Sun 23 Dec 22:23:01 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ich-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ich-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ich-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-parrot-hancs ############### 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 22:23:11 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/hancs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ich-2.0-parrot-hancs/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-hancs.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-hancs.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 5977 atoms. Observations/parameters ratio is 2.11 ------------------------------------------------------ Starting model: R = 0.3298 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2783 (Rfree = 0.000) for 5977 atoms. Found 204 (204 requested) and removed 107 (102 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.02 1.99 NCS extension: 0 residues added, 6074 seeds are put forward Round 1: 530 peptides, 45 chains. Longest chain 38 peptides. Score 0.790 Round 2: 570 peptides, 27 chains. Longest chain 94 peptides. Score 0.884 Round 3: 600 peptides, 20 chains. Longest chain 100 peptides. Score 0.917 Round 4: 604 peptides, 17 chains. Longest chain 144 peptides. Score 0.925 Round 5: 611 peptides, 15 chains. Longest chain 151 peptides. Score 0.932 Taking the results from Round 5 Chains 16, Residues 596, Estimated correctness of the model 99.5 % 14 chains (583 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 10 A and 15 A Built loop between residues 31 A and 34 A Built loop between residues 92 A and 98 A Built loop between residues 177 A and 181 A Built loop between residues 101 B and 104 B Built loop between residues 148 B and 151 B Built loop between residues 198 B and 204 B Built loop between residues 302 B and 305 B Built loop between residues 319 B and 322 B 6 chains (619 residues) following loop building 5 chains (610 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5656 restraints for refining 5618 atoms. 605 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2959 (Rfree = 0.000) for 5618 atoms. Found 180 (192 requested) and removed 111 (96 requested) atoms. Cycle 2: After refmac, R = 0.2597 (Rfree = 0.000) for 5672 atoms. Found 161 (190 requested) and removed 70 (97 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2391 (Rfree = 0.000) for 5732 atoms. Found 135 (193 requested) and removed 52 (98 requested) atoms. Cycle 4: After refmac, R = 0.2250 (Rfree = 0.000) for 5790 atoms. Found 124 (195 requested) and removed 28 (99 requested) atoms. Cycle 5: After refmac, R = 0.2159 (Rfree = 0.000) for 5868 atoms. Found 113 (197 requested) and removed 51 (100 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.94 1.91 NCS extension: 14 residues added (252 deleted due to clashes), 5949 seeds are put forward Round 1: 613 peptides, 14 chains. Longest chain 140 peptides. Score 0.935 Round 2: 620 peptides, 11 chains. Longest chain 151 peptides. Score 0.944 Round 3: 618 peptides, 12 chains. Longest chain 151 peptides. Score 0.941 Round 4: 620 peptides, 11 chains. Longest chain 233 peptides. Score 0.944 Round 5: 604 peptides, 17 chains. Longest chain 140 peptides. Score 0.925 Taking the results from Round 4 Chains 15, Residues 609, Estimated correctness of the model 99.6 % 11 chains (590 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 94 A and 98 A Built loop between residues 176 A and 183 A Built loop between residues 95 B and 98 B Built loop between residues 149 B and 152 B Built loop between residues 176 B and 179 B Built loop between residues 302 B and 305 B 7 chains (620 residues) following loop building 5 chains (607 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5717 restraints for refining 5771 atoms. 680 conditional restraints added. Observations/parameters ratio is 2.18 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2259 (Rfree = 0.000) for 5771 atoms. Found 167 (193 requested) and removed 101 (98 requested) atoms. Cycle 7: After refmac, R = 0.2117 (Rfree = 0.000) for 5822 atoms. Found 123 (191 requested) and removed 46 (99 requested) atoms. Cycle 8: After refmac, R = 0.2028 (Rfree = 0.000) for 5890 atoms. Found 114 (194 requested) and removed 41 (101 requested) atoms. Cycle 9: After refmac, R = 0.1977 (Rfree = 0.000) for 5957 atoms. Found 108 (196 requested) and removed 62 (102 requested) atoms. Cycle 10: After refmac, R = 0.1953 (Rfree = 0.000) for 5994 atoms. Found 114 (193 requested) and removed 65 (102 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.92 1.89 NCS extension: 5 residues added (259 deleted due to clashes), 6049 seeds are put forward Round 1: 615 peptides, 13 chains. Longest chain 151 peptides. Score 0.938 Round 2: 619 peptides, 11 chains. Longest chain 151 peptides. Score 0.943 Round 3: 619 peptides, 14 chains. Longest chain 221 peptides. Score 0.937 Round 4: 614 peptides, 12 chains. Longest chain 152 peptides. Score 0.940 Round 5: 613 peptides, 18 chains. Longest chain 151 peptides. Score 0.926 Taking the results from Round 2 Chains 12, Residues 608, Estimated correctness of the model 99.6 % 9 chains (591 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 182 A Built loop between residues 177 B and 181 B 10 chains (614 residues) following loop building 7 chains (597 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5830 restraints for refining 5810 atoms. 861 conditional restraints added. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2109 (Rfree = 0.000) for 5810 atoms. Found 171 (183 requested) and removed 70 (99 requested) atoms. Cycle 12: After refmac, R = 0.1996 (Rfree = 0.000) for 5902 atoms. Found 132 (186 requested) and removed 56 (101 requested) atoms. Cycle 13: After refmac, R = 0.1939 (Rfree = 0.000) for 5972 atoms. Found 116 (188 requested) and removed 55 (102 requested) atoms. Cycle 14: After refmac, R = 0.1893 (Rfree = 0.000) for 6028 atoms. Found 103 (190 requested) and removed 64 (103 requested) atoms. Cycle 15: After refmac, R = 0.1877 (Rfree = 0.000) for 6064 atoms. Found 120 (186 requested) and removed 69 (103 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.92 1.89 NCS extension: 30 residues added (18 deleted due to clashes), 6148 seeds are put forward Round 1: 615 peptides, 13 chains. Longest chain 150 peptides. Score 0.938 Round 2: 620 peptides, 10 chains. Longest chain 236 peptides. Score 0.946 Round 3: 615 peptides, 15 chains. Longest chain 151 peptides. Score 0.934 Round 4: 616 peptides, 14 chains. Longest chain 151 peptides. Score 0.936 Round 5: 618 peptides, 12 chains. Longest chain 210 peptides. Score 0.941 Taking the results from Round 2 Chains 11, Residues 610, Estimated correctness of the model 99.7 % 8 chains (596 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 162 A and 165 A Built loop between residues 178 A and 188 A Built loop between residues 93 B and 96 B 7 chains (619 residues) following loop building 5 chains (609 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5722 restraints for refining 5864 atoms. 681 conditional restraints added. Observations/parameters ratio is 2.15 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2056 (Rfree = 0.000) for 5864 atoms. Found 176 (176 requested) and removed 71 (100 requested) atoms. Failed to save intermediate PDB Cycle 17: After refmac, R = 0.1976 (Rfree = 0.000) for 5964 atoms. Found 113 (180 requested) and removed 64 (102 requested) atoms. Cycle 18: After refmac, R = 0.1916 (Rfree = 0.000) for 6006 atoms. Found 120 (176 requested) and removed 75 (102 requested) atoms. Cycle 19: After refmac, R = 0.1898 (Rfree = 0.000) for 6045 atoms. Found 120 (174 requested) and removed 84 (103 requested) atoms. Cycle 20: After refmac, R = 0.1870 (Rfree = 0.000) for 6074 atoms. Found 125 (171 requested) and removed 92 (104 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.92 1.89 NCS extension: 146 residues added (267 deleted due to clashes), 6258 seeds are put forward Round 1: 621 peptides, 10 chains. Longest chain 236 peptides. Score 0.946 Round 2: 622 peptides, 9 chains. Longest chain 227 peptides. Score 0.948 Round 3: 618 peptides, 14 chains. Longest chain 217 peptides. Score 0.937 Round 4: 624 peptides, 8 chains. Longest chain 265 peptides. Score 0.951 Round 5: 618 peptides, 12 chains. Longest chain 265 peptides. Score 0.941 Taking the results from Round 4 Chains 11, Residues 616, Estimated correctness of the model 99.7 % 9 chains (610 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 153 A and 156 A Built loop between residues 179 A and 186 A Built loop between residues 300 A and 304 A Built loop between residues 13 B and 16 B 5 chains (623 residues) following loop building 5 chains (623 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5694 restraints for refining 5880 atoms. 588 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2060 (Rfree = 0.000) for 5880 atoms. Found 161 (161 requested) and removed 79 (100 requested) atoms. Cycle 22: After refmac, R = 0.1955 (Rfree = 0.000) for 5955 atoms. Found 113 (163 requested) and removed 61 (102 requested) atoms. Cycle 23: After refmac, R = 0.1907 (Rfree = 0.000) for 6002 atoms. Found 116 (160 requested) and removed 57 (102 requested) atoms. Cycle 24: After refmac, R = 0.1874 (Rfree = 0.000) for 6058 atoms. Found 92 (161 requested) and removed 68 (103 requested) atoms. Cycle 25: After refmac, R = 0.1858 (Rfree = 0.000) for 6071 atoms. Found 112 (158 requested) and removed 77 (104 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.90 NCS extension: 12 residues added (252 deleted due to clashes), 6122 seeds are put forward Round 1: 623 peptides, 9 chains. Longest chain 265 peptides. Score 0.948 Round 2: 622 peptides, 10 chains. Longest chain 227 peptides. Score 0.946 Round 3: 615 peptides, 15 chains. Longest chain 151 peptides. Score 0.934 Round 4: 623 peptides, 9 chains. Longest chain 252 peptides. Score 0.948 Round 5: 613 peptides, 15 chains. Longest chain 151 peptides. Score 0.933 Taking the results from Round 4 Chains 13, Residues 614, Estimated correctness of the model 99.7 % 10 chains (606 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 176 A and 183 A Built loop between residues 317 A and 322 A Built loop between residues 13 B and 16 B Built loop between residues 93 B and 96 B Built loop between residues 156 B and 159 B 6 chains (623 residues) following loop building 5 chains (622 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5667 restraints for refining 5882 atoms. 566 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2028 (Rfree = 0.000) for 5882 atoms. Found 149 (149 requested) and removed 73 (100 requested) atoms. Cycle 27: After refmac, R = 0.1940 (Rfree = 0.000) for 5951 atoms. Found 128 (151 requested) and removed 59 (102 requested) atoms. Cycle 28: After refmac, R = 0.1898 (Rfree = 0.000) for 6018 atoms. Found 114 (152 requested) and removed 55 (103 requested) atoms. Cycle 29: After refmac, R = 0.1870 (Rfree = 0.000) for 6072 atoms. Found 109 (154 requested) and removed 79 (104 requested) atoms. Cycle 30: After refmac, R = 0.1855 (Rfree = 0.000) for 6091 atoms. Found 123 (150 requested) and removed 88 (104 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.92 1.89 NCS extension: 11 residues added (253 deleted due to clashes), 6144 seeds are put forward Round 1: 615 peptides, 12 chains. Longest chain 151 peptides. Score 0.940 Round 2: 616 peptides, 11 chains. Longest chain 151 peptides. Score 0.943 Round 3: 615 peptides, 14 chains. Longest chain 228 peptides. Score 0.936 Round 4: 614 peptides, 14 chains. Longest chain 151 peptides. Score 0.935 Round 5: 616 peptides, 12 chains. Longest chain 173 peptides. Score 0.940 Taking the results from Round 2 Chains 11, Residues 605, Estimated correctness of the model 99.6 % 9 chains (588 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 177 A and 181 A Built loop between residues 145 B and 148 B Built loop between residues 177 B and 181 B 8 chains (613 residues) following loop building 6 chains (596 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5915 restraints for refining 5886 atoms. 952 conditional restraints added. Observations/parameters ratio is 2.14 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2042 (Rfree = 0.000) for 5886 atoms. Found 141 (141 requested) and removed 63 (100 requested) atoms. Cycle 32: After refmac, R = 0.1933 (Rfree = 0.000) for 5961 atoms. Found 123 (143 requested) and removed 41 (102 requested) atoms. Cycle 33: After refmac, R = 0.1893 (Rfree = 0.000) for 6039 atoms. Found 113 (145 requested) and removed 53 (103 requested) atoms. Cycle 34: After refmac, R = 0.1868 (Rfree = 0.000) for 6091 atoms. Found 100 (146 requested) and removed 73 (104 requested) atoms. Cycle 35: After refmac, R = 0.1847 (Rfree = 0.000) for 6114 atoms. Found 106 (142 requested) and removed 69 (104 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.92 1.89 NCS extension: 32 residues added (265 deleted due to clashes), 6188 seeds are put forward Round 1: 613 peptides, 12 chains. Longest chain 166 peptides. Score 0.939 Round 2: 615 peptides, 11 chains. Longest chain 157 peptides. Score 0.942 Round 3: 612 peptides, 16 chains. Longest chain 143 peptides. Score 0.930 Round 4: 615 peptides, 10 chains. Longest chain 222 peptides. Score 0.944 Round 5: 615 peptides, 15 chains. Longest chain 153 peptides. Score 0.934 Taking the results from Round 4 Chains 15, Residues 605, Estimated correctness of the model 99.6 % 11 chains (593 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 13 A and 17 A Built loop between residues 102 A and 112 A Built loop between residues 176 A and 183 A Built loop between residues 13 B and 16 B Built loop between residues 93 B and 96 B Built loop between residues 157 B and 160 B Built loop between residues 177 B and 181 B 5 chains (622 residues) following loop building 4 chains (620 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5749 restraints for refining 5933 atoms. 659 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2071 (Rfree = 0.000) for 5933 atoms. Found 134 (134 requested) and removed 93 (101 requested) atoms. Cycle 37: After refmac, R = 0.1955 (Rfree = 0.000) for 5962 atoms. Found 131 (131 requested) and removed 40 (102 requested) atoms. Cycle 38: After refmac, R = 0.1899 (Rfree = 0.000) for 6047 atoms. Found 111 (132 requested) and removed 58 (103 requested) atoms. Cycle 39: After refmac, R = 0.1869 (Rfree = 0.000) for 6094 atoms. Found 113 (129 requested) and removed 70 (104 requested) atoms. Cycle 40: After refmac, R = 0.1851 (Rfree = 0.000) for 6131 atoms. Found 114 (126 requested) and removed 90 (105 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added (30 deleted due to clashes), 6160 seeds are put forward Round 1: 616 peptides, 10 chains. Longest chain 151 peptides. Score 0.945 Round 2: 614 peptides, 13 chains. Longest chain 156 peptides. Score 0.938 Round 3: 617 peptides, 10 chains. Longest chain 153 peptides. Score 0.945 Round 4: 619 peptides, 10 chains. Longest chain 144 peptides. Score 0.945 Round 5: 613 peptides, 16 chains. Longest chain 134 peptides. Score 0.931 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 184 A and 188 A Built loop between residues 319 A and 322 A Built loop between residues 102 B and 105 B Built loop between residues 185 B and 188 B 7 chains (618 residues) following loop building 5 chains (608 residues) in sequence following loop building ------------------------------------------------------ 50384 reflections ( 99.43 % complete ) and 5801 restraints for refining 5902 atoms. 774 conditional restraints added. Observations/parameters ratio is 2.13 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2057 (Rfree = 0.000) for 5902 atoms. Found 117 (117 requested) and removed 75 (101 requested) atoms. Cycle 42: After refmac, R = 0.1939 (Rfree = 0.000) for 5936 atoms. Found 114 (114 requested) and removed 35 (101 requested) atoms. Cycle 43: After refmac, R = 0.1877 (Rfree = 0.000) for 6006 atoms. Found 98 (115 requested) and removed 47 (103 requested) atoms. Cycle 44: After refmac, R = 0.1843 (Rfree = 0.000) for 6050 atoms. Found 93 (116 requested) and removed 60 (103 requested) atoms. Cycle 45: After refmac, R = 0.1820 (Rfree = 0.000) for 6076 atoms. Found 102 (112 requested) and removed 71 (104 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.93 1.90 NCS extension: 22 residues added (242 deleted due to clashes), 6132 seeds are put forward Round 1: 611 peptides, 13 chains. Longest chain 139 peptides. Score 0.937 Round 2: 616 peptides, 11 chains. Longest chain 161 peptides. Score 0.943 Round 3: 615 peptides, 12 chains. Longest chain 150 peptides. Score 0.940 Round 4: 607 peptides, 14 chains. Longest chain 144 peptides. Score 0.933 Round 5: 612 peptides, 12 chains. Longest chain 151 peptides. Score 0.939 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 605, Estimated correctness of the model 99.6 % 11 chains (590 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 101 A and 104 A Built loop between residues 156 A and 159 A Built loop between residues 177 A and 184 A Built loop between residues 318 A and 322 A Built loop between residues 12 B and 16 B Built loop between residues 102 B and 105 B Built loop between residues 177 B and 181 B 5 chains (620 residues) following loop building 4 chains (611 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 50384 reflections ( 99.43 % complete ) and 5050 restraints for refining 4909 atoms. Observations/parameters ratio is 2.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2699 (Rfree = 0.000) for 4909 atoms. Found 87 (87 requested) and removed 0 (87 requested) atoms. Cycle 47: After refmac, R = 0.2547 (Rfree = 0.000) for 4909 atoms. Found 68 (89 requested) and removed 0 (85 requested) atoms. Cycle 48: After refmac, R = 0.2417 (Rfree = 0.000) for 4909 atoms. Found 37 (90 requested) and removed 5 (86 requested) atoms. Cycle 49: After refmac, R = 0.2352 (Rfree = 0.000) for 4909 atoms. TimeTaking 93.78