null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ii1-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:12 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/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-hancs/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-hancs.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-hancs.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 10639 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3114 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2341 (Rfree = 0.000) for 10639 atoms. Found 44 (95 requested) and removed 122 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 10639 seeds are put forward NCS extension: 0 residues added, 10639 seeds are put forward Round 1: 391 peptides, 81 chains. Longest chain 11 peptides. Score 0.281 Round 2: 481 peptides, 88 chains. Longest chain 13 peptides. Score 0.374 Round 3: 551 peptides, 98 chains. Longest chain 14 peptides. Score 0.414 Round 4: 521 peptides, 91 chains. Longest chain 12 peptides. Score 0.413 Round 5: 554 peptides, 92 chains. Longest chain 15 peptides. Score 0.453 Taking the results from Round 5 Chains 93, Residues 462, Estimated correctness of the model 0.0 % 11 chains (59 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20061 restraints for refining 8791 atoms. 18174 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2227 (Rfree = 0.000) for 8791 atoms. Found 57 (78 requested) and removed 55 (39 requested) atoms. Cycle 2: After refmac, R = 0.2088 (Rfree = 0.000) for 8734 atoms. Found 27 (78 requested) and removed 44 (39 requested) atoms. Cycle 3: After refmac, R = 0.2022 (Rfree = 0.000) for 8701 atoms. Found 12 (78 requested) and removed 40 (39 requested) atoms. Cycle 4: After refmac, R = 0.1989 (Rfree = 0.000) for 8657 atoms. Found 6 (77 requested) and removed 39 (38 requested) atoms. Cycle 5: After refmac, R = 0.1967 (Rfree = 0.000) for 8612 atoms. Found 13 (77 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 8708 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 8724 seeds are put forward Round 1: 513 peptides, 96 chains. Longest chain 22 peptides. Score 0.372 Round 2: 566 peptides, 88 chains. Longest chain 16 peptides. Score 0.491 Round 3: 600 peptides, 99 chains. Longest chain 23 peptides. Score 0.474 Round 4: 595 peptides, 92 chains. Longest chain 18 peptides. Score 0.506 Round 5: 616 peptides, 99 chains. Longest chain 20 peptides. Score 0.494 Taking the results from Round 4 Chains 92, Residues 503, Estimated correctness of the model 13.3 % 13 chains (63 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20046 restraints for refining 8793 atoms. 17996 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2263 (Rfree = 0.000) for 8793 atoms. Found 47 (78 requested) and removed 50 (39 requested) atoms. Cycle 7: After refmac, R = 0.2129 (Rfree = 0.000) for 8765 atoms. Found 18 (78 requested) and removed 42 (39 requested) atoms. Cycle 8: After refmac, R = 0.2076 (Rfree = 0.000) for 8730 atoms. Found 10 (78 requested) and removed 39 (39 requested) atoms. Cycle 9: After refmac, R = 0.2060 (Rfree = 0.000) for 8694 atoms. Found 8 (78 requested) and removed 39 (39 requested) atoms. Cycle 10: After refmac, R = 0.2028 (Rfree = 0.000) for 8656 atoms. Found 9 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.10 3.50 Search for helices and strands: 0 residues in 0 chains, 8754 seeds are put forward NCS extension: 13 residues added (5 deleted due to clashes), 8767 seeds are put forward Round 1: 514 peptides, 96 chains. Longest chain 16 peptides. Score 0.373 Round 2: 597 peptides, 93 chains. Longest chain 21 peptides. Score 0.503 Round 3: 595 peptides, 90 chains. Longest chain 21 peptides. Score 0.517 Round 4: 586 peptides, 93 chains. Longest chain 16 peptides. Score 0.489 Round 5: 587 peptides, 89 chains. Longest chain 18 peptides. Score 0.512 Taking the results from Round 3 Chains 93, Residues 505, Estimated correctness of the model 16.8 % 18 chains (112 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 19726 restraints for refining 8792 atoms. 17513 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2236 (Rfree = 0.000) for 8792 atoms. Found 45 (78 requested) and removed 54 (39 requested) atoms. Cycle 12: After refmac, R = 0.2058 (Rfree = 0.000) for 8760 atoms. Found 17 (78 requested) and removed 41 (39 requested) atoms. Cycle 13: After refmac, R = 0.2032 (Rfree = 0.000) for 8723 atoms. Found 16 (78 requested) and removed 42 (39 requested) atoms. Cycle 14: After refmac, R = 0.1953 (Rfree = 0.000) for 8679 atoms. Found 22 (78 requested) and removed 43 (39 requested) atoms. Cycle 15: After refmac, R = 0.1851 (Rfree = 0.000) for 8623 atoms. Found 18 (77 requested) and removed 47 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 8731 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 8749 seeds are put forward Round 1: 507 peptides, 95 chains. Longest chain 14 peptides. Score 0.369 Round 2: 562 peptides, 87 chains. Longest chain 21 peptides. Score 0.492 Round 3: 564 peptides, 88 chains. Longest chain 19 peptides. Score 0.489 Round 4: 570 peptides, 84 chains. Longest chain 26 peptides. Score 0.518 Round 5: 578 peptides, 89 chains. Longest chain 17 peptides. Score 0.501 Taking the results from Round 4 Chains 86, Residues 486, Estimated correctness of the model 17.1 % 13 chains (87 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 19761 restraints for refining 8707 atoms. 17683 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2080 (Rfree = 0.000) for 8707 atoms. Found 38 (78 requested) and removed 56 (39 requested) atoms. Cycle 17: After refmac, R = 0.1953 (Rfree = 0.000) for 8676 atoms. Found 16 (77 requested) and removed 45 (38 requested) atoms. Cycle 18: After refmac, R = 0.1881 (Rfree = 0.000) for 8642 atoms. Found 14 (77 requested) and removed 38 (38 requested) atoms. Cycle 19: After refmac, R = 0.1849 (Rfree = 0.000) for 8613 atoms. Found 14 (77 requested) and removed 38 (38 requested) atoms. Cycle 20: After refmac, R = 0.1812 (Rfree = 0.000) for 8584 atoms. Found 11 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 8686 seeds are put forward NCS extension: 27 residues added (5 deleted due to clashes), 8713 seeds are put forward Round 1: 513 peptides, 93 chains. Longest chain 17 peptides. Score 0.390 Round 2: 567 peptides, 91 chains. Longest chain 22 peptides. Score 0.476 Round 3: 575 peptides, 89 chains. Longest chain 28 peptides. Score 0.497 Round 4: 586 peptides, 92 chains. Longest chain 22 peptides. Score 0.494 Round 5: 592 peptides, 88 chains. Longest chain 23 peptides. Score 0.523 Taking the results from Round 5 Chains 89, Residues 504, Estimated correctness of the model 18.7 % 10 chains (63 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 19835 restraints for refining 8793 atoms. 17736 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2017 (Rfree = 0.000) for 8793 atoms. Found 43 (78 requested) and removed 56 (39 requested) atoms. Cycle 22: After refmac, R = 0.1882 (Rfree = 0.000) for 8764 atoms. Found 20 (78 requested) and removed 43 (39 requested) atoms. Cycle 23: After refmac, R = 0.1826 (Rfree = 0.000) for 8732 atoms. Found 20 (78 requested) and removed 41 (39 requested) atoms. Cycle 24: After refmac, R = 0.2001 (Rfree = 0.000) for 8701 atoms. Found 39 (78 requested) and removed 43 (39 requested) atoms. Cycle 25: After refmac, R = 0.1714 (Rfree = 0.000) for 8688 atoms. Found 11 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 8828 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 8853 seeds are put forward Round 1: 502 peptides, 97 chains. Longest chain 15 peptides. Score 0.349 Round 2: 571 peptides, 98 chains. Longest chain 17 peptides. Score 0.441 Round 3: 567 peptides, 97 chains. Longest chain 17 peptides. Score 0.441 Round 4: 572 peptides, 94 chains. Longest chain 17 peptides. Score 0.465 Round 5: 572 peptides, 90 chains. Longest chain 18 peptides. Score 0.488 Taking the results from Round 5 Chains 91, Residues 482, Estimated correctness of the model 7.4 % 11 chains (82 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 19787 restraints for refining 8793 atoms. 17723 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1997 (Rfree = 0.000) for 8793 atoms. Found 39 (78 requested) and removed 56 (39 requested) atoms. Cycle 27: After refmac, R = 0.1878 (Rfree = 0.000) for 8767 atoms. Found 18 (78 requested) and removed 42 (39 requested) atoms. Cycle 28: After refmac, R = 0.1822 (Rfree = 0.000) for 8737 atoms. Found 8 (78 requested) and removed 39 (39 requested) atoms. Cycle 29: After refmac, R = 0.1760 (Rfree = 0.000) for 8703 atoms. Found 14 (78 requested) and removed 39 (39 requested) atoms. Cycle 30: After refmac, R = 0.1724 (Rfree = 0.000) for 8675 atoms. Found 7 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 8789 seeds are put forward NCS extension: 13 residues added (2 deleted due to clashes), 8802 seeds are put forward Round 1: 502 peptides, 97 chains. Longest chain 17 peptides. Score 0.349 Round 2: 512 peptides, 87 chains. Longest chain 14 peptides. Score 0.425 Round 3: 531 peptides, 86 chains. Longest chain 16 peptides. Score 0.457 Round 4: 540 peptides, 85 chains. Longest chain 22 peptides. Score 0.474 Round 5: 539 peptides, 88 chains. Longest chain 16 peptides. Score 0.456 Taking the results from Round 4 Chains 88, Residues 455, Estimated correctness of the model 2.7 % 8 chains (54 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20385 restraints for refining 8793 atoms. 18510 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1928 (Rfree = 0.000) for 8793 atoms. Found 32 (78 requested) and removed 45 (39 requested) atoms. Cycle 32: After refmac, R = 0.1813 (Rfree = 0.000) for 8777 atoms. Found 14 (78 requested) and removed 39 (39 requested) atoms. Cycle 33: After refmac, R = 0.1732 (Rfree = 0.000) for 8747 atoms. Found 8 (78 requested) and removed 39 (39 requested) atoms. Cycle 34: After refmac, R = 0.1816 (Rfree = 0.000) for 8711 atoms. Found 35 (78 requested) and removed 39 (39 requested) atoms. Cycle 35: After refmac, R = 0.1676 (Rfree = 0.000) for 8700 atoms. Found 13 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 8801 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8820 seeds are put forward Round 1: 441 peptides, 88 chains. Longest chain 12 peptides. Score 0.314 Round 2: 493 peptides, 78 chains. Longest chain 17 peptides. Score 0.452 Round 3: 490 peptides, 81 chains. Longest chain 14 peptides. Score 0.430 Round 4: 497 peptides, 78 chains. Longest chain 16 peptides. Score 0.458 Round 5: 506 peptides, 78 chains. Longest chain 22 peptides. Score 0.470 Taking the results from Round 5 Chains 78, Residues 428, Estimated correctness of the model 1.4 % 5 chains (27 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20897 restraints for refining 8793 atoms. 19196 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1841 (Rfree = 0.000) for 8793 atoms. Found 27 (78 requested) and removed 41 (39 requested) atoms. Cycle 37: After refmac, R = 0.1737 (Rfree = 0.000) for 8771 atoms. Found 14 (78 requested) and removed 40 (39 requested) atoms. Cycle 38: After refmac, R = 0.1719 (Rfree = 0.000) for 8740 atoms. Found 11 (78 requested) and removed 39 (39 requested) atoms. Cycle 39: After refmac, R = 0.1695 (Rfree = 0.000) for 8709 atoms. Found 23 (78 requested) and removed 39 (39 requested) atoms. Cycle 40: After refmac, R = 0.1574 (Rfree = 0.000) for 8691 atoms. Found 11 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 8807 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 8826 seeds are put forward Round 1: 399 peptides, 77 chains. Longest chain 11 peptides. Score 0.321 Round 2: 470 peptides, 76 chains. Longest chain 15 peptides. Score 0.433 Round 3: 449 peptides, 75 chains. Longest chain 15 peptides. Score 0.409 Round 4: 483 peptides, 81 chains. Longest chain 13 peptides. Score 0.421 Round 5: 467 peptides, 76 chains. Longest chain 13 peptides. Score 0.428 Taking the results from Round 2 Chains 78, Residues 394, Estimated correctness of the model 0.0 % 7 chains (39 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20544 restraints for refining 8791 atoms. 18936 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1682 (Rfree = 0.000) for 8791 atoms. Found 44 (78 requested) and removed 45 (39 requested) atoms. Cycle 42: After refmac, R = 0.1559 (Rfree = 0.000) for 8780 atoms. Found 13 (78 requested) and removed 41 (39 requested) atoms. Cycle 43: After refmac, R = 0.1507 (Rfree = 0.000) for 8746 atoms. Found 6 (78 requested) and removed 39 (39 requested) atoms. Cycle 44: After refmac, R = 0.1494 (Rfree = 0.000) for 8710 atoms. Found 11 (78 requested) and removed 39 (39 requested) atoms. Cycle 45: After refmac, R = 0.1469 (Rfree = 0.000) for 8681 atoms. Found 11 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 3.49 Search for helices and strands: 0 residues in 0 chains, 8786 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 8807 seeds are put forward Round 1: 416 peptides, 81 chains. Longest chain 14 peptides. Score 0.321 Round 2: 455 peptides, 75 chains. Longest chain 15 peptides. Score 0.418 Round 3: 463 peptides, 81 chains. Longest chain 15 peptides. Score 0.392 Round 4: 440 peptides, 74 chains. Longest chain 20 peptides. Score 0.402 Round 5: 436 peptides, 70 chains. Longest chain 15 peptides. Score 0.422 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 71, Residues 366, Estimated correctness of the model 0.0 % 7 chains (36 residues) have been docked in sequence Sequence coverage is 9 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 72 A and 85 A 70 chains (371 residues) following loop building 6 chains (48 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16190 reflections ( 91.24 % complete ) and 20499 restraints for refining 8791 atoms. 18966 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1765 (Rfree = 0.000) for 8791 atoms. Found 0 (78 requested) and removed 39 (39 requested) atoms. Cycle 47: After refmac, R = 0.1760 (Rfree = 0.000) for 8742 atoms. Found 0 (78 requested) and removed 38 (39 requested) atoms. Cycle 48: After refmac, R = 0.2067 (Rfree = 0.000) for 8698 atoms. Found 0 (78 requested) and removed 39 (39 requested) atoms. Cycle 49: After refmac, R = 0.1778 (Rfree = 0.000) for 8651 atoms. Found 0 (77 requested) and removed 38 (38 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:40:48 GMT 2018 Job finished. TimeTaking 132.85 Used memory is bytes: 15959648