Mon 24 Dec 00:57:11 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 1vl4-2.3-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-2.3-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vl4-2.3-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-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/1vl4-2.3-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-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 00:57:16 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/1vl4-2.3-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-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 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-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: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-2.3-parrot-mrncs.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 7912 atoms. Observations/parameters ratio is 1.42 ------------------------------------------------------ Starting model: R = 0.3166 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2513 (Rfree = 0.000) for 7912 atoms. Found 99 (177 requested) and removed 132 (88 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.37 2.28 NCS extension: 0 residues added, 7879 seeds are put forward Round 1: 610 peptides, 78 chains. Longest chain 29 peptides. Score 0.617 Round 2: 692 peptides, 54 chains. Longest chain 41 peptides. Score 0.788 Round 3: 745 peptides, 47 chains. Longest chain 55 peptides. Score 0.840 Round 4: 774 peptides, 34 chains. Longest chain 65 peptides. Score 0.884 Round 5: 791 peptides, 29 chains. Longest chain 125 peptides. Score 0.901 Taking the results from Round 5 Chains 33, Residues 762, Estimated correctness of the model 98.3 % 15 chains (645 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 141 A Built loop between residues 258 A and 262 A Built loop between residues 136 B and 139 B Built loop between residues 177 B and 180 B 29 chains (771 residues) following loop building 11 chains (655 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 8218 restraints for refining 7059 atoms. 2589 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2706 (Rfree = 0.000) for 7059 atoms. Found 158 (158 requested) and removed 105 (79 requested) atoms. Cycle 2: After refmac, R = 0.2447 (Rfree = 0.000) for 7032 atoms. Found 114 (156 requested) and removed 90 (79 requested) atoms. Cycle 3: After refmac, R = 0.2313 (Rfree = 0.000) for 7012 atoms. Found 98 (152 requested) and removed 83 (79 requested) atoms. Cycle 4: After refmac, R = 0.2235 (Rfree = 0.000) for 7002 atoms. Found 81 (148 requested) and removed 80 (78 requested) atoms. Cycle 5: After refmac, R = 0.2188 (Rfree = 0.000) for 6992 atoms. Found 74 (144 requested) and removed 81 (78 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.36 2.27 NCS extension: 80 residues added (204 deleted due to clashes), 7076 seeds are put forward Round 1: 794 peptides, 21 chains. Longest chain 123 peptides. Score 0.917 Round 2: 802 peptides, 15 chains. Longest chain 130 peptides. Score 0.930 Round 3: 804 peptides, 22 chains. Longest chain 131 peptides. Score 0.918 Round 4: 806 peptides, 24 chains. Longest chain 91 peptides. Score 0.915 Round 5: 813 peptides, 20 chains. Longest chain 118 peptides. Score 0.924 Taking the results from Round 2 Chains 16, Residues 787, Estimated correctness of the model 99.1 % 11 chains (754 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 233 A and 239 A Built loop between residues 96 B and 104 B Built loop between residues 166 B and 169 B Built loop between residues 306 B and 311 B 10 chains (802 residues) following loop building 7 chains (772 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7351 restraints for refining 7079 atoms. 1165 conditional restraints added. Observations/parameters ratio is 1.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2318 (Rfree = 0.000) for 7079 atoms. Found 142 (142 requested) and removed 92 (79 requested) atoms. Cycle 7: After refmac, R = 0.2143 (Rfree = 0.000) for 7104 atoms. Found 105 (140 requested) and removed 82 (79 requested) atoms. Cycle 8: After refmac, R = 0.2078 (Rfree = 0.000) for 7111 atoms. Found 97 (137 requested) and removed 84 (79 requested) atoms. Cycle 9: After refmac, R = 0.2016 (Rfree = 0.000) for 7119 atoms. Found 112 (134 requested) and removed 86 (79 requested) atoms. Cycle 10: After refmac, R = 0.1968 (Rfree = 0.000) for 7135 atoms. Found 112 (131 requested) and removed 87 (80 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.34 2.25 NCS extension: 133 residues added (394 deleted due to clashes), 7302 seeds are put forward Round 1: 817 peptides, 14 chains. Longest chain 142 peptides. Score 0.935 Round 2: 822 peptides, 20 chains. Longest chain 146 peptides. Score 0.926 Round 3: 829 peptides, 18 chains. Longest chain 147 peptides. Score 0.931 Round 4: 828 peptides, 24 chains. Longest chain 87 peptides. Score 0.921 Round 5: 825 peptides, 24 chains. Longest chain 129 peptides. Score 0.920 Taking the results from Round 1 Chains 14, Residues 803, Estimated correctness of the model 99.2 % 13 chains (800 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 A and 51 A Built loop between residues 80 A and 83 A Built loop between residues 96 A and 104 A Built loop between residues 232 A and 240 A Built loop between residues 97 B and 102 B Built loop between residues 233 B and 237 B Built loop between residues 308 B and 311 B Built loop between residues 355 B and 364 B Built loop between residues 393 B and 400 B 5 chains (844 residues) following loop building 4 chains (841 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7267 restraints for refining 7312 atoms. 595 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2165 (Rfree = 0.000) for 7312 atoms. Found 131 (131 requested) and removed 99 (82 requested) atoms. Cycle 12: After refmac, R = 0.1997 (Rfree = 0.000) for 7335 atoms. Found 125 (128 requested) and removed 87 (82 requested) atoms. Cycle 13: After refmac, R = 0.1912 (Rfree = 0.000) for 7364 atoms. Found 105 (125 requested) and removed 86 (82 requested) atoms. Cycle 14: After refmac, R = 0.1881 (Rfree = 0.000) for 7377 atoms. Found 112 (122 requested) and removed 87 (82 requested) atoms. Cycle 15: After refmac, R = 0.1851 (Rfree = 0.000) for 7396 atoms. Found 73 (120 requested) and removed 90 (83 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.35 2.26 NCS extension: 115 residues added (270 deleted due to clashes), 7505 seeds are put forward Round 1: 841 peptides, 15 chains. Longest chain 118 peptides. Score 0.939 Round 2: 845 peptides, 14 chains. Longest chain 141 peptides. Score 0.941 Round 3: 841 peptides, 15 chains. Longest chain 149 peptides. Score 0.939 Round 4: 842 peptides, 16 chains. Longest chain 141 peptides. Score 0.938 Round 5: 839 peptides, 24 chains. Longest chain 91 peptides. Score 0.924 Taking the results from Round 2 Chains 14, Residues 831, Estimated correctness of the model 99.4 % 11 chains (812 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 101 A Built loop between residues 240 A and 243 A Built loop between residues 277 A and 280 A Built loop between residues 307 A and 310 A Built loop between residues 96 B and 99 B Built loop between residues 232 B and 235 B Built loop between residues 307 B and 310 B Built loop between residues 394 B and 399 B 6 chains (850 residues) following loop building 3 chains (831 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7340 restraints for refining 7292 atoms. 710 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2028 (Rfree = 0.000) for 7292 atoms. Found 114 (114 requested) and removed 86 (81 requested) atoms. Cycle 17: After refmac, R = 0.1936 (Rfree = 0.000) for 7310 atoms. Found 105 (112 requested) and removed 84 (82 requested) atoms. Cycle 18: After refmac, R = 0.1891 (Rfree = 0.000) for 7324 atoms. Found 104 (108 requested) and removed 85 (82 requested) atoms. Cycle 19: After refmac, R = 0.1860 (Rfree = 0.000) for 7339 atoms. Found 105 (105 requested) and removed 87 (82 requested) atoms. Cycle 20: After refmac, R = 0.1843 (Rfree = 0.000) for 7353 atoms. Found 99 (102 requested) and removed 87 (82 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.34 2.25 NCS extension: 101 residues added (337 deleted due to clashes), 7470 seeds are put forward Round 1: 846 peptides, 15 chains. Longest chain 91 peptides. Score 0.940 Round 2: 848 peptides, 16 chains. Longest chain 137 peptides. Score 0.939 Round 3: 848 peptides, 16 chains. Longest chain 137 peptides. Score 0.939 Round 4: 837 peptides, 16 chains. Longest chain 93 peptides. Score 0.937 Round 5: 832 peptides, 23 chains. Longest chain 118 peptides. Score 0.924 Taking the results from Round 1 Chains 16, Residues 831, Estimated correctness of the model 99.3 % 15 chains (830 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 101 A Built loop between residues 166 A and 169 A Built loop between residues 189 A and 192 A Built loop between residues 277 A and 280 A Built loop between residues 308 A and 311 A Built loop between residues 319 A and 322 A Built loop between residues 390 A and 393 A Built loop between residues 97 B and 101 B Built loop between residues 190 B and 193 B Built loop between residues 225 B and 228 B Built loop between residues 287 B and 290 B Built loop between residues 338 B and 341 B Built loop between residues 394 B and 398 B 2 chains (859 residues) following loop building 2 chains (859 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7190 restraints for refining 7315 atoms. 381 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2007 (Rfree = 0.000) for 7315 atoms. Found 98 (98 requested) and removed 87 (82 requested) atoms. Cycle 22: After refmac, R = 0.1874 (Rfree = 0.000) for 7318 atoms. Found 95 (95 requested) and removed 83 (82 requested) atoms. Cycle 23: After refmac, R = 0.1833 (Rfree = 0.000) for 7327 atoms. Found 92 (92 requested) and removed 84 (82 requested) atoms. Cycle 24: After refmac, R = 0.1816 (Rfree = 0.000) for 7333 atoms. Found 89 (89 requested) and removed 84 (82 requested) atoms. Cycle 25: After refmac, R = 0.1819 (Rfree = 0.000) for 7332 atoms. Found 85 (85 requested) and removed 90 (82 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.34 2.25 NCS extension: 149 residues added (282 deleted due to clashes), 7478 seeds are put forward Round 1: 846 peptides, 11 chains. Longest chain 124 peptides. Score 0.946 Round 2: 846 peptides, 11 chains. Longest chain 138 peptides. Score 0.946 Round 3: 842 peptides, 17 chains. Longest chain 117 peptides. Score 0.936 Round 4: 842 peptides, 16 chains. Longest chain 186 peptides. Score 0.938 Round 5: 833 peptides, 19 chains. Longest chain 130 peptides. Score 0.931 Taking the results from Round 2 Chains 11, Residues 835, Estimated correctness of the model 99.5 % 9 chains (825 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 104 A Built loop between residues 240 A and 244 A Built loop between residues 338 A and 341 A Built loop between residues 97 B and 101 B Built loop between residues 190 B and 193 B Built loop between residues 277 B and 280 B Built loop between residues 361 B and 364 B 4 chains (855 residues) following loop building 2 chains (845 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7263 restraints for refining 7293 atoms. 543 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1978 (Rfree = 0.000) for 7293 atoms. Found 81 (81 requested) and removed 87 (81 requested) atoms. Cycle 27: After refmac, R = 0.1883 (Rfree = 0.000) for 7273 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1840 (Rfree = 0.000) for 7266 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Cycle 29: After refmac, R = 0.1827 (Rfree = 0.000) for 7263 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 30: After refmac, R = 0.1816 (Rfree = 0.000) for 7257 atoms. Found 81 (81 requested) and removed 82 (81 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.34 2.25 NCS extension: 157 residues added (269 deleted due to clashes), 7418 seeds are put forward Round 1: 848 peptides, 9 chains. Longest chain 209 peptides. Score 0.950 Round 2: 850 peptides, 9 chains. Longest chain 226 peptides. Score 0.950 Round 3: 843 peptides, 13 chains. Longest chain 142 peptides. Score 0.943 Round 4: 838 peptides, 15 chains. Longest chain 178 peptides. Score 0.938 Round 5: 836 peptides, 15 chains. Longest chain 130 peptides. Score 0.938 Taking the results from Round 2 Chains 9, Residues 841, Estimated correctness of the model 99.5 % 9 chains (841 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 50 A and 53 A Built loop between residues 97 A and 101 A Built loop between residues 166 A and 169 A Built loop between residues 189 A and 192 A Built loop between residues 216 A and 219 A Built loop between residues 98 B and 104 B Built loop between residues 310 B and 313 B 2 chains (859 residues) following loop building 2 chains (859 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7139 restraints for refining 7303 atoms. 314 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1964 (Rfree = 0.000) for 7303 atoms. Found 81 (81 requested) and removed 89 (81 requested) atoms. Cycle 32: After refmac, R = 0.1856 (Rfree = 0.000) for 7290 atoms. Found 81 (81 requested) and removed 81 (81 requested) atoms. Cycle 33: After refmac, R = 0.1814 (Rfree = 0.000) for 7288 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 34: After refmac, R = 0.1801 (Rfree = 0.000) for 7284 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 7277 atoms. Found 81 (81 requested) and removed 86 (81 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.34 2.25 NCS extension: 0 residues added, 7275 seeds are put forward Round 1: 842 peptides, 10 chains. Longest chain 149 peptides. Score 0.947 Round 2: 846 peptides, 11 chains. Longest chain 144 peptides. Score 0.946 Round 3: 841 peptides, 14 chains. Longest chain 131 peptides. Score 0.941 Round 4: 838 peptides, 19 chains. Longest chain 147 peptides. Score 0.932 Round 5: 838 peptides, 15 chains. Longest chain 127 peptides. Score 0.938 Taking the results from Round 1 Chains 13, Residues 832, Estimated correctness of the model 99.5 % 9 chains (812 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 104 A Built loop between residues 189 A and 192 A Built loop between residues 306 A and 309 A Built loop between residues 188 B and 192 B Built loop between residues 339 B and 342 B 7 chains (846 residues) following loop building 4 chains (827 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7368 restraints for refining 7213 atoms. 752 conditional restraints added. Observations/parameters ratio is 1.55 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1937 (Rfree = 0.000) for 7213 atoms. Found 80 (80 requested) and removed 83 (80 requested) atoms. Cycle 37: After refmac, R = 0.1845 (Rfree = 0.000) for 7203 atoms. Found 80 (80 requested) and removed 81 (80 requested) atoms. Cycle 38: After refmac, R = 0.1821 (Rfree = 0.000) for 7200 atoms. Found 80 (80 requested) and removed 81 (80 requested) atoms. Cycle 39: After refmac, R = 0.1814 (Rfree = 0.000) for 7195 atoms. Found 80 (80 requested) and removed 86 (80 requested) atoms. Cycle 40: After refmac, R = 0.1822 (Rfree = 0.000) for 7189 atoms. Found 80 (80 requested) and removed 83 (80 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.34 2.25 NCS extension: 249 residues added (592 deleted due to clashes), 7439 seeds are put forward Round 1: 849 peptides, 10 chains. Longest chain 204 peptides. Score 0.948 Round 2: 847 peptides, 10 chains. Longest chain 206 peptides. Score 0.948 Round 3: 849 peptides, 14 chains. Longest chain 177 peptides. Score 0.942 Round 4: 846 peptides, 16 chains. Longest chain 124 peptides. Score 0.939 Round 5: 835 peptides, 21 chains. Longest chain 149 peptides. Score 0.928 Taking the results from Round 2 Chains 10, Residues 837, Estimated correctness of the model 99.5 % 9 chains (824 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 102 A Built loop between residues 190 A and 193 A Built loop between residues 276 A and 279 A Built loop between residues 390 A and 394 A Built loop between residues 98 B and 105 B Built loop between residues 239 B and 242 B 4 chains (856 residues) following loop building 3 chains (843 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7242 restraints for refining 7257 atoms. 487 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1972 (Rfree = 0.000) for 7257 atoms. Found 81 (81 requested) and removed 86 (81 requested) atoms. Cycle 42: After refmac, R = 0.1862 (Rfree = 0.000) for 7248 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Cycle 43: After refmac, R = 0.1825 (Rfree = 0.000) for 7243 atoms. Found 81 (81 requested) and removed 81 (81 requested) atoms. Cycle 44: After refmac, R = 0.1793 (Rfree = 0.000) for 7242 atoms. Found 81 (81 requested) and removed 89 (81 requested) atoms. Cycle 45: After refmac, R = 0.1785 (Rfree = 0.000) for 7231 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.35 2.26 NCS extension: 190 residues added (266 deleted due to clashes), 7422 seeds are put forward Round 1: 845 peptides, 12 chains. Longest chain 204 peptides. Score 0.945 Round 2: 847 peptides, 11 chains. Longest chain 177 peptides. Score 0.946 Round 3: 845 peptides, 14 chains. Longest chain 120 peptides. Score 0.941 Round 4: 824 peptides, 22 chains. Longest chain 139 peptides. Score 0.923 Round 5: 825 peptides, 22 chains. Longest chain 91 peptides. Score 0.924 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 836, Estimated correctness of the model 99.5 % 10 chains (821 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 277 A and 280 A Built loop between residues 307 A and 310 A Built loop between residues 98 B and 104 B Built loop between residues 246 B and 249 B Built loop between residues 308 B and 311 B Built loop between residues 338 B and 341 B Built loop between residues 394 B and 399 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 6712 restraints for refining 6601 atoms. Observations/parameters ratio is 1.70 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2368 (Rfree = 0.000) for 6601 atoms. Found 64 (74 requested) and removed 0 (74 requested) atoms. Cycle 47: After refmac, R = 0.2196 (Rfree = 0.000) for 6601 atoms. Found 28 (74 requested) and removed 2 (74 requested) atoms. Cycle 48: After refmac, R = 0.2148 (Rfree = 0.000) for 6601 atoms. Found 12 (75 requested) and removed 3 (75 requested) atoms. Cycle 49: After refmac, R = 0.2130 (Rfree = 0.000) for 6601 atoms. TimeTaking 98.6