Mon 24 Dec 00:08:37 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 2anu-3.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2anu-3.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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/2anu-3.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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 ============================================================ Mon 24 Dec 00:08:41 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/2anu-3.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2anu-3.8-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 1241 and 0 Target number of residues in the AU: 1241 Target solvent content: 0.6322 Checking the provided sequence file Detected sequence length: 255 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1530 Adjusted target solvent content: 0.55 Input MTZ file: 2anu-3.8-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: 146 Cell parameters: 111.273 111.273 383.188 90.000 90.000 120.000 Input sequence file: 2anu-3.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12240 target number of atoms Had to go as low as 0.80 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: 127.729 3.800 Wilson plot Bfac: 67.68 17399 reflections ( 99.75 % complete ) and 0 restraints for refining 13564 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.2902 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2862 (Rfree = 0.000) for 13564 atoms. Found 74 (74 requested) and removed 58 (37 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.53 3.30 Search for helices and strands: 0 residues in 0 chains, 13824 seeds are put forward NCS extension: 0 residues added, 13824 seeds are put forward Round 1: 613 peptides, 113 chains. Longest chain 13 peptides. Score 0.335 Round 2: 818 peptides, 113 chains. Longest chain 23 peptides. Score 0.512 Round 3: 880 peptides, 120 chains. Longest chain 24 peptides. Score 0.535 Round 4: 889 peptides, 105 chains. Longest chain 26 peptides. Score 0.589 Round 5: 903 peptides, 107 chains. Longest chain 27 peptides. Score 0.593 Taking the results from Round 5 Chains 107, Residues 796, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 25664 restraints for refining 11062 atoms. 22587 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2471 (Rfree = 0.000) for 11062 atoms. Found 60 (60 requested) and removed 60 (30 requested) atoms. Cycle 2: After refmac, R = 0.2349 (Rfree = 0.000) for 10860 atoms. Found 60 (60 requested) and removed 51 (30 requested) atoms. Cycle 3: After refmac, R = 0.2002 (Rfree = 0.000) for 10771 atoms. Found 39 (59 requested) and removed 46 (29 requested) atoms. Cycle 4: After refmac, R = 0.2141 (Rfree = 0.000) for 10718 atoms. Found 59 (59 requested) and removed 53 (29 requested) atoms. Cycle 5: After refmac, R = 0.1882 (Rfree = 0.000) for 10685 atoms. Found 27 (58 requested) and removed 44 (29 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 11057 seeds are put forward NCS extension: 26 residues added (2 deleted due to clashes), 11083 seeds are put forward Round 1: 770 peptides, 125 chains. Longest chain 23 peptides. Score 0.430 Round 2: 847 peptides, 112 chains. Longest chain 24 peptides. Score 0.537 Round 3: 832 peptides, 111 chains. Longest chain 23 peptides. Score 0.529 Round 4: 842 peptides, 108 chains. Longest chain 21 peptides. Score 0.547 Round 5: 826 peptides, 101 chains. Longest chain 28 peptides. Score 0.558 Taking the results from Round 5 Chains 102, Residues 725, Estimated correctness of the model 0.0 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26075 restraints for refining 11069 atoms. 23205 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2192 (Rfree = 0.000) for 11069 atoms. Found 56 (60 requested) and removed 63 (30 requested) atoms. Cycle 7: After refmac, R = 0.2154 (Rfree = 0.000) for 10973 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 8: After refmac, R = 0.2076 (Rfree = 0.000) for 10924 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Cycle 9: After refmac, R = 0.1760 (Rfree = 0.000) for 10888 atoms. Found 13 (60 requested) and removed 37 (30 requested) atoms. Cycle 10: After refmac, R = 0.1896 (Rfree = 0.000) for 10832 atoms. Found 59 (59 requested) and removed 37 (29 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 11222 seeds are put forward NCS extension: 38 residues added (1 deleted due to clashes), 11260 seeds are put forward Round 1: 771 peptides, 123 chains. Longest chain 26 peptides. Score 0.439 Round 2: 832 peptides, 112 chains. Longest chain 21 peptides. Score 0.526 Round 3: 817 peptides, 108 chains. Longest chain 19 peptides. Score 0.528 Round 4: 838 peptides, 107 chains. Longest chain 19 peptides. Score 0.547 Round 5: 856 peptides, 106 chains. Longest chain 23 peptides. Score 0.563 Taking the results from Round 5 Chains 106, Residues 750, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26123 restraints for refining 11068 atoms. 23229 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2098 (Rfree = 0.000) for 11068 atoms. Found 60 (60 requested) and removed 44 (30 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2037 (Rfree = 0.000) for 10998 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Cycle 13: After refmac, R = 0.1956 (Rfree = 0.000) for 10957 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. Cycle 14: After refmac, R = 0.1857 (Rfree = 0.000) for 10936 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. Cycle 15: After refmac, R = 0.1601 (Rfree = 0.000) for 10925 atoms. Found 17 (60 requested) and removed 36 (30 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11249 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 11272 seeds are put forward Round 1: 726 peptides, 120 chains. Longest chain 16 peptides. Score 0.411 Round 2: 793 peptides, 109 chains. Longest chain 24 peptides. Score 0.507 Round 3: 807 peptides, 106 chains. Longest chain 21 peptides. Score 0.528 Round 4: 816 peptides, 109 chains. Longest chain 24 peptides. Score 0.524 Round 5: 782 peptides, 112 chains. Longest chain 19 peptides. Score 0.487 Taking the results from Round 3 Chains 108, Residues 701, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26162 restraints for refining 11069 atoms. 23419 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2101 (Rfree = 0.000) for 11069 atoms. Found 60 (60 requested) and removed 47 (30 requested) atoms. Cycle 17: After refmac, R = 0.2062 (Rfree = 0.000) for 11026 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. Cycle 18: After refmac, R = 0.1920 (Rfree = 0.000) for 11012 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1994 (Rfree = 0.000) for 10996 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Cycle 20: After refmac, R = 0.1913 (Rfree = 0.000) for 10982 atoms. Found 60 (60 requested) and removed 33 (30 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 11324 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 11346 seeds are put forward Round 1: 683 peptides, 119 chains. Longest chain 15 peptides. Score 0.377 Round 2: 759 peptides, 112 chains. Longest chain 19 peptides. Score 0.469 Round 3: 789 peptides, 113 chains. Longest chain 19 peptides. Score 0.489 Round 4: 777 peptides, 103 chains. Longest chain 20 peptides. Score 0.515 Round 5: 782 peptides, 109 chains. Longest chain 22 peptides. Score 0.498 Taking the results from Round 4 Chains 103, Residues 674, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26488 restraints for refining 11070 atoms. 23895 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2106 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 22: After refmac, R = 0.2099 (Rfree = 0.000) for 11039 atoms. Found 60 (60 requested) and removed 48 (30 requested) atoms. Cycle 23: After refmac, R = 0.2037 (Rfree = 0.000) for 11014 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 24: After refmac, R = 0.1923 (Rfree = 0.000) for 11004 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 25: After refmac, R = 0.1926 (Rfree = 0.000) for 10999 atoms. Found 60 (60 requested) and removed 43 (30 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.24 Search for helices and strands: 0 residues in 0 chains, 11376 seeds are put forward NCS extension: 26 residues added (3 deleted due to clashes), 11402 seeds are put forward Round 1: 636 peptides, 109 chains. Longest chain 16 peptides. Score 0.373 Round 2: 723 peptides, 111 chains. Longest chain 19 peptides. Score 0.443 Round 3: 733 peptides, 111 chains. Longest chain 24 peptides. Score 0.451 Round 4: 720 peptides, 104 chains. Longest chain 19 peptides. Score 0.466 Round 5: 734 peptides, 100 chains. Longest chain 32 peptides. Score 0.492 Taking the results from Round 5 Chains 102, Residues 634, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 26747 restraints for refining 11071 atoms. 24242 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2130 (Rfree = 0.000) for 11071 atoms. Found 60 (60 requested) and removed 46 (30 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2071 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 28: After refmac, R = 0.2023 (Rfree = 0.000) for 11010 atoms. Found 60 (60 requested) and removed 40 (30 requested) atoms. Cycle 29: After refmac, R = 0.1775 (Rfree = 0.000) for 10989 atoms. Found 29 (60 requested) and removed 42 (30 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1718 (Rfree = 0.000) for 10949 atoms. Found 28 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.47 3.25 Search for helices and strands: 0 residues in 0 chains, 11195 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 11215 seeds are put forward Round 1: 650 peptides, 124 chains. Longest chain 13 peptides. Score 0.326 Round 2: 671 peptides, 102 chains. Longest chain 18 peptides. Score 0.432 Round 3: 695 peptides, 104 chains. Longest chain 18 peptides. Score 0.445 Round 4: 702 peptides, 103 chains. Longest chain 18 peptides. Score 0.455 Round 5: 696 peptides, 105 chains. Longest chain 18 peptides. Score 0.442 Taking the results from Round 4 Chains 103, Residues 599, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 27297 restraints for refining 11068 atoms. 25004 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2087 (Rfree = 0.000) for 11068 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Cycle 32: After refmac, R = 0.2256 (Rfree = 0.000) for 11035 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 33: After refmac, R = 0.2038 (Rfree = 0.000) for 11024 atoms. Found 60 (60 requested) and removed 33 (30 requested) atoms. Cycle 34: After refmac, R = 0.2133 (Rfree = 0.000) for 11009 atoms. Found 60 (60 requested) and removed 39 (30 requested) atoms. Cycle 35: After refmac, R = 0.2050 (Rfree = 0.000) for 10997 atoms. Found 60 (60 requested) and removed 37 (30 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 3.22 Search for helices and strands: 0 residues in 0 chains, 11307 seeds are put forward NCS extension: 21 residues added (0 deleted due to clashes), 11328 seeds are put forward Round 1: 597 peptides, 112 chains. Longest chain 16 peptides. Score 0.324 Round 2: 648 peptides, 107 chains. Longest chain 14 peptides. Score 0.392 Round 3: 662 peptides, 101 chains. Longest chain 17 peptides. Score 0.428 Round 4: 666 peptides, 100 chains. Longest chain 19 peptides. Score 0.435 Round 5: 648 peptides, 98 chains. Longest chain 22 peptides. Score 0.428 Taking the results from Round 4 Chains 100, Residues 566, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 27383 restraints for refining 11067 atoms. 25219 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2132 (Rfree = 0.000) for 11067 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2203 (Rfree = 0.000) for 11050 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Cycle 38: After refmac, R = 0.2116 (Rfree = 0.000) for 11034 atoms. Found 60 (60 requested) and removed 38 (30 requested) atoms. Cycle 39: After refmac, R = 0.2042 (Rfree = 0.000) for 11022 atoms. Found 60 (60 requested) and removed 35 (30 requested) atoms. Cycle 40: After refmac, R = 0.2096 (Rfree = 0.000) for 11030 atoms. Found 60 (60 requested) and removed 41 (30 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.49 3.26 Search for helices and strands: 0 residues in 0 chains, 11388 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 11414 seeds are put forward Round 1: 583 peptides, 113 chains. Longest chain 13 peptides. Score 0.306 Round 2: 663 peptides, 115 chains. Longest chain 17 peptides. Score 0.374 Round 3: 671 peptides, 111 chains. Longest chain 18 peptides. Score 0.397 Round 4: 691 peptides, 109 chains. Longest chain 17 peptides. Score 0.423 Round 5: 680 peptides, 108 chains. Longest chain 16 peptides. Score 0.417 Taking the results from Round 4 Chains 109, Residues 582, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 17399 reflections ( 99.75 % complete ) and 27105 restraints for refining 11070 atoms. 24886 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2078 (Rfree = 0.000) for 11070 atoms. Found 60 (60 requested) and removed 42 (30 requested) atoms. Cycle 42: After refmac, R = 0.2057 (Rfree = 0.000) for 11028 atoms. Found 60 (60 requested) and removed 37 (30 requested) atoms. Cycle 43: After refmac, R = 0.2091 (Rfree = 0.000) for 11009 atoms. Found 60 (60 requested) and removed 45 (30 requested) atoms. Cycle 44: After refmac, R = 0.1713 (Rfree = 0.000) for 10985 atoms. Found 42 (60 requested) and removed 34 (30 requested) atoms. Cycle 45: After refmac, R = 0.1628 (Rfree = 0.000) for 10971 atoms. Found 22 (60 requested) and removed 32 (30 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.26 Search for helices and strands: 0 residues in 0 chains, 11260 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 11279 seeds are put forward Round 1: 529 peptides, 104 chains. Longest chain 14 peptides. Score 0.290 Round 2: 600 peptides, 104 chains. Longest chain 21 peptides. Score 0.360 Round 3: 626 peptides, 104 chains. Longest chain 14 peptides. Score 0.384 Round 4: 606 peptides, 95 chains. Longest chain 21 peptides. Score 0.402 Round 5: 628 peptides, 100 chains. Longest chain 17 peptides. Score 0.402 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 100, Residues 528, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2anu-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 17399 reflections ( 99.75 % complete ) and 27564 restraints for refining 11071 atoms. 25552 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2183 (Rfree = 0.000) for 11071 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2034 (Rfree = 0.000) for 10959 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 48: After refmac, R = 0.1966 (Rfree = 0.000) for 10886 atoms. Found 0 (60 requested) and removed 30 (30 requested) atoms. Cycle 49: After refmac, R = 0.1967 (Rfree = 0.000) for 10814 atoms. TimeTaking 134.02