Sun 23 Dec 22:23:10 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 1vl4-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vl4-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-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/1vl4-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-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 22:23:18 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/1vl4-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-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 902 and 0 Target number of residues in the AU: 902 Target solvent content: 0.5256 Checking the provided sequence file Detected sequence length: 447 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 894 Adjusted target solvent content: 0.53 Input MTZ file: 1vl4-2.3-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: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 7152 target number of atoms Had to go as low as 0.50 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: 79.862 2.320 Wilson plot Bfac: 29.14 44794 reflections ( 98.68 % complete ) and 0 restraints for refining 7966 atoms. Observations/parameters ratio is 1.41 ------------------------------------------------------ Starting model: R = 0.3105 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2340 (Rfree = 0.000) for 7966 atoms. Found 98 (178 requested) and removed 124 (89 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.36 2.27 NCS extension: 0 residues added, 7940 seeds are put forward Round 1: 645 peptides, 82 chains. Longest chain 33 peptides. Score 0.635 Round 2: 705 peptides, 56 chains. Longest chain 51 peptides. Score 0.790 Round 3: 760 peptides, 38 chains. Longest chain 117 peptides. Score 0.869 Round 4: 789 peptides, 31 chains. Longest chain 83 peptides. Score 0.896 Round 5: 800 peptides, 36 chains. Longest chain 83 peptides. Score 0.889 Taking the results from Round 4 Chains 34, Residues 758, Estimated correctness of the model 98.2 % 16 chains (640 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 168 A and 171 A Built loop between residues 380 A and 389 A Built loop between residues 399 A and 409 A Built loop between residues 97 B and 105 B Built loop between residues 213 B and 217 B Built loop between residues 233 B and 242 B Built loop between residues 333 B and 336 B 23 chains (787 residues) following loop building 9 chains (679 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 8468 restraints for refining 7403 atoms. 2653 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2765 (Rfree = 0.000) for 7403 atoms. Found 158 (166 requested) and removed 118 (83 requested) atoms. Cycle 2: After refmac, R = 0.2500 (Rfree = 0.000) for 7324 atoms. Found 99 (164 requested) and removed 90 (83 requested) atoms. Cycle 3: After refmac, R = 0.2410 (Rfree = 0.000) for 7261 atoms. Found 112 (157 requested) and removed 87 (82 requested) atoms. Cycle 4: After refmac, R = 0.2328 (Rfree = 0.000) for 7247 atoms. Found 85 (153 requested) and removed 86 (81 requested) atoms. Cycle 5: After refmac, R = 0.2274 (Rfree = 0.000) for 7213 atoms. Found 96 (149 requested) and removed 81 (81 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.35 2.26 NCS extension: 323 residues added (280 deleted due to clashes), 7578 seeds are put forward Round 1: 807 peptides, 18 chains. Longest chain 125 peptides. Score 0.926 Round 2: 823 peptides, 19 chains. Longest chain 120 peptides. Score 0.928 Round 3: 818 peptides, 20 chains. Longest chain 123 peptides. Score 0.925 Round 4: 829 peptides, 18 chains. Longest chain 108 peptides. Score 0.931 Round 5: 829 peptides, 20 chains. Longest chain 155 peptides. Score 0.928 Taking the results from Round 4 Chains 19, Residues 811, Estimated correctness of the model 99.1 % 13 chains (765 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 251 A and 260 A Built loop between residues 292 A and 295 A Built loop between residues 390 A and 393 A Built loop between residues 93 B and 104 B Built loop between residues 129 B and 132 B Built loop between residues 190 B and 193 B Built loop between residues 257 B and 261 B Built loop between residues 359 B and 364 B 9 chains (839 residues) following loop building 5 chains (798 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7293 restraints for refining 7256 atoms. 850 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2465 (Rfree = 0.000) for 7256 atoms. Found 123 (146 requested) and removed 99 (81 requested) atoms. Cycle 7: After refmac, R = 0.2223 (Rfree = 0.000) for 7242 atoms. Found 107 (143 requested) and removed 83 (81 requested) atoms. Cycle 8: After refmac, R = 0.2122 (Rfree = 0.000) for 7244 atoms. Found 88 (140 requested) and removed 84 (81 requested) atoms. Cycle 9: After refmac, R = 0.2040 (Rfree = 0.000) for 7236 atoms. Found 82 (136 requested) and removed 82 (81 requested) atoms. Cycle 10: After refmac, R = 0.1989 (Rfree = 0.000) for 7224 atoms. Found 100 (133 requested) and removed 85 (81 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.37 2.28 NCS extension: 15 residues added (50 deleted due to clashes), 7266 seeds are put forward Round 1: 834 peptides, 18 chains. Longest chain 127 peptides. Score 0.933 Round 2: 845 peptides, 13 chains. Longest chain 134 peptides. Score 0.943 Round 3: 842 peptides, 16 chains. Longest chain 160 peptides. Score 0.938 Round 4: 840 peptides, 16 chains. Longest chain 213 peptides. Score 0.937 Round 5: 826 peptides, 24 chains. Longest chain 117 peptides. Score 0.920 Taking the results from Round 2 Chains 13, Residues 832, Estimated correctness of the model 99.4 % 12 chains (826 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 103 A Built loop between residues 216 A and 222 A Built loop between residues 257 A and 260 A Built loop between residues 392 A and 395 A Built loop between residues 93 B and 98 B Built loop between residues 227 B and 230 B Built loop between residues 276 B and 279 B Built loop between residues 328 B and 331 B Built loop between residues 359 B and 363 B Built loop between residues 395 B and 397 B 3 chains (860 residues) following loop building 2 chains (854 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7210 restraints for refining 7360 atoms. 423 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2179 (Rfree = 0.000) for 7360 atoms. Found 132 (132 requested) and removed 97 (82 requested) atoms. Cycle 12: After refmac, R = 0.1980 (Rfree = 0.000) for 7385 atoms. Found 105 (129 requested) and removed 83 (82 requested) atoms. Cycle 13: After refmac, R = 0.1913 (Rfree = 0.000) for 7392 atoms. Found 76 (126 requested) and removed 85 (83 requested) atoms. Cycle 14: After refmac, R = 0.1883 (Rfree = 0.000) for 7369 atoms. Found 92 (122 requested) and removed 85 (82 requested) atoms. Cycle 15: After refmac, R = 0.1858 (Rfree = 0.000) for 7371 atoms. Found 90 (119 requested) and removed 84 (82 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.36 2.27 NCS extension: 5 residues added (9 deleted due to clashes), 7390 seeds are put forward Round 1: 846 peptides, 10 chains. Longest chain 121 peptides. Score 0.948 Round 2: 847 peptides, 12 chains. Longest chain 162 peptides. Score 0.945 Round 3: 847 peptides, 11 chains. Longest chain 172 peptides. Score 0.946 Round 4: 834 peptides, 20 chains. Longest chain 205 peptides. Score 0.929 Round 5: 841 peptides, 16 chains. Longest chain 175 peptides. Score 0.937 Taking the results from Round 1 Chains 11, Residues 836, Estimated correctness of the model 99.5 % 10 chains (832 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 100 A Built loop between residues 189 A and 192 A Built loop between residues 308 A and 311 A Built loop between residues 395 A and 402 A Built loop between residues 97 B and 103 B Built loop between residues 189 B and 192 B Built loop between residues 311 B and 314 B Built loop between residues 395 B and 398 B 2 chains (858 residues) following loop building 2 chains (858 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7207 restraints for refining 7366 atoms. 407 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2036 (Rfree = 0.000) for 7366 atoms. Found 115 (115 requested) and removed 94 (82 requested) atoms. Cycle 17: After refmac, R = 0.1906 (Rfree = 0.000) for 7374 atoms. Found 112 (112 requested) and removed 88 (82 requested) atoms. Cycle 18: After refmac, R = 0.1857 (Rfree = 0.000) for 7395 atoms. Found 95 (110 requested) and removed 90 (83 requested) atoms. Cycle 19: After refmac, R = 0.1833 (Rfree = 0.000) for 7398 atoms. Found 96 (106 requested) and removed 87 (83 requested) atoms. Cycle 20: After refmac, R = 0.1821 (Rfree = 0.000) for 7404 atoms. Found 100 (103 requested) and removed 94 (83 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.34 2.25 NCS extension: 0 residues added, 7414 seeds are put forward Round 1: 849 peptides, 10 chains. Longest chain 138 peptides. Score 0.948 Round 2: 851 peptides, 12 chains. Longest chain 168 peptides. Score 0.946 Round 3: 855 peptides, 11 chains. Longest chain 209 peptides. Score 0.948 Round 4: 849 peptides, 13 chains. Longest chain 259 peptides. Score 0.944 Round 5: 842 peptides, 17 chains. Longest chain 176 peptides. Score 0.936 Taking the results from Round 3 Chains 11, Residues 844, Estimated correctness of the model 99.5 % 10 chains (838 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 221 A and 224 A Built loop between residues 276 A and 279 A Built loop between residues 395 A and 398 A Built loop between residues 98 B and 102 B Built loop between residues 190 B and 193 B Built loop between residues 232 B and 235 B Built loop between residues 247 B and 250 B Built loop between residues 397 B and 400 B 3 chains (861 residues) following loop building 2 chains (855 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7194 restraints for refining 7332 atoms. 400 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1990 (Rfree = 0.000) for 7332 atoms. Found 98 (98 requested) and removed 89 (82 requested) atoms. Cycle 22: After refmac, R = 0.1876 (Rfree = 0.000) for 7331 atoms. Found 95 (95 requested) and removed 82 (82 requested) atoms. Cycle 23: After refmac, R = 0.1833 (Rfree = 0.000) for 7341 atoms. Found 92 (92 requested) and removed 85 (82 requested) atoms. Cycle 24: After refmac, R = 0.1807 (Rfree = 0.000) for 7343 atoms. Found 89 (89 requested) and removed 86 (82 requested) atoms. Cycle 25: After refmac, R = 0.1787 (Rfree = 0.000) for 7344 atoms. Found 85 (85 requested) and removed 90 (82 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.33 2.24 NCS extension: 187 residues added (255 deleted due to clashes), 7529 seeds are put forward Round 1: 848 peptides, 14 chains. Longest chain 137 peptides. Score 0.942 Round 2: 844 peptides, 13 chains. Longest chain 113 peptides. Score 0.943 Round 3: 840 peptides, 17 chains. Longest chain 118 peptides. Score 0.936 Round 4: 841 peptides, 16 chains. Longest chain 117 peptides. Score 0.937 Round 5: 839 peptides, 20 chains. Longest chain 131 peptides. Score 0.930 Taking the results from Round 2 Chains 14, Residues 831, Estimated correctness of the model 99.4 % 13 chains (827 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 99 A and 103 A Built loop between residues 170 A and 176 A Built loop between residues 259 A and 262 A Built loop between residues 275 A and 278 A Built loop between residues 310 A and 313 A Built loop between residues 395 A and 398 A Built loop between residues 119 B and 124 B Built loop between residues 189 B and 192 B Built loop between residues 276 B and 279 B Built loop between residues 390 B and 394 B 2 chains (856 residues) following loop building 2 chains (856 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7188 restraints for refining 7337 atoms. 391 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2016 (Rfree = 0.000) for 7337 atoms. Found 82 (82 requested) and removed 99 (82 requested) atoms. Cycle 27: After refmac, R = 0.1886 (Rfree = 0.000) for 7309 atoms. Found 82 (82 requested) and removed 83 (82 requested) atoms. Cycle 28: After refmac, R = 0.1840 (Rfree = 0.000) for 7304 atoms. Found 82 (82 requested) and removed 85 (82 requested) atoms. Cycle 29: After refmac, R = 0.1830 (Rfree = 0.000) for 7299 atoms. Found 81 (81 requested) and removed 90 (81 requested) atoms. Cycle 30: After refmac, R = 0.1829 (Rfree = 0.000) for 7287 atoms. Found 81 (81 requested) and removed 90 (81 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.32 2.23 NCS extension: 148 residues added (280 deleted due to clashes), 7430 seeds are put forward Round 1: 843 peptides, 11 chains. Longest chain 121 peptides. Score 0.946 Round 2: 849 peptides, 11 chains. Longest chain 137 peptides. Score 0.947 Round 3: 843 peptides, 17 chains. Longest chain 101 peptides. Score 0.936 Round 4: 838 peptides, 19 chains. Longest chain 87 peptides. Score 0.932 Round 5: 846 peptides, 17 chains. Longest chain 147 peptides. Score 0.937 Taking the results from Round 2 Chains 13, Residues 838, Estimated correctness of the model 99.5 % 12 chains (836 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A Built loop between residues 188 A and 193 A Built loop between residues 246 A and 249 A Built loop between residues 307 A and 310 A Built loop between residues 26 B and 29 B Built loop between residues 98 B and 102 B Built loop between residues 232 B and 235 B Built loop between residues 313 B and 316 B Built loop between residues 361 B and 364 B 3 chains (857 residues) following loop building 3 chains (857 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7145 restraints for refining 7300 atoms. 346 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1999 (Rfree = 0.000) for 7300 atoms. Found 81 (81 requested) and removed 82 (81 requested) atoms. Cycle 32: After refmac, R = 0.1885 (Rfree = 0.000) for 7286 atoms. Found 81 (81 requested) and removed 82 (81 requested) atoms. Cycle 33: After refmac, R = 0.1828 (Rfree = 0.000) for 7280 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 34: After refmac, R = 0.1809 (Rfree = 0.000) for 7272 atoms. Found 81 (81 requested) and removed 85 (81 requested) atoms. Cycle 35: After refmac, R = 0.1788 (Rfree = 0.000) for 7262 atoms. Found 81 (81 requested) and removed 85 (81 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.33 2.24 NCS extension: 0 residues added, 7262 seeds are put forward Round 1: 849 peptides, 10 chains. Longest chain 240 peptides. Score 0.948 Round 2: 846 peptides, 14 chains. Longest chain 212 peptides. Score 0.942 Round 3: 849 peptides, 13 chains. Longest chain 210 peptides. Score 0.944 Round 4: 836 peptides, 17 chains. Longest chain 115 peptides. Score 0.935 Round 5: 831 peptides, 21 chains. Longest chain 114 peptides. Score 0.927 Taking the results from Round 1 Chains 12, Residues 839, Estimated correctness of the model 99.5 % 11 chains (838 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 29 A Built loop between residues 98 A and 102 A Built loop between residues 190 A and 193 A Built loop between residues 231 A and 234 A Built loop between residues 390 A and 394 A Built loop between residues 66 B and 69 B Built loop between residues 308 B and 311 B Built loop between residues 394 B and 398 B 3 chains (857 residues) following loop building 3 chains (857 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7127 restraints for refining 7289 atoms. 328 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1967 (Rfree = 0.000) for 7289 atoms. Found 81 (81 requested) and removed 88 (81 requested) atoms. Cycle 37: After refmac, R = 0.1852 (Rfree = 0.000) for 7273 atoms. Found 81 (81 requested) and removed 82 (81 requested) atoms. Cycle 38: After refmac, R = 0.1805 (Rfree = 0.000) for 7271 atoms. Found 81 (81 requested) and removed 86 (81 requested) atoms. Cycle 39: After refmac, R = 0.1784 (Rfree = 0.000) for 7263 atoms. Found 81 (81 requested) and removed 87 (81 requested) atoms. Cycle 40: After refmac, R = 0.1774 (Rfree = 0.000) for 7255 atoms. Found 81 (81 requested) and removed 89 (81 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.33 2.24 NCS extension: 172 residues added (258 deleted due to clashes), 7422 seeds are put forward Round 1: 845 peptides, 9 chains. Longest chain 243 peptides. Score 0.949 Round 2: 843 peptides, 15 chains. Longest chain 163 peptides. Score 0.939 Round 3: 844 peptides, 17 chains. Longest chain 168 peptides. Score 0.936 Round 4: 843 peptides, 17 chains. Longest chain 130 peptides. Score 0.936 Round 5: 844 peptides, 20 chains. Longest chain 144 peptides. Score 0.932 Taking the results from Round 1 Chains 12, Residues 836, Estimated correctness of the model 99.5 % 10 chains (831 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 66 A Built loop between residues 305 A and 311 A Built loop between residues 390 A and 398 A Built loop between residues 428 A and 431 A Built loop between residues 81 B and 84 B Built loop between residues 319 B and 322 B Built loop between residues 394 B and 398 B 3 chains (856 residues) following loop building 3 chains (856 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7171 restraints for refining 7312 atoms. 383 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1946 (Rfree = 0.000) for 7312 atoms. Found 82 (82 requested) and removed 88 (82 requested) atoms. Cycle 42: After refmac, R = 0.1825 (Rfree = 0.000) for 7297 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 43: After refmac, R = 0.1773 (Rfree = 0.000) for 7294 atoms. Found 81 (81 requested) and removed 86 (81 requested) atoms. Cycle 44: After refmac, R = 0.1771 (Rfree = 0.000) for 7285 atoms. Found 81 (81 requested) and removed 86 (81 requested) atoms. Cycle 45: After refmac, R = 0.1772 (Rfree = 0.000) for 7276 atoms. Found 81 (81 requested) and removed 91 (81 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.35 2.26 NCS extension: 191 residues added (238 deleted due to clashes), 7459 seeds are put forward Round 1: 848 peptides, 10 chains. Longest chain 213 peptides. Score 0.948 Round 2: 846 peptides, 15 chains. Longest chain 180 peptides. Score 0.940 Round 3: 849 peptides, 12 chains. Longest chain 200 peptides. Score 0.945 Round 4: 846 peptides, 19 chains. Longest chain 91 peptides. Score 0.934 Round 5: 851 peptides, 13 chains. Longest chain 156 peptides. Score 0.944 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 838, Estimated correctness of the model 99.5 % 9 chains (823 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 190 A and 193 A Built loop between residues 231 A and 234 A Built loop between residues 80 B and 84 B Built loop between residues 98 B and 104 B Built loop between residues 208 B and 211 B Built loop between residues 394 B and 398 B 4 chains (854 residues) following loop building 3 chains (840 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 44794 reflections ( 98.68 % complete ) and 6711 restraints for refining 6600 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2363 (Rfree = 0.000) for 6600 atoms. Found 69 (74 requested) and removed 0 (74 requested) atoms. Cycle 47: After refmac, R = 0.2180 (Rfree = 0.000) for 6600 atoms. Found 34 (74 requested) and removed 1 (74 requested) atoms. Cycle 48: After refmac, R = 0.2116 (Rfree = 0.000) for 6600 atoms. Found 12 (75 requested) and removed 2 (75 requested) atoms. Cycle 49: After refmac, R = 0.2088 (Rfree = 0.000) for 6600 atoms. Found 13 (75 requested) and removed 4 (75 requested) atoms. Writing output files ... TimeTaking 118.15