Mon 24 Dec 01:10:59 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 2opk-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2opk-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-2.1-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/2opk-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-2.1-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 01:11:03 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/2opk-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2opk-2.1-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 592 and 0 Target number of residues in the AU: 592 Target solvent content: 0.4361 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-2.1-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-2.1-parrot-mrncs.fasta_lf Building free atoms model in initial map for 3584 target number of atoms Had to go as low as 0.60 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: 28.177 2.101 Wilson plot Bfac: 12.57 34444 reflections ( 99.66 % complete ) and 0 restraints for refining 3955 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Starting model: R = 0.3153 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2761 (Rfree = 0.000) for 3955 atoms. Found 117 (117 requested) and removed 63 (58 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.96 1.78 NCS extension: 0 residues added, 4009 seeds are put forward Round 1: 368 peptides, 31 chains. Longest chain 42 peptides. Score 0.762 Round 2: 404 peptides, 18 chains. Longest chain 66 peptides. Score 0.871 Round 3: 421 peptides, 13 chains. Longest chain 88 peptides. Score 0.903 Round 4: 427 peptides, 6 chains. Longest chain 108 peptides. Score 0.930 Round 5: 413 peptides, 9 chains. Longest chain 99 peptides. Score 0.913 Taking the results from Round 4 Chains 6, Residues 421, Estimated correctness of the model 99.4 % 5 chains (418 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A 5 chains (423 residues) following loop building 4 chains (420 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 3893 restraints for refining 3817 atoms. 512 conditional restraints added. Observations/parameters ratio is 2.26 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2879 (Rfree = 0.000) for 3817 atoms. Found 113 (113 requested) and removed 44 (56 requested) atoms. Cycle 2: After refmac, R = 0.2728 (Rfree = 0.000) for 3878 atoms. Found 108 (115 requested) and removed 10 (57 requested) atoms. Cycle 3: After refmac, R = 0.2632 (Rfree = 0.000) for 3972 atoms. Found 87 (118 requested) and removed 16 (59 requested) atoms. Cycle 4: After refmac, R = 0.2556 (Rfree = 0.000) for 4031 atoms. Found 73 (120 requested) and removed 17 (60 requested) atoms. Cycle 5: After refmac, R = 0.2462 (Rfree = 0.000) for 4076 atoms. Found 72 (121 requested) and removed 15 (60 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.85 1.68 NCS extension: 0 residues added (45 deleted due to clashes), 4136 seeds are put forward Round 1: 428 peptides, 6 chains. Longest chain 110 peptides. Score 0.931 Round 2: 429 peptides, 4 chains. Longest chain 110 peptides. Score 0.938 Round 3: 428 peptides, 5 chains. Longest chain 110 peptides. Score 0.934 Round 4: 426 peptides, 8 chains. Longest chain 107 peptides. Score 0.923 Round 5: 427 peptides, 7 chains. Longest chain 109 peptides. Score 0.927 Taking the results from Round 2 Chains 4, Residues 425, Estimated correctness of the model 99.5 % 4 chains (425 residues) have been docked in sequence Building loops using Loopy2018 4 chains (425 residues) following loop building 4 chains (425 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 3909 restraints for refining 3953 atoms. 493 conditional restraints added. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2483 (Rfree = 0.000) for 3953 atoms. Found 117 (117 requested) and removed 46 (58 requested) atoms. Cycle 7: After refmac, R = 0.2364 (Rfree = 0.000) for 4017 atoms. Found 92 (119 requested) and removed 17 (59 requested) atoms. Cycle 8: After refmac, R = 0.2277 (Rfree = 0.000) for 4083 atoms. Found 84 (121 requested) and removed 16 (60 requested) atoms. Cycle 9: After refmac, R = 0.2231 (Rfree = 0.000) for 4149 atoms. Found 69 (123 requested) and removed 22 (61 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2195 (Rfree = 0.000) for 4182 atoms. Found 53 (124 requested) and removed 28 (62 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.81 1.65 NCS extension: 2 residues added (1 deleted due to clashes), 4210 seeds are put forward Round 1: 430 peptides, 4 chains. Longest chain 110 peptides. Score 0.938 Round 2: 429 peptides, 6 chains. Longest chain 110 peptides. Score 0.931 Round 3: 427 peptides, 6 chains. Longest chain 109 peptides. Score 0.930 Round 4: 427 peptides, 8 chains. Longest chain 97 peptides. Score 0.924 Round 5: 430 peptides, 5 chains. Longest chain 110 peptides. Score 0.935 Taking the results from Round 1 Chains 4, Residues 426, Estimated correctness of the model 99.5 % 4 chains (426 residues) have been docked in sequence Building loops using Loopy2018 4 chains (426 residues) following loop building 4 chains (426 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 3956 restraints for refining 4055 atoms. 531 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2278 (Rfree = 0.000) for 4055 atoms. Found 118 (118 requested) and removed 32 (60 requested) atoms. Cycle 12: After refmac, R = 0.2203 (Rfree = 0.000) for 4133 atoms. Found 95 (121 requested) and removed 22 (61 requested) atoms. Cycle 13: After refmac, R = 0.2174 (Rfree = 0.000) for 4199 atoms. Found 85 (122 requested) and removed 31 (62 requested) atoms. Cycle 14: After refmac, R = 0.2154 (Rfree = 0.000) for 4247 atoms. Found 69 (123 requested) and removed 31 (63 requested) atoms. Cycle 15: After refmac, R = 0.2124 (Rfree = 0.000) for 4273 atoms. Found 91 (124 requested) and removed 23 (63 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.79 1.63 NCS extension: 0 residues added, 4342 seeds are put forward Round 1: 428 peptides, 5 chains. Longest chain 109 peptides. Score 0.934 Round 2: 429 peptides, 4 chains. Longest chain 109 peptides. Score 0.938 Round 3: 422 peptides, 8 chains. Longest chain 104 peptides. Score 0.921 Round 4: 426 peptides, 7 chains. Longest chain 109 peptides. Score 0.927 Round 5: 426 peptides, 7 chains. Longest chain 107 peptides. Score 0.927 Taking the results from Round 2 Chains 4, Residues 425, Estimated correctness of the model 99.5 % 4 chains (425 residues) have been docked in sequence Building loops using Loopy2018 4 chains (425 residues) following loop building 4 chains (425 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4049 restraints for refining 4117 atoms. 632 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2240 (Rfree = 0.000) for 4117 atoms. Found 120 (120 requested) and removed 27 (61 requested) atoms. Cycle 17: After refmac, R = 0.2183 (Rfree = 0.000) for 4206 atoms. Found 81 (122 requested) and removed 26 (62 requested) atoms. Cycle 18: After refmac, R = 0.2141 (Rfree = 0.000) for 4258 atoms. Found 86 (123 requested) and removed 22 (63 requested) atoms. Cycle 19: After refmac, R = 0.2138 (Rfree = 0.000) for 4321 atoms. Found 63 (125 requested) and removed 43 (64 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2131 (Rfree = 0.000) for 4333 atoms. Found 92 (124 requested) and removed 33 (64 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.78 1.62 NCS extension: 0 residues added, 4393 seeds are put forward Round 1: 425 peptides, 6 chains. Longest chain 107 peptides. Score 0.930 Round 2: 429 peptides, 5 chains. Longest chain 110 peptides. Score 0.935 Round 3: 427 peptides, 8 chains. Longest chain 97 peptides. Score 0.924 Round 4: 426 peptides, 9 chains. Longest chain 110 peptides. Score 0.920 Round 5: 429 peptides, 6 chains. Longest chain 111 peptides. Score 0.931 Taking the results from Round 2 Chains 5, Residues 424, Estimated correctness of the model 99.4 % 5 chains (424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 D and 61 D 4 chains (426 residues) following loop building 4 chains (426 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4056 restraints for refining 4179 atoms. 631 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2209 (Rfree = 0.000) for 4179 atoms. Found 119 (119 requested) and removed 35 (62 requested) atoms. Cycle 22: After refmac, R = 0.2161 (Rfree = 0.000) for 4258 atoms. Found 90 (121 requested) and removed 26 (63 requested) atoms. Cycle 23: After refmac, R = 0.2138 (Rfree = 0.000) for 4320 atoms. Found 77 (123 requested) and removed 28 (64 requested) atoms. Cycle 24: After refmac, R = 0.2125 (Rfree = 0.000) for 4360 atoms. Found 75 (125 requested) and removed 47 (65 requested) atoms. Cycle 25: After refmac, R = 0.2111 (Rfree = 0.000) for 4382 atoms. Found 83 (122 requested) and removed 47 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.77 1.61 NCS extension: 0 residues added, 4419 seeds are put forward Round 1: 427 peptides, 5 chains. Longest chain 107 peptides. Score 0.934 Round 2: 430 peptides, 5 chains. Longest chain 111 peptides. Score 0.935 Round 3: 430 peptides, 9 chains. Longest chain 107 peptides. Score 0.922 Round 4: 428 peptides, 5 chains. Longest chain 111 peptides. Score 0.934 Round 5: 426 peptides, 9 chains. Longest chain 105 peptides. Score 0.920 Taking the results from Round 2 Chains 5, Residues 425, Estimated correctness of the model 99.4 % 5 chains (425 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 71 A 4 chains (427 residues) following loop building 4 chains (427 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4135 restraints for refining 4206 atoms. 701 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2203 (Rfree = 0.000) for 4206 atoms. Found 115 (115 requested) and removed 32 (62 requested) atoms. Cycle 27: After refmac, R = 0.2159 (Rfree = 0.000) for 4282 atoms. Found 86 (117 requested) and removed 25 (63 requested) atoms. Cycle 28: After refmac, R = 0.2111 (Rfree = 0.000) for 4339 atoms. Found 84 (119 requested) and removed 30 (64 requested) atoms. Cycle 29: After refmac, R = 0.2085 (Rfree = 0.000) for 4387 atoms. Found 86 (120 requested) and removed 36 (65 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2089 (Rfree = 0.000) for 4425 atoms. Found 95 (121 requested) and removed 52 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.76 1.60 NCS extension: 3 residues added (3 deleted due to clashes), 4473 seeds are put forward Round 1: 428 peptides, 6 chains. Longest chain 109 peptides. Score 0.931 Round 2: 428 peptides, 5 chains. Longest chain 109 peptides. Score 0.934 Round 3: 426 peptides, 7 chains. Longest chain 109 peptides. Score 0.927 Round 4: 424 peptides, 8 chains. Longest chain 109 peptides. Score 0.922 Round 5: 428 peptides, 7 chains. Longest chain 109 peptides. Score 0.928 Taking the results from Round 2 Chains 5, Residues 423, Estimated correctness of the model 99.4 % 5 chains (423 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 D and 72 D 4 chains (426 residues) following loop building 4 chains (426 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4189 restraints for refining 4230 atoms. 765 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2169 (Rfree = 0.000) for 4230 atoms. Found 112 (112 requested) and removed 27 (62 requested) atoms. Cycle 32: After refmac, R = 0.2120 (Rfree = 0.000) for 4309 atoms. Found 112 (115 requested) and removed 21 (64 requested) atoms. Cycle 33: After refmac, R = 0.2094 (Rfree = 0.000) for 4396 atoms. Found 98 (117 requested) and removed 51 (65 requested) atoms. Cycle 34: After refmac, R = 0.2135 (Rfree = 0.000) for 4438 atoms. Found 95 (116 requested) and removed 50 (66 requested) atoms. Cycle 35: After refmac, R = 0.2100 (Rfree = 0.000) for 4478 atoms. Found 77 (114 requested) and removed 59 (66 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.77 1.61 NCS extension: 0 residues added, 4497 seeds are put forward Round 1: 428 peptides, 6 chains. Longest chain 109 peptides. Score 0.931 Round 2: 430 peptides, 4 chains. Longest chain 110 peptides. Score 0.938 Round 3: 426 peptides, 7 chains. Longest chain 105 peptides. Score 0.927 Round 4: 425 peptides, 9 chains. Longest chain 97 peptides. Score 0.919 Round 5: 429 peptides, 5 chains. Longest chain 110 peptides. Score 0.935 Taking the results from Round 2 Chains 4, Residues 426, Estimated correctness of the model 99.5 % 4 chains (426 residues) have been docked in sequence Building loops using Loopy2018 4 chains (426 residues) following loop building 4 chains (426 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4194 restraints for refining 4243 atoms. 770 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 4243 atoms. Found 106 (106 requested) and removed 26 (63 requested) atoms. Cycle 37: After refmac, R = 0.2190 (Rfree = 0.000) for 4317 atoms. Found 108 (108 requested) and removed 19 (64 requested) atoms. Cycle 38: After refmac, R = 0.2187 (Rfree = 0.000) for 4405 atoms. Found 78 (110 requested) and removed 43 (65 requested) atoms. Cycle 39: After refmac, R = 0.2160 (Rfree = 0.000) for 4436 atoms. Found 93 (108 requested) and removed 35 (66 requested) atoms. Cycle 40: After refmac, R = 0.2164 (Rfree = 0.000) for 4492 atoms. Found 74 (109 requested) and removed 51 (66 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.76 1.60 NCS extension: 0 residues added, 4516 seeds are put forward Round 1: 425 peptides, 5 chains. Longest chain 109 peptides. Score 0.933 Round 2: 428 peptides, 5 chains. Longest chain 110 peptides. Score 0.934 Round 3: 431 peptides, 5 chains. Longest chain 109 peptides. Score 0.936 Round 4: 431 peptides, 6 chains. Longest chain 109 peptides. Score 0.932 Round 5: 430 peptides, 6 chains. Longest chain 109 peptides. Score 0.932 Taking the results from Round 3 Chains 5, Residues 426, Estimated correctness of the model 99.5 % 5 chains (426 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 D and 72 D 4 chains (429 residues) following loop building 4 chains (429 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4215 restraints for refining 4310 atoms. 767 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2209 (Rfree = 0.000) for 4310 atoms. Found 102 (102 requested) and removed 28 (64 requested) atoms. Cycle 42: After refmac, R = 0.2137 (Rfree = 0.000) for 4380 atoms. Found 104 (104 requested) and removed 15 (65 requested) atoms. Cycle 43: After refmac, R = 0.2124 (Rfree = 0.000) for 4464 atoms. Found 84 (106 requested) and removed 46 (66 requested) atoms. Cycle 44: After refmac, R = 0.2104 (Rfree = 0.000) for 4489 atoms. Found 104 (104 requested) and removed 52 (66 requested) atoms. Cycle 45: After refmac, R = 0.2106 (Rfree = 0.000) for 4532 atoms. Found 97 (105 requested) and removed 62 (67 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.75 1.59 NCS extension: 0 residues added, 4568 seeds are put forward Round 1: 428 peptides, 6 chains. Longest chain 110 peptides. Score 0.931 Round 2: 425 peptides, 7 chains. Longest chain 110 peptides. Score 0.926 Round 3: 430 peptides, 5 chains. Longest chain 110 peptides. Score 0.935 Round 4: 424 peptides, 10 chains. Longest chain 105 peptides. Score 0.915 Round 5: 431 peptides, 6 chains. Longest chain 110 peptides. Score 0.932 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 425, Estimated correctness of the model 99.4 % 5 chains (421 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 49 C and 55 C 4 chains (426 residues) following loop building 4 chains (426 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 34444 reflections ( 99.66 % complete ) and 3423 restraints for refining 3309 atoms. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2712 (Rfree = 0.000) for 3309 atoms. Found 56 (74 requested) and removed 0 (74 requested) atoms. Cycle 47: After refmac, R = 0.2541 (Rfree = 0.000) for 3309 atoms. Found 12 (76 requested) and removed 0 (50 requested) atoms. Cycle 48: After refmac, R = 0.2470 (Rfree = 0.000) for 3309 atoms. Found 9 (76 requested) and removed 1 (50 requested) atoms. Cycle 49: After refmac, R = 0.2419 (Rfree = 0.000) for 3309 atoms. TimeTaking 52.12