Mon 24 Dec 01:00:39 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 2obn-2.3-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-2.3-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2obn-2.3-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-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/2obn-2.3-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-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 01:00:43 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/2obn-2.3-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2obn-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 1172 and 0 Target number of residues in the AU: 1172 Target solvent content: 0.5306 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-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: 4 Cell parameters: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-2.3-parrot-mrncs.fasta_lf Building free atoms model in initial map for 11168 target number of atoms Had to go as low as 0.45 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: 73.214 2.300 Wilson plot Bfac: 30.44 58827 reflections ( 99.75 % complete ) and 0 restraints for refining 12392 atoms. Observations/parameters ratio is 1.19 ------------------------------------------------------ Starting model: R = 0.3025 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2099 (Rfree = 0.000) for 12392 atoms. Found 185 (285 requested) and removed 156 (142 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.31 2.50 NCS extension: 0 residues added, 12421 seeds are put forward Round 1: 858 peptides, 118 chains. Longest chain 24 peptides. Score 0.606 Round 2: 1000 peptides, 82 chains. Longest chain 39 peptides. Score 0.805 Round 3: 1096 peptides, 65 chains. Longest chain 73 peptides. Score 0.873 Round 4: 1142 peptides, 59 chains. Longest chain 74 peptides. Score 0.895 Round 5: 1170 peptides, 53 chains. Longest chain 143 peptides. Score 0.909 Taking the results from Round 5 Chains 58, Residues 1117, Estimated correctness of the model 98.6 % 28 chains (938 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 272 A and 276 A Built loop between residues 311 A and 315 A Built loop between residues 44 C and 47 C Built loop between residues 164 C and 167 C Built loop between residues 216 C and 219 C Built loop between residues 235 C and 238 C Built loop between residues 271 C and 280 C Built loop between residues 310 C and 313 C Built loop between residues 182 B and 185 B Built loop between residues 205 B and 208 B Built loop between residues 150 D and 153 D Built loop between residues 234 D and 238 D Built loop between residues 292 D and 296 D Built loop between residues 312 D and 319 D 42 chains (1156 residues) following loop building 14 chains (980 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 12940 restraints for refining 10641 atoms. 4884 conditional restraints added. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2499 (Rfree = 0.000) for 10641 atoms. Found 201 (244 requested) and removed 143 (122 requested) atoms. Cycle 2: After refmac, R = 0.2215 (Rfree = 0.000) for 10596 atoms. Found 158 (241 requested) and removed 125 (123 requested) atoms. Cycle 3: After refmac, R = 0.2094 (Rfree = 0.000) for 10560 atoms. Found 132 (234 requested) and removed 123 (122 requested) atoms. Cycle 4: After refmac, R = 0.2009 (Rfree = 0.000) for 10533 atoms. Found 115 (228 requested) and removed 93 (121 requested) atoms. Cycle 5: After refmac, R = 0.1944 (Rfree = 0.000) for 10532 atoms. Found 100 (223 requested) and removed 63 (121 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.30 2.49 NCS extension: 259 residues added (1336 deleted due to clashes), 10858 seeds are put forward Round 1: 1190 peptides, 43 chains. Longest chain 126 peptides. Score 0.926 Round 2: 1224 peptides, 35 chains. Longest chain 195 peptides. Score 0.940 Round 3: 1227 peptides, 41 chains. Longest chain 156 peptides. Score 0.934 Round 4: 1225 peptides, 46 chains. Longest chain 100 peptides. Score 0.928 Round 5: 1251 peptides, 35 chains. Longest chain 218 peptides. Score 0.944 Taking the results from Round 5 Chains 40, Residues 1216, Estimated correctness of the model 99.4 % 23 chains (996 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 126 A and 130 A Built loop between residues 164 A and 167 A Built loop between residues 182 A and 185 A Built loop between residues 206 A and 209 A Built loop between residues 84 C and 95 C Built loop between residues 123 C and 130 C Built loop between residues 309 C and 315 C Built loop between residues 322 C and 325 C Built loop between residues 43 B and 53 B Built loop between residues 117 B and 120 B Built loop between residues 144 B and 147 B Built loop between residues 174 D and 177 D 26 chains (1246 residues) following loop building 11 chains (1043 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11956 restraints for refining 10588 atoms. 3351 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2222 (Rfree = 0.000) for 10588 atoms. Found 209 (219 requested) and removed 133 (121 requested) atoms. Cycle 7: After refmac, R = 0.2027 (Rfree = 0.000) for 10638 atoms. Found 120 (216 requested) and removed 124 (122 requested) atoms. Cycle 8: After refmac, R = 0.1942 (Rfree = 0.000) for 10616 atoms. Found 79 (210 requested) and removed 123 (122 requested) atoms. Cycle 9: After refmac, R = 0.1906 (Rfree = 0.000) for 10561 atoms. Found 95 (204 requested) and removed 62 (121 requested) atoms. Cycle 10: After refmac, R = 0.1866 (Rfree = 0.000) for 10583 atoms. Found 73 (199 requested) and removed 59 (121 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.30 2.49 NCS extension: 1532 residues added (1661 deleted due to clashes), 12166 seeds are put forward Round 1: 1225 peptides, 40 chains. Longest chain 127 peptides. Score 0.935 Round 2: 1242 peptides, 36 chains. Longest chain 188 peptides. Score 0.941 Round 3: 1249 peptides, 32 chains. Longest chain 221 peptides. Score 0.946 Round 4: 1248 peptides, 42 chains. Longest chain 92 peptides. Score 0.936 Round 5: 1257 peptides, 40 chains. Longest chain 192 peptides. Score 0.939 Taking the results from Round 3 Chains 37, Residues 1217, Estimated correctness of the model 99.5 % 19 chains (1069 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 163 A and 166 A Built loop between residues 243 A and 246 A Built loop between residues 120 C and 130 C Built loop between residues 22 B and 25 B Built loop between residues 124 B and 128 B Built loop between residues 134 D and 143 D Built loop between residues 157 D and 160 D Built loop between residues 209 D and 212 D Built loop between residues 300 D and 303 D 26 chains (1240 residues) following loop building 10 chains (1101 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11594 restraints for refining 10590 atoms. 2717 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2044 (Rfree = 0.000) for 10590 atoms. Found 194 (194 requested) and removed 132 (121 requested) atoms. Cycle 12: After refmac, R = 0.1890 (Rfree = 0.000) for 10634 atoms. Found 112 (191 requested) and removed 122 (122 requested) atoms. Cycle 13: After refmac, R = 0.1845 (Rfree = 0.000) for 10619 atoms. Found 94 (185 requested) and removed 83 (122 requested) atoms. Cycle 14: After refmac, R = 0.1816 (Rfree = 0.000) for 10617 atoms. Found 91 (181 requested) and removed 69 (122 requested) atoms. Cycle 15: After refmac, R = 0.1799 (Rfree = 0.000) for 10630 atoms. Found 74 (176 requested) and removed 62 (122 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.30 2.49 NCS extension: 663 residues added (402 deleted due to clashes), 11319 seeds are put forward Round 1: 1248 peptides, 35 chains. Longest chain 182 peptides. Score 0.943 Round 2: 1264 peptides, 26 chains. Longest chain 229 peptides. Score 0.954 Round 3: 1244 peptides, 39 chains. Longest chain 182 peptides. Score 0.939 Round 4: 1245 peptides, 33 chains. Longest chain 209 peptides. Score 0.945 Round 5: 1239 peptides, 44 chains. Longest chain 211 peptides. Score 0.933 Taking the results from Round 2 Chains 28, Residues 1238, Estimated correctness of the model 99.6 % 14 chains (1081 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 84 C and 91 C Built loop between residues 312 B and 315 B 26 chains (1245 residues) following loop building 12 chains (1089 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11739 restraints for refining 10590 atoms. 2900 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1979 (Rfree = 0.000) for 10590 atoms. Found 170 (170 requested) and removed 130 (121 requested) atoms. Cycle 17: After refmac, R = 0.1862 (Rfree = 0.000) for 10621 atoms. Found 122 (166 requested) and removed 122 (122 requested) atoms. Cycle 18: After refmac, R = 0.1808 (Rfree = 0.000) for 10614 atoms. Found 109 (161 requested) and removed 77 (122 requested) atoms. Cycle 19: After refmac, R = 0.1774 (Rfree = 0.000) for 10642 atoms. Found 75 (156 requested) and removed 59 (122 requested) atoms. Cycle 20: After refmac, R = 0.1754 (Rfree = 0.000) for 10651 atoms. Found 84 (152 requested) and removed 61 (122 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.30 2.49 NCS extension: 177 residues added (235 deleted due to clashes), 10865 seeds are put forward Round 1: 1264 peptides, 30 chains. Longest chain 163 peptides. Score 0.950 Round 2: 1261 peptides, 25 chains. Longest chain 183 peptides. Score 0.954 Round 3: 1259 peptides, 38 chains. Longest chain 124 peptides. Score 0.942 Round 4: 1262 peptides, 30 chains. Longest chain 147 peptides. Score 0.950 Round 5: 1257 peptides, 44 chains. Longest chain 127 peptides. Score 0.935 Taking the results from Round 2 Chains 31, Residues 1236, Estimated correctness of the model 99.6 % 18 chains (1128 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 120 A and 130 A Built loop between residues 200 A and 203 A Built loop between residues 84 C and 91 C Built loop between residues 160 C and 166 C Built loop between residues 163 B and 166 B Built loop between residues 116 D and 119 D Built loop between residues 196 D and 202 D 22 chains (1260 residues) following loop building 11 chains (1159 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11397 restraints for refining 10721 atoms. 2187 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1967 (Rfree = 0.000) for 10721 atoms. Found 148 (148 requested) and removed 134 (123 requested) atoms. Cycle 22: After refmac, R = 0.1835 (Rfree = 0.000) for 10724 atoms. Found 143 (143 requested) and removed 123 (123 requested) atoms. Cycle 23: After refmac, R = 0.1786 (Rfree = 0.000) for 10736 atoms. Found 138 (138 requested) and removed 90 (123 requested) atoms. Cycle 24: After refmac, R = 0.1748 (Rfree = 0.000) for 10778 atoms. Found 117 (134 requested) and removed 87 (124 requested) atoms. Cycle 25: After refmac, R = 0.1731 (Rfree = 0.000) for 10799 atoms. Found 119 (129 requested) and removed 72 (124 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.29 2.48 NCS extension: 418 residues added (496 deleted due to clashes), 11271 seeds are put forward Round 1: 1245 peptides, 38 chains. Longest chain 158 peptides. Score 0.940 Round 2: 1271 peptides, 26 chains. Longest chain 223 peptides. Score 0.955 Round 3: 1267 peptides, 35 chains. Longest chain 150 peptides. Score 0.946 Round 4: 1250 peptides, 41 chains. Longest chain 148 peptides. Score 0.937 Round 5: 1264 peptides, 36 chains. Longest chain 125 peptides. Score 0.944 Taking the results from Round 2 Chains 30, Residues 1245, Estimated correctness of the model 99.6 % 17 chains (1151 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 271 A and 274 A Built loop between residues 84 C and 91 C Built loop between residues 124 C and 131 C Built loop between residues 300 C and 303 C Built loop between residues 122 B and 131 B Built loop between residues 163 B and 166 B Built loop between residues 312 D and 315 D 22 chains (1268 residues) following loop building 10 chains (1179 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11450 restraints for refining 10806 atoms. 2135 conditional restraints added. Observations/parameters ratio is 1.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1923 (Rfree = 0.000) for 10806 atoms. Found 124 (124 requested) and removed 136 (124 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1807 (Rfree = 0.000) for 10782 atoms. Found 124 (124 requested) and removed 125 (124 requested) atoms. Cycle 28: After refmac, R = 0.1767 (Rfree = 0.000) for 10778 atoms. Found 106 (123 requested) and removed 96 (123 requested) atoms. Cycle 29: After refmac, R = 0.1750 (Rfree = 0.000) for 10775 atoms. Found 116 (124 requested) and removed 81 (124 requested) atoms. Cycle 30: After refmac, R = 0.1734 (Rfree = 0.000) for 10804 atoms. Found 92 (124 requested) and removed 86 (124 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.30 2.49 NCS extension: 1001 residues added (441 deleted due to clashes), 11817 seeds are put forward Round 1: 1272 peptides, 32 chains. Longest chain 185 peptides. Score 0.949 Round 2: 1287 peptides, 19 chains. Longest chain 253 peptides. Score 0.963 Round 3: 1269 peptides, 35 chains. Longest chain 127 peptides. Score 0.946 Round 4: 1277 peptides, 32 chains. Longest chain 175 peptides. Score 0.950 Round 5: 1265 peptides, 42 chains. Longest chain 86 peptides. Score 0.938 Taking the results from Round 2 Chains 21, Residues 1268, Estimated correctness of the model 99.7 % 14 chains (1213 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 300 A and 303 A Built loop between residues 46 D and 56 D Built loop between residues 123 D and 130 D Built loop between residues 336 D and 339 D 17 chains (1287 residues) following loop building 10 chains (1232 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11302 restraints for refining 10896 atoms. 1731 conditional restraints added. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1910 (Rfree = 0.000) for 10896 atoms. Found 125 (125 requested) and removed 134 (125 requested) atoms. Cycle 32: After refmac, R = 0.1793 (Rfree = 0.000) for 10879 atoms. Found 119 (125 requested) and removed 125 (125 requested) atoms. Cycle 33: After refmac, R = 0.1757 (Rfree = 0.000) for 10869 atoms. Found 105 (125 requested) and removed 125 (125 requested) atoms. Cycle 34: After refmac, R = 0.1730 (Rfree = 0.000) for 10835 atoms. Found 104 (124 requested) and removed 94 (124 requested) atoms. Cycle 35: After refmac, R = 0.1710 (Rfree = 0.000) for 10841 atoms. Found 104 (124 requested) and removed 73 (124 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.30 2.49 NCS extension: 239 residues added (113 deleted due to clashes), 11115 seeds are put forward Round 1: 1268 peptides, 30 chains. Longest chain 174 peptides. Score 0.951 Round 2: 1279 peptides, 25 chains. Longest chain 220 peptides. Score 0.956 Round 3: 1272 peptides, 31 chains. Longest chain 166 peptides. Score 0.950 Round 4: 1266 peptides, 30 chains. Longest chain 183 peptides. Score 0.950 Round 5: 1266 peptides, 40 chains. Longest chain 167 peptides. Score 0.941 Taking the results from Round 2 Chains 28, Residues 1254, Estimated correctness of the model 99.6 % 18 chains (1183 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 118 A and 122 A Built loop between residues 294 A and 297 A Built loop between residues 315 A and 318 A Built loop between residues 84 C and 90 C Built loop between residues 269 C and 273 C Built loop between residues 312 C and 315 C Built loop between residues 82 B and 88 B Built loop between residues 306 B and 309 B Built loop between residues 123 D and 129 D Built loop between residues 164 D and 167 D 18 chains (1285 residues) following loop building 8 chains (1214 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11368 restraints for refining 10841 atoms. 1881 conditional restraints added. Observations/parameters ratio is 1.36 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1891 (Rfree = 0.000) for 10841 atoms. Found 124 (124 requested) and removed 129 (124 requested) atoms. Cycle 37: After refmac, R = 0.1780 (Rfree = 0.000) for 10831 atoms. Found 124 (124 requested) and removed 124 (124 requested) atoms. Cycle 38: After refmac, R = 0.1736 (Rfree = 0.000) for 10825 atoms. Found 101 (124 requested) and removed 114 (124 requested) atoms. Cycle 39: After refmac, R = 0.1723 (Rfree = 0.000) for 10805 atoms. Found 111 (124 requested) and removed 86 (124 requested) atoms. Cycle 40: After refmac, R = 0.1700 (Rfree = 0.000) for 10822 atoms. Found 89 (124 requested) and removed 88 (124 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.31 2.50 NCS extension: 1059 residues added (682 deleted due to clashes), 11889 seeds are put forward Round 1: 1273 peptides, 29 chains. Longest chain 185 peptides. Score 0.952 Round 2: 1291 peptides, 21 chains. Longest chain 227 peptides. Score 0.961 Round 3: 1277 peptides, 34 chains. Longest chain 118 peptides. Score 0.948 Round 4: 1269 peptides, 31 chains. Longest chain 227 peptides. Score 0.950 Round 5: 1271 peptides, 38 chains. Longest chain 158 peptides. Score 0.943 Taking the results from Round 2 Chains 22, Residues 1270, Estimated correctness of the model 99.7 % 17 chains (1236 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 A and 87 A Built loop between residues 251 A and 255 A Built loop between residues 300 A and 303 A Built loop between residues 84 C and 88 C Built loop between residues 300 C and 303 C Built loop between residues 83 B and 91 B Built loop between residues 123 B and 130 B Built loop between residues 296 B and 299 B Built loop between residues 46 D and 56 D Built loop between residues 118 D and 122 D 12 chains (1311 residues) following loop building 7 chains (1277 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11084 restraints for refining 11001 atoms. 1235 conditional restraints added. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1905 (Rfree = 0.000) for 11001 atoms. Found 126 (126 requested) and removed 135 (126 requested) atoms. Cycle 42: After refmac, R = 0.1777 (Rfree = 0.000) for 10980 atoms. Found 126 (126 requested) and removed 126 (126 requested) atoms. Cycle 43: After refmac, R = 0.1724 (Rfree = 0.000) for 10975 atoms. Found 118 (126 requested) and removed 127 (126 requested) atoms. Cycle 44: After refmac, R = 0.1707 (Rfree = 0.000) for 10957 atoms. Found 96 (126 requested) and removed 99 (126 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1696 (Rfree = 0.000) for 10938 atoms. Found 108 (125 requested) and removed 87 (125 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.30 2.49 NCS extension: 822 residues added (344 deleted due to clashes), 11795 seeds are put forward Round 1: 1278 peptides, 28 chains. Longest chain 149 peptides. Score 0.954 Round 2: 1293 peptides, 21 chains. Longest chain 253 peptides. Score 0.961 Round 3: 1278 peptides, 28 chains. Longest chain 214 peptides. Score 0.954 Round 4: 1263 peptides, 40 chains. Longest chain 117 peptides. Score 0.940 Round 5: 1268 peptides, 30 chains. Longest chain 185 peptides. Score 0.951 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 23, Residues 1272, Estimated correctness of the model 99.7 % 16 chains (1235 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 83 A and 91 A Built loop between residues 120 A and 130 A Built loop between residues 46 C and 56 C Built loop between residues 82 C and 96 C Built loop between residues 18 B and 21 B Built loop between residues 54 B and 57 B Built loop between residues 84 B and 87 B Built loop between residues 125 B and 128 B Built loop between residues 163 B and 166 B Built loop between residues 45 D and 58 D Built loop between residues 82 D and 88 D 10 chains (1333 residues) following loop building 5 chains (1300 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 58827 reflections ( 99.75 % complete ) and 10029 restraints for refining 9841 atoms. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2495 (Rfree = 0.000) for 9841 atoms. Found 95 (113 requested) and removed 0 (113 requested) atoms. Cycle 47: After refmac, R = 0.2293 (Rfree = 0.000) for 9841 atoms. Found 31 (114 requested) and removed 5 (114 requested) atoms. Cycle 48: After refmac, R = 0.2233 (Rfree = 0.000) for 9841 atoms. Found 29 (114 requested) and removed 5 (114 requested) atoms. Cycle 49: After refmac, R = 0.2190 (Rfree = 0.000) for 9841 atoms. Found 12 (114 requested) and removed 6 (114 requested) atoms. Writing output files ... TimeTaking 133.1