Mon 24 Dec 07:29:30 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ig6-1.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-1.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ig6-1.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-parrot-noncs ############### 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 07:29:35 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/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ig6-1.8-parrot-noncs/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-noncs.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-noncs.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 2647 atoms. Observations/parameters ratio is 3.25 ------------------------------------------------------ Starting model: R = 0.3247 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2654 (Rfree = 0.000) for 2647 atoms. Found 122 (122 requested) and removed 62 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.96 1.81 NCS extension: 0 residues added, 2707 seeds are put forward Round 1: 247 peptides, 16 chains. Longest chain 66 peptides. Score 0.813 Round 2: 255 peptides, 16 chains. Longest chain 37 peptides. Score 0.826 Round 3: 260 peptides, 11 chains. Longest chain 101 peptides. Score 0.870 Round 4: 262 peptides, 12 chains. Longest chain 85 peptides. Score 0.866 Round 5: 273 peptides, 9 chains. Longest chain 85 peptides. Score 0.897 Taking the results from Round 5 Chains 10, Residues 264, Estimated correctness of the model 99.2 % 6 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 32 A Built loop between residues 68 A and 71 A Built loop between residues 38 B and 41 B Built loop between residues 53 B and 56 B 5 chains (272 residues) following loop building 2 chains (255 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2670 restraints for refining 2557 atoms. 514 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2677 (Rfree = 0.000) for 2557 atoms. Found 114 (118 requested) and removed 63 (59 requested) atoms. Cycle 2: After refmac, R = 0.2316 (Rfree = 0.000) for 2606 atoms. Found 98 (118 requested) and removed 27 (60 requested) atoms. Cycle 3: After refmac, R = 0.2169 (Rfree = 0.000) for 2671 atoms. Found 73 (121 requested) and removed 17 (61 requested) atoms. Cycle 4: After refmac, R = 0.2075 (Rfree = 0.000) for 2719 atoms. Found 63 (123 requested) and removed 25 (63 requested) atoms. Cycle 5: After refmac, R = 0.2032 (Rfree = 0.000) for 2745 atoms. Found 70 (124 requested) and removed 24 (63 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.94 1.79 NCS extension: 5 residues added (0 deleted due to clashes), 2798 seeds are put forward Round 1: 271 peptides, 7 chains. Longest chain 111 peptides. Score 0.907 Round 2: 273 peptides, 6 chains. Longest chain 80 peptides. Score 0.914 Round 3: 271 peptides, 8 chains. Longest chain 112 peptides. Score 0.901 Round 4: 276 peptides, 5 chains. Longest chain 130 peptides. Score 0.922 Round 5: 269 peptides, 11 chains. Longest chain 73 peptides. Score 0.881 Taking the results from Round 4 Chains 6, Residues 271, Estimated correctness of the model 99.5 % 3 chains (260 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A 5 chains (273 residues) following loop building 2 chains (262 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2710 restraints for refining 2661 atoms. 525 conditional restraints added. Observations/parameters ratio is 3.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2165 (Rfree = 0.000) for 2661 atoms. Found 118 (121 requested) and removed 46 (61 requested) atoms. Cycle 7: After refmac, R = 0.2079 (Rfree = 0.000) for 2733 atoms. Found 81 (123 requested) and removed 35 (63 requested) atoms. Cycle 8: After refmac, R = 0.2032 (Rfree = 0.000) for 2774 atoms. Found 78 (125 requested) and removed 43 (64 requested) atoms. Cycle 9: After refmac, R = 0.1991 (Rfree = 0.000) for 2801 atoms. Found 72 (124 requested) and removed 34 (64 requested) atoms. Cycle 10: After refmac, R = 0.1946 (Rfree = 0.000) for 2836 atoms. Found 72 (126 requested) and removed 35 (65 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.94 1.79 NCS extension: 4 residues added (0 deleted due to clashes), 2879 seeds are put forward Round 1: 270 peptides, 7 chains. Longest chain 102 peptides. Score 0.906 Round 2: 269 peptides, 8 chains. Longest chain 91 peptides. Score 0.899 Round 3: 272 peptides, 7 chains. Longest chain 121 peptides. Score 0.908 Round 4: 273 peptides, 7 chains. Longest chain 119 peptides. Score 0.909 Round 5: 272 peptides, 7 chains. Longest chain 82 peptides. Score 0.908 Taking the results from Round 4 Chains 8, Residues 266, Estimated correctness of the model 99.4 % 4 chains (248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 32 A Built loop between residues 47 B and 50 B 6 chains (270 residues) following loop building 2 chains (252 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2917 restraints for refining 2679 atoms. 800 conditional restraints added. Observations/parameters ratio is 3.21 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2101 (Rfree = 0.000) for 2679 atoms. Found 106 (118 requested) and removed 34 (61 requested) atoms. Cycle 12: After refmac, R = 0.2015 (Rfree = 0.000) for 2748 atoms. Found 87 (122 requested) and removed 25 (63 requested) atoms. Cycle 13: After refmac, R = 0.1971 (Rfree = 0.000) for 2808 atoms. Found 63 (124 requested) and removed 44 (64 requested) atoms. Cycle 14: After refmac, R = 0.1940 (Rfree = 0.000) for 2823 atoms. Found 61 (122 requested) and removed 39 (65 requested) atoms. Cycle 15: After refmac, R = 0.1921 (Rfree = 0.000) for 2842 atoms. Found 56 (121 requested) and removed 32 (65 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.95 1.80 NCS extension: 1 residues added (6 deleted due to clashes), 2869 seeds are put forward Round 1: 268 peptides, 9 chains. Longest chain 92 peptides. Score 0.892 Round 2: 272 peptides, 6 chains. Longest chain 128 peptides. Score 0.914 Round 3: 271 peptides, 8 chains. Longest chain 110 peptides. Score 0.901 Round 4: 273 peptides, 5 chains. Longest chain 135 peptides. Score 0.920 Round 5: 270 peptides, 8 chains. Longest chain 135 peptides. Score 0.900 Taking the results from Round 4 Chains 6, Residues 268, Estimated correctness of the model 99.5 % 3 chains (258 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 B and 32 B 5 chains (270 residues) following loop building 2 chains (260 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2832 restraints for refining 2716 atoms. 671 conditional restraints added. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2087 (Rfree = 0.000) for 2716 atoms. Found 108 (112 requested) and removed 43 (62 requested) atoms. Cycle 17: After refmac, R = 0.2034 (Rfree = 0.000) for 2773 atoms. Found 77 (115 requested) and removed 30 (64 requested) atoms. Cycle 18: After refmac, R = 0.1945 (Rfree = 0.000) for 2816 atoms. Found 72 (117 requested) and removed 26 (65 requested) atoms. Cycle 19: After refmac, R = 0.1921 (Rfree = 0.000) for 2853 atoms. Found 64 (119 requested) and removed 39 (66 requested) atoms. Cycle 20: After refmac, R = 0.1920 (Rfree = 0.000) for 2868 atoms. Found 61 (117 requested) and removed 43 (66 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.94 1.79 NCS extension: 2 residues added (1 deleted due to clashes), 2889 seeds are put forward Round 1: 271 peptides, 7 chains. Longest chain 109 peptides. Score 0.907 Round 2: 271 peptides, 6 chains. Longest chain 82 peptides. Score 0.913 Round 3: 269 peptides, 8 chains. Longest chain 101 peptides. Score 0.899 Round 4: 269 peptides, 8 chains. Longest chain 82 peptides. Score 0.899 Round 5: 267 peptides, 11 chains. Longest chain 92 peptides. Score 0.878 Taking the results from Round 2 Chains 6, Residues 265, Estimated correctness of the model 99.4 % 4 chains (257 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 71 A Built loop between residues 93 B and 96 B 4 chains (269 residues) following loop building 2 chains (261 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2839 restraints for refining 2725 atoms. 676 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2068 (Rfree = 0.000) for 2725 atoms. Found 98 (108 requested) and removed 38 (63 requested) atoms. Cycle 22: After refmac, R = 0.2002 (Rfree = 0.000) for 2779 atoms. Found 73 (110 requested) and removed 38 (64 requested) atoms. Cycle 23: After refmac, R = 0.1935 (Rfree = 0.000) for 2811 atoms. Found 83 (109 requested) and removed 26 (65 requested) atoms. Cycle 24: After refmac, R = 0.1946 (Rfree = 0.000) for 2864 atoms. Found 68 (111 requested) and removed 50 (66 requested) atoms. Cycle 25: After refmac, R = 0.1923 (Rfree = 0.000) for 2875 atoms. Found 80 (109 requested) and removed 55 (66 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.94 1.79 NCS extension: 7 residues added (6 deleted due to clashes), 2907 seeds are put forward Round 1: 272 peptides, 5 chains. Longest chain 129 peptides. Score 0.919 Round 2: 272 peptides, 6 chains. Longest chain 133 peptides. Score 0.914 Round 3: 271 peptides, 7 chains. Longest chain 92 peptides. Score 0.907 Round 4: 268 peptides, 10 chains. Longest chain 94 peptides. Score 0.886 Round 5: 274 peptides, 5 chains. Longest chain 141 peptides. Score 0.921 Taking the results from Round 5 Chains 5, Residues 269, Estimated correctness of the model 99.5 % 3 chains (258 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 B and 50 B 4 chains (271 residues) following loop building 2 chains (260 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2895 restraints for refining 2739 atoms. 727 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2108 (Rfree = 0.000) for 2739 atoms. Found 101 (101 requested) and removed 46 (63 requested) atoms. Cycle 27: After refmac, R = 0.2011 (Rfree = 0.000) for 2785 atoms. Found 79 (103 requested) and removed 40 (64 requested) atoms. Cycle 28: After refmac, R = 0.1955 (Rfree = 0.000) for 2820 atoms. Found 71 (101 requested) and removed 42 (65 requested) atoms. Cycle 29: After refmac, R = 0.1935 (Rfree = 0.000) for 2845 atoms. Found 69 (100 requested) and removed 50 (65 requested) atoms. Cycle 30: After refmac, R = 0.1917 (Rfree = 0.000) for 2859 atoms. Found 78 (98 requested) and removed 49 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.94 1.79 NCS extension: 7 residues added (3 deleted due to clashes), 2897 seeds are put forward Round 1: 273 peptides, 5 chains. Longest chain 128 peptides. Score 0.920 Round 2: 272 peptides, 6 chains. Longest chain 81 peptides. Score 0.914 Round 3: 274 peptides, 5 chains. Longest chain 129 peptides. Score 0.921 Round 4: 272 peptides, 8 chains. Longest chain 81 peptides. Score 0.902 Round 5: 277 peptides, 4 chains. Longest chain 131 peptides. Score 0.928 Taking the results from Round 5 Chains 5, 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 29 A and 32 A 4 chains (275 residues) following loop building 2 chains (270 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2780 restraints for refining 2721 atoms. 546 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2052 (Rfree = 0.000) for 2721 atoms. Found 90 (90 requested) and removed 38 (62 requested) atoms. Cycle 32: After refmac, R = 0.2005 (Rfree = 0.000) for 2770 atoms. Found 73 (92 requested) and removed 33 (64 requested) atoms. Cycle 33: After refmac, R = 0.1932 (Rfree = 0.000) for 2809 atoms. Found 75 (93 requested) and removed 39 (64 requested) atoms. Cycle 34: After refmac, R = 0.1916 (Rfree = 0.000) for 2841 atoms. Found 55 (92 requested) and removed 41 (65 requested) atoms. Cycle 35: After refmac, R = 0.1897 (Rfree = 0.000) for 2846 atoms. Found 76 (90 requested) and removed 42 (66 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.94 1.79 NCS extension: 4 residues added (0 deleted due to clashes), 2889 seeds are put forward Round 1: 274 peptides, 5 chains. Longest chain 130 peptides. Score 0.921 Round 2: 276 peptides, 3 chains. Longest chain 141 peptides. Score 0.933 Round 3: 269 peptides, 9 chains. Longest chain 80 peptides. Score 0.893 Round 4: 275 peptides, 4 chains. Longest chain 130 peptides. Score 0.927 Round 5: 273 peptides, 6 chains. Longest chain 122 peptides. Score 0.914 Taking the results from Round 2 Chains 3, Residues 273, Estimated correctness of the model 99.6 % 2 chains (269 residues) have been docked in sequence Building loops using Loopy2018 3 chains (273 residues) following loop building 2 chains (269 residues) in sequence following loop building ------------------------------------------------------ 34433 reflections ( 97.40 % complete ) and 2817 restraints for refining 2743 atoms. 593 conditional restraints added. Observations/parameters ratio is 3.14 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2062 (Rfree = 0.000) for 2743 atoms. Found 83 (83 requested) and removed 49 (63 requested) atoms. Cycle 37: After refmac, R = 0.2007 (Rfree = 0.000) for 2769 atoms. Found 82 (82 requested) and removed 38 (64 requested) atoms. Cycle 38: After refmac, R = 0.1936 (Rfree = 0.000) for 2809 atoms. Found 76 (83 requested) and removed 47 (65 requested) atoms. Cycle 39: After refmac, R = 0.1905 (Rfree = 0.000) for 2834 atoms. Found 78 (81 requested) and removed 44 (65 requested) atoms. Cycle 40: After refmac, R = 0.1882 (Rfree = 0.000) for 2862 atoms. Found 79 (79 requested) and removed 44 (66 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.94 1.79 NCS extension: 3 residues added (0 deleted due to clashes), 2901 seeds are put forward Round 1: 274 peptides, 5 chains. Longest chain 130 peptides. Score 0.921 Round 2: 276 peptides, 4 chains. Longest chain 131 peptides. Score 0.927 Round 3: 271 peptides, 8 chains. Longest chain 101 peptides. Score 0.901 Round 4: 274 peptides, 6 chains. Longest chain 131 peptides. Score 0.915 Round 5: 272 peptides, 7 chains. Longest chain 121 peptides. Score 0.908 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 2802 restraints for refining 2736 atoms. 576 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2039 (Rfree = 0.000) for 2736 atoms. Found 73 (73 requested) and removed 38 (63 requested) atoms. Cycle 42: After refmac, R = 0.1957 (Rfree = 0.000) for 2766 atoms. Found 72 (72 requested) and removed 25 (64 requested) atoms. Cycle 43: After refmac, R = 0.1920 (Rfree = 0.000) for 2805 atoms. Found 73 (73 requested) and removed 29 (65 requested) atoms. Cycle 44: After refmac, R = 0.1891 (Rfree = 0.000) for 2846 atoms. Found 65 (73 requested) and removed 38 (65 requested) atoms. Cycle 45: After refmac, R = 0.1876 (Rfree = 0.000) for 2869 atoms. Found 64 (71 requested) and removed 47 (66 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.94 1.79 NCS extension: 0 residues added, 2888 seeds are put forward Round 1: 273 peptides, 4 chains. Longest chain 128 peptides. Score 0.925 Round 2: 272 peptides, 6 chains. Longest chain 103 peptides. Score 0.914 Round 3: 275 peptides, 4 chains. Longest chain 129 peptides. Score 0.927 Round 4: 273 peptides, 5 chains. Longest chain 83 peptides. Score 0.920 Round 5: 273 peptides, 5 chains. Longest chain 129 peptides. Score 0.920 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 271, Estimated correctness of the model 99.6 % 3 chains (267 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 B and 32 B 3 chains (273 residues) following loop building 2 chains (269 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 34433 reflections ( 97.40 % complete ) and 2225 restraints for refining 2182 atoms. Observations/parameters ratio is 3.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2693 (Rfree = 0.000) for 2182 atoms. Found 52 (52 requested) and removed 0 (52 requested) atoms. Cycle 47: After refmac, R = 0.2526 (Rfree = 0.000) for 2182 atoms. Found 36 (54 requested) and removed 1 (51 requested) atoms. Cycle 48: After refmac, R = 0.2392 (Rfree = 0.000) for 2182 atoms. Found 22 (54 requested) and removed 2 (52 requested) atoms. Cycle 49: After refmac, R = 0.2329 (Rfree = 0.000) for 2182 atoms. TimeTaking 40.07