Sun 23 Dec 22:23:05 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 2ig6-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ig6-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-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/2ig6-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-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 ============================================================ Sun 23 Dec 22:23:13 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/2ig6-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-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 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-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: 19 Cell parameters: 52.413 65.299 108.709 90.000 90.000 90.000 Input sequence file: 2ig6-1.8-parrot-hancs.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 2667 atoms. Observations/parameters ratio is 3.23 ------------------------------------------------------ Starting model: R = 0.3199 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2584 (Rfree = 0.000) for 2667 atoms. Found 123 (123 requested) and removed 61 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.96 1.81 NCS extension: 0 residues added, 2729 seeds are put forward Round 1: 240 peptides, 17 chains. Longest chain 51 peptides. Score 0.792 Round 2: 255 peptides, 11 chains. Longest chain 94 peptides. Score 0.864 Round 3: 268 peptides, 7 chains. Longest chain 122 peptides. Score 0.904 Round 4: 271 peptides, 10 chains. Longest chain 85 peptides. Score 0.889 Round 5: 276 peptides, 5 chains. Longest chain 133 peptides. Score 0.922 Taking the results from Round 5 Chains 5, Residues 271, Estimated correctness of the model 99.5 % 3 chains (259 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 106 B and 109 B 4 chains (273 residues) following loop building 2 chains (261 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2650 restraints for refining 2586 atoms. 460 conditional restraints added. Observations/parameters ratio is 3.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2608 (Rfree = 0.000) for 2586 atoms. Found 119 (119 requested) and removed 55 (59 requested) atoms. Cycle 2: After refmac, R = 0.2289 (Rfree = 0.000) for 2645 atoms. Found 89 (122 requested) and removed 25 (61 requested) atoms. Cycle 3: After refmac, R = 0.2141 (Rfree = 0.000) for 2696 atoms. Found 77 (125 requested) and removed 29 (62 requested) atoms. Cycle 4: After refmac, R = 0.2073 (Rfree = 0.000) for 2738 atoms. Found 68 (126 requested) and removed 29 (63 requested) atoms. Cycle 5: After refmac, R = 0.2014 (Rfree = 0.000) for 2765 atoms. Found 71 (128 requested) and removed 30 (64 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.95 1.80 NCS extension: 0 residues added, 2807 seeds are put forward Round 1: 270 peptides, 6 chains. Longest chain 130 peptides. Score 0.912 Round 2: 273 peptides, 7 chains. Longest chain 85 peptides. Score 0.909 Round 3: 278 peptides, 3 chains. Longest chain 140 peptides. Score 0.934 Round 4: 275 peptides, 7 chains. Longest chain 120 peptides. Score 0.910 Round 5: 271 peptides, 7 chains. Longest chain 99 peptides. Score 0.907 Taking the results from Round 3 Chains 4, Residues 275, Estimated correctness of the model 99.7 % 2 chains (265 residues) have been docked in sequence Building loops using Loopy2018 4 chains (275 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2697 restraints for refining 2664 atoms. 489 conditional restraints added. Observations/parameters ratio is 3.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2145 (Rfree = 0.000) for 2664 atoms. Found 98 (123 requested) and removed 45 (61 requested) atoms. Cycle 7: After refmac, R = 0.2033 (Rfree = 0.000) for 2711 atoms. Found 74 (125 requested) and removed 29 (62 requested) atoms. Cycle 8: After refmac, R = 0.1956 (Rfree = 0.000) for 2753 atoms. Found 71 (127 requested) and removed 25 (63 requested) atoms. Cycle 9: After refmac, R = 0.1928 (Rfree = 0.000) for 2793 atoms. Found 69 (129 requested) and removed 38 (64 requested) atoms. Cycle 10: After refmac, R = 0.1900 (Rfree = 0.000) for 2819 atoms. Found 62 (127 requested) and removed 48 (65 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.94 1.79 NCS extension: 4 residues added (0 deleted due to clashes), 2839 seeds are put forward Round 1: 274 peptides, 4 chains. Longest chain 130 peptides. Score 0.926 Round 2: 276 peptides, 5 chains. Longest chain 140 peptides. Score 0.922 Round 3: 276 peptides, 6 chains. Longest chain 111 peptides. Score 0.917 Round 4: 275 peptides, 5 chains. Longest chain 140 peptides. Score 0.921 Round 5: 277 peptides, 5 chains. Longest chain 120 peptides. Score 0.923 Taking the results from Round 1 Chains 4, Residues 270, Estimated correctness of the model 99.6 % 3 chains (266 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A 3 chains (272 residues) following loop building 2 chains (268 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2735 restraints for refining 2713 atoms. 525 conditional restraints added. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2044 (Rfree = 0.000) for 2713 atoms. Found 104 (120 requested) and removed 45 (62 requested) atoms. Cycle 12: After refmac, R = 0.1977 (Rfree = 0.000) for 2767 atoms. Found 83 (123 requested) and removed 35 (64 requested) atoms. Cycle 13: After refmac, R = 0.1922 (Rfree = 0.000) for 2812 atoms. Found 75 (125 requested) and removed 52 (65 requested) atoms. Cycle 14: After refmac, R = 0.1903 (Rfree = 0.000) for 2830 atoms. Found 73 (123 requested) and removed 57 (65 requested) atoms. Cycle 15: After refmac, R = 0.1898 (Rfree = 0.000) for 2839 atoms. Found 65 (121 requested) and removed 51 (65 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2855 seeds are put forward Round 1: 275 peptides, 4 chains. Longest chain 131 peptides. Score 0.927 Round 2: 274 peptides, 6 chains. Longest chain 140 peptides. Score 0.915 Round 3: 273 peptides, 6 chains. Longest chain 111 peptides. Score 0.914 Round 4: 272 peptides, 8 chains. Longest chain 121 peptides. Score 0.902 Round 5: 274 peptides, 6 chains. Longest chain 108 peptides. Score 0.915 Taking the results from Round 1 Chains 5, Residues 271, Estimated correctness of the model 99.6 % 3 chains (266 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A 4 chains (273 residues) following loop building 2 chains (268 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2729 restraints for refining 2716 atoms. 517 conditional restraints added. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2028 (Rfree = 0.000) for 2716 atoms. Found 101 (112 requested) and removed 45 (62 requested) atoms. Cycle 17: After refmac, R = 0.1964 (Rfree = 0.000) for 2768 atoms. Found 70 (115 requested) and removed 42 (64 requested) atoms. Cycle 18: After refmac, R = 0.1926 (Rfree = 0.000) for 2792 atoms. Found 79 (114 requested) and removed 42 (64 requested) atoms. Cycle 19: After refmac, R = 0.1898 (Rfree = 0.000) for 2823 atoms. Found 76 (112 requested) and removed 53 (65 requested) atoms. Cycle 20: After refmac, R = 0.1889 (Rfree = 0.000) for 2840 atoms. Found 80 (110 requested) and removed 57 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.94 1.79 NCS extension: 8 residues added (2 deleted due to clashes), 2873 seeds are put forward Round 1: 275 peptides, 4 chains. Longest chain 130 peptides. Score 0.927 Round 2: 275 peptides, 5 chains. Longest chain 140 peptides. Score 0.921 Round 3: 273 peptides, 7 chains. Longest chain 93 peptides. Score 0.909 Round 4: 276 peptides, 4 chains. Longest chain 131 peptides. Score 0.927 Round 5: 270 peptides, 8 chains. Longest chain 120 peptides. Score 0.900 Taking the results from Round 4 Chains 6, Residues 272, Estimated correctness of the model 99.6 % 3 chains (264 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A 5 chains (274 residues) following loop building 2 chains (266 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2715 restraints for refining 2707 atoms. 506 conditional restraints added. Observations/parameters ratio is 3.18 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2051 (Rfree = 0.000) for 2707 atoms. Found 102 (102 requested) and removed 38 (62 requested) atoms. Cycle 22: After refmac, R = 0.1974 (Rfree = 0.000) for 2769 atoms. Found 75 (105 requested) and removed 31 (64 requested) atoms. Cycle 23: After refmac, R = 0.1933 (Rfree = 0.000) for 2809 atoms. Found 70 (107 requested) and removed 43 (65 requested) atoms. Cycle 24: After refmac, R = 0.1911 (Rfree = 0.000) for 2829 atoms. Found 63 (105 requested) and removed 51 (65 requested) atoms. Cycle 25: After refmac, R = 0.1893 (Rfree = 0.000) for 2833 atoms. Found 77 (102 requested) and removed 44 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2868 seeds are put forward Round 1: 273 peptides, 4 chains. Longest chain 129 peptides. Score 0.925 Round 2: 275 peptides, 4 chains. Longest chain 140 peptides. Score 0.927 Round 3: 273 peptides, 6 chains. Longest chain 83 peptides. Score 0.914 Round 4: 276 peptides, 4 chains. Longest chain 140 peptides. Score 0.927 Round 5: 272 peptides, 8 chains. Longest chain 78 peptides. Score 0.902 Taking the results from Round 4 Chains 5, Residues 272, Estimated correctness of the model 99.6 % 3 chains (262 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 B and 50 B 4 chains (274 residues) following loop building 2 chains (264 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2719 restraints for refining 2704 atoms. 523 conditional restraints added. Observations/parameters ratio is 3.18 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2055 (Rfree = 0.000) for 2704 atoms. Found 95 (95 requested) and removed 32 (62 requested) atoms. Cycle 27: After refmac, R = 0.1974 (Rfree = 0.000) for 2763 atoms. Found 67 (97 requested) and removed 34 (63 requested) atoms. Cycle 28: After refmac, R = 0.1927 (Rfree = 0.000) for 2789 atoms. Found 72 (95 requested) and removed 30 (64 requested) atoms. Cycle 29: After refmac, R = 0.1903 (Rfree = 0.000) for 2827 atoms. Found 70 (96 requested) and removed 40 (65 requested) atoms. Cycle 30: After refmac, R = 0.1895 (Rfree = 0.000) for 2854 atoms. Found 67 (95 requested) and removed 54 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.94 1.79 NCS extension: 4 residues added (0 deleted due to clashes), 2873 seeds are put forward Round 1: 270 peptides, 6 chains. Longest chain 129 peptides. Score 0.912 Round 2: 271 peptides, 6 chains. Longest chain 131 peptides. Score 0.913 Round 3: 273 peptides, 6 chains. Longest chain 130 peptides. Score 0.914 Round 4: 273 peptides, 6 chains. Longest chain 139 peptides. Score 0.914 Round 5: 269 peptides, 9 chains. Longest chain 108 peptides. Score 0.893 Taking the results from Round 4 Chains 6, Residues 267, Estimated correctness of the model 99.4 % 5 chains (261 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 Built loop between residues 92 B and 95 B 3 chains (273 residues) following loop building 2 chains (267 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2732 restraints for refining 2720 atoms. 523 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2035 (Rfree = 0.000) for 2720 atoms. Found 87 (87 requested) and removed 38 (62 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1989 (Rfree = 0.000) for 2764 atoms. Found 87 (90 requested) and removed 27 (64 requested) atoms. Cycle 33: After refmac, R = 0.1940 (Rfree = 0.000) for 2822 atoms. Found 73 (91 requested) and removed 40 (65 requested) atoms. Cycle 34: After refmac, R = 0.1923 (Rfree = 0.000) for 2852 atoms. Found 57 (90 requested) and removed 59 (66 requested) atoms. Cycle 35: After refmac, R = 0.1911 (Rfree = 0.000) for 2843 atoms. Found 79 (86 requested) and removed 39 (65 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.93 1.78 NCS extension: 6 residues added (3 deleted due to clashes), 2890 seeds are put forward Round 1: 270 peptides, 5 chains. Longest chain 119 peptides. Score 0.917 Round 2: 272 peptides, 3 chains. Longest chain 139 peptides. Score 0.930 Round 3: 271 peptides, 5 chains. Longest chain 119 peptides. Score 0.918 Round 4: 270 peptides, 6 chains. Longest chain 83 peptides. Score 0.912 Round 5: 269 peptides, 7 chains. Longest chain 92 peptides. Score 0.905 Taking the results from Round 2 Chains 3, Residues 269, Estimated correctness of the model 99.6 % 2 chains (265 residues) have been docked in sequence Building loops using Loopy2018 3 chains (269 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2786 restraints for refining 2712 atoms. 602 conditional restraints added. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2036 (Rfree = 0.000) for 2712 atoms. Found 82 (82 requested) and removed 37 (62 requested) atoms. Cycle 37: After refmac, R = 0.1970 (Rfree = 0.000) for 2753 atoms. Found 63 (84 requested) and removed 32 (63 requested) atoms. Cycle 38: After refmac, R = 0.1939 (Rfree = 0.000) for 2779 atoms. Found 73 (82 requested) and removed 36 (64 requested) atoms. Cycle 39: After refmac, R = 0.1906 (Rfree = 0.000) for 2811 atoms. Found 58 (83 requested) and removed 40 (65 requested) atoms. Cycle 40: After refmac, R = 0.1876 (Rfree = 0.000) for 2827 atoms. Found 71 (81 requested) and removed 49 (65 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.94 1.79 NCS extension: 3 residues added (0 deleted due to clashes), 2852 seeds are put forward Round 1: 270 peptides, 5 chains. Longest chain 129 peptides. Score 0.917 Round 2: 270 peptides, 6 chains. Longest chain 131 peptides. Score 0.912 Round 3: 268 peptides, 8 chains. Longest chain 91 peptides. Score 0.898 Round 4: 271 peptides, 5 chains. Longest chain 131 peptides. Score 0.918 Round 5: 270 peptides, 6 chains. Longest chain 111 peptides. Score 0.912 Taking the results from Round 4 Chains 5, Residues 266, Estimated correctness of the model 99.5 % 3 chains (256 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 B and 96 B 4 chains (268 residues) following loop building 2 chains (258 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2822 restraints for refining 2698 atoms. 668 conditional restraints added. Observations/parameters ratio is 3.19 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2023 (Rfree = 0.000) for 2698 atoms. Found 74 (74 requested) and removed 28 (62 requested) atoms. Cycle 42: After refmac, R = 0.1964 (Rfree = 0.000) for 2742 atoms. Found 76 (76 requested) and removed 30 (63 requested) atoms. Cycle 43: After refmac, R = 0.1930 (Rfree = 0.000) for 2785 atoms. Found 76 (77 requested) and removed 36 (64 requested) atoms. Cycle 44: After refmac, R = 0.1923 (Rfree = 0.000) for 2816 atoms. Found 76 (78 requested) and removed 49 (65 requested) atoms. Cycle 45: After refmac, R = 0.1912 (Rfree = 0.000) for 2841 atoms. Found 70 (76 requested) and removed 51 (65 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2861 seeds are put forward Round 1: 268 peptides, 6 chains. Longest chain 111 peptides. Score 0.910 Round 2: 270 peptides, 4 chains. Longest chain 131 peptides. Score 0.923 Round 3: 265 peptides, 8 chains. Longest chain 82 peptides. Score 0.895 Round 4: 268 peptides, 6 chains. Longest chain 131 peptides. Score 0.910 Round 5: 267 peptides, 7 chains. Longest chain 111 peptides. Score 0.903 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 266, Estimated correctness of the model 99.5 % 2 chains (257 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 4 chains (266 residues) following loop building 2 chains (257 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 34433 reflections ( 97.40 % complete ) and 2139 restraints for refining 2101 atoms. Observations/parameters ratio is 4.10 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2727 (Rfree = 0.000) for 2101 atoms. Found 54 (54 requested) and removed 0 (54 requested) atoms. Cycle 47: After refmac, R = 0.2590 (Rfree = 0.000) for 2101 atoms. Found 42 (55 requested) and removed 0 (49 requested) atoms. Cycle 48: After refmac, R = 0.2435 (Rfree = 0.000) for 2101 atoms. Found 15 (57 requested) and removed 1 (50 requested) atoms. Cycle 49: After refmac, R = 0.2356 (Rfree = 0.000) for 2101 atoms. TimeTaking 57.68