Mon 24 Dec 07:26:24 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 2aj7-2.2-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2aj7-2.2-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2aj7-2.2-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-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/2aj7-2.2-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-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 07:26:28 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/noncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2aj7-2.2-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 512 and 0 Target number of residues in the AU: 512 Target solvent content: 0.5104 Checking the provided sequence file Detected sequence length: 163 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 326 Adjusted target solvent content: 0.69 Input MTZ file: 2aj7-2.2-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: 173 Cell parameters: 108.801 108.801 82.811 90.000 90.000 120.000 Input sequence file: 2aj7-2.2-parrot-noncs.fasta_lf Building free atoms model in initial map for 2608 target number of atoms Had to go as low as 1.00 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: 94.224 2.240 Wilson plot Bfac: 25.68 26900 reflections ( 99.98 % complete ) and 0 restraints for refining 2921 atoms. Observations/parameters ratio is 2.30 ------------------------------------------------------ Starting model: R = 0.3545 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3115 (Rfree = 0.000) for 2921 atoms. Found 72 (72 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.31 1.77 NCS extension: 0 residues added, 2954 seeds are put forward Round 1: 238 peptides, 29 chains. Longest chain 20 peptides. Score 0.541 Round 2: 271 peptides, 26 chains. Longest chain 34 peptides. Score 0.644 Round 3: 258 peptides, 16 chains. Longest chain 61 peptides. Score 0.710 Round 4: 280 peptides, 11 chains. Longest chain 76 peptides. Score 0.784 Round 5: 281 peptides, 11 chains. Longest chain 100 peptides. Score 0.785 Taking the results from Round 5 Chains 14, Residues 270, Estimated correctness of the model 93.9 % 4 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 117 A 12 chains (274 residues) following loop building 3 chains (206 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 3399 restraints for refining 2832 atoms. 1460 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3124 (Rfree = 0.000) for 2832 atoms. Found 70 (70 requested) and removed 42 (35 requested) atoms. Cycle 2: After refmac, R = 0.2885 (Rfree = 0.000) for 2841 atoms. Found 69 (69 requested) and removed 37 (35 requested) atoms. Cycle 3: After refmac, R = 0.2701 (Rfree = 0.000) for 2858 atoms. Found 68 (68 requested) and removed 35 (35 requested) atoms. Cycle 4: After refmac, R = 0.2573 (Rfree = 0.000) for 2877 atoms. Found 50 (67 requested) and removed 27 (35 requested) atoms. Cycle 5: After refmac, R = 0.2461 (Rfree = 0.000) for 2885 atoms. Found 51 (65 requested) and removed 26 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.23 1.71 NCS extension: 168 residues added (121 deleted due to clashes), 3080 seeds are put forward Round 1: 281 peptides, 10 chains. Longest chain 89 peptides. Score 0.792 Round 2: 285 peptides, 9 chains. Longest chain 101 peptides. Score 0.804 Round 3: 275 peptides, 12 chains. Longest chain 65 peptides. Score 0.769 Round 4: 287 peptides, 9 chains. Longest chain 102 peptides. Score 0.807 Round 5: 283 peptides, 9 chains. Longest chain 88 peptides. Score 0.802 Taking the results from Round 4 Chains 12, Residues 278, Estimated correctness of the model 95.0 % 7 chains (255 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 43 A Built loop between residues 141 A and 144 A Built loop between residues 111 B and 116 B 7 chains (283 residues) following loop building 4 chains (263 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2945 restraints for refining 2850 atoms. 717 conditional restraints added. Observations/parameters ratio is 2.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2525 (Rfree = 0.000) for 2850 atoms. Found 63 (63 requested) and removed 35 (35 requested) atoms. Cycle 7: After refmac, R = 0.2321 (Rfree = 0.000) for 2874 atoms. Found 62 (62 requested) and removed 19 (35 requested) atoms. Cycle 8: After refmac, R = 0.2191 (Rfree = 0.000) for 2906 atoms. Found 59 (63 requested) and removed 28 (36 requested) atoms. Cycle 9: After refmac, R = 0.2115 (Rfree = 0.000) for 2929 atoms. Found 58 (63 requested) and removed 29 (36 requested) atoms. Cycle 10: After refmac, R = 0.2061 (Rfree = 0.000) for 2955 atoms. Found 64 (64 requested) and removed 27 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.20 1.69 NCS extension: 67 residues added (94 deleted due to clashes), 3060 seeds are put forward Round 1: 289 peptides, 6 chains. Longest chain 101 peptides. Score 0.829 Round 2: 290 peptides, 7 chains. Longest chain 102 peptides. Score 0.824 Round 3: 290 peptides, 7 chains. Longest chain 102 peptides. Score 0.824 Round 4: 289 peptides, 8 chains. Longest chain 88 peptides. Score 0.816 Round 5: 285 peptides, 6 chains. Longest chain 102 peptides. Score 0.825 Taking the results from Round 1 Chains 8, Residues 283, Estimated correctness of the model 96.0 % 5 chains (269 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 B and 116 B Built loop between residues 141 B and 145 B 4 chains (287 residues) following loop building 3 chains (275 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2904 restraints for refining 2873 atoms. 614 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2226 (Rfree = 0.000) for 2873 atoms. Found 62 (62 requested) and removed 36 (35 requested) atoms. Cycle 12: After refmac, R = 0.2094 (Rfree = 0.000) for 2897 atoms. Found 61 (61 requested) and removed 21 (35 requested) atoms. Cycle 13: After refmac, R = 0.2014 (Rfree = 0.000) for 2933 atoms. Found 62 (62 requested) and removed 37 (36 requested) atoms. Cycle 14: After refmac, R = 0.1955 (Rfree = 0.000) for 2953 atoms. Found 61 (61 requested) and removed 39 (36 requested) atoms. Cycle 15: After refmac, R = 0.1925 (Rfree = 0.000) for 2969 atoms. Found 60 (60 requested) and removed 37 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.19 1.68 NCS extension: 16 residues added (49 deleted due to clashes), 3010 seeds are put forward Round 1: 284 peptides, 8 chains. Longest chain 71 peptides. Score 0.810 Round 2: 288 peptides, 6 chains. Longest chain 100 peptides. Score 0.828 Round 3: 289 peptides, 6 chains. Longest chain 88 peptides. Score 0.829 Round 4: 289 peptides, 6 chains. Longest chain 88 peptides. Score 0.829 Round 5: 289 peptides, 6 chains. Longest chain 88 peptides. Score 0.829 Taking the results from Round 5 Chains 6, Residues 283, Estimated correctness of the model 96.0 % 5 chains (271 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 59 A Built loop between residues 114 A and 117 A 4 chains (287 residues) following loop building 3 chains (275 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2835 restraints for refining 2840 atoms. 542 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2140 (Rfree = 0.000) for 2840 atoms. Found 56 (56 requested) and removed 35 (35 requested) atoms. Cycle 17: After refmac, R = 0.2008 (Rfree = 0.000) for 2854 atoms. Found 55 (55 requested) and removed 14 (35 requested) atoms. Cycle 18: After refmac, R = 0.1919 (Rfree = 0.000) for 2889 atoms. Found 55 (55 requested) and removed 20 (35 requested) atoms. Cycle 19: After refmac, R = 0.1879 (Rfree = 0.000) for 2920 atoms. Found 56 (56 requested) and removed 28 (36 requested) atoms. Cycle 20: After refmac, R = 0.1836 (Rfree = 0.000) for 2946 atoms. Found 54 (57 requested) and removed 38 (36 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.18 1.67 NCS extension: 18 residues added (43 deleted due to clashes), 2981 seeds are put forward Round 1: 289 peptides, 6 chains. Longest chain 99 peptides. Score 0.829 Round 2: 289 peptides, 5 chains. Longest chain 100 peptides. Score 0.836 Round 3: 293 peptides, 5 chains. Longest chain 100 peptides. Score 0.840 Round 4: 289 peptides, 5 chains. Longest chain 101 peptides. Score 0.836 Round 5: 292 peptides, 5 chains. Longest chain 100 peptides. Score 0.839 Taking the results from Round 3 Chains 5, Residues 288, Estimated correctness of the model 96.4 % 4 chains (275 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 114 A 4 chains (290 residues) following loop building 3 chains (277 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2870 restraints for refining 2847 atoms. 560 conditional restraints added. Observations/parameters ratio is 2.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2042 (Rfree = 0.000) for 2847 atoms. Found 53 (53 requested) and removed 25 (35 requested) atoms. Cycle 22: After refmac, R = 0.1917 (Rfree = 0.000) for 2869 atoms. Found 54 (54 requested) and removed 10 (35 requested) atoms. Cycle 23: After refmac, R = 0.1864 (Rfree = 0.000) for 2911 atoms. Found 55 (55 requested) and removed 29 (36 requested) atoms. Cycle 24: After refmac, R = 0.1826 (Rfree = 0.000) for 2935 atoms. Found 53 (53 requested) and removed 31 (36 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1808 (Rfree = 0.000) for 2957 atoms. Found 53 (53 requested) and removed 36 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.18 1.67 NCS extension: 18 residues added (45 deleted due to clashes), 2992 seeds are put forward Round 1: 289 peptides, 8 chains. Longest chain 71 peptides. Score 0.816 Round 2: 290 peptides, 4 chains. Longest chain 101 peptides. Score 0.843 Round 3: 290 peptides, 6 chains. Longest chain 101 peptides. Score 0.830 Round 4: 291 peptides, 5 chains. Longest chain 101 peptides. Score 0.838 Round 5: 292 peptides, 7 chains. Longest chain 88 peptides. Score 0.826 Taking the results from Round 2 Chains 4, Residues 286, Estimated correctness of the model 96.6 % 4 chains (286 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 111 A and 115 A Built loop between residues 111 B and 115 B 2 chains (292 residues) following loop building 2 chains (292 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2764 restraints for refining 2862 atoms. 383 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2004 (Rfree = 0.000) for 2862 atoms. Found 49 (49 requested) and removed 28 (35 requested) atoms. Cycle 27: After refmac, R = 0.1900 (Rfree = 0.000) for 2879 atoms. Found 48 (48 requested) and removed 17 (35 requested) atoms. Cycle 28: After refmac, R = 0.1829 (Rfree = 0.000) for 2909 atoms. Found 49 (49 requested) and removed 32 (36 requested) atoms. Cycle 29: After refmac, R = 0.1808 (Rfree = 0.000) for 2924 atoms. Found 48 (48 requested) and removed 37 (36 requested) atoms. Cycle 30: After refmac, R = 0.1785 (Rfree = 0.000) for 2934 atoms. Found 46 (46 requested) and removed 39 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.18 1.67 NCS extension: 0 residues added, 2941 seeds are put forward Round 1: 292 peptides, 6 chains. Longest chain 68 peptides. Score 0.833 Round 2: 291 peptides, 6 chains. Longest chain 101 peptides. Score 0.832 Round 3: 290 peptides, 6 chains. Longest chain 101 peptides. Score 0.830 Round 4: 290 peptides, 7 chains. Longest chain 68 peptides. Score 0.824 Round 5: 293 peptides, 6 chains. Longest chain 104 peptides. Score 0.834 Taking the results from Round 5 Chains 6, Residues 287, Estimated correctness of the model 96.2 % 5 chains (282 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 113 A and 116 A Built loop between residues 76 B and 80 B Built loop between residues 105 B and 115 B 2 chains (296 residues) following loop building 2 chains (296 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2720 restraints for refining 2861 atoms. 299 conditional restraints added. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2093 (Rfree = 0.000) for 2861 atoms. Found 43 (43 requested) and removed 35 (35 requested) atoms. Cycle 32: After refmac, R = 0.1936 (Rfree = 0.000) for 2866 atoms. Found 43 (43 requested) and removed 26 (35 requested) atoms. Cycle 33: After refmac, R = 0.1860 (Rfree = 0.000) for 2881 atoms. Found 41 (41 requested) and removed 16 (35 requested) atoms. Cycle 34: After refmac, R = 0.1815 (Rfree = 0.000) for 2906 atoms. Found 42 (42 requested) and removed 26 (36 requested) atoms. Cycle 35: After refmac, R = 0.1795 (Rfree = 0.000) for 2921 atoms. Found 40 (40 requested) and removed 35 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.18 1.67 NCS extension: 0 residues added, 2930 seeds are put forward Round 1: 293 peptides, 6 chains. Longest chain 104 peptides. Score 0.834 Round 2: 294 peptides, 4 chains. Longest chain 104 peptides. Score 0.847 Round 3: 294 peptides, 6 chains. Longest chain 105 peptides. Score 0.835 Round 4: 293 peptides, 4 chains. Longest chain 103 peptides. Score 0.846 Round 5: 294 peptides, 7 chains. Longest chain 79 peptides. Score 0.828 Taking the results from Round 2 Chains 4, Residues 290, Estimated correctness of the model 96.7 % 4 chains (290 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 112 A and 115 A Built loop between residues 111 B and 115 B 2 chains (295 residues) following loop building 2 chains (295 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2706 restraints for refining 2841 atoms. 296 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2002 (Rfree = 0.000) for 2841 atoms. Found 38 (38 requested) and removed 28 (35 requested) atoms. Cycle 37: After refmac, R = 0.1874 (Rfree = 0.000) for 2849 atoms. Found 36 (36 requested) and removed 16 (35 requested) atoms. Cycle 38: After refmac, R = 0.1821 (Rfree = 0.000) for 2869 atoms. Found 37 (37 requested) and removed 19 (35 requested) atoms. Cycle 39: After refmac, R = 0.1770 (Rfree = 0.000) for 2886 atoms. Found 35 (35 requested) and removed 30 (35 requested) atoms. Cycle 40: After refmac, R = 0.1760 (Rfree = 0.000) for 2891 atoms. Found 35 (35 requested) and removed 26 (35 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.18 1.67 NCS extension: 0 residues added, 2901 seeds are put forward Round 1: 291 peptides, 4 chains. Longest chain 101 peptides. Score 0.844 Round 2: 295 peptides, 4 chains. Longest chain 105 peptides. Score 0.848 Round 3: 292 peptides, 4 chains. Longest chain 102 peptides. Score 0.845 Round 4: 291 peptides, 6 chains. Longest chain 101 peptides. Score 0.832 Round 5: 293 peptides, 6 chains. Longest chain 79 peptides. Score 0.834 Taking the results from Round 2 Chains 4, Residues 291, Estimated correctness of the model 96.8 % 4 chains (291 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 113 B and 116 B 2 chains (295 residues) following loop building 2 chains (295 residues) in sequence following loop building ------------------------------------------------------ 26900 reflections ( 99.98 % complete ) and 2723 restraints for refining 2833 atoms. 313 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1954 (Rfree = 0.000) for 2833 atoms. Found 35 (35 requested) and removed 27 (35 requested) atoms. Cycle 42: After refmac, R = 0.1854 (Rfree = 0.000) for 2840 atoms. Found 35 (35 requested) and removed 12 (35 requested) atoms. Cycle 43: After refmac, R = 0.1799 (Rfree = 0.000) for 2862 atoms. Found 35 (35 requested) and removed 13 (35 requested) atoms. Cycle 44: After refmac, R = 0.1760 (Rfree = 0.000) for 2884 atoms. Found 35 (35 requested) and removed 25 (35 requested) atoms. Cycle 45: After refmac, R = 0.1731 (Rfree = 0.000) for 2894 atoms. Found 35 (35 requested) and removed 28 (35 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.18 1.67 NCS extension: 0 residues added, 2902 seeds are put forward Round 1: 290 peptides, 6 chains. Longest chain 101 peptides. Score 0.830 Round 2: 290 peptides, 5 chains. Longest chain 101 peptides. Score 0.837 Round 3: 293 peptides, 4 chains. Longest chain 104 peptides. Score 0.846 Round 4: 289 peptides, 7 chains. Longest chain 103 peptides. Score 0.823 Round 5: 290 peptides, 8 chains. Longest chain 79 peptides. Score 0.817 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 289, Estimated correctness of the model 96.7 % 4 chains (289 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 113 A and 116 A Built loop between residues 111 B and 115 B 2 chains (294 residues) following loop building 2 chains (294 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 26900 reflections ( 99.98 % complete ) and 2399 restraints for refining 2348 atoms. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2500 (Rfree = 0.000) for 2348 atoms. Found 29 (29 requested) and removed 0 (29 requested) atoms. Cycle 47: After refmac, R = 0.2344 (Rfree = 0.000) for 2348 atoms. Found 29 (29 requested) and removed 0 (29 requested) atoms. Cycle 48: After refmac, R = 0.2238 (Rfree = 0.000) for 2348 atoms. Found 29 (29 requested) and removed 1 (29 requested) atoms. Cycle 49: After refmac, R = 0.2168 (Rfree = 0.000) for 2348 atoms. TimeTaking 49.18