Tue 25 Dec 19:27:55 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 1vkd-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkd-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-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/1vkd-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-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 ============================================================ Tue 25 Dec 19:28:05 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/1vkd-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkd-3.2-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 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-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: 19 Cell parameters: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.2-parrot-hancs.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 17918 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.2853 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2287 (Rfree = 0.000) for 17918 atoms. Found 160 (160 requested) and removed 130 (80 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.88 2.84 Search for helices and strands: 0 residues in 0 chains, 18144 seeds are put forward NCS extension: 0 residues added, 18144 seeds are put forward Round 1: 1199 peptides, 193 chains. Longest chain 21 peptides. Score 0.484 Round 2: 1457 peptides, 175 chains. Longest chain 33 peptides. Score 0.666 Round 3: 1562 peptides, 153 chains. Longest chain 54 peptides. Score 0.748 Round 4: 1588 peptides, 144 chains. Longest chain 37 peptides. Score 0.771 Round 5: 1646 peptides, 126 chains. Longest chain 49 peptides. Score 0.814 Taking the results from Round 5 Chains 148, Residues 1520, Estimated correctness of the model 85.5 % 38 chains (788 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 218 A and 221 A Built loop between residues 314 A and 318 A Built loop between residues 230 B and 235 B Built loop between residues 227 E and 230 E Built loop between residues 290 E and 293 E Built loop between residues 248 D and 252 D Built loop between residues 271 D and 274 D Built loop between residues 315 D and 321 D 135 chains (1535 residues) following loop building 30 chains (811 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 9422 restraints for refining 15389 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2566 (Rfree = 0.000) for 15389 atoms. Found 128 (138 requested) and removed 188 (69 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2346 (Rfree = 0.000) for 15329 atoms. Found 79 (134 requested) and removed 98 (68 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2241 (Rfree = 0.000) for 15310 atoms. Found 61 (132 requested) and removed 88 (68 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2172 (Rfree = 0.000) for 15283 atoms. Found 49 (129 requested) and removed 83 (68 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2020 (Rfree = 0.000) for 15249 atoms. Found 35 (125 requested) and removed 84 (68 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.89 2.85 Search for helices and strands: 0 residues in 0 chains, 15443 seeds are put forward NCS extension: 16 residues added (50 deleted due to clashes), 15459 seeds are put forward Round 1: 1502 peptides, 146 chains. Longest chain 43 peptides. Score 0.739 Round 2: 1620 peptides, 129 chains. Longest chain 59 peptides. Score 0.803 Round 3: 1647 peptides, 134 chains. Longest chain 46 peptides. Score 0.803 Round 4: 1633 peptides, 128 chains. Longest chain 44 peptides. Score 0.808 Round 5: 1604 peptides, 132 chains. Longest chain 63 peptides. Score 0.794 Taking the results from Round 4 Chains 156, Residues 1505, Estimated correctness of the model 84.6 % 45 chains (824 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 286 A and 292 A Built loop between residues 314 A and 321 A Built loop between residues 289 B and 295 B Built loop between residues 285 E and 288 E Built loop between residues 42 D and 51 D Built loop between residues 156 D and 159 D Built loop between residues 219 D and 222 D Built loop between residues 249 D and 252 D Built loop between residues 262 D and 265 D Built loop between residues 278 D and 281 D Built loop between residues 314 D and 318 D Built loop between residues 282 F and 285 F 138 chains (1531 residues) following loop building 33 chains (865 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 37988 reflections ( 99.76 % complete ) and 9571 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2486 (Rfree = 0.000) for 14812 atoms. Found 119 (119 requested) and removed 158 (66 requested) atoms. Cycle 7: After refmac, R = 0.2226 (Rfree = 0.000) for 14773 atoms. Found 68 (116 requested) and removed 87 (66 requested) atoms. Cycle 8: After refmac, R = 0.2115 (Rfree = 0.000) for 14754 atoms. Found 36 (114 requested) and removed 73 (66 requested) atoms. Cycle 9: After refmac, R = 0.2087 (Rfree = 0.000) for 14717 atoms. Found 41 (111 requested) and removed 69 (66 requested) atoms. Cycle 10: After refmac, R = 0.2044 (Rfree = 0.000) for 14689 atoms. Found 35 (107 requested) and removed 70 (65 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.88 2.84 Search for helices and strands: 0 residues in 0 chains, 14906 seeds are put forward NCS extension: 74 residues added (40 deleted due to clashes), 14980 seeds are put forward Round 1: 1502 peptides, 148 chains. Longest chain 43 peptides. Score 0.735 Round 2: 1551 peptides, 113 chains. Longest chain 54 peptides. Score 0.806 Round 3: 1563 peptides, 125 chains. Longest chain 54 peptides. Score 0.792 Round 4: 1612 peptides, 118 chains. Longest chain 52 peptides. Score 0.816 Round 5: 1602 peptides, 123 chains. Longest chain 52 peptides. Score 0.806 Taking the results from Round 4 Chains 139, Residues 1494, Estimated correctness of the model 85.8 % 32 chains (747 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 160 A and 168 A Built loop between residues 289 A and 295 A Built loop between residues 39 D and 48 D Built loop between residues 156 D and 161 D Built loop between residues 300 D and 305 D 131 chains (1508 residues) following loop building 27 chains (775 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 9212 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2378 (Rfree = 0.000) for 14812 atoms. Found 106 (106 requested) and removed 132 (66 requested) atoms. Cycle 12: After refmac, R = 0.2186 (Rfree = 0.000) for 14786 atoms. Found 61 (103 requested) and removed 78 (66 requested) atoms. Cycle 13: After refmac, R = 0.2102 (Rfree = 0.000) for 14769 atoms. Found 48 (100 requested) and removed 75 (66 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2019 (Rfree = 0.000) for 14742 atoms. Found 38 (98 requested) and removed 68 (66 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1957 (Rfree = 0.000) for 14712 atoms. Found 33 (95 requested) and removed 70 (66 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.88 2.84 Search for helices and strands: 0 residues in 0 chains, 14902 seeds are put forward NCS extension: 42 residues added (22 deleted due to clashes), 14944 seeds are put forward Round 1: 1453 peptides, 148 chains. Longest chain 41 peptides. Score 0.717 Round 2: 1551 peptides, 128 chains. Longest chain 63 peptides. Score 0.784 Round 3: 1570 peptides, 133 chains. Longest chain 40 peptides. Score 0.782 Round 4: 1561 peptides, 126 chains. Longest chain 57 peptides. Score 0.790 Round 5: 1563 peptides, 136 chains. Longest chain 51 peptides. Score 0.776 Taking the results from Round 4 Chains 143, Residues 1435, Estimated correctness of the model 81.9 % 31 chains (705 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 207 A and 218 A Built loop between residues 248 A and 252 A Built loop between residues 161 B and 165 B Built loop between residues 147 D and 150 D 136 chains (1447 residues) following loop building 26 chains (723 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 37988 reflections ( 99.76 % complete ) and 8815 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2327 (Rfree = 0.000) for 14812 atoms. Found 92 (92 requested) and removed 152 (66 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2163 (Rfree = 0.000) for 14752 atoms. Found 81 (90 requested) and removed 75 (66 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2099 (Rfree = 0.000) for 14758 atoms. Found 33 (87 requested) and removed 73 (66 requested) atoms. Cycle 19: After refmac, R = 0.2053 (Rfree = 0.000) for 14718 atoms. Found 44 (84 requested) and removed 67 (66 requested) atoms. Cycle 20: After refmac, R = 0.2021 (Rfree = 0.000) for 14695 atoms. Found 30 (81 requested) and removed 69 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.90 2.86 Search for helices and strands: 0 residues in 0 chains, 14880 seeds are put forward NCS extension: 65 residues added (44 deleted due to clashes), 14945 seeds are put forward Round 1: 1391 peptides, 144 chains. Longest chain 46 peptides. Score 0.699 Round 2: 1492 peptides, 133 chains. Longest chain 51 peptides. Score 0.757 Round 3: 1515 peptides, 141 chains. Longest chain 30 peptides. Score 0.752 Round 4: 1523 peptides, 130 chains. Longest chain 53 peptides. Score 0.772 Round 5: 1531 peptides, 139 chains. Longest chain 46 peptides. Score 0.761 Taking the results from Round 4 Chains 141, Residues 1393, Estimated correctness of the model 78.9 % 23 chains (497 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 160 A and 169 A Built loop between residues 180 A and 191 A Built loop between residues 238 A and 247 A Built loop between residues 289 A and 297 A 132 chains (1409 residues) following loop building 19 chains (530 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 7806 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2302 (Rfree = 0.000) for 14812 atoms. Found 79 (79 requested) and removed 100 (66 requested) atoms. Cycle 22: After refmac, R = 0.2118 (Rfree = 0.000) for 14791 atoms. Found 54 (77 requested) and removed 71 (66 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 23: After refmac, R = 0.2037 (Rfree = 0.000) for 14774 atoms. Found 25 (74 requested) and removed 69 (66 requested) atoms. Cycle 24: After refmac, R = 0.2000 (Rfree = 0.000) for 14730 atoms. Found 21 (71 requested) and removed 67 (66 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1975 (Rfree = 0.000) for 14684 atoms. Found 14 (68 requested) and removed 66 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.92 2.88 Search for helices and strands: 0 residues in 0 chains, 14817 seeds are put forward NCS extension: 28 residues added (5 deleted due to clashes), 14845 seeds are put forward Round 1: 1355 peptides, 163 chains. Longest chain 29 peptides. Score 0.644 Round 2: 1483 peptides, 152 chains. Longest chain 35 peptides. Score 0.721 Round 3: 1494 peptides, 137 chains. Longest chain 55 peptides. Score 0.751 Round 4: 1496 peptides, 137 chains. Longest chain 33 peptides. Score 0.752 Round 5: 1496 peptides, 141 chains. Longest chain 38 peptides. Score 0.745 Taking the results from Round 4 Chains 151, Residues 1359, Estimated correctness of the model 75.4 % 29 chains (515 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 313 A and 318 A Built loop between residues 264 D and 267 D Built loop between residues 289 D and 294 D 147 chains (1366 residues) following loop building 26 chains (525 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 7589 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2237 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 109 (66 requested) atoms. Cycle 27: After refmac, R = 0.2070 (Rfree = 0.000) for 14769 atoms. Found 38 (66 requested) and removed 73 (66 requested) atoms. Cycle 28: After refmac, R = 0.1981 (Rfree = 0.000) for 14734 atoms. Found 27 (66 requested) and removed 69 (66 requested) atoms. Cycle 29: After refmac, R = 0.1931 (Rfree = 0.000) for 14692 atoms. Found 19 (65 requested) and removed 65 (65 requested) atoms. Cycle 30: After refmac, R = 0.1887 (Rfree = 0.000) for 14646 atoms. Failed to save intermediate PDB Found 13 (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, 14778 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 14792 seeds are put forward Round 1: 1298 peptides, 162 chains. Longest chain 27 peptides. Score 0.618 Round 2: 1436 peptides, 142 chains. Longest chain 36 peptides. Score 0.721 Round 3: 1428 peptides, 144 chains. Longest chain 34 peptides. Score 0.714 Round 4: 1425 peptides, 144 chains. Longest chain 49 peptides. Score 0.713 Round 5: 1409 peptides, 139 chains. Longest chain 38 peptides. Score 0.716 Taking the results from Round 2 Chains 160, Residues 1294, Estimated correctness of the model 69.5 % 29 chains (467 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 43 A Built loop between residues 179 A and 184 A Built loop between residues 261 A and 267 A Built loop between residues 287 A and 296 A 153 chains (1301 residues) following loop building 25 chains (486 residues) in sequence following loop building ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 7096 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2151 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 107 (66 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1987 (Rfree = 0.000) for 14771 atoms. Found 40 (66 requested) and removed 67 (66 requested) atoms. Cycle 33: After refmac, R = 0.1936 (Rfree = 0.000) for 14744 atoms. Found 26 (66 requested) and removed 68 (66 requested) atoms. Cycle 34: After refmac, R = 0.1910 (Rfree = 0.000) for 14702 atoms. Found 11 (65 requested) and removed 65 (65 requested) atoms. Cycle 35: After refmac, R = 0.1901 (Rfree = 0.000) for 14648 atoms. Found 13 (65 requested) and removed 65 (65 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.93 2.89 Search for helices and strands: 0 residues in 0 chains, 14757 seeds are put forward NCS extension: 36 residues added (56 deleted due to clashes), 14793 seeds are put forward Round 1: 1220 peptides, 150 chains. Longest chain 33 peptides. Score 0.606 Round 2: 1343 peptides, 142 chains. Longest chain 34 peptides. Score 0.683 Round 3: 1358 peptides, 150 chains. Longest chain 41 peptides. Score 0.673 Round 4: 1349 peptides, 144 chains. Longest chain 30 peptides. Score 0.681 Round 5: 1343 peptides, 145 chains. Longest chain 40 peptides. Score 0.676 Taking the results from Round 2 Chains 158, Residues 1201, Estimated correctness of the model 61.5 % 31 chains (442 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 37988 reflections ( 99.76 % complete ) and 6526 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2078 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 99 (66 requested) atoms. Cycle 37: After refmac, R = 0.1982 (Rfree = 0.000) for 14779 atoms. Found 36 (66 requested) and removed 68 (66 requested) atoms. Cycle 38: After refmac, R = 0.1909 (Rfree = 0.000) for 14747 atoms. Found 25 (66 requested) and removed 70 (66 requested) atoms. Cycle 39: After refmac, R = 0.1872 (Rfree = 0.000) for 14702 atoms. Found 27 (65 requested) and removed 66 (65 requested) atoms. Cycle 40: After refmac, R = 0.1862 (Rfree = 0.000) for 14663 atoms. Found 19 (65 requested) and removed 65 (65 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.92 2.88 Search for helices and strands: 0 residues in 0 chains, 14792 seeds are put forward NCS extension: 11 residues added (15 deleted due to clashes), 14803 seeds are put forward Round 1: 1165 peptides, 161 chains. Longest chain 25 peptides. Score 0.548 Round 2: 1296 peptides, 141 chains. Longest chain 26 peptides. Score 0.664 Round 3: 1276 peptides, 147 chains. Longest chain 26 peptides. Score 0.641 Round 4: 1304 peptides, 147 chains. Longest chain 28 peptides. Score 0.654 Round 5: 1312 peptides, 148 chains. Longest chain 27 peptides. Score 0.656 Taking the results from Round 2 Chains 146, Residues 1155, Estimated correctness of the model 57.2 % 23 chains (373 residues) have been docked in sequence ------------------------------------------------------ 37988 reflections ( 99.76 % complete ) and 6069 restraints for refining 14812 atoms. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2083 (Rfree = 0.000) for 14812 atoms. Found 66 (66 requested) and removed 96 (66 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1924 (Rfree = 0.000) for 14782 atoms. Found 33 (66 requested) and removed 67 (66 requested) atoms. Cycle 43: After refmac, R = 0.1891 (Rfree = 0.000) for 14748 atoms. Found 28 (66 requested) and removed 69 (66 requested) atoms. Cycle 44: After refmac, R = 0.1851 (Rfree = 0.000) for 14707 atoms. Found 20 (65 requested) and removed 65 (65 requested) atoms. Cycle 45: After refmac, R = 0.1839 (Rfree = 0.000) for 14662 atoms. Found 12 (65 requested) and removed 66 (65 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.93 2.89 Search for helices and strands: 0 residues in 0 chains, 14791 seeds are put forward NCS extension: 8 residues added (13 deleted due to clashes), 14799 seeds are put forward Round 1: 1118 peptides, 156 chains. Longest chain 22 peptides. Score 0.534 Round 2: 1263 peptides, 145 chains. Longest chain 31 peptides. Score 0.639 Round 3: 1255 peptides, 143 chains. Longest chain 37 peptides. Score 0.640 Round 4: 1259 peptides, 143 chains. Longest chain 46 peptides. Score 0.642 Round 5: 1300 peptides, 153 chains. Longest chain 35 peptides. Score 0.639 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 148, Residues 1116, Estimated correctness of the model 51.9 % 16 chains (278 residues) have been docked in sequence Sequence coverage is 24 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 69 A and 81 A Built loop between residues 261 A and 274 A 144 chains (1124 residues) following loop building 13 chains (301 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 37988 reflections ( 99.76 % complete ) and 5548 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 27 (66 requested) atoms. Cycle 47: After refmac, R = 0.2009 (Rfree = 0.000) for 14785 atoms. Found 0 (66 requested) and removed 31 (66 requested) atoms. Cycle 48: After refmac, R = 0.1976 (Rfree = 0.000) for 14754 atoms. Found 0 (66 requested) and removed 33 (66 requested) atoms. Cycle 49: After refmac, R = 0.1905 (Rfree = 0.000) for 14721 atoms. Found 0 (66 requested) and removed 32 (66 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 23:06:11 GMT 2018 Job finished. TimeTaking 218.27