Sun 23 Dec 22:22:53 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 1vp4-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vp4-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-1.8-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/1vp4-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-1.8-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 22:23:02 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/1vp4-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vp4-1.8-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 982 and 0 Target number of residues in the AU: 982 Target solvent content: 0.5064 Checking the provided sequence file Detected sequence length: 425 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 850 Adjusted target solvent content: 0.57 Input MTZ file: 1vp4-1.8-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: 170 Cell parameters: 164.860 164.860 68.609 90.000 90.000 120.000 Input sequence file: 1vp4-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 6800 target number of atoms Had to go as low as 0.50 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: 142.773 1.820 Wilson plot Bfac: 24.83 94163 reflections ( 98.74 % complete ) and 0 restraints for refining 7567 atoms. Observations/parameters ratio is 3.11 ------------------------------------------------------ Starting model: R = 0.3232 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2731 (Rfree = 0.000) for 7567 atoms. Found 280 (339 requested) and removed 173 (169 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.14 1.95 NCS extension: 0 residues added, 7674 seeds are put forward Round 1: 668 peptides, 62 chains. Longest chain 33 peptides. Score 0.728 Round 2: 743 peptides, 38 chains. Longest chain 57 peptides. Score 0.851 Round 3: 772 peptides, 19 chains. Longest chain 138 peptides. Score 0.906 Round 4: 780 peptides, 22 chains. Longest chain 133 peptides. Score 0.902 Round 5: 794 peptides, 15 chains. Longest chain 225 peptides. Score 0.920 Taking the results from Round 5 Chains 18, Residues 779, Estimated correctness of the model 99.5 % 10 chains (722 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 103 A Built loop between residues 138 A and 143 A Built loop between residues 112 B and 115 B Built loop between residues 137 B and 142 B Built loop between residues 152 B and 157 B Built loop between residues 184 B and 187 B Built loop between residues 198 B and 201 B 8 chains (796 residues) following loop building 3 chains (744 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7656 restraints for refining 7321 atoms. 1321 conditional restraints added. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2804 (Rfree = 0.000) for 7321 atoms. Found 291 (328 requested) and removed 170 (164 requested) atoms. Cycle 2: After refmac, R = 0.2510 (Rfree = 0.000) for 7426 atoms. Found 206 (326 requested) and removed 89 (166 requested) atoms. Cycle 3: After refmac, R = 0.2351 (Rfree = 0.000) for 7488 atoms. Found 137 (331 requested) and removed 54 (169 requested) atoms. Cycle 4: After refmac, R = 0.2224 (Rfree = 0.000) for 7518 atoms. Found 155 (332 requested) and removed 58 (169 requested) atoms. Cycle 5: After refmac, R = 0.2154 (Rfree = 0.000) for 7578 atoms. Found 151 (334 requested) and removed 62 (170 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.03 1.85 NCS extension: 33 residues added (402 deleted due to clashes), 7705 seeds are put forward Round 1: 811 peptides, 12 chains. Longest chain 136 peptides. Score 0.930 Round 2: 815 peptides, 9 chains. Longest chain 225 peptides. Score 0.936 Round 3: 811 peptides, 12 chains. Longest chain 135 peptides. Score 0.930 Round 4: 818 peptides, 9 chains. Longest chain 225 peptides. Score 0.937 Round 5: 812 peptides, 12 chains. Longest chain 209 peptides. Score 0.930 Taking the results from Round 4 Chains 14, Residues 809, Estimated correctness of the model 99.7 % 9 chains (802 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 31 A Built loop between residues 139 A and 143 A Built loop between residues 184 A and 187 A Built loop between residues 198 A and 201 A Built loop between residues 138 B and 143 B Built loop between residues 196 B and 201 B Built loop between residues 259 B and 262 B 3 chains (824 residues) following loop building 2 chains (823 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7319 restraints for refining 7451 atoms. 551 conditional restraints added. Observations/parameters ratio is 3.16 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2324 (Rfree = 0.000) for 7451 atoms. Found 277 (326 requested) and removed 168 (166 requested) atoms. Cycle 7: After refmac, R = 0.2121 (Rfree = 0.000) for 7553 atoms. Found 184 (324 requested) and removed 80 (169 requested) atoms. Cycle 8: After refmac, R = 0.2018 (Rfree = 0.000) for 7646 atoms. Found 169 (329 requested) and removed 77 (171 requested) atoms. Cycle 9: After refmac, R = 0.1951 (Rfree = 0.000) for 7718 atoms. Found 151 (332 requested) and removed 82 (173 requested) atoms. Cycle 10: After refmac, R = 0.1914 (Rfree = 0.000) for 7769 atoms. Found 185 (328 requested) and removed 105 (174 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.01 1.83 NCS extension: 11 residues added (7 deleted due to clashes), 7864 seeds are put forward Round 1: 816 peptides, 10 chains. Longest chain 135 peptides. Score 0.934 Round 2: 816 peptides, 9 chains. Longest chain 225 peptides. Score 0.936 Round 3: 817 peptides, 10 chains. Longest chain 135 peptides. Score 0.935 Round 4: 820 peptides, 8 chains. Longest chain 225 peptides. Score 0.939 Round 5: 816 peptides, 11 chains. Longest chain 135 peptides. Score 0.933 Taking the results from Round 4 Chains 10, Residues 812, Estimated correctness of the model 99.7 % 8 chains (805 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 28 A and 36 A Built loop between residues 140 A and 143 A Built loop between residues 196 A and 201 A Built loop between residues 115 B and 118 B Built loop between residues 140 B and 143 B Built loop between residues 198 B and 201 B 2 chains (824 residues) following loop building 2 chains (824 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7340 restraints for refining 7534 atoms. 565 conditional restraints added. Observations/parameters ratio is 3.12 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2082 (Rfree = 0.000) for 7534 atoms. Found 299 (310 requested) and removed 173 (168 requested) atoms. Cycle 12: After refmac, R = 0.1989 (Rfree = 0.000) for 7655 atoms. Found 203 (309 requested) and removed 102 (171 requested) atoms. Cycle 13: After refmac, R = 0.1921 (Rfree = 0.000) for 7749 atoms. Found 211 (305 requested) and removed 96 (173 requested) atoms. Cycle 14: After refmac, R = 0.1899 (Rfree = 0.000) for 7851 atoms. Found 187 (310 requested) and removed 133 (176 requested) atoms. Cycle 15: After refmac, R = 0.1874 (Rfree = 0.000) for 7897 atoms. Found 213 (304 requested) and removed 142 (177 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.01 1.83 NCS extension: 0 residues added, 7970 seeds are put forward Round 1: 815 peptides, 10 chains. Longest chain 135 peptides. Score 0.934 Round 2: 815 peptides, 10 chains. Longest chain 225 peptides. Score 0.934 Round 3: 815 peptides, 11 chains. Longest chain 135 peptides. Score 0.932 Round 4: 818 peptides, 7 chains. Longest chain 225 peptides. Score 0.940 Round 5: 814 peptides, 12 chains. Longest chain 135 peptides. Score 0.930 Taking the results from Round 4 Chains 9, Residues 811, Estimated correctness of the model 99.7 % 7 chains (807 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 115 A and 118 A Built loop between residues 138 A and 141 A Built loop between residues 198 A and 201 A Built loop between residues 26 B and 33 B Built loop between residues 198 B and 201 B 3 chains (824 residues) following loop building 2 chains (821 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7382 restraints for refining 7583 atoms. 622 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2041 (Rfree = 0.000) for 7583 atoms. Found 285 (285 requested) and removed 148 (169 requested) atoms. Cycle 17: After refmac, R = 0.1960 (Rfree = 0.000) for 7711 atoms. Found 190 (284 requested) and removed 97 (173 requested) atoms. Cycle 18: After refmac, R = 0.1892 (Rfree = 0.000) for 7796 atoms. Found 199 (279 requested) and removed 102 (174 requested) atoms. Cycle 19: After refmac, R = 0.1872 (Rfree = 0.000) for 7886 atoms. Found 176 (275 requested) and removed 155 (176 requested) atoms. Cycle 20: After refmac, R = 0.1832 (Rfree = 0.000) for 7899 atoms. Found 211 (269 requested) and removed 128 (177 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.00 1.82 NCS extension: 0 residues added, 7986 seeds are put forward Round 1: 814 peptides, 9 chains. Longest chain 135 peptides. Score 0.936 Round 2: 814 peptides, 9 chains. Longest chain 225 peptides. Score 0.936 Round 3: 817 peptides, 9 chains. Longest chain 169 peptides. Score 0.936 Round 4: 818 peptides, 10 chains. Longest chain 225 peptides. Score 0.935 Round 5: 814 peptides, 12 chains. Longest chain 135 peptides. Score 0.930 Taking the results from Round 3 Chains 12, Residues 808, Estimated correctness of the model 99.7 % 9 chains (801 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 32 A Built loop between residues 199 A and 202 A Built loop between residues 288 A and 291 A Built loop between residues 137 B and 143 B Built loop between residues 184 B and 187 B Built loop between residues 198 B and 201 B Built loop between residues 288 B and 291 B 3 chains (824 residues) following loop building 2 chains (821 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 94163 reflections ( 98.74 % complete ) and 7340 restraints for refining 7569 atoms. 580 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2033 (Rfree = 0.000) for 7569 atoms. Found 251 (251 requested) and removed 132 (169 requested) atoms. Cycle 22: After refmac, R = 0.1940 (Rfree = 0.000) for 7679 atoms. Found 201 (248 requested) and removed 89 (172 requested) atoms. Cycle 23: After refmac, R = 0.1884 (Rfree = 0.000) for 7784 atoms. Found 208 (251 requested) and removed 122 (174 requested) atoms. Cycle 24: After refmac, R = 0.1864 (Rfree = 0.000) for 7862 atoms. Found 201 (246 requested) and removed 143 (176 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1866 (Rfree = 0.000) for 7917 atoms. Found 207 (241 requested) and removed 172 (177 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.01 1.83 NCS extension: 11 residues added (6 deleted due to clashes), 7969 seeds are put forward Round 1: 818 peptides, 12 chains. Longest chain 135 peptides. Score 0.932 Round 2: 821 peptides, 10 chains. Longest chain 225 peptides. Score 0.936 Round 3: 820 peptides, 11 chains. Longest chain 135 peptides. Score 0.934 Round 4: 820 peptides, 11 chains. Longest chain 225 peptides. Score 0.934 Round 5: 820 peptides, 12 chains. Longest chain 135 peptides. Score 0.932 Taking the results from Round 2 Chains 12, Residues 811, Estimated correctness of the model 99.7 % 9 chains (806 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 26 A and 32 A Built loop between residues 140 A and 143 A Built loop between residues 198 A and 201 A Built loop between residues 335 A and 338 A Built loop between residues 59 B and 62 B Built loop between residues 139 B and 142 B Built loop between residues 198 B and 201 B 4 chains (827 residues) following loop building 2 chains (823 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7346 restraints for refining 7579 atoms. 568 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2035 (Rfree = 0.000) for 7579 atoms. Found 224 (224 requested) and removed 128 (169 requested) atoms. Cycle 27: After refmac, R = 0.1937 (Rfree = 0.000) for 7665 atoms. Found 212 (220 requested) and removed 88 (172 requested) atoms. Cycle 28: After refmac, R = 0.1902 (Rfree = 0.000) for 7786 atoms. Found 213 (223 requested) and removed 147 (174 requested) atoms. Cycle 29: After refmac, R = 0.1885 (Rfree = 0.000) for 7848 atoms. Found 200 (218 requested) and removed 171 (175 requested) atoms. Cycle 30: After refmac, R = 0.1876 (Rfree = 0.000) for 7871 atoms. Found 208 (212 requested) and removed 159 (176 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.01 1.83 NCS extension: 10 residues added (7 deleted due to clashes), 7934 seeds are put forward Round 1: 817 peptides, 13 chains. Longest chain 135 peptides. Score 0.930 Round 2: 817 peptides, 9 chains. Longest chain 225 peptides. Score 0.936 Round 3: 819 peptides, 15 chains. Longest chain 135 peptides. Score 0.927 Round 4: 822 peptides, 11 chains. Longest chain 225 peptides. Score 0.934 Round 5: 818 peptides, 15 chains. Longest chain 135 peptides. Score 0.926 Taking the results from Round 2 Chains 9, Residues 808, Estimated correctness of the model 99.7 % 7 chains (789 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 139 A and 142 A Built loop between residues 197 A and 201 A Built loop between residues 115 B and 118 B Built loop between residues 140 B and 144 B Built loop between residues 198 B and 201 B 4 chains (820 residues) following loop building 2 chains (801 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7487 restraints for refining 7523 atoms. 817 conditional restraints added. Observations/parameters ratio is 3.13 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2009 (Rfree = 0.000) for 7523 atoms. Found 195 (195 requested) and removed 107 (168 requested) atoms. Cycle 32: After refmac, R = 0.1910 (Rfree = 0.000) for 7607 atoms. Found 191 (191 requested) and removed 86 (170 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1864 (Rfree = 0.000) for 7710 atoms. Found 193 (193 requested) and removed 114 (172 requested) atoms. Cycle 34: After refmac, R = 0.1858 (Rfree = 0.000) for 7784 atoms. Found 188 (188 requested) and removed 153 (174 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1850 (Rfree = 0.000) for 7815 atoms. Found 182 (182 requested) and removed 161 (175 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.00 1.82 NCS extension: 10 residues added (9 deleted due to clashes), 7848 seeds are put forward Round 1: 815 peptides, 14 chains. Longest chain 135 peptides. Score 0.927 Round 2: 817 peptides, 12 chains. Longest chain 225 peptides. Score 0.931 Round 3: 821 peptides, 12 chains. Longest chain 135 peptides. Score 0.932 Round 4: 819 peptides, 13 chains. Longest chain 225 peptides. Score 0.930 Round 5: 819 peptides, 15 chains. Longest chain 135 peptides. Score 0.927 Taking the results from Round 3 Chains 13, Residues 809, Estimated correctness of the model 99.6 % 11 chains (799 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 33 A Built loop between residues 140 A and 143 A Built loop between residues 198 A and 201 A Built loop between residues 288 A and 291 A Built loop between residues 115 B and 118 B Built loop between residues 139 B and 144 B Built loop between residues 198 B and 201 B Built loop between residues 259 B and 264 B Built loop between residues 288 B and 291 B 3 chains (831 residues) following loop building 2 chains (824 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7384 restraints for refining 7594 atoms. 582 conditional restraints added. Observations/parameters ratio is 3.10 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2038 (Rfree = 0.000) for 7594 atoms. Found 170 (170 requested) and removed 142 (170 requested) atoms. Cycle 37: After refmac, R = 0.1937 (Rfree = 0.000) for 7617 atoms. Found 170 (170 requested) and removed 69 (170 requested) atoms. Cycle 38: After refmac, R = 0.1881 (Rfree = 0.000) for 7713 atoms. Found 172 (172 requested) and removed 104 (172 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1847 (Rfree = 0.000) for 7776 atoms. Found 174 (174 requested) and removed 132 (174 requested) atoms. Cycle 40: After refmac, R = 0.1858 (Rfree = 0.000) for 7815 atoms. Found 175 (175 requested) and removed 146 (175 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.01 1.83 NCS extension: 10 residues added (7 deleted due to clashes), 7857 seeds are put forward Round 1: 823 peptides, 11 chains. Longest chain 135 peptides. Score 0.934 Round 2: 823 peptides, 12 chains. Longest chain 225 peptides. Score 0.933 Round 3: 822 peptides, 11 chains. Longest chain 135 peptides. Score 0.934 Round 4: 825 peptides, 10 chains. Longest chain 225 peptides. Score 0.936 Round 5: 821 peptides, 15 chains. Longest chain 135 peptides. Score 0.927 Taking the results from Round 4 Chains 10, Residues 815, Estimated correctness of the model 99.7 % 9 chains (808 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 32 A Built loop between residues 140 A and 143 A Built loop between residues 198 A and 201 A Built loop between residues 59 B and 62 B Built loop between residues 115 B and 118 B Built loop between residues 140 B and 144 B Built loop between residues 198 B and 201 B 3 chains (832 residues) following loop building 2 chains (825 residues) in sequence following loop building ------------------------------------------------------ 94163 reflections ( 98.74 % complete ) and 7380 restraints for refining 7567 atoms. 567 conditional restraints added. Observations/parameters ratio is 3.11 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2016 (Rfree = 0.000) for 7567 atoms. Found 169 (169 requested) and removed 135 (169 requested) atoms. Cycle 42: After refmac, R = 0.1916 (Rfree = 0.000) for 7598 atoms. Found 170 (170 requested) and removed 54 (170 requested) atoms. Cycle 43: After refmac, R = 0.1862 (Rfree = 0.000) for 7707 atoms. Found 172 (172 requested) and removed 100 (172 requested) atoms. Cycle 44: After refmac, R = 0.1840 (Rfree = 0.000) for 7775 atoms. Found 174 (174 requested) and removed 110 (174 requested) atoms. Cycle 45: After refmac, R = 0.1814 (Rfree = 0.000) for 7834 atoms. Found 175 (175 requested) and removed 138 (175 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.00 1.82 NCS extension: 10 residues added (7 deleted due to clashes), 7885 seeds are put forward Round 1: 819 peptides, 13 chains. Longest chain 135 peptides. Score 0.930 Round 2: 822 peptides, 13 chains. Longest chain 195 peptides. Score 0.931 Round 3: 823 peptides, 11 chains. Longest chain 135 peptides. Score 0.934 Round 4: 823 peptides, 10 chains. Longest chain 225 peptides. Score 0.936 Round 5: 821 peptides, 13 chains. Longest chain 134 peptides. Score 0.930 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 12, Residues 813, Estimated correctness of the model 99.7 % 9 chains (790 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 26 A and 32 A Built loop between residues 115 A and 118 A Built loop between residues 138 A and 141 A Built loop between residues 198 A and 201 A Built loop between residues 115 B and 118 B Built loop between residues 138 B and 141 B Built loop between residues 197 B and 201 B 4 chains (830 residues) following loop building 2 chains (808 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 94163 reflections ( 98.74 % complete ) and 6733 restraints for refining 6598 atoms. Observations/parameters ratio is 3.57 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2442 (Rfree = 0.000) for 6598 atoms. Found 147 (147 requested) and removed 0 (147 requested) atoms. Cycle 47: After refmac, R = 0.2257 (Rfree = 0.000) for 6598 atoms. Found 71 (151 requested) and removed 3 (151 requested) atoms. Cycle 48: After refmac, R = 0.2111 (Rfree = 0.000) for 6598 atoms. Found 37 (152 requested) and removed 9 (152 requested) atoms. Cycle 49: After refmac, R = 0.2045 (Rfree = 0.000) for 6598 atoms. Found 20 (153 requested) and removed 7 (153 requested) atoms. Writing output files ... TimeTaking 124.02