Mon 24 Dec 00:07:30 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 2p10-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2p10-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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/2p10-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:07:35 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/2p10-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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 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-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-2.1-parrot-mrncs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.75 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 15395 atoms. Observations/parameters ratio is 1.93 ------------------------------------------------------ Starting model: R = 0.3209 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2670 (Rfree = 0.000) for 15395 atoms. Found 440 (440 requested) and removed 221 (220 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.41 2.11 NCS extension: 0 residues added, 15614 seeds are put forward Round 1: 1220 peptides, 142 chains. Longest chain 37 peptides. Score 0.616 Round 2: 1355 peptides, 99 chains. Longest chain 66 peptides. Score 0.759 Round 3: 1435 peptides, 70 chains. Longest chain 95 peptides. Score 0.827 Round 4: 1461 peptides, 60 chains. Longest chain 110 peptides. Score 0.847 Round 5: 1442 peptides, 59 chains. Longest chain 113 peptides. Score 0.844 Taking the results from Round 4 Chains 69, Residues 1401, Estimated correctness of the model 97.2 % 34 chains (1186 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 124 A and 130 A Built loop between residues 220 A and 225 A Built loop between residues 252 A and 256 A Built loop between residues 175 C and 179 C Built loop between residues 88 B and 92 B Built loop between residues 95 E and 98 E Built loop between residues 179 E and 183 E Built loop between residues 232 E and 235 E Built loop between residues 272 E and 276 E Built loop between residues 38 D and 42 D Built loop between residues 55 D and 58 D Built loop between residues 128 D and 132 D Built loop between residues 148 D and 153 D 52 chains (1435 residues) following loop building 21 chains (1226 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 10062 restraints for refining 13590 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2747 (Rfree = 0.000) for 13590 atoms. Found 389 (389 requested) and removed 212 (194 requested) atoms. Cycle 2: After refmac, R = 0.2465 (Rfree = 0.000) for 13767 atoms. Found 334 (386 requested) and removed 124 (197 requested) atoms. Cycle 3: After refmac, R = 0.2286 (Rfree = 0.000) for 13977 atoms. Found 213 (392 requested) and removed 93 (200 requested) atoms. Cycle 4: After refmac, R = 0.2181 (Rfree = 0.000) for 14097 atoms. Found 168 (395 requested) and removed 86 (201 requested) atoms. Cycle 5: After refmac, R = 0.2106 (Rfree = 0.000) for 14179 atoms. Found 154 (389 requested) and removed 94 (202 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.35 2.05 NCS extension: 11 residues added (88 deleted due to clashes), 14266 seeds are put forward Round 1: 1468 peptides, 43 chains. Longest chain 113 peptides. Score 0.870 Round 2: 1486 peptides, 39 chains. Longest chain 119 peptides. Score 0.878 Round 3: 1488 peptides, 49 chains. Longest chain 101 peptides. Score 0.867 Round 4: 1487 peptides, 42 chains. Longest chain 132 peptides. Score 0.875 Round 5: 1482 peptides, 51 chains. Longest chain 119 peptides. Score 0.863 Taking the results from Round 2 Chains 42, Residues 1447, Estimated correctness of the model 98.2 % 22 chains (1248 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 58 A Built loop between residues 126 C and 130 C Built loop between residues 147 C and 150 C Built loop between residues 67 B and 70 B Built loop between residues 124 D and 131 D Built loop between residues 141 D and 150 D 33 chains (1460 residues) following loop building 16 chains (1273 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 10412 restraints for refining 13323 atoms. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2409 (Rfree = 0.000) for 13323 atoms. Found 358 (358 requested) and removed 134 (190 requested) atoms. Cycle 7: After refmac, R = 0.2154 (Rfree = 0.000) for 13547 atoms. Found 295 (364 requested) and removed 73 (193 requested) atoms. Cycle 8: After refmac, R = 0.2023 (Rfree = 0.000) for 13769 atoms. Found 185 (370 requested) and removed 87 (197 requested) atoms. Cycle 9: After refmac, R = 0.1943 (Rfree = 0.000) for 13867 atoms. Found 194 (373 requested) and removed 86 (198 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1889 (Rfree = 0.000) for 13975 atoms. Found 171 (376 requested) and removed 93 (200 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.34 2.04 NCS extension: 2 residues added (144 deleted due to clashes), 14067 seeds are put forward Round 1: 1471 peptides, 38 chains. Longest chain 115 peptides. Score 0.876 Round 2: 1502 peptides, 33 chains. Longest chain 118 peptides. Score 0.888 Round 3: 1489 peptides, 40 chains. Longest chain 113 peptides. Score 0.877 Round 4: 1498 peptides, 37 chains. Longest chain 116 peptides. Score 0.883 Round 5: 1470 peptides, 50 chains. Longest chain 83 peptides. Score 0.862 Taking the results from Round 2 Chains 41, Residues 1469, Estimated correctness of the model 98.4 % 23 chains (1341 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 102 A Built loop between residues 126 A and 131 A Built loop between residues 126 C and 130 C Built loop between residues 140 C and 143 C Built loop between residues 195 C and 205 C Built loop between residues 50 B and 56 B Built loop between residues 126 E and 130 E Built loop between residues 125 D and 130 D Built loop between residues 112 F and 116 F Built loop between residues 159 F and 162 F 26 chains (1495 residues) following loop building 13 chains (1382 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 10988 restraints for refining 13528 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2334 (Rfree = 0.000) for 13528 atoms. Found 356 (356 requested) and removed 164 (193 requested) atoms. Cycle 12: After refmac, R = 0.2097 (Rfree = 0.000) for 13720 atoms. Found 255 (361 requested) and removed 97 (196 requested) atoms. Cycle 13: After refmac, R = 0.1982 (Rfree = 0.000) for 13878 atoms. Found 203 (365 requested) and removed 99 (198 requested) atoms. Cycle 14: After refmac, R = 0.1913 (Rfree = 0.000) for 13982 atoms. Found 192 (368 requested) and removed 96 (200 requested) atoms. Cycle 15: After refmac, R = 0.1865 (Rfree = 0.000) for 14078 atoms. Found 177 (371 requested) and removed 118 (201 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.33 2.04 NCS extension: 17 residues added (19 deleted due to clashes), 14170 seeds are put forward Round 1: 1505 peptides, 40 chains. Longest chain 117 peptides. Score 0.880 Round 2: 1498 peptides, 38 chains. Longest chain 119 peptides. Score 0.881 Round 3: 1487 peptides, 41 chains. Longest chain 112 peptides. Score 0.876 Round 4: 1487 peptides, 46 chains. Longest chain 115 peptides. Score 0.870 Round 5: 1497 peptides, 53 chains. Longest chain 118 peptides. Score 0.864 Taking the results from Round 2 Chains 43, Residues 1460, Estimated correctness of the model 98.2 % 26 chains (1235 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 140 A and 143 A Built loop between residues 195 A and 205 A Built loop between residues 254 A and 257 A Built loop between residues 36 C and 42 C Built loop between residues 254 B and 263 B Built loop between residues 87 E and 91 E Built loop between residues 266 E and 269 E Built loop between residues 38 D and 42 D 31 chains (1482 residues) following loop building 18 chains (1269 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 10490 restraints for refining 13522 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2180 (Rfree = 0.000) for 13522 atoms. Found 348 (348 requested) and removed 174 (193 requested) atoms. Cycle 17: After refmac, R = 0.1990 (Rfree = 0.000) for 13696 atoms. Found 260 (353 requested) and removed 71 (196 requested) atoms. Cycle 18: After refmac, R = 0.1890 (Rfree = 0.000) for 13885 atoms. Found 203 (357 requested) and removed 98 (198 requested) atoms. Cycle 19: After refmac, R = 0.1832 (Rfree = 0.000) for 13990 atoms. Found 213 (360 requested) and removed 114 (200 requested) atoms. Cycle 20: After refmac, R = 0.1791 (Rfree = 0.000) for 14089 atoms. Found 208 (355 requested) and removed 121 (201 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.33 2.04 NCS extension: 6 residues added (57 deleted due to clashes), 14193 seeds are put forward Round 1: 1491 peptides, 38 chains. Longest chain 117 peptides. Score 0.880 Round 2: 1498 peptides, 37 chains. Longest chain 121 peptides. Score 0.883 Round 3: 1498 peptides, 37 chains. Longest chain 116 peptides. Score 0.883 Round 4: 1494 peptides, 41 chains. Longest chain 112 peptides. Score 0.877 Round 5: 1479 peptides, 45 chains. Longest chain 116 peptides. Score 0.870 Taking the results from Round 3 Chains 42, Residues 1461, Estimated correctness of the model 98.3 % 24 chains (1351 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 A and 61 A Built loop between residues 120 A and 130 A Built loop between residues 123 C and 130 C Built loop between residues 195 C and 205 C Built loop between residues 47 B and 56 B Built loop between residues 126 B and 130 B Built loop between residues 55 E and 58 E Built loop between residues 126 E and 131 E Built loop between residues 147 E and 150 E Built loop between residues 126 D and 131 D Built loop between residues 91 F and 94 F Built loop between residues 122 F and 130 F Built loop between residues 147 F and 150 F 26 chains (1507 residues) following loop building 11 chains (1410 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11136 restraints for refining 13556 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2284 (Rfree = 0.000) for 13556 atoms. Found 334 (334 requested) and removed 169 (194 requested) atoms. Cycle 22: After refmac, R = 0.2023 (Rfree = 0.000) for 13721 atoms. Found 329 (329 requested) and removed 84 (196 requested) atoms. Cycle 23: After refmac, R = 0.1901 (Rfree = 0.000) for 13966 atoms. Found 225 (335 requested) and removed 110 (199 requested) atoms. Cycle 24: After refmac, R = 0.1840 (Rfree = 0.000) for 14081 atoms. Found 208 (339 requested) and removed 103 (201 requested) atoms. Cycle 25: After refmac, R = 0.1796 (Rfree = 0.000) for 14186 atoms. Found 215 (341 requested) and removed 123 (203 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.33 2.04 NCS extension: 2 residues added (22 deleted due to clashes), 14287 seeds are put forward Round 1: 1494 peptides, 36 chains. Longest chain 118 peptides. Score 0.883 Round 2: 1512 peptides, 31 chains. Longest chain 118 peptides. Score 0.892 Round 3: 1494 peptides, 38 chains. Longest chain 113 peptides. Score 0.881 Round 4: 1491 peptides, 39 chains. Longest chain 154 peptides. Score 0.879 Round 5: 1499 peptides, 45 chains. Longest chain 110 peptides. Score 0.874 Taking the results from Round 2 Chains 34, Residues 1481, Estimated correctness of the model 98.5 % 23 chains (1419 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 104 A and 107 A Built loop between residues 122 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 194 C and 204 C Built loop between residues 107 B and 114 B Built loop between residues 127 B and 130 B Built loop between residues 147 B and 150 B Built loop between residues 128 E and 132 E Built loop between residues 172 E and 175 E Built loop between residues 193 E and 204 E Built loop between residues 124 D and 130 D Built loop between residues 194 D and 205 D Built loop between residues 127 F and 130 F 18 chains (1540 residues) following loop building 9 chains (1485 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11527 restraints for refining 13735 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2184 (Rfree = 0.000) for 13735 atoms. Found 322 (322 requested) and removed 206 (196 requested) atoms. Cycle 27: After refmac, R = 0.2000 (Rfree = 0.000) for 13851 atoms. Found 276 (317 requested) and removed 93 (198 requested) atoms. Cycle 28: After refmac, R = 0.1900 (Rfree = 0.000) for 14034 atoms. Found 244 (321 requested) and removed 98 (200 requested) atoms. Cycle 29: After refmac, R = 0.1837 (Rfree = 0.000) for 14180 atoms. Found 201 (324 requested) and removed 109 (202 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1788 (Rfree = 0.000) for 14272 atoms. Found 211 (318 requested) and removed 130 (204 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.33 2.04 NCS extension: 11 residues added (15 deleted due to clashes), 14381 seeds are put forward Round 1: 1494 peptides, 36 chains. Longest chain 118 peptides. Score 0.883 Round 2: 1508 peptides, 27 chains. Longest chain 119 peptides. Score 0.895 Round 3: 1497 peptides, 39 chains. Longest chain 121 peptides. Score 0.880 Round 4: 1494 peptides, 41 chains. Longest chain 110 peptides. Score 0.877 Round 5: 1474 peptides, 42 chains. Longest chain 113 peptides. Score 0.872 Taking the results from Round 2 Chains 31, Residues 1481, Estimated correctness of the model 98.6 % 20 chains (1424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 127 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 87 B and 90 B Built loop between residues 122 B and 131 B Built loop between residues 126 E and 130 E Built loop between residues 124 D and 131 D Built loop between residues 195 D and 205 D Built loop between residues 125 F and 131 F 19 chains (1514 residues) following loop building 11 chains (1465 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 11384 restraints for refining 13653 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2080 (Rfree = 0.000) for 13653 atoms. Found 296 (296 requested) and removed 174 (195 requested) atoms. Cycle 32: After refmac, R = 0.1923 (Rfree = 0.000) for 13775 atoms. Found 292 (292 requested) and removed 72 (197 requested) atoms. Cycle 33: After refmac, R = 0.1846 (Rfree = 0.000) for 13995 atoms. Found 248 (296 requested) and removed 114 (200 requested) atoms. Cycle 34: After refmac, R = 0.1799 (Rfree = 0.000) for 14129 atoms. Found 237 (299 requested) and removed 138 (202 requested) atoms. Cycle 35: After refmac, R = 0.1774 (Rfree = 0.000) for 14228 atoms. Found 260 (293 requested) and removed 170 (203 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.33 2.04 NCS extension: 17 residues added (13 deleted due to clashes), 14345 seeds are put forward Round 1: 1509 peptides, 29 chains. Longest chain 118 peptides. Score 0.893 Round 2: 1498 peptides, 35 chains. Longest chain 184 peptides. Score 0.885 Round 3: 1499 peptides, 35 chains. Longest chain 115 peptides. Score 0.885 Round 4: 1510 peptides, 36 chains. Longest chain 132 peptides. Score 0.886 Round 5: 1487 peptides, 41 chains. Longest chain 115 peptides. Score 0.876 Taking the results from Round 1 Chains 33, Residues 1480, Estimated correctness of the model 98.5 % 22 chains (1424 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 122 A and 130 A Built loop between residues 126 C and 130 C Built loop between residues 193 C and 204 C Built loop between residues 73 B and 76 B Built loop between residues 92 B and 95 B Built loop between residues 126 B and 130 B Built loop between residues 250 B and 253 B Built loop between residues 126 E and 130 E Built loop between residues 125 D and 131 D Built loop between residues 194 D and 205 D Built loop between residues 127 F and 131 F 19 chains (1528 residues) following loop building 10 chains (1476 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11464 restraints for refining 13718 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2093 (Rfree = 0.000) for 13718 atoms. Found 274 (274 requested) and removed 171 (196 requested) atoms. Cycle 37: After refmac, R = 0.1928 (Rfree = 0.000) for 13821 atoms. Found 269 (269 requested) and removed 76 (197 requested) atoms. Cycle 38: After refmac, R = 0.1842 (Rfree = 0.000) for 14014 atoms. Found 222 (273 requested) and removed 95 (200 requested) atoms. Cycle 39: After refmac, R = 0.1783 (Rfree = 0.000) for 14141 atoms. Found 213 (275 requested) and removed 121 (202 requested) atoms. Cycle 40: After refmac, R = 0.1754 (Rfree = 0.000) for 14233 atoms. Found 191 (269 requested) and removed 140 (203 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.33 2.04 NCS extension: 13 residues added (16 deleted due to clashes), 14308 seeds are put forward Round 1: 1487 peptides, 31 chains. Longest chain 117 peptides. Score 0.887 Round 2: 1503 peptides, 34 chains. Longest chain 119 peptides. Score 0.887 Round 3: 1506 peptides, 37 chains. Longest chain 118 peptides. Score 0.884 Round 4: 1511 peptides, 42 chains. Longest chain 118 peptides. Score 0.879 Round 5: 1495 peptides, 41 chains. Longest chain 119 peptides. Score 0.877 Taking the results from Round 2 Chains 40, Residues 1469, Estimated correctness of the model 98.4 % 24 chains (1388 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 88 A and 91 A Built loop between residues 104 A and 111 A Built loop between residues 254 A and 257 A Built loop between residues 126 C and 129 C Built loop between residues 194 C and 205 C Built loop between residues 147 B and 150 B Built loop between residues 124 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 151 D and 154 D 29 chains (1509 residues) following loop building 14 chains (1432 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11192 restraints for refining 13657 atoms. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2221 (Rfree = 0.000) for 13657 atoms. Found 250 (250 requested) and removed 163 (195 requested) atoms. Cycle 42: After refmac, R = 0.1982 (Rfree = 0.000) for 13744 atoms. Found 244 (244 requested) and removed 70 (196 requested) atoms. Cycle 43: After refmac, R = 0.1863 (Rfree = 0.000) for 13918 atoms. Found 202 (247 requested) and removed 76 (199 requested) atoms. Cycle 44: After refmac, R = 0.1795 (Rfree = 0.000) for 14044 atoms. Found 193 (249 requested) and removed 84 (201 requested) atoms. Cycle 45: After refmac, R = 0.1756 (Rfree = 0.000) for 14153 atoms. Found 184 (251 requested) and removed 105 (202 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.33 2.04 NCS extension: 25 residues added (72 deleted due to clashes), 14267 seeds are put forward Round 1: 1490 peptides, 33 chains. Longest chain 117 peptides. Score 0.886 Round 2: 1504 peptides, 32 chains. Longest chain 119 peptides. Score 0.889 Round 3: 1508 peptides, 37 chains. Longest chain 118 peptides. Score 0.884 Round 4: 1502 peptides, 43 chains. Longest chain 114 peptides. Score 0.876 Round 5: 1517 peptides, 41 chains. Longest chain 119 peptides. Score 0.882 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 38, Residues 1472, Estimated correctness of the model 98.4 % 23 chains (1325 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 74 A and 77 A Built loop between residues 85 A and 89 A Built loop between residues 122 A and 131 A Built loop between residues 126 C and 129 C Built loop between residues 192 C and 205 C Built loop between residues 88 B and 91 B Built loop between residues 126 B and 130 B Built loop between residues 171 E and 174 E Built loop between residues 194 E and 205 E Built loop between residues 195 D and 205 D Built loop between residues 52 F and 56 F Built loop between residues 124 F and 131 F 20 chains (1519 residues) following loop building 11 chains (1387 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 119082 reflections ( 97.35 % complete ) and 10997 restraints for refining 10853 atoms. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2877 (Rfree = 0.000) for 10853 atoms. Found 186 (186 requested) and removed 0 (186 requested) atoms. Cycle 47: After refmac, R = 0.2672 (Rfree = 0.000) for 10853 atoms. Found 107 (190 requested) and removed 2 (158 requested) atoms. Cycle 48: After refmac, R = 0.2528 (Rfree = 0.000) for 10853 atoms. Found 72 (191 requested) and removed 18 (159 requested) atoms. Cycle 49: After refmac, R = 0.2492 (Rfree = 0.000) for 10853 atoms. TimeTaking 237.5