null Sun 23 Dec 22:22:40 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 1zko-1.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1zko-1.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1zko-1.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-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/1zko-1.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-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 22:22:49 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/1zko-1.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-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 252 and 0 Target number of residues in the AU: 252 Target solvent content: 0.4413 Checking the provided sequence file Detected sequence length: 136 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 272 Adjusted target solvent content: 0.40 Input MTZ file: 1zko-1.6-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: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-1.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.45 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: 47.500 1.560 Wilson plot Bfac: 13.08 31574 reflections ( 88.87 % complete ) and 0 restraints for refining 2423 atoms. Observations/parameters ratio is 3.26 ------------------------------------------------------ Starting model: R = 0.3740 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3273 (Rfree = 0.000) for 2423 atoms. Found 91 (168 requested) and removed 96 (84 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.63 1.87 NCS extension: 0 residues added, 2418 seeds are put forward Round 1: 218 peptides, 17 chains. Longest chain 55 peptides. Score 0.859 Round 2: 239 peptides, 9 chains. Longest chain 93 peptides. Score 0.939 Round 3: 241 peptides, 12 chains. Longest chain 61 peptides. Score 0.924 Round 4: 246 peptides, 4 chains. Longest chain 128 peptides. Score 0.966 Round 5: 247 peptides, 7 chains. Longest chain 113 peptides. Score 0.954 Taking the results from Round 4 Chains 4, Residues 242, Estimated correctness of the model 99.9 % 2 chains (218 residues) have been docked in sequence Building loops using Loopy2018 4 chains (242 residues) following loop building 2 chains (218 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2553 restraints for refining 2290 atoms. 708 conditional restraints added. Observations/parameters ratio is 3.45 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3372 (Rfree = 0.000) for 2290 atoms. Found 119 (159 requested) and removed 82 (79 requested) atoms. Cycle 2: After refmac, R = 0.3179 (Rfree = 0.000) for 2324 atoms. Found 73 (158 requested) and removed 34 (80 requested) atoms. Cycle 3: After refmac, R = 0.3041 (Rfree = 0.000) for 2349 atoms. Found 71 (161 requested) and removed 11 (82 requested) atoms. Cycle 4: After refmac, R = 0.2844 (Rfree = 0.000) for 2403 atoms. Found 71 (164 requested) and removed 15 (83 requested) atoms. Cycle 5: After refmac, R = 0.2760 (Rfree = 0.000) for 2438 atoms. Found 71 (168 requested) and removed 10 (85 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.57 1.80 NCS extension: 0 residues added (22 deleted due to clashes), 2500 seeds are put forward Round 1: 250 peptides, 6 chains. Longest chain 66 peptides. Score 0.960 Round 2: 256 peptides, 2 chains. Longest chain 129 peptides. Score 0.978 Round 3: 254 peptides, 3 chains. Longest chain 128 peptides. Score 0.974 Round 4: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Round 5: 255 peptides, 2 chains. Longest chain 128 peptides. Score 0.978 Taking the results from Round 5 Chains 2, Residues 253, Estimated correctness of the model 100.0 % 2 chains (253 residues) have been docked in sequence Building loops using Loopy2018 2 chains (253 residues) following loop building 2 chains (253 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2344 restraints for refining 2427 atoms. 293 conditional restraints added. Observations/parameters ratio is 3.25 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2949 (Rfree = 0.000) for 2427 atoms. Found 110 (165 requested) and removed 46 (84 requested) atoms. Cycle 7: After refmac, R = 0.2813 (Rfree = 0.000) for 2487 atoms. Found 69 (170 requested) and removed 10 (86 requested) atoms. Cycle 8: After refmac, R = 0.2727 (Rfree = 0.000) for 2535 atoms. Found 60 (173 requested) and removed 9 (88 requested) atoms. Cycle 9: After refmac, R = 0.2661 (Rfree = 0.000) for 2576 atoms. Found 56 (175 requested) and removed 5 (89 requested) atoms. Cycle 10: After refmac, R = 0.2616 (Rfree = 0.000) for 2611 atoms. Found 56 (178 requested) and removed 13 (91 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.58 1.81 NCS extension: 0 residues added, 2657 seeds are put forward Round 1: 251 peptides, 4 chains. Longest chain 75 peptides. Score 0.969 Round 2: 249 peptides, 6 chains. Longest chain 72 peptides. Score 0.959 Round 3: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 4: 248 peptides, 5 chains. Longest chain 85 peptides. Score 0.963 Round 5: 248 peptides, 5 chains. Longest chain 72 peptides. Score 0.963 Taking the results from Round 3 Chains 3, Residues 248, Estimated correctness of the model 100.0 % 3 chains (248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 79 B and 82 B 2 chains (250 residues) following loop building 2 chains (250 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2478 restraints for refining 2502 atoms. 456 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2702 (Rfree = 0.000) for 2502 atoms. Found 110 (171 requested) and removed 49 (87 requested) atoms. Cycle 12: After refmac, R = 0.2647 (Rfree = 0.000) for 2557 atoms. Found 62 (174 requested) and removed 15 (89 requested) atoms. Cycle 13: After refmac, R = 0.2581 (Rfree = 0.000) for 2597 atoms. Found 47 (177 requested) and removed 10 (90 requested) atoms. Cycle 14: After refmac, R = 0.2527 (Rfree = 0.000) for 2620 atoms. Found 57 (179 requested) and removed 9 (91 requested) atoms. Cycle 15: After refmac, R = 0.2494 (Rfree = 0.000) for 2654 atoms. Found 59 (181 requested) and removed 14 (92 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.57 1.80 NCS extension: 1 residues added (2 deleted due to clashes), 2700 seeds are put forward Round 1: 250 peptides, 3 chains. Longest chain 125 peptides. Score 0.972 Round 2: 250 peptides, 3 chains. Longest chain 125 peptides. Score 0.972 Round 3: 247 peptides, 6 chains. Longest chain 87 peptides. Score 0.958 Round 4: 250 peptides, 5 chains. Longest chain 106 peptides. Score 0.964 Round 5: 250 peptides, 5 chains. Longest chain 107 peptides. Score 0.964 Taking the results from Round 2 Chains 3, Residues 247, Estimated correctness of the model 100.0 % 3 chains (247 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 B and 84 B 2 chains (249 residues) following loop building 2 chains (249 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2483 restraints for refining 2535 atoms. 460 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2619 (Rfree = 0.000) for 2535 atoms. Found 105 (172 requested) and removed 45 (88 requested) atoms. Cycle 17: After refmac, R = 0.2576 (Rfree = 0.000) for 2584 atoms. Found 61 (176 requested) and removed 13 (90 requested) atoms. Cycle 18: After refmac, R = 0.2538 (Rfree = 0.000) for 2626 atoms. Found 60 (179 requested) and removed 9 (91 requested) atoms. Cycle 19: After refmac, R = 0.2497 (Rfree = 0.000) for 2663 atoms. Found 58 (182 requested) and removed 11 (93 requested) atoms. Cycle 20: After refmac, R = 0.2475 (Rfree = 0.000) for 2693 atoms. Found 62 (184 requested) and removed 13 (94 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.57 1.80 NCS extension: 0 residues added, 2742 seeds are put forward Round 1: 249 peptides, 3 chains. Longest chain 124 peptides. Score 0.972 Round 2: 249 peptides, 4 chains. Longest chain 87 peptides. Score 0.968 Round 3: 251 peptides, 3 chains. Longest chain 126 peptides. Score 0.973 Round 4: 251 peptides, 3 chains. Longest chain 126 peptides. Score 0.973 Round 5: 249 peptides, 4 chains. Longest chain 126 peptides. Score 0.968 Taking the results from Round 4 Chains 3, Residues 248, Estimated correctness of the model 100.0 % 3 chains (248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 B and 47 B 2 chains (250 residues) following loop building 2 chains (250 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2456 restraints for refining 2571 atoms. 427 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2639 (Rfree = 0.000) for 2571 atoms. Found 128 (174 requested) and removed 47 (89 requested) atoms. Cycle 22: After refmac, R = 0.2562 (Rfree = 0.000) for 2638 atoms. Found 82 (180 requested) and removed 6 (92 requested) atoms. Cycle 23: After refmac, R = 0.2496 (Rfree = 0.000) for 2706 atoms. Found 39 (184 requested) and removed 13 (94 requested) atoms. Cycle 24: After refmac, R = 0.2440 (Rfree = 0.000) for 2718 atoms. Found 49 (186 requested) and removed 6 (95 requested) atoms. Cycle 25: After refmac, R = 0.2429 (Rfree = 0.000) for 2746 atoms. Found 45 (188 requested) and removed 7 (96 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 2784 seeds are put forward Round 1: 247 peptides, 4 chains. Longest chain 124 peptides. Score 0.967 Round 2: 248 peptides, 3 chains. Longest chain 124 peptides. Score 0.971 Round 3: 248 peptides, 4 chains. Longest chain 66 peptides. Score 0.967 Round 4: 248 peptides, 4 chains. Longest chain 125 peptides. Score 0.967 Round 5: 249 peptides, 3 chains. Longest chain 125 peptides. Score 0.972 Taking the results from Round 5 Chains 3, Residues 246, Estimated correctness of the model 100.0 % 3 chains (246 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 81 B and 84 B 2 chains (248 residues) following loop building 2 chains (248 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2578 restraints for refining 2613 atoms. 571 conditional restraints added. Observations/parameters ratio is 3.02 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2605 (Rfree = 0.000) for 2613 atoms. Found 125 (177 requested) and removed 42 (90 requested) atoms. Cycle 27: After refmac, R = 0.2584 (Rfree = 0.000) for 2682 atoms. Found 59 (183 requested) and removed 17 (93 requested) atoms. Cycle 28: After refmac, R = 0.2483 (Rfree = 0.000) for 2716 atoms. Found 60 (185 requested) and removed 12 (94 requested) atoms. Cycle 29: After refmac, R = 0.2429 (Rfree = 0.000) for 2749 atoms. Found 47 (188 requested) and removed 6 (96 requested) atoms. Cycle 30: After refmac, R = 0.2398 (Rfree = 0.000) for 2770 atoms. Found 55 (190 requested) and removed 8 (97 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 2817 seeds are put forward Round 1: 247 peptides, 4 chains. Longest chain 124 peptides. Score 0.967 Round 2: 246 peptides, 5 chains. Longest chain 87 peptides. Score 0.962 Round 3: 249 peptides, 3 chains. Longest chain 125 peptides. Score 0.972 Round 4: 249 peptides, 3 chains. Longest chain 125 peptides. Score 0.972 Round 5: 248 peptides, 4 chains. Longest chain 125 peptides. Score 0.967 Taking the results from Round 4 Chains 3, Residues 246, Estimated correctness of the model 100.0 % 3 chains (246 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 B and 47 B 2 chains (248 residues) following loop building 2 chains (248 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2665 restraints for refining 2644 atoms. 658 conditional restraints added. Observations/parameters ratio is 2.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2726 (Rfree = 0.000) for 2644 atoms. Found 121 (179 requested) and removed 38 (91 requested) atoms. Cycle 32: After refmac, R = 0.2561 (Rfree = 0.000) for 2720 atoms. Found 93 (185 requested) and removed 17 (94 requested) atoms. Cycle 33: After refmac, R = 0.2499 (Rfree = 0.000) for 2768 atoms. Found 62 (190 requested) and removed 11 (97 requested) atoms. Cycle 34: After refmac, R = 0.2426 (Rfree = 0.000) for 2803 atoms. Found 64 (192 requested) and removed 11 (98 requested) atoms. Cycle 35: After refmac, R = 0.2400 (Rfree = 0.000) for 2847 atoms. Found 56 (194 requested) and removed 12 (99 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.55 1.77 NCS extension: 0 residues added, 2891 seeds are put forward Round 1: 246 peptides, 4 chains. Longest chain 123 peptides. Score 0.966 Round 2: 247 peptides, 3 chains. Longest chain 125 peptides. Score 0.971 Round 3: 244 peptides, 6 chains. Longest chain 63 peptides. Score 0.957 Round 4: 246 peptides, 4 chains. Longest chain 123 peptides. Score 0.966 Round 5: 247 peptides, 3 chains. Longest chain 123 peptides. Score 0.971 Taking the results from Round 5 Chains 3, Residues 244, Estimated correctness of the model 100.0 % 3 chains (244 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 B and 85 B 2 chains (246 residues) following loop building 2 chains (246 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2758 restraints for refining 2700 atoms. 768 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2566 (Rfree = 0.000) for 2700 atoms. Found 125 (183 requested) and removed 43 (93 requested) atoms. Cycle 37: After refmac, R = 0.2507 (Rfree = 0.000) for 2773 atoms. Found 68 (189 requested) and removed 13 (96 requested) atoms. Cycle 38: After refmac, R = 0.2437 (Rfree = 0.000) for 2824 atoms. Found 46 (192 requested) and removed 9 (98 requested) atoms. Cycle 39: After refmac, R = 0.2397 (Rfree = 0.000) for 2847 atoms. Found 54 (194 requested) and removed 9 (99 requested) atoms. Cycle 40: After refmac, R = 0.2354 (Rfree = 0.000) for 2879 atoms. Found 50 (197 requested) and removed 13 (100 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 2916 seeds are put forward Round 1: 246 peptides, 5 chains. Longest chain 123 peptides. Score 0.962 Round 2: 247 peptides, 5 chains. Longest chain 78 peptides. Score 0.963 Round 3: 249 peptides, 4 chains. Longest chain 124 peptides. Score 0.968 Round 4: 251 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 5: 248 peptides, 5 chains. Longest chain 88 peptides. Score 0.963 Taking the results from Round 4 Chains 2, Residues 249, Estimated correctness of the model 100.0 % 2 chains (249 residues) have been docked in sequence Building loops using Loopy2018 2 chains (249 residues) following loop building 2 chains (249 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2755 restraints for refining 2710 atoms. 748 conditional restraints added. Observations/parameters ratio is 2.91 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2576 (Rfree = 0.000) for 2710 atoms. Found 145 (184 requested) and removed 51 (94 requested) atoms. Cycle 42: After refmac, R = 0.2519 (Rfree = 0.000) for 2794 atoms. Found 71 (191 requested) and removed 12 (97 requested) atoms. Cycle 43: After refmac, R = 0.2432 (Rfree = 0.000) for 2843 atoms. Found 63 (194 requested) and removed 13 (99 requested) atoms. Cycle 44: After refmac, R = 0.2387 (Rfree = 0.000) for 2878 atoms. Found 56 (197 requested) and removed 16 (100 requested) atoms. Cycle 45: After refmac, R = 0.2342 (Rfree = 0.000) for 2907 atoms. Found 65 (198 requested) and removed 18 (101 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.55 1.77 NCS extension: 0 residues added, 2954 seeds are put forward Round 1: 245 peptides, 6 chains. Longest chain 107 peptides. Score 0.957 Round 2: 245 peptides, 5 chains. Longest chain 88 peptides. Score 0.962 Round 3: 247 peptides, 4 chains. Longest chain 124 peptides. Score 0.967 Round 4: 248 peptides, 3 chains. Longest chain 124 peptides. Score 0.971 Round 5: 248 peptides, 3 chains. Longest chain 124 peptides. Score 0.971 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 245, Estimated correctness of the model 100.0 % 3 chains (245 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 72 A and 75 A 2 chains (247 residues) following loop building 2 chains (247 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 31574 reflections ( 88.87 % complete ) and 1996 restraints for refining 1960 atoms. Observations/parameters ratio is 4.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3090 (Rfree = 0.000) for 1960 atoms. Found 40 (133 requested) and removed 0 (133 requested) atoms. Cycle 47: After refmac, R = 0.2879 (Rfree = 0.000) for 1960 atoms. Found 11 (136 requested) and removed 0 (69 requested) atoms. Cycle 48: After refmac, R = 0.2810 (Rfree = 0.000) for 1960 atoms. Found 3 (136 requested) and removed 1 (69 requested) atoms. Cycle 49: After refmac, R = 0.2772 (Rfree = 0.000) for 1960 atoms. Found 3 (137 requested) and removed 1 (70 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:17:22 GMT 2018 Job finished. TimeTaking 54.7 Used memory is bytes: 16892824