Mon 24 Dec 07:48:16 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 2it9-1.9-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2it9-1.9-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2it9-1.9-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-1.9-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/2it9-1.9-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-1.9-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 07:48:21 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/2it9-1.9-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2it9-1.9-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 556 and 0 Target number of residues in the AU: 556 Target solvent content: 0.4999 Checking the provided sequence file Detected sequence length: 127 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 508 Adjusted target solvent content: 0.54 Input MTZ file: 2it9-1.9-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: 19 Cell parameters: 59.723 81.014 124.347 90.000 90.000 90.000 Input sequence file: 2it9-1.9-parrot-noncs.fasta_lf Building free atoms model in initial map for 4064 target number of atoms Had to go as low as 0.60 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: 67.879 1.900 Wilson plot Bfac: 23.36 48134 reflections ( 99.64 % complete ) and 0 restraints for refining 4488 atoms. Observations/parameters ratio is 2.68 ------------------------------------------------------ Starting model: R = 0.3777 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3247 (Rfree = 0.000) for 4488 atoms. Found 149 (177 requested) and removed 98 (88 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.07 1.96 NCS extension: 0 residues added, 4539 seeds are put forward Round 1: 328 peptides, 47 chains. Longest chain 21 peptides. Score 0.546 Round 2: 346 peptides, 35 chains. Longest chain 23 peptides. Score 0.684 Round 3: 360 peptides, 25 chains. Longest chain 33 peptides. Score 0.774 Round 4: 371 peptides, 24 chains. Longest chain 37 peptides. Score 0.793 Round 5: 386 peptides, 25 chains. Longest chain 54 peptides. Score 0.804 Taking the results from Round 5 Chains 30, Residues 361, Estimated correctness of the model 97.0 % 9 chains (227 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 77 A Built loop between residues 92 A and 99 A Built loop between residues 93 B and 102 B 24 chains (371 residues) following loop building 6 chains (244 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 6008 restraints for refining 4190 atoms. 3483 conditional restraints added. Observations/parameters ratio is 2.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3389 (Rfree = 0.000) for 4190 atoms. Found 166 (166 requested) and removed 94 (83 requested) atoms. Cycle 2: After refmac, R = 0.3062 (Rfree = 0.000) for 4240 atoms. Found 133 (165 requested) and removed 86 (84 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2862 (Rfree = 0.000) for 4275 atoms. Found 110 (162 requested) and removed 52 (84 requested) atoms. Cycle 4: After refmac, R = 0.2718 (Rfree = 0.000) for 4324 atoms. Found 105 (164 requested) and removed 42 (85 requested) atoms. Cycle 5: After refmac, R = 0.2605 (Rfree = 0.000) for 4379 atoms. Found 97 (166 requested) and removed 44 (86 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.00 1.90 NCS extension: 43 residues added (68 deleted due to clashes), 4489 seeds are put forward Round 1: 415 peptides, 24 chains. Longest chain 60 peptides. Score 0.838 Round 2: 427 peptides, 16 chains. Longest chain 85 peptides. Score 0.882 Round 3: 433 peptides, 19 chains. Longest chain 63 peptides. Score 0.874 Round 4: 441 peptides, 16 chains. Longest chain 102 peptides. Score 0.891 Round 5: 440 peptides, 17 chains. Longest chain 89 peptides. Score 0.887 Taking the results from Round 4 Chains 20, Residues 425, Estimated correctness of the model 99.0 % 13 chains (395 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 12 A and 18 A Built loop between residues 59 A and 64 A Built loop between residues 13 C and 20 C Built loop between residues 94 B and 100 B Built loop between residues 107 B and 110 B Built loop between residues 28 D and 32 D Built loop between residues 94 D and 98 D 12 chains (451 residues) following loop building 6 chains (423 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4797 restraints for refining 4531 atoms. 1153 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2664 (Rfree = 0.000) for 4531 atoms. Found 143 (172 requested) and removed 97 (89 requested) atoms. Cycle 7: After refmac, R = 0.2416 (Rfree = 0.000) for 4565 atoms. Found 104 (170 requested) and removed 90 (90 requested) atoms. Cycle 8: After refmac, R = 0.2267 (Rfree = 0.000) for 4572 atoms. Found 100 (167 requested) and removed 56 (90 requested) atoms. Cycle 9: After refmac, R = 0.2153 (Rfree = 0.000) for 4610 atoms. Found 85 (165 requested) and removed 61 (91 requested) atoms. Cycle 10: After refmac, R = 0.2089 (Rfree = 0.000) for 4623 atoms. Found 98 (161 requested) and removed 59 (91 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.99 1.89 NCS extension: 25 residues added (79 deleted due to clashes), 4693 seeds are put forward Round 1: 450 peptides, 17 chains. Longest chain 72 peptides. Score 0.893 Round 2: 459 peptides, 13 chains. Longest chain 102 peptides. Score 0.912 Round 3: 459 peptides, 14 chains. Longest chain 79 peptides. Score 0.909 Round 4: 460 peptides, 15 chains. Longest chain 56 peptides. Score 0.906 Round 5: 457 peptides, 14 chains. Longest chain 79 peptides. Score 0.908 Taking the results from Round 2 Chains 18, Residues 446, Estimated correctness of the model 99.3 % 12 chains (419 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 99 A Built loop between residues 18 C and 21 C Built loop between residues 14 B and 18 B Built loop between residues 60 B and 64 B Built loop between residues 18 D and 21 D 12 chains (459 residues) following loop building 7 chains (434 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4714 restraints for refining 4532 atoms. 997 conditional restraints added. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2257 (Rfree = 0.000) for 4532 atoms. Found 128 (154 requested) and removed 95 (89 requested) atoms. Cycle 12: After refmac, R = 0.2120 (Rfree = 0.000) for 4562 atoms. Found 105 (152 requested) and removed 58 (90 requested) atoms. Cycle 13: After refmac, R = 0.2028 (Rfree = 0.000) for 4604 atoms. Found 91 (149 requested) and removed 47 (91 requested) atoms. Cycle 14: After refmac, R = 0.1980 (Rfree = 0.000) for 4643 atoms. Found 88 (147 requested) and removed 58 (92 requested) atoms. Cycle 15: After refmac, R = 0.1923 (Rfree = 0.000) for 4672 atoms. Found 80 (144 requested) and removed 46 (92 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.00 1.90 NCS extension: 15 residues added (64 deleted due to clashes), 4729 seeds are put forward Round 1: 460 peptides, 14 chains. Longest chain 100 peptides. Score 0.909 Round 2: 463 peptides, 9 chains. Longest chain 117 peptides. Score 0.927 Round 3: 465 peptides, 11 chains. Longest chain 101 peptides. Score 0.921 Round 4: 464 peptides, 12 chains. Longest chain 117 peptides. Score 0.918 Round 5: 464 peptides, 12 chains. Longest chain 92 peptides. Score 0.918 Taking the results from Round 2 Chains 10, Residues 454, Estimated correctness of the model 99.5 % 8 chains (439 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 92 C and 99 C Built loop between residues 78 B and 82 B Built loop between residues 70 D and 76 D 6 chains (465 residues) following loop building 5 chains (453 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4581 restraints for refining 4571 atoms. 748 conditional restraints added. Observations/parameters ratio is 2.63 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2152 (Rfree = 0.000) for 4571 atoms. Found 132 (138 requested) and removed 93 (90 requested) atoms. Cycle 17: After refmac, R = 0.2020 (Rfree = 0.000) for 4603 atoms. Found 103 (135 requested) and removed 46 (91 requested) atoms. Cycle 18: After refmac, R = 0.1938 (Rfree = 0.000) for 4656 atoms. Found 85 (136 requested) and removed 46 (92 requested) atoms. Cycle 19: After refmac, R = 0.1892 (Rfree = 0.000) for 4692 atoms. Found 75 (134 requested) and removed 59 (93 requested) atoms. Cycle 20: After refmac, R = 0.1870 (Rfree = 0.000) for 4698 atoms. Found 85 (130 requested) and removed 60 (93 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 1.89 NCS extension: 33 residues added (95 deleted due to clashes), 4761 seeds are put forward Round 1: 466 peptides, 9 chains. Longest chain 119 peptides. Score 0.928 Round 2: 468 peptides, 9 chains. Longest chain 118 peptides. Score 0.929 Round 3: 467 peptides, 11 chains. Longest chain 101 peptides. Score 0.922 Round 4: 463 peptides, 13 chains. Longest chain 73 peptides. Score 0.914 Round 5: 469 peptides, 9 chains. Longest chain 106 peptides. Score 0.929 Taking the results from Round 5 Chains 11, Residues 460, Estimated correctness of the model 99.5 % 9 chains (457 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 A and 111 A Built loop between residues 80 C and 83 C Built loop between residues 92 C and 99 C Built loop between residues 73 B and 78 B Built loop between residues 80 D and 83 D 5 chains (474 residues) following loop building 4 chains (473 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4396 restraints for refining 4593 atoms. 441 conditional restraints added. Observations/parameters ratio is 2.62 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2141 (Rfree = 0.000) for 4593 atoms. Found 124 (124 requested) and removed 97 (91 requested) atoms. Cycle 22: After refmac, R = 0.2006 (Rfree = 0.000) for 4615 atoms. Found 121 (121 requested) and removed 47 (91 requested) atoms. Cycle 23: After refmac, R = 0.1928 (Rfree = 0.000) for 4687 atoms. Found 92 (122 requested) and removed 52 (92 requested) atoms. Cycle 24: After refmac, R = 0.1884 (Rfree = 0.000) for 4721 atoms. Found 88 (120 requested) and removed 52 (93 requested) atoms. Cycle 25: After refmac, R = 0.1863 (Rfree = 0.000) for 4746 atoms. Found 83 (117 requested) and removed 60 (94 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 1.89 NCS extension: 6 residues added (11 deleted due to clashes), 4777 seeds are put forward Round 1: 469 peptides, 9 chains. Longest chain 103 peptides. Score 0.929 Round 2: 467 peptides, 11 chains. Longest chain 119 peptides. Score 0.922 Round 3: 471 peptides, 7 chains. Longest chain 119 peptides. Score 0.936 Round 4: 466 peptides, 12 chains. Longest chain 78 peptides. Score 0.919 Round 5: 469 peptides, 11 chains. Longest chain 92 peptides. Score 0.923 Taking the results from Round 3 Chains 9, Residues 464, Estimated correctness of the model 99.6 % 7 chains (460 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 C and 99 C Built loop between residues 70 B and 76 B Built loop between residues 80 D and 83 D 5 chains (473 residues) following loop building 4 chains (472 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4414 restraints for refining 4631 atoms. 467 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2113 (Rfree = 0.000) for 4631 atoms. Found 110 (110 requested) and removed 96 (91 requested) atoms. Cycle 27: After refmac, R = 0.1976 (Rfree = 0.000) for 4642 atoms. Found 105 (107 requested) and removed 51 (92 requested) atoms. Cycle 28: After refmac, R = 0.1909 (Rfree = 0.000) for 4695 atoms. Found 79 (108 requested) and removed 50 (93 requested) atoms. Cycle 29: After refmac, R = 0.1864 (Rfree = 0.000) for 4721 atoms. Found 90 (105 requested) and removed 53 (93 requested) atoms. Cycle 30: After refmac, R = 0.1835 (Rfree = 0.000) for 4756 atoms. Found 100 (102 requested) and removed 62 (94 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 1.89 NCS extension: 12 residues added (63 deleted due to clashes), 4814 seeds are put forward Round 1: 469 peptides, 9 chains. Longest chain 119 peptides. Score 0.929 Round 2: 470 peptides, 8 chains. Longest chain 119 peptides. Score 0.933 Round 3: 468 peptides, 10 chains. Longest chain 79 peptides. Score 0.926 Round 4: 467 peptides, 11 chains. Longest chain 93 peptides. Score 0.922 Round 5: 467 peptides, 11 chains. Longest chain 119 peptides. Score 0.922 Taking the results from Round 2 Chains 11, Residues 462, Estimated correctness of the model 99.6 % 8 chains (455 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 76 A Built loop between residues 93 A and 99 A Built loop between residues 67 C and 74 C Built loop between residues 73 D and 78 D 5 chains (473 residues) following loop building 4 chains (472 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4418 restraints for refining 4624 atoms. 471 conditional restraints added. Observations/parameters ratio is 2.60 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2107 (Rfree = 0.000) for 4624 atoms. Found 95 (95 requested) and removed 100 (91 requested) atoms. Cycle 32: After refmac, R = 0.1957 (Rfree = 0.000) for 4610 atoms. Found 91 (91 requested) and removed 38 (91 requested) atoms. Cycle 33: After refmac, R = 0.1886 (Rfree = 0.000) for 4661 atoms. Found 76 (92 requested) and removed 42 (92 requested) atoms. Cycle 34: After refmac, R = 0.1851 (Rfree = 0.000) for 4689 atoms. Found 80 (93 requested) and removed 46 (93 requested) atoms. Cycle 35: After refmac, R = 0.1824 (Rfree = 0.000) for 4717 atoms. Found 92 (93 requested) and removed 43 (93 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.00 1.90 NCS extension: 11 residues added (63 deleted due to clashes), 4786 seeds are put forward Round 1: 467 peptides, 10 chains. Longest chain 103 peptides. Score 0.925 Round 2: 466 peptides, 12 chains. Longest chain 79 peptides. Score 0.919 Round 3: 468 peptides, 10 chains. Longest chain 119 peptides. Score 0.926 Round 4: 465 peptides, 12 chains. Longest chain 73 peptides. Score 0.918 Round 5: 467 peptides, 11 chains. Longest chain 74 peptides. Score 0.922 Taking the results from Round 3 Chains 11, Residues 458, Estimated correctness of the model 99.5 % 8 chains (449 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 82 A Built loop between residues 73 C and 82 C Built loop between residues 93 C and 99 C Built loop between residues 71 B and 75 B 6 chains (475 residues) following loop building 4 chains (473 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4433 restraints for refining 4643 atoms. 475 conditional restraints added. Observations/parameters ratio is 2.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2157 (Rfree = 0.000) for 4643 atoms. Found 92 (92 requested) and removed 100 (92 requested) atoms. Cycle 37: After refmac, R = 0.1999 (Rfree = 0.000) for 4630 atoms. Found 91 (91 requested) and removed 47 (91 requested) atoms. Cycle 38: After refmac, R = 0.1929 (Rfree = 0.000) for 4670 atoms. Found 67 (92 requested) and removed 39 (92 requested) atoms. Cycle 39: After refmac, R = 0.1893 (Rfree = 0.000) for 4693 atoms. Found 69 (93 requested) and removed 29 (93 requested) atoms. Cycle 40: After refmac, R = 0.1855 (Rfree = 0.000) for 4730 atoms. Found 65 (93 requested) and removed 46 (93 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.00 1.90 NCS extension: 24 residues added (94 deleted due to clashes), 4778 seeds are put forward Round 1: 460 peptides, 13 chains. Longest chain 102 peptides. Score 0.913 Round 2: 465 peptides, 11 chains. Longest chain 79 peptides. Score 0.921 Round 3: 463 peptides, 12 chains. Longest chain 72 peptides. Score 0.917 Round 4: 467 peptides, 10 chains. Longest chain 79 peptides. Score 0.925 Round 5: 467 peptides, 10 chains. Longest chain 120 peptides. Score 0.925 Taking the results from Round 5 Chains 11, Residues 457, Estimated correctness of the model 99.5 % 9 chains (450 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 82 A Built loop between residues 93 A and 99 A Built loop between residues 16 C and 19 C Built loop between residues 71 C and 75 C Built loop between residues 73 D and 78 D 4 chains (473 residues) following loop building 4 chains (473 residues) in sequence following loop building ------------------------------------------------------ 48134 reflections ( 99.64 % complete ) and 4421 restraints for refining 4615 atoms. 467 conditional restraints added. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2132 (Rfree = 0.000) for 4615 atoms. Found 91 (91 requested) and removed 99 (91 requested) atoms. Cycle 42: After refmac, R = 0.1997 (Rfree = 0.000) for 4599 atoms. Found 91 (91 requested) and removed 33 (91 requested) atoms. Cycle 43: After refmac, R = 0.1935 (Rfree = 0.000) for 4653 atoms. Found 65 (92 requested) and removed 31 (92 requested) atoms. Cycle 44: After refmac, R = 0.1890 (Rfree = 0.000) for 4681 atoms. Found 79 (92 requested) and removed 32 (92 requested) atoms. Cycle 45: After refmac, R = 0.1868 (Rfree = 0.000) for 4726 atoms. Found 73 (93 requested) and removed 46 (93 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.00 1.90 NCS extension: 28 residues added (96 deleted due to clashes), 4788 seeds are put forward Round 1: 467 peptides, 10 chains. Longest chain 120 peptides. Score 0.925 Round 2: 465 peptides, 15 chains. Longest chain 73 peptides. Score 0.909 Round 3: 471 peptides, 11 chains. Longest chain 101 peptides. Score 0.924 Round 4: 468 peptides, 12 chains. Longest chain 92 peptides. Score 0.920 Round 5: 462 peptides, 15 chains. Longest chain 75 peptides. Score 0.907 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 457, Estimated correctness of the model 99.5 % 10 chains (452 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 18 A and 21 A Built loop between residues 69 A and 75 A Built loop between residues 71 C and 75 C Built loop between residues 108 C and 111 C Built loop between residues 73 D and 77 D Built loop between residues 93 D and 100 D 4 chains (473 residues) following loop building 4 chains (473 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 48134 reflections ( 99.64 % complete ) and 3954 restraints for refining 3870 atoms. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2672 (Rfree = 0.000) for 3870 atoms. Found 76 (76 requested) and removed 0 (76 requested) atoms. Cycle 47: After refmac, R = 0.2472 (Rfree = 0.000) for 3870 atoms. Found 43 (78 requested) and removed 0 (78 requested) atoms. Cycle 48: After refmac, R = 0.2319 (Rfree = 0.000) for 3870 atoms. Found 29 (79 requested) and removed 2 (79 requested) atoms. Cycle 49: After refmac, R = 0.2277 (Rfree = 0.000) for 3870 atoms. TimeTaking 69.28