null Mon 24 Dec 01:08:35 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 1vkd-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkd-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 01:08:39 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/1vkd-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1743 and 0 Target number of residues in the AU: 1743 Target solvent content: 0.5806 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-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.2-parrot-mrncs.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 3.200 Wilson plot Bfac: 45.23 37988 reflections ( 99.76 % complete ) and 0 restraints for refining 18041 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2842 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2288 (Rfree = 0.000) for 18041 atoms. Found 153 (161 requested) and removed 122 (80 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.89 2.85 Search for helices and strands: 0 residues in 0 chains, 18253 seeds are put forward NCS extension: 0 residues added, 18253 seeds are put forward Round 1: 1209 peptides, 189 chains. Longest chain 18 peptides. Score 0.501 Round 2: 1481 peptides, 163 chains. Longest chain 30 peptides. Score 0.700 Round 3: 1489 peptides, 145 chains. Longest chain 33 peptides. Score 0.736 Round 4: 1586 peptides, 137 chains. Longest chain 42 peptides. Score 0.781 Round 5: 1581 peptides, 133 chains. Longest chain 60 peptides. Score 0.786 Taking the results from Round 5 Chains 153, Residues 1448, Estimated correctness of the model 81.2 % 36 chains (678 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 160 A and 165 A Built loop between residues 290 B and 298 B Built loop between residues 261 E and 267 E Built loop between residues 282 E and 292 E Built loop between residues 160 D and 163 D Built loop between residues 183 D and 193 D Built loop between residues 280 F and 287 F 139 chains (1465 residues) following loop building 29 chains (720 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 8661 restraints for refining 15123 atoms. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2655 (Rfree = 0.000) for 15123 atoms. Found 135 (135 requested) and removed 202 (67 requested) atoms. Cycle 2: After refmac, R = 0.2328 (Rfree = 0.000) for 15056 atoms. Found 82 (132 requested) and removed 114 (67 requested) atoms. Cycle 3: After refmac, R = 0.2204 (Rfree = 0.000) for 15024 atoms. Found 47 (129 requested) and removed 96 (67 requested) atoms. Cycle 4: After refmac, R = 0.2073 (Rfree = 0.000) for 14975 atoms. Found 30 (126 requested) and removed 76 (67 requested) atoms. Cycle 5: After refmac, R = 0.2025 (Rfree = 0.000) for 14929 atoms. Found 25 (122 requested) and removed 71 (66 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.90 2.86 Search for helices and strands: 0 residues in 0 chains, 15159 seeds are put forward NCS extension: 14 residues added (48 deleted due to clashes), 15173 seeds are put forward Round 1: 1454 peptides, 156 chains. Longest chain 34 peptides. Score 0.702 Round 2: 1553 peptides, 127 chains. Longest chain 44 peptides. Score 0.786 Round 3: 1613 peptides, 122 chains. Longest chain 55 peptides. Score 0.811 Round 4: 1585 peptides, 118 chains. Longest chain 52 peptides. Score 0.808 Round 5: 1596 peptides, 112 chains. Longest chain 46 peptides. Score 0.820 Taking the results from Round 5 Chains 131, Residues 1484, Estimated correctness of the model 86.3 % 35 chains (798 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 64 A and 67 A Built loop between residues 214 A and 219 A Built loop between residues 261 A and 264 A Built loop between residues 279 B and 286 B Built loop between residues 272 E and 276 E Built loop between residues 137 D and 141 D Built loop between residues 156 D and 164 D Built loop between residues 181 D and 189 D Built loop between residues 227 D and 230 D Built loop between residues 314 D and 318 D Built loop between residues 220 F and 222 F Built loop between residues 257 F and 261 F 110 chains (1507 residues) following loop building 23 chains (841 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 9542 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2484 (Rfree = 0.000) for 14812 atoms. Found 119 (119 requested) and removed 176 (66 requested) atoms. Cycle 7: After refmac, R = 0.2246 (Rfree = 0.000) for 14755 atoms. Found 90 (116 requested) and removed 84 (66 requested) atoms. Cycle 8: After refmac, R = 0.2113 (Rfree = 0.000) for 14761 atoms. Found 47 (114 requested) and removed 77 (66 requested) atoms. Cycle 9: After refmac, R = 0.2042 (Rfree = 0.000) for 14731 atoms. Found 29 (111 requested) and removed 71 (66 requested) atoms. Cycle 10: After refmac, R = 0.2013 (Rfree = 0.000) for 14689 atoms. Found 33 (107 requested) and removed 69 (65 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.89 2.85 Search for helices and strands: 0 residues in 0 chains, 14924 seeds are put forward NCS extension: 83 residues added (116 deleted due to clashes), 15007 seeds are put forward Round 1: 1472 peptides, 140 chains. Longest chain 57 peptides. Score 0.738 Round 2: 1559 peptides, 112 chains. Longest chain 111 peptides. Score 0.810 Round 3: 1529 peptides, 126 chains. Longest chain 111 peptides. Score 0.780 Round 4: 1536 peptides, 120 chains. Longest chain 56 peptides. Score 0.792 Round 5: 1532 peptides, 121 chains. Longest chain 57 peptides. Score 0.789 Taking the results from Round 2 Chains 124, Residues 1447, Estimated correctness of the model 84.9 % 34 chains (806 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 247 E and 250 E Built loop between residues 63 D and 66 D Built loop between residues 156 D and 164 D Built loop between residues 215 D and 219 D Built loop between residues 230 D and 236 D Built loop between residues 282 D and 292 D Built loop between residues 315 D and 319 D Built loop between residues 276 F and 283 F 114 chains (1481 residues) following loop building 26 chains (843 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 9561 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2311 (Rfree = 0.000) for 14812 atoms. Found 106 (106 requested) and removed 154 (66 requested) atoms. Cycle 12: After refmac, R = 0.2130 (Rfree = 0.000) for 14764 atoms. Found 43 (103 requested) and removed 78 (66 requested) atoms. Cycle 13: After refmac, R = 0.2085 (Rfree = 0.000) for 14729 atoms. Found 33 (100 requested) and removed 69 (66 requested) atoms. Cycle 14: After refmac, R = 0.2037 (Rfree = 0.000) for 14693 atoms. Found 25 (97 requested) and removed 69 (65 requested) atoms. Cycle 15: After refmac, R = 0.2015 (Rfree = 0.000) for 14649 atoms. Found 22 (94 requested) and removed 71 (65 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.92 2.88 Search for helices and strands: 0 residues in 0 chains, 14794 seeds are put forward NCS extension: 37 residues added (59 deleted due to clashes), 14831 seeds are put forward Round 1: 1445 peptides, 139 chains. Longest chain 41 peptides. Score 0.730 Round 2: 1506 peptides, 128 chains. Longest chain 54 peptides. Score 0.770 Round 3: 1529 peptides, 121 chains. Longest chain 51 peptides. Score 0.788 Round 4: 1517 peptides, 129 chains. Longest chain 53 peptides. Score 0.772 Round 5: 1509 peptides, 128 chains. Longest chain 56 peptides. Score 0.771 Taking the results from Round 3 Chains 144, Residues 1408, Estimated correctness of the model 81.6 % 37 chains (769 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 227 E and 230 E Built loop between residues 76 D and 85 D Built loop between residues 259 F and 263 F 140 chains (1416 residues) following loop building 34 chains (782 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 8960 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2297 (Rfree = 0.000) for 14812 atoms. Found 92 (92 requested) and removed 142 (66 requested) atoms. Cycle 17: After refmac, R = 0.2140 (Rfree = 0.000) for 14762 atoms. Found 51 (90 requested) and removed 71 (66 requested) atoms. Cycle 18: After refmac, R = 0.2033 (Rfree = 0.000) for 14742 atoms. Found 40 (87 requested) and removed 71 (66 requested) atoms. Cycle 19: After refmac, R = 0.1998 (Rfree = 0.000) for 14711 atoms. Found 29 (84 requested) and removed 70 (66 requested) atoms. Cycle 20: After refmac, R = 0.1962 (Rfree = 0.000) for 14670 atoms. Found 24 (81 requested) and removed 68 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.91 2.87 Search for helices and strands: 0 residues in 0 chains, 14860 seeds are put forward NCS extension: 19 residues added (14 deleted due to clashes), 14879 seeds are put forward Round 1: 1371 peptides, 143 chains. Longest chain 37 peptides. Score 0.693 Round 2: 1474 peptides, 126 chains. Longest chain 51 peptides. Score 0.763 Round 3: 1490 peptides, 129 chains. Longest chain 53 peptides. Score 0.763 Round 4: 1471 peptides, 136 chains. Longest chain 36 peptides. Score 0.745 Round 5: 1440 peptides, 127 chains. Longest chain 51 peptides. Score 0.749 Taking the results from Round 3 Chains 144, Residues 1361, Estimated correctness of the model 77.4 % 29 chains (567 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 305 A and 314 A Built loop between residues 252 D and 258 D 140 chains (1364 residues) following loop building 27 chains (580 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 7800 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2372 (Rfree = 0.000) for 14812 atoms. Found 79 (79 requested) and removed 135 (66 requested) atoms. Cycle 22: After refmac, R = 0.2090 (Rfree = 0.000) for 14756 atoms. Found 53 (77 requested) and removed 78 (66 requested) atoms. Cycle 23: After refmac, R = 0.2024 (Rfree = 0.000) for 14731 atoms. Found 34 (74 requested) and removed 71 (66 requested) atoms. Cycle 24: After refmac, R = 0.1979 (Rfree = 0.000) for 14694 atoms. Found 34 (71 requested) and removed 72 (65 requested) atoms. Cycle 25: After refmac, R = 0.1904 (Rfree = 0.000) for 14656 atoms. Found 41 (68 requested) and removed 69 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.90 2.86 Search for helices and strands: 0 residues in 0 chains, 14856 seeds are put forward NCS extension: 69 residues added (3 deleted due to clashes), 14925 seeds are put forward Round 1: 1299 peptides, 152 chains. Longest chain 29 peptides. Score 0.641 Round 2: 1365 peptides, 136 chains. Longest chain 36 peptides. Score 0.704 Round 3: 1417 peptides, 139 chains. Longest chain 40 peptides. Score 0.719 Round 4: 1366 peptides, 137 chains. Longest chain 35 peptides. Score 0.702 Round 5: 1414 peptides, 147 chains. Longest chain 47 peptides. Score 0.703 Taking the results from Round 3 Chains 153, Residues 1278, Estimated correctness of the model 69.1 % 23 chains (427 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 265 B and 268 B Built loop between residues 282 B and 287 B 151 chains (1283 residues) following loop building 21 chains (433 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 6870 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2322 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 115 (66 requested) atoms. Cycle 27: After refmac, R = 0.2040 (Rfree = 0.000) for 14763 atoms. Found 52 (66 requested) and removed 76 (66 requested) atoms. Cycle 28: After refmac, R = 0.1962 (Rfree = 0.000) for 14739 atoms. Found 37 (66 requested) and removed 75 (66 requested) atoms. Cycle 29: After refmac, R = 0.1892 (Rfree = 0.000) for 14701 atoms. Found 26 (65 requested) and removed 67 (65 requested) atoms. Cycle 30: After refmac, R = 0.1854 (Rfree = 0.000) for 14660 atoms. Found 25 (65 requested) and removed 66 (65 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.92 2.88 Search for helices and strands: 0 residues in 0 chains, 14804 seeds are put forward NCS extension: 60 residues added (55 deleted due to clashes), 14864 seeds are put forward Round 1: 1280 peptides, 154 chains. Longest chain 34 peptides. Score 0.627 Round 2: 1402 peptides, 139 chains. Longest chain 38 peptides. Score 0.713 Round 3: 1406 peptides, 141 chains. Longest chain 39 peptides. Score 0.711 Round 4: 1428 peptides, 140 chains. Longest chain 37 peptides. Score 0.722 Round 5: 1415 peptides, 143 chains. Longest chain 42 peptides. Score 0.711 Taking the results from Round 4 Chains 155, Residues 1288, Estimated correctness of the model 69.7 % 24 chains (394 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 314 A and 318 A Built loop between residues 217 B and 224 B Built loop between residues 261 B and 265 B Built loop between residues 279 B and 288 B 149 chains (1296 residues) following loop building 20 chains (414 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 6824 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2221 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 118 (66 requested) atoms. Cycle 32: After refmac, R = 0.1990 (Rfree = 0.000) for 14760 atoms. Found 63 (66 requested) and removed 68 (66 requested) atoms. Cycle 33: After refmac, R = 0.1868 (Rfree = 0.000) for 14755 atoms. Found 40 (66 requested) and removed 68 (66 requested) atoms. Cycle 34: After refmac, R = 0.1797 (Rfree = 0.000) for 14727 atoms. Found 14 (66 requested) and removed 66 (66 requested) atoms. Cycle 35: After refmac, R = 0.1771 (Rfree = 0.000) for 14675 atoms. Found 15 (65 requested) and removed 66 (65 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.93 2.89 Search for helices and strands: 0 residues in 0 chains, 14863 seeds are put forward NCS extension: 48 residues added (21 deleted due to clashes), 14911 seeds are put forward Round 1: 1309 peptides, 171 chains. Longest chain 38 peptides. Score 0.603 Round 2: 1413 peptides, 150 chains. Longest chain 38 peptides. Score 0.697 Round 3: 1429 peptides, 150 chains. Longest chain 34 peptides. Score 0.703 Round 4: 1430 peptides, 147 chains. Longest chain 38 peptides. Score 0.709 Round 5: 1420 peptides, 151 chains. Longest chain 39 peptides. Score 0.698 Taking the results from Round 4 Chains 164, Residues 1283, Estimated correctness of the model 67.1 % 24 chains (392 residues) have been docked in sequence Building loops using Loopy2018 164 chains (1283 residues) following loop building 24 chains (392 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 6715 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2092 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 115 (66 requested) atoms. Cycle 37: After refmac, R = 0.1918 (Rfree = 0.000) for 14763 atoms. Found 61 (66 requested) and removed 72 (66 requested) atoms. Cycle 38: After refmac, R = 0.1834 (Rfree = 0.000) for 14752 atoms. Found 35 (66 requested) and removed 69 (66 requested) atoms. Cycle 39: After refmac, R = 0.1754 (Rfree = 0.000) for 14718 atoms. Found 21 (66 requested) and removed 66 (66 requested) atoms. Cycle 40: After refmac, R = 0.1739 (Rfree = 0.000) for 14673 atoms. Found 15 (65 requested) and removed 65 (65 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.94 2.90 Search for helices and strands: 0 residues in 0 chains, 14809 seeds are put forward NCS extension: 13 residues added (32 deleted due to clashes), 14822 seeds are put forward Round 1: 1270 peptides, 173 chains. Longest chain 33 peptides. Score 0.578 Round 2: 1371 peptides, 141 chains. Longest chain 42 peptides. Score 0.697 Round 3: 1374 peptides, 152 chains. Longest chain 42 peptides. Score 0.676 Round 4: 1372 peptides, 146 chains. Longest chain 39 peptides. Score 0.687 Round 5: 1383 peptides, 143 chains. Longest chain 41 peptides. Score 0.698 Taking the results from Round 5 Chains 159, Residues 1240, Estimated correctness of the model 64.8 % 25 chains (404 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 6494 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2074 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 103 (66 requested) atoms. Cycle 42: After refmac, R = 0.1940 (Rfree = 0.000) for 14775 atoms. Found 45 (66 requested) and removed 73 (66 requested) atoms. Cycle 43: After refmac, R = 0.1873 (Rfree = 0.000) for 14747 atoms. Found 39 (66 requested) and removed 71 (66 requested) atoms. Cycle 44: After refmac, R = 0.1808 (Rfree = 0.000) for 14715 atoms. Found 30 (66 requested) and removed 68 (66 requested) atoms. Cycle 45: After refmac, R = 0.1772 (Rfree = 0.000) for 14677 atoms. Found 22 (65 requested) and removed 70 (65 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.93 2.89 Search for helices and strands: 0 residues in 0 chains, 14818 seeds are put forward NCS extension: 17 residues added (12 deleted due to clashes), 14835 seeds are put forward Round 1: 1163 peptides, 162 chains. Longest chain 29 peptides. Score 0.545 Round 2: 1281 peptides, 142 chains. Longest chain 40 peptides. Score 0.654 Round 3: 1319 peptides, 153 chains. Longest chain 39 peptides. Score 0.649 Round 4: 1341 peptides, 149 chains. Longest chain 46 peptides. Score 0.667 Round 5: 1326 peptides, 143 chains. Longest chain 45 peptides. Score 0.673 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 152, Residues 1183, Estimated correctness of the model 59.2 % 19 chains (327 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 227 A and 236 A Built loop between residues 258 C and 264 C 148 chains (1189 residues) following loop building 17 chains (340 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 37988 reflections ( 99.76 % complete ) and 6080 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2107 (Rfree = 0.000) for 14812 atoms. Found 0 (66 requested) and removed 31 (66 requested) atoms. Cycle 47: After refmac, R = 0.1995 (Rfree = 0.000) for 14781 atoms. Found 0 (66 requested) and removed 27 (66 requested) atoms. Cycle 48: After refmac, R = 0.1927 (Rfree = 0.000) for 14754 atoms. Found 0 (66 requested) and removed 48 (66 requested) atoms. Cycle 49: After refmac, R = 0.1876 (Rfree = 0.000) for 14706 atoms. Found 0 (65 requested) and removed 32 (65 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 03:50:02 GMT 2018 Job finished. TimeTaking 161.45 Used memory is bytes: 8941336