Mon 24 Dec 00:57:01 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 2pbl-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2pbl-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-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/2pbl-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:57:05 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/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-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 1033 and 0 Target number of residues in the AU: 1033 Target solvent content: 0.4463 Checking the provided sequence file Detected sequence length: 262 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1048 Adjusted target solvent content: 0.44 Input MTZ file: 2pbl-1.8-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: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 8384 target number of atoms Had to go as low as 0.40 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. Conditional restraints will be used 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: 87.858 1.790 Wilson plot Bfac: 14.00 93715 reflections ( 99.87 % complete ) and 0 restraints for refining 9283 atoms. Observations/parameters ratio is 2.52 ------------------------------------------------------ Starting model: R = 0.3659 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3259 (Rfree = 0.000) for 9283 atoms. Found 436 (436 requested) and removed 234 (218 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.73 1.87 NCS extension: 0 residues added, 9485 seeds are put forward Round 1: 893 peptides, 57 chains. Longest chain 76 peptides. Score 0.883 Round 2: 979 peptides, 31 chains. Longest chain 101 peptides. Score 0.945 Round 3: 989 peptides, 28 chains. Longest chain 158 peptides. Score 0.950 Round 4: 998 peptides, 25 chains. Longest chain 158 peptides. Score 0.955 Round 5: 1002 peptides, 25 chains. Longest chain 151 peptides. Score 0.955 Taking the results from Round 5 Chains 30, Residues 977, Estimated correctness of the model 99.8 % 20 chains (927 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 38 A Built loop between residues 103 A and 106 A Built loop between residues 187 A and 190 A Built loop between residues 172 C and 175 C Built loop between residues 34 B and 38 B Built loop between residues 71 B and 74 B Built loop between residues 103 B and 106 B Built loop between residues 32 D and 37 D Built loop between residues 103 D and 106 D Built loop between residues 155 D and 158 D Built loop between residues 204 D and 207 D 19 chains (1005 residues) following loop building 9 chains (955 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9520 restraints for refining 8929 atoms. 1714 conditional restraints added. Observations/parameters ratio is 2.62 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3098 (Rfree = 0.000) for 8929 atoms. Found 372 (419 requested) and removed 240 (209 requested) atoms. Cycle 2: After refmac, R = 0.2876 (Rfree = 0.000) for 9049 atoms. Found 296 (416 requested) and removed 95 (212 requested) atoms. Cycle 3: After refmac, R = 0.2785 (Rfree = 0.000) for 9221 atoms. Found 303 (425 requested) and removed 68 (217 requested) atoms. Cycle 4: After refmac, R = 0.2698 (Rfree = 0.000) for 9438 atoms. Found 261 (435 requested) and removed 87 (222 requested) atoms. Cycle 5: After refmac, R = 0.2602 (Rfree = 0.000) for 9589 atoms. Found 307 (442 requested) and removed 62 (225 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.74 1.89 NCS extension: 9 residues added (64 deleted due to clashes), 9848 seeds are put forward Round 1: 1016 peptides, 19 chains. Longest chain 157 peptides. Score 0.964 Round 2: 1021 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 3: 1021 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 4: 1021 peptides, 19 chains. Longest chain 151 peptides. Score 0.964 Round 5: 1022 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Taking the results from Round 5 Chains 18, Residues 1006, Estimated correctness of the model 99.9 % 15 chains (1001 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 13 A and 17 A Built loop between residues 34 A and 38 A Built loop between residues 71 A and 74 A Built loop between residues 103 A and 106 A Built loop between residues 187 A and 190 A Built loop between residues 103 C and 106 C Built loop between residues 14 B and 18 B Built loop between residues 34 B and 38 B Built loop between residues 103 B and 106 B Built loop between residues 103 D and 106 D Built loop between residues 208 D and 211 D 6 chains (1031 residues) following loop building 4 chains (1027 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9170 restraints for refining 9445 atoms. 984 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2774 (Rfree = 0.000) for 9445 atoms. Found 395 (434 requested) and removed 149 (221 requested) atoms. Cycle 7: After refmac, R = 0.2574 (Rfree = 0.000) for 9673 atoms. Found 336 (446 requested) and removed 104 (227 requested) atoms. Cycle 8: After refmac, R = 0.2483 (Rfree = 0.000) for 9868 atoms. Found 320 (456 requested) and removed 101 (232 requested) atoms. Cycle 9: After refmac, R = 0.2413 (Rfree = 0.000) for 10066 atoms. Found 281 (465 requested) and removed 106 (237 requested) atoms. Cycle 10: After refmac, R = 0.2382 (Rfree = 0.000) for 10217 atoms. Found 251 (471 requested) and removed 127 (240 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.74 1.89 NCS extension: 0 residues added, 10343 seeds are put forward Round 1: 1015 peptides, 20 chains. Longest chain 104 peptides. Score 0.962 Round 2: 1023 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 3: 1019 peptides, 18 chains. Longest chain 157 peptides. Score 0.965 Round 4: 1025 peptides, 16 chains. Longest chain 157 peptides. Score 0.968 Round 5: 1023 peptides, 19 chains. Longest chain 151 peptides. Score 0.964 Taking the results from Round 2 Chains 19, Residues 1008, Estimated correctness of the model 99.9 % 15 chains (999 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 38 A Built loop between residues 208 A and 211 A Built loop between residues 72 C and 75 C Built loop between residues 101 C and 106 C Built loop between residues 14 B and 20 B Built loop between residues 34 B and 37 B Built loop between residues 100 B and 106 B Built loop between residues 208 B and 211 B 11 chains (1032 residues) following loop building 7 chains (1024 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9789 restraints for refining 9847 atoms. 1629 conditional restraints added. Observations/parameters ratio is 2.38 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2635 (Rfree = 0.000) for 9847 atoms. Found 377 (444 requested) and removed 172 (231 requested) atoms. Cycle 12: After refmac, R = 0.2456 (Rfree = 0.000) for 10029 atoms. Found 290 (453 requested) and removed 115 (236 requested) atoms. Cycle 13: After refmac, R = 0.2378 (Rfree = 0.000) for 10170 atoms. Found 277 (460 requested) and removed 101 (239 requested) atoms. Cycle 14: After refmac, R = 0.2333 (Rfree = 0.000) for 10321 atoms. Found 274 (467 requested) and removed 132 (243 requested) atoms. Cycle 15: After refmac, R = 0.2310 (Rfree = 0.000) for 10434 atoms. Found 265 (471 requested) and removed 129 (245 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.73 1.87 NCS extension: 4 residues added (9 deleted due to clashes), 10579 seeds are put forward Round 1: 1022 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 2: 1027 peptides, 12 chains. Longest chain 157 peptides. Score 0.972 Round 3: 1028 peptides, 13 chains. Longest chain 157 peptides. Score 0.971 Round 4: 1027 peptides, 12 chains. Longest chain 190 peptides. Score 0.972 Round 5: 1023 peptides, 18 chains. Longest chain 123 peptides. Score 0.965 Taking the results from Round 4 Chains 12, Residues 1015, Estimated correctness of the model 99.9 % 11 chains (1011 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 17 A and 20 A Built loop between residues 208 A and 211 A Built loop between residues 71 C and 74 C Built loop between residues 103 C and 106 C Built loop between residues 69 B and 76 B Built loop between residues 103 B and 106 B Built loop between residues 103 D and 106 D 5 chains (1033 residues) following loop building 4 chains (1029 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9717 restraints for refining 9922 atoms. 1511 conditional restraints added. Observations/parameters ratio is 2.36 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2589 (Rfree = 0.000) for 9922 atoms. Found 402 (447 requested) and removed 151 (233 requested) atoms. Cycle 17: After refmac, R = 0.2405 (Rfree = 0.000) for 10155 atoms. Found 294 (459 requested) and removed 109 (239 requested) atoms. Cycle 18: After refmac, R = 0.2348 (Rfree = 0.000) for 10314 atoms. Found 252 (466 requested) and removed 113 (242 requested) atoms. Cycle 19: After refmac, R = 0.2306 (Rfree = 0.000) for 10424 atoms. Found 260 (471 requested) and removed 109 (245 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.2266 (Rfree = 0.000) for 10548 atoms. Found 241 (476 requested) and removed 140 (248 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.73 1.87 NCS extension: 0 residues added (25 deleted due to clashes), 10650 seeds are put forward Round 1: 1021 peptides, 14 chains. Longest chain 157 peptides. Score 0.969 Round 2: 1020 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Round 3: 1021 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 4: 1027 peptides, 15 chains. Longest chain 156 peptides. Score 0.969 Round 5: 1022 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Taking the results from Round 4 Chains 20, Residues 1012, Estimated correctness of the model 99.9 % 13 chains (987 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 75 A Built loop between residues 98 A and 106 A Built loop between residues 136 C and 139 C Built loop between residues 14 B and 20 B Built loop between residues 33 B and 36 B Built loop between residues 99 B and 107 B Built loop between residues 177 B and 180 B 11 chains (1033 residues) following loop building 6 chains (1015 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 93715 reflections ( 99.87 % complete ) and 10049 restraints for refining 10052 atoms. 1898 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2570 (Rfree = 0.000) for 10052 atoms. Found 421 (444 requested) and removed 189 (236 requested) atoms. Cycle 22: After refmac, R = 0.2396 (Rfree = 0.000) for 10265 atoms. Found 324 (454 requested) and removed 102 (241 requested) atoms. Cycle 23: After refmac, R = 0.2336 (Rfree = 0.000) for 10447 atoms. Found 273 (462 requested) and removed 140 (246 requested) atoms. Cycle 24: After refmac, R = 0.2283 (Rfree = 0.000) for 10565 atoms. Found 263 (457 requested) and removed 138 (248 requested) atoms. Cycle 25: After refmac, R = 0.2254 (Rfree = 0.000) for 10669 atoms. Found 251 (452 requested) and removed 172 (251 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.73 1.87 NCS extension: 134 residues added (95 deleted due to clashes), 10886 seeds are put forward Round 1: 1014 peptides, 18 chains. Longest chain 157 peptides. Score 0.965 Round 2: 1015 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 3: 1017 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 4: 1020 peptides, 18 chains. Longest chain 124 peptides. Score 0.965 Round 5: 1014 peptides, 18 chains. Longest chain 156 peptides. Score 0.965 Taking the results from Round 3 Chains 19, Residues 1000, Estimated correctness of the model 99.9 % 16 chains (994 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 106 A Built loop between residues 158 A and 161 A Built loop between residues 34 C and 38 C Built loop between residues 103 C and 106 C Built loop between residues 14 B and 22 B Built loop between residues 33 B and 36 B Built loop between residues 70 B and 73 B Built loop between residues 103 B and 106 B Built loop between residues 137 B and 141 B Built loop between residues 69 D and 73 D Built loop between residues 103 D and 106 D 7 chains (1029 residues) following loop building 5 chains (1024 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10016 restraints for refining 10079 atoms. 1856 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2578 (Rfree = 0.000) for 10079 atoms. Found 416 (416 requested) and removed 139 (236 requested) atoms. Cycle 27: After refmac, R = 0.2377 (Rfree = 0.000) for 10342 atoms. Found 307 (428 requested) and removed 118 (243 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2329 (Rfree = 0.000) for 10494 atoms. Found 263 (435 requested) and removed 127 (247 requested) atoms. Cycle 29: After refmac, R = 0.2286 (Rfree = 0.000) for 10606 atoms. Found 252 (439 requested) and removed 124 (249 requested) atoms. Cycle 30: After refmac, R = 0.2255 (Rfree = 0.000) for 10700 atoms. Found 259 (444 requested) and removed 130 (252 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.73 1.87 NCS extension: 0 residues added (78 deleted due to clashes), 10833 seeds are put forward Round 1: 1013 peptides, 18 chains. Longest chain 157 peptides. Score 0.964 Round 2: 1020 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Round 3: 1026 peptides, 12 chains. Longest chain 157 peptides. Score 0.972 Round 4: 1017 peptides, 17 chains. Longest chain 124 peptides. Score 0.966 Round 5: 1024 peptides, 16 chains. Longest chain 151 peptides. Score 0.968 Taking the results from Round 3 Chains 13, Residues 1014, Estimated correctness of the model 99.9 % 11 chains (1006 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 14 A and 20 A Built loop between residues 103 A and 106 A Built loop between residues 208 A and 211 A Built loop between residues 103 C and 106 C Built loop between residues 208 D and 211 D 8 chains (1027 residues) following loop building 6 chains (1019 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10149 restraints for refining 10114 atoms. 2009 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2545 (Rfree = 0.000) for 10114 atoms. Found 408 (408 requested) and removed 122 (237 requested) atoms. Cycle 32: After refmac, R = 0.2360 (Rfree = 0.000) for 10381 atoms. Found 323 (420 requested) and removed 89 (244 requested) atoms. Cycle 33: After refmac, R = 0.2309 (Rfree = 0.000) for 10589 atoms. Found 292 (428 requested) and removed 145 (249 requested) atoms. Cycle 34: After refmac, R = 0.2287 (Rfree = 0.000) for 10711 atoms. Found 277 (433 requested) and removed 157 (252 requested) atoms. Cycle 35: After refmac, R = 0.2267 (Rfree = 0.000) for 10794 atoms. Found 269 (428 requested) and removed 169 (254 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.73 1.87 NCS extension: 0 residues added (22 deleted due to clashes), 10896 seeds are put forward Round 1: 1019 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 2: 1023 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 3: 1023 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Round 4: 1018 peptides, 19 chains. Longest chain 124 peptides. Score 0.964 Round 5: 1019 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Taking the results from Round 3 Chains 19, Residues 1009, Estimated correctness of the model 99.9 % 14 chains (995 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 107 A Built loop between residues 158 A and 161 A Built loop between residues 35 C and 38 C Built loop between residues 103 C and 106 C Built loop between residues 14 B and 20 B Built loop between residues 33 B and 36 B Built loop between residues 208 B and 211 B Built loop between residues 101 D and 106 D 11 chains (1033 residues) following loop building 6 chains (1019 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10305 restraints for refining 10205 atoms. 2164 conditional restraints added. Observations/parameters ratio is 2.30 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2577 (Rfree = 0.000) for 10205 atoms. Found 393 (393 requested) and removed 169 (239 requested) atoms. Cycle 37: After refmac, R = 0.2387 (Rfree = 0.000) for 10399 atoms. Found 340 (402 requested) and removed 92 (245 requested) atoms. Cycle 38: After refmac, R = 0.2329 (Rfree = 0.000) for 10617 atoms. Found 282 (410 requested) and removed 116 (250 requested) atoms. Cycle 39: After refmac, R = 0.2300 (Rfree = 0.000) for 10764 atoms. Found 267 (415 requested) and removed 155 (253 requested) atoms. Cycle 40: After refmac, R = 0.2285 (Rfree = 0.000) for 10847 atoms. Found 268 (409 requested) and removed 165 (255 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.73 1.87 NCS extension: 4 residues added (263 deleted due to clashes), 10960 seeds are put forward Round 1: 1017 peptides, 18 chains. Longest chain 157 peptides. Score 0.965 Round 2: 1023 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 3: 1017 peptides, 14 chains. Longest chain 157 peptides. Score 0.969 Round 4: 1021 peptides, 15 chains. Longest chain 151 peptides. Score 0.968 Round 5: 1018 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Taking the results from Round 3 Chains 14, Residues 1003, Estimated correctness of the model 99.9 % 14 chains (1003 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 106 A Built loop between residues 135 A and 139 A Built loop between residues 103 C and 106 C Built loop between residues 14 B and 21 B Built loop between residues 70 B and 73 B Built loop between residues 103 B and 106 B Built loop between residues 208 B and 211 B Built loop between residues 71 D and 79 D Built loop between residues 103 D and 106 D Built loop between residues 154 D and 158 D 4 chains (1034 residues) following loop building 4 chains (1034 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10114 restraints for refining 10222 atoms. 1888 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2574 (Rfree = 0.000) for 10222 atoms. Found 374 (374 requested) and removed 166 (240 requested) atoms. Cycle 42: After refmac, R = 0.2382 (Rfree = 0.000) for 10406 atoms. Found 363 (382 requested) and removed 92 (245 requested) atoms. Cycle 43: After refmac, R = 0.2343 (Rfree = 0.000) for 10636 atoms. Found 314 (391 requested) and removed 145 (250 requested) atoms. Cycle 44: After refmac, R = 0.2310 (Rfree = 0.000) for 10771 atoms. Found 263 (395 requested) and removed 152 (253 requested) atoms. Cycle 45: After refmac, R = 0.2285 (Rfree = 0.000) for 10844 atoms. Found 283 (388 requested) and removed 123 (255 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.73 1.87 NCS extension: 3 residues added (115 deleted due to clashes), 11013 seeds are put forward Round 1: 1014 peptides, 18 chains. Longest chain 157 peptides. Score 0.965 Round 2: 1014 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 3: 1018 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 4: 1015 peptides, 17 chains. Longest chain 155 peptides. Score 0.966 Round 5: 1015 peptides, 19 chains. Longest chain 151 peptides. Score 0.964 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 1002, Estimated correctness of the model 99.9 % 14 chains (968 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 158 A and 161 A Built loop between residues 35 C and 38 C Built loop between residues 103 C and 106 C Built loop between residues 13 B and 20 B Built loop between residues 34 B and 37 B Built loop between residues 102 B and 106 B Built loop between residues 152 B and 155 B Built loop between residues 69 D and 75 D Built loop between residues 101 D and 107 D 8 chains (1029 residues) following loop building 5 chains (997 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 93715 reflections ( 99.87 % complete ) and 8061 restraints for refining 7858 atoms. Observations/parameters ratio is 2.98 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3470 (Rfree = 0.000) for 7858 atoms. Found 280 (280 requested) and removed 0 (280 requested) atoms. Cycle 47: After refmac, R = 0.3065 (Rfree = 0.000) for 7858 atoms. Found 184 (290 requested) and removed 3 (191 requested) atoms. Cycle 48: After refmac, R = 0.2880 (Rfree = 0.000) for 7858 atoms. Found 76 (296 requested) and removed 9 (195 requested) atoms. Cycle 49: After refmac, R = 0.2795 (Rfree = 0.000) for 7858 atoms. TimeTaking 145.73