Mon 24 Dec 07:33:09 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2pbl-1.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-1.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2pbl-1.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:33:14 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2pbl-1.8-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 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-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 77.197 74.438 95.727 90.000 113.394 90.000 Input sequence file: 2pbl-1.8-parrot-noncs.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 9316 atoms. Observations/parameters ratio is 2.51 ------------------------------------------------------ Starting model: R = 0.3567 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3224 (Rfree = 0.000) for 9316 atoms. Found 437 (437 requested) and removed 236 (218 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.74 1.89 NCS extension: 0 residues added, 9517 seeds are put forward Round 1: 871 peptides, 66 chains. Longest chain 38 peptides. Score 0.856 Round 2: 946 peptides, 32 chains. Longest chain 95 peptides. Score 0.938 Round 3: 978 peptides, 30 chains. Longest chain 77 peptides. Score 0.946 Round 4: 984 peptides, 24 chains. Longest chain 158 peptides. Score 0.954 Round 5: 999 peptides, 22 chains. Longest chain 113 peptides. Score 0.958 Taking the results from Round 5 Chains 27, Residues 977, Estimated correctness of the model 99.9 % 19 chains (918 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 181 A and 184 A Built loop between residues 220 A and 223 A Built loop between residues 103 C and 106 C Built loop between residues 217 C and 220 C Built loop between residues 33 B and 38 B Built loop between residues 103 B and 106 B Built loop between residues 187 B and 190 B Built loop between residues 31 D and 38 D Built loop between residues 199 D and 203 D Built loop between residues 225 D and 228 D 16 chains (1006 residues) following loop building 8 chains (947 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9350 restraints for refining 8828 atoms. 1589 conditional restraints added. Observations/parameters ratio is 2.65 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3090 (Rfree = 0.000) for 8828 atoms. Found 415 (415 requested) and removed 246 (207 requested) atoms. Cycle 2: After refmac, R = 0.2868 (Rfree = 0.000) for 8979 atoms. Found 354 (414 requested) and removed 86 (211 requested) atoms. Cycle 3: After refmac, R = 0.2761 (Rfree = 0.000) for 9217 atoms. Found 330 (425 requested) and removed 66 (217 requested) atoms. Cycle 4: After refmac, R = 0.2630 (Rfree = 0.000) for 9435 atoms. Found 286 (436 requested) and removed 81 (222 requested) atoms. Cycle 5: After refmac, R = 0.2541 (Rfree = 0.000) for 9609 atoms. Found 255 (444 requested) and removed 64 (226 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.75 1.90 NCS extension: 7 residues added (99 deleted due to clashes), 9809 seeds are put forward Round 1: 1012 peptides, 20 chains. Longest chain 157 peptides. Score 0.962 Round 2: 1020 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Round 3: 1023 peptides, 12 chains. Longest chain 225 peptides. Score 0.972 Round 4: 1019 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 5: 1016 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Taking the results from Round 3 Chains 16, Residues 1011, Estimated correctness of the model 99.9 % 11 chains (998 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 38 A Built loop between residues 14 C and 20 C Built loop between residues 33 C and 39 C Built loop between residues 102 C and 107 C Built loop between residues 198 C and 201 C Built loop between residues 103 B and 106 B 10 chains (1033 residues) following loop building 5 chains (1020 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9265 restraints for refining 9459 atoms. 1101 conditional restraints added. Observations/parameters ratio is 2.48 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2759 (Rfree = 0.000) for 9459 atoms. Found 367 (435 requested) and removed 201 (222 requested) atoms. Cycle 7: After refmac, R = 0.2569 (Rfree = 0.000) for 9608 atoms. Found 344 (434 requested) and removed 97 (226 requested) atoms. Cycle 8: After refmac, R = 0.2494 (Rfree = 0.000) for 9820 atoms. Found 318 (444 requested) and removed 101 (231 requested) atoms. Cycle 9: After refmac, R = 0.2431 (Rfree = 0.000) for 10013 atoms. Found 284 (452 requested) and removed 124 (235 requested) atoms. Cycle 10: After refmac, R = 0.2408 (Rfree = 0.000) for 10141 atoms. Found 281 (459 requested) and removed 131 (239 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.74 1.89 NCS extension: 6 residues added (102 deleted due to clashes), 10304 seeds are put forward Round 1: 1020 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 2: 1025 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 3: 1026 peptides, 16 chains. Longest chain 157 peptides. Score 0.968 Round 4: 1024 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Round 5: 1030 peptides, 13 chains. Longest chain 157 peptides. Score 0.971 Taking the results from Round 5 Chains 17, Residues 1017, Estimated correctness of the model 99.9 % 13 chains (1005 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 106 A Built loop between residues 34 C and 38 C Built loop between residues 101 C and 107 C Built loop between residues 158 C and 161 C Built loop between residues 34 B and 37 B Built loop between residues 71 B and 74 B Built loop between residues 158 B and 161 B Built loop between residues 101 D and 106 D 8 chains (1038 residues) following loop building 5 chains (1029 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9569 restraints for refining 9748 atoms. 1352 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2688 (Rfree = 0.000) for 9748 atoms. Found 407 (440 requested) and removed 204 (229 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2500 (Rfree = 0.000) for 9929 atoms. Found 328 (439 requested) and removed 109 (233 requested) atoms. Cycle 13: After refmac, R = 0.2427 (Rfree = 0.000) for 10117 atoms. Found 285 (447 requested) and removed 122 (238 requested) atoms. Cycle 14: After refmac, R = 0.2381 (Rfree = 0.000) for 10255 atoms. Found 262 (454 requested) and removed 131 (241 requested) atoms. Cycle 15: After refmac, R = 0.2345 (Rfree = 0.000) for 10363 atoms. Found 259 (459 requested) and removed 130 (244 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.74 1.89 NCS extension: 0 residues added, 10498 seeds are put forward Round 1: 1026 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 2: 1034 peptides, 10 chains. Longest chain 225 peptides. Score 0.975 Round 3: 1035 peptides, 10 chains. Longest chain 158 peptides. Score 0.975 Round 4: 1029 peptides, 16 chains. Longest chain 157 peptides. Score 0.968 Round 5: 1025 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Taking the results from Round 3 Chains 10, Residues 1025, Estimated correctness of the model 99.9 % 10 chains (1025 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 106 A Built loop between residues 34 C and 38 C Built loop between residues 102 C and 105 C Built loop between residues 103 B and 106 B Built loop between residues 34 D and 37 D Built loop between residues 103 D and 106 D 4 chains (1038 residues) following loop building 4 chains (1038 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9536 restraints for refining 9867 atoms. 1280 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2656 (Rfree = 0.000) for 9867 atoms. Found 411 (426 requested) and removed 145 (231 requested) atoms. Cycle 17: After refmac, R = 0.2461 (Rfree = 0.000) for 10108 atoms. Found 328 (438 requested) and removed 122 (238 requested) atoms. Cycle 18: After refmac, R = 0.2405 (Rfree = 0.000) for 10268 atoms. Found 289 (445 requested) and removed 133 (242 requested) atoms. Cycle 19: After refmac, R = 0.2367 (Rfree = 0.000) for 10393 atoms. Found 296 (450 requested) and removed 129 (244 requested) atoms. Cycle 20: After refmac, R = 0.2349 (Rfree = 0.000) for 10535 atoms. Found 219 (456 requested) and removed 145 (248 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.75 1.90 NCS extension: 4 residues added (29 deleted due to clashes), 10619 seeds are put forward Round 1: 1026 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Round 2: 1029 peptides, 12 chains. Longest chain 157 peptides. Score 0.972 Round 3: 1031 peptides, 12 chains. Longest chain 157 peptides. Score 0.972 Round 4: 1028 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Round 5: 1022 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Taking the results from Round 3 Chains 15, Residues 1019, 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 17 A Built loop between residues 33 A and 38 A Built loop between residues 103 A and 106 A Built loop between residues 34 B and 37 B Built loop between residues 100 B and 106 B Built loop between residues 103 D and 106 D 9 chains (1036 residues) following loop building 5 chains (1023 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9858 restraints for refining 10022 atoms. 1669 conditional restraints added. Observations/parameters ratio is 2.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2632 (Rfree = 0.000) for 10022 atoms. Found 420 (423 requested) and removed 176 (235 requested) atoms. Cycle 22: After refmac, R = 0.2436 (Rfree = 0.000) for 10236 atoms. Found 303 (434 requested) and removed 113 (241 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2390 (Rfree = 0.000) for 10377 atoms. Found 302 (440 requested) and removed 110 (244 requested) atoms. Cycle 24: After refmac, R = 0.2339 (Rfree = 0.000) for 10542 atoms. Found 243 (446 requested) and removed 142 (248 requested) atoms. Cycle 25: After refmac, R = 0.2318 (Rfree = 0.000) for 10612 atoms. Found 248 (440 requested) and removed 113 (250 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.74 1.89 NCS extension: 5 residues added (190 deleted due to clashes), 10757 seeds are put forward Round 1: 1022 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Round 2: 1028 peptides, 12 chains. Longest chain 157 peptides. Score 0.972 Round 3: 1029 peptides, 13 chains. Longest chain 157 peptides. Score 0.971 Round 4: 1028 peptides, 14 chains. Longest chain 151 peptides. Score 0.970 Round 5: 1022 peptides, 16 chains. Longest chain 103 peptides. Score 0.967 Taking the results from Round 2 Chains 14, Residues 1016, Estimated correctness of the model 99.9 % 12 chains (1012 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 103 A and 106 A Built loop between residues 33 B and 38 B Built loop between residues 71 B and 75 B Built loop between residues 103 D and 106 D 9 chains (1029 residues) following loop building 7 chains (1025 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9969 restraints for refining 10093 atoms. 1816 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2615 (Rfree = 0.000) for 10093 atoms. Found 417 (417 requested) and removed 161 (237 requested) atoms. Cycle 27: After refmac, R = 0.2422 (Rfree = 0.000) for 10320 atoms. Found 350 (428 requested) and removed 102 (243 requested) atoms. Cycle 28: After refmac, R = 0.2378 (Rfree = 0.000) for 10519 atoms. Found 229 (436 requested) and removed 152 (248 requested) atoms. Cycle 29: After refmac, R = 0.2338 (Rfree = 0.000) for 10562 atoms. Found 260 (427 requested) and removed 108 (248 requested) atoms. Cycle 30: After refmac, R = 0.2311 (Rfree = 0.000) for 10683 atoms. Found 252 (433 requested) and removed 146 (251 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.74 1.89 NCS extension: 12 residues added (194 deleted due to clashes), 10802 seeds are put forward Round 1: 1022 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Round 2: 1026 peptides, 12 chains. Longest chain 157 peptides. Score 0.972 Round 3: 1020 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 4: 1023 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 5: 1024 peptides, 17 chains. Longest chain 157 peptides. Score 0.967 Taking the results from Round 2 Chains 14, Residues 1014, Estimated correctness of the model 99.9 % 12 chains (1010 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 37 A Built loop between residues 71 A and 75 A Built loop between residues 103 A and 106 A Built loop between residues 69 C and 72 C Built loop between residues 101 C and 106 C Built loop between residues 69 B and 75 B Built loop between residues 101 B and 106 B Built loop between residues 103 D and 106 D 6 chains (1038 residues) following loop building 4 chains (1035 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10038 restraints for refining 10129 atoms. 1795 conditional restraints added. Observations/parameters ratio is 2.31 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2629 (Rfree = 0.000) for 10129 atoms. Found 400 (400 requested) and removed 179 (238 requested) atoms. Cycle 32: After refmac, R = 0.2487 (Rfree = 0.000) for 10320 atoms. Found 320 (408 requested) and removed 129 (243 requested) atoms. Cycle 33: After refmac, R = 0.2404 (Rfree = 0.000) for 10485 atoms. Found 286 (414 requested) and removed 124 (246 requested) atoms. Cycle 34: After refmac, R = 0.2359 (Rfree = 0.000) for 10597 atoms. Found 287 (420 requested) and removed 115 (250 requested) atoms. Cycle 35: After refmac, R = 0.2324 (Rfree = 0.000) for 10728 atoms. Found 233 (425 requested) and removed 136 (253 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.75 1.90 NCS extension: 6 residues added (198 deleted due to clashes), 10840 seeds are put forward Round 1: 1017 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 2: 1026 peptides, 13 chains. Longest chain 157 peptides. Score 0.971 Round 3: 1024 peptides, 15 chains. Longest chain 157 peptides. Score 0.969 Round 4: 1023 peptides, 14 chains. Longest chain 151 peptides. Score 0.970 Round 5: 1024 peptides, 16 chains. Longest chain 156 peptides. Score 0.968 Taking the results from Round 2 Chains 13, Residues 1013, Estimated correctness of the model 99.9 % 13 chains (1013 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 75 A and 79 A Built loop between residues 103 A and 106 A Built loop between residues 71 C and 74 C Built loop between residues 103 C and 106 C Built loop between residues 70 B and 75 B Built loop between residues 103 B and 106 B Built loop between residues 103 D and 106 D Built loop between residues 154 D and 158 D 5 chains (1033 residues) following loop building 5 chains (1033 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 9900 restraints for refining 10110 atoms. 1697 conditional restraints added. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2600 (Rfree = 0.000) for 10110 atoms. Found 389 (389 requested) and removed 124 (237 requested) atoms. Cycle 37: After refmac, R = 0.2416 (Rfree = 0.000) for 10341 atoms. Found 309 (399 requested) and removed 82 (243 requested) atoms. Cycle 38: After refmac, R = 0.2363 (Rfree = 0.000) for 10523 atoms. Found 267 (407 requested) and removed 98 (248 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2314 (Rfree = 0.000) for 10656 atoms. Found 247 (412 requested) and removed 107 (251 requested) atoms. Cycle 40: After refmac, R = 0.2287 (Rfree = 0.000) for 10765 atoms. Found 251 (416 requested) and removed 124 (253 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.74 1.89 NCS extension: 0 residues added (88 deleted due to clashes), 10894 seeds are put forward Round 1: 1016 peptides, 18 chains. Longest chain 157 peptides. Score 0.965 Round 2: 1018 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 3: 1021 peptides, 16 chains. Longest chain 157 peptides. Score 0.967 Round 4: 1014 peptides, 17 chains. Longest chain 157 peptides. Score 0.966 Round 5: 1016 peptides, 18 chains. Longest chain 105 peptides. Score 0.965 Taking the results from Round 3 Chains 18, Residues 1005, Estimated correctness of the model 99.9 % 16 chains (1000 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 37 A Built loop between residues 100 A and 106 A Built loop between residues 158 A and 161 A Built loop between residues 69 C and 72 C Built loop between residues 14 B and 20 B Built loop between residues 33 B and 38 B Built loop between residues 71 B and 75 B Built loop between residues 103 B and 106 B Built loop between residues 136 B and 139 B Built loop between residues 208 B and 211 B Built loop between residues 103 D and 106 D 7 chains (1034 residues) following loop building 5 chains (1031 residues) in sequence following loop building ------------------------------------------------------ 93715 reflections ( 99.87 % complete ) and 10024 restraints for refining 10163 atoms. 1812 conditional restraints added. Observations/parameters ratio is 2.31 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2592 (Rfree = 0.000) for 10163 atoms. Found 391 (391 requested) and removed 152 (238 requested) atoms. Cycle 42: After refmac, R = 0.2412 (Rfree = 0.000) for 10373 atoms. Found 350 (400 requested) and removed 82 (244 requested) atoms. Cycle 43: After refmac, R = 0.2348 (Rfree = 0.000) for 10581 atoms. Found 279 (410 requested) and removed 115 (250 requested) atoms. Cycle 44: After refmac, R = 0.2322 (Rfree = 0.000) for 10709 atoms. Found 248 (413 requested) and removed 124 (252 requested) atoms. Cycle 45: After refmac, R = 0.2281 (Rfree = 0.000) for 10793 atoms. Found 245 (417 requested) and removed 128 (254 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.74 1.89 NCS extension: 4 residues added (346 deleted due to clashes), 10917 seeds are put forward Round 1: 1011 peptides, 16 chains. Longest chain 157 peptides. Score 0.966 Round 2: 1011 peptides, 19 chains. Longest chain 157 peptides. Score 0.963 Round 3: 1019 peptides, 15 chains. Longest chain 157 peptides. Score 0.968 Round 4: 1020 peptides, 17 chains. Longest chain 151 peptides. Score 0.966 Round 5: 1024 peptides, 14 chains. Longest chain 157 peptides. Score 0.970 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 16, Residues 1010, Estimated correctness of the model 99.9 % 13 chains (1003 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 70 A and 76 A Built loop between residues 103 C and 106 C Built loop between residues 14 B and 17 B Built loop between residues 32 B and 38 B Built loop between residues 103 B and 106 B Built loop between residues 136 B and 139 B Built loop between residues 210 B and 213 B Built loop between residues 101 D and 106 D 7 chains (1032 residues) following loop building 5 chains (1027 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 93715 reflections ( 99.87 % complete ) and 8194 restraints for refining 7982 atoms. Observations/parameters ratio is 2.94 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3448 (Rfree = 0.000) for 7982 atoms. Found 265 (300 requested) and removed 0 (300 requested) atoms. Cycle 47: After refmac, R = 0.3021 (Rfree = 0.000) for 7982 atoms. Found 151 (310 requested) and removed 5 (193 requested) atoms. Cycle 48: After refmac, R = 0.2870 (Rfree = 0.000) for 7982 atoms. Found 99 (315 requested) and removed 8 (197 requested) atoms. Cycle 49: After refmac, R = 0.2761 (Rfree = 0.000) for 7982 atoms. TimeTaking 122.3