Mon 24 Dec 00:04:36 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1zko-1.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-1.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1zko-1.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-parrot-mrncs ############### 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 00:04:41 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/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1zko-1.6-parrot-mrncs/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-mrncs.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-mrncs.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 2411 atoms. Observations/parameters ratio is 3.27 ------------------------------------------------------ Starting model: R = 0.3782 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3324 (Rfree = 0.000) for 2411 atoms. Found 74 (167 requested) and removed 87 (83 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.62 1.85 NCS extension: 0 residues added, 2398 seeds are put forward Round 1: 209 peptides, 19 chains. Longest chain 30 peptides. Score 0.823 Round 2: 236 peptides, 13 chains. Longest chain 62 peptides. Score 0.913 Round 3: 246 peptides, 9 chains. Longest chain 51 peptides. Score 0.943 Round 4: 240 peptides, 9 chains. Longest chain 64 peptides. Score 0.939 Round 5: 247 peptides, 8 chains. Longest chain 57 peptides. Score 0.949 Taking the results from Round 5 Chains 9, Residues 239, Estimated correctness of the model 99.9 % 6 chains (215 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 30 A Built loop between residues 45 B and 48 B Built loop between residues 78 B and 81 B 6 chains (245 residues) following loop building 3 chains (221 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2505 restraints for refining 2297 atoms. 631 conditional restraints added. Observations/parameters ratio is 3.44 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3337 (Rfree = 0.000) for 2297 atoms. Found 111 (159 requested) and removed 84 (79 requested) atoms. Cycle 2: After refmac, R = 0.3176 (Rfree = 0.000) for 2317 atoms. Found 66 (158 requested) and removed 35 (80 requested) atoms. Cycle 3: After refmac, R = 0.2948 (Rfree = 0.000) for 2338 atoms. Found 74 (156 requested) and removed 29 (81 requested) atoms. Cycle 4: After refmac, R = 0.2853 (Rfree = 0.000) for 2353 atoms. Found 70 (158 requested) and removed 8 (82 requested) atoms. Cycle 5: After refmac, R = 0.2768 (Rfree = 0.000) for 2399 atoms. Found 62 (160 requested) and removed 13 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.58 1.81 NCS extension: 0 residues added (152 deleted due to clashes), 2449 seeds are put forward Round 1: 249 peptides, 6 chains. Longest chain 64 peptides. Score 0.959 Round 2: 252 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 3: 252 peptides, 3 chains. Longest chain 128 peptides. Score 0.973 Round 4: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 5: 249 peptides, 5 chains. Longest chain 65 peptides. Score 0.963 Taking the results from Round 4 Chains 4, Residues 248, Estimated correctness of the model 100.0 % 3 chains (245 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 B and 47 B 3 chains (250 residues) following loop building 2 chains (247 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2316 restraints for refining 2368 atoms. 308 conditional restraints added. Observations/parameters ratio is 3.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2808 (Rfree = 0.000) for 2368 atoms. Found 107 (157 requested) and removed 61 (82 requested) atoms. Cycle 7: After refmac, R = 0.2715 (Rfree = 0.000) for 2410 atoms. Found 75 (157 requested) and removed 10 (83 requested) atoms. Cycle 8: After refmac, R = 0.2647 (Rfree = 0.000) for 2467 atoms. Found 57 (162 requested) and removed 9 (86 requested) atoms. Cycle 9: After refmac, R = 0.2591 (Rfree = 0.000) for 2505 atoms. Found 37 (164 requested) and removed 4 (87 requested) atoms. Cycle 10: After refmac, R = 0.2556 (Rfree = 0.000) for 2529 atoms. Found 60 (165 requested) and removed 9 (88 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.57 1.80 NCS extension: 0 residues added (3 deleted due to clashes), 2580 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 126 peptides. Score 0.972 Round 3: 251 peptides, 4 chains. Longest chain 125 peptides. Score 0.969 Round 4: 252 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 5: 249 peptides, 5 chains. Longest chain 89 peptides. Score 0.963 Taking the results from Round 4 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 2350 restraints for refining 2452 atoms. 332 conditional restraints added. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2683 (Rfree = 0.000) for 2452 atoms. Found 104 (160 requested) and removed 42 (85 requested) atoms. Cycle 12: After refmac, R = 0.2621 (Rfree = 0.000) for 2509 atoms. Found 66 (164 requested) and removed 16 (87 requested) atoms. Cycle 13: After refmac, R = 0.2571 (Rfree = 0.000) for 2553 atoms. Found 65 (166 requested) and removed 10 (88 requested) atoms. Cycle 14: After refmac, R = 0.2538 (Rfree = 0.000) for 2599 atoms. Found 52 (170 requested) and removed 9 (90 requested) atoms. Cycle 15: After refmac, R = 0.2515 (Rfree = 0.000) for 2630 atoms. Found 64 (172 requested) and removed 11 (91 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.58 1.81 NCS extension: 0 residues added, 2683 seeds are put forward Round 1: 252 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 2: 248 peptides, 6 chains. Longest chain 90 peptides. Score 0.959 Round 3: 251 peptides, 3 chains. Longest chain 127 peptides. Score 0.973 Round 4: 250 peptides, 4 chains. Longest chain 127 peptides. Score 0.968 Round 5: 249 peptides, 5 chains. Longest chain 91 peptides. Score 0.963 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 2415 restraints for refining 2538 atoms. 397 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2634 (Rfree = 0.000) for 2538 atoms. Found 116 (165 requested) and removed 44 (88 requested) atoms. Cycle 17: After refmac, R = 0.2575 (Rfree = 0.000) for 2599 atoms. Found 88 (170 requested) and removed 7 (90 requested) atoms. Cycle 18: After refmac, R = 0.2516 (Rfree = 0.000) for 2672 atoms. Found 44 (175 requested) and removed 10 (93 requested) atoms. Cycle 19: After refmac, R = 0.2472 (Rfree = 0.000) for 2697 atoms. Found 66 (177 requested) and removed 9 (94 requested) atoms. Cycle 20: After refmac, R = 0.2449 (Rfree = 0.000) for 2739 atoms. Found 62 (180 requested) and removed 16 (95 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.57 1.80 NCS extension: 0 residues added, 2785 seeds are put forward Round 1: 252 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 2: 248 peptides, 5 chains. Longest chain 91 peptides. Score 0.963 Round 3: 250 peptides, 4 chains. Longest chain 89 peptides. Score 0.968 Round 4: 250 peptides, 5 chains. Longest chain 91 peptides. Score 0.964 Round 5: 251 peptides, 3 chains. Longest chain 127 peptides. Score 0.973 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 2496 restraints for refining 2616 atoms. 478 conditional restraints added. Observations/parameters ratio is 3.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2567 (Rfree = 0.000) for 2616 atoms. Found 127 (170 requested) and removed 34 (90 requested) atoms. Cycle 22: After refmac, R = 0.2513 (Rfree = 0.000) for 2697 atoms. Found 77 (177 requested) and removed 13 (94 requested) atoms. Cycle 23: After refmac, R = 0.2466 (Rfree = 0.000) for 2755 atoms. Found 47 (180 requested) and removed 8 (96 requested) atoms. Cycle 24: After refmac, R = 0.2445 (Rfree = 0.000) for 2777 atoms. Found 53 (182 requested) and removed 8 (97 requested) atoms. Cycle 25: After refmac, R = 0.2386 (Rfree = 0.000) for 2815 atoms. Found 55 (184 requested) and removed 8 (98 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 2862 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: 249 peptides, 5 chains. Longest chain 91 peptides. Score 0.963 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 2534 restraints for refining 2669 atoms. 516 conditional restraints added. Observations/parameters ratio is 2.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2639 (Rfree = 0.000) for 2669 atoms. Found 124 (174 requested) and removed 35 (92 requested) atoms. Cycle 27: After refmac, R = 0.2506 (Rfree = 0.000) for 2750 atoms. Found 62 (180 requested) and removed 17 (95 requested) atoms. Cycle 28: After refmac, R = 0.2437 (Rfree = 0.000) for 2787 atoms. Found 56 (182 requested) and removed 10 (97 requested) atoms. Cycle 29: After refmac, R = 0.2411 (Rfree = 0.000) for 2824 atoms. Found 43 (185 requested) and removed 11 (98 requested) atoms. Cycle 30: After refmac, R = 0.2380 (Rfree = 0.000) for 2836 atoms. Found 56 (186 requested) and removed 12 (99 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.57 1.80 NCS extension: 0 residues added, 2880 seeds are put forward Round 1: 250 peptides, 3 chains. Longest chain 124 peptides. Score 0.972 Round 2: 251 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 3: 248 peptides, 5 chains. Longest chain 124 peptides. Score 0.963 Round 4: 252 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 5: 249 peptides, 4 chains. Longest chain 125 peptides. Score 0.968 Taking the results from Round 4 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 2584 restraints for refining 2676 atoms. 566 conditional restraints added. Observations/parameters ratio is 2.95 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2654 (Rfree = 0.000) for 2676 atoms. Found 140 (175 requested) and removed 36 (93 requested) atoms. Cycle 32: After refmac, R = 0.2513 (Rfree = 0.000) for 2773 atoms. Found 77 (181 requested) and removed 15 (96 requested) atoms. Cycle 33: After refmac, R = 0.2446 (Rfree = 0.000) for 2825 atoms. Found 73 (185 requested) and removed 6 (98 requested) atoms. Cycle 34: After refmac, R = 0.2403 (Rfree = 0.000) for 2884 atoms. Found 45 (189 requested) and removed 9 (100 requested) atoms. Cycle 35: After refmac, R = 0.2357 (Rfree = 0.000) for 2908 atoms. Found 45 (191 requested) and removed 8 (101 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 2945 seeds are put forward Round 1: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 2: 249 peptides, 4 chains. Longest chain 125 peptides. Score 0.968 Round 3: 252 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Round 4: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 5: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Taking the results from Round 3 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 ------------------------------------------------------ Failed to save intermediate PDB 31574 reflections ( 88.87 % complete ) and 2627 restraints for refining 2733 atoms. 609 conditional restraints added. Observations/parameters ratio is 2.89 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2651 (Rfree = 0.000) for 2733 atoms. Found 130 (179 requested) and removed 38 (95 requested) atoms. Cycle 37: After refmac, R = 0.2528 (Rfree = 0.000) for 2820 atoms. Found 85 (184 requested) and removed 17 (98 requested) atoms. Cycle 38: After refmac, R = 0.2473 (Rfree = 0.000) for 2876 atoms. Found 74 (188 requested) and removed 14 (100 requested) atoms. Cycle 39: After refmac, R = 0.2441 (Rfree = 0.000) for 2927 atoms. Found 53 (192 requested) and removed 12 (102 requested) atoms. Cycle 40: After refmac, R = 0.2415 (Rfree = 0.000) for 2944 atoms. Found 69 (194 requested) and removed 13 (103 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 3000 seeds are put forward Round 1: 249 peptides, 4 chains. Longest chain 125 peptides. Score 0.968 Round 2: 248 peptides, 5 chains. Longest chain 125 peptides. Score 0.963 Round 3: 248 peptides, 4 chains. Longest chain 75 peptides. Score 0.967 Round 4: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Round 5: 251 peptides, 3 chains. Longest chain 125 peptides. Score 0.973 Taking the results from Round 5 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 98 B and 101 B 2 chains (250 residues) following loop building 2 chains (250 residues) in sequence following loop building ------------------------------------------------------ 31574 reflections ( 88.87 % complete ) and 2709 restraints for refining 2761 atoms. 691 conditional restraints added. Observations/parameters ratio is 2.86 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2583 (Rfree = 0.000) for 2761 atoms. Found 165 (180 requested) and removed 38 (96 requested) atoms. Cycle 42: After refmac, R = 0.2507 (Rfree = 0.000) for 2879 atoms. Found 86 (188 requested) and removed 17 (100 requested) atoms. Cycle 43: After refmac, R = 0.2436 (Rfree = 0.000) for 2941 atoms. Found 65 (193 requested) and removed 18 (102 requested) atoms. Cycle 44: After refmac, R = 0.2381 (Rfree = 0.000) for 2979 atoms. Found 57 (195 requested) and removed 21 (103 requested) atoms. Cycle 45: After refmac, R = 0.2357 (Rfree = 0.000) for 3002 atoms. Found 64 (196 requested) and removed 19 (104 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.56 1.79 NCS extension: 0 residues added, 3047 seeds are put forward Round 1: 250 peptides, 3 chains. Longest chain 124 peptides. Score 0.972 Round 2: 248 peptides, 4 chains. Longest chain 124 peptides. Score 0.967 Round 3: 250 peptides, 3 chains. Longest chain 124 peptides. Score 0.972 Round 4: 248 peptides, 4 chains. Longest chain 124 peptides. Score 0.967 Round 5: 251 peptides, 2 chains. Longest chain 127 peptides. Score 0.977 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 249, Estimated correctness of the model 100.0 % 2 chains (249 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (249 residues) following loop building 2 chains (249 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 31574 reflections ( 88.87 % complete ) and 2012 restraints for refining 1975 atoms. Observations/parameters ratio is 4.00 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3136 (Rfree = 0.000) for 1975 atoms. Found 44 (129 requested) and removed 0 (129 requested) atoms. Cycle 47: After refmac, R = 0.2828 (Rfree = 0.000) for 1975 atoms. Found 14 (132 requested) and removed 0 (70 requested) atoms. Cycle 48: After refmac, R = 0.2748 (Rfree = 0.000) for 1975 atoms. Found 2 (133 requested) and removed 1 (70 requested) atoms. Cycle 49: After refmac, R = 0.2716 (Rfree = 0.000) for 1975 atoms. TimeTaking 38.63