Mon 24 Dec 07:58:47 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 1vkd-2.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-2.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-2.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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/1vkd-2.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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 07:58:52 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/1vkd-2.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-2.6-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 1921 and 0 Target number of residues in the AU: 1921 Target solvent content: 0.5377 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-2.6-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: 19 Cell parameters: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-2.6-parrot-noncs.fasta_lf Building free atoms model in initial map for 16224 target number of atoms Had to go as low as 0.65 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. 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: 127.440 2.600 Wilson plot Bfac: 32.25 69678 reflections ( 99.15 % complete ) and 0 restraints for refining 18095 atoms. Observations/parameters ratio is 0.96 ------------------------------------------------------ Starting model: R = 0.3327 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2458 (Rfree = 0.000) for 18095 atoms. Found 149 (293 requested) and removed 191 (146 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.46 2.43 NCS extension: 0 residues added, 18053 seeds are put forward Round 1: 1054 peptides, 208 chains. Longest chain 14 peptides. Score 0.341 Round 2: 1174 peptides, 183 chains. Longest chain 23 peptides. Score 0.495 Round 3: 1305 peptides, 180 chains. Longest chain 28 peptides. Score 0.580 Round 4: 1367 peptides, 174 chains. Longest chain 36 peptides. Score 0.626 Round 5: 1408 peptides, 169 chains. Longest chain 32 peptides. Score 0.656 Taking the results from Round 5 Chains 183, Residues 1239, Estimated correctness of the model 76.8 % 25 chains (337 residues) have been docked in sequence ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 6151 restraints for refining 15238 atoms. Observations/parameters ratio is 1.14 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2805 (Rfree = 0.000) for 15238 atoms. Found 247 (247 requested) and removed 159 (123 requested) atoms. Cycle 2: After refmac, R = 0.2591 (Rfree = 0.000) for 15326 atoms. Found 144 (248 requested) and removed 136 (124 requested) atoms. Cycle 3: After refmac, R = 0.2489 (Rfree = 0.000) for 15334 atoms. Found 92 (248 requested) and removed 128 (124 requested) atoms. Cycle 4: After refmac, R = 0.2426 (Rfree = 0.000) for 15298 atoms. Found 69 (248 requested) and removed 125 (124 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2392 (Rfree = 0.000) for 15242 atoms. Found 69 (247 requested) and removed 129 (123 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.47 2.44 NCS extension: 184 residues added (61 deleted due to clashes), 15453 seeds are put forward Round 1: 1357 peptides, 156 chains. Longest chain 79 peptides. Score 0.660 Round 2: 1441 peptides, 145 chains. Longest chain 73 peptides. Score 0.717 Round 3: 1422 peptides, 147 chains. Longest chain 73 peptides. Score 0.706 Round 4: 1478 peptides, 143 chains. Longest chain 73 peptides. Score 0.735 Round 5: 1496 peptides, 140 chains. Longest chain 64 peptides. Score 0.747 Taking the results from Round 5 Chains 160, Residues 1356, Estimated correctness of the model 86.8 % 30 chains (533 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 71 A Built loop between residues 165 D and 173 D Built loop between residues 301 D and 305 D 156 chains (1369 residues) following loop building 27 chains (553 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 7685 restraints for refining 15125 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2756 (Rfree = 0.000) for 15125 atoms. Found 245 (245 requested) and removed 166 (122 requested) atoms. Cycle 7: After refmac, R = 0.2523 (Rfree = 0.000) for 15204 atoms. Found 154 (241 requested) and removed 127 (123 requested) atoms. Cycle 8: After refmac, R = 0.2427 (Rfree = 0.000) for 15231 atoms. Found 93 (237 requested) and removed 129 (123 requested) atoms. Cycle 9: After refmac, R = 0.2369 (Rfree = 0.000) for 15195 atoms. Found 83 (231 requested) and removed 127 (123 requested) atoms. Cycle 10: After refmac, R = 0.2401 (Rfree = 0.000) for 15151 atoms. Found 88 (225 requested) and removed 126 (122 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.48 2.45 NCS extension: 496 residues added (335 deleted due to clashes), 15708 seeds are put forward Round 1: 1400 peptides, 150 chains. Longest chain 43 peptides. Score 0.691 Round 2: 1450 peptides, 134 chains. Longest chain 55 peptides. Score 0.741 Round 3: 1469 peptides, 138 chains. Longest chain 83 peptides. Score 0.740 Round 4: 1465 peptides, 131 chains. Longest chain 63 peptides. Score 0.751 Round 5: 1484 peptides, 130 chains. Longest chain 67 peptides. Score 0.759 Taking the results from Round 5 Chains 139, Residues 1354, Estimated correctness of the model 87.9 % 27 chains (605 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 38 A and 45 A Built loop between residues 183 A and 192 A Built loop between residues 279 A and 282 A Built loop between residues 261 C and 267 C Built loop between residues 302 D and 310 D 132 chains (1377 residues) following loop building 22 chains (633 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 8114 restraints for refining 15125 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2706 (Rfree = 0.000) for 15125 atoms. Found 220 (220 requested) and removed 162 (122 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2477 (Rfree = 0.000) for 15183 atoms. Found 128 (216 requested) and removed 132 (123 requested) atoms. Cycle 13: After refmac, R = 0.2382 (Rfree = 0.000) for 15179 atoms. Found 63 (212 requested) and removed 124 (123 requested) atoms. Cycle 14: After refmac, R = 0.2342 (Rfree = 0.000) for 15118 atoms. Found 74 (206 requested) and removed 122 (122 requested) atoms. Cycle 15: After refmac, R = 0.2320 (Rfree = 0.000) for 15070 atoms. Found 74 (200 requested) and removed 122 (122 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.48 2.45 NCS extension: 466 residues added (425 deleted due to clashes), 15556 seeds are put forward Round 1: 1384 peptides, 142 chains. Longest chain 42 peptides. Score 0.700 Round 2: 1466 peptides, 126 chains. Longest chain 64 peptides. Score 0.760 Round 3: 1463 peptides, 125 chains. Longest chain 40 peptides. Score 0.760 Round 4: 1496 peptides, 115 chains. Longest chain 70 peptides. Score 0.787 Round 5: 1456 peptides, 121 chains. Longest chain 64 peptides. Score 0.765 Taking the results from Round 4 Chains 126, Residues 1381, Estimated correctness of the model 90.3 % 28 chains (680 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 67 A Built loop between residues 261 A and 267 A Built loop between residues 244 B and 252 B Built loop between residues 263 F and 267 F 119 chains (1393 residues) following loop building 24 chains (699 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 8451 restraints for refining 15125 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2619 (Rfree = 0.000) for 15125 atoms. Found 196 (196 requested) and removed 165 (122 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2454 (Rfree = 0.000) for 15156 atoms. Found 132 (191 requested) and removed 125 (122 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2354 (Rfree = 0.000) for 15163 atoms. Found 82 (186 requested) and removed 122 (122 requested) atoms. Cycle 19: After refmac, R = 0.2317 (Rfree = 0.000) for 15123 atoms. Found 77 (181 requested) and removed 123 (122 requested) atoms. Cycle 20: After refmac, R = 0.2303 (Rfree = 0.000) for 15077 atoms. Found 75 (176 requested) and removed 123 (122 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.46 2.43 NCS extension: 574 residues added (512 deleted due to clashes), 15654 seeds are put forward Round 1: 1412 peptides, 125 chains. Longest chain 88 peptides. Score 0.743 Round 2: 1477 peptides, 105 chains. Longest chain 80 peptides. Score 0.797 Round 3: 1499 peptides, 111 chains. Longest chain 105 peptides. Score 0.794 Round 4: 1509 peptides, 113 chains. Longest chain 86 peptides. Score 0.794 Round 5: 1516 peptides, 113 chains. Longest chain 76 peptides. Score 0.796 Taking the results from Round 2 Chains 122, Residues 1372, Estimated correctness of the model 91.2 % 35 chains (818 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 63 A and 68 A Built loop between residues 142 A and 148 A Built loop between residues 279 A and 282 A Built loop between residues 257 B and 267 B Built loop between residues 301 B and 306 B Built loop between residues 63 D and 73 D Built loop between residues 159 D and 163 D 111 chains (1397 residues) following loop building 28 chains (854 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 9202 restraints for refining 15204 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2594 (Rfree = 0.000) for 15204 atoms. Found 172 (172 requested) and removed 161 (123 requested) atoms. Cycle 22: After refmac, R = 0.2432 (Rfree = 0.000) for 15215 atoms. Found 130 (167 requested) and removed 123 (123 requested) atoms. Cycle 23: After refmac, R = 0.2356 (Rfree = 0.000) for 15222 atoms. Found 97 (162 requested) and removed 123 (123 requested) atoms. Cycle 24: After refmac, R = 0.2301 (Rfree = 0.000) for 15196 atoms. Found 75 (157 requested) and removed 123 (123 requested) atoms. Cycle 25: After refmac, R = 0.2284 (Rfree = 0.000) for 15148 atoms. Found 72 (152 requested) and removed 123 (122 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.49 2.46 NCS extension: 539 residues added (506 deleted due to clashes), 15659 seeds are put forward Round 1: 1413 peptides, 115 chains. Longest chain 86 peptides. Score 0.760 Round 2: 1469 peptides, 99 chains. Longest chain 107 peptides. Score 0.803 Round 3: 1482 peptides, 113 chains. Longest chain 64 peptides. Score 0.786 Round 4: 1466 peptides, 111 chains. Longest chain 75 peptides. Score 0.784 Round 5: 1474 peptides, 112 chains. Longest chain 65 peptides. Score 0.785 Taking the results from Round 2 Chains 109, Residues 1370, Estimated correctness of the model 91.6 % 27 chains (820 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 264 A and 267 A Built loop between residues 301 A and 306 A Built loop between residues 262 D and 265 D 105 chains (1380 residues) following loop building 23 chains (830 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 9015 restraints for refining 15138 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2494 (Rfree = 0.000) for 15138 atoms. Found 147 (147 requested) and removed 157 (122 requested) atoms. Cycle 27: After refmac, R = 0.2371 (Rfree = 0.000) for 15128 atoms. Found 119 (142 requested) and removed 122 (122 requested) atoms. Cycle 28: After refmac, R = 0.2315 (Rfree = 0.000) for 15125 atoms. Found 71 (137 requested) and removed 122 (122 requested) atoms. Cycle 29: After refmac, R = 0.2293 (Rfree = 0.000) for 15074 atoms. Found 54 (132 requested) and removed 125 (122 requested) atoms. Cycle 30: After refmac, R = 0.2270 (Rfree = 0.000) for 15003 atoms. Found 74 (126 requested) and removed 114 (121 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.48 2.45 NCS extension: 683 residues added (553 deleted due to clashes), 15663 seeds are put forward Round 1: 1402 peptides, 115 chains. Longest chain 94 peptides. Score 0.756 Round 2: 1457 peptides, 110 chains. Longest chain 100 peptides. Score 0.783 Round 3: 1467 peptides, 105 chains. Longest chain 94 peptides. Score 0.794 Round 4: 1466 peptides, 109 chains. Longest chain 63 peptides. Score 0.787 Round 5: 1475 peptides, 110 chains. Longest chain 96 peptides. Score 0.788 Taking the results from Round 3 Chains 122, Residues 1362, Estimated correctness of the model 90.9 % 32 chains (739 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 264 A and 267 A Built loop between residues 300 B and 304 B Built loop between residues 55 E and 66 E Built loop between residues 266 E and 269 E Built loop between residues 282 E and 287 E Built loop between residues 53 D and 63 D 114 chains (1375 residues) following loop building 26 chains (769 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 69678 reflections ( 99.15 % complete ) and 8595 restraints for refining 15125 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2554 (Rfree = 0.000) for 15125 atoms. Found 122 (122 requested) and removed 160 (122 requested) atoms. Cycle 32: After refmac, R = 0.2391 (Rfree = 0.000) for 15087 atoms. Found 122 (122 requested) and removed 124 (122 requested) atoms. Cycle 33: After refmac, R = 0.2322 (Rfree = 0.000) for 15085 atoms. Found 99 (122 requested) and removed 122 (122 requested) atoms. Cycle 34: After refmac, R = 0.2284 (Rfree = 0.000) for 15062 atoms. Found 84 (122 requested) and removed 123 (122 requested) atoms. Cycle 35: After refmac, R = 0.2261 (Rfree = 0.000) for 15023 atoms. Found 80 (121 requested) and removed 110 (121 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.48 2.45 NCS extension: 371 residues added (532 deleted due to clashes), 15429 seeds are put forward Round 1: 1387 peptides, 110 chains. Longest chain 95 peptides. Score 0.760 Round 2: 1480 peptides, 104 chains. Longest chain 114 peptides. Score 0.799 Round 3: 1448 peptides, 102 chains. Longest chain 114 peptides. Score 0.792 Round 4: 1486 peptides, 110 chains. Longest chain 71 peptides. Score 0.792 Round 5: 1460 peptides, 111 chains. Longest chain 72 peptides. Score 0.782 Taking the results from Round 2 Chains 113, Residues 1376, Estimated correctness of the model 91.3 % 24 chains (725 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 A and 71 A Built loop between residues 106 A and 117 A Built loop between residues 135 A and 140 A Built loop between residues 216 A and 219 A Built loop between residues 248 A and 259 A Built loop between residues 265 C and 268 C Built loop between residues 226 B and 233 B Built loop between residues 233 F and 238 F 101 chains (1396 residues) following loop building 16 chains (765 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 8780 restraints for refining 15125 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2458 (Rfree = 0.000) for 15125 atoms. Found 122 (122 requested) and removed 147 (122 requested) atoms. Cycle 37: After refmac, R = 0.2345 (Rfree = 0.000) for 15100 atoms. Found 122 (122 requested) and removed 123 (122 requested) atoms. Cycle 38: After refmac, R = 0.2288 (Rfree = 0.000) for 15099 atoms. Found 100 (122 requested) and removed 123 (122 requested) atoms. Cycle 39: After refmac, R = 0.2265 (Rfree = 0.000) for 15076 atoms. Found 91 (122 requested) and removed 109 (122 requested) atoms. Cycle 40: After refmac, R = 0.2240 (Rfree = 0.000) for 15058 atoms. Found 90 (122 requested) and removed 106 (122 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.47 2.44 NCS extension: 674 residues added (728 deleted due to clashes), 15751 seeds are put forward Round 1: 1387 peptides, 123 chains. Longest chain 73 peptides. Score 0.737 Round 2: 1476 peptides, 99 chains. Longest chain 95 peptides. Score 0.805 Round 3: 1480 peptides, 107 chains. Longest chain 98 peptides. Score 0.794 Round 4: 1478 peptides, 105 chains. Longest chain 70 peptides. Score 0.797 Round 5: 1479 peptides, 114 chains. Longest chain 71 peptides. Score 0.783 Taking the results from Round 2 Chains 112, Residues 1377, Estimated correctness of the model 91.8 % 32 chains (857 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 198 A and 209 A Built loop between residues 227 A and 236 A Built loop between residues 302 A and 307 A Built loop between residues 214 C and 222 C Built loop between residues 63 B and 67 B Built loop between residues 264 E and 267 E Built loop between residues 229 D and 233 D Built loop between residues 282 D and 285 D Built loop between residues 299 F and 303 F 100 chains (1413 residues) following loop building 23 chains (899 residues) in sequence following loop building ------------------------------------------------------ 69678 reflections ( 99.15 % complete ) and 9492 restraints for refining 15271 atoms. Observations/parameters ratio is 1.14 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2498 (Rfree = 0.000) for 15271 atoms. Found 123 (123 requested) and removed 170 (123 requested) atoms. Cycle 42: After refmac, R = 0.2382 (Rfree = 0.000) for 15224 atoms. Found 123 (123 requested) and removed 124 (123 requested) atoms. Cycle 43: After refmac, R = 0.2326 (Rfree = 0.000) for 15223 atoms. Found 90 (123 requested) and removed 125 (123 requested) atoms. Cycle 44: After refmac, R = 0.2290 (Rfree = 0.000) for 15188 atoms. Found 102 (123 requested) and removed 125 (123 requested) atoms. Cycle 45: After refmac, R = 0.2268 (Rfree = 0.000) for 15165 atoms. Found 83 (122 requested) and removed 122 (122 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.48 2.45 NCS extension: 694 residues added (600 deleted due to clashes), 15848 seeds are put forward Round 1: 1389 peptides, 120 chains. Longest chain 97 peptides. Score 0.743 Round 2: 1460 peptides, 100 chains. Longest chain 72 peptides. Score 0.799 Round 3: 1470 peptides, 103 chains. Longest chain 73 peptides. Score 0.798 Round 4: 1464 peptides, 98 chains. Longest chain 102 peptides. Score 0.803 Round 5: 1438 peptides, 115 chains. Longest chain 62 peptides. Score 0.769 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 111, Residues 1366, Estimated correctness of the model 91.6 % 31 chains (860 residues) have been docked in sequence Sequence coverage is 62 % Consider running further cycles of model building using 1vkd-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 134 A and 140 A Built loop between residues 227 A and 231 A Built loop between residues 248 A and 251 A Built loop between residues 214 C and 222 C Built loop between residues 217 B and 230 B Built loop between residues 98 D and 107 D Built loop between residues 227 D and 230 D Built loop between residues 316 D and 322 D Built loop between residues 226 F and 229 F 98 chains (1400 residues) following loop building 22 chains (906 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 69678 reflections ( 99.15 % complete ) and 9441 restraints for refining 15125 atoms. Observations/parameters ratio is 1.15 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2533 (Rfree = 0.000) for 15125 atoms. Found 0 (122 requested) and removed 27 (122 requested) atoms. Cycle 47: After refmac, R = 0.2459 (Rfree = 0.000) for 15098 atoms. Found 0 (122 requested) and removed 4 (122 requested) atoms. Cycle 48: After refmac, R = 0.2444 (Rfree = 0.000) for 15094 atoms. Found 0 (122 requested) and removed 8 (122 requested) atoms. Cycle 49: After refmac, R = 0.2422 (Rfree = 0.000) for 15086 atoms. TimeTaking 198.63