null Mon 24 Dec 07:57:14 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ii1-3.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ii1-3.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:57:19 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 795 and 0 Target number of residues in the AU: 795 Target solvent content: 0.6125 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-3.2-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-3.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 9632 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 91.283 3.200 Wilson plot Bfac: 57.95 16190 reflections ( 91.24 % complete ) and 0 restraints for refining 10735 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3286 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2739 (Rfree = 0.000) for 10735 atoms. Found 58 (96 requested) and removed 138 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 10726 seeds are put forward NCS extension: 0 residues added, 10726 seeds are put forward Round 1: 287 peptides, 64 chains. Longest chain 8 peptides. Score 0.225 Round 2: 390 peptides, 80 chains. Longest chain 10 peptides. Score 0.286 Round 3: 434 peptides, 87 chains. Longest chain 11 peptides. Score 0.310 Round 4: 411 peptides, 80 chains. Longest chain 11 peptides. Score 0.320 Round 5: 417 peptides, 76 chains. Longest chain 16 peptides. Score 0.355 Taking the results from Round 5 Chains 80, Residues 341, Estimated correctness of the model 0.0 % 13 chains (73 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20256 restraints for refining 8790 atoms. 18778 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2378 (Rfree = 0.000) for 8790 atoms. Found 45 (78 requested) and removed 54 (39 requested) atoms. Cycle 2: After refmac, R = 0.2357 (Rfree = 0.000) for 8715 atoms. Found 28 (78 requested) and removed 42 (39 requested) atoms. Cycle 3: After refmac, R = 0.2253 (Rfree = 0.000) for 8663 atoms. Found 25 (78 requested) and removed 42 (39 requested) atoms. Cycle 4: After refmac, R = 0.2197 (Rfree = 0.000) for 8619 atoms. Found 23 (77 requested) and removed 46 (38 requested) atoms. Cycle 5: After refmac, R = 0.2158 (Rfree = 0.000) for 8585 atoms. Found 18 (77 requested) and removed 43 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 8676 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 8689 seeds are put forward Round 1: 424 peptides, 90 chains. Longest chain 11 peptides. Score 0.274 Round 2: 494 peptides, 91 chains. Longest chain 17 peptides. Score 0.375 Round 3: 495 peptides, 87 chains. Longest chain 17 peptides. Score 0.401 Round 4: 494 peptides, 81 chains. Longest chain 17 peptides. Score 0.436 Round 5: 494 peptides, 85 chains. Longest chain 19 peptides. Score 0.412 Taking the results from Round 4 Chains 83, Residues 413, Estimated correctness of the model 0.0 % 11 chains (68 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 19713 restraints for refining 8623 atoms. 17960 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2313 (Rfree = 0.000) for 8623 atoms. Found 54 (77 requested) and removed 64 (38 requested) atoms. Cycle 7: After refmac, R = 0.2167 (Rfree = 0.000) for 8589 atoms. Found 20 (77 requested) and removed 48 (38 requested) atoms. Cycle 8: After refmac, R = 0.2101 (Rfree = 0.000) for 8545 atoms. Found 16 (76 requested) and removed 43 (38 requested) atoms. Cycle 9: After refmac, R = 0.2060 (Rfree = 0.000) for 8506 atoms. Found 16 (76 requested) and removed 39 (38 requested) atoms. Cycle 10: After refmac, R = 0.2074 (Rfree = 0.000) for 8471 atoms. Found 14 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 8566 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8583 seeds are put forward Round 1: 420 peptides, 86 chains. Longest chain 12 peptides. Score 0.294 Round 2: 485 peptides, 82 chains. Longest chain 20 peptides. Score 0.417 Round 3: 512 peptides, 86 chains. Longest chain 17 peptides. Score 0.431 Round 4: 499 peptides, 81 chains. Longest chain 22 peptides. Score 0.443 Round 5: 498 peptides, 82 chains. Longest chain 16 peptides. Score 0.435 Taking the results from Round 4 Chains 84, Residues 418, Estimated correctness of the model 0.0 % 14 chains (85 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 19921 restraints for refining 8712 atoms. 18110 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2186 (Rfree = 0.000) for 8712 atoms. Found 48 (78 requested) and removed 62 (39 requested) atoms. Cycle 12: After refmac, R = 0.2043 (Rfree = 0.000) for 8677 atoms. Found 25 (78 requested) and removed 42 (39 requested) atoms. Cycle 13: After refmac, R = 0.1982 (Rfree = 0.000) for 8647 atoms. Found 13 (77 requested) and removed 41 (38 requested) atoms. Cycle 14: After refmac, R = 0.1949 (Rfree = 0.000) for 8612 atoms. Found 10 (77 requested) and removed 42 (38 requested) atoms. Cycle 15: After refmac, R = 0.1927 (Rfree = 0.000) for 8575 atoms. Found 12 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 8703 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 8717 seeds are put forward Round 1: 429 peptides, 88 chains. Longest chain 11 peptides. Score 0.295 Round 2: 470 peptides, 81 chains. Longest chain 14 peptides. Score 0.402 Round 3: 469 peptides, 83 chains. Longest chain 15 peptides. Score 0.388 Round 4: 492 peptides, 85 chains. Longest chain 12 peptides. Score 0.409 Round 5: 476 peptides, 78 chains. Longest chain 13 peptides. Score 0.429 Taking the results from Round 5 Chains 79, Residues 398, Estimated correctness of the model 0.0 % 10 chains (65 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20398 restraints for refining 8793 atoms. 18733 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2054 (Rfree = 0.000) for 8793 atoms. Found 53 (78 requested) and removed 50 (39 requested) atoms. Cycle 17: After refmac, R = 0.1928 (Rfree = 0.000) for 8773 atoms. Found 27 (78 requested) and removed 46 (39 requested) atoms. Cycle 18: After refmac, R = 0.1910 (Rfree = 0.000) for 8748 atoms. Found 24 (78 requested) and removed 45 (39 requested) atoms. Cycle 19: After refmac, R = 0.1891 (Rfree = 0.000) for 8711 atoms. Found 20 (78 requested) and removed 45 (39 requested) atoms. Cycle 20: After refmac, R = 0.1837 (Rfree = 0.000) for 8682 atoms. Found 16 (77 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 8818 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 8839 seeds are put forward Round 1: 402 peptides, 85 chains. Longest chain 9 peptides. Score 0.272 Round 2: 450 peptides, 85 chains. Longest chain 14 peptides. Score 0.347 Round 3: 455 peptides, 84 chains. Longest chain 14 peptides. Score 0.361 Round 4: 452 peptides, 85 chains. Longest chain 10 peptides. Score 0.350 Round 5: 464 peptides, 82 chains. Longest chain 13 peptides. Score 0.387 Taking the results from Round 5 Chains 82, Residues 382, Estimated correctness of the model 0.0 % 6 chains (25 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20736 restraints for refining 8793 atoms. 19223 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1929 (Rfree = 0.000) for 8793 atoms. Found 40 (78 requested) and removed 46 (39 requested) atoms. Cycle 22: After refmac, R = 0.1791 (Rfree = 0.000) for 8772 atoms. Found 17 (78 requested) and removed 41 (39 requested) atoms. Cycle 23: After refmac, R = 0.1801 (Rfree = 0.000) for 8744 atoms. Found 21 (78 requested) and removed 42 (39 requested) atoms. Cycle 24: After refmac, R = 0.1766 (Rfree = 0.000) for 8715 atoms. Found 19 (78 requested) and removed 39 (39 requested) atoms. Cycle 25: After refmac, R = 0.1725 (Rfree = 0.000) for 8688 atoms. Found 16 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 8834 seeds are put forward NCS extension: 17 residues added (0 deleted due to clashes), 8851 seeds are put forward Round 1: 400 peptides, 86 chains. Longest chain 13 peptides. Score 0.262 Round 2: 435 peptides, 79 chains. Longest chain 14 peptides. Score 0.363 Round 3: 433 peptides, 79 chains. Longest chain 13 peptides. Score 0.360 Round 4: 437 peptides, 77 chains. Longest chain 11 peptides. Score 0.379 Round 5: 424 peptides, 73 chains. Longest chain 14 peptides. Score 0.385 Taking the results from Round 5 Chains 74, Residues 351, Estimated correctness of the model 0.0 % 9 chains (48 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20716 restraints for refining 8791 atoms. 19260 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1880 (Rfree = 0.000) for 8791 atoms. Found 44 (78 requested) and removed 53 (39 requested) atoms. Cycle 27: After refmac, R = 0.1767 (Rfree = 0.000) for 8774 atoms. Found 14 (78 requested) and removed 40 (39 requested) atoms. Cycle 28: After refmac, R = 0.1752 (Rfree = 0.000) for 8739 atoms. Found 10 (78 requested) and removed 39 (39 requested) atoms. Cycle 29: After refmac, R = 0.1716 (Rfree = 0.000) for 8703 atoms. Found 18 (78 requested) and removed 39 (39 requested) atoms. Cycle 30: After refmac, R = 0.1736 (Rfree = 0.000) for 8679 atoms. Found 18 (77 requested) and removed 39 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 8830 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 8842 seeds are put forward Round 1: 407 peptides, 85 chains. Longest chain 10 peptides. Score 0.280 Round 2: 459 peptides, 84 chains. Longest chain 12 peptides. Score 0.367 Round 3: 455 peptides, 82 chains. Longest chain 11 peptides. Score 0.374 Round 4: 455 peptides, 79 chains. Longest chain 16 peptides. Score 0.393 Round 5: 462 peptides, 79 chains. Longest chain 13 peptides. Score 0.403 Taking the results from Round 5 Chains 80, Residues 383, Estimated correctness of the model 0.0 % 9 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20251 restraints for refining 8793 atoms. 18655 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1858 (Rfree = 0.000) for 8793 atoms. Found 39 (78 requested) and removed 43 (39 requested) atoms. Cycle 32: After refmac, R = 0.1747 (Rfree = 0.000) for 8775 atoms. Found 29 (78 requested) and removed 41 (39 requested) atoms. Cycle 33: After refmac, R = 0.1737 (Rfree = 0.000) for 8751 atoms. Found 24 (78 requested) and removed 40 (39 requested) atoms. Cycle 34: After refmac, R = 0.1708 (Rfree = 0.000) for 8722 atoms. Found 30 (78 requested) and removed 40 (39 requested) atoms. Cycle 35: After refmac, R = 0.1716 (Rfree = 0.000) for 8700 atoms. Found 23 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 8848 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 8861 seeds are put forward Round 1: 366 peptides, 81 chains. Longest chain 8 peptides. Score 0.240 Round 2: 398 peptides, 78 chains. Longest chain 11 peptides. Score 0.313 Round 3: 426 peptides, 81 chains. Longest chain 11 peptides. Score 0.337 Round 4: 440 peptides, 80 chains. Longest chain 12 peptides. Score 0.364 Round 5: 430 peptides, 75 chains. Longest chain 11 peptides. Score 0.381 Taking the results from Round 5 Chains 75, Residues 355, Estimated correctness of the model 0.0 % 8 chains (45 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20502 restraints for refining 8793 atoms. 19055 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1853 (Rfree = 0.000) for 8793 atoms. Found 40 (78 requested) and removed 44 (39 requested) atoms. Cycle 37: After refmac, R = 0.1778 (Rfree = 0.000) for 8781 atoms. Found 31 (78 requested) and removed 43 (39 requested) atoms. Cycle 38: After refmac, R = 0.1769 (Rfree = 0.000) for 8761 atoms. Found 20 (78 requested) and removed 39 (39 requested) atoms. Cycle 39: After refmac, R = 0.1708 (Rfree = 0.000) for 8738 atoms. Found 17 (78 requested) and removed 39 (39 requested) atoms. Cycle 40: After refmac, R = 0.1708 (Rfree = 0.000) for 8706 atoms. Found 13 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.04 3.43 Search for helices and strands: 0 residues in 0 chains, 8779 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 8790 seeds are put forward Round 1: 335 peptides, 74 chains. Longest chain 8 peptides. Score 0.236 Round 2: 387 peptides, 76 chains. Longest chain 9 peptides. Score 0.309 Round 3: 411 peptides, 74 chains. Longest chain 13 peptides. Score 0.359 Round 4: 405 peptides, 75 chains. Longest chain 10 peptides. Score 0.344 Round 5: 378 peptides, 71 chains. Longest chain 11 peptides. Score 0.328 Taking the results from Round 3 Chains 74, Residues 337, Estimated correctness of the model 0.0 % 4 chains (16 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20674 restraints for refining 8792 atoms. 19366 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1840 (Rfree = 0.000) for 8792 atoms. Found 42 (78 requested) and removed 43 (39 requested) atoms. Cycle 42: After refmac, R = 0.1776 (Rfree = 0.000) for 8777 atoms. Found 30 (78 requested) and removed 41 (39 requested) atoms. Cycle 43: After refmac, R = 0.1743 (Rfree = 0.000) for 8764 atoms. Found 31 (78 requested) and removed 40 (39 requested) atoms. Cycle 44: After refmac, R = 0.1711 (Rfree = 0.000) for 8754 atoms. Found 33 (78 requested) and removed 39 (39 requested) atoms. Cycle 45: After refmac, R = 0.1700 (Rfree = 0.000) for 8740 atoms. Found 27 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.03 3.42 Search for helices and strands: 0 residues in 0 chains, 8832 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 8845 seeds are put forward Round 1: 337 peptides, 75 chains. Longest chain 9 peptides. Score 0.233 Round 2: 370 peptides, 76 chains. Longest chain 9 peptides. Score 0.281 Round 3: 387 peptides, 73 chains. Longest chain 8 peptides. Score 0.329 Round 4: 381 peptides, 72 chains. Longest chain 11 peptides. Score 0.326 Round 5: 370 peptides, 68 chains. Longest chain 10 peptides. Score 0.336 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 68, Residues 302, Estimated correctness of the model 0.0 % 8 chains (45 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 68 chains (302 residues) following loop building 8 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16190 reflections ( 91.24 % complete ) and 20668 restraints for refining 8793 atoms. 19434 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1741 (Rfree = 0.000) for 8793 atoms. Found 0 (78 requested) and removed 39 (39 requested) atoms. Cycle 47: After refmac, R = 0.1753 (Rfree = 0.000) for 8744 atoms. Found 0 (78 requested) and removed 35 (39 requested) atoms. Cycle 48: After refmac, R = 0.1710 (Rfree = 0.000) for 8703 atoms. Found 0 (78 requested) and removed 39 (39 requested) atoms. Cycle 49: After refmac, R = 0.1765 (Rfree = 0.000) for 8658 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 09:14:58 GMT 2018 Job finished. TimeTaking 77.73 Used memory is bytes: 2411072