Mon 24 Dec 07:30:50 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl6-2.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-2.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl6-2.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-parrot-noncs ############### 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 07:30:55 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/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-parrot-noncs/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-noncs.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-noncs.fasta_lf Building free atoms model in initial map for 12416 target number of atoms Had to go as low as 0.80 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 13849 atoms. Observations/parameters ratio is 0.85 ------------------------------------------------------ Starting model: R = 0.3277 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2908 (Rfree = 0.000) for 13849 atoms. Found 172 (181 requested) and removed 220 (90 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 14049 seeds are put forward NCS extension: 0 residues added, 14049 seeds are put forward Round 1: 785 peptides, 131 chains. Longest chain 28 peptides. Score 0.408 Round 2: 932 peptides, 122 chains. Longest chain 24 peptides. Score 0.548 Round 3: 965 peptides, 109 chains. Longest chain 35 peptides. Score 0.607 Round 4: 1034 peptides, 106 chains. Longest chain 44 peptides. Score 0.655 Round 5: 1011 peptides, 104 chains. Longest chain 45 peptides. Score 0.648 Taking the results from Round 4 Chains 110, Residues 928, Estimated correctness of the model 70.5 % 20 chains (394 residues) have been docked in sequence ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 20570 restraints for refining 11458 atoms. 15485 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2935 (Rfree = 0.000) for 11458 atoms. Found 143 (150 requested) and removed 124 (75 requested) atoms. Cycle 2: After refmac, R = 0.3007 (Rfree = 0.000) for 11286 atoms. Found 150 (150 requested) and removed 109 (75 requested) atoms. Cycle 3: After refmac, R = 0.2881 (Rfree = 0.000) for 11191 atoms. Found 148 (148 requested) and removed 103 (74 requested) atoms. Cycle 4: After refmac, R = 0.2801 (Rfree = 0.000) for 11119 atoms. Found 147 (147 requested) and removed 103 (73 requested) atoms. Cycle 5: After refmac, R = 0.2714 (Rfree = 0.000) for 11096 atoms. Found 146 (146 requested) and removed 88 (73 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.91 2.65 Search for helices and strands: 0 residues in 0 chains, 11514 seeds are put forward NCS extension: 293 residues added (46 deleted due to clashes), 11807 seeds are put forward Round 1: 1033 peptides, 115 chains. Longest chain 47 peptides. Score 0.631 Round 2: 1072 peptides, 92 chains. Longest chain 48 peptides. Score 0.709 Round 3: 1091 peptides, 96 chains. Longest chain 51 peptides. Score 0.709 Round 4: 1099 peptides, 92 chains. Longest chain 54 peptides. Score 0.722 Round 5: 1115 peptides, 82 chains. Longest chain 56 peptides. Score 0.750 Taking the results from Round 5 Chains 96, Residues 1033, Estimated correctness of the model 83.6 % 27 chains (637 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 130 A and 133 A Built loop between residues 141 A and 146 A Built loop between residues 173 C and 176 C Built loop between residues 141 B and 144 B Built loop between residues 324 B and 327 B 90 chains (1043 residues) following loop building 22 chains (649 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 17827 restraints for refining 11473 atoms. 11307 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2695 (Rfree = 0.000) for 11473 atoms. Found 142 (150 requested) and removed 128 (75 requested) atoms. Cycle 7: After refmac, R = 0.2536 (Rfree = 0.000) for 11408 atoms. Found 135 (147 requested) and removed 107 (75 requested) atoms. Cycle 8: After refmac, R = 0.2460 (Rfree = 0.000) for 11383 atoms. Found 133 (144 requested) and removed 101 (75 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2410 (Rfree = 0.000) for 11381 atoms. Found 134 (140 requested) and removed 92 (74 requested) atoms. Cycle 10: After refmac, R = 0.2374 (Rfree = 0.000) for 11388 atoms. Found 126 (137 requested) and removed 86 (74 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.91 2.65 Search for helices and strands: 0 residues in 0 chains, 11831 seeds are put forward NCS extension: 353 residues added (253 deleted due to clashes), 12184 seeds are put forward Round 1: 1061 peptides, 91 chains. Longest chain 76 peptides. Score 0.706 Round 2: 1107 peptides, 93 chains. Longest chain 69 peptides. Score 0.723 Round 3: 1122 peptides, 91 chains. Longest chain 76 peptides. Score 0.734 Round 4: 1121 peptides, 92 chains. Longest chain 61 peptides. Score 0.732 Round 5: 1117 peptides, 97 chains. Longest chain 54 peptides. Score 0.719 Taking the results from Round 3 Chains 101, Residues 1031, Estimated correctness of the model 81.7 % 28 chains (582 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 48 A Built loop between residues 82 A and 84 A Built loop between residues 100 A and 103 A Built loop between residues 261 A and 272 A Built loop between residues 100 D and 109 D 93 chains (1043 residues) following loop building 23 chains (605 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 18331 restraints for refining 11472 atoms. 12027 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2496 (Rfree = 0.000) for 11472 atoms. Found 118 (135 requested) and removed 122 (75 requested) atoms. Cycle 12: After refmac, R = 0.2399 (Rfree = 0.000) for 11418 atoms. Found 124 (132 requested) and removed 88 (75 requested) atoms. Cycle 13: After refmac, R = 0.2358 (Rfree = 0.000) for 11420 atoms. Found 115 (129 requested) and removed 97 (75 requested) atoms. Cycle 14: After refmac, R = 0.2321 (Rfree = 0.000) for 11412 atoms. Found 101 (126 requested) and removed 81 (75 requested) atoms. Cycle 15: After refmac, R = 0.2273 (Rfree = 0.000) for 11404 atoms. Found 91 (123 requested) and removed 78 (75 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11768 seeds are put forward NCS extension: 133 residues added (240 deleted due to clashes), 11901 seeds are put forward Round 1: 1066 peptides, 95 chains. Longest chain 86 peptides. Score 0.699 Round 2: 1141 peptides, 92 chains. Longest chain 77 peptides. Score 0.740 Round 3: 1138 peptides, 85 chains. Longest chain 54 peptides. Score 0.754 Round 4: 1139 peptides, 99 chains. Longest chain 50 peptides. Score 0.724 Round 5: 1157 peptides, 92 chains. Longest chain 47 peptides. Score 0.747 Taking the results from Round 3 Chains 91, Residues 1053, Estimated correctness of the model 84.1 % 25 chains (626 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 132 A and 134 A Built loop between residues 143 A and 147 A Built loop between residues 199 A and 202 A Built loop between residues 230 A and 238 A Built loop between residues 267 A and 274 A Built loop between residues 101 C and 105 C 82 chains (1066 residues) following loop building 19 chains (648 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 17663 restraints for refining 11475 atoms. 11040 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2576 (Rfree = 0.000) for 11475 atoms. Found 120 (120 requested) and removed 114 (75 requested) atoms. Cycle 17: After refmac, R = 0.2441 (Rfree = 0.000) for 11434 atoms. Found 117 (117 requested) and removed 106 (75 requested) atoms. Cycle 18: After refmac, R = 0.2324 (Rfree = 0.000) for 11397 atoms. Found 114 (114 requested) and removed 89 (75 requested) atoms. Cycle 19: After refmac, R = 0.2069 (Rfree = 0.000) for 11395 atoms. Found 78 (110 requested) and removed 84 (74 requested) atoms. Cycle 20: After refmac, R = 0.1987 (Rfree = 0.000) for 11374 atoms. Found 58 (107 requested) and removed 80 (74 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11743 seeds are put forward NCS extension: 1124 residues added (801 deleted due to clashes), 12867 seeds are put forward Round 1: 1109 peptides, 93 chains. Longest chain 51 peptides. Score 0.724 Round 2: 1172 peptides, 90 chains. Longest chain 64 peptides. Score 0.757 Round 3: 1169 peptides, 82 chains. Longest chain 49 peptides. Score 0.772 Round 4: 1129 peptides, 87 chains. Longest chain 57 peptides. Score 0.746 Round 5: 1102 peptides, 88 chains. Longest chain 54 peptides. Score 0.732 Taking the results from Round 3 Chains 90, Residues 1087, Estimated correctness of the model 86.2 % 30 chains (712 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 293 A and 302 A Built loop between residues 325 A and 329 A Built loop between residues 372 A and 376 A Built loop between residues 81 B and 87 B Built loop between residues 131 B and 134 B Built loop between residues 143 B and 146 B Built loop between residues 185 B and 188 B Built loop between residues 235 B and 239 B Built loop between residues 258 B and 263 B Built loop between residues 293 B and 297 B Built loop between residues 321 B and 325 B Built loop between residues 345 B and 348 B 76 chains (1121 residues) following loop building 18 chains (752 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16491 restraints for refining 11475 atoms. 9169 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2476 (Rfree = 0.000) for 11475 atoms. Found 105 (105 requested) and removed 143 (75 requested) atoms. Cycle 22: After refmac, R = 0.2283 (Rfree = 0.000) for 11393 atoms. Found 102 (102 requested) and removed 106 (75 requested) atoms. Cycle 23: After refmac, R = 0.2193 (Rfree = 0.000) for 11364 atoms. Found 83 (98 requested) and removed 79 (74 requested) atoms. Cycle 24: After refmac, R = 0.2160 (Rfree = 0.000) for 11334 atoms. Found 77 (95 requested) and removed 79 (74 requested) atoms. Cycle 25: After refmac, R = 0.2150 (Rfree = 0.000) for 11323 atoms. Found 73 (92 requested) and removed 76 (74 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.92 2.66 Search for helices and strands: 0 residues in 0 chains, 11687 seeds are put forward NCS extension: 1506 residues added (1206 deleted due to clashes), 13193 seeds are put forward Round 1: 1108 peptides, 83 chains. Longest chain 86 peptides. Score 0.745 Round 2: 1151 peptides, 77 chains. Longest chain 67 peptides. Score 0.775 Round 3: 1130 peptides, 77 chains. Longest chain 92 peptides. Score 0.767 Round 4: 1132 peptides, 82 chains. Longest chain 76 peptides. Score 0.757 Round 5: 1137 peptides, 79 chains. Longest chain 46 peptides. Score 0.766 Taking the results from Round 2 Chains 88, Residues 1074, Estimated correctness of the model 86.5 % 29 chains (723 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 87 A Built loop between residues 93 A and 97 A Built loop between residues 129 A and 132 A Built loop between residues 140 A and 149 A Built loop between residues 325 A and 328 A Built loop between residues 117 C and 125 C Built loop between residues 126 B and 129 B Built loop between residues 144 B and 148 B Built loop between residues 233 B and 238 B Built loop between residues 320 B and 323 B 75 chains (1105 residues) following loop building 19 chains (765 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16486 restraints for refining 11475 atoms. 9189 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2315 (Rfree = 0.000) for 11475 atoms. Found 90 (90 requested) and removed 105 (75 requested) atoms. Cycle 27: After refmac, R = 0.2179 (Rfree = 0.000) for 11416 atoms. Found 87 (87 requested) and removed 87 (75 requested) atoms. Cycle 28: After refmac, R = 0.2166 (Rfree = 0.000) for 11393 atoms. Found 83 (83 requested) and removed 77 (74 requested) atoms. Cycle 29: After refmac, R = 0.2125 (Rfree = 0.000) for 11381 atoms. Found 80 (80 requested) and removed 80 (74 requested) atoms. Cycle 30: After refmac, R = 0.2082 (Rfree = 0.000) for 11368 atoms. Found 77 (77 requested) and removed 100 (74 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.88 2.62 Search for helices and strands: 0 residues in 0 chains, 11739 seeds are put forward NCS extension: 372 residues added (497 deleted due to clashes), 12111 seeds are put forward Round 1: 1087 peptides, 77 chains. Longest chain 66 peptides. Score 0.749 Round 2: 1119 peptides, 76 chains. Longest chain 94 peptides. Score 0.764 Round 3: 1149 peptides, 78 chains. Longest chain 54 peptides. Score 0.772 Round 4: 1126 peptides, 77 chains. Longest chain 47 peptides. Score 0.765 Round 5: 1111 peptides, 79 chains. Longest chain 110 peptides. Score 0.755 Taking the results from Round 3 Chains 87, Residues 1071, Estimated correctness of the model 86.2 % 29 chains (748 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 83 A Built loop between residues 103 A and 108 A Built loop between residues 143 A and 147 A Built loop between residues 183 A and 192 A Built loop between residues 269 A and 272 A Built loop between residues 300 A and 303 A Built loop between residues 129 C and 132 C Built loop between residues 142 C and 149 C Built loop between residues 67 B and 70 B Built loop between residues 114 B and 117 B Built loop between residues 144 B and 152 B Built loop between residues 100 D and 109 D Built loop between residues 140 D and 146 D 70 chains (1115 residues) following loop building 16 chains (801 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16051 restraints for refining 11474 atoms. 8541 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2395 (Rfree = 0.000) for 11474 atoms. Found 75 (75 requested) and removed 117 (75 requested) atoms. Cycle 32: After refmac, R = 0.2271 (Rfree = 0.000) for 11383 atoms. Found 75 (75 requested) and removed 97 (75 requested) atoms. Cycle 33: After refmac, R = 0.2214 (Rfree = 0.000) for 11323 atoms. Found 74 (74 requested) and removed 82 (74 requested) atoms. Cycle 34: After refmac, R = 0.2169 (Rfree = 0.000) for 11293 atoms. Found 74 (74 requested) and removed 76 (74 requested) atoms. Cycle 35: After refmac, R = 0.2129 (Rfree = 0.000) for 11267 atoms. Found 74 (74 requested) and removed 76 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.90 2.64 Search for helices and strands: 0 residues in 0 chains, 11633 seeds are put forward NCS extension: 826 residues added (606 deleted due to clashes), 12459 seeds are put forward Round 1: 1085 peptides, 78 chains. Longest chain 92 peptides. Score 0.746 Round 2: 1131 peptides, 67 chains. Longest chain 76 peptides. Score 0.787 Round 3: 1116 peptides, 80 chains. Longest chain 66 peptides. Score 0.755 Round 4: 1123 peptides, 79 chains. Longest chain 104 peptides. Score 0.760 Round 5: 1119 peptides, 82 chains. Longest chain 83 peptides. Score 0.752 Taking the results from Round 2 Chains 72, Residues 1064, Estimated correctness of the model 87.8 % 31 chains (835 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 80 A and 83 A Built loop between residues 124 A and 127 A Built loop between residues 141 A and 145 A Built loop between residues 185 A and 190 A Built loop between residues 236 A and 240 A Built loop between residues 261 A and 270 A Built loop between residues 286 A and 289 A Built loop between residues 294 A and 301 A Built loop between residues 338 A and 341 A Built loop between residues 124 C and 127 C Built loop between residues 99 B and 104 B Built loop between residues 270 B and 273 B Built loop between residues 292 B and 295 B Built loop between residues 324 B and 327 B Built loop between residues 117 D and 120 D Built loop between residues 143 D and 153 D 53 chains (1109 residues) following loop building 15 chains (890 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15248 restraints for refining 11473 atoms. 7445 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2326 (Rfree = 0.000) for 11473 atoms. Found 75 (75 requested) and removed 109 (75 requested) atoms. Cycle 37: After refmac, R = 0.2208 (Rfree = 0.000) for 11403 atoms. Found 75 (75 requested) and removed 93 (75 requested) atoms. Cycle 38: After refmac, R = 0.2137 (Rfree = 0.000) for 11363 atoms. Found 74 (74 requested) and removed 96 (74 requested) atoms. Cycle 39: After refmac, R = 0.2114 (Rfree = 0.000) for 11324 atoms. Found 74 (74 requested) and removed 85 (74 requested) atoms. Cycle 40: After refmac, R = 0.2066 (Rfree = 0.000) for 11297 atoms. Found 74 (74 requested) and removed 80 (74 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11655 seeds are put forward NCS extension: 1325 residues added (1191 deleted due to clashes), 12980 seeds are put forward Round 1: 1082 peptides, 75 chains. Longest chain 86 peptides. Score 0.751 Round 2: 1118 peptides, 71 chains. Longest chain 87 peptides. Score 0.774 Round 3: 1151 peptides, 85 chains. Longest chain 96 peptides. Score 0.759 Round 4: 1133 peptides, 79 chains. Longest chain 66 peptides. Score 0.764 Round 5: 1158 peptides, 79 chains. Longest chain 80 peptides. Score 0.774 Taking the results from Round 5 Chains 87, Residues 1079, Estimated correctness of the model 86.4 % 28 chains (714 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 48 A Built loop between residues 79 A and 86 A Built loop between residues 124 A and 133 A Built loop between residues 140 A and 144 A Built loop between residues 189 A and 192 A Built loop between residues 238 A and 249 A Built loop between residues 294 A and 297 A Built loop between residues 78 C and 84 C Built loop between residues 94 C and 100 C Built loop between residues 44 B and 47 B 72 chains (1106 residues) following loop building 18 chains (759 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16934 restraints for refining 11475 atoms. 9732 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2382 (Rfree = 0.000) for 11475 atoms. Found 75 (75 requested) and removed 108 (75 requested) atoms. Cycle 42: After refmac, R = 0.2234 (Rfree = 0.000) for 11413 atoms. Found 75 (75 requested) and removed 90 (75 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2205 (Rfree = 0.000) for 11374 atoms. Found 74 (74 requested) and removed 78 (74 requested) atoms. Cycle 44: After refmac, R = 0.2141 (Rfree = 0.000) for 11350 atoms. Found 74 (74 requested) and removed 77 (74 requested) atoms. Cycle 45: After refmac, R = 0.2105 (Rfree = 0.000) for 11331 atoms. Found 74 (74 requested) and removed 77 (74 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11706 seeds are put forward NCS extension: 572 residues added (544 deleted due to clashes), 12278 seeds are put forward Round 1: 1097 peptides, 81 chains. Longest chain 68 peptides. Score 0.745 Round 2: 1115 peptides, 72 chains. Longest chain 122 peptides. Score 0.771 Round 3: 1122 peptides, 78 chains. Longest chain 79 peptides. Score 0.762 Round 4: 1118 peptides, 81 chains. Longest chain 71 peptides. Score 0.754 Round 5: 1106 peptides, 79 chains. Longest chain 62 peptides. Score 0.753 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 79, Residues 1043, Estimated correctness of the model 86.1 % 25 chains (735 residues) have been docked in sequence Sequence coverage is 70 % Consider running further cycles of model building using 1vl6-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 126 A and 132 A Built loop between residues 140 A and 144 A Built loop between residues 238 A and 241 A Built loop between residues 262 A and 267 A Built loop between residues 358 C and 361 C Built loop between residues 131 B and 135 B Built loop between residues 143 B and 155 B Built loop between residues 182 B and 185 B 68 chains (1072 residues) following loop building 16 chains (769 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 47203 reflections ( 99.93 % complete ) and 16636 restraints for refining 11473 atoms. 9450 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2278 (Rfree = 0.000) for 11473 atoms. Found 0 (75 requested) and removed 47 (75 requested) atoms. Cycle 47: After refmac, R = 0.2205 (Rfree = 0.000) for 11396 atoms. Found 0 (75 requested) and removed 43 (75 requested) atoms. Cycle 48: After refmac, R = 0.2167 (Rfree = 0.000) for 11338 atoms. Found 0 (74 requested) and removed 45 (74 requested) atoms. Cycle 49: After refmac, R = 0.2106 (Rfree = 0.000) for 11281 atoms. TimeTaking 156.35