Mon 24 Dec 00:58:01 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 2od6-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2od6-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-1.8-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/2od6-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-1.8-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 00:58:06 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/2od6-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2od6-1.8-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 437 and 0 Target number of residues in the AU: 437 Target solvent content: 0.5168 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-1.8-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: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3520 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: 29.066 1.849 Wilson plot Bfac: 27.04 42951 reflections ( 99.78 % complete ) and 0 restraints for refining 3889 atoms. Observations/parameters ratio is 2.76 ------------------------------------------------------ Starting model: R = 0.3363 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3006 (Rfree = 0.000) for 3889 atoms. Found 88 (166 requested) and removed 88 (83 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.14 2.11 NCS extension: 0 residues added, 3889 seeds are put forward Round 1: 327 peptides, 32 chains. Longest chain 36 peptides. Score 0.737 Round 2: 369 peptides, 22 chains. Longest chain 53 peptides. Score 0.856 Round 3: 391 peptides, 18 chains. Longest chain 65 peptides. Score 0.893 Round 4: 393 peptides, 15 chains. Longest chain 82 peptides. Score 0.907 Round 5: 398 peptides, 13 chains. Longest chain 83 peptides. Score 0.917 Taking the results from Round 5 Chains 16, Residues 385, Estimated correctness of the model 99.4 % 9 chains (344 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 58 A Built loop between residues 35 C and 39 C Built loop between residues 84 C and 91 C 12 chains (394 residues) following loop building 6 chains (355 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 4065 restraints for refining 3670 atoms. 938 conditional restraints added. Observations/parameters ratio is 2.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2994 (Rfree = 0.000) for 3670 atoms. Found 110 (157 requested) and removed 80 (78 requested) atoms. Cycle 2: After refmac, R = 0.2757 (Rfree = 0.000) for 3683 atoms. Found 76 (155 requested) and removed 42 (79 requested) atoms. Cycle 3: After refmac, R = 0.2626 (Rfree = 0.000) for 3705 atoms. Found 66 (153 requested) and removed 21 (79 requested) atoms. Cycle 4: After refmac, R = 0.2544 (Rfree = 0.000) for 3736 atoms. Found 58 (154 requested) and removed 17 (80 requested) atoms. Cycle 5: After refmac, R = 0.2476 (Rfree = 0.000) for 3770 atoms. Found 38 (155 requested) and removed 20 (80 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.13 2.10 NCS extension: 13 residues added (8 deleted due to clashes), 3804 seeds are put forward Round 1: 402 peptides, 10 chains. Longest chain 106 peptides. Score 0.930 Round 2: 406 peptides, 9 chains. Longest chain 107 peptides. Score 0.936 Round 3: 404 peptides, 12 chains. Longest chain 81 peptides. Score 0.924 Round 4: 399 peptides, 12 chains. Longest chain 82 peptides. Score 0.922 Round 5: 410 peptides, 8 chains. Longest chain 107 peptides. Score 0.941 Taking the results from Round 5 Chains 9, Residues 402, Estimated correctness of the model 99.7 % 7 chains (392 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 31 A and 34 A Built loop between residues 31 D and 34 D 7 chains (406 residues) following loop building 5 chains (396 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3873 restraints for refining 3792 atoms. 524 conditional restraints added. Observations/parameters ratio is 2.83 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2539 (Rfree = 0.000) for 3792 atoms. Found 103 (152 requested) and removed 82 (81 requested) atoms. Cycle 7: After refmac, R = 0.2400 (Rfree = 0.000) for 3808 atoms. Found 89 (150 requested) and removed 24 (81 requested) atoms. Cycle 8: After refmac, R = 0.2329 (Rfree = 0.000) for 3871 atoms. Found 75 (152 requested) and removed 19 (82 requested) atoms. Cycle 9: After refmac, R = 0.2276 (Rfree = 0.000) for 3922 atoms. Found 71 (155 requested) and removed 26 (84 requested) atoms. Cycle 10: After refmac, R = 0.2233 (Rfree = 0.000) for 3961 atoms. Found 64 (155 requested) and removed 26 (84 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.13 2.10 NCS extension: 17 residues added (21 deleted due to clashes), 4017 seeds are put forward Round 1: 411 peptides, 5 chains. Longest chain 107 peptides. Score 0.950 Round 2: 411 peptides, 5 chains. Longest chain 107 peptides. Score 0.950 Round 3: 401 peptides, 11 chains. Longest chain 77 peptides. Score 0.926 Round 4: 410 peptides, 7 chains. Longest chain 107 peptides. Score 0.944 Round 5: 407 peptides, 9 chains. Longest chain 107 peptides. Score 0.936 Taking the results from Round 2 Chains 5, Residues 406, Estimated correctness of the model 99.8 % 5 chains (406 residues) have been docked in sequence Building loops using Loopy2018 5 chains (406 residues) following loop building 5 chains (406 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3885 restraints for refining 3891 atoms. 492 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2372 (Rfree = 0.000) for 3891 atoms. Found 113 (153 requested) and removed 72 (83 requested) atoms. Cycle 12: After refmac, R = 0.2288 (Rfree = 0.000) for 3928 atoms. Found 91 (151 requested) and removed 33 (84 requested) atoms. Cycle 13: After refmac, R = 0.2237 (Rfree = 0.000) for 3983 atoms. Found 77 (153 requested) and removed 31 (85 requested) atoms. Cycle 14: After refmac, R = 0.2188 (Rfree = 0.000) for 4023 atoms. Found 74 (155 requested) and removed 23 (86 requested) atoms. Cycle 15: After refmac, R = 0.2155 (Rfree = 0.000) for 4067 atoms. Found 65 (157 requested) and removed 36 (87 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.13 2.10 NCS extension: 25 residues added (26 deleted due to clashes), 4122 seeds are put forward Round 1: 411 peptides, 5 chains. Longest chain 107 peptides. Score 0.950 Round 2: 413 peptides, 5 chains. Longest chain 107 peptides. Score 0.951 Round 3: 413 peptides, 5 chains. Longest chain 107 peptides. Score 0.951 Round 4: 408 peptides, 9 chains. Longest chain 107 peptides. Score 0.936 Round 5: 404 peptides, 10 chains. Longest chain 81 peptides. Score 0.931 Taking the results from Round 3 Chains 6, Residues 408, Estimated correctness of the model 99.8 % 4 chains (395 residues) have been docked in sequence Building loops using Loopy2018 6 chains (408 residues) following loop building 4 chains (395 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3970 restraints for refining 3938 atoms. 613 conditional restraints added. Observations/parameters ratio is 2.73 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2348 (Rfree = 0.000) for 3938 atoms. Found 126 (148 requested) and removed 63 (84 requested) atoms. Cycle 17: After refmac, R = 0.2252 (Rfree = 0.000) for 3994 atoms. Found 85 (150 requested) and removed 19 (85 requested) atoms. Cycle 18: After refmac, R = 0.2176 (Rfree = 0.000) for 4057 atoms. Found 62 (152 requested) and removed 24 (86 requested) atoms. Cycle 19: After refmac, R = 0.2133 (Rfree = 0.000) for 4090 atoms. Found 50 (154 requested) and removed 19 (87 requested) atoms. Cycle 20: After refmac, R = 0.2105 (Rfree = 0.000) for 4113 atoms. Found 53 (155 requested) and removed 26 (88 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.13 2.10 NCS extension: 11 residues added (16 deleted due to clashes), 4151 seeds are put forward Round 1: 417 peptides, 6 chains. Longest chain 107 peptides. Score 0.950 Round 2: 419 peptides, 6 chains. Longest chain 107 peptides. Score 0.950 Round 3: 417 peptides, 8 chains. Longest chain 107 peptides. Score 0.943 Round 4: 410 peptides, 9 chains. Longest chain 107 peptides. Score 0.937 Round 5: 415 peptides, 8 chains. Longest chain 107 peptides. Score 0.943 Taking the results from Round 2 Chains 8, Residues 413, Estimated correctness of the model 99.8 % 5 chains (405 residues) have been docked in sequence Building loops using Loopy2018 8 chains (413 residues) following loop building 5 chains (405 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3892 restraints for refining 3977 atoms. 477 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2304 (Rfree = 0.000) for 3977 atoms. Found 138 (150 requested) and removed 61 (85 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2251 (Rfree = 0.000) for 4045 atoms. Found 86 (152 requested) and removed 27 (86 requested) atoms. Cycle 23: After refmac, R = 0.2181 (Rfree = 0.000) for 4099 atoms. Found 69 (154 requested) and removed 33 (87 requested) atoms. Cycle 24: After refmac, R = 0.2157 (Rfree = 0.000) for 4129 atoms. Found 71 (156 requested) and removed 34 (88 requested) atoms. Cycle 25: After refmac, R = 0.2128 (Rfree = 0.000) for 4161 atoms. Found 64 (157 requested) and removed 33 (89 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.13 2.10 NCS extension: 23 residues added (30 deleted due to clashes), 4217 seeds are put forward Round 1: 411 peptides, 5 chains. Longest chain 107 peptides. Score 0.950 Round 2: 411 peptides, 5 chains. Longest chain 107 peptides. Score 0.950 Round 3: 406 peptides, 9 chains. Longest chain 107 peptides. Score 0.936 Round 4: 409 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Round 5: 411 peptides, 7 chains. Longest chain 107 peptides. Score 0.944 Taking the results from Round 2 Chains 5, Residues 406, Estimated correctness of the model 99.8 % 5 chains (406 residues) have been docked in sequence Building loops using Loopy2018 5 chains (406 residues) following loop building 5 chains (406 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3922 restraints for refining 3983 atoms. 529 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2313 (Rfree = 0.000) for 3983 atoms. Found 124 (146 requested) and removed 67 (85 requested) atoms. Cycle 27: After refmac, R = 0.2231 (Rfree = 0.000) for 4036 atoms. Found 83 (145 requested) and removed 23 (86 requested) atoms. Cycle 28: After refmac, R = 0.2182 (Rfree = 0.000) for 4091 atoms. Found 61 (147 requested) and removed 33 (87 requested) atoms. Cycle 29: After refmac, R = 0.2148 (Rfree = 0.000) for 4112 atoms. Found 64 (144 requested) and removed 32 (88 requested) atoms. Cycle 30: After refmac, R = 0.2118 (Rfree = 0.000) for 4138 atoms. Found 65 (145 requested) and removed 38 (88 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.13 2.10 NCS extension: 25 residues added (26 deleted due to clashes), 4190 seeds are put forward Round 1: 409 peptides, 5 chains. Longest chain 105 peptides. Score 0.950 Round 2: 410 peptides, 6 chains. Longest chain 107 peptides. Score 0.947 Round 3: 408 peptides, 8 chains. Longest chain 107 peptides. Score 0.940 Round 4: 412 peptides, 6 chains. Longest chain 107 peptides. Score 0.948 Round 5: 406 peptides, 10 chains. Longest chain 105 peptides. Score 0.932 Taking the results from Round 1 Chains 5, Residues 404, Estimated correctness of the model 99.8 % 5 chains (404 residues) have been docked in sequence Building loops using Loopy2018 5 chains (404 residues) following loop building 5 chains (404 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3950 restraints for refining 3988 atoms. 574 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2298 (Rfree = 0.000) for 3988 atoms. Found 119 (136 requested) and removed 69 (85 requested) atoms. Cycle 32: After refmac, R = 0.2243 (Rfree = 0.000) for 4035 atoms. Found 80 (135 requested) and removed 30 (86 requested) atoms. Cycle 33: After refmac, R = 0.2191 (Rfree = 0.000) for 4081 atoms. Found 70 (136 requested) and removed 24 (87 requested) atoms. Cycle 34: After refmac, R = 0.2161 (Rfree = 0.000) for 4121 atoms. Found 67 (137 requested) and removed 48 (88 requested) atoms. Cycle 35: After refmac, R = 0.2144 (Rfree = 0.000) for 4134 atoms. Found 67 (135 requested) and removed 38 (88 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.13 2.10 NCS extension: 24 residues added (27 deleted due to clashes), 4187 seeds are put forward Round 1: 409 peptides, 6 chains. Longest chain 107 peptides. Score 0.947 Round 2: 408 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Round 3: 409 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Round 4: 406 peptides, 10 chains. Longest chain 107 peptides. Score 0.932 Round 5: 407 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Taking the results from Round 1 Chains 7, Residues 403, Estimated correctness of the model 99.7 % 5 chains (398 residues) have been docked in sequence Building loops using Loopy2018 7 chains (403 residues) following loop building 5 chains (398 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 4024 restraints for refining 3993 atoms. 676 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2303 (Rfree = 0.000) for 3993 atoms. Found 121 (127 requested) and removed 62 (85 requested) atoms. Cycle 37: After refmac, R = 0.2238 (Rfree = 0.000) for 4043 atoms. Found 87 (125 requested) and removed 28 (86 requested) atoms. Cycle 38: After refmac, R = 0.2189 (Rfree = 0.000) for 4095 atoms. Found 71 (126 requested) and removed 47 (87 requested) atoms. Cycle 39: After refmac, R = 0.2160 (Rfree = 0.000) for 4117 atoms. Found 75 (123 requested) and removed 31 (88 requested) atoms. Cycle 40: After refmac, R = 0.2213 (Rfree = 0.000) for 4157 atoms. Found 75 (125 requested) and removed 39 (89 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.12 2.09 NCS extension: 36 residues added (37 deleted due to clashes), 4232 seeds are put forward Round 1: 405 peptides, 7 chains. Longest chain 107 peptides. Score 0.942 Round 2: 406 peptides, 8 chains. Longest chain 107 peptides. Score 0.939 Round 3: 409 peptides, 8 chains. Longest chain 107 peptides. Score 0.940 Round 4: 409 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Round 5: 408 peptides, 8 chains. Longest chain 107 peptides. Score 0.940 Taking the results from Round 4 Chains 8, Residues 402, Estimated correctness of the model 99.7 % 6 chains (396 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 92 A 7 chains (404 residues) following loop building 5 chains (398 residues) in sequence following loop building ------------------------------------------------------ 42951 reflections ( 99.78 % complete ) and 3988 restraints for refining 3999 atoms. 636 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2316 (Rfree = 0.000) for 3999 atoms. Found 116 (116 requested) and removed 71 (85 requested) atoms. Cycle 42: After refmac, R = 0.2232 (Rfree = 0.000) for 4038 atoms. Found 95 (114 requested) and removed 25 (86 requested) atoms. Cycle 43: After refmac, R = 0.2174 (Rfree = 0.000) for 4102 atoms. Found 85 (116 requested) and removed 28 (88 requested) atoms. Cycle 44: After refmac, R = 0.2131 (Rfree = 0.000) for 4153 atoms. Found 59 (117 requested) and removed 40 (89 requested) atoms. Cycle 45: After refmac, R = 0.2122 (Rfree = 0.000) for 4165 atoms. Found 74 (114 requested) and removed 38 (89 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.13 2.10 NCS extension: 41 residues added (32 deleted due to clashes), 4243 seeds are put forward Round 1: 408 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Round 2: 408 peptides, 7 chains. Longest chain 107 peptides. Score 0.943 Round 3: 409 peptides, 7 chains. Longest chain 106 peptides. Score 0.943 Round 4: 409 peptides, 8 chains. Longest chain 107 peptides. Score 0.940 Round 5: 410 peptides, 6 chains. Longest chain 107 peptides. Score 0.947 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 404, Estimated correctness of the model 99.7 % 6 chains (404 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 92 D and 96 D 5 chains (407 residues) following loop building 5 chains (407 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 42951 reflections ( 99.78 % complete ) and 3402 restraints for refining 3331 atoms. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2881 (Rfree = 0.000) for 3331 atoms. Found 49 (88 requested) and removed 0 (88 requested) atoms. Cycle 47: After refmac, R = 0.2726 (Rfree = 0.000) for 3331 atoms. Found 26 (89 requested) and removed 0 (72 requested) atoms. Cycle 48: After refmac, R = 0.2615 (Rfree = 0.000) for 3331 atoms. Found 20 (90 requested) and removed 0 (72 requested) atoms. Cycle 49: After refmac, R = 0.2553 (Rfree = 0.000) for 3331 atoms. TimeTaking 60.33