Mon 24 Dec 00:26:56 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 2okc-2.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-2.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2okc-2.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-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/2okc-2.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-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 00:27:01 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2okc-2.2-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 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-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: 75.340 85.750 152.600 90.000 90.000 90.000 Input sequence file: 2okc-2.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 7120 target number of atoms Had to go as low as 0.55 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 7912 atoms. Observations/parameters ratio is 1.47 ------------------------------------------------------ Starting model: R = 0.3126 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2653 (Rfree = 0.000) for 7912 atoms. Found 145 (206 requested) and removed 110 (103 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.39 2.36 NCS extension: 0 residues added, 7947 seeds are put forward Round 1: 521 peptides, 84 chains. Longest chain 21 peptides. Score 0.481 Round 2: 630 peptides, 64 chains. Longest chain 35 peptides. Score 0.714 Round 3: 674 peptides, 54 chains. Longest chain 49 peptides. Score 0.787 Round 4: 691 peptides, 42 chains. Longest chain 48 peptides. Score 0.836 Round 5: 695 peptides, 43 chains. Longest chain 48 peptides. Score 0.835 Taking the results from Round 4 Chains 53, Residues 649, Estimated correctness of the model 96.5 % 18 chains (454 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 233 A and 236 A Built loop between residues 262 A and 269 A Built loop between residues 315 A and 326 A Built loop between residues 355 A and 360 A Built loop between residues 195 B and 206 B Built loop between residues 340 B and 349 B 43 chains (681 residues) following loop building 12 chains (494 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9914 restraints for refining 7125 atoms. 5286 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3019 (Rfree = 0.000) for 7125 atoms. Found 158 (186 requested) and removed 105 (93 requested) atoms. Cycle 2: After refmac, R = 0.2791 (Rfree = 0.000) for 7138 atoms. Found 99 (183 requested) and removed 93 (93 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2664 (Rfree = 0.000) for 7105 atoms. Found 88 (179 requested) and removed 93 (93 requested) atoms. Cycle 4: After refmac, R = 0.2543 (Rfree = 0.000) for 7082 atoms. Found 80 (174 requested) and removed 70 (92 requested) atoms. Cycle 5: After refmac, R = 0.2462 (Rfree = 0.000) for 7070 atoms. Found 60 (170 requested) and removed 54 (92 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.29 2.26 NCS extension: 368 residues added (271 deleted due to clashes), 7457 seeds are put forward Round 1: 685 peptides, 45 chains. Longest chain 66 peptides. Score 0.824 Round 2: 731 peptides, 31 chains. Longest chain 90 peptides. Score 0.884 Round 3: 735 peptides, 34 chains. Longest chain 112 peptides. Score 0.878 Round 4: 733 peptides, 35 chains. Longest chain 86 peptides. Score 0.875 Round 5: 745 peptides, 39 chains. Longest chain 98 peptides. Score 0.870 Taking the results from Round 2 Chains 34, Residues 700, Estimated correctness of the model 98.1 % 15 chains (569 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 324 A and 328 A Built loop between residues 72 B and 76 B Built loop between residues 155 B and 159 B Built loop between residues 314 B and 318 B Built loop between residues 358 B and 361 B Built loop between residues 375 B and 379 B 26 chains (714 residues) following loop building 9 chains (586 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8636 restraints for refining 7032 atoms. 3426 conditional restraints added. Observations/parameters ratio is 1.65 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2702 (Rfree = 0.000) for 7032 atoms. Found 134 (165 requested) and removed 104 (91 requested) atoms. Cycle 7: After refmac, R = 0.2499 (Rfree = 0.000) for 7049 atoms. Found 80 (162 requested) and removed 95 (92 requested) atoms. Cycle 8: After refmac, R = 0.2413 (Rfree = 0.000) for 7021 atoms. Found 72 (157 requested) and removed 60 (91 requested) atoms. Cycle 9: After refmac, R = 0.2351 (Rfree = 0.000) for 7020 atoms. Found 62 (154 requested) and removed 36 (91 requested) atoms. Cycle 10: After refmac, R = 0.2302 (Rfree = 0.000) for 7039 atoms. Found 67 (150 requested) and removed 42 (91 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.28 2.25 NCS extension: 42 residues added (147 deleted due to clashes), 7113 seeds are put forward Round 1: 726 peptides, 39 chains. Longest chain 75 peptides. Score 0.862 Round 2: 732 peptides, 30 chains. Longest chain 157 peptides. Score 0.886 Round 3: 718 peptides, 35 chains. Longest chain 82 peptides. Score 0.868 Round 4: 721 peptides, 39 chains. Longest chain 89 peptides. Score 0.859 Round 5: 713 peptides, 31 chains. Longest chain 93 peptides. Score 0.876 Taking the results from Round 2 Chains 36, Residues 702, Estimated correctness of the model 98.2 % 15 chains (533 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 57 A and 60 A Built loop between residues 71 A and 77 A Built loop between residues 178 A and 181 A Built loop between residues 340 A and 345 A Built loop between residues 170 B and 172 B Built loop between residues 196 B and 206 B Built loop between residues 258 B and 261 B 26 chains (720 residues) following loop building 8 chains (558 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 46493 reflections ( 91.25 % complete ) and 8761 restraints for refining 6985 atoms. 3689 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2587 (Rfree = 0.000) for 6985 atoms. Found 127 (146 requested) and removed 102 (91 requested) atoms. Cycle 12: After refmac, R = 0.2421 (Rfree = 0.000) for 7000 atoms. Found 107 (143 requested) and removed 91 (91 requested) atoms. Cycle 13: After refmac, R = 0.2339 (Rfree = 0.000) for 7011 atoms. Found 77 (139 requested) and removed 45 (91 requested) atoms. Cycle 14: After refmac, R = 0.2277 (Rfree = 0.000) for 7036 atoms. Found 60 (135 requested) and removed 39 (91 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2229 (Rfree = 0.000) for 7052 atoms. Found 69 (132 requested) and removed 32 (92 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.29 2.26 NCS extension: 252 residues added (347 deleted due to clashes), 7353 seeds are put forward Round 1: 708 peptides, 35 chains. Longest chain 89 peptides. Score 0.864 Round 2: 719 peptides, 31 chains. Longest chain 165 peptides. Score 0.879 Round 3: 729 peptides, 32 chains. Longest chain 90 peptides. Score 0.880 Round 4: 727 peptides, 38 chains. Longest chain 95 peptides. Score 0.865 Round 5: 716 peptides, 35 chains. Longest chain 89 peptides. Score 0.867 Taking the results from Round 3 Chains 33, Residues 697, Estimated correctness of the model 98.0 % 12 chains (555 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 196 A and 206 A Built loop between residues 284 A and 287 A Built loop between residues 307 A and 311 A Built loop between residues 375 A and 378 A Built loop between residues 233 B and 236 B Built loop between residues 266 B and 269 B Built loop between residues 357 B and 361 B 25 chains (717 residues) following loop building 5 chains (578 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8699 restraints for refining 7015 atoms. 3519 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2543 (Rfree = 0.000) for 7015 atoms. Found 132 (132 requested) and removed 99 (91 requested) atoms. Cycle 17: After refmac, R = 0.2365 (Rfree = 0.000) for 7044 atoms. Found 100 (129 requested) and removed 67 (92 requested) atoms. Cycle 18: After refmac, R = 0.2260 (Rfree = 0.000) for 7069 atoms. Found 81 (125 requested) and removed 48 (92 requested) atoms. Cycle 19: After refmac, R = 0.2201 (Rfree = 0.000) for 7096 atoms. Found 60 (122 requested) and removed 47 (92 requested) atoms. Cycle 20: After refmac, R = 0.2148 (Rfree = 0.000) for 7105 atoms. Found 57 (118 requested) and removed 38 (92 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.25 2.22 NCS extension: 232 residues added (552 deleted due to clashes), 7368 seeds are put forward Round 1: 721 peptides, 37 chains. Longest chain 91 peptides. Score 0.865 Round 2: 721 peptides, 32 chains. Longest chain 171 peptides. Score 0.877 Round 3: 718 peptides, 32 chains. Longest chain 97 peptides. Score 0.876 Round 4: 718 peptides, 34 chains. Longest chain 98 peptides. Score 0.871 Round 5: 729 peptides, 36 chains. Longest chain 96 peptides. Score 0.871 Taking the results from Round 2 Chains 33, Residues 689, Estimated correctness of the model 97.9 % 10 chains (515 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 228 B and 231 B Built loop between residues 257 B and 260 B 31 chains (693 residues) following loop building 8 chains (519 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9326 restraints for refining 7004 atoms. 4475 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2403 (Rfree = 0.000) for 7004 atoms. Found 113 (113 requested) and removed 100 (91 requested) atoms. Cycle 22: After refmac, R = 0.2271 (Rfree = 0.000) for 7016 atoms. Found 78 (110 requested) and removed 41 (91 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2183 (Rfree = 0.000) for 7051 atoms. Found 65 (107 requested) and removed 31 (92 requested) atoms. Cycle 24: After refmac, R = 0.2142 (Rfree = 0.000) for 7082 atoms. Found 60 (107 requested) and removed 29 (92 requested) atoms. Cycle 25: After refmac, R = 0.2107 (Rfree = 0.000) for 7107 atoms. Found 60 (107 requested) and removed 38 (92 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.24 2.21 NCS extension: 44 residues added (204 deleted due to clashes), 7177 seeds are put forward Round 1: 711 peptides, 37 chains. Longest chain 107 peptides. Score 0.860 Round 2: 733 peptides, 27 chains. Longest chain 107 peptides. Score 0.893 Round 3: 724 peptides, 39 chains. Longest chain 97 peptides. Score 0.861 Round 4: 717 peptides, 34 chains. Longest chain 81 peptides. Score 0.870 Round 5: 721 peptides, 36 chains. Longest chain 65 peptides. Score 0.867 Taking the results from Round 2 Chains 34, Residues 706, Estimated correctness of the model 98.4 % 10 chains (530 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 229 B and 238 B 32 chains (710 residues) following loop building 9 chains (538 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9141 restraints for refining 7102 atoms. 4177 conditional restraints added. Observations/parameters ratio is 1.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2530 (Rfree = 0.000) for 7102 atoms. Found 104 (104 requested) and removed 113 (92 requested) atoms. Cycle 27: After refmac, R = 0.2366 (Rfree = 0.000) for 7089 atoms. Found 87 (100 requested) and removed 85 (92 requested) atoms. Cycle 28: After refmac, R = 0.2268 (Rfree = 0.000) for 7083 atoms. Found 75 (96 requested) and removed 39 (92 requested) atoms. Cycle 29: After refmac, R = 0.2217 (Rfree = 0.000) for 7114 atoms. Found 59 (92 requested) and removed 37 (92 requested) atoms. Cycle 30: After refmac, R = 0.2175 (Rfree = 0.000) for 7132 atoms. Found 51 (93 requested) and removed 33 (93 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.26 2.23 NCS extension: 161 residues added (280 deleted due to clashes), 7327 seeds are put forward Round 1: 700 peptides, 34 chains. Longest chain 90 peptides. Score 0.863 Round 2: 711 peptides, 35 chains. Longest chain 78 peptides. Score 0.865 Round 3: 702 peptides, 36 chains. Longest chain 66 peptides. Score 0.858 Round 4: 706 peptides, 34 chains. Longest chain 110 peptides. Score 0.865 Round 5: 692 peptides, 39 chains. Longest chain 60 peptides. Score 0.845 Taking the results from Round 4 Chains 35, Residues 672, Estimated correctness of the model 97.5 % 10 chains (491 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 197 A and 206 A Built loop between residues 179 B and 182 B Built loop between residues 330 B and 333 B Built loop between residues 353 B and 357 B 30 chains (684 residues) following loop building 6 chains (506 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 9357 restraints for refining 6998 atoms. 4623 conditional restraints added. Observations/parameters ratio is 1.66 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2513 (Rfree = 0.000) for 6998 atoms. Found 91 (91 requested) and removed 104 (91 requested) atoms. Cycle 32: After refmac, R = 0.2342 (Rfree = 0.000) for 6980 atoms. Found 85 (91 requested) and removed 63 (91 requested) atoms. Cycle 33: After refmac, R = 0.2240 (Rfree = 0.000) for 6999 atoms. Found 68 (91 requested) and removed 38 (91 requested) atoms. Cycle 34: After refmac, R = 0.2182 (Rfree = 0.000) for 7028 atoms. Found 64 (91 requested) and removed 30 (91 requested) atoms. Cycle 35: After refmac, R = 0.2140 (Rfree = 0.000) for 7058 atoms. Found 46 (92 requested) and removed 29 (92 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.26 2.23 NCS extension: 131 residues added (581 deleted due to clashes), 7214 seeds are put forward Round 1: 699 peptides, 37 chains. Longest chain 115 peptides. Score 0.854 Round 2: 724 peptides, 31 chains. Longest chain 97 peptides. Score 0.881 Round 3: 719 peptides, 35 chains. Longest chain 106 peptides. Score 0.869 Round 4: 725 peptides, 37 chains. Longest chain 98 peptides. Score 0.866 Round 5: 723 peptides, 38 chains. Longest chain 99 peptides. Score 0.863 Taking the results from Round 2 Chains 34, Residues 693, Estimated correctness of the model 98.0 % 16 chains (591 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 169 A and 172 A Built loop between residues 196 A and 201 A Built loop between residues 233 A and 236 A Built loop between residues 257 A and 260 A Built loop between residues 315 A and 318 A Built loop between residues 356 A and 360 A Built loop between residues 374 A and 379 A Built loop between residues 163 B and 171 B Built loop between residues 299 B and 302 B 23 chains (717 residues) following loop building 7 chains (619 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8465 restraints for refining 7142 atoms. 3106 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2446 (Rfree = 0.000) for 7142 atoms. Found 93 (93 requested) and removed 108 (93 requested) atoms. Cycle 37: After refmac, R = 0.2291 (Rfree = 0.000) for 7126 atoms. Found 93 (93 requested) and removed 79 (93 requested) atoms. Cycle 38: After refmac, R = 0.2230 (Rfree = 0.000) for 7135 atoms. Found 71 (93 requested) and removed 48 (93 requested) atoms. Cycle 39: After refmac, R = 0.2173 (Rfree = 0.000) for 7155 atoms. Found 70 (93 requested) and removed 39 (93 requested) atoms. Cycle 40: After refmac, R = 0.2141 (Rfree = 0.000) for 7182 atoms. Found 62 (93 requested) and removed 50 (93 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.25 2.22 NCS extension: 193 residues added (301 deleted due to clashes), 7395 seeds are put forward Round 1: 721 peptides, 35 chains. Longest chain 91 peptides. Score 0.870 Round 2: 729 peptides, 29 chains. Longest chain 131 peptides. Score 0.887 Round 3: 722 peptides, 35 chains. Longest chain 96 peptides. Score 0.870 Round 4: 717 peptides, 40 chains. Longest chain 70 peptides. Score 0.855 Round 5: 712 peptides, 36 chains. Longest chain 74 peptides. Score 0.863 Taking the results from Round 2 Chains 38, Residues 700, Estimated correctness of the model 98.2 % 14 chains (584 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 176 A and 181 A Built loop between residues 256 A and 260 A Built loop between residues 197 B and 201 B Built loop between residues 292 B and 295 B Built loop between residues 374 B and 379 B 30 chains (712 residues) following loop building 9 chains (600 residues) in sequence following loop building ------------------------------------------------------ 46493 reflections ( 91.25 % complete ) and 8566 restraints for refining 7124 atoms. 3322 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2399 (Rfree = 0.000) for 7124 atoms. Found 93 (93 requested) and removed 110 (93 requested) atoms. Cycle 42: After refmac, R = 0.2263 (Rfree = 0.000) for 7103 atoms. Found 92 (92 requested) and removed 62 (92 requested) atoms. Cycle 43: After refmac, R = 0.2193 (Rfree = 0.000) for 7129 atoms. Found 79 (93 requested) and removed 47 (93 requested) atoms. Cycle 44: After refmac, R = 0.2146 (Rfree = 0.000) for 7159 atoms. Found 75 (93 requested) and removed 47 (93 requested) atoms. Cycle 45: After refmac, R = 0.2117 (Rfree = 0.000) for 7186 atoms. Found 72 (93 requested) and removed 54 (93 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.25 2.22 NCS extension: 125 residues added (416 deleted due to clashes), 7338 seeds are put forward Round 1: 708 peptides, 38 chains. Longest chain 64 peptides. Score 0.856 Round 2: 734 peptides, 29 chains. Longest chain 157 peptides. Score 0.889 Round 3: 711 peptides, 39 chains. Longest chain 67 peptides. Score 0.855 Round 4: 729 peptides, 32 chains. Longest chain 148 peptides. Score 0.880 Round 5: 709 peptides, 33 chains. Longest chain 98 peptides. Score 0.869 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 705, Estimated correctness of the model 98.3 % 9 chains (558 residues) have been docked in sequence Sequence coverage is 79 % Consider running further cycles of model building using 2okc-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 169 A and 171 A Built loop between residues 197 A and 201 A Built loop between residues 344 A and 356 A Built loop between residues 194 B and 206 B Built loop between residues 225 B and 236 B 22 chains (729 residues) following loop building 4 chains (594 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 46493 reflections ( 91.25 % complete ) and 8699 restraints for refining 7209 atoms. 3414 conditional restraints added. Observations/parameters ratio is 1.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2437 (Rfree = 0.000) for 7209 atoms. Found 0 (94 requested) and removed 4 (94 requested) atoms. Cycle 47: After refmac, R = 0.2308 (Rfree = 0.000) for 7199 atoms. Found 0 (94 requested) and removed 3 (94 requested) atoms. Cycle 48: After refmac, R = 0.2250 (Rfree = 0.000) for 7192 atoms. Found 0 (93 requested) and removed 0 (93 requested) atoms. Cycle 49: After refmac, R = 0.2217 (Rfree = 0.000) for 7187 atoms. Found 0 (93 requested) and removed 3 (93 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 85.92