Sun 23 Dec 23:51:07 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 2fna-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2fna-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-2.0-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/2fna-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-2.0-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 ============================================================ Sun 23 Dec 23:51:12 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/2fna-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2fna-2.0-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 717 and 0 Target number of residues in the AU: 717 Target solvent content: 0.5347 Checking the provided sequence file Detected sequence length: 357 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 714 Adjusted target solvent content: 0.54 Input MTZ file: 2fna-2.0-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: 55.380 108.390 70.600 90.000 100.307 90.000 Input sequence file: 2fna-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5712 target number of atoms Had to go as low as 0.55 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: 69.461 2.000 Wilson plot Bfac: 31.44 53519 reflections ( 96.80 % complete ) and 0 restraints for refining 6300 atoms. Observations/parameters ratio is 2.12 ------------------------------------------------------ Starting model: R = 0.3292 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2822 (Rfree = 0.000) for 6300 atoms. Found 168 (215 requested) and removed 110 (107 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.27 2.15 NCS extension: 0 residues added, 6358 seeds are put forward Round 1: 483 peptides, 63 chains. Longest chain 22 peptides. Score 0.602 Round 2: 552 peptides, 49 chains. Longest chain 49 peptides. Score 0.757 Round 3: 591 peptides, 33 chains. Longest chain 75 peptides. Score 0.848 Round 4: 596 peptides, 29 chains. Longest chain 83 peptides. Score 0.864 Round 5: 614 peptides, 23 chains. Longest chain 104 peptides. Score 0.890 Taking the results from Round 5 Chains 25, Residues 591, Estimated correctness of the model 98.8 % 12 chains (517 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A Built loop between residues 269 A and 278 A 22 chains (598 residues) following loop building 10 chains (527 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 7140 restraints for refining 6071 atoms. 2390 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2875 (Rfree = 0.000) for 6071 atoms. Found 191 (207 requested) and removed 110 (103 requested) atoms. Cycle 2: After refmac, R = 0.2616 (Rfree = 0.000) for 6124 atoms. Found 109 (206 requested) and removed 81 (105 requested) atoms. Cycle 3: After refmac, R = 0.2479 (Rfree = 0.000) for 6123 atoms. Found 93 (202 requested) and removed 42 (105 requested) atoms. Cycle 4: After refmac, R = 0.2385 (Rfree = 0.000) for 6155 atoms. Found 82 (203 requested) and removed 32 (105 requested) atoms. Cycle 5: After refmac, R = 0.2317 (Rfree = 0.000) for 6191 atoms. Found 82 (204 requested) and removed 25 (106 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.18 2.07 NCS extension: 40 residues added (72 deleted due to clashes), 6293 seeds are put forward Round 1: 626 peptides, 18 chains. Longest chain 114 peptides. Score 0.908 Round 2: 633 peptides, 18 chains. Longest chain 135 peptides. Score 0.911 Round 3: 623 peptides, 24 chains. Longest chain 73 peptides. Score 0.892 Round 4: 632 peptides, 19 chains. Longest chain 119 peptides. Score 0.908 Round 5: 638 peptides, 19 chains. Longest chain 101 peptides. Score 0.910 Taking the results from Round 2 Chains 18, Residues 615, Estimated correctness of the model 99.2 % 10 chains (571 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 29 A Built loop between residues 281 A and 292 A Built loop between residues 188 B and 199 B 14 chains (634 residues) following loop building 7 chains (593 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6911 restraints for refining 6284 atoms. 1735 conditional restraints added. Observations/parameters ratio is 2.13 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2441 (Rfree = 0.000) for 6284 atoms. Found 147 (206 requested) and removed 110 (107 requested) atoms. Cycle 7: After refmac, R = 0.2281 (Rfree = 0.000) for 6306 atoms. Found 122 (203 requested) and removed 59 (108 requested) atoms. Cycle 8: After refmac, R = 0.2186 (Rfree = 0.000) for 6361 atoms. Found 102 (205 requested) and removed 45 (109 requested) atoms. Cycle 9: After refmac, R = 0.2108 (Rfree = 0.000) for 6412 atoms. Found 86 (206 requested) and removed 31 (109 requested) atoms. Cycle 10: After refmac, R = 0.2061 (Rfree = 0.000) for 6460 atoms. Found 81 (208 requested) and removed 49 (110 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.18 2.07 NCS extension: 32 residues added (70 deleted due to clashes), 6529 seeds are put forward Round 1: 639 peptides, 16 chains. Longest chain 159 peptides. Score 0.918 Round 2: 650 peptides, 14 chains. Longest chain 169 peptides. Score 0.926 Round 3: 651 peptides, 12 chains. Longest chain 162 peptides. Score 0.931 Round 4: 648 peptides, 20 chains. Longest chain 132 peptides. Score 0.912 Round 5: 643 peptides, 17 chains. Longest chain 158 peptides. Score 0.917 Taking the results from Round 3 Chains 13, Residues 639, Estimated correctness of the model 99.5 % 9 chains (621 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 189 A and 193 A Built loop between residues 275 A and 278 A Built loop between residues 285 B and 288 B Built loop between residues 313 B and 323 B Built loop between residues 340 B and 344 B 7 chains (657 residues) following loop building 4 chains (640 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6556 restraints for refining 6414 atoms. 1084 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2289 (Rfree = 0.000) for 6414 atoms. Found 172 (201 requested) and removed 109 (109 requested) atoms. Cycle 12: After refmac, R = 0.2161 (Rfree = 0.000) for 6471 atoms. Found 85 (199 requested) and removed 58 (110 requested) atoms. Cycle 13: After refmac, R = 0.2076 (Rfree = 0.000) for 6497 atoms. Found 91 (195 requested) and removed 35 (111 requested) atoms. Cycle 14: After refmac, R = 0.2032 (Rfree = 0.000) for 6548 atoms. Found 71 (197 requested) and removed 48 (112 requested) atoms. Cycle 15: After refmac, R = 0.1983 (Rfree = 0.000) for 6569 atoms. Found 97 (193 requested) and removed 53 (112 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.19 2.08 NCS extension: 0 residues added, 6618 seeds are put forward Round 1: 646 peptides, 16 chains. Longest chain 158 peptides. Score 0.920 Round 2: 658 peptides, 15 chains. Longest chain 141 peptides. Score 0.926 Round 3: 655 peptides, 15 chains. Longest chain 147 peptides. Score 0.925 Round 4: 653 peptides, 19 chains. Longest chain 117 peptides. Score 0.916 Round 5: 652 peptides, 17 chains. Longest chain 141 peptides. Score 0.920 Taking the results from Round 2 Chains 16, Residues 643, Estimated correctness of the model 99.4 % 12 chains (623 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 29 A Built loop between residues 143 A and 146 A Built loop between residues 285 A and 288 A Built loop between residues 316 A and 320 A Built loop between residues 47 B and 51 B Built loop between residues 143 B and 146 B Built loop between residues 187 B and 191 B Built loop between residues 311 B and 314 B 8 chains (662 residues) following loop building 4 chains (642 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6510 restraints for refining 6436 atoms. 1007 conditional restraints added. Observations/parameters ratio is 2.08 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2207 (Rfree = 0.000) for 6436 atoms. Found 185 (185 requested) and removed 106 (110 requested) atoms. Cycle 17: After refmac, R = 0.2082 (Rfree = 0.000) for 6510 atoms. Found 105 (183 requested) and removed 49 (111 requested) atoms. Cycle 18: After refmac, R = 0.1998 (Rfree = 0.000) for 6559 atoms. Found 108 (184 requested) and removed 32 (112 requested) atoms. Cycle 19: After refmac, R = 0.1950 (Rfree = 0.000) for 6635 atoms. Found 90 (186 requested) and removed 57 (113 requested) atoms. Cycle 20: After refmac, R = 0.1918 (Rfree = 0.000) for 6667 atoms. Found 109 (182 requested) and removed 55 (114 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.19 2.08 NCS extension: 0 residues added, 6723 seeds are put forward Round 1: 663 peptides, 17 chains. Longest chain 158 peptides. Score 0.924 Round 2: 670 peptides, 11 chains. Longest chain 235 peptides. Score 0.938 Round 3: 667 peptides, 16 chains. Longest chain 193 peptides. Score 0.927 Round 4: 656 peptides, 13 chains. Longest chain 235 peptides. Score 0.930 Round 5: 667 peptides, 16 chains. Longest chain 154 peptides. Score 0.927 Taking the results from Round 2 Chains 12, Residues 659, Estimated correctness of the model 99.6 % 8 chains (633 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 46 A and 49 A Built loop between residues 157 A and 168 A Built loop between residues 285 A and 288 A 8 chains (667 residues) following loop building 5 chains (647 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6549 restraints for refining 6527 atoms. 1002 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2166 (Rfree = 0.000) for 6527 atoms. Found 169 (174 requested) and removed 113 (111 requested) atoms. Cycle 22: After refmac, R = 0.2045 (Rfree = 0.000) for 6578 atoms. Found 129 (171 requested) and removed 57 (112 requested) atoms. Cycle 23: After refmac, R = 0.1979 (Rfree = 0.000) for 6645 atoms. Found 104 (173 requested) and removed 77 (113 requested) atoms. Cycle 24: After refmac, R = 0.1936 (Rfree = 0.000) for 6669 atoms. Found 123 (169 requested) and removed 67 (114 requested) atoms. Cycle 25: After refmac, R = 0.1924 (Rfree = 0.000) for 6724 atoms. Found 120 (166 requested) and removed 88 (115 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.19 2.08 NCS extension: 4 residues added (28 deleted due to clashes), 6762 seeds are put forward Round 1: 666 peptides, 14 chains. Longest chain 212 peptides. Score 0.931 Round 2: 668 peptides, 15 chains. Longest chain 190 peptides. Score 0.929 Round 3: 667 peptides, 15 chains. Longest chain 147 peptides. Score 0.929 Round 4: 667 peptides, 16 chains. Longest chain 123 peptides. Score 0.927 Round 5: 668 peptides, 13 chains. Longest chain 165 peptides. Score 0.934 Taking the results from Round 5 Chains 13, Residues 655, Estimated correctness of the model 99.5 % 11 chains (638 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 48 A Built loop between residues 189 A and 193 A Built loop between residues 26 B and 29 B Built loop between residues 73 B and 76 B Built loop between residues 165 B and 168 B Built loop between residues 291 B and 294 B Built loop between residues 316 B and 324 B 6 chains (675 residues) following loop building 4 chains (658 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6482 restraints for refining 6548 atoms. 857 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2210 (Rfree = 0.000) for 6548 atoms. Found 157 (157 requested) and removed 115 (112 requested) atoms. Cycle 27: After refmac, R = 0.2076 (Rfree = 0.000) for 6586 atoms. Found 140 (153 requested) and removed 59 (112 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1995 (Rfree = 0.000) for 6665 atoms. Found 112 (155 requested) and removed 58 (114 requested) atoms. Cycle 29: After refmac, R = 0.1954 (Rfree = 0.000) for 6714 atoms. Found 100 (152 requested) and removed 73 (115 requested) atoms. Cycle 30: After refmac, R = 0.1923 (Rfree = 0.000) for 6738 atoms. Found 106 (147 requested) and removed 71 (115 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.19 2.08 NCS extension: 2 residues added (1 deleted due to clashes), 6780 seeds are put forward Round 1: 667 peptides, 14 chains. Longest chain 158 peptides. Score 0.931 Round 2: 676 peptides, 10 chains. Longest chain 196 peptides. Score 0.942 Round 3: 674 peptides, 13 chains. Longest chain 146 peptides. Score 0.935 Round 4: 661 peptides, 17 chains. Longest chain 120 peptides. Score 0.923 Round 5: 668 peptides, 10 chains. Longest chain 184 peptides. Score 0.940 Taking the results from Round 2 Chains 11, Residues 666, Estimated correctness of the model 99.6 % 8 chains (647 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 29 A Built loop between residues 143 A and 146 A Built loop between residues 311 A and 314 A Built loop between residues 316 B and 320 B 7 chains (675 residues) following loop building 4 chains (656 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6499 restraints for refining 6540 atoms. 884 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2148 (Rfree = 0.000) for 6540 atoms. Found 139 (139 requested) and removed 107 (112 requested) atoms. Cycle 32: After refmac, R = 0.2027 (Rfree = 0.000) for 6571 atoms. Found 135 (135 requested) and removed 45 (112 requested) atoms. Cycle 33: After refmac, R = 0.1977 (Rfree = 0.000) for 6658 atoms. Found 111 (137 requested) and removed 70 (114 requested) atoms. Cycle 34: After refmac, R = 0.1940 (Rfree = 0.000) for 6694 atoms. Found 115 (133 requested) and removed 62 (114 requested) atoms. Cycle 35: After refmac, R = 0.1922 (Rfree = 0.000) for 6744 atoms. Found 105 (129 requested) and removed 75 (115 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.19 2.08 NCS extension: 0 residues added, 6778 seeds are put forward Round 1: 669 peptides, 11 chains. Longest chain 212 peptides. Score 0.938 Round 2: 677 peptides, 11 chains. Longest chain 191 peptides. Score 0.940 Round 3: 672 peptides, 13 chains. Longest chain 193 peptides. Score 0.935 Round 4: 667 peptides, 14 chains. Longest chain 153 peptides. Score 0.931 Round 5: 667 peptides, 13 chains. Longest chain 193 peptides. Score 0.933 Taking the results from Round 2 Chains 11, Residues 666, Estimated correctness of the model 99.6 % 9 chains (647 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 76 A Built loop between residues 165 A and 168 A Built loop between residues 285 A and 288 A Built loop between residues 320 A and 323 A Built loop between residues 311 B and 314 B 6 chains (676 residues) following loop building 4 chains (657 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6548 restraints for refining 6585 atoms. 924 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2137 (Rfree = 0.000) for 6585 atoms. Found 121 (121 requested) and removed 111 (112 requested) atoms. Cycle 37: After refmac, R = 0.2017 (Rfree = 0.000) for 6593 atoms. Found 117 (117 requested) and removed 37 (112 requested) atoms. Cycle 38: After refmac, R = 0.1948 (Rfree = 0.000) for 6670 atoms. Found 111 (119 requested) and removed 43 (114 requested) atoms. Cycle 39: After refmac, R = 0.1904 (Rfree = 0.000) for 6737 atoms. Found 108 (120 requested) and removed 57 (115 requested) atoms. Cycle 40: After refmac, R = 0.1877 (Rfree = 0.000) for 6787 atoms. Found 82 (116 requested) and removed 71 (116 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.18 2.07 NCS extension: 1 residues added (14 deleted due to clashes), 6801 seeds are put forward Round 1: 674 peptides, 13 chains. Longest chain 167 peptides. Score 0.935 Round 2: 672 peptides, 13 chains. Longest chain 170 peptides. Score 0.935 Round 3: 666 peptides, 15 chains. Longest chain 165 peptides. Score 0.929 Round 4: 665 peptides, 13 chains. Longest chain 116 peptides. Score 0.933 Round 5: 658 peptides, 17 chains. Longest chain 159 peptides. Score 0.922 Taking the results from Round 2 Chains 13, Residues 659, Estimated correctness of the model 99.5 % 11 chains (640 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 29 A Built loop between residues 73 A and 76 A Built loop between residues 143 A and 146 A Built loop between residues 304 A and 307 A Built loop between residues 73 B and 76 B Built loop between residues 143 B and 146 B Built loop between residues 314 B and 319 B 6 chains (675 residues) following loop building 4 chains (656 residues) in sequence following loop building ------------------------------------------------------ 53519 reflections ( 96.80 % complete ) and 6545 restraints for refining 6600 atoms. 929 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2117 (Rfree = 0.000) for 6600 atoms. Found 113 (113 requested) and removed 105 (113 requested) atoms. Cycle 42: After refmac, R = 0.1990 (Rfree = 0.000) for 6608 atoms. Found 113 (113 requested) and removed 32 (113 requested) atoms. Cycle 43: After refmac, R = 0.1912 (Rfree = 0.000) for 6686 atoms. Found 104 (114 requested) and removed 45 (114 requested) atoms. Cycle 44: After refmac, R = 0.1874 (Rfree = 0.000) for 6739 atoms. Found 101 (115 requested) and removed 60 (115 requested) atoms. Cycle 45: After refmac, R = 0.1842 (Rfree = 0.000) for 6780 atoms. Found 98 (116 requested) and removed 61 (116 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.18 2.07 NCS extension: 1 residues added (14 deleted due to clashes), 6820 seeds are put forward Round 1: 670 peptides, 12 chains. Longest chain 170 peptides. Score 0.936 Round 2: 671 peptides, 13 chains. Longest chain 184 peptides. Score 0.934 Round 3: 661 peptides, 18 chains. Longest chain 145 peptides. Score 0.921 Round 4: 660 peptides, 14 chains. Longest chain 224 peptides. Score 0.929 Round 5: 656 peptides, 19 chains. Longest chain 152 peptides. Score 0.917 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 13, Residues 658, Estimated correctness of the model 99.5 % 9 chains (633 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 26 A and 29 A Built loop between residues 143 A and 146 A Built loop between residues 314 A and 323 A Built loop between residues 143 B and 146 B Built loop between residues 311 B and 314 B 8 chains (674 residues) following loop building 4 chains (649 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 53519 reflections ( 96.80 % complete ) and 5580 restraints for refining 5475 atoms. Observations/parameters ratio is 2.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2704 (Rfree = 0.000) for 5475 atoms. Found 56 (93 requested) and removed 0 (93 requested) atoms. Cycle 47: After refmac, R = 0.2529 (Rfree = 0.000) for 5475 atoms. Found 19 (94 requested) and removed 2 (94 requested) atoms. Cycle 48: After refmac, R = 0.2437 (Rfree = 0.000) for 5475 atoms. Found 25 (95 requested) and removed 3 (95 requested) atoms. Cycle 49: After refmac, R = 0.2366 (Rfree = 0.000) for 5475 atoms. Found 18 (95 requested) and removed 9 (95 requested) atoms. Writing output files ... TimeTaking 91.23