working dir: /home/casp11/multicom/ZCA_155705426023607/domain1/blast blast NR: /home/casp13/uniref//uniref50 toconvert blast output to aligconvert blast output to alignment... convert alignment to HMM... Query file is in A2M, A3M or FASTA format Read domain1.fasta.fas with 49 sequences Alignment in domain1.fasta.fas contains 218 match states 30 out of 49 sequences passed filter for 90% maximum sequence identity Effective number of sequences exp(entropy) = 4.7 Writing HMM to domain1.hhm predict secondary struture... Running PSI-BLAST with sequence on NRPredicting secondary structuPredicting secondary structure... Pass1 ... Pass2 ... Cleaning up ... Final output files: domain1.ss2 domain1.horiz Finished. add secondary structure into HMM... calibrate HMM model... Search results will be written to domain1.hhr Query file is in HHM format Read in HMM domain1 with 218 match states and effective number of sequences = 4.7 .............................................. Fitting scores with EVD (first round) ... Fitting scores with EVD (second round) ... Query domain1 Match_columns 218 No_of_seqs 30 Neff 4.7 Searched_HMMs 935 Date Sun May 5 22:07:07 2019 Command /home/chengji/software/hhsearch1.2/linux32//hhsearch -cal -i domain1.shhm -d /home/chengji/software/hhsearch1.2/linux32//cal.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 d1jg5a_ d.205.1.1 (A:) GTP cyc 9.8 4.8 0.0051 15.2 2.4 16 11-26 51-66 (83) 2 d1ctf__ d.45.1.1 (-) Ribosomal 8.3 4.7 0.0051 15.2 1.6 18 133-150 50-67 (68) 3 d1slua_ b.16.1.1 (A:) Ecotin, 6.0 8.3 0.0089 13.9 1.4 33 148-180 15-47 (133) 4 d1gqea_ e.38.1.1 (A:) Polypept 5.9 6.1 0.0065 14.6 0.7 17 20-36 154-170 (362) 5 d1gk8i_ d.73.1.1 (I:) Ribulose 5.6 22 0.024 11.6 3.3 21 8-28 18-41 (125) 6 d1ozbi_ g.74.1.1 (I:) Preprote 4.6 6.7 0.0072 14.4 -0.1 14 41-54 1-14 (26) 7 d1a9xa3 c.30.1.1 (A:1-127) Car 4.6 24 0.026 11.4 2.7 42 109-169 13-54 (127) 8 d1c4ka3 d.125.1.1 (A:570-730) 4.4 17 0.019 12.2 1.8 17 6-22 53-69 (161) 9 d1aln_1 c.97.1.1 (1-150) Two-d 4.2 12 0.013 13.0 0.7 8 111-118 129-136 (150) 10 d1jj2k_ c.12.1.1 (K:) Ribosoma 4.0 21 0.023 11.7 1.9 21 138-158 130-150 (150) Recording calibration coefficients in domain1.shhm Done search HMM against HMM database... Search results will be written to domain1.hhr Query file is in HHM format Read in HMM domain1 with 218 match states and effective number of sequences = 4.7 .................................................. 1000 HMMs searched .................................................. 2000 HMMs searched .................................................. 3000 HMMs searched .................................................. 4000 HMMs searched .................................................. 5000 HMMs searched .................................................. 6000 HMMs searched .................................................. 7000 HMMs searched .................................................. 8000 HMMs searched .................................................. 9000 HMMs searched .................................................. 10000 HMMs searched .................................................. 11000 HMMs searched .................................................. 12000 HMMs searched .................................................. 13000 HMMs searched .................................................. 14000 HMMs searched .................................................. 15000 HMMs searched .................................................. 16000 HMMs searched .................................................. 17000 HMMs searched .................................................. 18000 HMMs searched .................................................. 19000 HMMs searched .................................................. 20000 HMMs searched .................................................. 21000 HMMs searched .................................................. 22000 HMMs searched .................................................. 23000 HMMs searched .................................................. 24000 HMMs searched .................................................. 25000 HMMs searched .................................................. 26000 HMMs searched .................................................. 27000 HMMs searched .................................................. 28000 HMMs searched .................................................. 29000 HMMs searched .................................................. 30000 HMMs searched .................................................. 31000 HMMs searched .................................................. 32000 HMMs searched .................................................. 33000 HMMs searched .................................................. 34000 HMMs searched .................................................. 35000 HMMs searched .................................................. 36000 HMMs searched .................................................. 37000 HMMs searched .................................................. 38000 HMMs searched .................................................. 39000 HMMs searched .................................................. 40000 HMMs searched .................................................. 41000 HMMs searched .................................................. 42000 HMMs searched .................................................. 43000 HMMs searched .................................................. 44000 HMMs searched .................................................. 45000 HMMs searched .................................................. 46000 HMMs searched .................................................. 47000 HMMs searched .................................................. 48000 HMMs searched .................................................. 49000 HMMs searched .................................................. 50000 HMMs searched .................................................. 51000 HMMs searched .................................................. 52000 HMMs searched .................................................. 53000 HMMs searched .................................................. 54000 HMMs searched .................................................. 55000 HMMs searched ................................. Using lamda=0.433 and mu=3.02 from calibrated query HMM domain1. Note that HMMs need to be recalibrated when changing HMM-HMM alignment options. Query domain1 Match_columns 218 No_of_seqs 30 Neff 4.7 Searched_HMMs 55661 Date Sun May 5 22:14:14 2019 Command /home/chengji/software/hhsearch1.2/linux32//hhsearch -i domain1.shhm -d /home/chengji/software/prosys_database/fr_lib/hhsearchdb No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3UK8A 100.0 0 0 504.3 22.1 212 6-217 2-213 (214) 2 3BOHA 100.0 0 0 465.8 21.9 212 6-217 1-212 (213) 3 3BOBA 100.0 0 0 455.8 21.1 208 10-217 1-208 (209) 4 3PX3A 35.6 10 0.00018 22.9 2.3 41 121-162 196-236 (240) 5 3HBXA 33.8 8.3 0.00015 23.3 1.5 13 14-26 378-390 (436) 6 4NNBA 24.5 29 0.00052 20.5 2.1 18 1-18 151-168 (484) 7 3EYPA 23.3 60 0.0011 18.8 3.5 41 117-157 38-78 (459) 8 1F0KA 23.2 25 0.00045 20.8 1.5 29 12-40 17-46 (351) 9 2Y7GA 23.0 41 0.00073 19.7 2.5 17 2-18 18-34 (276) 10 2I1SA 21.6 47 0.00085 19.3 2.4 46 21-75 98-143 (178) Done generate ranking list... parse hhsearch output... generate combined PIR alignments... Use Modeller to generate tertiary structures... Generate a model from each template... Check if the local alignment file exists in the output dir. generate PIR alignments for easy template 1... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 3. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 5836.9399 Current Energy of Model 2: 5723.6816 Current Energy of Model 3: 5769.6421 Current Energy of Model 4: 6705.8506 Current Energy of Model 5: 5725.4707 Current Energy of Model 6: 5790.4985 Current Energy of Model 7: 5694.1025 Current Energy of Model 8: 5740.2202 Current Energy of Model 9: 5711.1470 Current Energy of Model 10: 5672.8218 the energy of the selected model 10 = 5672.8218 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 2... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 2. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 5392.6592 Current Energy of Model 2: 5485.4019 Current Energy of Model 3: 5425.0938 Current Energy of Model 4: 5396.2383 Current Energy of Model 5: 5367.0479 Current Energy of Model 6: 5373.7471 Current Energy of Model 7: 5419.8984 Current Energy of Model 8: 5423.6987 Current Energy of Model 9: 5399.3457 Current Energy of Model 10: 5376.0337 the energy of the selected model 5 = 5367.0479 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 3... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 1. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 932.8757 Current Energy of Model 2: 1005.7734 Current Energy of Model 3: 963.2396 Current Energy of Model 4: 991.8539 Current Energy of Model 5: 950.5729 Current Energy of Model 6: 1017.6270 Current Energy of Model 7: 1119.2109 Current Energy of Model 8: 1043.9844 Current Energy of Model 9: 1079.5088 Current Energy of Model 10: 956.2294 the energy of the selected model 1 = 932.8757 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 4... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 4. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 1358.2268 Current Energy of Model 2: 1589.9595 Current Energy of Model 3: 1277.7163 Current Energy of Model 4: 1204.4978 Current Energy of Model 5: 1089.4697 Current Energy of Model 6: 1203.8652 Current Energy of Model 7: 1737.8263 Current Energy of Model 8: 1297.6792 Current Energy of Model 9: 1393.8593 Current Energy of Model 10: 1057.4092 the energy of the selected model 10 = 1057.4092 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 5... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 3. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 1377.2284 Current Energy of Model 2: 1236.2024 Current Energy of Model 3: 1204.9104 Current Energy of Model 4: 1298.1652 Current Energy of Model 5: 1442.1716 Current Energy of Model 6: 1540.9414 Current Energy of Model 7: 1342.5793 Current Energy of Model 8: 1391.5697 Current Energy of Model 9: 1501.6600 Current Energy of Model 10: 1360.6511 the energy of the selected model 3 = 1204.9104 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 6... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 4. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 1316.8105 Current Energy of Model 2: 1450.4939 Current Energy of Model 3: 1424.1708 Current Energy of Model 4: 1309.8123 Current Energy of Model 5: 1343.7574 Current Energy of Model 6: 1423.2908 Current Energy of Model 7: 1283.9950 Current Energy of Model 8: 1420.4258 Current Energy of Model 9: 1401.7783 Current Energy of Model 10: 1342.9176 the energy of the selected model 7 = 1283.9950 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 7... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 3. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 1279.7151 Current Energy of Model 2: 1447.6050 Current Energy of Model 3: 1439.5116 Current Energy of Model 4: 1347.4692 Current Energy of Model 5: 1797.0181 Current Energy of Model 6: 1499.2529 Current Energy of Model 7: 1574.7006 Current Energy of Model 8: 1193.1925 Current Energy of Model 9: 1337.3379 Current Energy of Model 10: 1361.7468 the energy of the selected model 8 = 1193.1925 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 8... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 2. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 1055.8209 Current Energy of Model 2: 1062.4806 Current Energy of Model 3: 1103.3074 Current Energy of Model 4: 1012.7982 Current Energy of Model 5: 1064.0632 Current Energy of Model 6: 1039.1591 Current Energy of Model 7: 1207.7968 Current Energy of Model 8: 1011.2881 Current Energy of Model 9: 1181.3761 Current Energy of Model 10: 1006.5377 the energy of the selected model 10 = 1006.5377 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 9... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 2. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 941.8217 Current Energy of Model 2: 921.1481 Current Energy of Model 3: 1051.0704 Current Energy of Model 4: 1008.4496 Current Energy of Model 5: 967.7676 Current Energy of Model 6: 983.3694 Current Energy of Model 7: 1012.9215 Current Energy of Model 8: 960.4307 Current Energy of Model 9: 926.3275 Current Energy of Model 10: 1102.8552 the energy of the selected model 2 = 921.1481 Easy Comparative modelling for domain1 is done. generate PIR alignments for easy template 10... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 1. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 1029.9352 Current Energy of Model 2: 1004.0293 Current Energy of Model 3: 1034.5139 Current Energy of Model 4: 1005.1604 Current Energy of Model 5: 947.8609 Current Energy of Model 6: 1004.7991 Current Energy of Model 7: 1017.8729 Current Energy of Model 8: 1018.0251 Current Energy of Model 9: 1080.4132 Current Energy of Model 10: 1024.3431 the energy of the selected model 5 = 947.8609 Easy Comparative modelling for domain1 is done. Comparative modelling for domain1 is done. omain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 954.0032 Current Energy of Model 2: 947.8091 Current Energy of Model 3: 1026.9666 Current Energy of Model 4: 1076.9491 Current Energy of Model 5: 981.6770 Current Energy of Model 6: 1027.2092 Current Energy of Model 7: 985.9860 Current Energy of Model 8: 1004.5580 Current Energy of Model 9: 1069.5116 Current Energy of Model 10: 977.8611 the energy of the selected model 2 = 947.8091 Comparative modelling for domain1 is done. generate PIR alignments for easy template 10... Add structural information to blast pir alignments. Use Modeller to generate tertiary structures... Run Modeller version 9.16... Total number of templates used for initial model generation is 1. Structures are generated in iteration:1 model 1 is created:domain1.1.pdb model 2 is created:domain1.2.pdb model 3 is created:domain1.3.pdb model 4 is created:domain1.4.pdb model 5 is created:domain1.5.pdb model 6 is created:domain1.6.pdb model 7 is created:domain1.7.pdb model 8 is created:domain1.8.pdb model 9 is created:domain1.9.pdb model 10 is created:domain1.10.pdb Current Energy of Model 1: 1092.2181 Current Energy of Model 2: 1107.0291 Current Energy of Model 3: 1121.2499 Current Energy of Model 4: 1145.2345 Current Energy of Model 5: 1062.9111 Current Energy of Model 6: 1050.8733 Current Energy of Model 7: 1134.8945 Current Energy of Model 8: 1208.2150 Current Energy of Model 9: 1145.3164 Current Energy of Model 10: 1155.1075 the energy of the selected model 6 = 1050.8733 Comparative modelling for domain1 is done. Comparative modelling for domain1.fasta is done.