Tue 25 Dec 19:27:57 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 2ii1-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ii1-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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/2ii1-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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 19:28:07 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/2ii1-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ii1-1.9-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 1083 and 0 Target number of residues in the AU: 1083 Target solvent content: 0.4721 Checking the provided sequence file Detected sequence length: 301 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1204 Adjusted target solvent content: 0.41 Input MTZ file: 2ii1-1.9-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: 1 Cell parameters: 43.759 69.605 94.984 73.954 88.905 86.625 Input sequence file: 2ii1-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 9632 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 1 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: 91.283 1.950 Wilson plot Bfac: 18.16 70806 reflections ( 90.30 % complete ) and 0 restraints for refining 10608 atoms. Observations/parameters ratio is 1.67 ------------------------------------------------------ Starting model: R = 0.3340 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2800 (Rfree = 0.000) for 10608 atoms. Found 278 (390 requested) and removed 211 (195 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.94 2.19 NCS extension: 0 residues added, 10675 seeds are put forward Round 1: 781 peptides, 106 chains. Longest chain 19 peptides. Score 0.642 Round 2: 891 peptides, 70 chains. Longest chain 42 peptides. Score 0.833 Round 3: 941 peptides, 67 chains. Longest chain 52 peptides. Score 0.861 Round 4: 969 peptides, 61 chains. Longest chain 57 peptides. Score 0.882 Round 5: 1011 peptides, 52 chains. Longest chain 78 peptides. Score 0.909 Taking the results from Round 5 Chains 59, Residues 959, Estimated correctness of the model 99.2 % 24 chains (761 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 251 A and 256 A Built loop between residues 191 C and 195 C Built loop between residues 249 C and 256 C Built loop between residues 140 B and 150 B 53 chains (976 residues) following loop building 20 chains (783 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 12498 restraints for refining 9564 atoms. 5897 conditional restraints added. Observations/parameters ratio is 1.85 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3064 (Rfree = 0.000) for 9564 atoms. Found 280 (352 requested) and removed 183 (176 requested) atoms. Cycle 2: After refmac, R = 0.2753 (Rfree = 0.000) for 9631 atoms. Found 216 (348 requested) and removed 85 (177 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2555 (Rfree = 0.000) for 9696 atoms. Found 210 (352 requested) and removed 46 (179 requested) atoms. Cycle 4: After refmac, R = 0.2402 (Rfree = 0.000) for 9823 atoms. Found 156 (356 requested) and removed 37 (181 requested) atoms. Cycle 5: After refmac, R = 0.2291 (Rfree = 0.000) for 9907 atoms. Found 134 (359 requested) and removed 31 (183 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.91 2.16 NCS extension: 5 residues added (7 deleted due to clashes), 10035 seeds are put forward Round 1: 1032 peptides, 45 chains. Longest chain 87 peptides. Score 0.923 Round 2: 1071 peptides, 36 chains. Longest chain 151 peptides. Score 0.942 Round 3: 1074 peptides, 40 chains. Longest chain 90 peptides. Score 0.938 Round 4: 1068 peptides, 40 chains. Longest chain 119 peptides. Score 0.937 Round 5: 1083 peptides, 34 chains. Longest chain 118 peptides. Score 0.946 Taking the results from Round 5 Chains 36, Residues 1049, Estimated correctness of the model 99.7 % 21 chains (954 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 249 A and 252 A Built loop between residues 278 A and 281 A Built loop between residues 212 C and 219 C Built loop between residues 278 C and 281 C Built loop between residues 69 B and 72 B Built loop between residues 175 B and 178 B Built loop between residues 152 D and 155 D 28 chains (1065 residues) following loop building 14 chains (972 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 70806 reflections ( 90.30 % complete ) and 11156 restraints for refining 9852 atoms. 3473 conditional restraints added. Observations/parameters ratio is 1.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2447 (Rfree = 0.000) for 9852 atoms. Found 292 (355 requested) and removed 185 (181 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2262 (Rfree = 0.000) for 9931 atoms. Found 165 (351 requested) and removed 47 (183 requested) atoms. Cycle 8: After refmac, R = 0.2148 (Rfree = 0.000) for 10024 atoms. Found 146 (355 requested) and removed 31 (185 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2070 (Rfree = 0.000) for 10116 atoms. Found 118 (358 requested) and removed 28 (186 requested) atoms. Cycle 10: After refmac, R = 0.2009 (Rfree = 0.000) for 10188 atoms. Found 97 (360 requested) and removed 31 (187 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.91 2.16 NCS extension: 2 residues added (39 deleted due to clashes), 10260 seeds are put forward Round 1: 1069 peptides, 40 chains. Longest chain 85 peptides. Score 0.937 Round 2: 1093 peptides, 30 chains. Longest chain 127 peptides. Score 0.952 Round 3: 1093 peptides, 38 chains. Longest chain 90 peptides. Score 0.943 Round 4: 1101 peptides, 31 chains. Longest chain 90 peptides. Score 0.952 Round 5: 1097 peptides, 39 chains. Longest chain 82 peptides. Score 0.942 Taking the results from Round 4 Chains 33, Residues 1070, Estimated correctness of the model 99.7 % 20 chains (955 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 139 A Built loop between residues 149 A and 154 A Built loop between residues 140 C and 143 C Built loop between residues 186 C and 190 C Built loop between residues 152 B and 155 B Built loop between residues 186 B and 189 B Built loop between residues 215 B and 219 B Built loop between residues 131 D and 137 D 24 chains (1089 residues) following loop building 12 chains (978 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 11067 restraints for refining 9953 atoms. 3269 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2149 (Rfree = 0.000) for 9953 atoms. Found 244 (351 requested) and removed 118 (183 requested) atoms. Cycle 12: After refmac, R = 0.2020 (Rfree = 0.000) for 10068 atoms. Found 175 (356 requested) and removed 37 (185 requested) atoms. Cycle 13: After refmac, R = 0.1938 (Rfree = 0.000) for 10192 atoms. Found 146 (360 requested) and removed 25 (187 requested) atoms. Cycle 14: After refmac, R = 0.1875 (Rfree = 0.000) for 10300 atoms. Found 121 (364 requested) and removed 38 (189 requested) atoms. Cycle 15: After refmac, R = 0.1823 (Rfree = 0.000) for 10364 atoms. Found 143 (367 requested) and removed 42 (191 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.90 2.14 NCS extension: 5 residues added (206 deleted due to clashes), 10471 seeds are put forward Round 1: 1094 peptides, 33 chains. Longest chain 80 peptides. Score 0.949 Round 2: 1106 peptides, 32 chains. Longest chain 127 peptides. Score 0.951 Round 3: 1109 peptides, 34 chains. Longest chain 114 peptides. Score 0.949 Round 4: 1105 peptides, 34 chains. Longest chain 90 peptides. Score 0.949 Round 5: 1113 peptides, 34 chains. Longest chain 84 peptides. Score 0.950 Taking the results from Round 2 Chains 35, Residues 1074, Estimated correctness of the model 99.7 % 19 chains (937 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 278 C and 281 C Built loop between residues 41 B and 45 B Built loop between residues 61 B and 64 B Built loop between residues 152 B and 155 B Built loop between residues 278 B and 281 B Built loop between residues 136 D and 139 D Built loop between residues 216 D and 219 D 27 chains (1088 residues) following loop building 12 chains (952 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 11607 restraints for refining 10112 atoms. 3898 conditional restraints added. Observations/parameters ratio is 1.75 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2019 (Rfree = 0.000) for 10112 atoms. Found 256 (357 requested) and removed 121 (186 requested) atoms. Cycle 17: After refmac, R = 0.1906 (Rfree = 0.000) for 10233 atoms. Found 162 (362 requested) and removed 42 (188 requested) atoms. Cycle 18: After refmac, R = 0.1831 (Rfree = 0.000) for 10336 atoms. Found 158 (366 requested) and removed 32 (190 requested) atoms. Cycle 19: After refmac, R = 0.1780 (Rfree = 0.000) for 10450 atoms. Found 133 (370 requested) and removed 67 (192 requested) atoms. Cycle 20: After refmac, R = 0.1751 (Rfree = 0.000) for 10502 atoms. Found 167 (364 requested) and removed 71 (193 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.89 2.13 NCS extension: 8 residues added (23 deleted due to clashes), 10610 seeds are put forward Round 1: 1103 peptides, 32 chains. Longest chain 90 peptides. Score 0.951 Round 2: 1114 peptides, 30 chains. Longest chain 84 peptides. Score 0.954 Round 3: 1116 peptides, 30 chains. Longest chain 90 peptides. Score 0.954 Round 4: 1110 peptides, 31 chains. Longest chain 91 peptides. Score 0.953 Round 5: 1108 peptides, 31 chains. Longest chain 108 peptides. Score 0.952 Taking the results from Round 3 Chains 32, Residues 1086, Estimated correctness of the model 99.8 % 26 chains (1044 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 A and 87 A Built loop between residues 105 A and 109 A Built loop between residues 149 A and 154 A Built loop between residues 175 A and 178 A Built loop between residues 186 A and 190 A Built loop between residues 216 A and 219 A Built loop between residues 61 C and 64 C Built loop between residues 152 C and 155 C Built loop between residues 193 C and 196 C Built loop between residues 216 C and 219 C Built loop between residues 152 B and 158 B Built loop between residues 175 B and 178 B Built loop between residues 216 B and 219 B Built loop between residues 233 B and 236 B Built loop between residues 140 D and 143 D Built loop between residues 151 D and 154 D Built loop between residues 186 D and 191 D 15 chains (1129 residues) following loop building 9 chains (1087 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10426 restraints for refining 10214 atoms. 2055 conditional restraints added. Observations/parameters ratio is 1.73 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1959 (Rfree = 0.000) for 10214 atoms. Found 317 (353 requested) and removed 151 (188 requested) atoms. Cycle 22: After refmac, R = 0.1852 (Rfree = 0.000) for 10361 atoms. Found 217 (359 requested) and removed 68 (191 requested) atoms. Cycle 23: After refmac, R = 0.1777 (Rfree = 0.000) for 10494 atoms. Found 206 (363 requested) and removed 59 (193 requested) atoms. Cycle 24: After refmac, R = 0.1728 (Rfree = 0.000) for 10628 atoms. Found 175 (368 requested) and removed 87 (195 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1692 (Rfree = 0.000) for 10700 atoms. Found 180 (370 requested) and removed 92 (197 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.89 2.13 NCS extension: 24 residues added (188 deleted due to clashes), 10817 seeds are put forward Round 1: 1118 peptides, 26 chains. Longest chain 90 peptides. Score 0.959 Round 2: 1131 peptides, 20 chains. Longest chain 131 peptides. Score 0.966 Round 3: 1119 peptides, 29 chains. Longest chain 90 peptides. Score 0.956 Round 4: 1121 peptides, 25 chains. Longest chain 90 peptides. Score 0.960 Round 5: 1123 peptides, 25 chains. Longest chain 114 peptides. Score 0.960 Taking the results from Round 2 Chains 21, Residues 1111, Estimated correctness of the model 99.9 % 17 chains (1080 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 64 A Built loop between residues 134 A and 137 A Built loop between residues 61 C and 64 C Built loop between residues 135 C and 138 C Built loop between residues 216 C and 219 C Built loop between residues 135 B and 137 B Built loop between residues 185 B and 191 B Built loop between residues 216 B and 219 B 12 chains (1129 residues) following loop building 9 chains (1099 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10577 restraints for refining 10312 atoms. 2172 conditional restraints added. Observations/parameters ratio is 1.72 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1926 (Rfree = 0.000) for 10312 atoms. Found 336 (349 requested) and removed 132 (189 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1811 (Rfree = 0.000) for 10496 atoms. Found 206 (356 requested) and removed 67 (193 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1740 (Rfree = 0.000) for 10617 atoms. Found 187 (360 requested) and removed 78 (195 requested) atoms. Cycle 29: After refmac, R = 0.1696 (Rfree = 0.000) for 10711 atoms. Found 170 (362 requested) and removed 90 (197 requested) atoms. Cycle 30: After refmac, R = 0.1666 (Rfree = 0.000) for 10779 atoms. Found 180 (357 requested) and removed 96 (198 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.89 2.13 NCS extension: 11 residues added (189 deleted due to clashes), 10877 seeds are put forward Round 1: 1112 peptides, 28 chains. Longest chain 90 peptides. Score 0.956 Round 2: 1119 peptides, 26 chains. Longest chain 90 peptides. Score 0.959 Round 3: 1115 peptides, 24 chains. Longest chain 131 peptides. Score 0.960 Round 4: 1122 peptides, 27 chains. Longest chain 125 peptides. Score 0.958 Round 5: 1128 peptides, 25 chains. Longest chain 131 peptides. Score 0.961 Taking the results from Round 5 Chains 25, Residues 1103, Estimated correctness of the model 99.8 % 19 chains (1071 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 216 A and 219 A Built loop between residues 60 C and 64 C Built loop between residues 152 C and 155 C Built loop between residues 189 C and 192 C Built loop between residues 216 C and 219 C Built loop between residues 193 B and 196 B Built loop between residues 216 B and 219 B Built loop between residues 110 D and 113 D Built loop between residues 135 D and 137 D Built loop between residues 152 D and 155 D 14 chains (1125 residues) following loop building 8 chains (1093 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 70806 reflections ( 90.30 % complete ) and 10694 restraints for refining 10353 atoms. 2308 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1900 (Rfree = 0.000) for 10353 atoms. Found 335 (335 requested) and removed 132 (190 requested) atoms. Cycle 32: After refmac, R = 0.1789 (Rfree = 0.000) for 10531 atoms. Found 238 (341 requested) and removed 66 (194 requested) atoms. Cycle 33: After refmac, R = 0.1718 (Rfree = 0.000) for 10692 atoms. Found 179 (347 requested) and removed 89 (197 requested) atoms. Cycle 34: After refmac, R = 0.1678 (Rfree = 0.000) for 10769 atoms. Found 188 (349 requested) and removed 88 (198 requested) atoms. Cycle 35: After refmac, R = 0.1647 (Rfree = 0.000) for 10864 atoms. Found 166 (352 requested) and removed 118 (200 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.89 2.13 NCS extension: 12 residues added (157 deleted due to clashes), 10930 seeds are put forward Round 1: 1120 peptides, 29 chains. Longest chain 80 peptides. Score 0.956 Round 2: 1129 peptides, 29 chains. Longest chain 80 peptides. Score 0.957 Round 3: 1127 peptides, 27 chains. Longest chain 154 peptides. Score 0.959 Round 4: 1118 peptides, 32 chains. Longest chain 90 peptides. Score 0.953 Round 5: 1122 peptides, 29 chains. Longest chain 131 peptides. Score 0.956 Taking the results from Round 3 Chains 27, Residues 1100, Estimated correctness of the model 99.8 % 22 chains (1061 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 140 A and 143 A Built loop between residues 175 A and 178 A Built loop between residues 278 A and 281 A Built loop between residues 60 C and 64 C Built loop between residues 152 C and 155 C Built loop between residues 175 C and 178 C Built loop between residues 186 C and 195 C Built loop between residues 216 C and 219 C Built loop between residues 278 C and 281 C Built loop between residues 216 B and 219 B Built loop between residues 152 D and 158 D Built loop between residues 216 D and 219 D Built loop between residues 278 D and 281 D 12 chains (1135 residues) following loop building 8 chains (1099 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10662 restraints for refining 10379 atoms. 2219 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1896 (Rfree = 0.000) for 10379 atoms. Found 329 (329 requested) and removed 122 (191 requested) atoms. Cycle 37: After refmac, R = 0.1789 (Rfree = 0.000) for 10566 atoms. Found 173 (335 requested) and removed 76 (194 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1720 (Rfree = 0.000) for 10652 atoms. Found 182 (337 requested) and removed 61 (196 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 39: After refmac, R = 0.1677 (Rfree = 0.000) for 10759 atoms. Found 161 (341 requested) and removed 85 (198 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1658 (Rfree = 0.000) for 10821 atoms. Found 186 (334 requested) and removed 89 (199 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.89 2.13 NCS extension: 13 residues added (227 deleted due to clashes), 10934 seeds are put forward Round 1: 1117 peptides, 29 chains. Longest chain 81 peptides. Score 0.956 Round 2: 1134 peptides, 25 chains. Longest chain 127 peptides. Score 0.961 Round 3: 1129 peptides, 28 chains. Longest chain 128 peptides. Score 0.958 Round 4: 1133 peptides, 26 chains. Longest chain 111 peptides. Score 0.960 Round 5: 1132 peptides, 25 chains. Longest chain 131 peptides. Score 0.961 Taking the results from Round 5 Chains 26, Residues 1107, Estimated correctness of the model 99.8 % 22 chains (1088 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 135 A and 138 A Built loop between residues 151 A and 154 A Built loop between residues 216 A and 219 A Built loop between residues 60 C and 64 C Built loop between residues 135 C and 138 C Built loop between residues 150 C and 154 C Built loop between residues 190 C and 193 C Built loop between residues 215 C and 219 C Built loop between residues 193 B and 196 B Built loop between residues 203 B and 207 B Built loop between residues 216 B and 219 B Built loop between residues 255 B and 258 B Built loop between residues 61 D and 64 D Built loop between residues 134 D and 137 D Built loop between residues 216 D and 219 D 10 chains (1140 residues) following loop building 7 chains (1122 residues) in sequence following loop building ------------------------------------------------------ 70806 reflections ( 90.30 % complete ) and 10423 restraints for refining 10361 atoms. 1867 conditional restraints added. Observations/parameters ratio is 1.71 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1874 (Rfree = 0.000) for 10361 atoms. Found 320 (320 requested) and removed 117 (190 requested) atoms. Cycle 42: After refmac, R = 0.1773 (Rfree = 0.000) for 10542 atoms. Found 214 (326 requested) and removed 64 (194 requested) atoms. Cycle 43: After refmac, R = 0.1712 (Rfree = 0.000) for 10681 atoms. Found 167 (330 requested) and removed 67 (196 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1671 (Rfree = 0.000) for 10762 atoms. Found 159 (333 requested) and removed 92 (198 requested) atoms. Cycle 45: After refmac, R = 0.1646 (Rfree = 0.000) for 10817 atoms. Found 156 (326 requested) and removed 92 (199 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.89 2.13 NCS extension: 17 residues added (223 deleted due to clashes), 10899 seeds are put forward Round 1: 1120 peptides, 27 chains. Longest chain 90 peptides. Score 0.958 Round 2: 1122 peptides, 28 chains. Longest chain 81 peptides. Score 0.957 Round 3: 1134 peptides, 28 chains. Longest chain 101 peptides. Score 0.959 Round 4: 1122 peptides, 27 chains. Longest chain 128 peptides. Score 0.958 Round 5: 1119 peptides, 34 chains. Longest chain 90 peptides. Score 0.951 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 30, Residues 1106, Estimated correctness of the model 99.8 % 23 chains (1077 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 61 A and 64 A Built loop between residues 140 A and 143 A Built loop between residues 151 A and 154 A Built loop between residues 216 A and 219 A Built loop between residues 278 A and 281 A Built loop between residues 60 C and 64 C Built loop between residues 152 C and 155 C Built loop between residues 206 C and 219 C Built loop between residues 163 B and 166 B Built loop between residues 199 B and 203 B Built loop between residues 216 B and 219 B Built loop between residues 110 D and 113 D Built loop between residues 153 D and 156 D Built loop between residues 216 D and 219 D 15 chains (1138 residues) following loop building 9 chains (1117 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 70806 reflections ( 90.30 % complete ) and 8540 restraints for refining 8409 atoms. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2650 (Rfree = 0.000) for 8409 atoms. Found 168 (247 requested) and removed 0 (247 requested) atoms. Cycle 47: After refmac, R = 0.2405 (Rfree = 0.000) for 8409 atoms. Found 70 (252 requested) and removed 2 (157 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2333 (Rfree = 0.000) for 8409 atoms. Found 33 (254 requested) and removed 8 (159 requested) atoms. Cycle 49: After refmac, R = 0.2298 (Rfree = 0.000) for 8409 atoms. Found 16 (255 requested) and removed 4 (159 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 163.01