Mon 24 Dec 01:09:31 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 1vl6-2.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-2.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl6-2.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-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/1vl6-2.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-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 01:09:36 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/1vl6-2.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-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 1427 and 0 Target number of residues in the AU: 1427 Target solvent content: 0.6050 Checking the provided sequence file Detected sequence length: 388 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1552 Adjusted target solvent content: 0.57 Input MTZ file: 1vl6-2.8-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-2.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.85 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 3 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: 124.815 2.800 Wilson plot Bfac: 54.64 47203 reflections ( 99.93 % complete ) and 0 restraints for refining 13925 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Starting model: R = 0.3308 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2892 (Rfree = 0.000) for 13925 atoms. Found 182 (182 requested) and removed 117 (91 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.92 2.66 Search for helices and strands: 0 residues in 0 chains, 14291 seeds are put forward NCS extension: 0 residues added, 14291 seeds are put forward Round 1: 875 peptides, 136 chains. Longest chain 31 peptides. Score 0.462 Round 2: 1050 peptides, 115 chains. Longest chain 41 peptides. Score 0.641 Round 3: 1107 peptides, 110 chains. Longest chain 39 peptides. Score 0.684 Round 4: 1125 peptides, 102 chains. Longest chain 44 peptides. Score 0.711 Round 5: 1153 peptides, 98 chains. Longest chain 45 peptides. Score 0.733 Taking the results from Round 5 Chains 110, Residues 1055, Estimated correctness of the model 81.5 % 32 chains (590 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 B and 66 B Built loop between residues 124 B and 132 B Built loop between residues 268 B and 271 B Built loop between residues 282 B and 286 B Built loop between residues 324 B and 327 B 104 chains (1070 residues) following loop building 27 chains (608 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 18469 restraints for refining 11463 atoms. 12019 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2868 (Rfree = 0.000) for 11463 atoms. Found 150 (150 requested) and removed 185 (75 requested) atoms. Cycle 2: After refmac, R = 0.2741 (Rfree = 0.000) for 11245 atoms. Found 147 (147 requested) and removed 114 (75 requested) atoms. Cycle 3: After refmac, R = 0.2630 (Rfree = 0.000) for 11171 atoms. Found 128 (142 requested) and removed 92 (74 requested) atoms. Cycle 4: After refmac, R = 0.2558 (Rfree = 0.000) for 11148 atoms. Found 138 (138 requested) and removed 93 (73 requested) atoms. Cycle 5: After refmac, R = 0.2483 (Rfree = 0.000) for 11157 atoms. Found 134 (134 requested) and removed 86 (73 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.87 2.61 Search for helices and strands: 0 residues in 0 chains, 11576 seeds are put forward NCS extension: 231 residues added (159 deleted due to clashes), 11807 seeds are put forward Round 1: 1075 peptides, 90 chains. Longest chain 44 peptides. Score 0.715 Round 2: 1127 peptides, 76 chains. Longest chain 69 peptides. Score 0.768 Round 3: 1139 peptides, 83 chains. Longest chain 75 peptides. Score 0.758 Round 4: 1127 peptides, 89 chains. Longest chain 101 peptides. Score 0.741 Round 5: 1132 peptides, 86 chains. Longest chain 132 peptides. Score 0.749 Taking the results from Round 2 Chains 80, Residues 1051, Estimated correctness of the model 85.7 % 26 chains (694 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 293 C and 297 C Built loop between residues 45 B and 49 B Built loop between residues 57 B and 63 B Built loop between residues 123 B and 126 B Built loop between residues 140 B and 148 B Built loop between residues 195 B and 200 B Built loop between residues 233 B and 242 B Built loop between residues 294 B and 297 B Built loop between residues 313 B and 316 B Built loop between residues 325 B and 328 B 68 chains (1085 residues) following loop building 16 chains (732 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 17260 restraints for refining 11474 atoms. 10206 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2557 (Rfree = 0.000) for 11474 atoms. Found 127 (135 requested) and removed 125 (75 requested) atoms. Cycle 7: After refmac, R = 0.2404 (Rfree = 0.000) for 11392 atoms. Found 109 (132 requested) and removed 96 (75 requested) atoms. Cycle 8: After refmac, R = 0.2277 (Rfree = 0.000) for 11346 atoms. Found 91 (128 requested) and removed 88 (74 requested) atoms. Cycle 9: After refmac, R = 0.2225 (Rfree = 0.000) for 11318 atoms. Found 88 (125 requested) and removed 78 (74 requested) atoms. Cycle 10: After refmac, R = 0.2195 (Rfree = 0.000) for 11311 atoms. Found 93 (121 requested) and removed 79 (74 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.88 2.62 Search for helices and strands: 0 residues in 0 chains, 11671 seeds are put forward NCS extension: 878 residues added (693 deleted due to clashes), 12549 seeds are put forward Round 1: 1109 peptides, 80 chains. Longest chain 122 peptides. Score 0.752 Round 2: 1159 peptides, 68 chains. Longest chain 125 peptides. Score 0.795 Round 3: 1150 peptides, 74 chains. Longest chain 106 peptides. Score 0.780 Round 4: 1138 peptides, 75 chains. Longest chain 107 peptides. Score 0.774 Round 5: 1135 peptides, 73 chains. Longest chain 72 peptides. Score 0.777 Taking the results from Round 2 Chains 74, Residues 1091, Estimated correctness of the model 88.6 % 27 chains (746 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 47 A Built loop between residues 106 A and 109 A Built loop between residues 143 A and 147 A Built loop between residues 270 A and 273 A Built loop between residues 293 A and 297 A Built loop between residues 341 A and 344 A Built loop between residues 373 A and 383 A Built loop between residues 38 C and 49 C Built loop between residues 141 C and 148 C Built loop between residues 141 B and 146 B 62 chains (1129 residues) following loop building 17 chains (790 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16327 restraints for refining 11473 atoms. 8925 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2363 (Rfree = 0.000) for 11473 atoms. Found 117 (120 requested) and removed 102 (75 requested) atoms. Cycle 12: After refmac, R = 0.2191 (Rfree = 0.000) for 11443 atoms. Found 73 (117 requested) and removed 91 (75 requested) atoms. Cycle 13: After refmac, R = 0.2140 (Rfree = 0.000) for 11397 atoms. Found 70 (114 requested) and removed 80 (75 requested) atoms. Cycle 14: After refmac, R = 0.2105 (Rfree = 0.000) for 11365 atoms. Found 94 (110 requested) and removed 77 (74 requested) atoms. Cycle 15: After refmac, R = 0.2060 (Rfree = 0.000) for 11357 atoms. Found 74 (107 requested) and removed 75 (74 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11727 seeds are put forward NCS extension: 663 residues added (805 deleted due to clashes), 12390 seeds are put forward Round 1: 1112 peptides, 82 chains. Longest chain 51 peptides. Score 0.749 Round 2: 1161 peptides, 71 chains. Longest chain 102 peptides. Score 0.790 Round 3: 1167 peptides, 67 chains. Longest chain 104 peptides. Score 0.800 Round 4: 1148 peptides, 80 chains. Longest chain 79 peptides. Score 0.768 Round 5: 1142 peptides, 80 chains. Longest chain 73 peptides. Score 0.766 Taking the results from Round 3 Chains 76, Residues 1100, Estimated correctness of the model 89.1 % 26 chains (765 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 90 A Built loop between residues 126 A and 129 A Built loop between residues 136 A and 147 A Built loop between residues 233 A and 237 A Built loop between residues 269 A and 272 A Built loop between residues 142 C and 149 C Built loop between residues 97 B and 103 B Built loop between residues 126 B and 129 B Built loop between residues 141 B and 147 B Built loop between residues 182 B and 186 B Built loop between residues 349 B and 352 B 63 chains (1139 residues) following loop building 15 chains (812 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16009 restraints for refining 11473 atoms. 8392 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2350 (Rfree = 0.000) for 11473 atoms. Found 100 (105 requested) and removed 109 (75 requested) atoms. Cycle 17: After refmac, R = 0.2216 (Rfree = 0.000) for 11412 atoms. Found 77 (102 requested) and removed 82 (75 requested) atoms. Cycle 18: After refmac, R = 0.2188 (Rfree = 0.000) for 11387 atoms. Found 62 (98 requested) and removed 79 (74 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2144 (Rfree = 0.000) for 11350 atoms. Found 75 (95 requested) and removed 78 (74 requested) atoms. Cycle 20: After refmac, R = 0.1994 (Rfree = 0.000) for 11329 atoms. Found 32 (92 requested) and removed 76 (74 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 2.64 Search for helices and strands: 0 residues in 0 chains, 11632 seeds are put forward NCS extension: 1053 residues added (663 deleted due to clashes), 12685 seeds are put forward Round 1: 1097 peptides, 82 chains. Longest chain 78 peptides. Score 0.743 Round 2: 1162 peptides, 74 chains. Longest chain 123 peptides. Score 0.785 Round 3: 1162 peptides, 73 chains. Longest chain 92 peptides. Score 0.787 Round 4: 1126 peptides, 83 chains. Longest chain 55 peptides. Score 0.753 Round 5: 1132 peptides, 83 chains. Longest chain 51 peptides. Score 0.755 Taking the results from Round 3 Chains 80, Residues 1089, Estimated correctness of the model 87.8 % 30 chains (770 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 128 A Built loop between residues 141 A and 147 A Built loop between residues 199 A and 202 A Built loop between residues 223 A and 234 A Built loop between residues 267 A and 272 A Built loop between residues 288 A and 297 A Built loop between residues 359 A and 362 A Built loop between residues 143 C and 149 C Built loop between residues 141 B and 147 B Built loop between residues 182 B and 185 B Built loop between residues 199 B and 202 B 65 chains (1127 residues) following loop building 19 chains (819 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16048 restraints for refining 11475 atoms. 8464 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2407 (Rfree = 0.000) for 11475 atoms. Found 90 (90 requested) and removed 113 (75 requested) atoms. Cycle 22: After refmac, R = 0.2262 (Rfree = 0.000) for 11411 atoms. Found 87 (87 requested) and removed 88 (75 requested) atoms. Cycle 23: After refmac, R = 0.2182 (Rfree = 0.000) for 11383 atoms. Found 83 (83 requested) and removed 79 (74 requested) atoms. Cycle 24: After refmac, R = 0.2132 (Rfree = 0.000) for 11363 atoms. Found 80 (80 requested) and removed 79 (74 requested) atoms. Cycle 25: After refmac, R = 0.2113 (Rfree = 0.000) for 11348 atoms. Found 77 (77 requested) and removed 77 (74 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 2.64 Search for helices and strands: 0 residues in 0 chains, 11686 seeds are put forward NCS extension: 931 residues added (835 deleted due to clashes), 12617 seeds are put forward Round 1: 1096 peptides, 81 chains. Longest chain 85 peptides. Score 0.745 Round 2: 1172 peptides, 74 chains. Longest chain 104 peptides. Score 0.788 Round 3: 1152 peptides, 77 chains. Longest chain 68 peptides. Score 0.775 Round 4: 1151 peptides, 79 chains. Longest chain 65 peptides. Score 0.771 Round 5: 1120 peptides, 87 chains. Longest chain 49 peptides. Score 0.742 Taking the results from Round 2 Chains 86, Residues 1098, Estimated correctness of the model 87.9 % 28 chains (785 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 126 A Built loop between residues 141 A and 144 A Built loop between residues 183 A and 188 A Built loop between residues 226 A and 234 A Built loop between residues 263 A and 272 A Built loop between residues 293 A and 297 A Built loop between residues 142 B and 146 B Built loop between residues 165 B and 172 B Built loop between residues 199 B and 203 B Built loop between residues 282 B and 285 B 73 chains (1130 residues) following loop building 17 chains (825 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15845 restraints for refining 11474 atoms. 8208 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2339 (Rfree = 0.000) for 11474 atoms. Found 75 (75 requested) and removed 120 (75 requested) atoms. Cycle 27: After refmac, R = 0.2222 (Rfree = 0.000) for 11395 atoms. Found 75 (75 requested) and removed 84 (75 requested) atoms. Cycle 28: After refmac, R = 0.2190 (Rfree = 0.000) for 11360 atoms. Found 74 (74 requested) and removed 82 (74 requested) atoms. Cycle 29: After refmac, R = 0.2033 (Rfree = 0.000) for 11325 atoms. Found 55 (74 requested) and removed 76 (74 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1971 (Rfree = 0.000) for 11285 atoms. Found 36 (74 requested) and removed 74 (74 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.91 2.65 Search for helices and strands: 0 residues in 0 chains, 11615 seeds are put forward NCS extension: 811 residues added (777 deleted due to clashes), 12426 seeds are put forward Round 1: 1122 peptides, 87 chains. Longest chain 68 peptides. Score 0.743 Round 2: 1179 peptides, 74 chains. Longest chain 85 peptides. Score 0.791 Round 3: 1170 peptides, 77 chains. Longest chain 89 peptides. Score 0.782 Round 4: 1155 peptides, 78 chains. Longest chain 51 peptides. Score 0.775 Round 5: 1129 peptides, 89 chains. Longest chain 49 peptides. Score 0.742 Taking the results from Round 2 Chains 89, Residues 1105, Estimated correctness of the model 88.2 % 32 chains (807 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 106 A Built loop between residues 126 A and 129 A Built loop between residues 142 A and 145 A Built loop between residues 198 A and 204 A Built loop between residues 293 A and 297 A Built loop between residues 59 C and 66 C Built loop between residues 79 C and 90 C Built loop between residues 189 C and 199 C Built loop between residues 230 C and 233 C Built loop between residues 248 C and 251 C Built loop between residues 261 C and 265 C Built loop between residues 294 C and 297 C Built loop between residues 309 C and 320 C Built loop between residues 339 C and 342 C Built loop between residues 371 C and 375 C Built loop between residues 37 B and 46 B Built loop between residues 81 B and 88 B 65 chains (1163 residues) following loop building 15 chains (886 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15220 restraints for refining 11474 atoms. 7248 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2339 (Rfree = 0.000) for 11474 atoms. Found 75 (75 requested) and removed 116 (75 requested) atoms. Cycle 32: After refmac, R = 0.2185 (Rfree = 0.000) for 11383 atoms. Found 75 (75 requested) and removed 85 (75 requested) atoms. Cycle 33: After refmac, R = 0.2143 (Rfree = 0.000) for 11339 atoms. Found 66 (74 requested) and removed 81 (74 requested) atoms. Cycle 34: After refmac, R = 0.2108 (Rfree = 0.000) for 11307 atoms. Found 57 (74 requested) and removed 78 (74 requested) atoms. Cycle 35: After refmac, R = 0.2087 (Rfree = 0.000) for 11266 atoms. Found 74 (74 requested) and removed 75 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11619 seeds are put forward NCS extension: 948 residues added (774 deleted due to clashes), 12567 seeds are put forward Round 1: 1112 peptides, 73 chains. Longest chain 92 peptides. Score 0.768 Round 2: 1153 peptides, 76 chains. Longest chain 87 peptides. Score 0.778 Round 3: 1164 peptides, 81 chains. Longest chain 54 peptides. Score 0.772 Round 4: 1148 peptides, 79 chains. Longest chain 65 peptides. Score 0.770 Round 5: 1129 peptides, 82 chains. Longest chain 45 peptides. Score 0.756 Taking the results from Round 2 Chains 87, Residues 1077, Estimated correctness of the model 86.8 % 30 chains (772 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 47 A Built loop between residues 81 A and 89 A Built loop between residues 106 A and 109 A Built loop between residues 143 A and 147 A Built loop between residues 188 A and 191 A Built loop between residues 250 A and 253 A Built loop between residues 106 C and 109 C Built loop between residues 142 C and 149 C Built loop between residues 75 B and 85 B Built loop between residues 121 B and 131 B Built loop between residues 144 B and 147 B Built loop between residues 182 B and 185 B 71 chains (1115 residues) following loop building 18 chains (826 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15977 restraints for refining 11475 atoms. 8452 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2263 (Rfree = 0.000) for 11475 atoms. Found 75 (75 requested) and removed 120 (75 requested) atoms. Cycle 37: After refmac, R = 0.2181 (Rfree = 0.000) for 11386 atoms. Found 75 (75 requested) and removed 83 (75 requested) atoms. Cycle 38: After refmac, R = 0.2144 (Rfree = 0.000) for 11348 atoms. Found 74 (74 requested) and removed 78 (74 requested) atoms. Cycle 39: After refmac, R = 0.2105 (Rfree = 0.000) for 11314 atoms. Found 74 (74 requested) and removed 77 (74 requested) atoms. Cycle 40: After refmac, R = 0.2086 (Rfree = 0.000) for 11297 atoms. Found 67 (74 requested) and removed 75 (74 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.90 2.64 Search for helices and strands: 0 residues in 0 chains, 11643 seeds are put forward NCS extension: 1141 residues added (477 deleted due to clashes), 12784 seeds are put forward Round 1: 1103 peptides, 81 chains. Longest chain 58 peptides. Score 0.747 Round 2: 1162 peptides, 80 chains. Longest chain 63 peptides. Score 0.773 Round 3: 1156 peptides, 81 chains. Longest chain 54 peptides. Score 0.769 Round 4: 1158 peptides, 85 chains. Longest chain 74 peptides. Score 0.762 Round 5: 1128 peptides, 89 chains. Longest chain 48 peptides. Score 0.741 Taking the results from Round 2 Chains 89, Residues 1082, Estimated correctness of the model 86.3 % 29 chains (803 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 47 A Built loop between residues 82 A and 91 A Built loop between residues 144 A and 148 A Built loop between residues 261 A and 264 A Built loop between residues 354 A and 358 A Built loop between residues 37 C and 47 C Built loop between residues 124 C and 133 C Built loop between residues 145 C and 149 C Built loop between residues 167 C and 175 C Built loop between residues 44 B and 47 B Built loop between residues 122 B and 126 B Built loop between residues 144 B and 147 B Built loop between residues 184 B and 187 B Built loop between residues 293 B and 297 B Built loop between residues 323 B and 326 B Built loop between residues 93 D and 104 D 64 chains (1135 residues) following loop building 13 chains (877 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15399 restraints for refining 11475 atoms. 7603 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2287 (Rfree = 0.000) for 11475 atoms. Found 75 (75 requested) and removed 101 (75 requested) atoms. Cycle 42: After refmac, R = 0.2140 (Rfree = 0.000) for 11396 atoms. Found 75 (75 requested) and removed 84 (75 requested) atoms. Cycle 43: After refmac, R = 0.2081 (Rfree = 0.000) for 11357 atoms. Found 74 (74 requested) and removed 76 (74 requested) atoms. Cycle 44: After refmac, R = 0.2023 (Rfree = 0.000) for 11335 atoms. Found 65 (74 requested) and removed 76 (74 requested) atoms. Cycle 45: After refmac, R = 0.2022 (Rfree = 0.000) for 11311 atoms. Found 62 (74 requested) and removed 74 (74 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11653 seeds are put forward NCS extension: 253 residues added (782 deleted due to clashes), 11906 seeds are put forward Round 1: 1086 peptides, 77 chains. Longest chain 84 peptides. Score 0.749 Round 2: 1110 peptides, 68 chains. Longest chain 58 peptides. Score 0.777 Round 3: 1118 peptides, 73 chains. Longest chain 96 peptides. Score 0.770 Round 4: 1115 peptides, 78 chains. Longest chain 43 peptides. Score 0.759 Round 5: 1112 peptides, 76 chains. Longest chain 55 peptides. Score 0.762 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 73, Residues 1042, Estimated correctness of the model 86.7 % 30 chains (802 residues) have been docked in sequence Sequence coverage is 76 % Consider running further cycles of model building using 1vl6-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 38 A and 47 A Built loop between residues 87 A and 91 A Built loop between residues 97 A and 100 A Built loop between residues 145 A and 148 A Built loop between residues 185 A and 188 A Built loop between residues 229 A and 234 A Built loop between residues 290 A and 301 A Built loop between residues 350 A and 353 A Built loop between residues 128 C and 131 C Built loop between residues 140 C and 149 C Built loop between residues 77 B and 89 B Built loop between residues 100 B and 103 B Built loop between residues 119 B and 122 B Built loop between residues 142 B and 146 B Built loop between residues 183 B and 186 B Built loop between residues 295 B and 298 B Built loop between residues 315 B and 318 B Built loop between residues 327 B and 331 B 53 chains (1108 residues) following loop building 12 chains (872 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 47203 reflections ( 99.93 % complete ) and 15440 restraints for refining 11475 atoms. 7696 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2275 (Rfree = 0.000) for 11475 atoms. Found 0 (75 requested) and removed 39 (75 requested) atoms. Cycle 47: After refmac, R = 0.2134 (Rfree = 0.000) for 11391 atoms. Found 0 (75 requested) and removed 25 (75 requested) atoms. Cycle 48: After refmac, R = 0.2147 (Rfree = 0.000) for 11349 atoms. Found 0 (74 requested) and removed 19 (74 requested) atoms. Cycle 49: After refmac, R = 0.2129 (Rfree = 0.000) for 11315 atoms. TimeTaking 182.97