null Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pnk-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pnk-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-2.1-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-2.1-parrot-hancs ############### 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 19:28:05 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/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pnk-2.1-parrot-hancs/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-hancs.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-hancs.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 381160 reflections ( 94.42 % complete ) and 0 restraints for refining 45307 atoms. Observations/parameters ratio is 2.10 ------------------------------------------------------ Starting model: R = 0.2904 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2408 (Rfree = 0.000) for 45307 atoms. Found 1350 (1350 requested) and removed 375 (675 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.20 1.90 NCS extension: 0 residues added, 46282 seeds are put forward Round 1: 4056 peptides, 407 chains. Longest chain 57 peptides. Score 0.685 Round 2: 4467 peptides, 241 chains. Longest chain 101 peptides. Score 0.823 Round 3: 4626 peptides, 166 chains. Longest chain 133 peptides. Score 0.866 Round 4: 4738 peptides, 122 chains. Longest chain 192 peptides. Score 0.889 Round 5: 4764 peptides, 105 chains. Longest chain 292 peptides. Score 0.897 Taking the results from Round 5 Chains 115, Residues 4659, Estimated correctness of the model 98.7 % 75 chains (4323 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 216 A and 219 A Built loop between residues 230 A and 233 A Built loop between residues 230 C and 234 C Built loop between residues 124 B and 127 B Built loop between residues 172 B and 175 B Built loop between residues 267 B and 270 B Built loop between residues 322 B and 328 B Built loop between residues 111 E and 118 E Built loop between residues 153 E and 160 E Built loop between residues 228 E and 233 E Built loop between residues 267 E and 271 E Built loop between residues 284 E and 286 E Built loop between residues 352 E and 355 E Built loop between residues 68 D and 71 D Built loop between residues 393 D and 398 D Built loop between residues 34 G and 37 G Built loop between residues 62 G and 65 G Built loop between residues 118 G and 123 G Built loop between residues 24 F and 27 F Built loop between residues 64 F and 67 F Built loop between residues 108 F and 112 F Built loop between residues 230 F and 233 F Built loop between residues 322 F and 325 F Built loop between residues 54 I and 57 I Built loop between residues 157 I and 160 I Built loop between residues 206 I and 209 I Built loop between residues 94 H and 98 H Built loop between residues 172 H and 175 H Built loop between residues 228 H and 233 H Built loop between residues 328 H and 331 H Built loop between residues 353 H and 357 H Built loop between residues 105 K and 108 K Built loop between residues 355 K and 358 K Built loop between residues 60 J and 63 J Built loop between residues 229 J and 237 J Built loop between residues 258 J and 261 J Built loop between residues 322 J and 325 J Built loop between residues 53 L and 56 L 74 chains (4760 residues) following loop building 37 chains (4427 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 38522 restraints for refining 45148 atoms. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2616 (Rfree = 0.000) for 45148 atoms. Found 1345 (1345 requested) and removed 738 (672 requested) atoms. Cycle 2: After refmac, R = 0.2398 (Rfree = 0.000) for 45755 atoms. Found 1189 (1336 requested) and removed 232 (681 requested) atoms. Cycle 3: After refmac, R = 0.2259 (Rfree = 0.000) for 46712 atoms. Found 865 (1364 requested) and removed 185 (696 requested) atoms. Cycle 4: After refmac, R = 0.2153 (Rfree = 0.000) for 47392 atoms. Found 791 (1384 requested) and removed 207 (706 requested) atoms. Cycle 5: After refmac, R = 0.2074 (Rfree = 0.000) for 47976 atoms. Found 609 (1401 requested) and removed 171 (715 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.14 1.84 NCS extension: 7 residues added (9 deleted due to clashes), 48439 seeds are put forward Round 1: 4804 peptides, 86 chains. Longest chain 228 peptides. Score 0.905 Round 2: 4818 peptides, 85 chains. Longest chain 213 peptides. Score 0.906 Round 3: 4795 peptides, 103 chains. Longest chain 163 peptides. Score 0.899 Round 4: 4803 peptides, 91 chains. Longest chain 166 peptides. Score 0.903 Round 5: 4774 peptides, 127 chains. Longest chain 127 peptides. Score 0.890 Taking the results from Round 2 Chains 100, Residues 4733, Estimated correctness of the model 98.9 % 64 chains (4348 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 227 A and 230 A Built loop between residues 322 A and 325 A Built loop between residues 387 A and 392 A Built loop between residues 41 B and 51 B Built loop between residues 229 B and 234 B Built loop between residues 334 B and 340 B Built loop between residues 31 E and 34 E Built loop between residues 215 E and 218 E Built loop between residues 326 E and 336 E Built loop between residues 111 D and 122 D Built loop between residues 167 D and 173 D Built loop between residues 322 D and 327 D Built loop between residues 13 G and 16 G Built loop between residues 120 G and 123 G Built loop between residues 205 G and 208 G Built loop between residues 321 G and 327 G Built loop between residues 63 I and 67 I Built loop between residues 233 I and 236 I Built loop between residues 319 I and 322 I Built loop between residues 60 H and 67 H Built loop between residues 154 H and 160 H Built loop between residues 214 H and 219 H Built loop between residues 260 H and 269 H Built loop between residues 216 K and 219 K Built loop between residues 229 K and 233 K Built loop between residues 322 K and 325 K Built loop between residues 394 K and 398 K Built loop between residues 80 J and 83 J Built loop between residues 118 J and 123 J Built loop between residues 162 J and 165 J Built loop between residues 322 J and 325 J Built loop between residues 38 L and 40 L Built loop between residues 134 L and 139 L Built loop between residues 215 L and 218 L Built loop between residues 229 L and 236 L Built loop between residues 355 L and 358 L 50 chains (4831 residues) following loop building 28 chains (4482 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 39096 restraints for refining 46706 atoms. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2417 (Rfree = 0.000) for 46706 atoms. Found 1364 (1364 requested) and removed 795 (696 requested) atoms. Cycle 7: After refmac, R = 0.2230 (Rfree = 0.000) for 47275 atoms. Found 1024 (1353 requested) and removed 289 (704 requested) atoms. Cycle 8: After refmac, R = 0.2119 (Rfree = 0.000) for 48010 atoms. Found 639 (1374 requested) and removed 221 (715 requested) atoms. Cycle 9: After refmac, R = 0.2039 (Rfree = 0.000) for 48428 atoms. Found 499 (1385 requested) and removed 192 (721 requested) atoms. Cycle 10: After refmac, R = 0.1974 (Rfree = 0.000) for 48735 atoms. Found 476 (1394 requested) and removed 196 (726 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.14 1.84 NCS extension: 6 residues added (14 deleted due to clashes), 49064 seeds are put forward Round 1: 4824 peptides, 92 chains. Longest chain 225 peptides. Score 0.904 Round 2: 4842 peptides, 69 chains. Longest chain 321 peptides. Score 0.912 Round 3: 4781 peptides, 109 chains. Longest chain 128 peptides. Score 0.896 Round 4: 4796 peptides, 103 chains. Longest chain 308 peptides. Score 0.899 Round 5: 4800 peptides, 109 chains. Longest chain 151 peptides. Score 0.897 Taking the results from Round 2 Chains 79, Residues 4773, Estimated correctness of the model 99.0 % 58 chains (4556 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 59 A and 62 A Built loop between residues 154 A and 160 A Built loop between residues 227 A and 230 A Built loop between residues 388 A and 391 A Built loop between residues 66 C and 69 C Built loop between residues 161 C and 164 C Built loop between residues 102 B and 107 B Built loop between residues 150 B and 153 B Built loop between residues 182 B and 189 B Built loop between residues 206 B and 209 B Built loop between residues 322 B and 328 B Built loop between residues 230 E and 233 E Built loop between residues 59 D and 62 D Built loop between residues 48 G and 51 G Built loop between residues 113 G and 116 G Built loop between residues 136 G and 139 G Built loop between residues 152 G and 155 G Built loop between residues 322 G and 328 G Built loop between residues 46 F and 49 F Built loop between residues 96 F and 99 F Built loop between residues 352 F and 357 F Built loop between residues 120 I and 123 I Built loop between residues 230 I and 233 I Built loop between residues 326 I and 329 I Built loop between residues 394 I and 398 I Built loop between residues 54 H and 57 H Built loop between residues 110 H and 114 H Built loop between residues 105 J and 109 J Built loop between residues 318 J and 325 J 47 chains (4847 residues) following loop building 29 chains (4638 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 39970 restraints for refining 47135 atoms. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2270 (Rfree = 0.000) for 47135 atoms. Found 1349 (1349 requested) and removed 649 (702 requested) atoms. Cycle 12: After refmac, R = 0.2121 (Rfree = 0.000) for 47835 atoms. Found 861 (1368 requested) and removed 219 (712 requested) atoms. Cycle 13: After refmac, R = 0.2021 (Rfree = 0.000) for 48477 atoms. Found 759 (1387 requested) and removed 183 (722 requested) atoms. Cycle 14: After refmac, R = 0.1906 (Rfree = 0.000) for 49053 atoms. Found 589 (1404 requested) and removed 270 (731 requested) atoms. Cycle 15: After refmac, R = 0.1831 (Rfree = 0.000) for 49372 atoms. Found 572 (1412 requested) and removed 309 (735 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.14 1.84 NCS extension: 2 residues added (131 deleted due to clashes), 49647 seeds are put forward Round 1: 4832 peptides, 85 chains. Longest chain 229 peptides. Score 0.907 Round 2: 4844 peptides, 74 chains. Longest chain 257 peptides. Score 0.911 Round 3: 4801 peptides, 103 chains. Longest chain 227 peptides. Score 0.899 Round 4: 4805 peptides, 107 chains. Longest chain 194 peptides. Score 0.898 Round 5: 4813 peptides, 104 chains. Longest chain 223 peptides. Score 0.900 Taking the results from Round 2 Chains 87, Residues 4770, Estimated correctness of the model 99.0 % 72 chains (4671 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 60 A and 63 A Built loop between residues 90 A and 93 A Built loop between residues 110 A and 116 A Built loop between residues 227 A and 230 A Built loop between residues 322 A and 325 A Built loop between residues 40 C and 47 C Built loop between residues 61 C and 67 C Built loop between residues 157 C and 160 C Built loop between residues 171 C and 174 C Built loop between residues 322 C and 325 C Built loop between residues 351 C and 357 C Built loop between residues 104 B and 112 B Built loop between residues 198 B and 202 B Built loop between residues 362 B and 365 B Built loop between residues 63 E and 66 E Built loop between residues 95 E and 99 E Built loop between residues 323 E and 327 E Built loop between residues 194 D and 197 D Built loop between residues 355 D and 358 D Built loop between residues 26 G and 29 G Built loop between residues 63 G and 67 G Built loop between residues 120 G and 123 G Built loop between residues 206 G and 215 G Built loop between residues 229 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 13 F and 16 F Built loop between residues 54 F and 57 F Built loop between residues 230 F and 234 F Built loop between residues 322 F and 328 F Built loop between residues 393 F and 396 F Built loop between residues 65 I and 68 I Built loop between residues 162 I and 165 I Built loop between residues 228 I and 234 I Built loop between residues 270 I and 273 I Built loop between residues 320 I and 323 I Built loop between residues 198 H and 203 H Built loop between residues 322 H and 328 H Built loop between residues 406 H and 408 H Built loop between residues 61 K and 66 K Built loop between residues 121 K and 124 K Built loop between residues 156 K and 160 K Built loop between residues 216 K and 219 K Built loop between residues 230 K and 233 K Built loop between residues 394 K and 397 K Built loop between residues 80 J and 83 J Built loop between residues 110 J and 113 J Built loop between residues 231 J and 234 J Built loop between residues 322 J and 325 J Built loop between residues 60 L and 63 L Built loop between residues 105 L and 108 L Built loop between residues 152 L and 155 L Built loop between residues 204 L and 207 L Built loop between residues 267 L and 270 L Built loop between residues 320 L and 323 L 21 chains (4896 residues) following loop building 17 chains (4824 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 41093 restraints for refining 47256 atoms. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2218 (Rfree = 0.000) for 47256 atoms. Found 1324 (1324 requested) and removed 638 (704 requested) atoms. Cycle 17: After refmac, R = 0.2072 (Rfree = 0.000) for 47942 atoms. Found 1040 (1343 requested) and removed 229 (714 requested) atoms. Cycle 18: After refmac, R = 0.1988 (Rfree = 0.000) for 48753 atoms. Found 705 (1366 requested) and removed 267 (726 requested) atoms. Cycle 19: After refmac, R = 0.1873 (Rfree = 0.000) for 49191 atoms. Found 661 (1378 requested) and removed 301 (733 requested) atoms. Cycle 20: After refmac, R = 0.1851 (Rfree = 0.000) for 49551 atoms. Found 616 (1388 requested) and removed 324 (738 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.13 1.84 NCS extension: 12 residues added (14 deleted due to clashes), 49872 seeds are put forward Round 1: 4847 peptides, 77 chains. Longest chain 230 peptides. Score 0.910 Round 2: 4844 peptides, 67 chains. Longest chain 231 peptides. Score 0.913 Round 3: 4821 peptides, 104 chains. Longest chain 231 peptides. Score 0.900 Round 4: 4804 peptides, 95 chains. Longest chain 230 peptides. Score 0.902 Round 5: 4783 peptides, 127 chains. Longest chain 189 peptides. Score 0.890 Taking the results from Round 2 Chains 76, Residues 4777, Estimated correctness of the model 99.1 % 63 chains (4666 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 197 A and 203 A Built loop between residues 322 A and 328 A Built loop between residues 354 A and 357 A Built loop between residues 216 C and 219 C Built loop between residues 230 C and 233 C Built loop between residues 322 C and 328 C Built loop between residues 60 B and 65 B Built loop between residues 207 B and 210 B Built loop between residues 230 B and 233 B Built loop between residues 323 B and 328 B Built loop between residues 187 E and 191 E Built loop between residues 216 E and 219 E Built loop between residues 393 E and 398 E Built loop between residues 326 D and 329 D Built loop between residues 393 D and 396 D Built loop between residues 231 G and 234 G Built loop between residues 320 G and 323 G Built loop between residues 285 F and 288 F Built loop between residues 326 F and 329 F Built loop between residues 342 F and 345 F Built loop between residues 97 I and 100 I Built loop between residues 228 I and 234 I Built loop between residues 267 I and 273 I Built loop between residues 355 I and 358 I Built loop between residues 26 H and 29 H Built loop between residues 48 H and 51 H Built loop between residues 104 H and 114 H Built loop between residues 267 H and 276 H Built loop between residues 284 H and 286 H Built loop between residues 216 K and 219 K Built loop between residues 322 K and 325 K Built loop between residues 356 K and 359 K Built loop between residues 36 J and 38 J Built loop between residues 122 J and 127 J Built loop between residues 163 J and 166 J Built loop between residues 230 J and 233 J Built loop between residues 63 L and 66 L Built loop between residues 199 L and 202 L Built loop between residues 230 L and 233 L Built loop between residues 322 L and 325 L 30 chains (4878 residues) following loop building 23 chains (4781 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40796 restraints for refining 47370 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2185 (Rfree = 0.000) for 47370 atoms. Found 1299 (1299 requested) and removed 607 (706 requested) atoms. Cycle 22: After refmac, R = 0.1952 (Rfree = 0.000) for 48062 atoms. Found 1064 (1317 requested) and removed 270 (716 requested) atoms. Cycle 23: After refmac, R = 0.1844 (Rfree = 0.000) for 48856 atoms. Found 782 (1340 requested) and removed 314 (728 requested) atoms. Cycle 24: After refmac, R = 0.1810 (Rfree = 0.000) for 49324 atoms. Found 721 (1352 requested) and removed 348 (735 requested) atoms. Cycle 25: After refmac, R = 0.1780 (Rfree = 0.000) for 49697 atoms. Found 666 (1363 requested) and removed 395 (740 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.13 1.84 NCS extension: 14 residues added (6 deleted due to clashes), 49997 seeds are put forward Round 1: 4861 peptides, 70 chains. Longest chain 230 peptides. Score 0.913 Round 2: 4872 peptides, 63 chains. Longest chain 230 peptides. Score 0.916 Round 3: 4823 peptides, 97 chains. Longest chain 174 peptides. Score 0.903 Round 4: 4794 peptides, 105 chains. Longest chain 199 peptides. Score 0.898 Round 5: 4808 peptides, 105 chains. Longest chain 203 peptides. Score 0.899 Taking the results from Round 2 Chains 74, Residues 4809, Estimated correctness of the model 99.1 % 62 chains (4766 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 200 A and 203 A Built loop between residues 229 A and 233 A Built loop between residues 352 A and 355 A Built loop between residues 124 C and 127 C Built loop between residues 200 C and 203 C Built loop between residues 231 C and 237 C Built loop between residues 322 C and 325 C Built loop between residues 217 B and 220 B Built loop between residues 230 B and 233 B Built loop between residues 285 B and 288 B Built loop between residues 325 B and 331 B Built loop between residues 385 B and 391 B Built loop between residues 216 E and 219 E Built loop between residues 230 E and 233 E Built loop between residues 266 E and 269 E Built loop between residues 322 E and 325 E Built loop between residues 231 D and 234 D Built loop between residues 356 D and 359 D Built loop between residues 62 G and 65 G Built loop between residues 152 G and 160 G Built loop between residues 178 G and 181 G Built loop between residues 216 G and 219 G Built loop between residues 230 G and 233 G Built loop between residues 268 G and 275 G Built loop between residues 284 G and 287 G Built loop between residues 216 F and 219 F Built loop between residues 348 F and 351 F Built loop between residues 62 I and 65 I Built loop between residues 228 I and 234 I Built loop between residues 322 I and 325 I Built loop between residues 393 I and 396 I Built loop between residues 62 H and 65 H Built loop between residues 231 H and 234 H Built loop between residues 270 H and 273 H Built loop between residues 356 H and 358 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 110 J and 113 J Built loop between residues 206 J and 209 J Built loop between residues 322 J and 325 J Built loop between residues 393 J and 396 J Built loop between residues 322 L and 328 L Built loop between residues 354 L and 357 L 24 chains (4906 residues) following loop building 18 chains (4878 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 41334 restraints for refining 47403 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2148 (Rfree = 0.000) for 47403 atoms. Found 1272 (1272 requested) and removed 597 (706 requested) atoms. Cycle 27: After refmac, R = 0.1916 (Rfree = 0.000) for 48078 atoms. Found 1079 (1290 requested) and removed 220 (716 requested) atoms. Cycle 28: After refmac, R = 0.1858 (Rfree = 0.000) for 48937 atoms. Found 753 (1312 requested) and removed 319 (729 requested) atoms. Cycle 29: After refmac, R = 0.1773 (Rfree = 0.000) for 49371 atoms. Found 766 (1324 requested) and removed 356 (735 requested) atoms. Cycle 30: After refmac, R = 0.1720 (Rfree = 0.000) for 49781 atoms. Found 708 (1336 requested) and removed 494 (742 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.13 1.84 NCS extension: 12 residues added (14 deleted due to clashes), 50021 seeds are put forward Round 1: 4857 peptides, 66 chains. Longest chain 228 peptides. Score 0.914 Round 2: 4851 peptides, 68 chains. Longest chain 222 peptides. Score 0.913 Round 3: 4822 peptides, 94 chains. Longest chain 204 peptides. Score 0.903 Round 4: 4805 peptides, 105 chains. Longest chain 151 peptides. Score 0.899 Round 5: 4791 peptides, 100 chains. Longest chain 178 peptides. Score 0.900 Taking the results from Round 1 Chains 71, Residues 4791, Estimated correctness of the model 99.1 % 51 chains (4596 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 215 A and 218 A Built loop between residues 34 C and 39 C Built loop between residues 230 C and 233 C Built loop between residues 285 C and 288 C Built loop between residues 322 C and 325 C Built loop between residues 216 B and 219 B Built loop between residues 230 B and 233 B Built loop between residues 326 B and 330 B Built loop between residues 405 B and 408 B Built loop between residues 101 E and 104 E Built loop between residues 231 E and 234 E Built loop between residues 325 E and 328 E Built loop between residues 230 D and 234 D Built loop between residues 322 D and 325 D Built loop between residues 231 G and 235 G Built loop between residues 47 F and 50 F Built loop between residues 35 I and 38 I Built loop between residues 230 I and 233 I Built loop between residues 35 H and 38 H Built loop between residues 106 H and 109 H Built loop between residues 172 H and 174 H Built loop between residues 230 H and 233 H Built loop between residues 355 H and 358 H Built loop between residues 404 H and 407 H Built loop between residues 206 K and 209 K 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 109 J Built loop between residues 228 J and 234 J Built loop between residues 322 J and 325 J Built loop between residues 356 J and 359 J Built loop between residues 230 L and 234 L Built loop between residues 322 L and 325 L 35 chains (4863 residues) following loop building 18 chains (4674 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40069 restraints for refining 47310 atoms. Observations/parameters ratio is 2.01 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2124 (Rfree = 0.000) for 47310 atoms. Found 1241 (1241 requested) and removed 581 (705 requested) atoms. Cycle 32: After refmac, R = 0.1982 (Rfree = 0.000) for 47970 atoms. Found 1084 (1258 requested) and removed 187 (715 requested) atoms. Cycle 33: After refmac, R = 0.1896 (Rfree = 0.000) for 48867 atoms. Found 734 (1281 requested) and removed 274 (728 requested) atoms. Cycle 34: After refmac, R = 0.1839 (Rfree = 0.000) for 49327 atoms. Found 686 (1294 requested) and removed 272 (735 requested) atoms. Cycle 35: After refmac, R = 0.1793 (Rfree = 0.000) for 49741 atoms. Found 603 (1304 requested) and removed 338 (741 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.13 1.84 NCS extension: 6 residues added (22 deleted due to clashes), 50027 seeds are put forward Round 1: 4858 peptides, 65 chains. Longest chain 230 peptides. Score 0.914 Round 2: 4868 peptides, 63 chains. Longest chain 231 peptides. Score 0.916 Round 3: 4828 peptides, 100 chains. Longest chain 208 peptides. Score 0.902 Round 4: 4809 peptides, 99 chains. Longest chain 182 peptides. Score 0.901 Round 5: 4804 peptides, 110 chains. Longest chain 138 peptides. Score 0.897 Taking the results from Round 2 Chains 69, Residues 4805, Estimated correctness of the model 99.1 % 56 chains (4664 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 225 A and 233 A Built loop between residues 320 A and 323 A Built loop between residues 59 C and 62 C Built loop between residues 230 C and 233 C Built loop between residues 124 B and 127 B Built loop between residues 185 B and 188 B Built loop between residues 230 B and 233 B Built loop between residues 284 B and 287 B Built loop between residues 322 E and 325 E Built loop between residues 60 D and 65 D Built loop between residues 230 D and 233 D Built loop between residues 396 D and 399 D Built loop between residues 34 G and 37 G Built loop between residues 103 G and 112 G Built loop between residues 123 G and 126 G Built loop between residues 322 G and 325 G Built loop between residues 62 F and 65 F Built loop between residues 214 F and 218 F Built loop between residues 230 F and 233 F Built loop between residues 63 I and 66 I Built loop between residues 110 I and 113 I Built loop between residues 123 I and 126 I Built loop between residues 229 I and 234 I Built loop between residues 266 I and 269 I Built loop between residues 322 I and 325 I Built loop between residues 54 H and 57 H Built loop between residues 112 H and 115 H Built loop between residues 228 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 322 K and 325 K Built loop between residues 352 K and 357 K Built loop between residues 101 J and 105 J Built loop between residues 271 J and 274 J Built loop between residues 322 J and 325 J Built loop between residues 356 J and 359 J Built loop between residues 231 L and 234 L 26 chains (4889 residues) following loop building 19 chains (4761 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 40698 restraints for refining 47728 atoms. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2143 (Rfree = 0.000) for 47728 atoms. Found 1223 (1223 requested) and removed 647 (711 requested) atoms. Cycle 37: After refmac, R = 0.1995 (Rfree = 0.000) for 48304 atoms. Found 1013 (1209 requested) and removed 182 (719 requested) atoms. Cycle 38: After refmac, R = 0.1907 (Rfree = 0.000) for 49135 atoms. Found 718 (1230 requested) and removed 280 (732 requested) atoms. Cycle 39: After refmac, R = 0.1849 (Rfree = 0.000) for 49573 atoms. Found 634 (1241 requested) and removed 297 (738 requested) atoms. Cycle 40: After refmac, R = 0.1806 (Rfree = 0.000) for 49910 atoms. Found 595 (1249 requested) and removed 332 (743 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.13 1.84 NCS extension: 13 residues added (6 deleted due to clashes), 50198 seeds are put forward Round 1: 4847 peptides, 70 chains. Longest chain 228 peptides. Score 0.912 Round 2: 4838 peptides, 72 chains. Longest chain 281 peptides. Score 0.911 Round 3: 4808 peptides, 89 chains. Longest chain 199 peptides. Score 0.904 Round 4: 4806 peptides, 98 chains. Longest chain 215 peptides. Score 0.901 Round 5: 4790 peptides, 98 chains. Longest chain 267 peptides. Score 0.900 Taking the results from Round 1 Chains 73, Residues 4777, Estimated correctness of the model 99.0 % 55 chains (4306 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 230 A and 237 A Built loop between residues 231 C and 236 C Built loop between residues 48 B and 51 B Built loop between residues 62 B and 65 B Built loop between residues 178 B and 181 B Built loop between residues 230 B and 233 B Built loop between residues 322 E and 325 E Built loop between residues 185 D and 188 D Built loop between residues 230 D and 233 D Built loop between residues 34 G and 37 G Built loop between residues 229 G and 233 G Built loop between residues 285 G and 288 G Built loop between residues 24 F and 27 F Built loop between residues 54 I and 59 I Built loop between residues 230 I and 233 I Built loop between residues 322 I and 325 I Built loop between residues 62 H and 65 H Built loop between residues 230 H and 233 H Built loop between residues 322 H and 328 H Built loop between residues 102 K and 105 K Built loop between residues 230 K and 233 K Built loop between residues 322 K and 325 K Built loop between residues 101 J and 104 J Built loop between residues 230 J and 233 J Built loop between residues 230 L and 233 L Built loop between residues 322 L and 325 L Built loop between residues 405 L and 408 L 45 chains (4839 residues) following loop building 28 chains (4372 residues) in sequence following loop building ------------------------------------------------------ 381160 reflections ( 94.42 % complete ) and 38701 restraints for refining 48126 atoms. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2169 (Rfree = 0.000) for 48126 atoms. Found 1176 (1176 requested) and removed 677 (717 requested) atoms. Cycle 42: After refmac, R = 0.2004 (Rfree = 0.000) for 48625 atoms. Found 920 (1159 requested) and removed 175 (724 requested) atoms. Cycle 43: After refmac, R = 0.1905 (Rfree = 0.000) for 49370 atoms. Found 598 (1177 requested) and removed 214 (735 requested) atoms. Cycle 44: After refmac, R = 0.1845 (Rfree = 0.000) for 49754 atoms. Found 511 (1186 requested) and removed 227 (741 requested) atoms. Cycle 45: After refmac, R = 0.1795 (Rfree = 0.000) for 50038 atoms. Found 478 (1193 requested) and removed 267 (745 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.13 1.84 NCS extension: 7 residues added (19 deleted due to clashes), 50267 seeds are put forward Round 1: 4852 peptides, 68 chains. Longest chain 229 peptides. Score 0.913 Round 2: 4859 peptides, 69 chains. Longest chain 231 peptides. Score 0.913 Round 3: 4816 peptides, 101 chains. Longest chain 195 peptides. Score 0.901 Round 4: 4809 peptides, 103 chains. Longest chain 230 peptides. Score 0.900 Round 5: 4781 peptides, 112 chains. Longest chain 191 peptides. Score 0.895 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 77, Residues 4790, Estimated correctness of the model 99.1 % 63 chains (4704 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 106 A and 109 A Built loop between residues 136 A and 139 A Built loop between residues 161 A and 164 A Built loop between residues 227 A and 235 A Built loop between residues 326 A and 337 A Built loop between residues 351 A and 354 A Built loop between residues 97 C and 103 C Built loop between residues 145 C and 148 C Built loop between residues 230 C and 233 C Built loop between residues 322 C and 325 C Built loop between residues 124 B and 127 B Built loop between residues 185 B and 188 B Built loop between residues 216 B and 219 B Built loop between residues 230 B and 233 B Built loop between residues 393 B and 396 B Built loop between residues 155 E and 159 E Built loop between residues 229 E and 233 E Built loop between residues 322 E and 328 E Built loop between residues 405 E and 408 E Built loop between residues 113 D and 116 D Built loop between residues 185 D and 197 D Built loop between residues 396 D and 399 D Built loop between residues 35 G and 38 G Built loop between residues 109 G and 112 G Built loop between residues 267 G and 270 G Built loop between residues 63 F and 66 F Built loop between residues 103 F and 106 F Built loop between residues 186 F and 191 F Built loop between residues 214 F and 218 F Built loop between residues 266 F and 269 F Built loop between residues 372 F and 376 F Built loop between residues 55 I and 65 I Built loop between residues 216 I and 219 I Built loop between residues 230 I and 233 I Built loop between residues 322 I and 325 I Built loop between residues 396 I and 399 I Built loop between residues 60 H and 63 H Built loop between residues 109 H and 112 H Built loop between residues 228 H and 237 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 234 K Built loop between residues 322 K and 325 K Built loop between residues 352 K and 357 K Built loop between residues 110 J and 113 J Built loop between residues 230 J and 233 J Built loop between residues 213 L and 216 L Built loop between residues 322 L and 325 L 20 chains (4912 residues) following loop building 15 chains (4850 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 381160 reflections ( 94.42 % complete ) and 41178 restraints for refining 40194 atoms. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2617 (Rfree = 0.000) for 40194 atoms. Found 754 (934 requested) and removed 0 (934 requested) atoms. Cycle 47: After refmac, R = 0.2388 (Rfree = 0.000) for 40194 atoms. Found 369 (952 requested) and removed 7 (610 requested) atoms. Cycle 48: After refmac, R = 0.2301 (Rfree = 0.000) for 40194 atoms. Found 182 (960 requested) and removed 22 (615 requested) atoms. Cycle 49: After refmac, R = 0.2238 (Rfree = 0.000) for 40194 atoms. Found 139 (964 requested) and removed 46 (618 requested) atoms. Writing output files ... Normal termination of warpNtrace Wed 26 Dec 09:39:08 GMT 2018 Job finished. TimeTaking 851.22 Used memory is bytes: 36650400