Sun 23 Dec 23:55:39 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 1vr0-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vr0-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-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/1vr0-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-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 23:55:44 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/1vr0-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vr0-2.5-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 613 and 0 Target number of residues in the AU: 613 Target solvent content: 0.5471 Checking the provided sequence file Detected sequence length: 247 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 3 Adjusted target number of residues: 741 Adjusted target solvent content: 0.45 Input MTZ file: 1vr0-2.5-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: 20 Cell parameters: 46.686 69.193 453.518 90.000 90.000 90.000 Input sequence file: 1vr0-2.5-parrot-mrncs.fasta_lf Building free atoms model in initial map for 5928 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 3 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: 226.759 2.490 Wilson plot Bfac: 34.68 22751 reflections ( 85.61 % complete ) and 0 restraints for refining 6604 atoms. Observations/parameters ratio is 0.86 ------------------------------------------------------ Starting model: R = 0.3147 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2275 (Rfree = 0.000) for 6604 atoms. Found 66 (121 requested) and removed 82 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.43 2.60 NCS extension: 0 residues added, 6588 seeds are put forward Round 1: 419 peptides, 69 chains. Longest chain 16 peptides. Score 0.488 Round 2: 487 peptides, 47 chains. Longest chain 32 peptides. Score 0.739 Round 3: 535 peptides, 40 chains. Longest chain 63 peptides. Score 0.818 Round 4: 561 peptides, 40 chains. Longest chain 77 peptides. Score 0.837 Round 5: 558 peptides, 29 chains. Longest chain 100 peptides. Score 0.873 Taking the results from Round 5 Chains 34, Residues 529, Estimated correctness of the model 96.7 % 10 chains (341 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 144 B and 150 B 32 chains (533 residues) following loop building 9 chains (346 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 8286 restraints for refining 5554 atoms. 4917 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2825 (Rfree = 0.000) for 5554 atoms. Found 101 (101 requested) and removed 58 (50 requested) atoms. Cycle 2: After refmac, R = 0.2485 (Rfree = 0.000) for 5533 atoms. Found 65 (100 requested) and removed 56 (51 requested) atoms. Cycle 3: After refmac, R = 0.2326 (Rfree = 0.000) for 5510 atoms. Found 38 (97 requested) and removed 53 (50 requested) atoms. Cycle 4: After refmac, R = 0.2237 (Rfree = 0.000) for 5462 atoms. Found 39 (94 requested) and removed 52 (50 requested) atoms. Cycle 5: After refmac, R = 0.2255 (Rfree = 0.000) for 5433 atoms. Found 31 (91 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.43 2.60 NCS extension: 85 residues added (93 deleted due to clashes), 5517 seeds are put forward Round 1: 551 peptides, 30 chains. Longest chain 89 peptides. Score 0.865 Round 2: 577 peptides, 25 chains. Longest chain 103 peptides. Score 0.895 Round 3: 587 peptides, 29 chains. Longest chain 67 peptides. Score 0.888 Round 4: 581 peptides, 23 chains. Longest chain 55 peptides. Score 0.902 Round 5: 583 peptides, 26 chains. Longest chain 63 peptides. Score 0.895 Taking the results from Round 4 Chains 26, Residues 558, Estimated correctness of the model 98.0 % 14 chains (460 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 158 A and 162 A Built loop between residues 81 C and 91 C Built loop between residues 144 C and 149 C Built loop between residues 182 C and 186 C Built loop between residues 210 C and 213 C Built loop between residues 89 B and 96 B Built loop between residues 123 B and 126 B Built loop between residues 179 B and 182 B Built loop between residues 210 B and 213 B 16 chains (588 residues) following loop building 5 chains (493 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6786 restraints for refining 5558 atoms. 2558 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2435 (Rfree = 0.000) for 5558 atoms. Found 83 (91 requested) and removed 62 (50 requested) atoms. Cycle 7: After refmac, R = 0.2198 (Rfree = 0.000) for 5554 atoms. Found 59 (90 requested) and removed 56 (51 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2085 (Rfree = 0.000) for 5543 atoms. Found 52 (87 requested) and removed 54 (50 requested) atoms. Cycle 9: After refmac, R = 0.2020 (Rfree = 0.000) for 5534 atoms. Found 44 (85 requested) and removed 50 (50 requested) atoms. Cycle 10: After refmac, R = 0.1990 (Rfree = 0.000) for 5522 atoms. Found 38 (83 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.45 2.62 NCS extension: 208 residues added (425 deleted due to clashes), 5731 seeds are put forward Round 1: 599 peptides, 28 chains. Longest chain 99 peptides. Score 0.897 Round 2: 611 peptides, 20 chains. Longest chain 225 peptides. Score 0.922 Round 3: 608 peptides, 24 chains. Longest chain 68 peptides. Score 0.911 Round 4: 598 peptides, 28 chains. Longest chain 64 peptides. Score 0.896 Round 5: 610 peptides, 20 chains. Longest chain 116 peptides. Score 0.921 Taking the results from Round 2 Chains 22, Residues 591, Estimated correctness of the model 98.7 % 12 chains (534 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 144 A and 150 A Built loop between residues 182 A and 186 A Built loop between residues 204 A and 213 A Built loop between residues 136 C and 140 C 17 chains (605 residues) following loop building 8 chains (553 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6226 restraints for refining 5557 atoms. 1711 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2205 (Rfree = 0.000) for 5557 atoms. Found 81 (81 requested) and removed 56 (50 requested) atoms. Cycle 12: After refmac, R = 0.1996 (Rfree = 0.000) for 5570 atoms. Found 71 (80 requested) and removed 54 (51 requested) atoms. Cycle 13: After refmac, R = 0.1910 (Rfree = 0.000) for 5584 atoms. Found 40 (78 requested) and removed 52 (51 requested) atoms. Cycle 14: After refmac, R = 0.1883 (Rfree = 0.000) for 5565 atoms. Found 42 (75 requested) and removed 51 (51 requested) atoms. Cycle 15: After refmac, R = 0.1873 (Rfree = 0.000) for 5549 atoms. Found 56 (73 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.44 2.61 NCS extension: 469 residues added (786 deleted due to clashes), 6034 seeds are put forward Round 1: 603 peptides, 24 chains. Longest chain 99 peptides. Score 0.909 Round 2: 619 peptides, 17 chains. Longest chain 234 peptides. Score 0.931 Round 3: 614 peptides, 25 chains. Longest chain 94 peptides. Score 0.911 Round 4: 601 peptides, 22 chains. Longest chain 117 peptides. Score 0.913 Round 5: 600 peptides, 24 chains. Longest chain 96 peptides. Score 0.908 Taking the results from Round 2 Chains 21, Residues 602, Estimated correctness of the model 98.9 % 9 chains (524 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 86 A Built loop between residues 143 A and 149 A 19 chains (609 residues) following loop building 7 chains (531 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6362 restraints for refining 5558 atoms. 1894 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2039 (Rfree = 0.000) for 5558 atoms. Found 71 (71 requested) and removed 58 (50 requested) atoms. Cycle 17: After refmac, R = 0.1897 (Rfree = 0.000) for 5561 atoms. Found 69 (69 requested) and removed 51 (51 requested) atoms. Cycle 18: After refmac, R = 0.1830 (Rfree = 0.000) for 5573 atoms. Found 43 (67 requested) and removed 51 (51 requested) atoms. Cycle 19: After refmac, R = 0.1821 (Rfree = 0.000) for 5562 atoms. Found 60 (65 requested) and removed 51 (51 requested) atoms. Cycle 20: After refmac, R = 0.1789 (Rfree = 0.000) for 5568 atoms. Found 57 (63 requested) and removed 52 (51 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.42 2.59 NCS extension: 132 residues added (562 deleted due to clashes), 5710 seeds are put forward Round 1: 617 peptides, 25 chains. Longest chain 94 peptides. Score 0.912 Round 2: 617 peptides, 15 chains. Longest chain 134 peptides. Score 0.935 Round 3: 613 peptides, 24 chains. Longest chain 73 peptides. Score 0.913 Round 4: 613 peptides, 24 chains. Longest chain 92 peptides. Score 0.913 Round 5: 609 peptides, 25 chains. Longest chain 94 peptides. Score 0.909 Taking the results from Round 2 Chains 17, Residues 602, Estimated correctness of the model 99.0 % 8 chains (532 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 145 A and 151 A Built loop between residues 143 C and 148 C Built loop between residues 174 C and 178 C Built loop between residues 101 B and 107 B Built loop between residues 222 B and 225 B 11 chains (619 residues) following loop building 3 chains (551 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6199 restraints for refining 5558 atoms. 1622 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2020 (Rfree = 0.000) for 5558 atoms. Found 61 (61 requested) and removed 60 (50 requested) atoms. Cycle 22: After refmac, R = 0.1869 (Rfree = 0.000) for 5548 atoms. Found 59 (59 requested) and removed 52 (50 requested) atoms. Cycle 23: After refmac, R = 0.1793 (Rfree = 0.000) for 5553 atoms. Found 57 (57 requested) and removed 51 (50 requested) atoms. Cycle 24: After refmac, R = 0.1756 (Rfree = 0.000) for 5557 atoms. Found 55 (55 requested) and removed 53 (50 requested) atoms. Cycle 25: After refmac, R = 0.1737 (Rfree = 0.000) for 5556 atoms. Found 53 (53 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.44 2.61 NCS extension: 292 residues added (296 deleted due to clashes), 5852 seeds are put forward Round 1: 621 peptides, 17 chains. Longest chain 191 peptides. Score 0.932 Round 2: 615 peptides, 19 chains. Longest chain 116 peptides. Score 0.925 Round 3: 617 peptides, 20 chains. Longest chain 127 peptides. Score 0.924 Round 4: 611 peptides, 25 chains. Longest chain 145 peptides. Score 0.910 Round 5: 601 peptides, 28 chains. Longest chain 53 peptides. Score 0.898 Taking the results from Round 1 Chains 17, Residues 604, Estimated correctness of the model 99.0 % 9 chains (542 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 A and 43 A Built loop between residues 232 A and 235 A Built loop between residues 145 C and 151 C Built loop between residues 180 C and 183 C 13 chains (615 residues) following loop building 5 chains (553 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6143 restraints for refining 5558 atoms. 1551 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1959 (Rfree = 0.000) for 5558 atoms. Found 50 (50 requested) and removed 57 (50 requested) atoms. Cycle 27: After refmac, R = 0.1826 (Rfree = 0.000) for 5548 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 28: After refmac, R = 0.1782 (Rfree = 0.000) for 5543 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. Cycle 29: After refmac, R = 0.1758 (Rfree = 0.000) for 5537 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. Cycle 30: After refmac, R = 0.1736 (Rfree = 0.000) for 5536 atoms. Found 49 (50 requested) and removed 50 (50 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.43 2.60 NCS extension: 242 residues added (787 deleted due to clashes), 5786 seeds are put forward Round 1: 626 peptides, 21 chains. Longest chain 191 peptides. Score 0.925 Round 2: 630 peptides, 23 chains. Longest chain 94 peptides. Score 0.921 Round 3: 627 peptides, 19 chains. Longest chain 104 peptides. Score 0.929 Round 4: 613 peptides, 26 chains. Longest chain 122 peptides. Score 0.908 Round 5: 619 peptides, 23 chains. Longest chain 100 peptides. Score 0.917 Taking the results from Round 3 Chains 20, Residues 608, Estimated correctness of the model 98.9 % 11 chains (534 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 42 A Built loop between residues 178 A and 181 A Built loop between residues 200 C and 206 C Built loop between residues 232 C and 235 C Built loop between residues 133 B and 136 B 14 chains (617 residues) following loop building 6 chains (547 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6187 restraints for refining 5558 atoms. 1614 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2014 (Rfree = 0.000) for 5558 atoms. Found 50 (50 requested) and removed 70 (50 requested) atoms. Cycle 32: After refmac, R = 0.1831 (Rfree = 0.000) for 5533 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. Cycle 33: After refmac, R = 0.1777 (Rfree = 0.000) for 5529 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 34: After refmac, R = 0.1741 (Rfree = 0.000) for 5524 atoms. Found 49 (50 requested) and removed 51 (50 requested) atoms. Cycle 35: After refmac, R = 0.1712 (Rfree = 0.000) for 5518 atoms. Found 50 (50 requested) and removed 53 (50 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.43 2.60 NCS extension: 46 residues added (373 deleted due to clashes), 5568 seeds are put forward Round 1: 611 peptides, 28 chains. Longest chain 104 peptides. Score 0.902 Round 2: 620 peptides, 23 chains. Longest chain 82 peptides. Score 0.918 Round 3: 610 peptides, 19 chains. Longest chain 107 peptides. Score 0.924 Round 4: 618 peptides, 25 chains. Longest chain 90 peptides. Score 0.912 Round 5: 617 peptides, 24 chains. Longest chain 78 peptides. Score 0.914 Taking the results from Round 3 Chains 19, Residues 591, Estimated correctness of the model 98.7 % 11 chains (530 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 39 A and 43 A Built loop between residues 148 A and 151 A Built loop between residues 177 C and 181 C Built loop between residues 133 B and 136 B 15 chains (601 residues) following loop building 7 chains (540 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6299 restraints for refining 5558 atoms. 1832 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1944 (Rfree = 0.000) for 5558 atoms. Found 50 (50 requested) and removed 55 (50 requested) atoms. Cycle 37: After refmac, R = 0.1782 (Rfree = 0.000) for 5549 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 38: After refmac, R = 0.1732 (Rfree = 0.000) for 5544 atoms. Found 50 (50 requested) and removed 52 (50 requested) atoms. Cycle 39: After refmac, R = 0.1705 (Rfree = 0.000) for 5540 atoms. Found 50 (50 requested) and removed 53 (50 requested) atoms. Cycle 40: After refmac, R = 0.1675 (Rfree = 0.000) for 5535 atoms. Found 42 (50 requested) and removed 52 (50 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.45 2.62 NCS extension: 349 residues added (705 deleted due to clashes), 5879 seeds are put forward Round 1: 603 peptides, 24 chains. Longest chain 163 peptides. Score 0.909 Round 2: 615 peptides, 18 chains. Longest chain 98 peptides. Score 0.928 Round 3: 607 peptides, 27 chains. Longest chain 99 peptides. Score 0.903 Round 4: 611 peptides, 23 chains. Longest chain 109 peptides. Score 0.914 Round 5: 610 peptides, 24 chains. Longest chain 102 peptides. Score 0.912 Taking the results from Round 2 Chains 19, Residues 597, Estimated correctness of the model 98.8 % 12 chains (541 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A Built loop between residues 144 A and 151 A Built loop between residues 179 A and 183 A Built loop between residues 210 A and 213 A Built loop between residues 25 C and 28 C Built loop between residues 102 B and 107 B Built loop between residues 147 B and 150 B 12 chains (618 residues) following loop building 5 chains (562 residues) in sequence following loop building ------------------------------------------------------ 22751 reflections ( 85.61 % complete ) and 6010 restraints for refining 5558 atoms. 1386 conditional restraints added. Observations/parameters ratio is 1.02 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1962 (Rfree = 0.000) for 5558 atoms. Found 50 (50 requested) and removed 55 (50 requested) atoms. Cycle 42: After refmac, R = 0.1786 (Rfree = 0.000) for 5546 atoms. Found 50 (50 requested) and removed 54 (50 requested) atoms. Cycle 43: After refmac, R = 0.1714 (Rfree = 0.000) for 5539 atoms. Found 50 (50 requested) and removed 50 (50 requested) atoms. Cycle 44: After refmac, R = 0.1705 (Rfree = 0.000) for 5538 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. Cycle 45: After refmac, R = 0.1679 (Rfree = 0.000) for 5534 atoms. Found 50 (50 requested) and removed 51 (50 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.45 2.62 NCS extension: 521 residues added (468 deleted due to clashes), 6058 seeds are put forward Round 1: 603 peptides, 21 chains. Longest chain 126 peptides. Score 0.916 Round 2: 616 peptides, 18 chains. Longest chain 200 peptides. Score 0.928 Round 3: 600 peptides, 26 chains. Longest chain 80 peptides. Score 0.902 Round 4: 604 peptides, 22 chains. Longest chain 84 peptides. Score 0.914 Round 5: 597 peptides, 26 chains. Longest chain 64 peptides. Score 0.901 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 598, Estimated correctness of the model 98.8 % 10 chains (531 residues) have been docked in sequence Sequence coverage is 88 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 101 A and 104 A Built loop between residues 145 A and 151 A Built loop between residues 179 A and 183 A Built loop between residues 204 A and 213 A Built loop between residues 137 C and 148 C Built loop between residues 211 B and 224 B 9 chains (620 residues) following loop building 4 chains (571 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 22751 reflections ( 85.61 % complete ) and 4681 restraints for refining 4641 atoms. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2907 (Rfree = 0.000) for 4641 atoms. Found 37 (42 requested) and removed 0 (42 requested) atoms. Cycle 47: After refmac, R = 0.2700 (Rfree = 0.000) for 4641 atoms. Found 14 (42 requested) and removed 3 (42 requested) atoms. Cycle 48: After refmac, R = 0.2637 (Rfree = 0.000) for 4641 atoms. Found 6 (43 requested) and removed 2 (43 requested) atoms. Cycle 49: After refmac, R = 0.2592 (Rfree = 0.000) for 4641 atoms. Found 6 (43 requested) and removed 2 (43 requested) atoms. Writing output files ... TimeTaking 89.7