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 1vl6-2.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-2.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl6-2.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-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/1vl6-2.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-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 22:22:50 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/1vl6-2.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl6-2.8-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 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-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: 170 Cell parameters: 144.124 144.124 163.018 90.000 90.000 120.000 Input sequence file: 1vl6-2.8-parrot-hancs.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 = 0.3272 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2681 (Rfree = 0.000) for 13925 atoms. Found 182 (182 requested) and removed 139 (91 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 14236 seeds are put forward NCS extension: 0 residues added, 14236 seeds are put forward Round 1: 931 peptides, 134 chains. Longest chain 19 peptides. Score 0.510 Round 2: 1065 peptides, 112 chains. Longest chain 43 peptides. Score 0.657 Round 3: 1128 peptides, 105 chains. Longest chain 47 peptides. Score 0.706 Round 4: 1158 peptides, 90 chains. Longest chain 56 peptides. Score 0.752 Round 5: 1151 peptides, 82 chains. Longest chain 51 peptides. Score 0.765 Taking the results from Round 5 Chains 96, Residues 1069, Estimated correctness of the model 85.4 % 32 chains (655 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 99 A and 103 A Built loop between residues 125 A and 129 A Built loop between residues 183 A and 188 A Built loop between residues 78 B and 88 B Built loop between residues 106 B and 109 B Built loop between residues 197 B and 200 B Built loop between residues 233 B and 238 B Built loop between residues 251 B and 254 B Built loop between residues 376 B and 379 B 84 chains (1091 residues) following loop building 23 chains (686 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 17253 restraints for refining 11461 atoms. 10320 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2830 (Rfree = 0.000) for 11461 atoms. Found 150 (150 requested) and removed 154 (75 requested) atoms. Cycle 2: After refmac, R = 0.2670 (Rfree = 0.000) for 11242 atoms. Found 147 (147 requested) and removed 110 (75 requested) atoms. Cycle 3: After refmac, R = 0.2575 (Rfree = 0.000) for 11169 atoms. Found 142 (142 requested) and removed 98 (74 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2493 (Rfree = 0.000) for 11143 atoms. Found 111 (138 requested) and removed 88 (73 requested) atoms. Cycle 5: After refmac, R = 0.2460 (Rfree = 0.000) for 11116 atoms. Found 127 (134 requested) and removed 88 (73 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.90 2.64 Search for helices and strands: 0 residues in 0 chains, 11513 seeds are put forward NCS extension: 461 residues added (380 deleted due to clashes), 11974 seeds are put forward Round 1: 1118 peptides, 83 chains. Longest chain 67 peptides. Score 0.750 Round 2: 1182 peptides, 81 chains. Longest chain 50 peptides. Score 0.779 Round 3: 1183 peptides, 87 chains. Longest chain 60 peptides. Score 0.768 Round 4: 1183 peptides, 84 chains. Longest chain 46 peptides. Score 0.774 Round 5: 1171 peptides, 89 chains. Longest chain 61 peptides. Score 0.759 Taking the results from Round 2 Chains 92, Residues 1101, Estimated correctness of the model 86.9 % 35 chains (764 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 61 A Built loop between residues 107 A and 117 A Built loop between residues 141 A and 144 A Built loop between residues 181 A and 184 A Built loop between residues 326 A and 331 A Built loop between residues 55 C and 58 C Built loop between residues 45 B and 52 B Built loop between residues 58 B and 63 B Built loop between residues 370 B and 375 B Built loop between residues 143 D and 149 D 77 chains (1131 residues) following loop building 25 chains (806 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16211 restraints for refining 11470 atoms. 8697 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2500 (Rfree = 0.000) for 11470 atoms. Found 127 (135 requested) and removed 125 (75 requested) atoms. Cycle 7: After refmac, R = 0.2309 (Rfree = 0.000) for 11371 atoms. Found 89 (132 requested) and removed 110 (75 requested) atoms. Cycle 8: After refmac, R = 0.2233 (Rfree = 0.000) for 11299 atoms. Found 74 (128 requested) and removed 84 (74 requested) atoms. Cycle 9: After refmac, R = 0.2202 (Rfree = 0.000) for 11256 atoms. Found 67 (124 requested) and removed 82 (74 requested) atoms. Cycle 10: After refmac, R = 0.2165 (Rfree = 0.000) for 11223 atoms. Found 66 (121 requested) and removed 75 (73 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11553 seeds are put forward NCS extension: 357 residues added (646 deleted due to clashes), 11910 seeds are put forward Round 1: 1138 peptides, 84 chains. Longest chain 51 peptides. Score 0.756 Round 2: 1183 peptides, 80 chains. Longest chain 56 peptides. Score 0.781 Round 3: 1170 peptides, 86 chains. Longest chain 112 peptides. Score 0.765 Round 4: 1167 peptides, 90 chains. Longest chain 62 peptides. Score 0.755 Round 5: 1179 peptides, 83 chains. Longest chain 64 peptides. Score 0.774 Taking the results from Round 2 Chains 85, Residues 1103, Estimated correctness of the model 87.2 % 32 chains (807 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 53 A Built loop between residues 60 A and 63 A Built loop between residues 81 A and 91 A Built loop between residues 145 A and 148 A Built loop between residues 197 A and 200 A Built loop between residues 213 A and 216 A Built loop between residues 241 A and 244 A Built loop between residues 293 A and 297 A Built loop between residues 320 A and 327 A Built loop between residues 363 A and 366 A Built loop between residues 45 C and 48 C Built loop between residues 140 C and 143 C Built loop between residues 183 B and 186 B Built loop between residues 206 B and 209 B 68 chains (1140 residues) following loop building 18 chains (853 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15988 restraints for refining 11474 atoms. 8195 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2443 (Rfree = 0.000) for 11474 atoms. Found 116 (120 requested) and removed 119 (75 requested) atoms. Cycle 12: After refmac, R = 0.2304 (Rfree = 0.000) for 11425 atoms. Found 95 (117 requested) and removed 91 (75 requested) atoms. Cycle 13: After refmac, R = 0.2225 (Rfree = 0.000) for 11394 atoms. Found 92 (114 requested) and removed 83 (75 requested) atoms. Cycle 14: After refmac, R = 0.2203 (Rfree = 0.000) for 11388 atoms. Found 73 (110 requested) and removed 81 (74 requested) atoms. Cycle 15: After refmac, R = 0.2048 (Rfree = 0.000) for 11361 atoms. Found 37 (107 requested) and removed 80 (74 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11640 seeds are put forward NCS extension: 2037 residues added (1833 deleted due to clashes), 13677 seeds are put forward Round 1: 1166 peptides, 76 chains. Longest chain 79 peptides. Score 0.783 Round 2: 1195 peptides, 77 chains. Longest chain 62 peptides. Score 0.791 Round 3: 1186 peptides, 81 chains. Longest chain 53 peptides. Score 0.780 Round 4: 1169 peptides, 79 chains. Longest chain 92 peptides. Score 0.778 Round 5: 1175 peptides, 93 chains. Longest chain 64 peptides. Score 0.753 Taking the results from Round 2 Chains 87, Residues 1118, Estimated correctness of the model 88.2 % 33 chains (799 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 47 A Built loop between residues 61 A and 64 A Built loop between residues 189 A and 200 A Built loop between residues 213 A and 216 A Built loop between residues 242 A and 245 A Built loop between residues 294 A and 298 A Built loop between residues 323 A and 327 A Built loop between residues 79 C and 84 C Built loop between residues 144 C and 148 C Built loop between residues 80 B and 90 B Built loop between residues 96 B and 101 B Built loop between residues 125 B and 129 B Built loop between residues 140 B and 146 B Built loop between residues 186 B and 189 B Built loop between residues 267 B and 270 B Built loop between residues 292 B and 297 B Built loop between residues 319 B and 323 B Built loop between residues 349 B and 359 B Built loop between residues 141 D and 146 D 59 chains (1171 residues) following loop building 14 chains (875 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15635 restraints for refining 11474 atoms. 7649 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2388 (Rfree = 0.000) for 11474 atoms. Found 105 (105 requested) and removed 106 (75 requested) atoms. Cycle 17: After refmac, R = 0.2200 (Rfree = 0.000) for 11433 atoms. Found 79 (102 requested) and removed 89 (75 requested) atoms. Cycle 18: After refmac, R = 0.2168 (Rfree = 0.000) for 11391 atoms. Found 77 (98 requested) and removed 85 (74 requested) atoms. Cycle 19: After refmac, R = 0.2119 (Rfree = 0.000) for 11366 atoms. Found 95 (95 requested) and removed 76 (74 requested) atoms. Cycle 20: After refmac, R = 0.2110 (Rfree = 0.000) for 11363 atoms. Found 92 (92 requested) and removed 87 (74 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.88 2.62 Search for helices and strands: 0 residues in 0 chains, 11720 seeds are put forward NCS extension: 1100 residues added (1285 deleted due to clashes), 12820 seeds are put forward Round 1: 1158 peptides, 76 chains. Longest chain 93 peptides. Score 0.780 Round 2: 1190 peptides, 76 chains. Longest chain 69 peptides. Score 0.791 Round 3: 1198 peptides, 72 chains. Longest chain 148 peptides. Score 0.801 Round 4: 1161 peptides, 85 chains. Longest chain 79 peptides. Score 0.763 Round 5: 1160 peptides, 86 chains. Longest chain 69 peptides. Score 0.761 Taking the results from Round 3 Chains 80, Residues 1126, Estimated correctness of the model 89.2 % 31 chains (858 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 24 A and 32 A Built loop between residues 77 A and 82 A Built loop between residues 131 A and 134 A Built loop between residues 143 A and 148 A Built loop between residues 294 A and 297 A Built loop between residues 328 A and 331 A Built loop between residues 373 A and 376 A Built loop between residues 106 C and 109 C Built loop between residues 139 C and 149 C Built loop between residues 43 B and 47 B Built loop between residues 124 B and 127 B Built loop between residues 142 B and 147 B Built loop between residues 326 B and 331 B Built loop between residues 341 B and 344 B 64 chains (1164 residues) following loop building 17 chains (907 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 47203 reflections ( 99.93 % complete ) and 15290 restraints for refining 11475 atoms. 7246 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2363 (Rfree = 0.000) for 11475 atoms. Found 90 (90 requested) and removed 113 (75 requested) atoms. Cycle 22: After refmac, R = 0.2204 (Rfree = 0.000) for 11415 atoms. Found 87 (87 requested) and removed 90 (75 requested) atoms. Cycle 23: After refmac, R = 0.2148 (Rfree = 0.000) for 11395 atoms. Found 67 (83 requested) and removed 80 (74 requested) atoms. Cycle 24: After refmac, R = 0.2124 (Rfree = 0.000) for 11365 atoms. Found 65 (80 requested) and removed 82 (74 requested) atoms. Cycle 25: After refmac, R = 0.2078 (Rfree = 0.000) for 11336 atoms. Found 53 (77 requested) and removed 76 (74 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 2.64 Search for helices and strands: 0 residues in 0 chains, 11678 seeds are put forward NCS extension: 1286 residues added (1591 deleted due to clashes), 12964 seeds are put forward Round 1: 1109 peptides, 77 chains. Longest chain 86 peptides. Score 0.758 Round 2: 1170 peptides, 71 chains. Longest chain 86 peptides. Score 0.793 Round 3: 1156 peptides, 79 chains. Longest chain 51 peptides. Score 0.773 Round 4: 1176 peptides, 83 chains. Longest chain 81 peptides. Score 0.773 Round 5: 1173 peptides, 91 chains. Longest chain 59 peptides. Score 0.756 Taking the results from Round 2 Chains 80, Residues 1099, Estimated correctness of the model 88.4 % 33 chains (833 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 43 A and 47 A Built loop between residues 145 A and 148 A Built loop between residues 165 A and 169 A Built loop between residues 308 A and 317 A Built loop between residues 342 A and 345 A Built loop between residues 358 A and 365 A Built loop between residues 43 C and 49 C Built loop between residues 143 C and 147 C Built loop between residues 81 B and 87 B Built loop between residues 97 B and 100 B Built loop between residues 141 B and 147 B Built loop between residues 237 B and 240 B Built loop between residues 294 B and 303 B Built loop between residues 55 D and 62 D Built loop between residues 145 D and 151 D 59 chains (1147 residues) following loop building 18 chains (898 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15344 restraints for refining 11474 atoms. 7374 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2321 (Rfree = 0.000) for 11474 atoms. Found 75 (75 requested) and removed 100 (75 requested) atoms. Cycle 27: After refmac, R = 0.2202 (Rfree = 0.000) for 11413 atoms. Found 75 (75 requested) and removed 85 (75 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2106 (Rfree = 0.000) for 11374 atoms. Found 58 (74 requested) and removed 77 (74 requested) atoms. Cycle 29: After refmac, R = 0.2079 (Rfree = 0.000) for 11333 atoms. Found 54 (74 requested) and removed 76 (74 requested) atoms. Cycle 30: After refmac, R = 0.2083 (Rfree = 0.000) for 11301 atoms. Found 53 (74 requested) and removed 76 (74 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11638 seeds are put forward NCS extension: 515 residues added (943 deleted due to clashes), 12153 seeds are put forward Round 1: 1107 peptides, 70 chains. Longest chain 87 peptides. Score 0.772 Round 2: 1118 peptides, 82 chains. Longest chain 57 peptides. Score 0.752 Round 3: 1144 peptides, 75 chains. Longest chain 72 peptides. Score 0.776 Round 4: 1109 peptides, 87 chains. Longest chain 82 peptides. Score 0.737 Round 5: 1105 peptides, 85 chains. Longest chain 35 peptides. Score 0.740 Taking the results from Round 3 Chains 87, Residues 1069, Estimated correctness of the model 86.6 % 34 chains (814 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 49 A Built loop between residues 60 A and 63 A Built loop between residues 107 A and 113 A Built loop between residues 126 A and 133 A Built loop between residues 141 A and 144 A Built loop between residues 214 A and 217 A Built loop between residues 294 A and 299 A Built loop between residues 324 A and 327 A Built loop between residues 95 C and 99 C Built loop between residues 143 C and 149 C Built loop between residues 97 B and 102 B Built loop between residues 124 B and 127 B Built loop between residues 144 B and 148 B Built loop between residues 261 B and 264 B Built loop between residues 287 B and 298 B Built loop between residues 325 B and 328 B Built loop between residues 124 D and 127 D 67 chains (1117 residues) following loop building 17 chains (873 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 15635 restraints for refining 11475 atoms. 7864 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2293 (Rfree = 0.000) for 11475 atoms. Found 75 (75 requested) and removed 104 (75 requested) atoms. Cycle 32: After refmac, R = 0.2155 (Rfree = 0.000) for 11405 atoms. Found 75 (75 requested) and removed 87 (75 requested) atoms. Cycle 33: After refmac, R = 0.2093 (Rfree = 0.000) for 11371 atoms. Found 74 (74 requested) and removed 85 (74 requested) atoms. Cycle 34: After refmac, R = 0.2055 (Rfree = 0.000) for 11347 atoms. Found 71 (74 requested) and removed 82 (74 requested) atoms. Cycle 35: After refmac, R = 0.2028 (Rfree = 0.000) for 11319 atoms. Found 66 (74 requested) and removed 78 (74 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11690 seeds are put forward NCS extension: 340 residues added (395 deleted due to clashes), 12030 seeds are put forward Round 1: 1108 peptides, 76 chains. Longest chain 68 peptides. Score 0.760 Round 2: 1147 peptides, 76 chains. Longest chain 92 peptides. Score 0.775 Round 3: 1159 peptides, 75 chains. Longest chain 85 peptides. Score 0.782 Round 4: 1123 peptides, 80 chains. Longest chain 48 peptides. Score 0.758 Round 5: 1105 peptides, 87 chains. Longest chain 68 peptides. Score 0.736 Taking the results from Round 3 Chains 79, Residues 1084, Estimated correctness of the model 87.3 % 30 chains (793 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 127 A Built loop between residues 197 A and 208 A Built loop between residues 37 C and 48 C Built loop between residues 308 C and 317 C Built loop between residues 60 B and 63 B Built loop between residues 182 B and 191 B Built loop between residues 203 B and 207 B Built loop between residues 242 B and 245 B Built loop between residues 359 B and 362 B 65 chains (1113 residues) following loop building 21 chains (841 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16049 restraints for refining 11474 atoms. 8410 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2259 (Rfree = 0.000) for 11474 atoms. Found 75 (75 requested) and removed 116 (75 requested) atoms. Cycle 37: After refmac, R = 0.2103 (Rfree = 0.000) for 11398 atoms. Found 75 (75 requested) and removed 91 (75 requested) atoms. Cycle 38: After refmac, R = 0.2066 (Rfree = 0.000) for 11366 atoms. Found 74 (74 requested) and removed 80 (74 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2051 (Rfree = 0.000) for 11337 atoms. Found 74 (74 requested) and removed 81 (74 requested) atoms. Cycle 40: After refmac, R = 0.2043 (Rfree = 0.000) for 11320 atoms. Found 74 (74 requested) and removed 77 (74 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.89 2.63 Search for helices and strands: 0 residues in 0 chains, 11682 seeds are put forward NCS extension: 590 residues added (986 deleted due to clashes), 12272 seeds are put forward Round 1: 1115 peptides, 80 chains. Longest chain 46 peptides. Score 0.755 Round 2: 1158 peptides, 68 chains. Longest chain 92 peptides. Score 0.795 Round 3: 1159 peptides, 77 chains. Longest chain 74 peptides. Score 0.778 Round 4: 1165 peptides, 78 chains. Longest chain 87 peptides. Score 0.778 Round 5: 1132 peptides, 89 chains. Longest chain 48 peptides. Score 0.743 Taking the results from Round 2 Chains 83, Residues 1090, Estimated correctness of the model 88.6 % 28 chains (781 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 165 A and 168 A Built loop between residues 173 C and 176 C Built loop between residues 357 C and 360 C Built loop between residues 81 B and 86 B Built loop between residues 145 B and 148 B Built loop between residues 182 B and 185 B Built loop between residues 267 B and 272 B Built loop between residues 293 B and 297 B Built loop between residues 142 D and 149 D 72 chains (1111 residues) following loop building 19 chains (808 residues) in sequence following loop building ------------------------------------------------------ 47203 reflections ( 99.93 % complete ) and 16551 restraints for refining 11475 atoms. 9112 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2235 (Rfree = 0.000) for 11475 atoms. Found 75 (75 requested) and removed 105 (75 requested) atoms. Cycle 42: After refmac, R = 0.2143 (Rfree = 0.000) for 11415 atoms. Found 75 (75 requested) and removed 100 (75 requested) atoms. Cycle 43: After refmac, R = 0.2099 (Rfree = 0.000) for 11379 atoms. Found 74 (74 requested) and removed 78 (74 requested) atoms. Cycle 44: After refmac, R = 0.2054 (Rfree = 0.000) for 11367 atoms. Found 74 (74 requested) and removed 83 (74 requested) atoms. Cycle 45: After refmac, R = 0.2032 (Rfree = 0.000) for 11350 atoms. Found 74 (74 requested) and removed 81 (74 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.88 2.62 Search for helices and strands: 0 residues in 0 chains, 11702 seeds are put forward NCS extension: 723 residues added (933 deleted due to clashes), 12425 seeds are put forward Round 1: 1111 peptides, 73 chains. Longest chain 92 peptides. Score 0.767 Round 2: 1154 peptides, 74 chains. Longest chain 99 peptides. Score 0.782 Round 3: 1170 peptides, 75 chains. Longest chain 78 peptides. Score 0.786 Round 4: 1139 peptides, 82 chains. Longest chain 48 peptides. Score 0.760 Round 5: 1128 peptides, 72 chains. Longest chain 52 peptides. Score 0.776 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 85, Residues 1095, Estimated correctness of the model 87.7 % 31 chains (756 residues) have been docked in sequence Sequence coverage is 68 % Consider running further cycles of model building using 1vl6-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 44 A and 48 A Built loop between residues 127 A and 132 A Built loop between residues 140 A and 143 A Built loop between residues 185 A and 197 A Built loop between residues 205 A and 208 A Built loop between residues 229 A and 232 A Built loop between residues 270 A and 273 A Built loop between residues 324 A and 327 A Built loop between residues 357 A and 367 A Built loop between residues 80 C and 90 C Built loop between residues 141 C and 149 C Built loop between residues 66 B and 69 B Built loop between residues 81 B and 85 B Built loop between residues 96 B and 99 B Built loop between residues 121 B and 130 B Built loop between residues 144 B and 148 B Built loop between residues 294 B and 297 B Built loop between residues 331 B and 334 B Built loop between residues 359 B and 362 B 60 chains (1149 residues) following loop building 12 chains (833 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 47203 reflections ( 99.93 % complete ) and 15819 restraints for refining 11473 atoms. 8125 conditional restraints added. Observations/parameters ratio is 1.03 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2356 (Rfree = 0.000) for 11473 atoms. Found 0 (75 requested) and removed 51 (75 requested) atoms. Cycle 47: After refmac, R = 0.2220 (Rfree = 0.000) for 11386 atoms. Found 0 (74 requested) and removed 22 (74 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2198 (Rfree = 0.000) for 11338 atoms. Found 0 (74 requested) and removed 30 (74 requested) atoms. Cycle 49: After refmac, R = 0.2128 (Rfree = 0.000) for 11301 atoms. TimeTaking 194.57