Sun 23 Dec 23:42:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ii1-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ii1-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-mrncs ############### 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 ============================================================ Sun 23 Dec 23:42:34 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/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ii1-3.2-parrot-mrncs/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-mrncs.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-mrncs.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 10665 atoms. Observations/parameters ratio is 0.38 ------------------------------------------------------ Starting model: R = 0.3115 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2487 (Rfree = 0.000) for 10665 atoms. Found 43 (95 requested) and removed 340 (47 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.04 3.43 Search for helices and strands: 0 residues in 0 chains, 10441 seeds are put forward NCS extension: 0 residues added, 10441 seeds are put forward Round 1: 358 peptides, 73 chains. Longest chain 9 peptides. Score 0.282 Round 2: 418 peptides, 83 chains. Longest chain 13 peptides. Score 0.311 Round 3: 438 peptides, 79 chains. Longest chain 11 peptides. Score 0.368 Round 4: 453 peptides, 83 chains. Longest chain 11 peptides. Score 0.365 Round 5: 486 peptides, 81 chains. Longest chain 14 peptides. Score 0.425 Taking the results from Round 5 Chains 83, Residues 405, Estimated correctness of the model 0.0 % 14 chains (71 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20031 restraints for refining 8793 atoms. 18342 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2327 (Rfree = 0.000) for 8793 atoms. Found 37 (78 requested) and removed 87 (39 requested) atoms. Cycle 2: After refmac, R = 0.2119 (Rfree = 0.000) for 8699 atoms. Found 21 (78 requested) and removed 48 (39 requested) atoms. Cycle 3: After refmac, R = 0.2069 (Rfree = 0.000) for 8648 atoms. Found 13 (77 requested) and removed 45 (38 requested) atoms. Cycle 4: After refmac, R = 0.2117 (Rfree = 0.000) for 8603 atoms. Found 13 (77 requested) and removed 43 (38 requested) atoms. Cycle 5: After refmac, R = 0.2043 (Rfree = 0.000) for 8564 atoms. Found 13 (76 requested) and removed 40 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.06 3.45 Search for helices and strands: 0 residues in 0 chains, 8694 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8707 seeds are put forward Round 1: 429 peptides, 90 chains. Longest chain 10 peptides. Score 0.282 Round 2: 525 peptides, 95 chains. Longest chain 17 peptides. Score 0.395 Round 3: 511 peptides, 88 chains. Longest chain 16 peptides. Score 0.418 Round 4: 515 peptides, 85 chains. Longest chain 18 peptides. Score 0.441 Round 5: 538 peptides, 92 chains. Longest chain 16 peptides. Score 0.431 Taking the results from Round 4 Chains 87, Residues 430, Estimated correctness of the model 0.0 % 13 chains (95 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20012 restraints for refining 8793 atoms. 18157 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2279 (Rfree = 0.000) for 8793 atoms. Found 49 (78 requested) and removed 66 (39 requested) atoms. Cycle 7: After refmac, R = 0.2142 (Rfree = 0.000) for 8751 atoms. Found 14 (78 requested) and removed 43 (39 requested) atoms. Cycle 8: After refmac, R = 0.2080 (Rfree = 0.000) for 8704 atoms. Found 11 (78 requested) and removed 39 (39 requested) atoms. Cycle 9: After refmac, R = 0.2024 (Rfree = 0.000) for 8670 atoms. Found 4 (77 requested) and removed 39 (38 requested) atoms. Cycle 10: After refmac, R = 0.2029 (Rfree = 0.000) for 8629 atoms. Found 9 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.08 3.48 Search for helices and strands: 0 residues in 0 chains, 8744 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 8767 seeds are put forward Round 1: 476 peptides, 92 chains. Longest chain 17 peptides. Score 0.342 Round 2: 544 peptides, 93 chains. Longest chain 19 peptides. Score 0.433 Round 3: 524 peptides, 84 chains. Longest chain 16 peptides. Score 0.459 Round 4: 535 peptides, 84 chains. Longest chain 16 peptides. Score 0.474 Round 5: 558 peptides, 85 chains. Longest chain 16 peptides. Score 0.498 Taking the results from Round 5 Chains 85, Residues 473, Estimated correctness of the model 10.7 % 10 chains (52 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20397 restraints for refining 8792 atoms. 18474 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2512 (Rfree = 0.000) for 8792 atoms. Found 53 (78 requested) and removed 81 (39 requested) atoms. Cycle 12: After refmac, R = 0.2105 (Rfree = 0.000) for 8742 atoms. Found 35 (78 requested) and removed 44 (39 requested) atoms. Cycle 13: After refmac, R = 0.2101 (Rfree = 0.000) for 8717 atoms. Found 15 (78 requested) and removed 44 (39 requested) atoms. Cycle 14: After refmac, R = 0.1972 (Rfree = 0.000) for 8682 atoms. Found 17 (77 requested) and removed 43 (38 requested) atoms. Cycle 15: After refmac, R = 0.1946 (Rfree = 0.000) for 8652 atoms. Found 8 (77 requested) and removed 45 (38 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.07 3.47 Search for helices and strands: 0 residues in 0 chains, 8781 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 8800 seeds are put forward Round 1: 502 peptides, 97 chains. Longest chain 11 peptides. Score 0.349 Round 2: 544 peptides, 86 chains. Longest chain 15 peptides. Score 0.474 Round 3: 520 peptides, 82 chains. Longest chain 17 peptides. Score 0.465 Round 4: 549 peptides, 84 chains. Longest chain 18 peptides. Score 0.492 Round 5: 551 peptides, 86 chains. Longest chain 21 peptides. Score 0.483 Taking the results from Round 4 Chains 85, Residues 465, Estimated correctness of the model 8.7 % 7 chains (53 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20247 restraints for refining 8793 atoms. 18325 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2284 (Rfree = 0.000) for 8793 atoms. Found 47 (78 requested) and removed 60 (39 requested) atoms. Cycle 17: After refmac, R = 0.2044 (Rfree = 0.000) for 8768 atoms. Found 24 (78 requested) and removed 48 (39 requested) atoms. Cycle 18: After refmac, R = 0.2029 (Rfree = 0.000) for 8730 atoms. Found 8 (78 requested) and removed 39 (39 requested) atoms. Cycle 19: After refmac, R = 0.2011 (Rfree = 0.000) for 8693 atoms. Found 12 (78 requested) and removed 39 (39 requested) atoms. Cycle 20: After refmac, R = 0.1977 (Rfree = 0.000) for 8664 atoms. Found 4 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.05 3.44 Search for helices and strands: 0 residues in 0 chains, 8758 seeds are put forward NCS extension: 22 residues added (1 deleted due to clashes), 8780 seeds are put forward Round 1: 470 peptides, 86 chains. Longest chain 12 peptides. Score 0.371 Round 2: 517 peptides, 82 chains. Longest chain 18 peptides. Score 0.461 Round 3: 544 peptides, 82 chains. Longest chain 18 peptides. Score 0.496 Round 4: 520 peptides, 77 chains. Longest chain 23 peptides. Score 0.494 Round 5: 526 peptides, 77 chains. Longest chain 23 peptides. Score 0.502 Taking the results from Round 5 Chains 78, Residues 449, Estimated correctness of the model 12.0 % 12 chains (89 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 19970 restraints for refining 8792 atoms. 18025 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2166 (Rfree = 0.000) for 8792 atoms. Found 52 (78 requested) and removed 54 (39 requested) atoms. Cycle 22: After refmac, R = 0.2226 (Rfree = 0.000) for 8776 atoms. Found 53 (78 requested) and removed 48 (39 requested) atoms. Cycle 23: After refmac, R = 0.1895 (Rfree = 0.000) for 8766 atoms. Found 22 (78 requested) and removed 42 (39 requested) atoms. Cycle 24: After refmac, R = 0.2048 (Rfree = 0.000) for 8732 atoms. Found 39 (78 requested) and removed 48 (39 requested) atoms. Cycle 25: After refmac, R = 0.1852 (Rfree = 0.000) for 8714 atoms. Found 13 (78 requested) and removed 45 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.02 3.41 Search for helices and strands: 0 residues in 0 chains, 8851 seeds are put forward NCS extension: 18 residues added (0 deleted due to clashes), 8869 seeds are put forward Round 1: 432 peptides, 88 chains. Longest chain 14 peptides. Score 0.300 Round 2: 485 peptides, 79 chains. Longest chain 23 peptides. Score 0.435 Round 3: 489 peptides, 84 chains. Longest chain 14 peptides. Score 0.411 Round 4: 500 peptides, 81 chains. Longest chain 18 peptides. Score 0.444 Round 5: 489 peptides, 78 chains. Longest chain 19 peptides. Score 0.447 Taking the results from Round 5 Chains 78, Residues 411, Estimated correctness of the model 0.0 % 6 chains (30 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20656 restraints for refining 8793 atoms. 19018 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2067 (Rfree = 0.000) for 8793 atoms. Found 56 (78 requested) and removed 42 (39 requested) atoms. Cycle 27: After refmac, R = 0.1913 (Rfree = 0.000) for 8801 atoms. Found 25 (79 requested) and removed 39 (39 requested) atoms. Cycle 28: After refmac, R = 0.1863 (Rfree = 0.000) for 8783 atoms. Found 10 (78 requested) and removed 39 (39 requested) atoms. Cycle 29: After refmac, R = 0.1853 (Rfree = 0.000) for 8750 atoms. Found 11 (78 requested) and removed 39 (39 requested) atoms. Cycle 30: After refmac, R = 0.1884 (Rfree = 0.000) for 8719 atoms. Found 18 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.04 3.43 Search for helices and strands: 0 residues in 0 chains, 8846 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 8874 seeds are put forward Round 1: 436 peptides, 87 chains. Longest chain 10 peptides. Score 0.313 Round 2: 480 peptides, 90 chains. Longest chain 10 peptides. Score 0.360 Round 3: 495 peptides, 85 chains. Longest chain 11 peptides. Score 0.413 Round 4: 488 peptides, 85 chains. Longest chain 14 peptides. Score 0.403 Round 5: 464 peptides, 79 chains. Longest chain 13 peptides. Score 0.406 Taking the results from Round 3 Chains 85, Residues 410, Estimated correctness of the model 0.0 % 10 chains (51 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20466 restraints for refining 8792 atoms. 18798 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1978 (Rfree = 0.000) for 8792 atoms. Found 42 (78 requested) and removed 45 (39 requested) atoms. Cycle 32: After refmac, R = 0.1874 (Rfree = 0.000) for 8777 atoms. Found 14 (78 requested) and removed 40 (39 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1833 (Rfree = 0.000) for 8743 atoms. Found 9 (78 requested) and removed 39 (39 requested) atoms. Cycle 34: After refmac, R = 0.1820 (Rfree = 0.000) for 8710 atoms. Found 5 (78 requested) and removed 39 (39 requested) atoms. Cycle 35: After refmac, R = 0.1790 (Rfree = 0.000) for 8674 atoms. Found 7 (77 requested) and removed 38 (38 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.02 3.41 Search for helices and strands: 0 residues in 0 chains, 8793 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 8806 seeds are put forward Round 1: 386 peptides, 78 chains. Longest chain 10 peptides. Score 0.294 Round 2: 439 peptides, 81 chains. Longest chain 11 peptides. Score 0.356 Round 3: 450 peptides, 81 chains. Longest chain 15 peptides. Score 0.373 Round 4: 441 peptides, 82 chains. Longest chain 11 peptides. Score 0.353 Round 5: 434 peptides, 77 chains. Longest chain 16 peptides. Score 0.375 Taking the results from Round 5 Chains 77, Residues 357, Estimated correctness of the model 0.0 % 4 chains (18 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 21049 restraints for refining 8793 atoms. 19662 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2055 (Rfree = 0.000) for 8793 atoms. Found 58 (78 requested) and removed 39 (39 requested) atoms. Cycle 37: After refmac, R = 0.1940 (Rfree = 0.000) for 8801 atoms. Found 17 (79 requested) and removed 41 (39 requested) atoms. Cycle 38: After refmac, R = 0.1913 (Rfree = 0.000) for 8773 atoms. Found 12 (78 requested) and removed 39 (39 requested) atoms. Cycle 39: After refmac, R = 0.1879 (Rfree = 0.000) for 8745 atoms. Found 7 (78 requested) and removed 39 (39 requested) atoms. Cycle 40: After refmac, R = 0.1846 (Rfree = 0.000) for 8713 atoms. Found 10 (78 requested) and removed 39 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.03 3.42 Search for helices and strands: 0 residues in 0 chains, 8832 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 8847 seeds are put forward Round 1: 395 peptides, 84 chains. Longest chain 10 peptides. Score 0.267 Round 2: 460 peptides, 88 chains. Longest chain 12 peptides. Score 0.343 Round 3: 474 peptides, 86 chains. Longest chain 13 peptides. Score 0.377 Round 4: 456 peptides, 81 chains. Longest chain 14 peptides. Score 0.382 Round 5: 432 peptides, 77 chains. Longest chain 13 peptides. Score 0.372 Taking the results from Round 4 Chains 81, Residues 375, Estimated correctness of the model 0.0 % 7 chains (33 residues) have been docked in sequence ------------------------------------------------------ 16190 reflections ( 91.24 % complete ) and 20771 restraints for refining 8793 atoms. 19273 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2042 (Rfree = 0.000) for 8793 atoms. Found 57 (78 requested) and removed 41 (39 requested) atoms. Cycle 42: After refmac, R = 0.1915 (Rfree = 0.000) for 8802 atoms. Found 24 (79 requested) and removed 39 (39 requested) atoms. Cycle 43: After refmac, R = 0.1857 (Rfree = 0.000) for 8782 atoms. Found 11 (78 requested) and removed 39 (39 requested) atoms. Cycle 44: After refmac, R = 0.1816 (Rfree = 0.000) for 8750 atoms. Found 10 (78 requested) and removed 39 (39 requested) atoms. Cycle 45: After refmac, R = 0.1800 (Rfree = 0.000) for 8720 atoms. Found 9 (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, 8824 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 8842 seeds are put forward Round 1: 393 peptides, 82 chains. Longest chain 11 peptides. Score 0.278 Round 2: 413 peptides, 73 chains. Longest chain 14 peptides. Score 0.369 Round 3: 409 peptides, 70 chains. Longest chain 15 peptides. Score 0.382 Round 4: 413 peptides, 73 chains. Longest chain 16 peptides. Score 0.369 Round 5: 415 peptides, 75 chains. Longest chain 18 peptides. Score 0.359 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 339, Estimated correctness of the model 0.0 % 4 chains (24 residues) have been docked in sequence Sequence coverage is 7 % Consider running further cycles of model building using 2ii1-3_warpNtrace.pdb as input Building loops using Loopy2018 70 chains (339 residues) following loop building 4 chains (24 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 16190 reflections ( 91.24 % complete ) and 20577 restraints for refining 8749 atoms. 19231 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1948 (Rfree = 0.000) for 8749 atoms. Found 0 (78 requested) and removed 20 (39 requested) atoms. Cycle 47: After refmac, R = 0.1882 (Rfree = 0.000) for 8726 atoms. Found 0 (78 requested) and removed 12 (39 requested) atoms. Cycle 48: After refmac, R = 0.1861 (Rfree = 0.000) for 8711 atoms. Found 0 (78 requested) and removed 7 (39 requested) atoms. Cycle 49: After refmac, R = 0.1846 (Rfree = 0.000) for 8703 atoms. TimeTaking 83.17