Mon 24 Dec 07:28:55 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 2ich-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ich-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ich-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-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/2ich-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-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 07:28:59 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/2ich-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-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 706 and 0 Target number of residues in the AU: 706 Target solvent content: 0.4810 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-2.0-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: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 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: 29.160 2.000 Wilson plot Bfac: 19.68 50384 reflections ( 99.43 % complete ) and 0 restraints for refining 5959 atoms. Observations/parameters ratio is 2.11 ------------------------------------------------------ Starting model: R = 0.3388 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2929 (Rfree = 0.000) for 5959 atoms. Found 199 (204 requested) and removed 115 (102 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.02 1.99 NCS extension: 0 residues added, 6043 seeds are put forward Round 1: 482 peptides, 49 chains. Longest chain 40 peptides. Score 0.721 Round 2: 554 peptides, 32 chains. Longest chain 53 peptides. Score 0.859 Round 3: 571 peptides, 27 chains. Longest chain 59 peptides. Score 0.885 Round 4: 568 peptides, 24 chains. Longest chain 84 peptides. Score 0.892 Round 5: 586 peptides, 17 chains. Longest chain 136 peptides. Score 0.919 Taking the results from Round 5 Chains 17, Residues 569, Estimated correctness of the model 99.3 % 12 chains (532 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 39 A Built loop between residues 93 A and 103 A Built loop between residues 157 B and 161 B Built loop between residues 200 B and 204 B Built loop between residues 289 B and 292 B Built loop between residues 317 B and 321 B 10 chains (592 residues) following loop building 6 chains (558 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5988 restraints for refining 5574 atoms. 1251 conditional restraints added. Observations/parameters ratio is 2.26 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3181 (Rfree = 0.000) for 5574 atoms. Found 190 (190 requested) and removed 120 (95 requested) atoms. Cycle 2: After refmac, R = 0.2834 (Rfree = 0.000) for 5623 atoms. Found 171 (189 requested) and removed 96 (96 requested) atoms. Cycle 3: After refmac, R = 0.2632 (Rfree = 0.000) for 5653 atoms. Found 138 (187 requested) and removed 47 (97 requested) atoms. Cycle 4: After refmac, R = 0.2477 (Rfree = 0.000) for 5714 atoms. Found 124 (188 requested) and removed 33 (98 requested) atoms. Failed to save intermediate PDB Cycle 5: After refmac, R = 0.2374 (Rfree = 0.000) for 5787 atoms. Found 111 (190 requested) and removed 49 (99 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.95 1.92 NCS extension: 28 residues added (39 deleted due to clashes), 5890 seeds are put forward Round 1: 600 peptides, 17 chains. Longest chain 134 peptides. Score 0.924 Round 2: 604 peptides, 12 chains. Longest chain 143 peptides. Score 0.937 Round 3: 602 peptides, 13 chains. Longest chain 167 peptides. Score 0.934 Round 4: 607 peptides, 9 chains. Longest chain 149 peptides. Score 0.944 Round 5: 609 peptides, 13 chains. Longest chain 177 peptides. Score 0.936 Taking the results from Round 4 Chains 9, Residues 598, Estimated correctness of the model 99.6 % 9 chains (598 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 93 A and 96 A Built loop between residues 154 A and 159 A Built loop between residues 185 A and 188 A Built loop between residues 319 A and 322 A Built loop between residues 177 B and 182 B 4 chains (612 residues) following loop building 4 chains (612 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5606 restraints for refining 5720 atoms. 576 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2528 (Rfree = 0.000) for 5720 atoms. Found 164 (187 requested) and removed 104 (97 requested) atoms. Cycle 7: After refmac, R = 0.2291 (Rfree = 0.000) for 5775 atoms. Found 122 (186 requested) and removed 40 (99 requested) atoms. Cycle 8: After refmac, R = 0.2172 (Rfree = 0.000) for 5842 atoms. Found 115 (188 requested) and removed 47 (100 requested) atoms. Cycle 9: After refmac, R = 0.2078 (Rfree = 0.000) for 5898 atoms. Found 123 (190 requested) and removed 58 (101 requested) atoms. Cycle 10: After refmac, R = 0.2029 (Rfree = 0.000) for 5953 atoms. Found 113 (192 requested) and removed 80 (102 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.94 1.91 NCS extension: 7 residues added (32 deleted due to clashes), 5995 seeds are put forward Round 1: 614 peptides, 11 chains. Longest chain 149 peptides. Score 0.942 Round 2: 610 peptides, 13 chains. Longest chain 144 peptides. Score 0.936 Round 3: 617 peptides, 11 chains. Longest chain 149 peptides. Score 0.943 Round 4: 616 peptides, 13 chains. Longest chain 177 peptides. Score 0.938 Round 5: 617 peptides, 12 chains. Longest chain 151 peptides. Score 0.941 Taking the results from Round 3 Chains 11, Residues 606, Estimated correctness of the model 99.6 % 10 chains (597 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 177 A and 181 A Built loop between residues 319 A and 323 A Built loop between residues 13 B and 16 B Built loop between residues 31 B and 34 B Built loop between residues 95 B and 98 B Built loop between residues 177 B and 182 B 5 chains (622 residues) following loop building 4 chains (613 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5666 restraints for refining 5812 atoms. 596 conditional restraints added. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2174 (Rfree = 0.000) for 5812 atoms. Found 183 (183 requested) and removed 90 (99 requested) atoms. Cycle 12: After refmac, R = 0.2057 (Rfree = 0.000) for 5896 atoms. Found 111 (186 requested) and removed 58 (101 requested) atoms. Cycle 13: After refmac, R = 0.1972 (Rfree = 0.000) for 5947 atoms. Found 115 (183 requested) and removed 45 (101 requested) atoms. Cycle 14: After refmac, R = 0.1929 (Rfree = 0.000) for 6011 atoms. Found 93 (185 requested) and removed 74 (103 requested) atoms. Cycle 15: After refmac, R = 0.1897 (Rfree = 0.000) for 6020 atoms. Found 126 (181 requested) and removed 68 (103 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.93 1.90 NCS extension: 282 residues added (19 deleted due to clashes), 6361 seeds are put forward Round 1: 619 peptides, 11 chains. Longest chain 227 peptides. Score 0.943 Round 2: 620 peptides, 9 chains. Longest chain 217 peptides. Score 0.948 Round 3: 614 peptides, 16 chains. Longest chain 133 peptides. Score 0.931 Round 4: 615 peptides, 14 chains. Longest chain 151 peptides. Score 0.936 Round 5: 620 peptides, 10 chains. Longest chain 252 peptides. Score 0.946 Taking the results from Round 2 Chains 12, Residues 611, Estimated correctness of the model 99.7 % 8 chains (585 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 145 A and 148 A Built loop between residues 176 A and 183 A Built loop between residues 101 B and 104 B Built loop between residues 319 B and 323 B 7 chains (619 residues) following loop building 4 chains (598 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5748 restraints for refining 5834 atoms. 747 conditional restraints added. Observations/parameters ratio is 2.16 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2063 (Rfree = 0.000) for 5834 atoms. Found 171 (171 requested) and removed 65 (99 requested) atoms. Cycle 17: After refmac, R = 0.1950 (Rfree = 0.000) for 5934 atoms. Found 130 (175 requested) and removed 67 (101 requested) atoms. Cycle 18: After refmac, R = 0.1909 (Rfree = 0.000) for 5986 atoms. Found 115 (172 requested) and removed 59 (102 requested) atoms. Cycle 19: After refmac, R = 0.1881 (Rfree = 0.000) for 6036 atoms. Found 119 (169 requested) and removed 66 (103 requested) atoms. Cycle 20: After refmac, R = 0.1858 (Rfree = 0.000) for 6086 atoms. Found 113 (166 requested) and removed 81 (104 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.93 1.90 NCS extension: 261 residues added (15 deleted due to clashes), 6380 seeds are put forward Round 1: 614 peptides, 12 chains. Longest chain 149 peptides. Score 0.940 Round 2: 619 peptides, 11 chains. Longest chain 144 peptides. Score 0.943 Round 3: 616 peptides, 15 chains. Longest chain 138 peptides. Score 0.934 Round 4: 620 peptides, 12 chains. Longest chain 151 peptides. Score 0.942 Round 5: 610 peptides, 18 chains. Longest chain 125 peptides. Score 0.925 Taking the results from Round 2 Chains 11, Residues 608, Estimated correctness of the model 99.6 % 10 chains (603 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 13 A and 16 A Built loop between residues 162 A and 165 A Built loop between residues 177 A and 188 A Built loop between residues 13 B and 16 B Built loop between residues 96 B and 100 B Built loop between residues 185 B and 188 B 4 chains (624 residues) following loop building 4 chains (624 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5750 restraints for refining 5948 atoms. 630 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2109 (Rfree = 0.000) for 5948 atoms. Found 158 (158 requested) and removed 113 (101 requested) atoms. Cycle 22: After refmac, R = 0.1971 (Rfree = 0.000) for 5986 atoms. Found 123 (156 requested) and removed 62 (102 requested) atoms. Cycle 23: After refmac, R = 0.1913 (Rfree = 0.000) for 6041 atoms. Found 124 (153 requested) and removed 63 (103 requested) atoms. Cycle 24: After refmac, R = 0.1881 (Rfree = 0.000) for 6100 atoms. Found 125 (150 requested) and removed 87 (104 requested) atoms. Cycle 25: After refmac, R = 0.1871 (Rfree = 0.000) for 6132 atoms. Found 115 (147 requested) and removed 110 (105 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 6141 seeds are put forward Round 1: 619 peptides, 11 chains. Longest chain 219 peptides. Score 0.943 Round 2: 620 peptides, 11 chains. Longest chain 219 peptides. Score 0.944 Round 3: 618 peptides, 14 chains. Longest chain 139 peptides. Score 0.937 Round 4: 616 peptides, 11 chains. Longest chain 149 peptides. Score 0.943 Round 5: 615 peptides, 16 chains. Longest chain 215 peptides. Score 0.931 Taking the results from Round 2 Chains 11, Residues 609, Estimated correctness of the model 99.6 % 9 chains (595 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 165 A Built loop between residues 177 A and 188 A Built loop between residues 99 B and 102 B Built loop between residues 319 B and 322 B 6 chains (621 residues) following loop building 5 chains (611 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5773 restraints for refining 5883 atoms. 720 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2063 (Rfree = 0.000) for 5883 atoms. Found 137 (137 requested) and removed 70 (100 requested) atoms. Cycle 27: After refmac, R = 0.1953 (Rfree = 0.000) for 5942 atoms. Found 134 (134 requested) and removed 35 (101 requested) atoms. Cycle 28: After refmac, R = 0.1900 (Rfree = 0.000) for 6036 atoms. Found 109 (136 requested) and removed 71 (103 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1876 (Rfree = 0.000) for 6070 atoms. Found 110 (133 requested) and removed 77 (104 requested) atoms. Cycle 30: After refmac, R = 0.1857 (Rfree = 0.000) for 6096 atoms. Found 113 (130 requested) and removed 78 (104 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.90 NCS extension: 30 residues added (256 deleted due to clashes), 6164 seeds are put forward Round 1: 617 peptides, 12 chains. Longest chain 149 peptides. Score 0.941 Round 2: 617 peptides, 10 chains. Longest chain 151 peptides. Score 0.945 Round 3: 611 peptides, 16 chains. Longest chain 133 peptides. Score 0.930 Round 4: 619 peptides, 10 chains. Longest chain 151 peptides. Score 0.945 Round 5: 615 peptides, 13 chains. Longest chain 132 peptides. Score 0.938 Taking the results from Round 4 Chains 11, Residues 609, Estimated correctness of the model 99.6 % 9 chains (599 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 95 A and 98 A Built loop between residues 177 A and 181 A Built loop between residues 13 B and 16 B Built loop between residues 102 B and 105 B Built loop between residues 177 B and 181 B 6 chains (621 residues) following loop building 4 chains (611 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5753 restraints for refining 5887 atoms. 696 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2028 (Rfree = 0.000) for 5887 atoms. Found 121 (121 requested) and removed 70 (100 requested) atoms. Cycle 32: After refmac, R = 0.1923 (Rfree = 0.000) for 5927 atoms. Found 112 (118 requested) and removed 40 (101 requested) atoms. Cycle 33: After refmac, R = 0.1866 (Rfree = 0.000) for 5995 atoms. Found 102 (119 requested) and removed 44 (102 requested) atoms. Cycle 34: After refmac, R = 0.1832 (Rfree = 0.000) for 6048 atoms. Found 106 (120 requested) and removed 69 (103 requested) atoms. Cycle 35: After refmac, R = 0.1814 (Rfree = 0.000) for 6076 atoms. Found 116 (116 requested) and removed 87 (104 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.92 1.89 NCS extension: 3 residues added (35 deleted due to clashes), 6112 seeds are put forward Round 1: 611 peptides, 15 chains. Longest chain 140 peptides. Score 0.932 Round 2: 623 peptides, 9 chains. Longest chain 151 peptides. Score 0.948 Round 3: 618 peptides, 12 chains. Longest chain 151 peptides. Score 0.941 Round 4: 620 peptides, 12 chains. Longest chain 149 peptides. Score 0.942 Round 5: 620 peptides, 12 chains. Longest chain 151 peptides. Score 0.942 Taking the results from Round 2 Chains 9, Residues 614, Estimated correctness of the model 99.7 % 7 chains (594 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 177 A and 181 A Built loop between residues 101 B and 104 B Built loop between residues 177 B and 181 B 6 chains (622 residues) following loop building 4 chains (602 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5780 restraints for refining 5880 atoms. 752 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2031 (Rfree = 0.000) for 5880 atoms. Found 109 (109 requested) and removed 65 (100 requested) atoms. Cycle 37: After refmac, R = 0.1931 (Rfree = 0.000) for 5915 atoms. Found 105 (105 requested) and removed 35 (101 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1881 (Rfree = 0.000) for 5981 atoms. Found 96 (107 requested) and removed 59 (102 requested) atoms. Cycle 39: After refmac, R = 0.1850 (Rfree = 0.000) for 6010 atoms. Found 102 (103 requested) and removed 62 (103 requested) atoms. Cycle 40: After refmac, R = 0.1836 (Rfree = 0.000) for 6042 atoms. Found 97 (103 requested) and removed 69 (103 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.93 1.90 NCS extension: 11 residues added (253 deleted due to clashes), 6085 seeds are put forward Round 1: 617 peptides, 12 chains. Longest chain 151 peptides. Score 0.941 Round 2: 620 peptides, 11 chains. Longest chain 217 peptides. Score 0.944 Round 3: 617 peptides, 13 chains. Longest chain 225 peptides. Score 0.939 Round 4: 616 peptides, 14 chains. Longest chain 144 peptides. Score 0.936 Round 5: 616 peptides, 12 chains. Longest chain 133 peptides. Score 0.940 Taking the results from Round 2 Chains 11, Residues 609, Estimated correctness of the model 99.6 % 9 chains (595 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 188 A Built loop between residues 319 A and 322 A Built loop between residues 13 B and 16 B Built loop between residues 101 B and 104 B Built loop between residues 319 B and 322 B 5 chains (622 residues) following loop building 4 chains (612 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5775 restraints for refining 5878 atoms. 710 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2037 (Rfree = 0.000) for 5878 atoms. Found 100 (100 requested) and removed 73 (100 requested) atoms. Cycle 42: After refmac, R = 0.1922 (Rfree = 0.000) for 5900 atoms. Found 101 (101 requested) and removed 28 (101 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1864 (Rfree = 0.000) for 5972 atoms. Found 100 (102 requested) and removed 34 (102 requested) atoms. Cycle 44: After refmac, R = 0.1830 (Rfree = 0.000) for 6036 atoms. Found 98 (103 requested) and removed 71 (103 requested) atoms. Cycle 45: After refmac, R = 0.1812 (Rfree = 0.000) for 6060 atoms. Found 103 (103 requested) and removed 60 (103 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.90 NCS extension: 3 residues added (35 deleted due to clashes), 6108 seeds are put forward Round 1: 615 peptides, 12 chains. Longest chain 151 peptides. Score 0.940 Round 2: 618 peptides, 11 chains. Longest chain 142 peptides. Score 0.943 Round 3: 611 peptides, 15 chains. Longest chain 150 peptides. Score 0.932 Round 4: 618 peptides, 11 chains. Longest chain 177 peptides. Score 0.943 Round 5: 618 peptides, 11 chains. Longest chain 155 peptides. Score 0.943 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 607, Estimated correctness of the model 99.6 % 12 chains (596 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 13 A and 16 A Built loop between residues 156 A and 159 A Built loop between residues 177 A and 181 A Built loop between residues 13 B and 16 B Built loop between residues 93 B and 96 B Built loop between residues 161 B and 164 B Built loop between residues 177 B and 189 B Built loop between residues 318 B and 321 B 5 chains (623 residues) following loop building 4 chains (622 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 50384 reflections ( 99.43 % complete ) and 5103 restraints for refining 4958 atoms. Observations/parameters ratio is 2.54 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2672 (Rfree = 0.000) for 4958 atoms. Found 84 (84 requested) and removed 0 (84 requested) atoms. Cycle 47: After refmac, R = 0.2525 (Rfree = 0.000) for 4958 atoms. Found 67 (86 requested) and removed 3 (86 requested) atoms. Cycle 48: After refmac, R = 0.2403 (Rfree = 0.000) for 4958 atoms. Found 40 (87 requested) and removed 3 (87 requested) atoms. Cycle 49: After refmac, R = 0.2325 (Rfree = 0.000) for 4958 atoms. TimeTaking 80.82