Mon 24 Dec 08:06:35 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 2p10-2.1-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p10-2.1-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p10-2.1-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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/2p10-2.1-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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 08:06:40 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/2p10-2.1-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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 1935 and 0 Target number of residues in the AU: 1935 Target solvent content: 0.5487 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 286 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1716 Adjusted target solvent content: 0.60 Input MTZ file: 2p10-2.1-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-2.1-parrot-noncs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.80 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. 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: 119.449 2.130 Wilson plot Bfac: 35.19 119082 reflections ( 97.35 % complete ) and 0 restraints for refining 15456 atoms. Observations/parameters ratio is 1.93 ------------------------------------------------------ Starting model: R = 0.3211 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2714 (Rfree = 0.000) for 15456 atoms. Found 394 (442 requested) and removed 221 (221 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.41 2.11 NCS extension: 0 residues added, 15629 seeds are put forward Round 1: 1111 peptides, 148 chains. Longest chain 26 peptides. Score 0.543 Round 2: 1242 peptides, 117 chains. Longest chain 67 peptides. Score 0.681 Round 3: 1337 peptides, 83 chains. Longest chain 97 peptides. Score 0.779 Round 4: 1358 peptides, 75 chains. Longest chain 80 peptides. Score 0.799 Round 5: 1380 peptides, 66 chains. Longest chain 80 peptides. Score 0.818 Taking the results from Round 5 Chains 78, Residues 1314, Estimated correctness of the model 96.2 % 37 chains (1058 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 55 A and 65 A Built loop between residues 154 A and 157 A Built loop between residues 175 A and 179 A Built loop between residues 109 B and 112 B Built loop between residues 126 B and 130 B Built loop between residues 37 E and 44 E Built loop between residues 120 E and 130 E Built loop between residues 68 D and 74 D Built loop between residues 127 D and 130 D Built loop between residues 233 D and 236 D Built loop between residues 253 D and 256 D Built loop between residues 108 F and 117 F Built loop between residues 153 F and 157 F 60 chains (1360 residues) following loop building 24 chains (1114 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 9329 restraints for refining 13710 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3031 (Rfree = 0.000) for 13710 atoms. Found 392 (392 requested) and removed 212 (196 requested) atoms. Cycle 2: After refmac, R = 0.2654 (Rfree = 0.000) for 13890 atoms. Found 339 (389 requested) and removed 159 (198 requested) atoms. Cycle 3: After refmac, R = 0.2424 (Rfree = 0.000) for 14070 atoms. Found 268 (394 requested) and removed 116 (201 requested) atoms. Cycle 4: After refmac, R = 0.2282 (Rfree = 0.000) for 14222 atoms. Found 178 (399 requested) and removed 108 (203 requested) atoms. Cycle 5: After refmac, R = 0.2187 (Rfree = 0.000) for 14292 atoms. Found 158 (393 requested) and removed 82 (204 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.35 2.05 NCS extension: 18 residues added (128 deleted due to clashes), 14414 seeds are put forward Round 1: 1415 peptides, 54 chains. Longest chain 117 peptides. Score 0.844 Round 2: 1444 peptides, 51 chains. Longest chain 119 peptides. Score 0.855 Round 3: 1433 peptides, 50 chains. Longest chain 102 peptides. Score 0.854 Round 4: 1436 peptides, 52 chains. Longest chain 182 peptides. Score 0.852 Round 5: 1451 peptides, 47 chains. Longest chain 120 peptides. Score 0.861 Taking the results from Round 5 Chains 56, Residues 1404, Estimated correctness of the model 97.7 % 30 chains (1232 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 A and 59 A Built loop between residues 80 A and 83 A Built loop between residues 127 A and 131 A Built loop between residues 40 C and 50 C Built loop between residues 105 C and 112 C Built loop between residues 123 C and 129 C Built loop between residues 56 B and 60 B Built loop between residues 156 B and 159 B Built loop between residues 127 E and 131 E Built loop between residues 194 E and 205 E Built loop between residues 124 D and 130 D Built loop between residues 194 D and 205 D Built loop between residues 254 D and 257 D Built loop between residues 37 F and 41 F Built loop between residues 65 F and 68 F Built loop between residues 128 F and 132 F Built loop between residues 160 F and 166 F Built loop between residues 178 F and 182 F 32 chains (1465 residues) following loop building 12 chains (1310 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 10556 restraints for refining 13647 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2621 (Rfree = 0.000) for 13647 atoms. Found 367 (367 requested) and removed 203 (195 requested) atoms. Cycle 7: After refmac, R = 0.2329 (Rfree = 0.000) for 13811 atoms. Found 298 (363 requested) and removed 100 (197 requested) atoms. Cycle 8: After refmac, R = 0.2157 (Rfree = 0.000) for 14009 atoms. Found 201 (369 requested) and removed 76 (200 requested) atoms. Cycle 9: After refmac, R = 0.2052 (Rfree = 0.000) for 14134 atoms. Found 158 (372 requested) and removed 81 (202 requested) atoms. Cycle 10: After refmac, R = 0.1978 (Rfree = 0.000) for 14211 atoms. Found 168 (365 requested) and removed 83 (203 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.34 2.04 NCS extension: 11 residues added (119 deleted due to clashes), 14327 seeds are put forward Round 1: 1439 peptides, 39 chains. Longest chain 109 peptides. Score 0.869 Round 2: 1465 peptides, 41 chains. Longest chain 119 peptides. Score 0.872 Round 3: 1458 peptides, 51 chains. Longest chain 113 peptides. Score 0.858 Round 4: 1461 peptides, 46 chains. Longest chain 101 peptides. Score 0.865 Round 5: 1465 peptides, 46 chains. Longest chain 119 peptides. Score 0.866 Taking the results from Round 2 Chains 46, Residues 1424, Estimated correctness of the model 98.0 % 27 chains (1264 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 132 A Built loop between residues 195 A and 204 A Built loop between residues 45 C and 56 C Built loop between residues 127 C and 130 C Built loop between residues 88 B and 92 B Built loop between residues 127 B and 130 B Built loop between residues 126 E and 130 E Built loop between residues 151 E and 154 E Built loop between residues 36 D and 39 D Built loop between residues 123 D and 130 D Built loop between residues 193 D and 204 D Built loop between residues 244 D and 247 D Built loop between residues 261 D and 264 D 31 chains (1472 residues) following loop building 14 chains (1319 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 10611 restraints for refining 13681 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2385 (Rfree = 0.000) for 13681 atoms. Found 352 (352 requested) and removed 199 (195 requested) atoms. Cycle 12: After refmac, R = 0.2224 (Rfree = 0.000) for 13834 atoms. Found 244 (348 requested) and removed 58 (198 requested) atoms. Cycle 13: After refmac, R = 0.2037 (Rfree = 0.000) for 14020 atoms. Found 182 (353 requested) and removed 84 (200 requested) atoms. Cycle 14: After refmac, R = 0.1948 (Rfree = 0.000) for 14118 atoms. Found 161 (356 requested) and removed 65 (202 requested) atoms. Cycle 15: After refmac, R = 0.1885 (Rfree = 0.000) for 14214 atoms. Found 149 (357 requested) and removed 87 (203 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.34 2.04 NCS extension: 14 residues added (11 deleted due to clashes), 14308 seeds are put forward Round 1: 1471 peptides, 41 chains. Longest chain 150 peptides. Score 0.873 Round 2: 1484 peptides, 35 chains. Longest chain 120 peptides. Score 0.882 Round 3: 1483 peptides, 38 chains. Longest chain 118 peptides. Score 0.879 Round 4: 1471 peptides, 46 chains. Longest chain 118 peptides. Score 0.867 Round 5: 1447 peptides, 51 chains. Longest chain 113 peptides. Score 0.855 Taking the results from Round 2 Chains 45, Residues 1449, Estimated correctness of the model 98.3 % 27 chains (1328 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 A and 49 A Built loop between residues 88 A and 91 A Built loop between residues 114 A and 121 A Built loop between residues 127 A and 130 A Built loop between residues 125 C and 131 C Built loop between residues 195 C and 205 C Built loop between residues 254 C and 257 C Built loop between residues 76 B and 79 B Built loop between residues 122 B and 125 B Built loop between residues 151 E and 154 E Built loop between residues 245 E and 255 E Built loop between residues 130 D and 133 D Built loop between residues 195 D and 204 D Built loop between residues 97 F and 104 F Built loop between residues 128 F and 135 F 26 chains (1503 residues) following loop building 12 chains (1397 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11037 restraints for refining 13725 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2381 (Rfree = 0.000) for 13725 atoms. Found 337 (337 requested) and removed 192 (196 requested) atoms. Cycle 17: After refmac, R = 0.2109 (Rfree = 0.000) for 13870 atoms. Found 243 (333 requested) and removed 87 (198 requested) atoms. Cycle 18: After refmac, R = 0.1975 (Rfree = 0.000) for 14026 atoms. Found 198 (337 requested) and removed 79 (200 requested) atoms. Cycle 19: After refmac, R = 0.1901 (Rfree = 0.000) for 14145 atoms. Found 139 (339 requested) and removed 91 (202 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1852 (Rfree = 0.000) for 14193 atoms. Found 172 (333 requested) and removed 63 (203 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.34 2.04 NCS extension: 32 residues added (22 deleted due to clashes), 14354 seeds are put forward Round 1: 1474 peptides, 41 chains. Longest chain 106 peptides. Score 0.873 Round 2: 1485 peptides, 40 chains. Longest chain 120 peptides. Score 0.877 Round 3: 1501 peptides, 44 chains. Longest chain 118 peptides. Score 0.875 Round 4: 1482 peptides, 46 chains. Longest chain 119 peptides. Score 0.869 Round 5: 1463 peptides, 54 chains. Longest chain 113 peptides. Score 0.855 Taking the results from Round 2 Chains 50, Residues 1445, Estimated correctness of the model 98.1 % 29 chains (1339 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 126 A and 131 A Built loop between residues 194 A and 205 A Built loop between residues 254 A and 257 A Built loop between residues 43 C and 48 C Built loop between residues 88 C and 91 C Built loop between residues 104 C and 107 C Built loop between residues 38 B and 40 B Built loop between residues 172 B and 176 B Built loop between residues 243 B and 247 B Built loop between residues 261 B and 268 B Built loop between residues 123 E and 130 E Built loop between residues 193 E and 204 E Built loop between residues 217 E and 220 E Built loop between residues 130 D and 133 D Built loop between residues 194 D and 204 D Built loop between residues 92 F and 99 F Built loop between residues 123 F and 131 F Built loop between residues 244 F and 254 F 24 chains (1514 residues) following loop building 11 chains (1427 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 11162 restraints for refining 13769 atoms. Observations/parameters ratio is 2.16 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2228 (Rfree = 0.000) for 13769 atoms. Found 323 (323 requested) and removed 202 (197 requested) atoms. Cycle 22: After refmac, R = 0.2034 (Rfree = 0.000) for 13890 atoms. Found 245 (318 requested) and removed 95 (198 requested) atoms. Cycle 23: After refmac, R = 0.1939 (Rfree = 0.000) for 14040 atoms. Found 231 (321 requested) and removed 99 (200 requested) atoms. Cycle 24: After refmac, R = 0.1876 (Rfree = 0.000) for 14172 atoms. Found 172 (324 requested) and removed 102 (202 requested) atoms. Cycle 25: After refmac, R = 0.1829 (Rfree = 0.000) for 14242 atoms. Found 182 (317 requested) and removed 108 (203 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.34 2.04 NCS extension: 13 residues added (97 deleted due to clashes), 14352 seeds are put forward Round 1: 1490 peptides, 37 chains. Longest chain 118 peptides. Score 0.881 Round 2: 1507 peptides, 29 chains. Longest chain 116 peptides. Score 0.893 Round 3: 1494 peptides, 44 chains. Longest chain 116 peptides. Score 0.874 Round 4: 1492 peptides, 49 chains. Longest chain 102 peptides. Score 0.867 Round 5: 1478 peptides, 46 chains. Longest chain 142 peptides. Score 0.868 Taking the results from Round 2 Chains 37, Residues 1478, Estimated correctness of the model 98.5 % 20 chains (1376 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 97 A and 104 A Built loop between residues 123 A and 131 A Built loop between residues 120 C and 123 C Built loop between residues 126 B and 131 B Built loop between residues 126 E and 131 E Built loop between residues 194 E and 204 E Built loop between residues 126 D and 130 D Built loop between residues 195 D and 204 D Built loop between residues 124 F and 131 F Built loop between residues 254 F and 257 F 23 chains (1515 residues) following loop building 10 chains (1427 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 11199 restraints for refining 13705 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2316 (Rfree = 0.000) for 13705 atoms. Found 298 (298 requested) and removed 199 (196 requested) atoms. Cycle 27: After refmac, R = 0.2059 (Rfree = 0.000) for 13804 atoms. Found 268 (292 requested) and removed 86 (197 requested) atoms. Cycle 28: After refmac, R = 0.1947 (Rfree = 0.000) for 13986 atoms. Found 212 (296 requested) and removed 87 (200 requested) atoms. Cycle 29: After refmac, R = 0.1877 (Rfree = 0.000) for 14111 atoms. Found 194 (298 requested) and removed 104 (201 requested) atoms. Cycle 30: After refmac, R = 0.1830 (Rfree = 0.000) for 14201 atoms. Found 181 (292 requested) and removed 107 (203 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.33 2.04 NCS extension: 4 residues added (18 deleted due to clashes), 14293 seeds are put forward Round 1: 1479 peptides, 31 chains. Longest chain 116 peptides. Score 0.886 Round 2: 1496 peptides, 35 chains. Longest chain 118 peptides. Score 0.885 Round 3: 1492 peptides, 42 chains. Longest chain 98 peptides. Score 0.876 Round 4: 1476 peptides, 49 chains. Longest chain 114 peptides. Score 0.864 Round 5: 1491 peptides, 37 chains. Longest chain 115 peptides. Score 0.881 Taking the results from Round 1 Chains 32, Residues 1448, Estimated correctness of the model 98.4 % 22 chains (1336 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 122 A and 131 A Built loop between residues 93 C and 96 C Built loop between residues 127 C and 130 C Built loop between residues 194 C and 205 C Built loop between residues 127 B and 130 B Built loop between residues 126 E and 130 E Built loop between residues 126 D and 130 D Built loop between residues 193 D and 204 D Built loop between residues 127 F and 130 F Built loop between residues 250 F and 253 F 21 chains (1494 residues) following loop building 11 chains (1382 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 10977 restraints for refining 13650 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2252 (Rfree = 0.000) for 13650 atoms. Found 273 (273 requested) and removed 135 (195 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2019 (Rfree = 0.000) for 13788 atoms. Found 266 (276 requested) and removed 69 (197 requested) atoms. Cycle 33: After refmac, R = 0.1912 (Rfree = 0.000) for 13985 atoms. Found 175 (280 requested) and removed 81 (200 requested) atoms. Cycle 34: After refmac, R = 0.1856 (Rfree = 0.000) for 14079 atoms. Found 187 (282 requested) and removed 68 (201 requested) atoms. Cycle 35: After refmac, R = 0.1805 (Rfree = 0.000) for 14198 atoms. Found 164 (284 requested) and removed 99 (203 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.33 2.04 NCS extension: 18 residues added (197 deleted due to clashes), 14288 seeds are put forward Round 1: 1466 peptides, 36 chains. Longest chain 117 peptides. Score 0.878 Round 2: 1478 peptides, 35 chains. Longest chain 149 peptides. Score 0.881 Round 3: 1473 peptides, 41 chains. Longest chain 116 peptides. Score 0.873 Round 4: 1470 peptides, 44 chains. Longest chain 99 peptides. Score 0.869 Round 5: 1458 peptides, 47 chains. Longest chain 99 peptides. Score 0.863 Taking the results from Round 2 Chains 41, Residues 1443, Estimated correctness of the model 98.2 % 24 chains (1337 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 115 A and 118 A Built loop between residues 254 A and 257 A Built loop between residues 123 C and 130 C Built loop between residues 194 C and 203 C Built loop between residues 126 B and 131 B Built loop between residues 126 E and 130 E Built loop between residues 193 E and 204 E Built loop between residues 123 D and 130 D Built loop between residues 254 D and 257 D Built loop between residues 97 F and 107 F Built loop between residues 122 F and 131 F Built loop between residues 239 F and 242 F 26 chains (1495 residues) following loop building 12 chains (1399 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11029 restraints for refining 13661 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2136 (Rfree = 0.000) for 13661 atoms. Found 266 (266 requested) and removed 198 (195 requested) atoms. Cycle 37: After refmac, R = 0.1962 (Rfree = 0.000) for 13729 atoms. Found 259 (259 requested) and removed 82 (196 requested) atoms. Cycle 38: After refmac, R = 0.1874 (Rfree = 0.000) for 13906 atoms. Found 223 (263 requested) and removed 115 (199 requested) atoms. Cycle 39: After refmac, R = 0.1825 (Rfree = 0.000) for 14014 atoms. Found 233 (257 requested) and removed 128 (200 requested) atoms. Cycle 40: After refmac, R = 0.1793 (Rfree = 0.000) for 14119 atoms. Found 244 (250 requested) and removed 153 (202 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.34 2.04 NCS extension: 32 residues added (296 deleted due to clashes), 14258 seeds are put forward Round 1: 1463 peptides, 37 chains. Longest chain 117 peptides. Score 0.876 Round 2: 1482 peptides, 27 chains. Longest chain 184 peptides. Score 0.891 Round 3: 1468 peptides, 40 chains. Longest chain 118 peptides. Score 0.873 Round 4: 1466 peptides, 45 chains. Longest chain 100 peptides. Score 0.867 Round 5: 1451 peptides, 43 chains. Longest chain 102 peptides. Score 0.866 Taking the results from Round 2 Chains 34, Residues 1455, Estimated correctness of the model 98.5 % 22 chains (1400 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 147 A and 150 A Built loop between residues 125 C and 129 C Built loop between residues 194 C and 204 C Built loop between residues 97 B and 104 B Built loop between residues 160 B and 164 B Built loop between residues 116 E and 119 E Built loop between residues 127 E and 131 E Built loop between residues 193 D and 203 D Built loop between residues 123 F and 130 F 21 chains (1488 residues) following loop building 13 chains (1443 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11164 restraints for refining 13557 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2137 (Rfree = 0.000) for 13557 atoms. Found 233 (233 requested) and removed 201 (194 requested) atoms. Cycle 42: After refmac, R = 0.1962 (Rfree = 0.000) for 13589 atoms. Found 226 (226 requested) and removed 65 (194 requested) atoms. Cycle 43: After refmac, R = 0.1872 (Rfree = 0.000) for 13750 atoms. Found 228 (228 requested) and removed 78 (196 requested) atoms. Cycle 44: After refmac, R = 0.1818 (Rfree = 0.000) for 13900 atoms. Found 212 (230 requested) and removed 99 (198 requested) atoms. Cycle 45: After refmac, R = 0.1792 (Rfree = 0.000) for 14013 atoms. Found 210 (233 requested) and removed 141 (200 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.34 2.04 NCS extension: 8 residues added (7 deleted due to clashes), 14113 seeds are put forward Round 1: 1479 peptides, 33 chains. Longest chain 118 peptides. Score 0.884 Round 2: 1500 peptides, 32 chains. Longest chain 132 peptides. Score 0.889 Round 3: 1490 peptides, 37 chains. Longest chain 118 peptides. Score 0.881 Round 4: 1495 peptides, 41 chains. Longest chain 118 peptides. Score 0.877 Round 5: 1492 peptides, 44 chains. Longest chain 113 peptides. Score 0.873 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 36, Residues 1468, Estimated correctness of the model 98.4 % 24 chains (1409 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 97 A and 104 A Built loop between residues 123 A and 131 A Built loop between residues 254 A and 257 A Built loop between residues 126 C and 130 C Built loop between residues 254 C and 257 C Built loop between residues 88 B and 91 B Built loop between residues 126 B and 130 B Built loop between residues 126 E and 129 E Built loop between residues 194 E and 204 E Built loop between residues 244 E and 247 E Built loop between residues 141 D and 144 D Built loop between residues 195 D and 203 D Built loop between residues 93 F and 96 F Built loop between residues 123 F and 130 F 19 chains (1512 residues) following loop building 10 chains (1464 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 119082 reflections ( 97.35 % complete ) and 11346 restraints for refining 11189 atoms. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2766 (Rfree = 0.000) for 11189 atoms. Found 167 (179 requested) and removed 0 (179 requested) atoms. Cycle 47: After refmac, R = 0.2518 (Rfree = 0.000) for 11189 atoms. Found 74 (182 requested) and removed 1 (162 requested) atoms. Cycle 48: After refmac, R = 0.2375 (Rfree = 0.000) for 11189 atoms. Found 53 (183 requested) and removed 8 (163 requested) atoms. Cycle 49: After refmac, R = 0.2291 (Rfree = 0.000) for 11189 atoms. TimeTaking 230.55