 0 total=3664 Number of alignments=160 # 1f8rA read from 1f8rA/merged-good-all-a2m # found chain 1f8rA in template set T0334 3 :GKID 1f8rA 30 :TSNP T0334 7 :KILIVGGGTAGWMAASYLGK 1f8rA 35 :HVVIVGAGMAGLSAAYVLAG T0334 29 :QGT 1f8rA 55 :AGH T0334 33 :DITLLQAPD 1f8rA 58 :QVTVLEASE T0334 42 :IPTL 1f8rA 68 :PGGR T0334 69 :EWMRECNAS 1f8rA 100 :EYIRKFDLR T0334 96 :EARELDGGPDHFYHSFGLL 1f8rA 109 :LNEFSQENDNAWYFIKNIR T0334 115 :KYHE 1f8rA 136 :DPGL T0334 152 :ANRSPRRLDGSKVTNYAWHF 1f8rA 141 :KYPVKPSEAGKSAGQLYEES T0334 172 :DAHLVADFLRRFA 1f8rA 239 :GMDKLPTAMYRDI T0334 186 :EK 1f8rA 252 :QD T0334 191 :RHVED 1f8rA 254 :KVHFN T0334 196 :RVEHVQRDANG 1f8rA 260 :QVIKIQQNDQK T0334 209 :ESVRTA 1f8rA 271 :VTVVYE T0334 215 :TGR 1f8rA 279 :SKE T0334 218 :VFDADLFVDCS 1f8rA 284 :SVTADYVIVCT T0334 231 :RGLLI 1f8rA 295 :TSRAV T0334 237 :KAMEEPFLDM 1f8rA 300 :RLIKFNPPLL T0334 247 :SDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPM 1f8rA 319 :VHYRSGTKIFLTCTTKFWEDDGIHGGKSTTDLPSRFIYYPNH T0334 289 :LGRFGTGYVYSSRFATE 1f8rA 364 :NGVGVIIAYGIGDDANF T0334 306 :DEAVREFCEM 1f8rA 387 :KDCADIVFND T0334 316 :WHLDP 1f8rA 400 :IHQLP T0334 321 :ETQPLNRIRF 1f8rA 411 :FCYPSVIQKW T0334 331 :R 1f8rA 426 :A T0334 337 :RAWVGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKH 1f8rA 446 :TASQGRIYFAGEYTAQAHGWIDSTIKSGLRAARDVNLA Number of specific fragments extracted= 25 number of extra gaps= 0 total=3689 Number of alignments=161 # 1f8rA read from 1f8rA/merged-good-all-a2m # found chain 1f8rA in template set Warning: unaligning (T0334)D377 because last residue in template chain is (1f8rA)N486 T0334 3 :GKIDKILIVGGGTAGWMAASYLGK 1f8rA 31 :SNPKHVVIVGAGMAGLSAAYVLAG T0334 30 :GTADITLLQAPDIPT 1f8rA 55 :AGHQVTVLEASERPG T0334 45 :LGVGEATI 1f8rA 84 :ANLGPMRL T0334 53 :PNLQTAFFDFLGIPE 1f8rA 95 :HRIVREYIRKFDLRL T0334 73 :ECNASYKVAIKFINWRTA 1f8rA 111 :EFSQENDNAWYFIKNIRK T0334 91 :GEGTSEARELDGGPDHFYHSFGLLKYHEQIPLSHYWFDRSYRGKTVEPFDYACYKEPVILDANRSPRRLDGSKVTNYAWHFDAHLVADF 1f8rA 135 :KDPGLLKYPVKPSEAGKSAGQLYEESLGKVVEELKRTNCSYILNKYDTYSTKEYLIKEGDLSPGAVDMIGDLLNEDSGYYVSFIESLKH T0334 180 :LRRFATEKLG 1f8rA 243 :LPTAMYRDIQ T0334 191 :RHVEDRVEHVQRDANGNIESVRTATGR 1f8rA 255 :VHFNAQVIKIQQNDQKVTVVYETLSKE T0334 218 :VFDADLFVDCSGFRG 1f8rA 284 :SVTADYVIVCTTSRA T0334 238 :AMEEPFLD 1f8rA 299 :VRLIKFNP T0334 246 :MSDHLLNDSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGR 1f8rA 317 :RSVHYRSGTKIFLTCTTKFWEDDGIHGGKSTTDLPSRFIYYPNHNF T0334 292 :FGTGYVYSS 1f8rA 366 :VGVIIAYGI T0334 301 :RFATEDEAVREFCEMWHLDPETQ 1f8rA 382 :QALDFKDCADIVFNDLSLIHQLP T0334 324 :PLNRIRFRVGRNRRAW 1f8rA 427 :MGGITTFTPYQFQHFS T0334 340 :VGNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1f8rA 449 :QGRIYFAGEYTAQAHGWIDSTIKSGLRAARDVNLASE Number of specific fragments extracted= 15 number of extra gaps= 0 total=3704 Number of alignments=162 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvl/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lvl expands to /projects/compbio/data/pdb/1lvl.pdb.gz 1lvl:Warning: there is no chain 1lvl will retry with 1lvlA # T0334 read from 1lvl/merged-good-all-a2m # 1lvl read from 1lvl/merged-good-all-a2m # adding 1lvl to template set # found chain 1lvl in template set Warning: unaligning (T0334)N166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lvl)P157 Warning: unaligning (T0334)Y167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lvl)P157 Warning: unaligning (T0334)T213 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)G248 Warning: unaligning (T0334)A214 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)G248 Warning: unaligning (T0334)R217 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)L253 Warning: unaligning (T0334)K279 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)A375 Warning: unaligning (T0334)S280 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)A375 T0334 2 :SGKIDKILIVGGGTAGWMAASYLGKA 1lvl 2 :QTIQTTLLIIGGGPGGYVAAIRAGQL T0334 31 :TADITLLQAPDIPTLGVGEATIPN 1lvl 28 :GIPTVLVEGQALGGTCLNIGCIPS T0334 57 :TAF 1lvl 52 :KAL T0334 64 :GI 1lvl 81 :RL T0334 73 :ECNASYKVAIKFINWRTAGE 1lvl 83 :DIGQSVAWKDGIVDRLTTGV T0334 123 :SHYWFDRSYR 1lvl 103 :AALLKKHGVK T0334 142 :ACYKEPVILD 1lvl 113 :VVHGWAKVLD T0334 152 :ANRSPRRLDGSKVT 1lvl 142 :TGSSSVELPMLPLG T0334 168 :AW 1lvl 158 :VI T0334 170 :HFDAHLVADFLRRFA 1lvl 208 :PTYDSELTAPVAESL T0334 186 :EKLGVRHVED 1lvl 223 :KKLGIALHLG T0334 196 :RVEHV 1lvl 234 :SVEGY T0334 204 :ANG 1lvl 239 :ENG T0334 208 :IESVR 1lvl 242 :CLLAN T0334 215 :TG 1lvl 249 :KG T0334 218 :VFDADLFVDCSGFRGLL 1lvl 254 :RLEADRVLVAVGRRPRT T0334 239 :MEEPFLDMSDHLLN 1lvl 328 :AGKARRFEPAAIAA T0334 253 :DSAVAT 1lvl 347 :PEVVVV T0334 260 :VPHDDDA 1lvl 353 :GKTPEQA T0334 267 :NGVEPFTSAIAM 1lvl 362 :QGLDCIVAQFPF T0334 281 :GWTWKIPMLGR 1lvl 387 :GFVRVVARRDN T0334 292 :FGTGYVY 1lvl 399 :LILGWQA T0334 299 :SSRFA 1lvl 407 :GVAVS T0334 307 :EAVREFCEMW 1lvl 412 :ELSTAFAQSL T0334 317 :HLD 1lvl 432 :GTI Number of specific fragments extracted= 25 number of extra gaps= 4 total=3729 Number of alignments=163 # 1lvl read from 1lvl/merged-good-all-a2m # found chain 1lvl in template set Warning: unaligning (T0334)D105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1lvl)P157 Warning: unaligning (T0334)H106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1lvl)P157 Warning: unaligning (T0334)T215 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)G248 Warning: unaligning (T0334)G216 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)G248 T0334 3 :GKID 1lvl 2 :QTIQ T0334 7 :KILIVGGGTAGWMAASYLGK 1lvl 7 :TLLIIGGGPGGYVAAIRAGQ T0334 29 :QGT 1lvl 27 :LGI T0334 33 :DITLLQAPDIPTL 1lvl 30 :PTVLVEGQALGGT T0334 52 :IP 1lvl 76 :SV T0334 61 :DFLGIPEDEWMRECNASYKVAIKFINWRTAGEGTS 1lvl 78 :ASPRLDIGQSVAWKDGIVDRLTTGVAALLKKHGVK T0334 96 :EARELDG 1lvl 148 :ELPMLPL T0334 104 :P 1lvl 155 :G T0334 107 :FYHSFGLL 1lvl 158 :VISSTEAL T0334 115 :KYHEQIPLSHYWFDRSYRG 1lvl 169 :ALPQHLVVVGGGYIGLELG T0334 139 :FDYACYKEPVILD 1lvl 188 :IAYRKLGAQVSVV T0334 152 :ANRSPRRL 1lvl 202 :ARERILPT T0334 172 :DAHLVADFLRRFA 1lvl 210 :YDSELTAPVAESL T0334 186 :EKLGVRHVED 1lvl 223 :KKLGIALHLG T0334 196 :RVEHV 1lvl 234 :SVEGY T0334 203 :DANG 1lvl 239 :ENGC T0334 211 :VRTA 1lvl 243 :LLAN T0334 217 :R 1lvl 249 :K T0334 218 :VFDADLFVDCSGFRG 1lvl 254 :RLEADRVLVAVGRRP T0334 233 :LLINKAMEEPFL 1lvl 272 :GFNLECLDLKMN T0334 247 :SDHLLNDSAVATQVPHDDDANGV 1lvl 284 :GAAIAIDERCQTSMHNVWAIGDV Number of specific fragments extracted= 21 number of extra gaps= 2 total=3750 Number of alignments=164 # 1lvl read from 1lvl/merged-good-all-a2m # found chain 1lvl in template set Warning: unaligning (T0334)T213 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)G248 Warning: unaligning (T0334)A214 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)G248 Warning: unaligning (T0334)C351 because of BadResidue code BAD_PEPTIDE in next template residue (1lvl)E309 Warning: unaligning (T0334)E354 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)E309 Warning: unaligning (T0334)P355 because of BadResidue code BAD_PEPTIDE at template residue (1lvl)P310 T0334 5 :IDKILIVGGGTAGWMAASYLGK 1lvl 171 :PQHLVVVGGGYIGLELGIAYRK T0334 30 :GTADITLLQAPDI 1lvl 193 :LGAQVSVVEARER T0334 51 :TI 1lvl 206 :IL T0334 63 :LGIPE 1lvl 208 :PTYDS T0334 175 :LVADFLRRFATEKLGVRHVEDRVEHVQ 1lvl 213 :ELTAPVAESLKKLGIALHLGHSVEGYE T0334 205 :NG 1lvl 240 :NG T0334 208 :IESVR 1lvl 242 :CLLAN T0334 215 :TGR 1lvl 249 :KGG T0334 218 :VFDADLFVDCSGF 1lvl 254 :RLEADRVLVAVGR T0334 258 :TQV 1lvl 267 :RPR T0334 264 :DDANGVE 1lvl 270 :TKGFNLE T0334 322 :TQPLNRIRF 1lvl 277 :CLDLKMNGA T0334 331 :RVGRNRRAWVGNCVSIGTSS 1lvl 288 :AIDERCQTSMHNVWAIGDVA T0334 356 :LE 1lvl 311 :ML T0334 361 :IYFVYAALYQLVKHFPDKSLN 1lvl 313 :AHRAMAQGEMVAEIIAGKARR Number of specific fragments extracted= 15 number of extra gaps= 2 total=3765 Number of alignments=165 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pn0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1pn0A expands to /projects/compbio/data/pdb/1pn0.pdb.gz 1pn0A:# T0334 read from 1pn0A/merged-good-all-a2m # 1pn0A read from 1pn0A/merged-good-all-a2m # adding 1pn0A to template set # found chain 1pn0A in template set Warning: unaligning (T0334)S300 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pn0A)T305 T0334 4 :KIDKILIVGGGTAGWMAASYLGKAL 1pn0A 6 :SYCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAP 1pn0A 33 :KPDLKVRIIDKR T0334 41 :DIPTLGVGEATIPNLQTAF 1pn0A 46 :TKVYNGQADGLQCRTLESL T0334 61 :DFLGI 1pn0A 65 :KNLGL T0334 123 :SHYWFDRSYR 1pn0A 70 :ADKILSEAND T0334 136 :VEP 1pn0A 80 :MST T0334 141 :YACYKEPVILD 1pn0A 88 :PDENGHIRRTD T0334 154 :RSPRRLDGSKVTNYAW 1pn0A 99 :RIPDTLPGISRYHQVV T0334 171 :FDAHLVADFLRRFATEKLG 1pn0A 115 :LHQGRIERRILDSIAEISD T0334 190 :VRHVED 1pn0A 136 :IKVERP T0334 196 :RVEHVQR 1pn0A 143 :IPEKMEI T0334 203 :DANGNIESVRTA 1pn0A 156 :DPEAYPVTMTLR T0334 216 :G 1pn0A 211 :G T0334 217 :RVFDADLFVDCSGFRGLL 1pn0A 214 :ETVHCKYVIGCDGGHSWV T0334 236 :NKAMEEPFLDMSDH 1pn0A 232 :RRTLGFEMIGEQTD T0334 253 :DSAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPMLGR 1pn0A 246 :YIWGVLDAVPASNFPDIRSRCAIHSAESGSIMIIPRENN T0334 292 :FGTGYVYS 1pn0A 286 :VRFYVQLQ T0334 306 :DEAVREFCEMWHL 1pn0A 310 :EVVIANAKKIFHP T0334 322 :TQ 1pn0A 323 :YT T0334 324 :PLNRIRFRVGRNRRAWVG 1pn0A 332 :WFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHF 1pn0A 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKL T0334 378 :KSLNPVLTARFNREIETMFDDTRDFIQAHFYFSPRTD 1pn0A 390 :GRAKRDILKTYEEERQPFAQALIDFDHQFSRLFSGRP T0334 481 :VPDAPSPRLAHMPQATESVDEVFG 1pn0A 427 :AKDVADEMGVSMDVFKEAFVKGNE Number of specific fragments extracted= 23 number of extra gaps= 0 total=3788 Number of alignments=166 # 1pn0A read from 1pn0A/merged-good-all-a2m # found chain 1pn0A in template set Warning: unaligning (T0334)S2 because first residue in template chain is (1pn0A)T1 Warning: unaligning (T0334)S300 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pn0A)T305 T0334 3 :GKID 1pn0A 2 :KYSE T0334 7 :KILIVGGGTAGWMAASYLGK 1pn0A 9 :DVLIVGAGPAGLMAARVLSE T0334 28 :L 1pn0A 29 :Y T0334 29 :QGT 1pn0A 34 :PDL T0334 33 :DITLLQAPD 1pn0A 37 :KVRIIDKRS T0334 42 :IPTLGVGEATIPNLQTAF 1pn0A 47 :KVYNGQADGLQCRTLESL T0334 61 :DFLGIPED 1pn0A 65 :KNLGLADK T0334 103 :GPDHFYHSFGLL 1pn0A 79 :DMSTIALYNPDE T0334 115 :KYHE 1pn0A 92 :GHIR T0334 152 :ANRSPRRLDGSKVTNYAWHFDAHLVADFLRRFATEKLG 1pn0A 96 :RTDRIPDTLPGISRYHQVVLHQGRIERRILDSIAEISD T0334 190 :VRHVED 1pn0A 136 :IKVERP T0334 196 :RVEHVQR 1pn0A 143 :IPEKMEI T0334 203 :DANGNIESVRTAT 1pn0A 156 :DPEAYPVTMTLRY T0334 216 :GR 1pn0A 211 :GE T0334 218 :VFDADLFVDCSGFRGLLI 1pn0A 215 :TVHCKYVIGCDGGHSWVR T0334 237 :KAMEEPFLDM 1pn0A 233 :RTLGFEMIGE T0334 247 :SD 1pn0A 245 :DY T0334 254 :SAVATQVPHDDDANGVEPFTSAIAMKSGWTWKIPM 1pn0A 247 :IWGVLDAVPASNFPDIRSRCAIHSAESGSIMIIPR T0334 289 :LGRFGTGYVYS 1pn0A 283 :NNLVRFYVQLQ T0334 306 :DEAVREFCEMWHLDP 1pn0A 310 :EVVIANAKKIFHPYT T0334 321 :ETQPLNRIRFRVGRNRRAWVG 1pn0A 329 :QLDWFTAYHIGQRVTEKFSKD T0334 342 :NCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pn0A 351 :RVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFYFS 1pn0A 389 :TGRAKRDILKTYEEERQPFAQALIDFDHQFSRLF T0334 411 :PRTD 1pn0A 424 :GRPA T0334 427 :ADGMQEKIDMYRAGMAINA 1pn0A 438 :MDVFKEAFVKGNEFASGTA T0334 480 :LVPD 1pn0A 457 :INYD Number of specific fragments extracted= 26 number of extra gaps= 0 total=3814 Number of alignments=167 # 1pn0A read from 1pn0A/merged-good-all-a2m # found chain 1pn0A in template set Warning: unaligning (T0334)R301 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1pn0A)T305 T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 1pn0A 7 :YCDVLIVGAGPAGLMAARVLSEYV T0334 29 :QGTADITLLQAPDIPTL 1pn0A 33 :KPDLKVRIIDKRSTKVY T0334 46 :GVGEATIPNLQTAF 1pn0A 51 :GQADGLQCRTLESL T0334 61 :DFLGI 1pn0A 65 :KNLGL T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTSEARELDGG 1pn0A 70 :ADKILSEANDMSTIALYNPDENGHIRRTDRIPDTLP T0334 162 :SKVTNYAWHFDAHLVADFLRRFATEK 1pn0A 106 :GISRYHQVVLHQGRIERRILDSIAEI T0334 188 :LGVRHVEDRVEHVQRDANGN 1pn0A 135 :RIKVERPLIPEKMEIDSSKA T0334 214 :ATGR 1pn0A 209 :EAGE T0334 218 :VFDADLFVDCSGFRGLLIN 1pn0A 215 :TVHCKYVIGCDGGHSWVRR T0334 238 :AMEEPFLDMSDHLLNDSAVATQV 1pn0A 234 :TLGFEMIGEQTDYIWGVLDAVPA T0334 264 :DDANGVEPFTSAIAMKSGWTWKIPMLGRFGTGYVYSS 1pn0A 257 :SNFPDIRSRCAIHSAESGSIMIIPRENNLVRFYVQLQ T0334 307 :EAVREFCEMWHLDP 1pn0A 311 :VVIANAKKIFHPYT T0334 325 :LNRIRFRVGRNRRAWV 1pn0A 325 :FDVQQLDWFTAYHIGQ T0334 341 :GNCVSIGTSSCFVEPLESTGIYFVYAALYQLVKHFP 1pn0A 350 :ERVFIAGDACHTHSPKAGQGMNTSMMDTYNLGWKLG T0334 377 :DKSLNPVLTARFNREIETMFDDTRDFIQAHFY 1pn0A 393 :KRDILKTYEEERQPFAQALIDFDHQFSRLFSG T0334 442 :AINAPASDDA 1pn0A 425 :RPAKDVADEM T0334 452 :QLYYGNFEEEFRNFWNNSNYYC 1pn0A 439 :DVFKEAFVKGNEFASGTAINYD Number of specific fragments extracted= 17 number of extra gaps= 0 total=3831 Number of alignments=168 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kssA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kssA expands to /projects/compbio/data/pdb/1kss.pdb.gz 1kssA:# T0334 read from 1kssA/merged-good-all-a2m # 1kssA read from 1kssA/merged-good-all-a2m # adding 1kssA to template set # found chain 1kssA in template set T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1kssA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPDIPTLGVGEATI 1kssA 148 :SGAKVILIEKEPVIGGNAKLAAG T0334 57 :TAF 1kssA 178 :DQQ T0334 61 :DFLGI 1kssA 181 :KAKKI T0334 66 :PEDEWMRECNA 1kssA 188 :SPELMFEDTMK T0334 77 :SYKVAIKFINWR 1kssA 208 :LVKVLSSHSKDS T0334 123 :SHYWFDRSYR 1kssA 220 :VDWMTAMGAD T0334 141 :YACYKEPVI 1kssA 230 :LTDVGMMGG T0334 155 :SPRRL 1kssA 239 :ASVNR T0334 162 :SKVTNYAW 1kssA 244 :AHRPTGGA T0334 171 :FDAHLVADFLRRFAT 1kssA 252 :GVGAHVVQVLYDNAV T0334 187 :KLGVRHVED 1kssA 267 :KRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1kssA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :TG 1kssA 299 :KG T0334 217 :RVFDADLFVDCSGFRGL 1kssA 302 :YWVKADAVILATGGFAK T0334 234 :L 1kssA 323 :V T0334 236 :NKA 1kssA 324 :AKL T0334 246 :MSDHLLNDS 1kssA 330 :LKGFISTNQ T0334 267 :NGVE 1kssA 339 :PGAV T0334 272 :FTSAIAMKSGWTWKIPM 1kssA 351 :NAGGALKDMQYIQAHPT T0334 289 :LGRFGT 1kssA 371 :KGGVMV T0334 295 :GYVYSSRFATE 1kssA 384 :GAILVNREGKR T0334 306 :DEAVREFCEMW 1kssA 459 :KALTETVARYN T0334 317 :HLDPETQ 1kssA 475 :GKDTDFE T0334 324 :PLNRIRFRVG 1kssA 493 :NYYAIEVTPG T0334 334 :RNRRAWVGNCVSIG 1kssA 520 :NAKKQVIPGLYGAG T0334 348 :TSSCFVEPLESTGIYFVYAALYQLVKHF 1kssA 537 :GGVHGANRLGGNAISDIITFGRLAGEEA Number of specific fragments extracted= 27 number of extra gaps= 0 total=3858 Number of alignments=169 # 1kssA read from 1kssA/merged-good-all-a2m # found chain 1kssA in template set Warning: unaligning (T0334)P66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kssA)W176 Warning: unaligning (T0334)E67 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kssA)W176 T0334 3 :GKID 1kssA 122 :APHD T0334 7 :KILIVGGGTAGWMAASYLGK 1kssA 128 :DVVVVGSGGAGFSAAISATD T0334 29 :QGT 1kssA 148 :SGA T0334 33 :DITLLQAPD 1kssA 151 :KVILIEKEP T0334 42 :IPTL 1kssA 161 :IGGN T0334 59 :FFDFLGI 1kssA 168 :AAGGMNA T0334 68 :DEWMRECNASYKVAIKFINWRTAGEGTS 1kssA 177 :TDQQKAKKITDSPELMFEDTMKGGQNIN T0334 96 :EARELDGGPDHFYHSFGLL 1kssA 222 :WMTAMGADLTDVGMMGGAS T0334 115 :KYHE 1kssA 246 :RPTG T0334 152 :AN 1kssA 251 :AG T0334 172 :DAHLVADFLRRFA 1kssA 253 :VGAHVVQVLYDNA T0334 186 :EKLGVRHVED 1kssA 266 :VKRNIDLRMN T0334 196 :RVEHVQRDANGNIESVRTA 1kssA 277 :RGIEVLKDDKGTVKGILVK T0334 215 :T 1kssA 297 :M T0334 216 :GR 1kssA 299 :KG T0334 218 :VFDADLFVDCSGF 1kssA 303 :WVKADAVILATGG T0334 280 :SGWTWKIPM 1kssA 359 :MQYIQAHPT T0334 289 :LGR 1kssA 371 :KGG T0334 292 :FGTGYVYSSRFATE 1kssA 383 :NGAILVNREGKRFV T0334 306 :DEAVREFCEM 1kssA 462 :TETVARYNSL T0334 316 :WHLDPETQPLNRIRF 1kssA 473 :SSGKDTDFERPNLPR T0334 331 :RVGRNR 1kssA 500 :TPGVHA T0334 337 :RAWVGNCVSIGTSSCFVEP 1kssA 523 :KQVIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFP 1kssA 545 :LGGNAISDIITFGRLAGEEAA Number of specific fragments extracted= 24 number of extra gaps= 1 total=3882 Number of alignments=170 # 1kssA read from 1kssA/merged-good-all-a2m # found chain 1kssA in template set Warning: unaligning (T0334)K378 because of BadResidue code BAD_PEPTIDE in next template residue (1kssA)S568 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1kssA 125 :DTVDVVVVGSGGAGFSAAISATD T0334 30 :GTADITLLQAPD 1kssA 148 :SGAKVILIEKEP T0334 44 :TLGVGEATI 1kssA 160 :VIGGNAKLA T0334 57 :TAF 1kssA 178 :DQQ T0334 61 :DFLGI 1kssA 181 :KAKKI T0334 66 :PEDEWMR 1kssA 188 :SPELMFE T0334 113 :LLKYHEQIPLSHYWFDRSY 1kssA 195 :DTMKGGQNINDPALVKVLS T0334 137 :EPFDYACYKEPVILDANRSPRRLDGSKVTN 1kssA 214 :SHSKDSVDWMTAMGADLTDVGMMGGASVNR T0334 169 :WHF 1kssA 244 :AHR T0334 172 :DAHLVADFLRRFATEKLGVRHVEDRVEHVQRDANGNIESVRT 1kssA 253 :VGAHVVQVLYDNAVKRNIDLRMNTRGIEVLKDDKGTVKGILV T0334 214 :ATGR 1kssA 297 :MYKG T0334 218 :VFDADLFVDCSGFRG 1kssA 303 :WVKADAVILATGGFA T0334 233 :LLINK 1kssA 322 :RVAKL T0334 243 :FLDMSDHLLND 1kssA 327 :DPSLKGFISTN T0334 307 :EAVREFCEMWHLDP 1kssA 463 :ETVARYNSLVSSGK T0334 322 :TQ 1kssA 477 :DT T0334 324 :PLNRIRFRVGRNRRA 1kssA 493 :NYYAIEVTPGVHATM T0334 339 :WVGNCVSIGTSSCFVEP 1kssA 525 :VIPGLYGAGEVTGGVHG T0334 356 :LESTGIYFVYAALYQLVKHFPD 1kssA 545 :LGGNAISDIITFGRLAGEEAAK Number of specific fragments extracted= 19 number of extra gaps= 1 total=3901 Number of alignments=171 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m6iA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0334 read from 1m6iA/merged-good-all-a2m # 1m6iA read from 1m6iA/merged-good-all-a2m # found chain 1m6iA in training set Warning: unaligning (T0334)N326 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1m6iA)Y560 T0334 4 :KIDKILIVGGGTAGWMAASYLGK 1m6iA 130 :SHVPFLLIGGGTAAFAAARSIRA T0334 28 :LQGTADITLLQAPDIPTLGVGEAT 1m6iA 153 :RDPGARVLIVSEDPELPYMRPPLS T0334 56 :QTAF 1m6iA 177 :KELW T0334 62 :FLGI 1m6iA 270 :IDRA T0334 67 :EDEWMR 1m6iA 274 :GAEVKS T0334 73 :ECNASYKVAIK 1m6iA 289 :DFRSLEKISRE T0334 84 :FINWRTA 1m6iA 312 :GSELACA T0334 122 :LSHYWFDRSYR 1m6iA 319 :LGRKARALGTE T0334 170 :HFDAHLVADFLRRFA 1m6iA 342 :KILPEYLSNWTMEKV T0334 186 :EKLGVRHVED 1m6iA 357 :RREGVKVMPN T0334 196 :RVEHVQRDANG 1m6iA 368 :IVQSVGVSSGK T0334 209 :ESVRTATGRVFDADLFVDCSGFRGLL 1m6iA 379 :LLIKLKDGRKVETDHIVAAVGLEPNV T0334 235 :INKAMEEPFLDMSDH 1m6iA 406 :LAKTGGLEIDSDFGG T0334 266 :ANGVE 1m6iA 473 :AKPYW T0334 272 :FTSAIA 1m6iA 480 :SMFWSD T0334 278 :MKSGWTWKIPMLGR 1m6iA 487 :GPDVGYEAIGLVDS T0334 292 :FGTGYVYSS 1m6iA 502 :LPTVGVFAK T0334 301 :RFATE 1m6iA 513 :AQDNP T0334 327 :RIRFRVGRNRRAWV 1m6iA 561 :GKGVIFYLRDKVVV T0334 342 :NCVSIG 1m6iA 575 :GIVLWN T0334 398 :DTRDFIQAHFYFSPR 1m6iA 584 :RMPIARKIIKDGEQH T0334 483 :DAPSPRLAH 1m6iA 599 :EDLNEVAKL Number of specific fragments extracted= 22 number of extra gaps= 0 total=3923 Number of alignments=172 # 1m6iA read from 1m6iA/merged-good-all-a2m # found chain 1m6iA in training set T0334 5 :ID 1m6iA 130 :SH T0334 7 :KILIVGGGTAGWMAASYLGK 1m6iA 133 :PFLLIGGGTAAFAAARSIRA T0334 28 :L 1m6iA 153 :R T0334 29 :QGT 1m6iA 155 :PGA T0334 33 :DITLLQAPD 1m6iA 158 :RVLIVSEDP T0334 42 :IPTL 1m6iA 168 :LPYM T0334 139 :FDYACYKEPVILD 1m6iA 321 :RKARALGTEVIQL T0334 152 :ANRSPRRLD 1m6iA 335 :PEKGNMGKI T0334 172 :DAHLVADFLRRFA 1m6iA 344 :LPEYLSNWTMEKV T0334 186 :EKLGVRHVED 1m6iA 357 :RREGVKVMPN T0334 196 :RVEHVQRDANG 1m6iA 368 :IVQSVGVSSGK T0334 209 :ESVRTATGRVFDADLFVDCSGFRG 1m6iA 379 :LLIKLKDGRKVETDHIVAAVGLEP T0334 233 :LLINKAMEEPFLDMSDHLLNDSAV 1m6iA 404 :VELAKTGGLEIDSDFGGFRVNAEL T0334 338 :AWVGNCVSIGTSSCF 1m6iA 428 :QARSNIWVAGDAACF T0334 363 :FVYAALYQLVKHFPDKSLN 1m6iA 457 :HAVVSGRLAGENMTGAAKP Number of specific fragments extracted= 15 number of extra gaps= 0 total=3938 Number of alignments=173 # 1m6iA read from 1m6iA/merged-good-all-a2m # found chain 1m6iA in training set T0334 5 :IDKILIVGGGTAGWMAASYLGKAL 1m6iA 300 :VKSITIIGGGFLGSELACALGRKA T0334 29 :QGTADITLLQAPDI 1m6iA 325 :ALGTEVIQLFPEKG T0334 46 :GVGEATIPNLQTAF 1m6iA 339 :NMGKILPEYLSNWT T0334 181 :RRFATEKLGVRHVEDRVEHVQRDANG 1m6iA 353 :MEKVRREGVKVMPNAIVQSVGVSSGK T0334 209 :ESVRTATGRVFDADLFVDCSGF 1m6iA 379 :LLIKLKDGRKVETDHIVAAVGL T0334 235 :INKAMEEPFLDMSDH 1m6iA 406 :LAKTGGLEIDSDFGG T0334 297 :VYSSRFA 1m6iA 421 :FRVNAEL T0334 338 :AWVGNCVSIGTSSCFVE 1m6iA 428 :QARSNIWVAGDAACFYD T0334 359 :TGIYFVYAALYQLVKHFPDKS 1m6iA 453 :EHHDHAVVSGRLAGENMTGAA Number of specific fragments extracted= 9 number of extra gaps= 0 total=3947 Number of alignments=174 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 174 Adding 17814 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -1014.1150, CN propb: -1014.1150 weights: 0.1530 constraints: 1778 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 1778 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 1778 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 16036 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 16036 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 17814 # command: