Mon 24 Dec 07:50:50 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vl4-2.3-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-2.3-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vl4-2.3-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:50:55 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vl4-2.3-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 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-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 80.171 107.117 119.834 90.000 90.000 90.000 Input sequence file: 1vl4-2.3-parrot-noncs.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 = 0.3135 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2414 (Rfree = 0.000) for 7966 atoms. Found 87 (178 requested) and removed 102 (89 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.36 2.27 NCS extension: 0 residues added, 7951 seeds are put forward Round 1: 579 peptides, 83 chains. Longest chain 20 peptides. Score 0.554 Round 2: 664 peptides, 63 chains. Longest chain 48 peptides. Score 0.735 Round 3: 719 peptides, 50 chains. Longest chain 59 peptides. Score 0.817 Round 4: 735 peptides, 42 chains. Longest chain 62 peptides. Score 0.848 Round 5: 757 peptides, 34 chains. Longest chain 102 peptides. Score 0.878 Taking the results from Round 5 Chains 37, Residues 723, Estimated correctness of the model 97.6 % 17 chains (606 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 A and 47 A Built loop between residues 190 A and 193 A Built loop between residues 209 A and 212 A Built loop between residues 48 B and 55 B Built loop between residues 189 B and 193 B 31 chains (737 residues) following loop building 12 chains (621 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 8987 restraints for refining 7280 atoms. 3613 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2831 (Rfree = 0.000) for 7280 atoms. Found 142 (163 requested) and removed 109 (81 requested) atoms. Cycle 2: After refmac, R = 0.2567 (Rfree = 0.000) for 7217 atoms. Found 94 (161 requested) and removed 85 (82 requested) atoms. Cycle 3: After refmac, R = 0.2449 (Rfree = 0.000) for 7171 atoms. Found 87 (156 requested) and removed 82 (81 requested) atoms. Cycle 4: After refmac, R = 0.2384 (Rfree = 0.000) for 7139 atoms. Found 89 (151 requested) and removed 80 (80 requested) atoms. Cycle 5: After refmac, R = 0.2317 (Rfree = 0.000) for 7126 atoms. Found 69 (147 requested) and removed 81 (80 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.39 2.30 NCS extension: 286 residues added (119 deleted due to clashes), 7412 seeds are put forward Round 1: 789 peptides, 29 chains. Longest chain 103 peptides. Score 0.900 Round 2: 804 peptides, 23 chains. Longest chain 116 peptides. Score 0.916 Round 3: 800 peptides, 27 chains. Longest chain 103 peptides. Score 0.907 Round 4: 816 peptides, 22 chains. Longest chain 90 peptides. Score 0.921 Round 5: 794 peptides, 30 chains. Longest chain 131 peptides. Score 0.900 Taking the results from Round 4 Chains 25, Residues 794, Estimated correctness of the model 98.9 % 15 chains (749 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 96 A and 102 A Built loop between residues 190 A and 193 A Built loop between residues 390 A and 401 A Built loop between residues 40 B and 50 B Built loop between residues 96 B and 104 B Built loop between residues 181 B and 184 B Built loop between residues 231 B and 242 B Built loop between residues 266 B and 269 B Built loop between residues 391 B and 397 B Built loop between residues 410 B and 413 B 11 chains (836 residues) following loop building 5 chains (803 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7654 restraints for refining 7397 atoms. 1166 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2499 (Rfree = 0.000) for 7397 atoms. Found 149 (149 requested) and removed 116 (83 requested) atoms. Cycle 7: After refmac, R = 0.2276 (Rfree = 0.000) for 7387 atoms. Found 101 (146 requested) and removed 92 (83 requested) atoms. Cycle 8: After refmac, R = 0.2181 (Rfree = 0.000) for 7370 atoms. Found 83 (142 requested) and removed 84 (82 requested) atoms. Cycle 9: After refmac, R = 0.2110 (Rfree = 0.000) for 7351 atoms. Found 82 (139 requested) and removed 83 (82 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2070 (Rfree = 0.000) for 7333 atoms. Found 60 (134 requested) and removed 86 (82 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.38 2.29 NCS extension: 73 residues added (238 deleted due to clashes), 7399 seeds are put forward Round 1: 830 peptides, 16 chains. Longest chain 136 peptides. Score 0.935 Round 2: 830 peptides, 19 chains. Longest chain 168 peptides. Score 0.930 Round 3: 835 peptides, 16 chains. Longest chain 114 peptides. Score 0.936 Round 4: 825 peptides, 23 chains. Longest chain 79 peptides. Score 0.922 Round 5: 830 peptides, 18 chains. Longest chain 144 peptides. Score 0.932 Taking the results from Round 3 Chains 16, Residues 819, Estimated correctness of the model 99.3 % 12 chains (760 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 167 A and 178 A Built loop between residues 333 A and 336 A Built loop between residues 390 A and 399 A Built loop between residues 98 B and 102 B Built loop between residues 190 B and 193 B Built loop between residues 355 B and 358 B Built loop between residues 409 B and 415 B 9 chains (851 residues) following loop building 5 chains (792 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7718 restraints for refining 7408 atoms. 1218 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2291 (Rfree = 0.000) for 7408 atoms. Found 133 (133 requested) and removed 115 (83 requested) atoms. Cycle 12: After refmac, R = 0.2102 (Rfree = 0.000) for 7408 atoms. Found 98 (129 requested) and removed 90 (83 requested) atoms. Cycle 13: After refmac, R = 0.2028 (Rfree = 0.000) for 7403 atoms. Found 74 (126 requested) and removed 88 (83 requested) atoms. Cycle 14: After refmac, R = 0.1993 (Rfree = 0.000) for 7379 atoms. Found 87 (122 requested) and removed 88 (82 requested) atoms. Cycle 15: After refmac, R = 0.1959 (Rfree = 0.000) for 7368 atoms. Found 76 (119 requested) and removed 89 (82 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.35 2.26 NCS extension: 135 residues added (342 deleted due to clashes), 7500 seeds are put forward Round 1: 832 peptides, 12 chains. Longest chain 175 peptides. Score 0.942 Round 2: 842 peptides, 11 chains. Longest chain 208 peptides. Score 0.945 Round 3: 830 peptides, 19 chains. Longest chain 111 peptides. Score 0.930 Round 4: 827 peptides, 16 chains. Longest chain 131 peptides. Score 0.934 Round 5: 838 peptides, 18 chains. Longest chain 121 peptides. Score 0.934 Taking the results from Round 2 Chains 13, Residues 831, Estimated correctness of the model 99.4 % 11 chains (820 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 47 A and 50 A Built loop between residues 97 A and 104 A Built loop between residues 247 A and 250 A Built loop between residues 276 A and 279 A Built loop between residues 307 A and 310 A Built loop between residues 395 A and 399 A Built loop between residues 96 B and 103 B Built loop between residues 216 B and 219 B Built loop between residues 231 B and 238 B 3 chains (857 residues) following loop building 2 chains (851 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7255 restraints for refining 7382 atoms. 486 conditional restraints added. Observations/parameters ratio is 1.52 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2060 (Rfree = 0.000) for 7382 atoms. Found 115 (115 requested) and removed 93 (82 requested) atoms. Cycle 17: After refmac, R = 0.1930 (Rfree = 0.000) for 7384 atoms. Found 113 (113 requested) and removed 90 (83 requested) atoms. Cycle 18: After refmac, R = 0.1870 (Rfree = 0.000) for 7400 atoms. Found 110 (110 requested) and removed 85 (83 requested) atoms. Cycle 19: After refmac, R = 0.1837 (Rfree = 0.000) for 7423 atoms. Found 106 (106 requested) and removed 87 (83 requested) atoms. Cycle 20: After refmac, R = 0.1821 (Rfree = 0.000) for 7434 atoms. Found 102 (104 requested) and removed 90 (83 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.34 2.25 NCS extension: 185 residues added (256 deleted due to clashes), 7639 seeds are put forward Round 1: 838 peptides, 13 chains. Longest chain 200 peptides. Score 0.942 Round 2: 848 peptides, 14 chains. Longest chain 175 peptides. Score 0.942 Round 3: 846 peptides, 15 chains. Longest chain 136 peptides. Score 0.940 Round 4: 836 peptides, 15 chains. Longest chain 119 peptides. Score 0.938 Round 5: 845 peptides, 17 chains. Longest chain 123 peptides. Score 0.937 Taking the results from Round 2 Chains 15, Residues 834, Estimated correctness of the model 99.4 % 10 chains (801 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 A and 104 A Built loop between residues 138 A and 141 A Built loop between residues 190 A and 193 A Built loop between residues 276 A and 279 A Built loop between residues 98 B and 104 B Built loop between residues 277 B and 280 B 8 chains (848 residues) following loop building 4 chains (817 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7387 restraints for refining 7254 atoms. 781 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2049 (Rfree = 0.000) for 7254 atoms. Found 97 (97 requested) and removed 87 (81 requested) atoms. Cycle 22: After refmac, R = 0.1917 (Rfree = 0.000) for 7254 atoms. Found 95 (95 requested) and removed 82 (81 requested) atoms. Cycle 23: After refmac, R = 0.1857 (Rfree = 0.000) for 7260 atoms. Found 91 (91 requested) and removed 83 (81 requested) atoms. Cycle 24: After refmac, R = 0.1833 (Rfree = 0.000) for 7265 atoms. Found 88 (88 requested) and removed 85 (81 requested) atoms. Cycle 25: After refmac, R = 0.1826 (Rfree = 0.000) for 7262 atoms. Found 85 (85 requested) and removed 85 (81 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.34 2.25 NCS extension: 402 residues added (593 deleted due to clashes), 7671 seeds are put forward Round 1: 837 peptides, 14 chains. Longest chain 126 peptides. Score 0.940 Round 2: 850 peptides, 9 chains. Longest chain 263 peptides. Score 0.950 Round 3: 843 peptides, 16 chains. Longest chain 121 peptides. Score 0.938 Round 4: 845 peptides, 13 chains. Longest chain 171 peptides. Score 0.943 Round 5: 831 peptides, 20 chains. Longest chain 121 peptides. Score 0.929 Taking the results from Round 2 Chains 12, Residues 841, Estimated correctness of the model 99.5 % 9 chains (834 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 103 A Built loop between residues 190 A and 198 A Built loop between residues 237 A and 240 A Built loop between residues 276 A and 279 A Built loop between residues 274 B and 280 B Built loop between residues 393 B and 398 B 3 chains (859 residues) following loop building 3 chains (859 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 44794 reflections ( 98.68 % complete ) and 7116 restraints for refining 7308 atoms. 304 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2017 (Rfree = 0.000) for 7308 atoms. Found 82 (82 requested) and removed 96 (82 requested) atoms. Cycle 27: After refmac, R = 0.1905 (Rfree = 0.000) for 7284 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 28: After refmac, R = 0.1867 (Rfree = 0.000) for 7278 atoms. Found 81 (81 requested) and removed 82 (81 requested) atoms. Cycle 29: After refmac, R = 0.1830 (Rfree = 0.000) for 7276 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 30: After refmac, R = 0.1811 (Rfree = 0.000) for 7269 atoms. Found 81 (81 requested) and removed 85 (81 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.34 2.25 NCS extension: 177 residues added (253 deleted due to clashes), 7446 seeds are put forward Round 1: 839 peptides, 11 chains. Longest chain 211 peptides. Score 0.945 Round 2: 845 peptides, 11 chains. Longest chain 203 peptides. Score 0.946 Round 3: 844 peptides, 14 chains. Longest chain 163 peptides. Score 0.941 Round 4: 838 peptides, 18 chains. Longest chain 168 peptides. Score 0.934 Round 5: 842 peptides, 16 chains. Longest chain 175 peptides. Score 0.938 Taking the results from Round 2 Chains 14, Residues 834, Estimated correctness of the model 99.5 % 11 chains (827 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 62 A and 65 A Built loop between residues 189 A and 193 A Built loop between residues 204 A and 208 A Built loop between residues 330 A and 333 A Built loop between residues 394 A and 398 A Built loop between residues 97 B and 102 B Built loop between residues 137 B and 141 B Built loop between residues 239 B and 242 B 4 chains (854 residues) following loop building 3 chains (849 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7177 restraints for refining 7263 atoms. 436 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1991 (Rfree = 0.000) for 7263 atoms. Found 81 (81 requested) and removed 94 (81 requested) atoms. Cycle 32: After refmac, R = 0.1882 (Rfree = 0.000) for 7239 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1836 (Rfree = 0.000) for 7233 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Cycle 34: After refmac, R = 0.1812 (Rfree = 0.000) for 7229 atoms. Found 81 (81 requested) and removed 86 (81 requested) atoms. Cycle 35: After refmac, R = 0.1804 (Rfree = 0.000) for 7218 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.34 2.25 NCS extension: 5 residues added (13 deleted due to clashes), 7225 seeds are put forward Round 1: 847 peptides, 10 chains. Longest chain 138 peptides. Score 0.948 Round 2: 842 peptides, 13 chains. Longest chain 167 peptides. Score 0.942 Round 3: 842 peptides, 19 chains. Longest chain 150 peptides. Score 0.933 Round 4: 840 peptides, 18 chains. Longest chain 159 peptides. Score 0.934 Round 5: 844 peptides, 15 chains. Longest chain 163 peptides. Score 0.940 Taking the results from Round 1 Chains 10, Residues 837, Estimated correctness of the model 99.5 % 9 chains (834 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 97 B and 101 B Built loop between residues 189 B and 192 B Built loop between residues 308 B and 311 B Built loop between residues 390 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 7129 restraints for refining 7254 atoms. 329 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1974 (Rfree = 0.000) for 7254 atoms. Found 81 (81 requested) and removed 94 (81 requested) atoms. Cycle 37: After refmac, R = 0.1858 (Rfree = 0.000) for 7233 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Cycle 38: After refmac, R = 0.1832 (Rfree = 0.000) for 7231 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 39: After refmac, R = 0.1803 (Rfree = 0.000) for 7225 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1811 (Rfree = 0.000) for 7222 atoms. Found 81 (81 requested) and removed 90 (81 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.33 2.24 NCS extension: 0 residues added, 7220 seeds are put forward Round 1: 847 peptides, 10 chains. Longest chain 255 peptides. Score 0.948 Round 2: 842 peptides, 14 chains. Longest chain 167 peptides. Score 0.941 Round 3: 841 peptides, 17 chains. Longest chain 140 peptides. Score 0.936 Round 4: 832 peptides, 19 chains. Longest chain 174 peptides. Score 0.930 Round 5: 830 peptides, 19 chains. Longest chain 176 peptides. Score 0.930 Taking the results from Round 1 Chains 11, Residues 837, Estimated correctness of the model 99.5 % 10 chains (835 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 97 B and 101 B Built loop between residues 190 B and 193 B Built loop between residues 245 B and 248 B Built loop between residues 307 B and 310 B Built loop between residues 393 B and 398 B Built loop between residues 428 B and 431 B 2 chains (858 residues) following loop building 2 chains (858 residues) in sequence following loop building ------------------------------------------------------ 44794 reflections ( 98.68 % complete ) and 7124 restraints for refining 7262 atoms. 324 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1939 (Rfree = 0.000) for 7262 atoms. Found 81 (81 requested) and removed 90 (81 requested) atoms. Cycle 42: After refmac, R = 0.1840 (Rfree = 0.000) for 7250 atoms. Found 81 (81 requested) and removed 83 (81 requested) atoms. Cycle 43: After refmac, R = 0.1792 (Rfree = 0.000) for 7247 atoms. Found 81 (81 requested) and removed 84 (81 requested) atoms. Cycle 44: After refmac, R = 0.1770 (Rfree = 0.000) for 7241 atoms. Found 81 (81 requested) and removed 81 (81 requested) atoms. Cycle 45: After refmac, R = 0.1756 (Rfree = 0.000) for 7239 atoms. Found 81 (81 requested) and removed 86 (81 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.34 2.25 NCS extension: 0 residues added, 7237 seeds are put forward Round 1: 843 peptides, 11 chains. Longest chain 118 peptides. Score 0.946 Round 2: 841 peptides, 15 chains. Longest chain 91 peptides. Score 0.939 Round 3: 843 peptides, 16 chains. Longest chain 131 peptides. Score 0.938 Round 4: 844 peptides, 15 chains. Longest chain 168 peptides. Score 0.940 Round 5: 835 peptides, 23 chains. Longest chain 127 peptides. Score 0.924 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 832, Estimated correctness of the model 99.5 % 11 chains (832 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 81 A and 84 A Built loop between residues 97 A and 102 A Built loop between residues 189 A and 192 A Built loop between residues 308 A and 311 A Built loop between residues 390 A and 393 A Built loop between residues 98 B and 102 B Built loop between residues 189 B and 192 B Built loop between residues 308 B and 311 B Built loop between residues 390 B and 398 B 2 chains (858 residues) following loop building 2 chains (858 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 44794 reflections ( 98.68 % complete ) and 6800 restraints for refining 6686 atoms. Observations/parameters ratio is 1.67 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2320 (Rfree = 0.000) for 6686 atoms. Found 63 (75 requested) and removed 0 (75 requested) atoms. Cycle 47: After refmac, R = 0.2157 (Rfree = 0.000) for 6686 atoms. Found 25 (75 requested) and removed 1 (75 requested) atoms. Cycle 48: After refmac, R = 0.2106 (Rfree = 0.000) for 6686 atoms. Found 16 (75 requested) and removed 2 (75 requested) atoms. Cycle 49: After refmac, R = 0.2087 (Rfree = 0.000) for 6686 atoms. TimeTaking 102.13