Mon 24 Dec 00:35:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2f4l-2.5-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-2.5-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2f4l-2.5-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 00:35:54 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2f4l-2.5-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 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-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 80.030 103.980 155.130 90.000 90.000 90.000 Input sequence file: 2f4l-2.5-parrot-mrncs.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 10481 atoms. Observations/parameters ratio is 1.08 ------------------------------------------------------ Starting model: R = 0.3043 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2052 (Rfree = 0.000) for 10481 atoms. Found 108 (190 requested) and removed 136 (95 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.53 2.53 NCS extension: 0 residues added, 10453 seeds are put forward Round 1: 808 peptides, 91 chains. Longest chain 39 peptides. Score 0.677 Round 2: 905 peptides, 64 chains. Longest chain 51 peptides. Score 0.815 Round 3: 962 peptides, 53 chains. Longest chain 92 peptides. Score 0.862 Round 4: 1005 peptides, 40 chains. Longest chain 81 peptides. Score 0.898 Round 5: 1016 peptides, 38 chains. Longest chain 113 peptides. Score 0.904 Taking the results from Round 5 Chains 40, Residues 978, Estimated correctness of the model 98.0 % 25 chains (870 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 A and 111 A Built loop between residues 177 A and 181 A Built loop between residues 94 C and 102 C Built loop between residues 217 C and 221 C Built loop between residues 107 B and 110 B Built loop between residues 157 B and 160 B Built loop between residues 178 B and 181 B Built loop between residues 91 D and 94 D Built loop between residues 145 D and 148 D Built loop between residues 241 D and 245 D Built loop between residues 262 D and 266 D 28 chains (1005 residues) following loop building 14 chains (901 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 10762 restraints for refining 9323 atoms. 3218 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2337 (Rfree = 0.000) for 9323 atoms. Found 153 (169 requested) and removed 101 (84 requested) atoms. Cycle 2: After refmac, R = 0.2069 (Rfree = 0.000) for 9287 atoms. Found 91 (167 requested) and removed 93 (85 requested) atoms. Cycle 3: After refmac, R = 0.1966 (Rfree = 0.000) for 9233 atoms. Found 85 (161 requested) and removed 89 (84 requested) atoms. Cycle 4: After refmac, R = 0.1901 (Rfree = 0.000) for 9203 atoms. Found 73 (157 requested) and removed 87 (83 requested) atoms. Cycle 5: After refmac, R = 0.1876 (Rfree = 0.000) for 9171 atoms. Found 65 (153 requested) and removed 87 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.55 2.55 NCS extension: 79 residues added (1063 deleted due to clashes), 9242 seeds are put forward Round 1: 1046 peptides, 29 chains. Longest chain 115 peptides. Score 0.924 Round 2: 1056 peptides, 24 chains. Longest chain 132 peptides. Score 0.932 Round 3: 1053 peptides, 35 chains. Longest chain 115 peptides. Score 0.917 Round 4: 1061 peptides, 32 chains. Longest chain 114 peptides. Score 0.923 Round 5: 1052 peptides, 33 chains. Longest chain 116 peptides. Score 0.920 Taking the results from Round 2 Chains 27, Residues 1032, Estimated correctness of the model 98.9 % 21 chains (1004 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 106 A and 113 A Built loop between residues 126 A and 130 A Built loop between residues 178 A and 182 A Built loop between residues 225 A and 228 A Built loop between residues 122 C and 127 C Built loop between residues 203 C and 206 C Built loop between residues 241 C and 244 C Built loop between residues 280 C and 283 C Built loop between residues 123 B and 126 B Built loop between residues 160 B and 164 B Built loop between residues 163 D and 166 D Built loop between residues 179 D and 187 D Built loop between residues 196 D and 201 D 13 chains (1069 residues) following loop building 8 chains (1046 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9397 restraints for refining 9169 atoms. 1047 conditional restraints added. Observations/parameters ratio is 1.24 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2032 (Rfree = 0.000) for 9169 atoms. Found 149 (149 requested) and removed 109 (83 requested) atoms. Cycle 7: After refmac, R = 0.1814 (Rfree = 0.000) for 9190 atoms. Found 111 (147 requested) and removed 85 (83 requested) atoms. Cycle 8: After refmac, R = 0.1719 (Rfree = 0.000) for 9201 atoms. Found 93 (144 requested) and removed 95 (83 requested) atoms. Cycle 9: After refmac, R = 0.1670 (Rfree = 0.000) for 9184 atoms. Found 96 (139 requested) and removed 91 (83 requested) atoms. Cycle 10: After refmac, R = 0.1639 (Rfree = 0.000) for 9177 atoms. Found 100 (136 requested) and removed 93 (83 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.54 2.54 NCS extension: 7 residues added (6 deleted due to clashes), 9198 seeds are put forward Round 1: 1058 peptides, 26 chains. Longest chain 113 peptides. Score 0.930 Round 2: 1067 peptides, 26 chains. Longest chain 110 peptides. Score 0.932 Round 3: 1057 peptides, 26 chains. Longest chain 113 peptides. Score 0.930 Round 4: 1059 peptides, 29 chains. Longest chain 115 peptides. Score 0.926 Round 5: 1059 peptides, 28 chains. Longest chain 115 peptides. Score 0.928 Taking the results from Round 2 Chains 27, Residues 1041, Estimated correctness of the model 98.9 % 21 chains (985 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 138 A and 141 A Built loop between residues 178 A and 182 A Built loop between residues 195 A and 198 A Built loop between residues 178 C and 181 C Built loop between residues 195 C and 198 C Built loop between residues 138 B and 141 B Built loop between residues 178 B and 182 B Built loop between residues 201 B and 205 B Built loop between residues 243 B and 246 B Built loop between residues 28 D and 38 D Built loop between residues 183 D and 186 D 15 chains (1068 residues) following loop building 10 chains (1017 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9530 restraints for refining 8991 atoms. 1274 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1911 (Rfree = 0.000) for 8991 atoms. Found 130 (130 requested) and removed 95 (81 requested) atoms. Cycle 12: After refmac, R = 0.1733 (Rfree = 0.000) for 9014 atoms. Found 117 (127 requested) and removed 87 (81 requested) atoms. Cycle 13: After refmac, R = 0.1658 (Rfree = 0.000) for 9036 atoms. Found 98 (125 requested) and removed 88 (82 requested) atoms. Cycle 14: After refmac, R = 0.1617 (Rfree = 0.000) for 9044 atoms. Found 105 (121 requested) and removed 92 (82 requested) atoms. Cycle 15: After refmac, R = 0.1592 (Rfree = 0.000) for 9050 atoms. Found 115 (118 requested) and removed 87 (82 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.54 2.54 NCS extension: 14 residues added (502 deleted due to clashes), 9100 seeds are put forward Round 1: 1065 peptides, 25 chains. Longest chain 115 peptides. Score 0.933 Round 2: 1070 peptides, 22 chains. Longest chain 169 peptides. Score 0.938 Round 3: 1057 peptides, 29 chains. Longest chain 117 peptides. Score 0.926 Round 4: 1064 peptides, 27 chains. Longest chain 97 peptides. Score 0.930 Round 5: 1049 peptides, 31 chains. Longest chain 115 peptides. Score 0.922 Taking the results from Round 2 Chains 23, Residues 1048, Estimated correctness of the model 99.1 % 18 chains (1024 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 161 A and 164 A Built loop between residues 202 A and 205 A Built loop between residues 280 A and 283 A Built loop between residues 124 C and 127 C Built loop between residues 124 B and 127 B Built loop between residues 162 B and 166 B Built loop between residues 196 B and 201 B Built loop between residues 123 D and 126 D Built loop between residues 161 D and 164 D 13 chains (1067 residues) following loop building 9 chains (1045 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9287 restraints for refining 8906 atoms. 924 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1850 (Rfree = 0.000) for 8906 atoms. Found 113 (113 requested) and removed 93 (80 requested) atoms. Cycle 17: After refmac, R = 0.1671 (Rfree = 0.000) for 8916 atoms. Found 109 (109 requested) and removed 83 (80 requested) atoms. Cycle 18: After refmac, R = 0.1606 (Rfree = 0.000) for 8937 atoms. Found 107 (107 requested) and removed 96 (81 requested) atoms. Cycle 19: After refmac, R = 0.1548 (Rfree = 0.000) for 8944 atoms. Found 104 (104 requested) and removed 87 (81 requested) atoms. Cycle 20: After refmac, R = 0.1531 (Rfree = 0.000) for 8958 atoms. Found 100 (100 requested) and removed 91 (81 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.53 2.53 NCS extension: 4 residues added (250 deleted due to clashes), 8974 seeds are put forward Round 1: 1059 peptides, 29 chains. Longest chain 112 peptides. Score 0.926 Round 2: 1073 peptides, 23 chains. Longest chain 131 peptides. Score 0.937 Round 3: 1073 peptides, 26 chains. Longest chain 105 peptides. Score 0.933 Round 4: 1059 peptides, 23 chains. Longest chain 113 peptides. Score 0.934 Round 5: 1063 peptides, 29 chains. Longest chain 118 peptides. Score 0.927 Taking the results from Round 2 Chains 26, Residues 1050, Estimated correctness of the model 99.1 % 19 chains (1024 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 179 A and 182 A Built loop between residues 195 A and 198 A Built loop between residues 162 C and 165 C Built loop between residues 125 B and 129 B Built loop between residues 177 B and 180 B Built loop between residues 103 D and 106 D Built loop between residues 159 D and 166 D Built loop between residues 178 D and 181 D Built loop between residues 192 D and 197 D Built loop between residues 209 D and 212 D Built loop between residues 224 D and 227 D 12 chains (1071 residues) following loop building 8 chains (1053 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9166 restraints for refining 8909 atoms. 762 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1834 (Rfree = 0.000) for 8909 atoms. Found 97 (97 requested) and removed 87 (80 requested) atoms. Cycle 22: After refmac, R = 0.1655 (Rfree = 0.000) for 8910 atoms. Found 93 (93 requested) and removed 83 (80 requested) atoms. Cycle 23: After refmac, R = 0.1595 (Rfree = 0.000) for 8913 atoms. Found 90 (90 requested) and removed 87 (80 requested) atoms. Cycle 24: After refmac, R = 0.1556 (Rfree = 0.000) for 8913 atoms. Found 87 (87 requested) and removed 85 (80 requested) atoms. Cycle 25: After refmac, R = 0.1537 (Rfree = 0.000) for 8909 atoms. Found 84 (84 requested) and removed 91 (80 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.53 2.53 NCS extension: 0 residues added, 8911 seeds are put forward Round 1: 1065 peptides, 24 chains. Longest chain 113 peptides. Score 0.934 Round 2: 1073 peptides, 18 chains. Longest chain 156 peptides. Score 0.943 Round 3: 1058 peptides, 31 chains. Longest chain 77 peptides. Score 0.924 Round 4: 1060 peptides, 31 chains. Longest chain 120 peptides. Score 0.924 Round 5: 1060 peptides, 28 chains. Longest chain 116 peptides. Score 0.928 Taking the results from Round 2 Chains 21, Residues 1055, Estimated correctness of the model 99.2 % 15 chains (1030 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 140 A Built loop between residues 163 C and 166 C Built loop between residues 192 C and 195 C Built loop between residues 138 B and 141 B Built loop between residues 176 B and 180 B Built loop between residues 121 D and 127 D Built loop between residues 175 D and 179 D 11 chains (1067 residues) following loop building 8 chains (1050 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9194 restraints for refining 8906 atoms. 822 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1793 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 93 (80 requested) atoms. Cycle 27: After refmac, R = 0.1634 (Rfree = 0.000) for 8882 atoms. Found 80 (80 requested) and removed 88 (80 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.1581 (Rfree = 0.000) for 8869 atoms. Found 80 (80 requested) and removed 82 (80 requested) atoms. Cycle 29: After refmac, R = 0.1555 (Rfree = 0.000) for 8865 atoms. Found 80 (80 requested) and removed 88 (80 requested) atoms. Cycle 30: After refmac, R = 0.1541 (Rfree = 0.000) for 8852 atoms. Found 80 (80 requested) and removed 89 (80 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.52 2.52 NCS extension: 3 residues added (7 deleted due to clashes), 8851 seeds are put forward Round 1: 1063 peptides, 25 chains. Longest chain 112 peptides. Score 0.932 Round 2: 1076 peptides, 20 chains. Longest chain 131 peptides. Score 0.941 Round 3: 1065 peptides, 23 chains. Longest chain 116 peptides. Score 0.935 Round 4: 1063 peptides, 29 chains. Longest chain 110 peptides. Score 0.927 Round 5: 1058 peptides, 27 chains. Longest chain 115 peptides. Score 0.929 Taking the results from Round 2 Chains 21, Residues 1056, Estimated correctness of the model 99.2 % 15 chains (989 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 197 A and 200 A Built loop between residues 162 C and 165 C Built loop between residues 103 B and 106 B Built loop between residues 193 B and 196 B Built loop between residues 136 D and 142 D Built loop between residues 177 D and 180 D 14 chains (1068 residues) following loop building 9 chains (1004 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9516 restraints for refining 8906 atoms. 1306 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1781 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 92 (80 requested) atoms. Cycle 32: After refmac, R = 0.1646 (Rfree = 0.000) for 8884 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. Cycle 33: After refmac, R = 0.1594 (Rfree = 0.000) for 8879 atoms. Found 80 (80 requested) and removed 82 (80 requested) atoms. Cycle 34: After refmac, R = 0.1564 (Rfree = 0.000) for 8874 atoms. Found 80 (80 requested) and removed 88 (80 requested) atoms. Cycle 35: After refmac, R = 0.1531 (Rfree = 0.000) for 8863 atoms. Found 80 (80 requested) and removed 86 (80 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.53 2.53 NCS extension: 5 residues added (264 deleted due to clashes), 8866 seeds are put forward Round 1: 1051 peptides, 29 chains. Longest chain 112 peptides. Score 0.925 Round 2: 1077 peptides, 15 chains. Longest chain 232 peptides. Score 0.947 Round 3: 1059 peptides, 25 chains. Longest chain 116 peptides. Score 0.932 Round 4: 1058 peptides, 27 chains. Longest chain 115 peptides. Score 0.929 Round 5: 1063 peptides, 28 chains. Longest chain 112 peptides. Score 0.929 Taking the results from Round 2 Chains 18, Residues 1062, Estimated correctness of the model 99.3 % 12 chains (1045 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 136 A and 140 A Built loop between residues 175 A and 180 A Built loop between residues 125 D and 130 D Built loop between residues 163 D and 166 D 11 chains (1069 residues) following loop building 8 chains (1058 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9114 restraints for refining 8906 atoms. 705 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1781 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 90 (80 requested) atoms. Cycle 37: After refmac, R = 0.1625 (Rfree = 0.000) for 8891 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. Cycle 38: After refmac, R = 0.1561 (Rfree = 0.000) for 8881 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. Cycle 39: After refmac, R = 0.1526 (Rfree = 0.000) for 8873 atoms. Found 80 (80 requested) and removed 92 (80 requested) atoms. Cycle 40: After refmac, R = 0.1508 (Rfree = 0.000) for 8857 atoms. Found 80 (80 requested) and removed 82 (80 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.53 2.53 NCS extension: 2 residues added (5 deleted due to clashes), 8864 seeds are put forward Round 1: 1058 peptides, 25 chains. Longest chain 112 peptides. Score 0.932 Round 2: 1069 peptides, 24 chains. Longest chain 117 peptides. Score 0.935 Round 3: 1058 peptides, 26 chains. Longest chain 116 peptides. Score 0.930 Round 4: 1062 peptides, 27 chains. Longest chain 169 peptides. Score 0.930 Round 5: 1058 peptides, 32 chains. Longest chain 97 peptides. Score 0.922 Taking the results from Round 2 Chains 25, Residues 1045, Estimated correctness of the model 99.0 % 19 chains (1021 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 126 A Built loop between residues 161 A and 166 A Built loop between residues 178 A and 181 A Built loop between residues 196 A and 200 A Built loop between residues 123 C and 126 C Built loop between residues 138 C and 140 C Built loop between residues 193 C and 196 C Built loop between residues 126 B and 129 B Built loop between residues 175 B and 179 B Built loop between residues 161 D and 165 D Built loop between residues 196 D and 205 D 12 chains (1070 residues) following loop building 8 chains (1053 residues) in sequence following loop building ------------------------------------------------------ 45394 reflections ( 99.69 % complete ) and 9184 restraints for refining 8906 atoms. 784 conditional restraints added. Observations/parameters ratio is 1.27 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1781 (Rfree = 0.000) for 8906 atoms. Found 80 (80 requested) and removed 92 (80 requested) atoms. Cycle 42: After refmac, R = 0.1616 (Rfree = 0.000) for 8891 atoms. Found 80 (80 requested) and removed 85 (80 requested) atoms. Cycle 43: After refmac, R = 0.1565 (Rfree = 0.000) for 8879 atoms. Found 80 (80 requested) and removed 90 (80 requested) atoms. Cycle 44: After refmac, R = 0.1522 (Rfree = 0.000) for 8866 atoms. Found 80 (80 requested) and removed 88 (80 requested) atoms. Cycle 45: After refmac, R = 0.1508 (Rfree = 0.000) for 8854 atoms. Found 80 (80 requested) and removed 90 (80 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.52 2.52 NCS extension: 0 residues added, 8851 seeds are put forward Round 1: 1061 peptides, 24 chains. Longest chain 112 peptides. Score 0.933 Round 2: 1071 peptides, 20 chains. Longest chain 198 peptides. Score 0.940 Round 3: 1068 peptides, 26 chains. Longest chain 115 peptides. Score 0.932 Round 4: 1056 peptides, 30 chains. Longest chain 122 peptides. Score 0.925 Round 5: 1068 peptides, 28 chains. Longest chain 98 peptides. Score 0.930 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 20, Residues 1051, Estimated correctness of the model 99.2 % 16 chains (1034 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 199 A and 205 A Built loop between residues 243 A and 246 A Built loop between residues 95 C and 98 C Built loop between residues 178 B and 181 B Built loop between residues 197 B and 200 B Built loop between residues 124 D and 127 D Built loop between residues 137 D and 140 D Built loop between residues 176 D and 180 D 12 chains (1071 residues) following loop building 8 chains (1054 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 45394 reflections ( 99.69 % complete ) and 8408 restraints for refining 8239 atoms. Observations/parameters ratio is 1.38 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2248 (Rfree = 0.000) for 8239 atoms. Found 60 (74 requested) and removed 0 (74 requested) atoms. Cycle 47: After refmac, R = 0.2055 (Rfree = 0.000) for 8239 atoms. Found 35 (75 requested) and removed 7 (75 requested) atoms. Cycle 48: After refmac, R = 0.1987 (Rfree = 0.000) for 8239 atoms. Found 16 (75 requested) and removed 13 (75 requested) atoms. Cycle 49: After refmac, R = 0.1967 (Rfree = 0.000) for 8239 atoms. Found 23 (75 requested) and removed 12 (75 requested) atoms. Writing output files ... TimeTaking 121.5