Tue 25 Dec 20:46:19 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 2pnk-2.1-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-2.1-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pnk-2.1-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-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/2pnk-2.1-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 ============================================================ Tue 25 Dec 20:46:41 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/2pnk-2.1-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 6319 and 0 Target number of residues in the AU: 6319 Target solvent content: 0.5162 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 428 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 5136 Adjusted target solvent content: 0.61 Input MTZ file: 2pnk-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: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-2.1-parrot-noncs.fasta_lf Building free atoms model in initial map for 41088 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: 162.857 2.100 Wilson plot Bfac: 26.99 Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 0 restraints for refining 45844 atoms. Observations/parameters ratio is 2.08 ------------------------------------------------------ Starting model: R = 0.3019 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2521 (Rfree = 0.000) for 45844 atoms. Found 1366 (1366 requested) and removed 519 (683 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.22 1.91 NCS extension: 0 residues added, 46691 seeds are put forward Round 1: 3813 peptides, 464 chains. Longest chain 36 peptides. Score 0.608 Round 2: 4278 peptides, 292 chains. Longest chain 80 peptides. Score 0.780 Round 3: 4490 peptides, 226 chains. Longest chain 102 peptides. Score 0.831 Round 4: 4612 peptides, 170 chains. Longest chain 108 peptides. Score 0.864 Round 5: 4629 peptides, 162 chains. Longest chain 144 peptides. Score 0.868 Taking the results from Round 5 Chains 177, Residues 4467, Estimated correctness of the model 98.0 % 99 chains (3884 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 33 A Built loop between residues 93 A and 97 A Built loop between residues 208 A and 218 A Built loop between residues 93 C and 97 C Built loop between residues 109 C and 112 C Built loop between residues 150 C and 154 C Built loop between residues 215 C and 218 C Built loop between residues 262 C and 265 C Built loop between residues 350 C and 353 C Built loop between residues 230 B and 233 B Built loop between residues 152 E and 160 E Built loop between residues 389 E and 393 E Built loop between residues 27 G and 38 G Built loop between residues 57 G and 62 G Built loop between residues 98 G and 104 G Built loop between residues 126 G and 129 G Built loop between residues 162 G and 165 G Built loop between residues 212 G and 216 G Built loop between residues 232 G and 235 G Built loop between residues 346 G and 357 G Built loop between residues 26 F and 34 F Built loop between residues 322 F and 325 F Built loop between residues 64 I and 67 I Built loop between residues 112 I and 115 I Built loop between residues 168 I and 171 I Built loop between residues 231 I and 236 I Built loop between residues 383 I and 386 I Built loop between residues 45 H and 56 H Built loop between residues 198 H and 205 H Built loop between residues 231 H and 234 H Built loop between residues 105 K and 108 K Built loop between residues 217 K and 220 K Built loop between residues 264 K and 273 K Built loop between residues 374 K and 382 K Built loop between residues 65 J and 68 J Built loop between residues 110 J and 117 J Built loop between residues 230 J and 234 J Built loop between residues 326 J and 329 J Built loop between residues 111 L and 114 L Built loop between residues 353 L and 356 L 126 chains (4594 residues) following loop building 59 chains (4041 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 36088 restraints for refining 45990 atoms. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2798 (Rfree = 0.000) for 45990 atoms. Found 1370 (1370 requested) and removed 791 (685 requested) atoms. Cycle 2: After refmac, R = 0.2558 (Rfree = 0.000) for 46569 atoms. Found 1236 (1360 requested) and removed 390 (694 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2397 (Rfree = 0.000) for 47415 atoms. Found 844 (1385 requested) and removed 226 (706 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 4: After refmac, R = 0.2287 (Rfree = 0.000) for 48033 atoms. Found 651 (1402 requested) and removed 154 (715 requested) atoms. Cycle 5: After refmac, R = 0.2202 (Rfree = 0.000) for 48530 atoms. Found 528 (1417 requested) and removed 159 (723 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.15 1.85 NCS extension: 18 residues added (216 deleted due to clashes), 48956 seeds are put forward Round 1: 4694 peptides, 145 chains. Longest chain 205 peptides. Score 0.879 Round 2: 4753 peptides, 118 chains. Longest chain 158 peptides. Score 0.892 Round 3: 4760 peptides, 126 chains. Longest chain 173 peptides. Score 0.889 Round 4: 4758 peptides, 120 chains. Longest chain 228 peptides. Score 0.891 Round 5: 4736 peptides, 131 chains. Longest chain 168 peptides. Score 0.886 Taking the results from Round 2 Chains 127, Residues 4635, Estimated correctness of the model 98.6 % 79 chains (4210 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 163 A and 166 A Built loop between residues 231 A and 237 A Built loop between residues 270 A and 274 A Built loop between residues 354 A and 357 A Built loop between residues 30 C and 33 C Built loop between residues 157 C and 166 C Built loop between residues 322 C and 325 C Built loop between residues 388 C and 392 C Built loop between residues 322 B and 325 B Built loop between residues 48 E and 51 E Built loop between residues 104 E and 112 E Built loop between residues 151 E and 159 E Built loop between residues 263 E and 266 E Built loop between residues 30 D and 34 D Built loop between residues 33 G and 38 G Built loop between residues 59 G and 62 G Built loop between residues 91 G and 94 G Built loop between residues 112 G and 115 G Built loop between residues 158 G and 161 G Built loop between residues 270 G and 273 G Built loop between residues 322 G and 325 G Built loop between residues 333 G and 336 G Built loop between residues 406 G and 409 G Built loop between residues 60 I and 65 I Built loop between residues 163 I and 173 I Built loop between residues 230 I and 233 I Built loop between residues 319 I and 322 I Built loop between residues 31 H and 37 H Built loop between residues 70 H and 74 H Built loop between residues 312 H and 316 H Built loop between residues 356 H and 359 H Built loop between residues 110 K and 116 K Built loop between residues 230 K and 234 K Built loop between residues 323 K and 330 K Built loop between residues 111 J and 115 J Built loop between residues 260 J and 263 J Built loop between residues 379 J and 383 J Built loop between residues 111 L and 114 L Built loop between residues 218 L and 221 L Built loop between residues 321 L and 324 L Built loop between residues 333 L and 336 L 78 chains (4743 residues) following loop building 38 chains (4340 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 38122 restraints for refining 46904 atoms. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2476 (Rfree = 0.000) for 46904 atoms. Found 1370 (1370 requested) and removed 735 (699 requested) atoms. Cycle 7: After refmac, R = 0.2297 (Rfree = 0.000) for 47539 atoms. Found 986 (1360 requested) and removed 196 (708 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2177 (Rfree = 0.000) for 48329 atoms. Found 661 (1382 requested) and removed 179 (720 requested) atoms. Cycle 9: After refmac, R = 0.2092 (Rfree = 0.000) for 48811 atoms. Found 563 (1397 requested) and removed 162 (727 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 10: After refmac, R = 0.2025 (Rfree = 0.000) for 49212 atoms. Found 457 (1408 requested) and removed 183 (733 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.14 1.84 NCS extension: 13 residues added (99 deleted due to clashes), 49520 seeds are put forward Round 1: 4789 peptides, 103 chains. Longest chain 231 peptides. Score 0.899 Round 2: 4818 peptides, 93 chains. Longest chain 223 peptides. Score 0.904 Round 3: 4790 peptides, 112 chains. Longest chain 173 peptides. Score 0.896 Round 4: 4778 peptides, 110 chains. Longest chain 179 peptides. Score 0.896 Round 5: 4748 peptides, 131 chains. Longest chain 144 peptides. Score 0.887 Taking the results from Round 2 Chains 99, Residues 4725, Estimated correctness of the model 98.9 % 68 chains (4435 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 228 A and 235 A Built loop between residues 321 A and 324 A Built loop between residues 121 C and 126 C Built loop between residues 216 C and 219 C Built loop between residues 230 C and 233 C Built loop between residues 303 C and 306 C Built loop between residues 322 C and 327 C Built loop between residues 391 C and 395 C Built loop between residues 110 B and 113 B Built loop between residues 271 B and 274 B Built loop between residues 322 B and 325 B Built loop between residues 230 E and 233 E Built loop between residues 104 D and 107 D Built loop between residues 322 D and 327 D Built loop between residues 26 G and 29 G Built loop between residues 59 G and 62 G Built loop between residues 229 G and 236 G Built loop between residues 325 G and 329 G Built loop between residues 63 I and 66 I Built loop between residues 79 I and 82 I Built loop between residues 110 I and 113 I Built loop between residues 175 I and 178 I Built loop between residues 322 I and 328 I Built loop between residues 35 H and 38 H Built loop between residues 54 H and 56 H Built loop between residues 124 H and 127 H Built loop between residues 157 H and 160 H Built loop between residues 199 H and 202 H Built loop between residues 322 H and 325 H Built loop between residues 162 K and 165 K Built loop between residues 228 K and 234 K Built loop between residues 322 K and 325 K Built loop between residues 354 K and 357 K Built loop between residues 60 J and 63 J Built loop between residues 71 J and 76 J Built loop between residues 157 J and 161 J Built loop between residues 229 J and 235 J Built loop between residues 163 L and 166 L Built loop between residues 230 L and 233 L Built loop between residues 322 L and 328 L Built loop between residues 354 L and 357 L 54 chains (4825 residues) following loop building 27 chains (4547 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 39445 restraints for refining 47379 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2357 (Rfree = 0.000) for 47379 atoms. Found 1356 (1356 requested) and removed 723 (706 requested) atoms. Cycle 12: After refmac, R = 0.2175 (Rfree = 0.000) for 48012 atoms. Found 938 (1345 requested) and removed 174 (715 requested) atoms. Cycle 13: After refmac, R = 0.2072 (Rfree = 0.000) for 48776 atoms. Found 608 (1367 requested) and removed 194 (727 requested) atoms. Cycle 14: After refmac, R = 0.1999 (Rfree = 0.000) for 49190 atoms. Found 573 (1378 requested) and removed 195 (733 requested) atoms. Cycle 15: After refmac, R = 0.1939 (Rfree = 0.000) for 49568 atoms. Found 513 (1388 requested) and removed 257 (738 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.14 1.84 NCS extension: 11 residues added (29 deleted due to clashes), 49862 seeds are put forward Round 1: 4816 peptides, 91 chains. Longest chain 229 peptides. Score 0.904 Round 2: 4837 peptides, 78 chains. Longest chain 231 peptides. Score 0.909 Round 3: 4805 peptides, 106 chains. Longest chain 227 peptides. Score 0.899 Round 4: 4803 peptides, 101 chains. Longest chain 171 peptides. Score 0.900 Round 5: 4795 peptides, 113 chains. Longest chain 184 peptides. Score 0.896 Taking the results from Round 2 Chains 88, Residues 4759, Estimated correctness of the model 99.0 % 64 chains (4559 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 213 A and 218 A Built loop between residues 229 A and 233 A Built loop between residues 265 A and 269 A Built loop between residues 320 A and 323 A Built loop between residues 32 C and 39 C Built loop between residues 73 C and 78 C Built loop between residues 230 C and 237 C Built loop between residues 266 C and 269 C Built loop between residues 320 C and 323 C Built loop between residues 322 B and 325 B Built loop between residues 24 E and 35 E Built loop between residues 317 E and 322 E Built loop between residues 13 D and 16 D Built loop between residues 216 D and 219 D Built loop between residues 266 D and 269 D Built loop between residues 348 D and 357 D Built loop between residues 48 G and 51 G Built loop between residues 63 G and 66 G Built loop between residues 71 G and 76 G Built loop between residues 326 G and 329 G Built loop between residues 354 G and 357 G Built loop between residues 47 F and 49 F Built loop between residues 151 F and 154 F Built loop between residues 62 I and 67 I Built loop between residues 163 I and 166 I Built loop between residues 230 I and 233 I Built loop between residues 321 I and 324 I Built loop between residues 66 H and 69 H Built loop between residues 168 H and 171 H Built loop between residues 230 H and 233 H Built loop between residues 231 K and 234 K Built loop between residues 322 K and 325 K Built loop between residues 354 K and 357 K Built loop between residues 59 J and 62 J Built loop between residues 185 J and 188 J Built loop between residues 230 J and 233 J Built loop between residues 120 L and 123 L Built loop between residues 231 L and 234 L Built loop between residues 266 L and 269 L Built loop between residues 322 L and 327 L 40 chains (4854 residues) following loop building 24 chains (4674 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40085 restraints for refining 47608 atoms. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2285 (Rfree = 0.000) for 47608 atoms. Found 1305 (1305 requested) and removed 651 (709 requested) atoms. Cycle 17: After refmac, R = 0.2136 (Rfree = 0.000) for 48262 atoms. Found 966 (1323 requested) and removed 191 (719 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2042 (Rfree = 0.000) for 49037 atoms. Found 697 (1344 requested) and removed 171 (730 requested) atoms. Cycle 19: After refmac, R = 0.1971 (Rfree = 0.000) for 49563 atoms. Found 590 (1359 requested) and removed 273 (738 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 20: After refmac, R = 0.1920 (Rfree = 0.000) for 49880 atoms. Found 600 (1367 requested) and removed 294 (743 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.14 1.84 NCS extension: 13 residues added (4 deleted due to clashes), 50212 seeds are put forward Round 1: 4833 peptides, 81 chains. Longest chain 231 peptides. Score 0.908 Round 2: 4841 peptides, 79 chains. Longest chain 229 peptides. Score 0.909 Round 3: 4811 peptides, 101 chains. Longest chain 172 peptides. Score 0.901 Round 4: 4776 peptides, 113 chains. Longest chain 225 peptides. Score 0.895 Round 5: 4790 peptides, 116 chains. Longest chain 193 peptides. Score 0.894 Taking the results from Round 2 Chains 86, Residues 4762, Estimated correctness of the model 99.0 % 69 chains (4561 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 139 A Built loop between residues 200 A and 203 A Built loop between residues 228 A and 233 A Built loop between residues 320 A and 323 A Built loop between residues 157 C and 161 C Built loop between residues 184 C and 187 C Built loop between residues 265 C and 269 C Built loop between residues 355 C and 358 C Built loop between residues 25 B and 28 B Built loop between residues 124 B and 127 B Built loop between residues 162 B and 165 B Built loop between residues 266 B and 269 B Built loop between residues 322 B and 325 B Built loop between residues 185 D and 195 D Built loop between residues 230 D and 233 D Built loop between residues 320 D and 323 D Built loop between residues 32 G and 35 G Built loop between residues 54 G and 57 G Built loop between residues 119 G and 122 G Built loop between residues 198 G and 201 G Built loop between residues 322 G and 328 G Built loop between residues 108 F and 115 F Built loop between residues 229 F and 233 F Built loop between residues 326 F and 329 F Built loop between residues 396 F and 399 F Built loop between residues 60 I and 65 I Built loop between residues 102 I and 107 I Built loop between residues 216 I and 219 I Built loop between residues 326 I and 329 I Built loop between residues 351 I and 355 I Built loop between residues 31 H and 34 H Built loop between residues 227 H and 233 H Built loop between residues 230 K and 233 K Built loop between residues 322 K and 328 K Built loop between residues 105 J and 108 J Built loop between residues 231 J and 234 J Built loop between residues 322 J and 325 J Built loop between residues 347 J and 350 J Built loop between residues 104 L and 107 L Built loop between residues 154 L and 157 L Built loop between residues 206 L and 209 L Built loop between residues 230 L and 233 L Built loop between residues 348 L and 357 L Built loop between residues 396 L and 399 L 38 chains (4876 residues) following loop building 25 chains (4685 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 40294 restraints for refining 47876 atoms. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2242 (Rfree = 0.000) for 47876 atoms. Found 1313 (1313 requested) and removed 644 (713 requested) atoms. Cycle 22: After refmac, R = 0.2096 (Rfree = 0.000) for 48545 atoms. Found 947 (1331 requested) and removed 181 (723 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.1996 (Rfree = 0.000) for 49311 atoms. Found 642 (1351 requested) and removed 216 (734 requested) atoms. Cycle 24: After refmac, R = 0.1927 (Rfree = 0.000) for 49737 atoms. Found 626 (1363 requested) and removed 228 (741 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1877 (Rfree = 0.000) for 50135 atoms. Found 571 (1374 requested) and removed 293 (747 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.13 1.84 NCS extension: 11 residues added (3 deleted due to clashes), 50435 seeds are put forward Round 1: 4838 peptides, 81 chains. Longest chain 229 peptides. Score 0.908 Round 2: 4846 peptides, 72 chains. Longest chain 230 peptides. Score 0.912 Round 3: 4807 peptides, 105 chains. Longest chain 211 peptides. Score 0.899 Round 4: 4808 peptides, 110 chains. Longest chain 198 peptides. Score 0.897 Round 5: 4784 peptides, 115 chains. Longest chain 190 peptides. Score 0.894 Taking the results from Round 2 Chains 81, Residues 4774, Estimated correctness of the model 99.0 % 65 chains (4582 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 230 A and 233 A Built loop between residues 320 A and 323 A Built loop between residues 266 C and 269 C Built loop between residues 322 C and 325 C Built loop between residues 103 B and 106 B Built loop between residues 136 B and 139 B Built loop between residues 185 B and 195 B Built loop between residues 230 B and 233 B Built loop between residues 320 B and 323 B Built loop between residues 62 E and 65 E Built loop between residues 172 E and 175 E Built loop between residues 265 E and 269 E Built loop between residues 355 E and 358 E Built loop between residues 111 D and 116 D Built loop between residues 133 D and 137 D Built loop between residues 210 D and 218 D Built loop between residues 322 D and 325 D Built loop between residues 351 D and 357 D Built loop between residues 62 G and 65 G Built loop between residues 229 G and 233 G Built loop between residues 31 F and 38 F Built loop between residues 326 F and 329 F Built loop between residues 347 F and 350 F Built loop between residues 62 I and 67 I Built loop between residues 230 I and 234 I Built loop between residues 322 I and 328 I Built loop between residues 348 I and 357 I Built loop between residues 54 H and 57 H Built loop between residues 121 H and 126 H Built loop between residues 326 H and 329 H Built loop between residues 231 K and 234 K Built loop between residues 322 K and 328 K Built loop between residues 405 K and 408 K Built loop between residues 49 J and 52 J Built loop between residues 213 J and 220 J Built loop between residues 322 J and 325 J Built loop between residues 111 L and 114 L Built loop between residues 216 L and 219 L Built loop between residues 230 L and 233 L 35 chains (4881 residues) following loop building 26 chains (4705 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40171 restraints for refining 47645 atoms. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2234 (Rfree = 0.000) for 47645 atoms. Found 1278 (1278 requested) and removed 634 (710 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2090 (Rfree = 0.000) for 48289 atoms. Found 1061 (1295 requested) and removed 191 (719 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1992 (Rfree = 0.000) for 49159 atoms. Found 723 (1318 requested) and removed 210 (732 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1873 (Rfree = 0.000) for 49672 atoms. Found 648 (1332 requested) and removed 283 (740 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.1839 (Rfree = 0.000) for 50037 atoms. Found 605 (1342 requested) and removed 298 (745 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.13 1.84 NCS extension: 10 residues added (3 deleted due to clashes), 50387 seeds are put forward Round 1: 4846 peptides, 85 chains. Longest chain 229 peptides. Score 0.908 Round 2: 4860 peptides, 70 chains. Longest chain 261 peptides. Score 0.913 Round 3: 4809 peptides, 107 chains. Longest chain 231 peptides. Score 0.898 Round 4: 4838 peptides, 101 chains. Longest chain 193 peptides. Score 0.902 Round 5: 4789 peptides, 122 chains. Longest chain 168 peptides. Score 0.892 Taking the results from Round 2 Chains 78, Residues 4790, Estimated correctness of the model 99.1 % 60 chains (4583 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 214 A and 218 A Built loop between residues 229 A and 233 A Built loop between residues 322 A and 333 A Built loop between residues 354 A and 357 A Built loop between residues 199 C and 203 C Built loop between residues 322 C and 325 C Built loop between residues 321 B and 325 B Built loop between residues 62 E and 65 E Built loop between residues 213 E and 216 E Built loop between residues 230 E and 233 E Built loop between residues 266 E and 269 E Built loop between residues 323 E and 328 E Built loop between residues 150 D and 160 D Built loop between residues 179 D and 187 D Built loop between residues 231 D and 234 D Built loop between residues 265 D and 269 D Built loop between residues 322 D and 325 D Built loop between residues 345 D and 348 D Built loop between residues 90 G and 93 G Built loop between residues 110 G and 117 G Built loop between residues 363 G and 365 G Built loop between residues 25 F and 28 F Built loop between residues 60 F and 65 F Built loop between residues 163 F and 166 F Built loop between residues 185 F and 190 F Built loop between residues 31 I and 34 I Built loop between residues 216 I and 219 I Built loop between residues 229 I and 233 I Built loop between residues 355 I and 358 I Built loop between residues 393 I and 396 I Built loop between residues 32 H and 35 H Built loop between residues 48 H and 57 H Built loop between residues 106 H and 109 H Built loop between residues 230 H and 233 H Built loop between residues 230 K and 234 K Built loop between residues 322 K and 325 K Built loop between residues 79 J and 82 J Built loop between residues 194 J and 197 J Built loop between residues 216 J and 219 J Built loop between residues 229 J and 233 J Built loop between residues 322 J and 326 J Built loop between residues 230 L and 233 L Built loop between residues 322 L and 328 L 27 chains (4906 residues) following loop building 17 chains (4716 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 40600 restraints for refining 47909 atoms. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2199 (Rfree = 0.000) for 47909 atoms. Found 1285 (1285 requested) and removed 575 (714 requested) atoms. Cycle 32: After refmac, R = 0.2054 (Rfree = 0.000) for 48619 atoms. Found 995 (1304 requested) and removed 185 (724 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1957 (Rfree = 0.000) for 49429 atoms. Found 647 (1326 requested) and removed 233 (736 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1886 (Rfree = 0.000) for 49843 atoms. Found 556 (1336 requested) and removed 239 (742 requested) atoms. Cycle 35: After refmac, R = 0.1794 (Rfree = 0.000) for 50160 atoms. Found 577 (1345 requested) and removed 344 (747 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.13 1.84 NCS extension: 3 residues added (12 deleted due to clashes), 50412 seeds are put forward Round 1: 4869 peptides, 72 chains. Longest chain 230 peptides. Score 0.913 Round 2: 4861 peptides, 72 chains. Longest chain 350 peptides. Score 0.912 Round 3: 4823 peptides, 98 chains. Longest chain 177 peptides. Score 0.902 Round 4: 4817 peptides, 109 chains. Longest chain 193 peptides. Score 0.898 Round 5: 4790 peptides, 111 chains. Longest chain 186 peptides. Score 0.896 Taking the results from Round 1 Chains 76, Residues 4797, Estimated correctness of the model 99.1 % 58 chains (4515 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 200 A and 203 A Built loop between residues 230 A and 233 A Built loop between residues 322 A and 325 A Built loop between residues 405 A and 408 A Built loop between residues 230 C and 233 C Built loop between residues 285 C and 288 C Built loop between residues 323 C and 328 C Built loop between residues 104 B and 114 B Built loop between residues 187 B and 195 B Built loop between residues 216 B and 219 B Built loop between residues 230 B and 233 B Built loop between residues 249 B and 252 B Built loop between residues 322 B and 328 B Built loop between residues 105 E and 115 E Built loop between residues 145 E and 149 E Built loop between residues 229 E and 233 E Built loop between residues 322 E and 325 E Built loop between residues 230 D and 233 D Built loop between residues 322 D and 325 D Built loop between residues 230 F and 233 F Built loop between residues 185 I and 188 I Built loop between residues 230 I and 233 I Built loop between residues 326 I and 329 I Built loop between residues 356 I and 359 I Built loop between residues 35 H and 38 H Built loop between residues 230 H and 233 H Built loop between residues 322 H and 328 H Built loop between residues 230 K and 233 K Built loop between residues 405 K and 408 K Built loop between residues 59 J and 62 J Built loop between residues 163 J and 166 J Built loop between residues 185 J and 188 J Built loop between residues 230 J and 233 J Built loop between residues 322 J and 325 J Built loop between residues 230 L and 233 L Built loop between residues 355 L and 358 L Built loop between residues 405 L and 408 L 35 chains (4885 residues) following loop building 21 chains (4618 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 39982 restraints for refining 47888 atoms. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2150 (Rfree = 0.000) for 47888 atoms. Found 1256 (1256 requested) and removed 563 (713 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2009 (Rfree = 0.000) for 48581 atoms. Found 1048 (1274 requested) and removed 205 (724 requested) atoms. Cycle 38: After refmac, R = 0.1920 (Rfree = 0.000) for 49424 atoms. Found 691 (1296 requested) and removed 255 (736 requested) atoms. Cycle 39: After refmac, R = 0.1855 (Rfree = 0.000) for 49860 atoms. Found 591 (1308 requested) and removed 243 (743 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1812 (Rfree = 0.000) for 50208 atoms. Found 582 (1316 requested) and removed 299 (748 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.13 1.84 NCS extension: 12 residues added (0 deleted due to clashes), 50520 seeds are put forward Round 1: 4864 peptides, 65 chains. Longest chain 229 peptides. Score 0.915 Round 2: 4860 peptides, 71 chains. Longest chain 230 peptides. Score 0.913 Round 3: 4828 peptides, 91 chains. Longest chain 218 peptides. Score 0.905 Round 4: 4808 peptides, 110 chains. Longest chain 180 peptides. Score 0.897 Round 5: 4804 peptides, 117 chains. Longest chain 160 peptides. Score 0.895 Taking the results from Round 1 Chains 68, Residues 4799, Estimated correctness of the model 99.1 % 51 chains (4541 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 A and 160 A Built loop between residues 183 A and 186 A Built loop between residues 230 A and 233 A Built loop between residues 264 A and 267 A Built loop between residues 322 A and 325 A Built loop between residues 230 C and 233 C Built loop between residues 322 C and 328 C Built loop between residues 229 B and 233 B Built loop between residues 35 E and 38 E Built loop between residues 322 E and 325 E Built loop between residues 164 D and 167 D Built loop between residues 200 D and 203 D Built loop between residues 326 D and 329 D Built loop between residues 15 G and 18 G Built loop between residues 322 G and 325 G Built loop between residues 59 I and 62 I Built loop between residues 185 I and 188 I Built loop between residues 230 I and 233 I Built loop between residues 355 H and 358 H Built loop between residues 230 K and 234 K Built loop between residues 106 J and 109 J Built loop between residues 162 J and 166 J Built loop between residues 230 J and 233 J Built loop between residues 322 J and 325 J Built loop between residues 230 L and 234 L Built loop between residues 322 L and 328 L 42 chains (4865 residues) following loop building 25 chains (4607 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 39751 restraints for refining 48238 atoms. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2164 (Rfree = 0.000) for 48238 atoms. Found 1237 (1237 requested) and removed 681 (719 requested) atoms. Cycle 42: After refmac, R = 0.2021 (Rfree = 0.000) for 48794 atoms. Found 969 (1221 requested) and removed 183 (727 requested) atoms. Cycle 43: After refmac, R = 0.1932 (Rfree = 0.000) for 49580 atoms. Found 650 (1242 requested) and removed 244 (739 requested) atoms. Cycle 44: After refmac, R = 0.1872 (Rfree = 0.000) for 49986 atoms. Found 613 (1252 requested) and removed 234 (745 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1820 (Rfree = 0.000) for 50365 atoms. Found 547 (1261 requested) and removed 324 (750 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.13 1.84 NCS extension: 8 residues added (260 deleted due to clashes), 50605 seeds are put forward Round 1: 4869 peptides, 69 chains. Longest chain 229 peptides. Score 0.914 Round 2: 4871 peptides, 67 chains. Longest chain 261 peptides. Score 0.914 Round 3: 4827 peptides, 100 chains. Longest chain 228 peptides. Score 0.902 Round 4: 4827 peptides, 100 chains. Longest chain 212 peptides. Score 0.902 Round 5: 4791 peptides, 111 chains. Longest chain 127 peptides. Score 0.896 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 70, Residues 4804, Estimated correctness of the model 99.1 % 54 chains (4580 residues) have been docked in sequence Sequence coverage is 95 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 230 A and 233 A Built loop between residues 334 A and 337 A Built loop between residues 354 A and 357 A Built loop between residues 230 C and 235 C Built loop between residues 322 C and 327 C Built loop between residues 25 B and 28 B Built loop between residues 59 B and 62 B Built loop between residues 109 B and 112 B Built loop between residues 229 B and 233 B Built loop between residues 387 B and 396 B Built loop between residues 229 E and 234 E Built loop between residues 172 D and 175 D Built loop between residues 229 D and 233 D Built loop between residues 163 G and 166 G Built loop between residues 216 G and 219 G Built loop between residues 90 F and 93 F Built loop between residues 109 F and 112 F Built loop between residues 322 F and 328 F Built loop between residues 79 I and 82 I Built loop between residues 230 I and 233 I Built loop between residues 270 I and 273 I Built loop between residues 32 H and 35 H Built loop between residues 55 H and 67 H Built loop between residues 326 H and 329 H Built loop between residues 230 K and 234 K Built loop between residues 322 K and 325 K Built loop between residues 356 K and 359 K Built loop between residues 109 J and 112 J Built loop between residues 230 J and 233 J Built loop between residues 172 L and 175 L Built loop between residues 229 L and 233 L Built loop between residues 357 L and 360 L Built loop between residues 396 L and 399 L 33 chains (4883 residues) following loop building 21 chains (4674 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 381160 reflections ( 94.42 % complete ) and 40145 restraints for refining 39210 atoms. Observations/parameters ratio is 2.43 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2747 (Rfree = 0.000) for 39210 atoms. Found 708 (958 requested) and removed 0 (958 requested) atoms. Cycle 47: After refmac, R = 0.2537 (Rfree = 0.000) for 39210 atoms. Found 379 (975 requested) and removed 10 (594 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2452 (Rfree = 0.000) for 39210 atoms. Found 205 (984 requested) and removed 29 (600 requested) atoms. Cycle 49: After refmac, R = 0.2396 (Rfree = 0.000) for 39210 atoms. TimeTaking 824.95