working dir: /home/casp11/multicom/ZCA_155705426023607/domain0/blast blast NR: /home/casp13/uniref//uniref50 toconvert blast output to aligconvert bconvert alignment to HMM... Query file is in A2M, A3M or FASTA format Read domain0.fasta.fas with 2 sequences Alignment in domain0.fasta.fas contains 91 match states 1 out of 2 sequences passed filter for 90% maximum sequence identity Effective number of sequences exp(entropy) = 1.0 Writing HMM to domain0.hhm predict secondary struture... Running PSI-BLAST with sequence on NR database domain0.fasta ... Predicting secondary structuPredicPass1 ... Pass2 ... Cleaning up ... Final output files: domain0.Final output files: domain0.add secondary structure intoadd secocalibrate HMM model... Search results will be writtSearch results will be written to domain0.hhr Query file is in HHM format Read in HMM domain0 with 91 match states and effective number of sequences = 1 .............................................. Fitting scores with EVD (first round) ... Fitting scores with EVD (second round) ... Query domain0 Match_columns 91 No_of_seqs 1 Neff 1.0 Searched_HMMs 935 Date Sun May 5 12:58:55 2019 Command /home/chengji/software/hhsearch1.2/linux32//hhsearch -cal -i domain0.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 d1j2la_ g.20.1.1 (A:) Flavorid 17.3 0.6 0.00064 19.1 0.6 17 3-19 4-20 (68) 2 d1jzta_ c.104.1.1 (A:) Hypothe 13.9 3.3 0.0036 15.4 3.3 40 29-71 157-196 (243) 3 d1mxa_1 d.130.1.1 (1-102) S-ad 5.6 5.1 0.0055 14.5 0.0 10 58-67 1-10 (102) 4 d1oc0b_ g.64.1.1 (B:) Vitronec 5.1 10 0.011 13.0 1.2 13 2-14 6-18 (37) 5 d2pspa1 g.16.1.1 (A:1-53) Panc 5.1 5 0.0053 14.6 -0.4 16 3-18 19-34 (53) 6 d1gl1i_ g.4.1.1 (I:) Protease 4.6 5.5 0.0059 14.4 -0.6 16 3-18 16-32 (34) 7 d1d1ra_ d.64.1.1 (A:) YciH {Es 4.0 13 0.014 12.5 0.8 7 1-7 42-48 (83) 8 d1nyoa_ b.118.1.1 (A:) Immunog 3.6 8.7 0.0093 13.4 -0.5 7 56-62 70-76 (163) 9 d1d6ga_ g.33.1.1 (A:) Cholecys 3.2 24 0.025 11.3 1.2 21 50-70 10-30 (47) 10 d1ezvh_ f.28.1.1 (H:) Non-heme 3.0 27 0.029 11.0 1.1 10 14-23 24-33 (74) Recording calibration coefficients in domain0.shhm Done search HMM against HMM database... Search results will be written to domain0.hhr Query file is in HHM format Read in HMM domain0 with 91 match states and effective number of sequences = 1 .................................................. 1000 HMMs se............................. 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 se............................. 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 sear........................... 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=0.470 and mu=3. Using lamda=0.470 and mu=3.45 from calibrated query HMM domain0. Note that HMMs need to be recalibrated when changing HMM-HMM alignment options. Query domain0 Match_columns 91 No_of_seqs 1 Neff 1.0 Searched_HMMs 55661 Date Sun May 5 13:04:13 2019 Command /home/chengji/software/hhsearch1.2/linux32//hhsearch -i domain0.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 6D7LA 41.6 3.2 5.7E-05 24.3 1.1 41 2-47 137-177 (288) 2 2KAKA 37.0 5.2 9.4E-05 23.2 1.2 12 1-12 4-15 (53) 3 2MHKA 32.6 8.6 0.00015 22.1 1.3 13 3-15 19-31 (250) 4 1J2LA 24.1 15 0.00028 20.9 0.6 17 3-19 4-20 (68) 5 1JYPA 23.2 21 0.00039 20.2 1.1 17 3-19 4-20 (68) 6 2YIBA 20.9 24 0.00042 20.0 0.7 33 32-64 319-351 (789) 7 1L3XA 17.5 28 0.00051 19.6 0.2 17 3-19 6-22 (73) 8 6EK9A 16.5 41 0.00074 18.8 0.7 16 5-20 89-104 (121) 9 4Q34A 15.6 53 0.00094 18.3 0.9 8 52-59 286-293 (313) 10 3UCIA 15.0 56 0.001 18.1 0.8 16 generate ranking list... parse hhsearch output... Analyze local alignments... Remove redundant local alignments... Construct scalfolds of each template... Calculate the stuructural similarity between lCheck if the local Check if front or end domains are missing... Extend local alignments if necessary.... working dir: /home/casp11/multicom/ZCA_155705426023607/domain0/hhsearch/. Check if the local alignment file exists in the work dir. generate PIR alignments for easy template 1... local alignment 3 Structures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 584.9785 Current Energy of Model 2: 608.1185 Current Energy of Model 3: 622.4444 Current Energy of Model 4: 684.2470 Current Energy of Model 5: 629.0336 Current Energy of Model 6: 674.9561 Current Energy Structures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 632.5966 Current Energy of Model 2: 571.8757 Current Energy of ModelStructures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 491.2687 Current Energy of Model 2: 571.5041 Current Energy of Model 3: 526.3131 Current Energy of Model 4: 573.2347 Current Energy of Model 5: 496.4846 Current Energy of Model 6: 535.4307 Current Energy of Model 7: 524.1302 Current Energy of Model 8: 455.45Structures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 491.2687 CurreStructures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 471.5980 Current Energy of Model 2: 426.1702 Current Energy of Model 3: 484.1517 Current Energy of Model 4: 413.4847 Current Energy of Model 5: 454.5669 Current Energy of Model 6: 525.0193 Current Energy of Model 7: 402.3335 Current Energy of Model 8: 513.2099 Current Energy of Model 9: 521.1887 Current Energy Structures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:doStructures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 444.2024 Current Energy of Model 2: 443.9420 Current Energy of Model 3: 468.3298 Current Energy of Model 4: 463.0789 Current Energy of Model 5: 421.1686 Current Energy of Model 6: 517.6839 Current Energy of Model 7: 429.9413 Current Energy of Model 8: 409.1726 Current Energy of Model 9: 457.1002 Current Energy of Model 10: 516.9170 the energy of the selected model 8 = 409.1726 Easy Comparative modelling for domain0 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 moStructures are generaStructures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 485.8271 Current Energy of Model 2: 446.4160 Current Energy of Model 3: 456.2526 Current Energy of Model 4: 436.0899 Current Energy of Model 5: 493.0527 Current Energy of Model 6: 548.4163 Current Energy of Model 7: 422.1401 Current Energy of Model 8: 478.9701 Current Energy of Model 9: 468.8168 Current Energy of Model 10: 471.3433 the energy of the selected model 7 = 422.1401 Easy Comparative modelling for domain0 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 2. Structures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 560.8934 Current Energy of Model 2: 585.5677 Current Energy of Model 3: 611.8112 Current Energy of Model 4: 717.8954 Current Energy of Model 5: 572.2985 Current Energy of Model 6: 525.5435 Current Energy of Model 7: 553.4742 Current Energy of Model 8: 526.9467 Current Energy of Model 9: 565.8057 Current Energy of Model 10: 570.5068 the energy of the selected model 6 = 525.5435 Easy Comparative modelling for domain0 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 1. Structures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 496.3751 Current Energy of Model 2: 465.7533 Current Energy of Model 3: 480.4274 Current Energy of Model 4: 505.5728 Current Energy of Model 5: 471.7835 Current Energy of Model 6: 463.8891 Current Energy of Model 7: 475.6152 Current Energy of Model 8: 494.4150 Current Energy of Model 9: 469.0352 Current Energy of Model 10: 560.2485 the energy of the selected model 6 = 463.8891 Easy Comparative modelling for domain0 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 1. Structures are generated in iteration:1 model 1 is created:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 410.4548 Current Energy of Model 2: 416.4258 Current Energy of Model 3: 453.5049 Current Energy of Model 4: 419.8810 Current Energy of Model 5: 402.1494 Current Energy of Model 6: 404.9829 Current Energy of Model 7: 457.8396 Current Energy of Model 8: 422.6453 Current Energy of Model 9: 414.2793 Current Energy of Model 10: 394.1523 the energy of the selected model 10 = 394.1523 Easy Comparative modelling for domain0 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:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 434.6942 Current Energy of Model 2: 458.7316 Current Energy of Model 3: 445.6741 Current Energy of Model 4: 473.9771 Current Energy of Model 5: 399.9802 Current Energy of Model 6: 397.0856 Current Energy of Model 7: 495.8188 Current Energy of Model 8: 421.8748 Current Energy of Model 9: 445.9476 Current Energy of Model 10: 457.5322 the energy of the selected model 6 = 397.0856 Easy Comparative modelling for domain0 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:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 470.7254 Current Energy of Model 2: 402.0832 Current Energy of Model 3: 416.7844 Current Energy of Model 4: 435.0879 Current Energy of Model 5: 423.8414 Current Energy of Model 6: 378.7932 Current Energy of Model 7: 427.2247 Current Energy of Model 8: 429.5136 Current Energy of Model 9: 416.6210 Current Energy of Model 10: 382.3469 the energy of the selected model 6 = 378.7932 Easy Comparative modelling for domain0 is done. Comparative modelling for domain0 is done. 0.10.pdb Current Energy of Model 1: 514.5596 Current Energy of Model 2: 447.6222 Current Energy of Model 3: 414.5737 Current Energy of Model 4: 457.5719 Current Energy of Model 5: 452.1272 Current Energy of Model 6: 480.8907 Current Energy of Model 7: 461.5410 Current Energy of Model 8: 443.2879 Current Energy of Model 9: 446.0646 Current Energy of Model 10: 434.9659 the energy of the selected model 3 = 414.5737 Comparative modelling for domain0 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:domain0.1.pdb model 2 is created:domain0.2.pdb model 3 is created:domain0.3.pdb model 4 is created:domain0.4.pdb model 5 is created:domain0.5.pdb model 6 is created:domain0.6.pdb model 7 is created:domain0.7.pdb model 8 is created:domain0.8.pdb model 9 is created:domain0.9.pdb model 10 is created:domain0.10.pdb Current Energy of Model 1: 477.7766 Current Energy of Model 2: 404.0219 Current Energy of Model 3: 383.6111 Current Energy of Model 4: 431.0797 Current Energy of Model 5: 465.1320 Current Energy of Model 6: 431.8576 Current Energy of Model 7: 420.5324 Current Energy of Model 8: 412.4045 Current Energy of Model 9: 402.2566 Current Energy of Model 10: 410.7024 the energy of the selected model 3 = 383.6111 Comparative modelling for domain0 is done. Comparative modelling for domain0.fasta is done.