null Sun 23 Dec 22:22:41 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 2okc-2.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2okc-2.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2okc-2.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-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/2okc-2.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-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 22:22:51 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/2okc-2.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-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 864 and 0 Target number of residues in the AU: 864 Target solvent content: 0.5257 Checking the provided sequence file Detected sequence length: 445 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 890 Adjusted target solvent content: 0.51 Input MTZ file: 2okc-2.2-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: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-2.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 7120 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: 28.546 2.200 Wilson plot Bfac: 29.16 46493 reflections ( 91.25 % complete ) and 0 restraints for refining 7840 atoms. Observations/parameters ratio is 1.48 ------------------------------------------------------ Starting model: R = 0.3172 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2695 (Rfree = 0.000) for 7840 atoms. Found 141 (204 requested) and removed 107 (102 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.39 2.36 NCS extension: 0 residues added, 7874 seeds are put forward Round 1: 516 peptides, 88 chains. Longest chain 15 peptides. Score 0.448 Round 2: 606 peptides, 68 chains. Longest chain 30 peptides. Score 0.673 Round 3: 657 peptides, 54 chains. Longest chain 48 peptides. Score 0.775 Round 4: 689 peptides, 49 chains. Longest chain 50 peptides. Score 0.814 Round 5: 692 peptides, 42 chains. Longest chain 59 peptides. Score 0.836 Taking the results from Round 5 Chains 50, Residues 650, Estimated correctness of the model 96.5 % 13 chains (376 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 233 A and 240 A 48 chains (652 residues) following loop building 12 chains (382 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 10257 restraints for refining 6856 atoms. 6137 conditional restraints added. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3057 (Rfree = 0.000) for 6856 atoms. Found 153 (179 requested) and removed 100 (89 requested) atoms. Cycle 2: After refmac, R = 0.2828 (Rfree = 0.000) for 6875 atoms. Found 102 (176 requested) and removed 90 (90 requested) atoms. Cycle 3: After refmac, R = 0.2698 (Rfree = 0.000) for 6856 atoms. Found 82 (172 requested) and removed 74 (89 requested) atoms. Cycle 4: After refmac, R = 0.2607 (Rfree = 0.000) for 6842 atoms. Found 90 (168 requested) and removed 46 (89 requested) atoms. Cycle 5: After refmac, R = 0.2536 (Rfree = 0.000) for 6878 atoms. Found 68 (165 requested) and removed 53 (89 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.27 2.24 NCS extension: 108 residues added (66 deleted due to clashes), 7016 seeds are put forward Round 1: 679 peptides, 53 chains. Longest chain 51 peptides. Score 0.794 Round 2: 702 peptides, 37 chains. Longest chain 80 peptides. Score 0.856 Round 3: 703 peptides, 45 chains. Longest chain 57 peptides. Score 0.834 Round 4: 716 peptides, 41 chains. Longest chain 98 peptides. Score 0.852 Round 5: 703 peptides, 40 chains. Longest chain 68 peptides. Score 0.848 Taking the results from Round 2 Chains 39, Residues 665, Estimated correctness of the model 97.2 % 15 chains (458 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 54 A Built loop between residues 194 A and 205 A Built loop between residues 226 A and 236 A Built loop between residues 314 A and 321 A Built loop between residues 373 A and 383 A Built loop between residues 268 B and 271 B 30 chains (699 residues) following loop building 9 chains (499 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9484 restraints for refining 7058 atoms. 4707 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2859 (Rfree = 0.000) for 7058 atoms. Found 148 (166 requested) and removed 111 (92 requested) atoms. Cycle 7: After refmac, R = 0.2671 (Rfree = 0.000) for 7083 atoms. Found 73 (163 requested) and removed 92 (92 requested) atoms. Cycle 8: After refmac, R = 0.2552 (Rfree = 0.000) for 7055 atoms. Found 50 (158 requested) and removed 86 (92 requested) atoms. Cycle 9: After refmac, R = 0.2477 (Rfree = 0.000) for 7012 atoms. Found 61 (154 requested) and removed 60 (91 requested) atoms. Cycle 10: After refmac, R = 0.2423 (Rfree = 0.000) for 7012 atoms. Found 46 (150 requested) and removed 37 (91 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.26 2.23 NCS extension: 397 residues added (229 deleted due to clashes), 7437 seeds are put forward Round 1: 674 peptides, 43 chains. Longest chain 57 peptides. Score 0.823 Round 2: 704 peptides, 41 chains. Longest chain 68 peptides. Score 0.846 Round 3: 711 peptides, 38 chains. Longest chain 68 peptides. Score 0.857 Round 4: 702 peptides, 37 chains. Longest chain 98 peptides. Score 0.856 Round 5: 695 peptides, 46 chains. Longest chain 68 peptides. Score 0.826 Taking the results from Round 3 Chains 40, Residues 673, Estimated correctness of the model 97.3 % 16 chains (524 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 166 A and 171 A Built loop between residues 218 A and 226 A Built loop between residues 266 A and 269 A Built loop between residues 316 A and 325 A Built loop between residues 374 A and 378 A Built loop between residues 263 B and 266 B Built loop between residues 306 B and 316 B 28 chains (695 residues) following loop building 9 chains (559 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9077 restraints for refining 7063 atoms. 4058 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2738 (Rfree = 0.000) for 7063 atoms. Found 145 (147 requested) and removed 110 (92 requested) atoms. Cycle 12: After refmac, R = 0.2553 (Rfree = 0.000) for 7089 atoms. Found 74 (144 requested) and removed 92 (92 requested) atoms. Cycle 13: After refmac, R = 0.2445 (Rfree = 0.000) for 7065 atoms. Found 73 (140 requested) and removed 47 (92 requested) atoms. Cycle 14: After refmac, R = 0.2371 (Rfree = 0.000) for 7085 atoms. Found 61 (137 requested) and removed 36 (92 requested) atoms. Cycle 15: After refmac, R = 0.2313 (Rfree = 0.000) for 7102 atoms. Found 59 (133 requested) and removed 37 (92 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.27 2.24 NCS extension: 337 residues added (212 deleted due to clashes), 7474 seeds are put forward Round 1: 703 peptides, 41 chains. Longest chain 84 peptides. Score 0.845 Round 2: 720 peptides, 31 chains. Longest chain 174 peptides. Score 0.879 Round 3: 737 peptides, 34 chains. Longest chain 83 peptides. Score 0.879 Round 4: 728 peptides, 31 chains. Longest chain 120 peptides. Score 0.882 Round 5: 707 peptides, 43 chains. Longest chain 70 peptides. Score 0.842 Taking the results from Round 4 Chains 33, Residues 697, Estimated correctness of the model 98.1 % 13 chains (548 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 141 A and 151 A Built loop between residues 160 A and 171 A Built loop between residues 314 A and 317 A Built loop between residues 165 B and 170 B Built loop between residues 194 B and 203 B Built loop between residues 321 B and 324 B 26 chains (725 residues) following loop building 7 chains (583 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8901 restraints for refining 7219 atoms. 3709 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2757 (Rfree = 0.000) for 7219 atoms. Found 132 (132 requested) and removed 112 (94 requested) atoms. Cycle 17: After refmac, R = 0.2547 (Rfree = 0.000) for 7233 atoms. Found 97 (129 requested) and removed 94 (94 requested) atoms. Cycle 18: After refmac, R = 0.2410 (Rfree = 0.000) for 7225 atoms. Found 84 (124 requested) and removed 94 (94 requested) atoms. Cycle 19: After refmac, R = 0.2322 (Rfree = 0.000) for 7205 atoms. Found 77 (120 requested) and removed 56 (94 requested) atoms. Cycle 20: After refmac, R = 0.2250 (Rfree = 0.000) for 7221 atoms. Found 72 (117 requested) and removed 39 (94 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.27 2.24 NCS extension: 306 residues added (527 deleted due to clashes), 7580 seeds are put forward Round 1: 715 peptides, 40 chains. Longest chain 64 peptides. Score 0.854 Round 2: 738 peptides, 29 chains. Longest chain 94 peptides. Score 0.891 Round 3: 727 peptides, 34 chains. Longest chain 88 peptides. Score 0.875 Round 4: 696 peptides, 39 chains. Longest chain 92 peptides. Score 0.847 Round 5: 699 peptides, 40 chains. Longest chain 81 peptides. Score 0.846 Taking the results from Round 2 Chains 35, Residues 709, Estimated correctness of the model 98.3 % 13 chains (571 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 176 A Built loop between residues 182 A and 185 A Built loop between residues 301 A and 304 A Built loop between residues 103 B and 108 B Built loop between residues 165 B and 169 B Built loop between residues 250 B and 253 B Built loop between residues 265 B and 268 B 26 chains (728 residues) following loop building 6 chains (592 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8781 restraints for refining 7247 atoms. 3515 conditional restraints added. Observations/parameters ratio is 1.60 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2571 (Rfree = 0.000) for 7247 atoms. Found 113 (113 requested) and removed 108 (94 requested) atoms. Cycle 22: After refmac, R = 0.2416 (Rfree = 0.000) for 7250 atoms. Found 84 (110 requested) and removed 94 (94 requested) atoms. Cycle 23: After refmac, R = 0.2313 (Rfree = 0.000) for 7237 atoms. Found 81 (106 requested) and removed 38 (94 requested) atoms. Cycle 24: After refmac, R = 0.2252 (Rfree = 0.000) for 7274 atoms. Found 80 (106 requested) and removed 51 (95 requested) atoms. Cycle 25: After refmac, R = 0.2196 (Rfree = 0.000) for 7298 atoms. Found 67 (103 requested) and removed 47 (95 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.28 2.25 NCS extension: 237 residues added (266 deleted due to clashes), 7561 seeds are put forward Round 1: 725 peptides, 32 chains. Longest chain 91 peptides. Score 0.879 Round 2: 741 peptides, 30 chains. Longest chain 89 peptides. Score 0.890 Round 3: 737 peptides, 31 chains. Longest chain 92 peptides. Score 0.886 Round 4: 730 peptides, 37 chains. Longest chain 81 peptides. Score 0.869 Round 5: 708 peptides, 36 chains. Longest chain 98 peptides. Score 0.861 Taking the results from Round 2 Chains 32, Residues 711, Estimated correctness of the model 98.3 % 17 chains (528 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 50 A Built loop between residues 98 A and 103 A Built loop between residues 163 A and 166 A Built loop between residues 194 A and 204 A Built loop between residues 268 A and 271 A Built loop between residues 398 A and 407 A Built loop between residues 169 B and 173 B Built loop between residues 223 B and 226 B Built loop between residues 266 B and 269 B Built loop between residues 281 B and 284 B 21 chains (746 residues) following loop building 7 chains (565 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8744 restraints for refining 7193 atoms. 3612 conditional restraints added. Observations/parameters ratio is 1.62 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2613 (Rfree = 0.000) for 7193 atoms. Found 97 (97 requested) and removed 107 (93 requested) atoms. Cycle 27: After refmac, R = 0.2446 (Rfree = 0.000) for 7177 atoms. Found 93 (93 requested) and removed 93 (93 requested) atoms. Cycle 28: After refmac, R = 0.2343 (Rfree = 0.000) for 7177 atoms. Found 77 (93 requested) and removed 38 (93 requested) atoms. Cycle 29: After refmac, R = 0.2259 (Rfree = 0.000) for 7208 atoms. Found 68 (94 requested) and removed 36 (94 requested) atoms. Cycle 30: After refmac, R = 0.2208 (Rfree = 0.000) for 7239 atoms. Found 58 (94 requested) and removed 28 (94 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.27 2.24 NCS extension: 177 residues added (299 deleted due to clashes), 7474 seeds are put forward Round 1: 721 peptides, 39 chains. Longest chain 109 peptides. Score 0.859 Round 2: 729 peptides, 38 chains. Longest chain 88 peptides. Score 0.866 Round 3: 715 peptides, 42 chains. Longest chain 97 peptides. Score 0.849 Round 4: 724 peptides, 39 chains. Longest chain 97 peptides. Score 0.861 Round 5: 717 peptides, 41 chains. Longest chain 96 peptides. Score 0.852 Taking the results from Round 2 Chains 42, Residues 691, Estimated correctness of the model 97.6 % 19 chains (559 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 49 A Built loop between residues 63 A and 71 A Built loop between residues 198 A and 205 A Built loop between residues 230 A and 233 A Built loop between residues 314 A and 317 A Built loop between residues 401 A and 407 A Built loop between residues 169 B and 173 B Built loop between residues 196 B and 202 B Built loop between residues 224 B and 235 B Built loop between residues 266 B and 269 B Built loop between residues 298 B and 301 B Built loop between residues 314 B and 317 B 24 chains (729 residues) following loop building 7 chains (609 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8790 restraints for refining 7332 atoms. 3477 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2511 (Rfree = 0.000) for 7332 atoms. Found 95 (95 requested) and removed 112 (95 requested) atoms. Cycle 32: After refmac, R = 0.2355 (Rfree = 0.000) for 7305 atoms. Found 95 (95 requested) and removed 89 (95 requested) atoms. Cycle 33: After refmac, R = 0.2268 (Rfree = 0.000) for 7307 atoms. Found 90 (95 requested) and removed 44 (95 requested) atoms. Cycle 34: After refmac, R = 0.2197 (Rfree = 0.000) for 7348 atoms. Found 58 (95 requested) and removed 34 (95 requested) atoms. Cycle 35: After refmac, R = 0.2151 (Rfree = 0.000) for 7364 atoms. Found 59 (96 requested) and removed 38 (96 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.26 2.23 NCS extension: 115 residues added (210 deleted due to clashes), 7515 seeds are put forward Round 1: 699 peptides, 49 chains. Longest chain 60 peptides. Score 0.820 Round 2: 723 peptides, 33 chains. Longest chain 121 peptides. Score 0.876 Round 3: 723 peptides, 40 chains. Longest chain 60 peptides. Score 0.858 Round 4: 722 peptides, 37 chains. Longest chain 62 peptides. Score 0.865 Round 5: 705 peptides, 43 chains. Longest chain 51 peptides. Score 0.841 Taking the results from Round 2 Chains 38, Residues 690, Estimated correctness of the model 97.9 % 13 chains (549 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 233 A and 236 A Built loop between residues 163 B and 168 B Built loop between residues 248 B and 252 B Built loop between residues 267 B and 271 B Built loop between residues 297 B and 300 B 30 chains (700 residues) following loop building 8 chains (563 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9199 restraints for refining 7319 atoms. 4136 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2454 (Rfree = 0.000) for 7319 atoms. Found 95 (95 requested) and removed 114 (95 requested) atoms. Cycle 37: After refmac, R = 0.2306 (Rfree = 0.000) for 7298 atoms. Found 95 (95 requested) and removed 72 (95 requested) atoms. Cycle 38: After refmac, R = 0.2236 (Rfree = 0.000) for 7318 atoms. Found 80 (95 requested) and removed 30 (95 requested) atoms. Cycle 39: After refmac, R = 0.2166 (Rfree = 0.000) for 7365 atoms. Found 56 (96 requested) and removed 27 (96 requested) atoms. Cycle 40: After refmac, R = 0.2124 (Rfree = 0.000) for 7389 atoms. Found 52 (96 requested) and removed 24 (96 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.26 2.23 NCS extension: 53 residues added (33 deleted due to clashes), 7476 seeds are put forward Round 1: 671 peptides, 46 chains. Longest chain 67 peptides. Score 0.812 Round 2: 710 peptides, 37 chains. Longest chain 65 peptides. Score 0.859 Round 3: 683 peptides, 42 chains. Longest chain 58 peptides. Score 0.831 Round 4: 691 peptides, 39 chains. Longest chain 82 peptides. Score 0.845 Round 5: 707 peptides, 39 chains. Longest chain 114 peptides. Score 0.853 Taking the results from Round 2 Chains 43, Residues 673, Estimated correctness of the model 97.3 % 19 chains (517 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 48 A Built loop between residues 163 A and 169 A Built loop between residues 269 A and 272 A Built loop between residues 284 A and 288 A Built loop between residues 312 A and 315 A Built loop between residues 169 B and 173 B Built loop between residues 231 B and 234 B Built loop between residues 254 B and 257 B Built loop between residues 268 B and 272 B Built loop between residues 313 B and 323 B 30 chains (700 residues) following loop building 9 chains (551 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9208 restraints for refining 7306 atoms. 4260 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2379 (Rfree = 0.000) for 7306 atoms. Found 95 (95 requested) and removed 108 (95 requested) atoms. Cycle 42: After refmac, R = 0.2252 (Rfree = 0.000) for 7289 atoms. Found 95 (95 requested) and removed 50 (95 requested) atoms. Cycle 43: After refmac, R = 0.2178 (Rfree = 0.000) for 7333 atoms. Found 54 (95 requested) and removed 22 (95 requested) atoms. Cycle 44: After refmac, R = 0.2130 (Rfree = 0.000) for 7359 atoms. Found 45 (96 requested) and removed 28 (96 requested) atoms. Cycle 45: After refmac, R = 0.2098 (Rfree = 0.000) for 7371 atoms. Found 49 (96 requested) and removed 31 (96 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.26 2.23 NCS extension: 182 residues added (58 deleted due to clashes), 7583 seeds are put forward Round 1: 691 peptides, 40 chains. Longest chain 80 peptides. Score 0.842 Round 2: 706 peptides, 37 chains. Longest chain 63 peptides. Score 0.858 Round 3: 721 peptides, 33 chains. Longest chain 124 peptides. Score 0.875 Round 4: 683 peptides, 40 chains. Longest chain 135 peptides. Score 0.837 Round 5: 710 peptides, 39 chains. Longest chain 87 peptides. Score 0.854 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 688, Estimated correctness of the model 97.9 % 14 chains (535 residues) have been docked in sequence Sequence coverage is 77 % Consider running further cycles of model building using 2okc-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 44 A and 55 A Built loop between residues 73 A and 76 A Built loop between residues 105 A and 112 A Built loop between residues 134 A and 138 A Built loop between residues 179 A and 182 A Built loop between residues 193 A and 202 A Built loop between residues 324 A and 328 A Built loop between residues 400 A and 407 A Built loop between residues 196 B and 202 B 24 chains (724 residues) following loop building 5 chains (580 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 46493 reflections ( 91.25 % complete ) and 9042 restraints for refining 7444 atoms. 3816 conditional restraints added. Observations/parameters ratio is 1.56 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2475 (Rfree = 0.000) for 7444 atoms. Found 0 (97 requested) and removed 9 (97 requested) atoms. Cycle 47: After refmac, R = 0.2345 (Rfree = 0.000) for 7430 atoms. Found 0 (97 requested) and removed 2 (97 requested) atoms. Cycle 48: After refmac, R = 0.2280 (Rfree = 0.000) for 7422 atoms. Found 0 (96 requested) and removed 1 (96 requested) atoms. Cycle 49: After refmac, R = 0.2242 (Rfree = 0.000) for 7420 atoms. Found 0 (96 requested) and removed 3 (96 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:08:15 GMT 2018 Job finished. TimeTaking 105.57 Used memory is bytes: 17006960