Sun 23 Dec 22:22:59 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 2f4l-2.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-2.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2f4l-2.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-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/2f4l-2.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-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 22:23:08 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/2f4l-2.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-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 1047 and 0 Target number of residues in the AU: 1047 Target solvent content: 0.5611 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1188 Adjusted target solvent content: 0.50 Input MTZ file: 2f4l-2.5-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: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-2.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 9504 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 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: 86.372 2.500 Wilson plot Bfac: 38.78 45394 reflections ( 99.69 % complete ) and 0 restraints for refining 10632 atoms. Observations/parameters ratio is 1.07 ------------------------------------------------------ Starting model: R = 0.3065 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2145 (Rfree = 0.000) for 10632 atoms. Found 102 (192 requested) and removed 136 (96 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.54 2.54 NCS extension: 0 residues added, 10598 seeds are put forward Round 1: 814 peptides, 103 chains. Longest chain 25 peptides. Score 0.639 Round 2: 930 peptides, 69 chains. Longest chain 51 peptides. Score 0.815 Round 3: 966 peptides, 57 chains. Longest chain 59 peptides. Score 0.856 Round 4: 1006 peptides, 43 chains. Longest chain 96 peptides. Score 0.893 Round 5: 1020 peptides, 40 chains. Longest chain 98 peptides. Score 0.902 Taking the results from Round 5 Chains 49, Residues 980, Estimated correctness of the model 97.9 % 27 chains (835 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 107 A and 110 A Built loop between residues 195 A and 198 A Built loop between residues 123 C and 127 C Built loop between residues 138 C and 140 C Built loop between residues 160 C and 163 C Built loop between residues 176 C and 182 C Built loop between residues 202 C and 205 C Built loop between residues 246 C and 250 C Built loop between residues 280 C and 284 C Built loop between residues 123 B and 126 B Built loop between residues 194 B and 198 B Built loop between residues 277 B and 280 B Built loop between residues 124 D and 127 D Built loop between residues 262 D and 265 D 33 chains (1012 residues) following loop building 13 chains (869 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 11011 restraints for refining 9399 atoms. 3595 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2495 (Rfree = 0.000) for 9399 atoms. Found 161 (170 requested) and removed 118 (85 requested) atoms. Cycle 2: After refmac, R = 0.2209 (Rfree = 0.000) for 9341 atoms. Found 96 (168 requested) and removed 97 (85 requested) atoms. Cycle 3: After refmac, R = 0.2091 (Rfree = 0.000) for 9279 atoms. Found 72 (162 requested) and removed 86 (84 requested) atoms. Cycle 4: After refmac, R = 0.2026 (Rfree = 0.000) for 9225 atoms. Found 60 (158 requested) and removed 85 (84 requested) atoms. Cycle 5: After refmac, R = 0.1974 (Rfree = 0.000) for 9176 atoms. Found 58 (153 requested) and removed 84 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.55 2.55 NCS extension: 105 residues added (872 deleted due to clashes), 9270 seeds are put forward Round 1: 1047 peptides, 34 chains. Longest chain 104 peptides. Score 0.917 Round 2: 1062 peptides, 26 chains. Longest chain 116 peptides. Score 0.931 Round 3: 1055 peptides, 29 chains. Longest chain 122 peptides. Score 0.926 Round 4: 1060 peptides, 31 chains. Longest chain 112 peptides. Score 0.924 Round 5: 1054 peptides, 36 chains. Longest chain 98 peptides. Score 0.916 Taking the results from Round 2 Chains 28, Residues 1036, Estimated correctness of the model 98.9 % 20 chains (989 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 192 A and 201 A Built loop between residues 126 C and 129 C Built loop between residues 176 C and 180 C Built loop between residues 124 B and 127 B Built loop between residues 137 B and 140 B Built loop between residues 175 B and 180 B Built loop between residues 223 B and 227 B Built loop between residues 273 B and 276 B Built loop between residues 138 D and 142 D Built loop between residues 191 D and 195 D Built loop between residues 244 D and 247 D 15 chains (1063 residues) following loop building 9 chains (1023 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9630 restraints for refining 9229 atoms. 1413 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2170 (Rfree = 0.000) for 9229 atoms. Found 143 (150 requested) and removed 110 (83 requested) atoms. Cycle 7: After refmac, R = 0.1943 (Rfree = 0.000) for 9225 atoms. Found 104 (147 requested) and removed 87 (83 requested) atoms. Cycle 8: After refmac, R = 0.1846 (Rfree = 0.000) for 9221 atoms. Found 97 (144 requested) and removed 83 (83 requested) atoms. Cycle 9: After refmac, R = 0.1781 (Rfree = 0.000) for 9219 atoms. Found 101 (140 requested) and removed 89 (83 requested) atoms. Cycle 10: After refmac, R = 0.1731 (Rfree = 0.000) for 9224 atoms. Found 85 (137 requested) and removed 87 (83 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.55 2.55 NCS extension: 12 residues added (237 deleted due to clashes), 9248 seeds are put forward Round 1: 1065 peptides, 25 chains. Longest chain 116 peptides. Score 0.933 Round 2: 1069 peptides, 22 chains. Longest chain 155 peptides. Score 0.937 Round 3: 1057 peptides, 31 chains. Longest chain 221 peptides. Score 0.923 Round 4: 1052 peptides, 34 chains. Longest chain 133 peptides. Score 0.918 Round 5: 1069 peptides, 22 chains. Longest chain 134 peptides. Score 0.937 Taking the results from Round 5 Chains 24, Residues 1047, Estimated correctness of the model 99.1 % 18 chains (1012 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 132 A and 140 A Built loop between residues 159 A and 162 A Built loop between residues 121 C and 127 C Built loop between residues 177 C and 180 C Built loop between residues 236 C and 239 C Built loop between residues 272 C and 275 C Built loop between residues 179 B and 183 B Built loop between residues 233 B and 238 B Built loop between residues 154 D and 159 D Built loop between residues 178 D and 182 D 11 chains (1072 residues) following loop building 8 chains (1046 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9333 restraints for refining 9096 atoms. 960 conditional restraints added. Observations/parameters ratio is 1.25 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2052 (Rfree = 0.000) for 9096 atoms. Found 131 (131 requested) and removed 110 (82 requested) atoms. Cycle 12: After refmac, R = 0.1845 (Rfree = 0.000) for 9093 atoms. Found 122 (129 requested) and removed 89 (82 requested) atoms. Cycle 13: After refmac, R = 0.1752 (Rfree = 0.000) for 9119 atoms. Found 124 (125 requested) and removed 90 (82 requested) atoms. Cycle 14: After refmac, R = 0.1695 (Rfree = 0.000) for 9144 atoms. Found 119 (123 requested) and removed 95 (83 requested) atoms. Cycle 15: After refmac, R = 0.1662 (Rfree = 0.000) for 9159 atoms. Found 117 (120 requested) and removed 88 (83 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.53 2.53 NCS extension: 5 residues added (11 deleted due to clashes), 9198 seeds are put forward Round 1: 1060 peptides, 25 chains. Longest chain 112 peptides. Score 0.932 Round 2: 1058 peptides, 24 chains. Longest chain 102 peptides. Score 0.933 Round 3: 1048 peptides, 31 chains. Longest chain 110 peptides. Score 0.922 Round 4: 1056 peptides, 24 chains. Longest chain 125 peptides. Score 0.932 Round 5: 1047 peptides, 28 chains. Longest chain 128 peptides. Score 0.925 Taking the results from Round 2 Chains 24, Residues 1034, Estimated correctness of the model 99.0 % 20 chains (1017 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 161 A and 165 A Built loop between residues 191 A and 194 A Built loop between residues 123 C and 127 C Built loop between residues 195 C and 198 C Built loop between residues 139 B and 142 B Built loop between residues 178 B and 182 B Built loop between residues 195 B and 198 B Built loop between residues 226 B and 229 B Built loop between residues 124 D and 128 D Built loop between residues 177 D and 186 D Built loop between residues 196 D and 200 D Built loop between residues 249 D and 252 D 11 chains (1066 residues) following loop building 8 chains (1052 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9297 restraints for refining 9004 atoms. 916 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1916 (Rfree = 0.000) for 9004 atoms. Found 114 (114 requested) and removed 100 (81 requested) atoms. Cycle 17: After refmac, R = 0.1730 (Rfree = 0.000) for 9010 atoms. Found 111 (111 requested) and removed 86 (81 requested) atoms. Cycle 18: After refmac, R = 0.1654 (Rfree = 0.000) for 9029 atoms. Found 108 (108 requested) and removed 94 (81 requested) atoms. Cycle 19: After refmac, R = 0.1605 (Rfree = 0.000) for 9038 atoms. Found 105 (105 requested) and removed 91 (82 requested) atoms. Cycle 20: After refmac, R = 0.1568 (Rfree = 0.000) for 9047 atoms. Found 102 (102 requested) and removed 98 (82 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.52 2.52 NCS extension: 0 residues added, 9053 seeds are put forward Round 1: 1056 peptides, 24 chains. Longest chain 113 peptides. Score 0.932 Round 2: 1069 peptides, 22 chains. Longest chain 169 peptides. Score 0.937 Round 3: 1054 peptides, 35 chains. Longest chain 102 peptides. Score 0.917 Round 4: 1064 peptides, 23 chains. Longest chain 228 peptides. Score 0.935 Round 5: 1057 peptides, 30 chains. Longest chain 112 peptides. Score 0.925 Taking the results from Round 2 Chains 25, Residues 1047, Estimated correctness of the model 99.1 % 19 chains (1016 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 176 A and 183 A Built loop between residues 192 A and 202 A Built loop between residues 280 A and 283 A Built loop between residues 124 C and 128 C Built loop between residues 177 C and 180 C Built loop between residues 195 C and 198 C Built loop between residues 123 B and 127 B Built loop between residues 129 D and 132 D Built loop between residues 176 D and 181 D Built loop between residues 193 D and 196 D Built loop between residues 262 D and 265 D 11 chains (1072 residues) following loop building 8 chains (1053 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9207 restraints for refining 8968 atoms. 803 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1873 (Rfree = 0.000) for 8968 atoms. Found 97 (97 requested) and removed 95 (81 requested) atoms. Cycle 22: After refmac, R = 0.1696 (Rfree = 0.000) for 8963 atoms. Found 94 (94 requested) and removed 83 (81 requested) atoms. Cycle 23: After refmac, R = 0.1626 (Rfree = 0.000) for 8970 atoms. Found 91 (91 requested) and removed 87 (81 requested) atoms. Cycle 24: After refmac, R = 0.1606 (Rfree = 0.000) for 8970 atoms. Found 87 (87 requested) and removed 88 (81 requested) atoms. Cycle 25: After refmac, R = 0.1574 (Rfree = 0.000) for 8968 atoms. Found 84 (84 requested) and removed 94 (81 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.51 2.51 NCS extension: 32 residues added (196 deleted due to clashes), 9001 seeds are put forward Round 1: 1064 peptides, 25 chains. Longest chain 114 peptides. Score 0.933 Round 2: 1076 peptides, 20 chains. Longest chain 133 peptides. Score 0.941 Round 3: 1050 peptides, 33 chains. Longest chain 112 peptides. Score 0.919 Round 4: 1071 peptides, 24 chains. Longest chain 117 peptides. Score 0.935 Round 5: 1046 peptides, 33 chains. Longest chain 130 peptides. Score 0.918 Taking the results from Round 2 Chains 21, Residues 1056, Estimated correctness of the model 99.2 % 16 chains (982 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 178 A and 181 A Built loop between residues 197 A and 200 A Built loop between residues 182 C and 185 C Built loop between residues 123 B and 126 B Built loop between residues 137 B and 140 B Built loop between residues 178 B and 181 B Built loop between residues 195 B and 198 B Built loop between residues 49 D and 59 D Built loop between residues 160 D and 163 D 11 chains (1080 residues) following loop building 7 chains (1007 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9458 restraints for refining 8906 atoms. 1217 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1877 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 93 (80 requested) atoms. Cycle 27: After refmac, R = 0.1702 (Rfree = 0.000) for 8885 atoms. Found 80 (80 requested) and removed 83 (80 requested) atoms. Cycle 28: After refmac, R = 0.1630 (Rfree = 0.000) for 8879 atoms. Found 80 (80 requested) and removed 84 (80 requested) atoms. Cycle 29: After refmac, R = 0.1590 (Rfree = 0.000) for 8874 atoms. Found 80 (80 requested) and removed 91 (80 requested) atoms. Cycle 30: After refmac, R = 0.1570 (Rfree = 0.000) for 8862 atoms. Found 80 (80 requested) and removed 84 (80 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.52 2.52 NCS extension: 9 residues added (63 deleted due to clashes), 8874 seeds are put forward Round 1: 1064 peptides, 26 chains. Longest chain 113 peptides. Score 0.931 Round 2: 1072 peptides, 22 chains. Longest chain 139 peptides. Score 0.938 Round 3: 1072 peptides, 25 chains. Longest chain 116 peptides. Score 0.934 Round 4: 1060 peptides, 27 chains. Longest chain 116 peptides. Score 0.929 Round 5: 1066 peptides, 30 chains. Longest chain 113 peptides. Score 0.926 Taking the results from Round 2 Chains 26, Residues 1050, Estimated correctness of the model 99.1 % 19 chains (1030 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 127 A Built loop between residues 137 A and 140 A Built loop between residues 178 A and 182 A Built loop between residues 224 A and 228 A Built loop between residues 277 A and 280 A Built loop between residues 203 C and 206 C Built loop between residues 243 C and 246 C Built loop between residues 138 B and 141 B Built loop between residues 178 B and 181 B Built loop between residues 176 D and 180 D Built loop between residues 192 D and 201 D 11 chains (1076 residues) following loop building 8 chains (1062 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9080 restraints for refining 8906 atoms. 632 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1820 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 94 (80 requested) atoms. Cycle 32: After refmac, R = 0.1639 (Rfree = 0.000) for 8891 atoms. Found 80 (80 requested) and removed 83 (80 requested) atoms. Cycle 33: After refmac, R = 0.1586 (Rfree = 0.000) for 8885 atoms. Found 80 (80 requested) and removed 83 (80 requested) atoms. Cycle 34: After refmac, R = 0.1560 (Rfree = 0.000) for 8881 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. Cycle 35: After refmac, R = 0.1546 (Rfree = 0.000) for 8874 atoms. Found 80 (80 requested) and removed 87 (80 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.52 2.52 NCS extension: 0 residues added (5 deleted due to clashes), 8870 seeds are put forward Round 1: 1062 peptides, 24 chains. Longest chain 113 peptides. Score 0.934 Round 2: 1075 peptides, 19 chains. Longest chain 228 peptides. Score 0.942 Round 3: 1069 peptides, 24 chains. Longest chain 228 peptides. Score 0.935 Round 4: 1064 peptides, 27 chains. Longest chain 103 peptides. Score 0.930 Round 5: 1069 peptides, 27 chains. Longest chain 116 peptides. Score 0.931 Taking the results from Round 2 Chains 21, Residues 1056, Estimated correctness of the model 99.2 % 15 chains (1034 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 127 A Built loop between residues 137 A and 140 A Built loop between residues 156 A and 159 A Built loop between residues 177 A and 180 A Built loop between residues 123 C and 127 C Built loop between residues 176 C and 181 C Built loop between residues 191 B and 197 B 12 chains (1074 residues) following loop building 8 chains (1055 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9111 restraints for refining 8906 atoms. 691 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1778 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 92 (80 requested) atoms. Cycle 37: After refmac, R = 0.1627 (Rfree = 0.000) for 8890 atoms. Found 80 (80 requested) and removed 83 (80 requested) atoms. Cycle 38: After refmac, R = 0.1581 (Rfree = 0.000) for 8884 atoms. Found 80 (80 requested) and removed 84 (80 requested) atoms. Cycle 39: After refmac, R = 0.1549 (Rfree = 0.000) for 8876 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. Cycle 40: After refmac, R = 0.1538 (Rfree = 0.000) for 8864 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.52 2.52 NCS extension: 0 residues added, 8862 seeds are put forward Round 1: 1063 peptides, 24 chains. Longest chain 112 peptides. Score 0.934 Round 2: 1078 peptides, 20 chains. Longest chain 131 peptides. Score 0.941 Round 3: 1063 peptides, 30 chains. Longest chain 116 peptides. Score 0.926 Round 4: 1067 peptides, 30 chains. Longest chain 103 peptides. Score 0.927 Round 5: 1061 peptides, 31 chains. Longest chain 102 peptides. Score 0.924 Taking the results from Round 2 Chains 22, Residues 1058, Estimated correctness of the model 99.2 % 16 chains (1033 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 127 A Built loop between residues 138 A and 141 A Built loop between residues 177 A and 180 A Built loop between residues 250 A and 253 A Built loop between residues 176 C and 182 C Built loop between residues 195 C and 198 C Built loop between residues 196 B and 199 B Built loop between residues 162 D and 165 D 12 chains (1074 residues) following loop building 8 chains (1053 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9138 restraints for refining 8906 atoms. 722 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1783 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 91 (80 requested) atoms. Cycle 42: After refmac, R = 0.1626 (Rfree = 0.000) for 8892 atoms. Found 80 (80 requested) and removed 82 (80 requested) atoms. Cycle 43: After refmac, R = 0.1558 (Rfree = 0.000) for 8886 atoms. Found 80 (80 requested) and removed 86 (80 requested) atoms. Cycle 44: After refmac, R = 0.1531 (Rfree = 0.000) for 8874 atoms. Found 80 (80 requested) and removed 83 (80 requested) atoms. Cycle 45: After refmac, R = 0.1515 (Rfree = 0.000) for 8867 atoms. Found 80 (80 requested) and removed 86 (80 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.52 2.52 NCS extension: 0 residues added, 8864 seeds are put forward Round 1: 1069 peptides, 23 chains. Longest chain 112 peptides. Score 0.936 Round 2: 1065 peptides, 26 chains. Longest chain 116 peptides. Score 0.932 Round 3: 1062 peptides, 29 chains. Longest chain 117 peptides. Score 0.927 Round 4: 1068 peptides, 25 chains. Longest chain 131 peptides. Score 0.933 Round 5: 1059 peptides, 32 chains. Longest chain 171 peptides. Score 0.922 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 1046, Estimated correctness of the model 99.1 % 19 chains (1018 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 123 A and 129 A Built loop between residues 178 A and 182 A Built loop between residues 192 A and 198 A Built loop between residues 262 A and 265 A Built loop between residues 122 C and 127 C Built loop between residues 176 C and 180 C Built loop between residues 192 C and 195 C Built loop between residues 176 B and 181 B Built loop between residues 192 B and 195 B Built loop between residues 178 D and 181 D Built loop between residues 191 D and 194 D 12 chains (1074 residues) following loop building 8 chains (1052 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 45394 reflections ( 99.69 % complete ) and 8412 restraints for refining 8244 atoms. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2255 (Rfree = 0.000) for 8244 atoms. Found 65 (74 requested) and removed 0 (74 requested) atoms. Cycle 47: After refmac, R = 0.2046 (Rfree = 0.000) for 8244 atoms. Found 45 (75 requested) and removed 9 (75 requested) atoms. Cycle 48: After refmac, R = 0.1968 (Rfree = 0.000) for 8244 atoms. Found 21 (75 requested) and removed 17 (75 requested) atoms. Cycle 49: After refmac, R = 0.1945 (Rfree = 0.000) for 8244 atoms. Found 22 (75 requested) and removed 12 (75 requested) atoms. Writing output files ... TimeTaking 135.17