null Mon 24 Dec 07:27:56 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 1zko-1.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1zko-1.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1zko-1.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-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/1zko-1.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-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 07:28:01 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/1zko-1.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-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 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-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: 54.005 65.321 69.197 90.000 90.000 90.000 Input sequence file: 1zko-1.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 2176 target number of atoms Had to go as low as 0.40 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 2415 atoms. Observations/parameters ratio is 3.27 ------------------------------------------------------ Starting model: R = 0.3659 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3173 (Rfree = 0.000) for 2415 atoms. Found 108 (168 requested) and removed 95 (84 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.61 1.84 NCS extension: 0 residues added, 2428 seeds are put forward Round 1: 220 peptides, 12 chains. Longest chain 64 peptides. Score 0.902 Round 2: 236 peptides, 8 chains. Longest chain 59 peptides. Score 0.942 Round 3: 243 peptides, 5 chains. Longest chain 120 peptides. Score 0.961 Round 4: 246 peptides, 4 chains. Longest chain 96 peptides. Score 0.966 Round 5: 247 peptides, 5 chains. Longest chain 92 peptides. Score 0.963 Taking the results from Round 4 Chains 4, Residues 242, Estimated correctness of the model 99.9 % 4 chains (242 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 36 A and 39 A Built loop between residues 44 B and 47 B 2 chains (246 residues) following loop building 2 chains (246 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2305 restraints for refining 2302 atoms. 325 conditional restraints added. Observations/parameters ratio is 3.43 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3297 (Rfree = 0.000) for 2302 atoms. Found 102 (160 requested) and removed 84 (80 requested) atoms. Cycle 2: After refmac, R = 0.3132 (Rfree = 0.000) for 2316 atoms. Found 70 (158 requested) and removed 32 (80 requested) atoms. Cycle 3: After refmac, R = 0.2931 (Rfree = 0.000) for 2336 atoms. Found 59 (160 requested) and removed 12 (81 requested) atoms. Cycle 4: After refmac, R = 0.2814 (Rfree = 0.000) for 2362 atoms. Found 49 (162 requested) and removed 6 (82 requested) atoms. Cycle 5: After refmac, R = 0.2733 (Rfree = 0.000) for 2387 atoms. Found 45 (164 requested) and removed 11 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.59 1.82 NCS extension: 1 residues added (3 deleted due to clashes), 2423 seeds are put forward Round 1: 249 peptides, 3 chains. Longest chain 124 peptides. Score 0.972 Round 2: 252 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 3: 250 peptides, 3 chains. Longest chain 124 peptides. Score 0.972 Round 4: 251 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 5: 250 peptides, 4 chains. Longest chain 91 peptides. Score 0.968 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 2311 restraints for refining 2364 atoms. 299 conditional restraints added. Observations/parameters ratio is 3.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2906 (Rfree = 0.000) for 2364 atoms. Found 90 (161 requested) and removed 47 (82 requested) atoms. Cycle 7: After refmac, R = 0.2715 (Rfree = 0.000) for 2405 atoms. Found 71 (160 requested) and removed 4 (83 requested) atoms. Cycle 8: After refmac, R = 0.2652 (Rfree = 0.000) for 2465 atoms. Found 61 (164 requested) and removed 9 (85 requested) atoms. Cycle 9: After refmac, R = 0.2590 (Rfree = 0.000) for 2513 atoms. Found 62 (168 requested) and removed 7 (87 requested) atoms. Cycle 10: After refmac, R = 0.2567 (Rfree = 0.000) for 2558 atoms. Found 59 (171 requested) and removed 6 (89 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 2611 seeds are put forward Round 1: 252 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 2: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 3: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 4: 251 peptides, 3 chains. Longest chain 127 peptides. Score 0.973 Round 5: 250 peptides, 4 chains. Longest chain 119 peptides. Score 0.968 Taking the results from Round 1 Chains 2, Residues 250, Estimated correctness of the model 100.0 % 2 chains (250 residues) have been docked in sequence Building loops using Loopy2018 2 chains (250 residues) following loop building 2 chains (250 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2391 restraints for refining 2503 atoms. 368 conditional restraints added. Observations/parameters ratio is 3.15 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2650 (Rfree = 0.000) for 2503 atoms. Found 112 (167 requested) and removed 42 (87 requested) atoms. Cycle 12: After refmac, R = 0.2594 (Rfree = 0.000) for 2565 atoms. Found 67 (171 requested) and removed 8 (89 requested) atoms. Cycle 13: After refmac, R = 0.2555 (Rfree = 0.000) for 2621 atoms. Found 55 (175 requested) and removed 10 (91 requested) atoms. Cycle 14: After refmac, R = 0.2526 (Rfree = 0.000) for 2656 atoms. Found 55 (178 requested) and removed 7 (92 requested) atoms. Cycle 15: After refmac, R = 0.2480 (Rfree = 0.000) for 2694 atoms. Found 54 (180 requested) and removed 13 (94 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 2735 seeds are put forward Round 1: 250 peptides, 4 chains. Longest chain 125 peptides. Score 0.968 Round 2: 253 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 3: 250 peptides, 5 chains. Longest chain 119 peptides. Score 0.964 Round 4: 252 peptides, 3 chains. Longest chain 128 peptides. Score 0.973 Round 5: 253 peptides, 3 chains. Longest chain 128 peptides. Score 0.973 Taking the results from Round 2 Chains 2, Residues 251, Estimated correctness of the model 100.0 % 2 chains (251 residues) have been docked in sequence Building loops using Loopy2018 2 chains (251 residues) following loop building 2 chains (251 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2463 restraints for refining 2574 atoms. 429 conditional restraints added. Observations/parameters ratio is 3.07 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2719 (Rfree = 0.000) for 2574 atoms. Found 113 (172 requested) and removed 35 (89 requested) atoms. Cycle 17: After refmac, R = 0.2598 (Rfree = 0.000) for 2646 atoms. Found 74 (177 requested) and removed 11 (92 requested) atoms. Cycle 18: After refmac, R = 0.2520 (Rfree = 0.000) for 2702 atoms. Found 51 (180 requested) and removed 13 (94 requested) atoms. Cycle 19: After refmac, R = 0.2474 (Rfree = 0.000) for 2730 atoms. Found 58 (182 requested) and removed 11 (95 requested) atoms. Cycle 20: After refmac, R = 0.2451 (Rfree = 0.000) for 2768 atoms. Found 55 (185 requested) and removed 16 (96 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.55 1.77 NCS extension: 0 residues added, 2807 seeds are put forward Round 1: 253 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 2: 252 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 3: 249 peptides, 5 chains. Longest chain 104 peptides. Score 0.963 Round 4: 253 peptides, 2 chains. Longest chain 128 peptides. Score 0.977 Round 5: 250 peptides, 4 chains. Longest chain 125 peptides. Score 0.968 Taking the results from Round 4 Chains 2, Residues 251, Estimated correctness of the model 100.0 % 2 chains (251 residues) have been docked in sequence Building loops using Loopy2018 2 chains (251 residues) following loop building 2 chains (251 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2521 restraints for refining 2626 atoms. 487 conditional restraints added. Observations/parameters ratio is 3.01 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2566 (Rfree = 0.000) for 2626 atoms. Found 118 (175 requested) and removed 35 (91 requested) atoms. Cycle 22: After refmac, R = 0.2530 (Rfree = 0.000) for 2699 atoms. Found 66 (180 requested) and removed 8 (94 requested) atoms. Cycle 23: After refmac, R = 0.2487 (Rfree = 0.000) for 2751 atoms. Found 68 (183 requested) and removed 11 (95 requested) atoms. Cycle 24: After refmac, R = 0.2443 (Rfree = 0.000) for 2803 atoms. Found 68 (187 requested) and removed 13 (97 requested) atoms. Cycle 25: After refmac, R = 0.2434 (Rfree = 0.000) for 2848 atoms. Found 55 (190 requested) and removed 15 (99 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.55 1.77 NCS extension: 0 residues added, 2888 seeds are put forward Round 1: 250 peptides, 4 chains. Longest chain 125 peptides. Score 0.968 Round 2: 250 peptides, 4 chains. Longest chain 119 peptides. Score 0.968 Round 3: 249 peptides, 5 chains. Longest chain 68 peptides. Score 0.963 Round 4: 249 peptides, 4 chains. Longest chain 117 peptides. Score 0.968 Round 5: 251 peptides, 4 chains. Longest chain 125 peptides. Score 0.969 Taking the results from Round 5 Chains 5, Residues 247, Estimated correctness of the model 99.9 % 4 chains (246 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 B and 32 B Built loop between residues 98 B and 101 B 3 chains (251 residues) following loop building 2 chains (250 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2565 restraints for refining 2666 atoms. 533 conditional restraints added. Observations/parameters ratio is 2.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2711 (Rfree = 0.000) for 2666 atoms. Found 137 (178 requested) and removed 39 (92 requested) atoms. Cycle 27: After refmac, R = 0.2564 (Rfree = 0.000) for 2760 atoms. Found 62 (184 requested) and removed 9 (96 requested) atoms. Cycle 28: After refmac, R = 0.2473 (Rfree = 0.000) for 2803 atoms. Found 60 (187 requested) and removed 15 (97 requested) atoms. Cycle 29: After refmac, R = 0.2419 (Rfree = 0.000) for 2836 atoms. Found 57 (190 requested) and removed 16 (99 requested) atoms. Cycle 30: After refmac, R = 0.2437 (Rfree = 0.000) for 2860 atoms. Found 73 (192 requested) and removed 17 (100 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.54 1.76 NCS extension: 0 residues added, 2916 seeds are put forward Round 1: 250 peptides, 2 chains. Longest chain 125 peptides. Score 0.976 Round 2: 248 peptides, 4 chains. Longest chain 125 peptides. Score 0.967 Round 3: 244 peptides, 8 chains. Longest chain 69 peptides. Score 0.947 Round 4: 245 peptides, 4 chains. Longest chain 125 peptides. Score 0.966 Round 5: 244 peptides, 7 chains. Longest chain 60 peptides. Score 0.952 Taking the results from Round 1 Chains 2, Residues 248, Estimated correctness of the model 100.0 % 2 chains (248 residues) have been docked in sequence Building loops using Loopy2018 2 chains (248 residues) following loop building 2 chains (248 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2697 restraints for refining 2709 atoms. 696 conditional restraints added. Observations/parameters ratio is 2.91 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2563 (Rfree = 0.000) for 2709 atoms. Found 116 (180 requested) and removed 42 (94 requested) atoms. Cycle 32: After refmac, R = 0.2497 (Rfree = 0.000) for 2770 atoms. Found 73 (185 requested) and removed 13 (96 requested) atoms. Cycle 33: After refmac, R = 0.2443 (Rfree = 0.000) for 2825 atoms. Found 68 (188 requested) and removed 9 (98 requested) atoms. Cycle 34: After refmac, R = 0.2422 (Rfree = 0.000) for 2870 atoms. Found 63 (192 requested) and removed 15 (100 requested) atoms. Cycle 35: After refmac, R = 0.2398 (Rfree = 0.000) for 2908 atoms. Found 55 (194 requested) and removed 22 (101 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.54 1.76 NCS extension: 0 residues added, 2941 seeds are put forward Round 1: 247 peptides, 3 chains. Longest chain 125 peptides. Score 0.971 Round 2: 247 peptides, 5 chains. Longest chain 118 peptides. Score 0.963 Round 3: 246 peptides, 4 chains. Longest chain 125 peptides. Score 0.966 Round 4: 248 peptides, 4 chains. Longest chain 125 peptides. Score 0.967 Round 5: 247 peptides, 4 chains. Longest chain 118 peptides. Score 0.967 Taking the results from Round 1 Chains 3, Residues 244, Estimated correctness of the model 100.0 % 2 chains (240 residues) have been docked in sequence Building loops using Loopy2018 3 chains (244 residues) following loop building 2 chains (240 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2955 restraints for refining 2715 atoms. 1017 conditional restraints added. Observations/parameters ratio is 2.91 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2570 (Rfree = 0.000) for 2715 atoms. Found 135 (180 requested) and removed 35 (94 requested) atoms. Cycle 37: After refmac, R = 0.2507 (Rfree = 0.000) for 2810 atoms. Found 72 (187 requested) and removed 20 (97 requested) atoms. Cycle 38: After refmac, R = 0.2450 (Rfree = 0.000) for 2854 atoms. Found 70 (191 requested) and removed 10 (99 requested) atoms. Cycle 39: After refmac, R = 0.2426 (Rfree = 0.000) for 2898 atoms. Found 58 (194 requested) and removed 18 (101 requested) atoms. Cycle 40: After refmac, R = 0.2386 (Rfree = 0.000) for 2925 atoms. Found 71 (196 requested) and removed 20 (102 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.55 1.77 NCS extension: 0 residues added (6 deleted due to clashes), 2976 seeds are put forward Round 1: 243 peptides, 5 chains. Longest chain 117 peptides. Score 0.961 Round 2: 246 peptides, 5 chains. Longest chain 118 peptides. Score 0.962 Round 3: 251 peptides, 2 chains. Longest chain 126 peptides. Score 0.977 Round 4: 247 peptides, 3 chains. Longest chain 125 peptides. Score 0.971 Round 5: 248 peptides, 5 chains. Longest chain 73 peptides. Score 0.963 Taking the results from Round 3 Chains 3, Residues 249, Estimated correctness of the model 100.0 % 2 chains (248 residues) have been docked in sequence Building loops using Loopy2018 3 chains (249 residues) following loop building 2 chains (248 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2722 restraints for refining 2717 atoms. 712 conditional restraints added. Observations/parameters ratio is 2.91 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2559 (Rfree = 0.000) for 2717 atoms. Found 156 (180 requested) and removed 42 (94 requested) atoms. Cycle 42: After refmac, R = 0.2524 (Rfree = 0.000) for 2826 atoms. Found 76 (188 requested) and removed 14 (98 requested) atoms. Cycle 43: After refmac, R = 0.2445 (Rfree = 0.000) for 2882 atoms. Found 69 (192 requested) and removed 13 (100 requested) atoms. Cycle 44: After refmac, R = 0.2437 (Rfree = 0.000) for 2924 atoms. Found 60 (196 requested) and removed 20 (102 requested) atoms. Cycle 45: After refmac, R = 0.2389 (Rfree = 0.000) for 2949 atoms. Found 71 (198 requested) and removed 23 (103 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.54 1.76 NCS extension: 0 residues added, 2997 seeds are put forward Round 1: 246 peptides, 4 chains. Longest chain 117 peptides. Score 0.966 Round 2: 248 peptides, 5 chains. Longest chain 87 peptides. Score 0.963 Round 3: 250 peptides, 3 chains. Longest chain 125 peptides. Score 0.972 Round 4: 250 peptides, 5 chains. Longest chain 125 peptides. Score 0.964 Round 5: 244 peptides, 6 chains. Longest chain 57 peptides. Score 0.957 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 3, Residues 247, Estimated correctness of the model 100.0 % 3 chains (247 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 57 B and 61 B 2 chains (250 residues) following loop building 2 chains (250 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 31574 reflections ( 88.87 % complete ) and 2023 restraints for refining 1985 atoms. Observations/parameters ratio is 3.98 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3051 (Rfree = 0.000) for 1985 atoms. Found 41 (132 requested) and removed 0 (132 requested) atoms. Cycle 47: After refmac, R = 0.2833 (Rfree = 0.000) for 1985 atoms. Found 10 (134 requested) and removed 0 (70 requested) atoms. Cycle 48: After refmac, R = 0.2752 (Rfree = 0.000) for 1985 atoms. Found 7 (135 requested) and removed 2 (70 requested) atoms. Cycle 49: After refmac, R = 0.2712 (Rfree = 0.000) for 1985 atoms. Found 8 (135 requested) and removed 1 (70 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:05:04 GMT 2018 Job finished. TimeTaking 37.13 Used memory is bytes: 10053728