Tue 25 Dec 19:30:29 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 2pnk-2.1-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-2.1-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pnk-2.1-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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/2pnk-2.1-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 ============================================================ Tue 25 Dec 19:30:40 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-2.1-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pnk-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 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-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: 5 Cell parameters: 273.720 158.560 181.240 90.000 116.029 90.000 Input sequence file: 2pnk-2.1-parrot-mrncs.fasta_lf Building free atoms model in initial map for 41088 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: 162.857 2.100 Wilson plot Bfac: 26.99 Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 0 restraints for refining 46082 atoms. Observations/parameters ratio is 2.07 ------------------------------------------------------ Starting model: R = 0.2887 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2386 (Rfree = 0.000) for 46082 atoms. Found 1373 (1373 requested) and removed 468 (686 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.20 1.90 NCS extension: 0 residues added, 46987 seeds are put forward Round 1: 4050 peptides, 405 chains. Longest chain 44 peptides. Score 0.686 Round 2: 4472 peptides, 250 chains. Longest chain 108 peptides. Score 0.819 Round 3: 4635 peptides, 160 chains. Longest chain 111 peptides. Score 0.869 Round 4: 4715 peptides, 144 chains. Longest chain 155 peptides. Score 0.880 Round 5: 4769 peptides, 114 chains. Longest chain 229 peptides. Score 0.894 Taking the results from Round 5 Chains 127, Residues 4655, Estimated correctness of the model 98.6 % 83 chains (4141 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 121 A and 125 A Built loop between residues 223 A and 234 A Built loop between residues 250 A and 254 A Built loop between residues 264 A and 268 A Built loop between residues 67 C and 73 C Built loop between residues 228 C and 231 C Built loop between residues 267 C and 273 C Built loop between residues 322 C and 325 C Built loop between residues 230 B and 234 B Built loop between residues 270 B and 274 B Built loop between residues 355 E and 358 E Built loop between residues 389 E and 392 E Built loop between residues 71 D and 74 D Built loop between residues 98 D and 102 D Built loop between residues 115 D and 118 D Built loop between residues 200 D and 203 D Built loop between residues 35 G and 38 G Built loop between residues 109 G and 112 G Built loop between residues 198 G and 201 G Built loop between residues 230 G and 234 G Built loop between residues 325 G and 329 G Built loop between residues 347 G and 350 G Built loop between residues 258 F and 262 F Built loop between residues 303 F and 306 F Built loop between residues 34 I and 38 I Built loop between residues 63 I and 71 I Built loop between residues 109 I and 112 I Built loop between residues 183 I and 187 I Built loop between residues 231 I and 241 I Built loop between residues 323 I and 328 I Built loop between residues 347 I and 350 I Built loop between residues 45 H and 51 H Built loop between residues 62 H and 65 H Built loop between residues 103 H and 106 H Built loop between residues 163 H and 166 H Built loop between residues 262 H and 266 H Built loop between residues 385 H and 388 H Built loop between residues 229 K and 233 K Built loop between residues 259 K and 262 K Built loop between residues 325 K and 328 K Built loop between residues 43 J and 48 J Built loop between residues 102 J and 110 J Built loop between residues 230 J and 233 J Built loop between residues 329 J and 332 J Built loop between residues 170 L and 173 L Built loop between residues 195 L and 199 L Built loop between residues 232 L and 242 L Built loop between residues 266 L and 269 L 72 chains (4789 residues) following loop building 35 chains (4296 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 38077 restraints for refining 45444 atoms. Observations/parameters ratio is 2.10 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2656 (Rfree = 0.000) for 45444 atoms. Found 1354 (1354 requested) and removed 776 (677 requested) atoms. Failed to save intermediate PDB Cycle 2: After refmac, R = 0.2413 (Rfree = 0.000) for 46022 atoms. Found 1178 (1344 requested) and removed 311 (685 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2161 (Rfree = 0.000) for 46889 atoms. Found 950 (1369 requested) and removed 326 (698 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2079 (Rfree = 0.000) for 47513 atoms. Found 765 (1388 requested) and removed 206 (708 requested) atoms. Failed to save intermediate PDBFailed to save intermediate PDB Cycle 5: After refmac, R = 0.2004 (Rfree = 0.000) for 48072 atoms. Found 630 (1404 requested) and removed 214 (716 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.15 1.85 NCS extension: 5 residues added (52 deleted due to clashes), 48537 seeds are put forward Round 1: 4805 peptides, 97 chains. Longest chain 231 peptides. Score 0.902 Round 2: 4825 peptides, 78 chains. Longest chain 230 peptides. Score 0.909 Round 3: 4790 peptides, 105 chains. Longest chain 229 peptides. Score 0.898 Round 4: 4791 peptides, 101 chains. Longest chain 229 peptides. Score 0.900 Round 5: 4762 peptides, 120 chains. Longest chain 156 peptides. Score 0.891 Taking the results from Round 2 Chains 86, Residues 4747, Estimated correctness of the model 99.0 % 64 chains (4416 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 205 A and 209 A Built loop between residues 230 A and 233 A Built loop between residues 320 A and 323 A Built loop between residues 37 C and 39 C Built loop between residues 108 C and 114 C Built loop between residues 227 C and 233 C Built loop between residues 322 B and 328 B Built loop between residues 231 E and 233 E Built loop between residues 322 E and 325 E Built loop between residues 354 E and 357 E Built loop between residues 191 D and 194 D Built loop between residues 25 G and 28 G Built loop between residues 213 G and 218 G Built loop between residues 230 G and 233 G Built loop between residues 322 G and 325 G Built loop between residues 353 G and 356 G Built loop between residues 393 G and 398 G Built loop between residues 189 F and 200 F Built loop between residues 214 I and 218 I Built loop between residues 326 I and 329 I Built loop between residues 35 H and 38 H Built loop between residues 163 H and 174 H Built loop between residues 326 H and 329 H Built loop between residues 351 H and 354 H Built loop between residues 231 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 101 J and 104 J Built loop between residues 112 L and 116 L Built loop between residues 159 L and 162 L Built loop between residues 230 L and 234 L Built loop between residues 266 L and 269 L 47 chains (4828 residues) following loop building 32 chains (4511 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 39354 restraints for refining 46673 atoms. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2348 (Rfree = 0.000) for 46673 atoms. Found 1363 (1363 requested) and removed 773 (695 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.2163 (Rfree = 0.000) for 47263 atoms. Found 963 (1352 requested) and removed 230 (704 requested) atoms. Cycle 8: After refmac, R = 0.2046 (Rfree = 0.000) for 47996 atoms. Found 687 (1373 requested) and removed 214 (715 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.1965 (Rfree = 0.000) for 48469 atoms. Found 562 (1386 requested) and removed 209 (722 requested) atoms. Cycle 10: After refmac, R = 0.1906 (Rfree = 0.000) for 48822 atoms. Found 525 (1397 requested) and removed 220 (727 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.14 1.84 NCS extension: 11 residues added (38 deleted due to clashes), 49154 seeds are put forward Round 1: 4832 peptides, 76 chains. Longest chain 229 peptides. Score 0.910 Round 2: 4863 peptides, 67 chains. Longest chain 339 peptides. Score 0.914 Round 3: 4783 peptides, 113 chains. Longest chain 187 peptides. Score 0.895 Round 4: 4812 peptides, 98 chains. Longest chain 231 peptides. Score 0.902 Round 5: 4782 peptides, 124 chains. Longest chain 186 peptides. Score 0.891 Taking the results from Round 2 Chains 73, Residues 4796, Estimated correctness of the model 99.1 % 58 chains (4622 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 124 C and 127 C Built loop between residues 216 C and 219 C Built loop between residues 322 C and 328 C Built loop between residues 396 C and 399 C Built loop between residues 103 B and 106 B Built loop between residues 136 B and 139 B Built loop between residues 285 B and 288 B Built loop between residues 347 B and 350 B Built loop between residues 60 E and 63 E Built loop between residues 163 E and 166 E Built loop between residues 211 E and 217 E Built loop between residues 322 E and 325 E Built loop between residues 361 E and 364 E Built loop between residues 48 D and 51 D Built loop between residues 163 D and 166 D Built loop between residues 230 D and 233 D Built loop between residues 326 D and 329 D Built loop between residues 353 D and 357 D Built loop between residues 201 G and 209 G Built loop between residues 322 G and 325 G Built loop between residues 96 F and 99 F Built loop between residues 230 F and 233 F Built loop between residues 54 I and 57 I Built loop between residues 322 I and 325 I Built loop between residues 400 I and 403 I Built loop between residues 38 H and 42 H Built loop between residues 59 H and 62 H Built loop between residues 215 H and 219 H Built loop between residues 266 H and 269 H Built loop between residues 322 H and 325 H Built loop between residues 397 H and 400 H Built loop between residues 326 K and 329 K Built loop between residues 105 J and 108 J Built loop between residues 231 J and 234 J Built loop between residues 270 J and 273 J Built loop between residues 322 J and 325 J Built loop between residues 194 L and 197 L Built loop between residues 212 L and 216 L Built loop between residues 322 L and 325 L 31 chains (4882 residues) following loop building 19 chains (4715 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40397 restraints for refining 46994 atoms. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2236 (Rfree = 0.000) for 46994 atoms. Found 1344 (1344 requested) and removed 636 (700 requested) atoms. Cycle 12: After refmac, R = 0.2082 (Rfree = 0.000) for 47702 atoms. Found 957 (1365 requested) and removed 234 (711 requested) atoms. Cycle 13: After refmac, R = 0.1982 (Rfree = 0.000) for 48425 atoms. Found 676 (1385 requested) and removed 206 (721 requested) atoms. Cycle 14: After refmac, R = 0.1861 (Rfree = 0.000) for 48895 atoms. Found 646 (1399 requested) and removed 321 (728 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1791 (Rfree = 0.000) for 49220 atoms. Found 659 (1408 requested) and removed 323 (733 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.13 1.84 NCS extension: 15 residues added (6 deleted due to clashes), 49596 seeds are put forward Round 1: 4852 peptides, 69 chains. Longest chain 231 peptides. Score 0.913 Round 2: 4867 peptides, 62 chains. Longest chain 412 peptides. Score 0.916 Round 3: 4819 peptides, 87 chains. Longest chain 195 peptides. Score 0.906 Round 4: 4813 peptides, 99 chains. Longest chain 209 peptides. Score 0.901 Round 5: 4787 peptides, 113 chains. Longest chain 215 peptides. Score 0.895 Taking the results from Round 2 Chains 69, Residues 4805, Estimated correctness of the model 99.1 % 54 chains (4629 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 213 A and 218 A Built loop between residues 230 A and 233 A Built loop between residues 322 A and 328 A Built loop between residues 396 A and 399 A Built loop between residues 60 C and 63 C Built loop between residues 109 C and 112 C Built loop between residues 187 C and 197 C Built loop between residues 322 C and 325 C Built loop between residues 385 C and 388 C Built loop between residues 37 B and 39 B Built loop between residues 227 B and 233 B Built loop between residues 320 B and 323 B Built loop between residues 189 E and 195 E Built loop between residues 163 D and 166 D Built loop between residues 230 D and 233 D Built loop between residues 124 G and 127 G Built loop between residues 185 G and 188 G Built loop between residues 229 G and 234 G Built loop between residues 270 G and 274 G Built loop between residues 284 G and 287 G Built loop between residues 110 F and 113 F Built loop between residues 160 F and 163 F Built loop between residues 62 I and 65 I Built loop between residues 322 I and 325 I Built loop between residues 55 H and 58 H Built loop between residues 106 H and 109 H Built loop between residues 264 H and 268 H Built loop between residues 322 H and 328 H Built loop between residues 191 K and 194 K Built loop between residues 230 K and 235 K Built loop between residues 319 K and 322 K Built loop between residues 63 J and 66 J Built loop between residues 119 J and 123 J Built loop between residues 229 J and 233 J Built loop between residues 267 J and 273 J 31 chains (4900 residues) following loop building 19 chains (4730 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 40643 restraints for refining 47315 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2187 (Rfree = 0.000) for 47315 atoms. Found 1354 (1354 requested) and removed 650 (705 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.2032 (Rfree = 0.000) for 48019 atoms. Found 890 (1374 requested) and removed 228 (715 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1932 (Rfree = 0.000) for 48681 atoms. Found 666 (1393 requested) and removed 228 (725 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1865 (Rfree = 0.000) for 49119 atoms. Found 598 (1405 requested) and removed 261 (732 requested) atoms. Cycle 20: After refmac, R = 0.1815 (Rfree = 0.000) for 49456 atoms. Found 549 (1415 requested) and removed 295 (737 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.13 1.84 NCS extension: 13 residues added (9 deleted due to clashes), 49729 seeds are put forward Round 1: 4854 peptides, 73 chains. Longest chain 229 peptides. Score 0.912 Round 2: 4872 peptides, 57 chains. Longest chain 300 peptides. Score 0.918 Round 3: 4845 peptides, 92 chains. Longest chain 162 peptides. Score 0.905 Round 4: 4812 peptides, 100 chains. Longest chain 195 peptides. Score 0.901 Round 5: 4801 peptides, 114 chains. Longest chain 231 peptides. Score 0.896 Taking the results from Round 2 Chains 64, Residues 4815, Estimated correctness of the model 99.1 % 52 chains (4666 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 122 A and 125 A Built loop between residues 200 A and 203 A Built loop between residues 231 A and 237 A Built loop between residues 320 A and 323 A Built loop between residues 229 C and 233 C Built loop between residues 34 B and 37 B Built loop between residues 120 B and 123 B Built loop between residues 171 B and 174 B Built loop between residues 229 B and 233 B Built loop between residues 322 B and 328 B Built loop between residues 191 E and 194 E Built loop between residues 231 E and 234 E Built loop between residues 319 E and 322 E Built loop between residues 231 D and 234 D Built loop between residues 322 D and 328 D Built loop between residues 322 G and 325 G Built loop between residues 61 F and 64 F Built loop between residues 394 F and 398 F Built loop between residues 25 I and 28 I Built loop between residues 326 I and 329 I Built loop between residues 54 H and 57 H Built loop between residues 230 H and 234 H Built loop between residues 320 H and 323 H Built loop between residues 230 K and 234 K Built loop between residues 326 K and 329 K Built loop between residues 45 J and 49 J Built loop between residues 124 J and 127 J Built loop between residues 149 J and 153 J Built loop between residues 231 J and 234 J Built loop between residues 271 J and 274 J Built loop between residues 284 J and 287 J Built loop between residues 231 L and 234 L Built loop between residues 326 L and 329 L 28 chains (4894 residues) following loop building 19 chains (4748 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 40722 restraints for refining 47453 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2159 (Rfree = 0.000) for 47453 atoms. Found 1329 (1329 requested) and removed 586 (707 requested) atoms. Cycle 22: After refmac, R = 0.2006 (Rfree = 0.000) for 48196 atoms. Found 965 (1350 requested) and removed 197 (718 requested) atoms. Cycle 23: After refmac, R = 0.1918 (Rfree = 0.000) for 48964 atoms. Found 614 (1371 requested) and removed 235 (729 requested) atoms. Cycle 24: After refmac, R = 0.1801 (Rfree = 0.000) for 49343 atoms. Found 612 (1382 requested) and removed 291 (735 requested) atoms. Cycle 25: After refmac, R = 0.1771 (Rfree = 0.000) for 49664 atoms. Found 589 (1391 requested) and removed 377 (740 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.13 1.84 NCS extension: 12 residues added (4 deleted due to clashes), 49898 seeds are put forward Round 1: 4862 peptides, 73 chains. Longest chain 229 peptides. Score 0.912 Round 2: 4877 peptides, 63 chains. Longest chain 321 peptides. Score 0.916 Round 3: 4830 peptides, 96 chains. Longest chain 214 peptides. Score 0.903 Round 4: 4814 peptides, 101 chains. Longest chain 156 peptides. Score 0.901 Round 5: 4813 peptides, 109 chains. Longest chain 201 peptides. Score 0.898 Taking the results from Round 2 Chains 66, Residues 4814, Estimated correctness of the model 99.1 % 56 chains (4621 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 322 A and 327 A Built loop between residues 230 C and 234 C Built loop between residues 322 C and 325 C Built loop between residues 352 C and 357 C Built loop between residues 230 B and 233 B Built loop between residues 322 B and 327 B Built loop between residues 270 E and 273 E Built loop between residues 25 D and 28 D Built loop between residues 183 D and 186 D Built loop between residues 158 G and 161 G Built loop between residues 216 G and 219 G Built loop between residues 284 F and 287 F Built loop between residues 62 I and 65 I Built loop between residues 171 I and 174 I Built loop between residues 216 I and 219 I Built loop between residues 229 I and 233 I Built loop between residues 326 I and 329 I Built loop between residues 394 I and 397 I Built loop between residues 33 H and 37 H Built loop between residues 60 H and 65 H Built loop between residues 322 H and 325 H Built loop between residues 351 H and 354 H Built loop between residues 396 H and 399 H Built loop between residues 191 K and 194 K Built loop between residues 230 K and 235 K Built loop between residues 319 K and 322 K Built loop between residues 110 J and 113 J Built loop between residues 213 J and 218 J Built loop between residues 267 J and 270 J Built loop between residues 397 J and 400 J Built loop between residues 200 L and 203 L Built loop between residues 230 L and 233 L Built loop between residues 320 L and 323 L 30 chains (4891 residues) following loop building 23 chains (4702 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40395 restraints for refining 47414 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2121 (Rfree = 0.000) for 47414 atoms. Found 1300 (1300 requested) and removed 537 (706 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.1975 (Rfree = 0.000) for 48177 atoms. Found 957 (1321 requested) and removed 225 (718 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1886 (Rfree = 0.000) for 48909 atoms. Found 645 (1341 requested) and removed 272 (729 requested) atoms. Cycle 29: After refmac, R = 0.1824 (Rfree = 0.000) for 49282 atoms. Found 630 (1351 requested) and removed 290 (734 requested) atoms. Cycle 30: After refmac, R = 0.1779 (Rfree = 0.000) for 49622 atoms. Found 585 (1361 requested) and removed 321 (739 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.13 1.84 NCS extension: 11 residues added (15 deleted due to clashes), 49904 seeds are put forward Round 1: 4864 peptides, 67 chains. Longest chain 231 peptides. Score 0.914 Round 2: 4861 peptides, 71 chains. Longest chain 274 peptides. Score 0.913 Round 3: 4823 peptides, 102 chains. Longest chain 152 peptides. Score 0.901 Round 4: 4821 peptides, 97 chains. Longest chain 207 peptides. Score 0.902 Round 5: 4826 peptides, 102 chains. Longest chain 213 peptides. Score 0.901 Taking the results from Round 1 Chains 74, Residues 4797, Estimated correctness of the model 99.1 % 53 chains (4634 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 230 A and 234 A Built loop between residues 326 A and 329 A Built loop between residues 285 C and 288 C Built loop between residues 322 C and 325 C Built loop between residues 230 B and 233 B Built loop between residues 322 B and 328 B Built loop between residues 405 B and 408 B Built loop between residues 230 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 321 G and 328 G Built loop between residues 352 G and 355 G Built loop between residues 231 F and 234 F Built loop between residues 322 F and 328 F Built loop between residues 33 I and 38 I Built loop between residues 150 H and 153 H Built loop between residues 184 H and 187 H Built loop between residues 230 H and 233 H Built loop between residues 270 H and 274 H Built loop between residues 323 H and 333 H Built loop between residues 230 K and 234 K Built loop between residues 326 K and 329 K Built loop between residues 405 K and 408 K Built loop between residues 103 J and 106 J Built loop between residues 189 J and 195 J Built loop between residues 230 J and 233 J Built loop between residues 326 J and 329 J Built loop between residues 361 J and 364 J Built loop between residues 106 L and 109 L Built loop between residues 230 L and 234 L Built loop between residues 322 L and 327 L 36 chains (4879 residues) following loop building 21 chains (4726 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 40369 restraints for refining 47533 atoms. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2124 (Rfree = 0.000) for 47533 atoms. Found 1274 (1274 requested) and removed 524 (708 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.1979 (Rfree = 0.000) for 48283 atoms. Found 985 (1295 requested) and removed 185 (719 requested) atoms. Cycle 33: After refmac, R = 0.1822 (Rfree = 0.000) for 49083 atoms. Found 751 (1317 requested) and removed 315 (731 requested) atoms. Cycle 34: After refmac, R = 0.1745 (Rfree = 0.000) for 49519 atoms. Found 735 (1328 requested) and removed 355 (738 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1696 (Rfree = 0.000) for 49899 atoms. Found 716 (1338 requested) and removed 466 (743 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.13 1.84 NCS extension: 14 residues added (11 deleted due to clashes), 50186 seeds are put forward Round 1: 4873 peptides, 69 chains. Longest chain 230 peptides. Score 0.914 Round 2: 4883 peptides, 59 chains. Longest chain 230 peptides. Score 0.917 Round 3: 4841 peptides, 85 chains. Longest chain 229 peptides. Score 0.907 Round 4: 4833 peptides, 100 chains. Longest chain 181 peptides. Score 0.902 Round 5: 4826 peptides, 102 chains. Longest chain 208 peptides. Score 0.901 Taking the results from Round 2 Chains 63, Residues 4824, Estimated correctness of the model 99.1 % 53 chains (4548 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 230 A and 234 A Built loop between residues 258 A and 261 A Built loop between residues 325 A and 328 A Built loop between residues 25 C and 28 C Built loop between residues 230 C and 233 C Built loop between residues 396 C and 399 C Built loop between residues 24 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 216 B and 219 B Built loop between residues 266 B and 269 B Built loop between residues 319 B and 322 B Built loop between residues 33 E and 39 E Built loop between residues 110 E and 113 E Built loop between residues 230 E and 233 E Built loop between residues 322 E and 325 E Built loop between residues 163 D and 166 D Built loop between residues 322 D and 328 D Built loop between residues 351 D and 354 D Built loop between residues 326 F and 329 F Built loop between residues 30 I and 33 I Built loop between residues 63 I and 67 I Built loop between residues 90 I and 93 I Built loop between residues 231 I and 234 I Built loop between residues 319 I and 322 I Built loop between residues 47 H and 50 H Built loop between residues 123 H and 126 H Built loop between residues 209 H and 217 H Built loop between residues 231 K and 234 K Built loop between residues 105 J and 108 J Built loop between residues 230 J and 233 J Built loop between residues 322 J and 325 J Built loop between residues 333 J and 336 J Built loop between residues 216 L and 219 L Built loop between residues 229 L and 233 L Built loop between residues 326 L and 329 L Built loop between residues 396 L and 399 L 23 chains (4906 residues) following loop building 16 chains (4637 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40241 restraints for refining 47641 atoms. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2144 (Rfree = 0.000) for 47641 atoms. Found 1250 (1250 requested) and removed 655 (710 requested) atoms. Cycle 37: After refmac, R = 0.1979 (Rfree = 0.000) for 48236 atoms. Found 1093 (1236 requested) and removed 207 (718 requested) atoms. Cycle 38: After refmac, R = 0.1887 (Rfree = 0.000) for 49122 atoms. Found 668 (1259 requested) and removed 288 (732 requested) atoms. Cycle 39: After refmac, R = 0.1820 (Rfree = 0.000) for 49502 atoms. Found 631 (1268 requested) and removed 264 (737 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1773 (Rfree = 0.000) for 49869 atoms. Found 561 (1278 requested) and removed 366 (743 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.13 1.84 NCS extension: 12 residues added (2 deleted due to clashes), 50085 seeds are put forward Round 1: 4878 peptides, 62 chains. Longest chain 230 peptides. Score 0.916 Round 2: 4892 peptides, 51 chains. Longest chain 267 peptides. Score 0.920 Round 3: 4827 peptides, 96 chains. Longest chain 223 peptides. Score 0.903 Round 4: 4836 peptides, 90 chains. Longest chain 168 peptides. Score 0.905 Round 5: 4802 peptides, 114 chains. Longest chain 141 peptides. Score 0.896 Taking the results from Round 2 Chains 53, Residues 4841, Estimated correctness of the model 99.2 % 49 chains (4768 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 C and 62 C Built loop between residues 216 C and 219 C Built loop between residues 230 C and 233 C Built loop between residues 266 C and 269 C Built loop between residues 322 C and 328 C Built loop between residues 267 B and 270 B Built loop between residues 322 B and 325 B Built loop between residues 191 E and 195 E Built loop between residues 351 E and 354 E Built loop between residues 33 D and 38 D Built loop between residues 187 D and 196 D Built loop between residues 230 D and 233 D Built loop between residues 326 D and 329 D Built loop between residues 354 D and 357 D Built loop between residues 124 G and 127 G Built loop between residues 62 F and 65 F Built loop between residues 230 F and 233 F Built loop between residues 31 I and 34 I Built loop between residues 213 I and 216 I Built loop between residues 230 I and 233 I Built loop between residues 325 I and 328 I Built loop between residues 54 H and 57 H Built loop between residues 322 H and 325 H Built loop between residues 393 H and 396 H Built loop between residues 230 K and 233 K Built loop between residues 320 K and 323 K Built loop between residues 105 J and 108 J Built loop between residues 231 J and 235 J Built loop between residues 322 J and 325 J Built loop between residues 333 J and 336 J Built loop between residues 230 L and 234 L Built loop between residues 258 L and 261 L Built loop between residues 325 L and 328 L 18 chains (4919 residues) following loop building 16 chains (4848 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 381160 reflections ( 94.42 % complete ) and 41230 restraints for refining 47685 atoms. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2110 (Rfree = 0.000) for 47685 atoms. Found 1194 (1194 requested) and removed 491 (710 requested) atoms. Cycle 42: After refmac, R = 0.1972 (Rfree = 0.000) for 48388 atoms. Found 980 (1211 requested) and removed 190 (721 requested) atoms. Cycle 43: After refmac, R = 0.1890 (Rfree = 0.000) for 49177 atoms. Found 679 (1231 requested) and removed 263 (733 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1831 (Rfree = 0.000) for 49592 atoms. Found 595 (1242 requested) and removed 276 (739 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1789 (Rfree = 0.000) for 49911 atoms. Found 543 (1249 requested) and removed 313 (743 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.13 1.84 NCS extension: 9 residues added (3 deleted due to clashes), 50158 seeds are put forward Round 1: 4880 peptides, 69 chains. Longest chain 229 peptides. Score 0.914 Round 2: 4883 peptides, 58 chains. Longest chain 263 peptides. Score 0.918 Round 3: 4840 peptides, 103 chains. Longest chain 163 peptides. Score 0.901 Round 4: 4805 peptides, 102 chains. Longest chain 200 peptides. Score 0.900 Round 5: 4820 peptides, 96 chains. Longest chain 183 peptides. Score 0.903 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 62, Residues 4825, Estimated correctness of the model 99.1 % 54 chains (4787 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 124 A and 127 A Built loop between residues 216 A and 219 A Built loop between residues 270 A and 274 A Built loop between residues 348 A and 351 A Built loop between residues 25 C and 28 C Built loop between residues 153 C and 156 C Built loop between residues 230 C and 233 C Built loop between residues 266 C and 269 C Built loop between residues 322 C and 327 C Built loop between residues 250 B and 253 B Built loop between residues 322 B and 325 B Built loop between residues 33 E and 38 E Built loop between residues 113 E and 116 E Built loop between residues 230 E and 233 E Built loop between residues 322 E and 325 E Built loop between residues 347 E and 350 E Built loop between residues 231 D and 234 D Built loop between residues 266 D and 270 D Built loop between residues 283 D and 286 D Built loop between residues 322 D and 325 D Built loop between residues 216 G and 219 G Built loop between residues 231 G and 233 G Built loop between residues 322 G and 328 G Built loop between residues 393 G and 396 G Built loop between residues 230 F and 235 F Built loop between residues 322 F and 328 F Built loop between residues 90 I and 93 I Built loop between residues 117 I and 120 I Built loop between residues 182 I and 185 I Built loop between residues 321 I and 328 I Built loop between residues 36 H and 39 H Built loop between residues 62 H and 65 H Built loop between residues 326 H and 329 H Built loop between residues 163 K and 166 K Built loop between residues 230 K and 233 K Built loop between residues 322 K and 325 K Built loop between residues 351 K and 357 K Built loop between residues 101 J and 105 J Built loop between residues 230 J and 233 J Built loop between residues 231 L and 237 L Built loop between residues 355 L and 358 L 18 chains (4924 residues) following loop building 13 chains (4893 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 381160 reflections ( 94.42 % complete ) and 41467 restraints for refining 40468 atoms. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2532 (Rfree = 0.000) for 40468 atoms. Found 773 (989 requested) and removed 0 (989 requested) atoms. Cycle 47: After refmac, R = 0.2317 (Rfree = 0.000) for 40468 atoms. Found 356 (1008 requested) and removed 3 (614 requested) atoms. Cycle 48: After refmac, R = 0.2168 (Rfree = 0.000) for 40468 atoms. Found 222 (1016 requested) and removed 26 (619 requested) atoms. Cycle 49: After refmac, R = 0.2086 (Rfree = 0.000) for 40468 atoms. TimeTaking 903.68