Mon 24 Dec 00:23:24 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 2ig6-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ig6-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-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/2ig6-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-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 00:23:28 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/2ig6-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-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 341 and 0 Target number of residues in the AU: 341 Target solvent content: 0.5040 Checking the provided sequence file Detected sequence length: 150 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 300 Adjusted target solvent content: 0.56 Input MTZ file: 2ig6-1.8-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2400 target number of atoms Had to go as low as 0.55 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 1 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: 55.977 1.800 Wilson plot Bfac: 24.07 34433 reflections ( 97.40 % complete ) and 0 restraints for refining 2666 atoms. Observations/parameters ratio is 3.23 ------------------------------------------------------ Starting model: R = 0.3237 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2618 (Rfree = 0.000) for 2666 atoms. Found 123 (123 requested) and removed 67 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.96 1.81 NCS extension: 0 residues added, 2722 seeds are put forward Round 1: 247 peptides, 14 chains. Longest chain 88 peptides. Score 0.830 Round 2: 264 peptides, 9 chains. Longest chain 120 peptides. Score 0.888 Round 3: 267 peptides, 9 chains. Longest chain 111 peptides. Score 0.891 Round 4: 272 peptides, 7 chains. Longest chain 124 peptides. Score 0.908 Round 5: 270 peptides, 11 chains. Longest chain 88 peptides. Score 0.882 Taking the results from Round 4 Chains 8, Residues 265, Estimated correctness of the model 99.4 % 4 chains (249 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 28 A and 31 A Built loop between residues 38 A and 41 A 6 chains (269 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2763 restraints for refining 2576 atoms. 614 conditional restraints added. Observations/parameters ratio is 3.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2648 (Rfree = 0.000) for 2576 atoms. Found 115 (119 requested) and removed 52 (59 requested) atoms. Cycle 2: After refmac, R = 0.2308 (Rfree = 0.000) for 2636 atoms. Found 94 (122 requested) and removed 27 (61 requested) atoms. Cycle 3: After refmac, R = 0.2160 (Rfree = 0.000) for 2697 atoms. Found 82 (125 requested) and removed 25 (62 requested) atoms. Cycle 4: After refmac, R = 0.2059 (Rfree = 0.000) for 2743 atoms. Found 85 (127 requested) and removed 17 (63 requested) atoms. Cycle 5: After refmac, R = 0.2012 (Rfree = 0.000) for 2800 atoms. Found 71 (130 requested) and removed 35 (65 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.94 1.79 NCS extension: 2 residues added (6 deleted due to clashes), 2841 seeds are put forward Round 1: 274 peptides, 6 chains. Longest chain 130 peptides. Score 0.915 Round 2: 271 peptides, 7 chains. Longest chain 82 peptides. Score 0.907 Round 3: 274 peptides, 7 chains. Longest chain 93 peptides. Score 0.910 Round 4: 273 peptides, 6 chains. Longest chain 141 peptides. Score 0.914 Round 5: 271 peptides, 10 chains. Longest chain 92 peptides. Score 0.889 Taking the results from Round 1 Chains 6, Residues 268, Estimated correctness of the model 99.4 % 4 chains (257 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 B and 33 B Built loop between residues 47 B and 50 B 4 chains (272 residues) following loop building 2 chains (261 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2743 restraints for refining 2685 atoms. 552 conditional restraints added. Observations/parameters ratio is 3.21 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2093 (Rfree = 0.000) for 2685 atoms. Found 104 (124 requested) and removed 29 (62 requested) atoms. Cycle 7: After refmac, R = 0.2031 (Rfree = 0.000) for 2756 atoms. Found 66 (127 requested) and removed 47 (63 requested) atoms. Cycle 8: After refmac, R = 0.1961 (Rfree = 0.000) for 2768 atoms. Found 87 (125 requested) and removed 24 (64 requested) atoms. Cycle 9: After refmac, R = 0.1925 (Rfree = 0.000) for 2824 atoms. Found 63 (127 requested) and removed 38 (65 requested) atoms. Cycle 10: After refmac, R = 0.1900 (Rfree = 0.000) for 2843 atoms. Found 73 (126 requested) and removed 27 (65 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2891 seeds are put forward Round 1: 273 peptides, 5 chains. Longest chain 129 peptides. Score 0.920 Round 2: 273 peptides, 7 chains. Longest chain 133 peptides. Score 0.909 Round 3: 274 peptides, 6 chains. Longest chain 130 peptides. Score 0.915 Round 4: 274 peptides, 6 chains. Longest chain 121 peptides. Score 0.915 Round 5: 277 peptides, 4 chains. Longest chain 141 peptides. Score 0.928 Taking the results from Round 5 Chains 4, Residues 273, Estimated correctness of the model 99.6 % 3 chains (268 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 B and 50 B 3 chains (275 residues) following loop building 2 chains (270 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2732 restraints for refining 2712 atoms. 494 conditional restraints added. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2063 (Rfree = 0.000) for 2712 atoms. Found 113 (120 requested) and removed 38 (62 requested) atoms. Cycle 12: After refmac, R = 0.2008 (Rfree = 0.000) for 2779 atoms. Found 72 (123 requested) and removed 49 (64 requested) atoms. Cycle 13: After refmac, R = 0.1962 (Rfree = 0.000) for 2794 atoms. Found 83 (121 requested) and removed 30 (64 requested) atoms. Cycle 14: After refmac, R = 0.1910 (Rfree = 0.000) for 2843 atoms. Found 70 (123 requested) and removed 43 (65 requested) atoms. Cycle 15: After refmac, R = 0.1897 (Rfree = 0.000) for 2860 atoms. Found 69 (121 requested) and removed 39 (66 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2892 seeds are put forward Round 1: 273 peptides, 7 chains. Longest chain 102 peptides. Score 0.909 Round 2: 281 peptides, 4 chains. Longest chain 143 peptides. Score 0.931 Round 3: 275 peptides, 8 chains. Longest chain 93 peptides. Score 0.905 Round 4: 277 peptides, 5 chains. Longest chain 143 peptides. Score 0.923 Round 5: 277 peptides, 6 chains. Longest chain 141 peptides. Score 0.918 Taking the results from Round 2 Chains 5, Residues 277, Estimated correctness of the model 99.6 % 3 chains (268 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 B and 96 B 4 chains (279 residues) following loop building 2 chains (270 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 34433 reflections ( 97.40 % complete ) and 2785 restraints for refining 2753 atoms. 527 conditional restraints added. Observations/parameters ratio is 3.13 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2060 (Rfree = 0.000) for 2753 atoms. Found 114 (114 requested) and removed 45 (63 requested) atoms. Cycle 17: After refmac, R = 0.1988 (Rfree = 0.000) for 2816 atoms. Found 74 (117 requested) and removed 46 (65 requested) atoms. Cycle 18: After refmac, R = 0.1944 (Rfree = 0.000) for 2836 atoms. Found 78 (115 requested) and removed 44 (65 requested) atoms. Cycle 19: After refmac, R = 0.1915 (Rfree = 0.000) for 2865 atoms. Found 67 (114 requested) and removed 53 (66 requested) atoms. Cycle 20: After refmac, R = 0.1891 (Rfree = 0.000) for 2876 atoms. Found 77 (112 requested) and removed 39 (66 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2916 seeds are put forward Round 1: 277 peptides, 5 chains. Longest chain 120 peptides. Score 0.923 Round 2: 280 peptides, 4 chains. Longest chain 142 peptides. Score 0.930 Round 3: 277 peptides, 7 chains. Longest chain 93 peptides. Score 0.912 Round 4: 275 peptides, 5 chains. Longest chain 141 peptides. Score 0.921 Round 5: 273 peptides, 10 chains. Longest chain 102 peptides. Score 0.891 Taking the results from Round 2 Chains 6, Residues 276, Estimated correctness of the model 99.6 % 3 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 B and 96 B 5 chains (278 residues) following loop building 2 chains (269 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2734 restraints for refining 2732 atoms. 488 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2043 (Rfree = 0.000) for 2732 atoms. Found 103 (103 requested) and removed 34 (63 requested) atoms. Cycle 22: After refmac, R = 0.1992 (Rfree = 0.000) for 2794 atoms. Found 67 (106 requested) and removed 30 (64 requested) atoms. Cycle 23: After refmac, R = 0.1962 (Rfree = 0.000) for 2825 atoms. Found 66 (107 requested) and removed 40 (65 requested) atoms. Cycle 24: After refmac, R = 0.1918 (Rfree = 0.000) for 2845 atoms. Found 73 (105 requested) and removed 38 (65 requested) atoms. Cycle 25: After refmac, R = 0.1911 (Rfree = 0.000) for 2877 atoms. Found 62 (104 requested) and removed 49 (66 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.94 1.79 NCS extension: 6 residues added (2 deleted due to clashes), 2899 seeds are put forward Round 1: 278 peptides, 4 chains. Longest chain 130 peptides. Score 0.929 Round 2: 280 peptides, 4 chains. Longest chain 143 peptides. Score 0.930 Round 3: 279 peptides, 6 chains. Longest chain 132 peptides. Score 0.919 Round 4: 275 peptides, 6 chains. Longest chain 141 peptides. Score 0.916 Round 5: 276 peptides, 5 chains. Longest chain 130 peptides. Score 0.922 Taking the results from Round 2 Chains 6, Residues 276, Estimated correctness of the model 99.6 % 3 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 B and 96 B 5 chains (278 residues) following loop building 2 chains (269 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2774 restraints for refining 2737 atoms. 529 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2081 (Rfree = 0.000) for 2737 atoms. Found 96 (96 requested) and removed 33 (63 requested) atoms. Cycle 27: After refmac, R = 0.1989 (Rfree = 0.000) for 2797 atoms. Found 65 (98 requested) and removed 32 (64 requested) atoms. Cycle 28: After refmac, R = 0.1928 (Rfree = 0.000) for 2828 atoms. Found 58 (99 requested) and removed 33 (65 requested) atoms. Cycle 29: After refmac, R = 0.1902 (Rfree = 0.000) for 2847 atoms. Found 69 (97 requested) and removed 35 (65 requested) atoms. Cycle 30: After refmac, R = 0.1883 (Rfree = 0.000) for 2875 atoms. Found 56 (96 requested) and removed 41 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2893 seeds are put forward Round 1: 276 peptides, 4 chains. Longest chain 130 peptides. Score 0.927 Round 2: 278 peptides, 5 chains. Longest chain 142 peptides. Score 0.924 Round 3: 277 peptides, 7 chains. Longest chain 93 peptides. Score 0.912 Round 4: 276 peptides, 5 chains. Longest chain 133 peptides. Score 0.922 Round 5: 276 peptides, 7 chains. Longest chain 102 peptides. Score 0.911 Taking the results from Round 1 Chains 5, Residues 272, Estimated correctness of the model 99.6 % 3 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A 4 chains (274 residues) following loop building 2 chains (269 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2866 restraints for refining 2749 atoms. 642 conditional restraints added. Observations/parameters ratio is 3.13 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2056 (Rfree = 0.000) for 2749 atoms. Found 89 (89 requested) and removed 42 (63 requested) atoms. Cycle 32: After refmac, R = 0.1996 (Rfree = 0.000) for 2790 atoms. Found 68 (90 requested) and removed 26 (64 requested) atoms. Cycle 33: After refmac, R = 0.1948 (Rfree = 0.000) for 2827 atoms. Found 72 (91 requested) and removed 42 (65 requested) atoms. Cycle 34: After refmac, R = 0.1901 (Rfree = 0.000) for 2853 atoms. Found 72 (90 requested) and removed 40 (66 requested) atoms. Cycle 35: After refmac, R = 0.1897 (Rfree = 0.000) for 2881 atoms. Found 67 (88 requested) and removed 56 (66 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2894 seeds are put forward Round 1: 276 peptides, 5 chains. Longest chain 131 peptides. Score 0.922 Round 2: 276 peptides, 5 chains. Longest chain 111 peptides. Score 0.922 Round 3: 274 peptides, 6 chains. Longest chain 120 peptides. Score 0.915 Round 4: 277 peptides, 4 chains. Longest chain 142 peptides. Score 0.928 Round 5: 272 peptides, 10 chains. Longest chain 73 peptides. Score 0.890 Taking the results from Round 4 Chains 6, Residues 273, Estimated correctness of the model 99.6 % 2 chains (256 residues) have been docked in sequence Building loops using Loopy2018 6 chains (273 residues) following loop building 2 chains (256 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2966 restraints for refining 2741 atoms. 812 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2045 (Rfree = 0.000) for 2741 atoms. Found 81 (81 requested) and removed 33 (63 requested) atoms. Cycle 37: After refmac, R = 0.1982 (Rfree = 0.000) for 2784 atoms. Found 83 (83 requested) and removed 39 (64 requested) atoms. Cycle 38: After refmac, R = 0.1951 (Rfree = 0.000) for 2824 atoms. Found 78 (83 requested) and removed 36 (65 requested) atoms. Cycle 39: After refmac, R = 0.1936 (Rfree = 0.000) for 2864 atoms. Found 65 (84 requested) and removed 55 (66 requested) atoms. Cycle 40: After refmac, R = 0.1925 (Rfree = 0.000) for 2868 atoms. Found 67 (82 requested) and removed 39 (66 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.94 1.79 NCS extension: 4 residues added (3 deleted due to clashes), 2901 seeds are put forward Round 1: 275 peptides, 5 chains. Longest chain 120 peptides. Score 0.921 Round 2: 276 peptides, 4 chains. Longest chain 130 peptides. Score 0.927 Round 3: 274 peptides, 7 chains. Longest chain 120 peptides. Score 0.910 Round 4: 276 peptides, 6 chains. Longest chain 122 peptides. Score 0.917 Round 5: 275 peptides, 7 chains. Longest chain 120 peptides. Score 0.910 Taking the results from Round 2 Chains 5, Residues 272, Estimated correctness of the model 99.6 % 3 chains (267 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 71 A 4 chains (274 residues) following loop building 2 chains (269 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2897 restraints for refining 2767 atoms. 670 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2046 (Rfree = 0.000) for 2767 atoms. Found 76 (76 requested) and removed 42 (63 requested) atoms. Cycle 42: After refmac, R = 0.1989 (Rfree = 0.000) for 2795 atoms. Found 69 (75 requested) and removed 29 (64 requested) atoms. Cycle 43: After refmac, R = 0.1933 (Rfree = 0.000) for 2830 atoms. Found 76 (76 requested) and removed 29 (65 requested) atoms. Cycle 44: After refmac, R = 0.1921 (Rfree = 0.000) for 2874 atoms. Found 56 (77 requested) and removed 46 (66 requested) atoms. Cycle 45: After refmac, R = 0.1898 (Rfree = 0.000) for 2882 atoms. Found 74 (74 requested) and removed 39 (66 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.94 1.79 NCS extension: 3 residues added (0 deleted due to clashes), 2923 seeds are put forward Round 1: 276 peptides, 4 chains. Longest chain 130 peptides. Score 0.927 Round 2: 273 peptides, 7 chains. Longest chain 92 peptides. Score 0.909 Round 3: 275 peptides, 5 chains. Longest chain 130 peptides. Score 0.921 Round 4: 274 peptides, 6 chains. Longest chain 142 peptides. Score 0.915 Round 5: 272 peptides, 8 chains. Longest chain 108 peptides. Score 0.902 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 272, Estimated correctness of the model 99.6 % 3 chains (268 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 29 A and 32 A 3 chains (274 residues) following loop building 2 chains (270 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 34433 reflections ( 97.40 % complete ) and 2232 restraints for refining 2189 atoms. Observations/parameters ratio is 3.93 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2700 (Rfree = 0.000) for 2189 atoms. Found 55 (55 requested) and removed 0 (55 requested) atoms. Cycle 47: After refmac, R = 0.2524 (Rfree = 0.000) for 2189 atoms. Found 45 (56 requested) and removed 1 (51 requested) atoms. Cycle 48: After refmac, R = 0.2370 (Rfree = 0.000) for 2189 atoms. Found 20 (57 requested) and removed 3 (52 requested) atoms. Cycle 49: After refmac, R = 0.2300 (Rfree = 0.000) for 2189 atoms. TimeTaking 40.77