null Mon 24 Dec 00:28:18 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 1vme-1.8-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-1.8-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vme-1.8-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-1.8-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/1vme-1.8-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-1.8-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 00:28:22 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/1vme-1.8-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vme-1.8-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 901 and 0 Target number of residues in the AU: 901 Target solvent content: 0.4867 Checking the provided sequence file Detected sequence length: 410 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 820 Adjusted target solvent content: 0.53 Input MTZ file: 1vme-1.8-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: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-1.8-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.35 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: 48.998 1.802 Wilson plot Bfac: 20.79 81220 reflections ( 94.25 % complete ) and 0 restraints for refining 7285 atoms. Observations/parameters ratio is 2.79 ------------------------------------------------------ Starting model: R = 0.2993 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2496 (Rfree = 0.000) for 7285 atoms. Found 335 (335 requested) and removed 169 (167 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.88 1.81 NCS extension: 0 residues added, 7451 seeds are put forward Round 1: 717 peptides, 34 chains. Longest chain 82 peptides. Score 0.879 Round 2: 747 peptides, 25 chains. Longest chain 120 peptides. Score 0.910 Round 3: 755 peptides, 21 chains. Longest chain 92 peptides. Score 0.920 Round 4: 759 peptides, 18 chains. Longest chain 130 peptides. Score 0.927 Round 5: 761 peptides, 18 chains. Longest chain 155 peptides. Score 0.928 Taking the results from Round 5 Chains 19, Residues 743, Estimated correctness of the model 99.6 % 15 chains (711 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 161 A and 164 A Built loop between residues 208 A and 210 A Built loop between residues 249 A and 252 A Built loop between residues 309 A and 312 A Built loop between residues 328 A and 335 A Built loop between residues 362 A and 370 A Built loop between residues 390 A and 393 A Built loop between residues 22 B and 26 B Built loop between residues 43 B and 46 B Built loop between residues 327 B and 333 B Built loop between residues 362 B and 371 B 8 chains (783 residues) following loop building 4 chains (751 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7258 restraints for refining 6958 atoms. 984 conditional restraints added. Observations/parameters ratio is 2.92 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2612 (Rfree = 0.000) for 6958 atoms. Found 291 (320 requested) and removed 168 (160 requested) atoms. Cycle 2: After refmac, R = 0.2212 (Rfree = 0.000) for 7070 atoms. Found 241 (319 requested) and removed 94 (163 requested) atoms. Cycle 3: After refmac, R = 0.2055 (Rfree = 0.000) for 7200 atoms. Found 199 (325 requested) and removed 71 (166 requested) atoms. Cycle 4: After refmac, R = 0.1946 (Rfree = 0.000) for 7312 atoms. Found 201 (330 requested) and removed 79 (168 requested) atoms. Cycle 5: After refmac, R = 0.1890 (Rfree = 0.000) for 7421 atoms. Found 186 (335 requested) and removed 75 (171 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.86 1.79 NCS extension: 2 residues added (38 deleted due to clashes), 7547 seeds are put forward Round 1: 774 peptides, 13 chains. Longest chain 168 peptides. Score 0.940 Round 2: 776 peptides, 13 chains. Longest chain 137 peptides. Score 0.940 Round 3: 774 peptides, 13 chains. Longest chain 136 peptides. Score 0.940 Round 4: 774 peptides, 13 chains. Longest chain 168 peptides. Score 0.940 Round 5: 777 peptides, 14 chains. Longest chain 181 peptides. Score 0.939 Taking the results from Round 4 Chains 16, Residues 761, Estimated correctness of the model 99.7 % 13 chains (757 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 A and 26 A Built loop between residues 103 A and 106 A Built loop between residues 161 A and 164 A Built loop between residues 330 A and 337 A Built loop between residues 23 B and 27 B Built loop between residues 160 B and 164 B Built loop between residues 213 B and 216 B Built loop between residues 277 B and 280 B Built loop between residues 390 B and 395 B 6 chains (787 residues) following loop building 4 chains (784 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7104 restraints for refining 7277 atoms. 630 conditional restraints added. Observations/parameters ratio is 2.79 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2058 (Rfree = 0.000) for 7277 atoms. Found 253 (328 requested) and removed 184 (167 requested) atoms. Cycle 7: After refmac, R = 0.1922 (Rfree = 0.000) for 7342 atoms. Found 212 (324 requested) and removed 93 (169 requested) atoms. Cycle 8: After refmac, R = 0.1840 (Rfree = 0.000) for 7454 atoms. Found 193 (330 requested) and removed 90 (172 requested) atoms. Cycle 9: After refmac, R = 0.1797 (Rfree = 0.000) for 7554 atoms. Found 202 (334 requested) and removed 108 (174 requested) atoms. Cycle 10: After refmac, R = 0.1777 (Rfree = 0.000) for 7638 atoms. Found 177 (331 requested) and removed 110 (176 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.86 1.79 NCS extension: 0 residues added, 7709 seeds are put forward Round 1: 780 peptides, 11 chains. Longest chain 168 peptides. Score 0.945 Round 2: 781 peptides, 11 chains. Longest chain 253 peptides. Score 0.945 Round 3: 781 peptides, 13 chains. Longest chain 135 peptides. Score 0.941 Round 4: 777 peptides, 16 chains. Longest chain 137 peptides. Score 0.935 Round 5: 781 peptides, 11 chains. Longest chain 172 peptides. Score 0.945 Taking the results from Round 5 Chains 13, Residues 770, Estimated correctness of the model 99.7 % 11 chains (767 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 28 A Built loop between residues 157 A and 161 A Built loop between residues 329 A and 334 A Built loop between residues 362 A and 371 A Built loop between residues 23 B and 26 B Built loop between residues 103 B and 106 B Built loop between residues 161 B and 164 B Built loop between residues 203 B and 207 B Built loop between residues 330 B and 333 B 3 chains (798 residues) following loop building 2 chains (797 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7087 restraints for refining 7417 atoms. 517 conditional restraints added. Observations/parameters ratio is 2.74 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2012 (Rfree = 0.000) for 7417 atoms. Found 295 (314 requested) and removed 178 (170 requested) atoms. Cycle 12: After refmac, R = 0.1899 (Rfree = 0.000) for 7531 atoms. Found 228 (312 requested) and removed 105 (173 requested) atoms. Cycle 13: After refmac, R = 0.1827 (Rfree = 0.000) for 7649 atoms. Found 178 (317 requested) and removed 112 (176 requested) atoms. Cycle 14: After refmac, R = 0.1773 (Rfree = 0.000) for 7712 atoms. Found 184 (312 requested) and removed 90 (177 requested) atoms. Cycle 15: After refmac, R = 0.1742 (Rfree = 0.000) for 7801 atoms. Found 156 (316 requested) and removed 115 (179 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.86 1.79 NCS extension: 4 residues added (0 deleted due to clashes), 7855 seeds are put forward Round 1: 776 peptides, 12 chains. Longest chain 168 peptides. Score 0.942 Round 2: 780 peptides, 11 chains. Longest chain 168 peptides. Score 0.945 Round 3: 773 peptides, 13 chains. Longest chain 137 peptides. Score 0.940 Round 4: 774 peptides, 15 chains. Longest chain 168 peptides. Score 0.936 Round 5: 775 peptides, 16 chains. Longest chain 137 peptides. Score 0.935 Taking the results from Round 2 Chains 14, Residues 769, Estimated correctness of the model 99.7 % 11 chains (764 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 27 A Built loop between residues 161 A and 164 A Built loop between residues 363 A and 367 A Built loop between residues 23 B and 26 B Built loop between residues 161 B and 164 B Built loop between residues 190 B and 193 B Built loop between residues 360 B and 371 B 6 chains (791 residues) following loop building 4 chains (788 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7254 restraints for refining 7516 atoms. 752 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1981 (Rfree = 0.000) for 7516 atoms. Found 298 (298 requested) and removed 171 (173 requested) atoms. Cycle 17: After refmac, R = 0.1879 (Rfree = 0.000) for 7635 atoms. Found 191 (296 requested) and removed 100 (176 requested) atoms. Cycle 18: After refmac, R = 0.1797 (Rfree = 0.000) for 7724 atoms. Found 145 (292 requested) and removed 87 (178 requested) atoms. Cycle 19: After refmac, R = 0.1753 (Rfree = 0.000) for 7770 atoms. Found 168 (286 requested) and removed 89 (179 requested) atoms. Cycle 20: After refmac, R = 0.1727 (Rfree = 0.000) for 7845 atoms. Found 146 (282 requested) and removed 92 (180 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.86 1.79 NCS extension: 0 residues added, 7903 seeds are put forward Round 1: 773 peptides, 13 chains. Longest chain 138 peptides. Score 0.940 Round 2: 779 peptides, 12 chains. Longest chain 168 peptides. Score 0.943 Round 3: 778 peptides, 12 chains. Longest chain 162 peptides. Score 0.942 Round 4: 775 peptides, 16 chains. Longest chain 136 peptides. Score 0.935 Round 5: 773 peptides, 17 chains. Longest chain 137 peptides. Score 0.933 Taking the results from Round 2 Chains 14, Residues 767, Estimated correctness of the model 99.7 % 12 chains (764 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 26 A Built loop between residues 161 A and 164 A Built loop between residues 330 A and 335 A Built loop between residues 363 A and 367 A Built loop between residues 23 B and 27 B Built loop between residues 161 B and 164 B Built loop between residues 275 B and 278 B Built loop between residues 330 B and 334 B Built loop between residues 360 B and 371 B Built loop between residues 391 B and 394 B 3 chains (798 residues) following loop building 2 chains (797 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7173 restraints for refining 7543 atoms. 603 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1968 (Rfree = 0.000) for 7543 atoms. Found 264 (264 requested) and removed 163 (173 requested) atoms. Cycle 22: After refmac, R = 0.1872 (Rfree = 0.000) for 7629 atoms. Found 199 (260 requested) and removed 85 (176 requested) atoms. Cycle 23: After refmac, R = 0.1805 (Rfree = 0.000) for 7734 atoms. Found 178 (264 requested) and removed 92 (178 requested) atoms. Cycle 24: After refmac, R = 0.1769 (Rfree = 0.000) for 7813 atoms. Found 171 (259 requested) and removed 97 (180 requested) atoms. Cycle 25: After refmac, R = 0.1740 (Rfree = 0.000) for 7879 atoms. Found 172 (254 requested) and removed 108 (181 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.86 1.79 NCS extension: 12 residues added (14 deleted due to clashes), 7959 seeds are put forward Round 1: 779 peptides, 12 chains. Longest chain 166 peptides. Score 0.943 Round 2: 782 peptides, 12 chains. Longest chain 170 peptides. Score 0.943 Round 3: 776 peptides, 14 chains. Longest chain 137 peptides. Score 0.939 Round 4: 780 peptides, 13 chains. Longest chain 168 peptides. Score 0.941 Round 5: 776 peptides, 17 chains. Longest chain 137 peptides. Score 0.933 Taking the results from Round 2 Chains 15, Residues 770, Estimated correctness of the model 99.7 % 12 chains (765 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 26 A Built loop between residues 161 A and 164 A Built loop between residues 190 A and 193 A Built loop between residues 330 A and 334 A Built loop between residues 23 B and 27 B Built loop between residues 330 B and 333 B Built loop between residues 390 B and 395 B 7 chains (787 residues) following loop building 5 chains (783 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7320 restraints for refining 7524 atoms. 859 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1939 (Rfree = 0.000) for 7524 atoms. Found 235 (235 requested) and removed 145 (173 requested) atoms. Cycle 27: After refmac, R = 0.1847 (Rfree = 0.000) for 7604 atoms. Found 203 (232 requested) and removed 64 (175 requested) atoms. Cycle 28: After refmac, R = 0.1787 (Rfree = 0.000) for 7737 atoms. Found 172 (236 requested) and removed 79 (178 requested) atoms. Cycle 29: After refmac, R = 0.1754 (Rfree = 0.000) for 7829 atoms. Found 161 (238 requested) and removed 101 (180 requested) atoms. Cycle 30: After refmac, R = 0.1729 (Rfree = 0.000) for 7883 atoms. Found 177 (232 requested) and removed 97 (181 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.86 1.79 NCS extension: 14 residues added (340 deleted due to clashes), 7980 seeds are put forward Round 1: 779 peptides, 13 chains. Longest chain 166 peptides. Score 0.941 Round 2: 783 peptides, 11 chains. Longest chain 168 peptides. Score 0.945 Round 3: 783 peptides, 10 chains. Longest chain 164 peptides. Score 0.947 Round 4: 782 peptides, 13 chains. Longest chain 168 peptides. Score 0.942 Round 5: 777 peptides, 15 chains. Longest chain 125 peptides. Score 0.937 Taking the results from Round 3 Chains 11, Residues 773, Estimated correctness of the model 99.8 % 9 chains (739 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 26 A Built loop between residues 161 A and 168 A Built loop between residues 330 A and 334 A Built loop between residues 41 B and 48 B Built loop between residues 278 B and 281 B 5 chains (788 residues) following loop building 4 chains (758 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7577 restraints for refining 7540 atoms. 1217 conditional restraints added. Observations/parameters ratio is 2.69 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1933 (Rfree = 0.000) for 7540 atoms. Found 215 (215 requested) and removed 155 (173 requested) atoms. Cycle 32: After refmac, R = 0.1831 (Rfree = 0.000) for 7593 atoms. Found 202 (210 requested) and removed 58 (175 requested) atoms. Cycle 33: After refmac, R = 0.1772 (Rfree = 0.000) for 7730 atoms. Found 162 (214 requested) and removed 61 (178 requested) atoms. Cycle 34: After refmac, R = 0.1735 (Rfree = 0.000) for 7827 atoms. Found 140 (217 requested) and removed 81 (180 requested) atoms. Cycle 35: After refmac, R = 0.1704 (Rfree = 0.000) for 7881 atoms. Found 163 (211 requested) and removed 87 (181 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.86 1.79 NCS extension: 25 residues added (296 deleted due to clashes), 7985 seeds are put forward Round 1: 778 peptides, 13 chains. Longest chain 168 peptides. Score 0.941 Round 2: 774 peptides, 13 chains. Longest chain 138 peptides. Score 0.940 Round 3: 778 peptides, 14 chains. Longest chain 168 peptides. Score 0.939 Round 4: 778 peptides, 13 chains. Longest chain 167 peptides. Score 0.941 Round 5: 775 peptides, 17 chains. Longest chain 168 peptides. Score 0.933 Taking the results from Round 4 Chains 16, Residues 765, Estimated correctness of the model 99.7 % 13 chains (762 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 26 A Built loop between residues 161 A and 164 A Built loop between residues 329 A and 334 A Built loop between residues 363 A and 367 A Built loop between residues 23 B and 27 B Built loop between residues 161 B and 164 B Built loop between residues 277 B and 282 B Built loop between residues 330 B and 333 B Built loop between residues 362 B and 371 B Built loop between residues 390 B and 394 B 4 chains (796 residues) following loop building 3 chains (795 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7220 restraints for refining 7565 atoms. 663 conditional restraints added. Observations/parameters ratio is 2.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1969 (Rfree = 0.000) for 7565 atoms. Found 195 (195 requested) and removed 162 (174 requested) atoms. Cycle 37: After refmac, R = 0.1844 (Rfree = 0.000) for 7589 atoms. Found 189 (189 requested) and removed 51 (175 requested) atoms. Cycle 38: After refmac, R = 0.1780 (Rfree = 0.000) for 7720 atoms. Found 189 (192 requested) and removed 81 (178 requested) atoms. Cycle 39: After refmac, R = 0.1739 (Rfree = 0.000) for 7822 atoms. Found 173 (194 requested) and removed 98 (180 requested) atoms. Cycle 40: After refmac, R = 0.1712 (Rfree = 0.000) for 7894 atoms. Found 164 (189 requested) and removed 98 (182 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.86 1.79 NCS extension: 24 residues added (332 deleted due to clashes), 7991 seeds are put forward Round 1: 775 peptides, 14 chains. Longest chain 168 peptides. Score 0.938 Round 2: 777 peptides, 13 chains. Longest chain 168 peptides. Score 0.941 Round 3: 773 peptides, 17 chains. Longest chain 119 peptides. Score 0.933 Round 4: 780 peptides, 14 chains. Longest chain 137 peptides. Score 0.940 Round 5: 777 peptides, 15 chains. Longest chain 125 peptides. Score 0.937 Taking the results from Round 2 Chains 16, Residues 764, Estimated correctness of the model 99.7 % 13 chains (759 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 27 A Built loop between residues 161 A and 164 A Built loop between residues 327 A and 333 A Built loop between residues 362 A and 371 A Built loop between residues 390 A and 395 A Built loop between residues 22 B and 26 B Built loop between residues 161 B and 164 B Built loop between residues 190 B and 193 B Built loop between residues 330 B and 334 B Built loop between residues 363 B and 367 B Built loop between residues 389 B and 393 B 3 chains (798 residues) following loop building 2 chains (797 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7195 restraints for refining 7583 atoms. 625 conditional restraints added. Observations/parameters ratio is 2.68 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1951 (Rfree = 0.000) for 7583 atoms. Found 174 (174 requested) and removed 155 (174 requested) atoms. Cycle 42: After refmac, R = 0.1828 (Rfree = 0.000) for 7592 atoms. Found 175 (175 requested) and removed 49 (175 requested) atoms. Cycle 43: After refmac, R = 0.1767 (Rfree = 0.000) for 7711 atoms. Found 174 (177 requested) and removed 63 (177 requested) atoms. Cycle 44: After refmac, R = 0.1730 (Rfree = 0.000) for 7811 atoms. Found 172 (180 requested) and removed 100 (180 requested) atoms. Cycle 45: After refmac, R = 0.1702 (Rfree = 0.000) for 7879 atoms. Found 181 (181 requested) and removed 108 (181 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.86 1.79 NCS extension: 1 residues added (2 deleted due to clashes), 7959 seeds are put forward Round 1: 776 peptides, 13 chains. Longest chain 165 peptides. Score 0.940 Round 2: 775 peptides, 14 chains. Longest chain 136 peptides. Score 0.938 Round 3: 777 peptides, 14 chains. Longest chain 165 peptides. Score 0.939 Round 4: 774 peptides, 16 chains. Longest chain 136 peptides. Score 0.935 Round 5: 771 peptides, 14 chains. Longest chain 137 peptides. Score 0.937 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 763, Estimated correctness of the model 99.7 % 13 chains (759 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 23 A and 26 A Built loop between residues 161 A and 164 A Built loop between residues 327 A and 334 A Built loop between residues 363 A and 367 A Built loop between residues 22 B and 26 B Built loop between residues 41 B and 44 B Built loop between residues 161 B and 164 B Built loop between residues 275 B and 278 B Built loop between residues 330 B and 333 B Built loop between residues 359 B and 371 B Built loop between residues 390 B and 394 B 3 chains (798 residues) following loop building 2 chains (797 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 81220 reflections ( 94.25 % complete ) and 6570 restraints for refining 6415 atoms. Observations/parameters ratio is 3.17 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2439 (Rfree = 0.000) for 6415 atoms. Found 143 (147 requested) and removed 0 (147 requested) atoms. Cycle 47: After refmac, R = 0.2203 (Rfree = 0.000) for 6415 atoms. Found 61 (151 requested) and removed 0 (151 requested) atoms. Cycle 48: After refmac, R = 0.2044 (Rfree = 0.000) for 6415 atoms. Found 57 (152 requested) and removed 3 (152 requested) atoms. Cycle 49: After refmac, R = 0.1992 (Rfree = 0.000) for 6415 atoms. Found 15 (153 requested) and removed 2 (153 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 02:01:26 GMT 2018 Job finished. TimeTaking 93.13 Used memory is bytes: 10117160