null Sun 23 Dec 22:23:10 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 1vme-1.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vme-1.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vme-1.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-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/1vme-1.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-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 22:23:19 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/1vme-1.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vme-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 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-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: 4 Cell parameters: 55.242 95.831 90.130 90.000 95.426 90.000 Input sequence file: 1vme-1.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 6560 target number of atoms Had to go as low as 0.40 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 48.998 1.802 Wilson plot Bfac: 20.79 81220 reflections ( 94.25 % complete ) and 0 restraints for refining 7226 atoms. Observations/parameters ratio is 2.81 ------------------------------------------------------ Starting model: R = 0.3025 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2522 (Rfree = 0.000) for 7226 atoms. Found 333 (333 requested) and removed 171 (166 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.88 1.81 NCS extension: 0 residues added, 7388 seeds are put forward Round 1: 689 peptides, 38 chains. Longest chain 56 peptides. Score 0.855 Round 2: 731 peptides, 24 chains. Longest chain 150 peptides. Score 0.907 Round 3: 746 peptides, 19 chains. Longest chain 122 peptides. Score 0.922 Round 4: 755 peptides, 19 chains. Longest chain 115 peptides. Score 0.924 Round 5: 756 peptides, 21 chains. Longest chain 117 peptides. Score 0.921 Taking the results from Round 4 Chains 22, Residues 736, Estimated correctness of the model 99.5 % 17 chains (711 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 A and 26 A Built loop between residues 42 A and 48 A Built loop between residues 161 A and 164 A Built loop between residues 201 A and 204 A Built loop between residues 271 A and 275 A Built loop between residues 330 A and 333 A Built loop between residues 360 A and 371 A Built loop between residues 23 B and 27 B Built loop between residues 102 B and 105 B Built loop between residues 161 B and 164 B Built loop between residues 274 B and 277 B Built loop between residues 327 B and 335 B Built loop between residues 362 B and 373 B 8 chains (788 residues) following loop building 4 chains (764 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7125 restraints for refining 6994 atoms. 729 conditional restraints added. Observations/parameters ratio is 2.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2591 (Rfree = 0.000) for 6994 atoms. Found 274 (322 requested) and removed 167 (161 requested) atoms. Cycle 2: After refmac, R = 0.2190 (Rfree = 0.000) for 7092 atoms. Found 237 (320 requested) and removed 80 (163 requested) atoms. Cycle 3: After refmac, R = 0.2038 (Rfree = 0.000) for 7233 atoms. Found 210 (327 requested) and removed 85 (167 requested) atoms. Cycle 4: After refmac, R = 0.1925 (Rfree = 0.000) for 7337 atoms. Found 207 (332 requested) and removed 65 (169 requested) atoms. Cycle 5: After refmac, R = 0.1863 (Rfree = 0.000) for 7466 atoms. Found 178 (337 requested) and removed 99 (172 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.86 1.79 NCS extension: 7 residues added (369 deleted due to clashes), 7565 seeds are put forward Round 1: 775 peptides, 14 chains. Longest chain 170 peptides. Score 0.938 Round 2: 783 peptides, 10 chains. Longest chain 200 peptides. Score 0.947 Round 3: 777 peptides, 12 chains. Longest chain 170 peptides. Score 0.942 Round 4: 774 peptides, 15 chains. Longest chain 137 peptides. Score 0.936 Round 5: 768 peptides, 17 chains. Longest chain 137 peptides. Score 0.931 Taking the results from Round 2 Chains 11, Residues 773, Estimated correctness of the model 99.8 % 9 chains (742 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 A and 26 A Built loop between residues 330 A and 334 A Built loop between residues 363 A and 369 A Built loop between residues 159 B and 164 B Built loop between residues 362 B and 370 B Built loop between residues 390 B and 394 B 4 chains (795 residues) following loop building 3 chains (767 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7331 restraints for refining 7323 atoms. 890 conditional restraints added. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2249 (Rfree = 0.000) for 7323 atoms. Found 224 (324 requested) and removed 180 (168 requested) atoms. Cycle 7: After refmac, R = 0.2124 (Rfree = 0.000) for 7366 atoms. Found 182 (319 requested) and removed 51 (169 requested) atoms. Cycle 8: After refmac, R = 0.1957 (Rfree = 0.000) for 7491 atoms. Found 166 (324 requested) and removed 65 (172 requested) atoms. Cycle 9: After refmac, R = 0.1862 (Rfree = 0.000) for 7581 atoms. Found 174 (329 requested) and removed 67 (175 requested) atoms. Cycle 10: After refmac, R = 0.1820 (Rfree = 0.000) for 7681 atoms. Found 167 (333 requested) and removed 101 (177 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.86 1.79 NCS extension: 35 residues added (358 deleted due to clashes), 7788 seeds are put forward Round 1: 777 peptides, 14 chains. Longest chain 167 peptides. Score 0.939 Round 2: 779 peptides, 12 chains. Longest chain 167 peptides. Score 0.943 Round 3: 781 peptides, 12 chains. Longest chain 166 peptides. Score 0.943 Round 4: 776 peptides, 16 chains. Longest chain 137 peptides. Score 0.935 Round 5: 777 peptides, 16 chains. Longest chain 136 peptides. Score 0.935 Taking the results from Round 3 Chains 14, Residues 769, Estimated correctness of the model 99.7 % 12 chains (767 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 A and 25 A Built loop between residues 161 A and 164 A Built loop between residues 328 A and 334 A Built loop between residues 363 A and 367 A Built loop between residues 390 A and 395 A Built loop between residues 23 B and 27 B Built loop between residues 161 B and 164 B Built loop between residues 209 B and 214 B Built loop between residues 276 B and 279 B Built loop between residues 364 B and 370 B 2 chains (799 residues) following loop building 2 chains (799 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7144 restraints for refining 7491 atoms. 555 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2025 (Rfree = 0.000) for 7491 atoms. Found 268 (317 requested) and removed 183 (172 requested) atoms. Cycle 12: After refmac, R = 0.1910 (Rfree = 0.000) for 7572 atoms. Found 190 (314 requested) and removed 89 (174 requested) atoms. Cycle 13: After refmac, R = 0.1850 (Rfree = 0.000) for 7669 atoms. Found 154 (318 requested) and removed 105 (176 requested) atoms. Cycle 14: After refmac, R = 0.1807 (Rfree = 0.000) for 7713 atoms. Found 173 (312 requested) and removed 89 (177 requested) atoms. Cycle 15: After refmac, R = 0.1799 (Rfree = 0.000) for 7787 atoms. Found 159 (309 requested) and removed 115 (179 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.86 1.79 NCS extension: 0 residues added, 7838 seeds are put forward Round 1: 773 peptides, 15 chains. Longest chain 137 peptides. Score 0.936 Round 2: 777 peptides, 14 chains. Longest chain 168 peptides. Score 0.939 Round 3: 779 peptides, 12 chains. Longest chain 137 peptides. Score 0.943 Round 4: 777 peptides, 16 chains. Longest chain 121 peptides. Score 0.935 Round 5: 783 peptides, 12 chains. Longest chain 137 peptides. Score 0.943 Taking the results from Round 5 Chains 13, Residues 771, Estimated correctness of the model 99.7 % 11 chains (763 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 A and 26 A Built loop between residues 161 A and 164 A Built loop between residues 216 A and 227 A Built loop between residues 328 A and 334 A Built loop between residues 363 A and 367 A Built loop between residues 142 B and 145 B Built loop between residues 161 B and 164 B Built loop between residues 277 B and 280 B Built loop between residues 363 B and 371 B 2 chains (799 residues) following loop building 2 chains (799 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7102 restraints for refining 7452 atoms. 513 conditional restraints added. Observations/parameters ratio is 2.72 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2006 (Rfree = 0.000) for 7452 atoms. Found 287 (288 requested) and removed 163 (171 requested) atoms. Cycle 17: After refmac, R = 0.1910 (Rfree = 0.000) for 7569 atoms. Found 180 (286 requested) and removed 83 (174 requested) atoms. Cycle 18: After refmac, R = 0.1832 (Rfree = 0.000) for 7661 atoms. Found 168 (289 requested) and removed 73 (176 requested) atoms. Cycle 19: After refmac, R = 0.1787 (Rfree = 0.000) for 7754 atoms. Found 160 (293 requested) and removed 102 (178 requested) atoms. Cycle 20: After refmac, R = 0.1756 (Rfree = 0.000) for 7805 atoms. Found 188 (288 requested) and removed 99 (180 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.86 1.79 NCS extension: 1 residues added (3 deleted due to clashes), 7899 seeds are put forward Round 1: 788 peptides, 11 chains. Longest chain 170 peptides. Score 0.946 Round 2: 788 peptides, 10 chains. Longest chain 157 peptides. Score 0.948 Round 3: 782 peptides, 13 chains. Longest chain 170 peptides. Score 0.942 Round 4: 785 peptides, 12 chains. Longest chain 194 peptides. Score 0.944 Round 5: 784 peptides, 13 chains. Longest chain 137 peptides. Score 0.942 Taking the results from Round 2 Chains 11, Residues 778, Estimated correctness of the model 99.8 % 10 chains (777 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 A and 26 A Built loop between residues 119 A and 122 A Built loop between residues 277 A and 280 A Built loop between residues 367 A and 372 A Built loop between residues 23 B and 26 B Built loop between residues 161 B and 164 B Built loop between residues 274 B and 278 B Built loop between residues 330 B and 334 B 3 chains (799 residues) following loop building 2 chains (798 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7182 restraints for refining 7482 atoms. 601 conditional restraints added. Observations/parameters ratio is 2.71 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1968 (Rfree = 0.000) for 7482 atoms. Found 269 (269 requested) and removed 170 (172 requested) atoms. Cycle 22: After refmac, R = 0.1878 (Rfree = 0.000) for 7576 atoms. Found 197 (265 requested) and removed 98 (174 requested) atoms. Cycle 23: After refmac, R = 0.1815 (Rfree = 0.000) for 7672 atoms. Found 186 (268 requested) and removed 98 (176 requested) atoms. Cycle 24: After refmac, R = 0.1782 (Rfree = 0.000) for 7750 atoms. Found 182 (264 requested) and removed 118 (178 requested) atoms. Cycle 25: After refmac, R = 0.1741 (Rfree = 0.000) for 7808 atoms. Found 195 (259 requested) and removed 107 (180 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.86 1.79 NCS extension: 9 residues added (36 deleted due to clashes), 7910 seeds are put forward Round 1: 787 peptides, 10 chains. Longest chain 169 peptides. Score 0.948 Round 2: 792 peptides, 11 chains. Longest chain 168 peptides. Score 0.947 Round 3: 786 peptides, 15 chains. Longest chain 125 peptides. Score 0.939 Round 4: 789 peptides, 15 chains. Longest chain 129 peptides. Score 0.940 Round 5: 789 peptides, 16 chains. Longest chain 137 peptides. Score 0.938 Taking the results from Round 1 Chains 11, Residues 777, Estimated correctness of the model 99.8 % 10 chains (774 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 23 A and 26 A Built loop between residues 159 A and 164 A Built loop between residues 331 A and 334 A Built loop between residues 362 A and 369 A Built loop between residues 23 B and 26 B Built loop between residues 161 B and 164 B Built loop between residues 328 B and 334 B Built loop between residues 366 B and 369 B 2 chains (799 residues) following loop building 2 chains (799 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7199 restraints for refining 7520 atoms. 610 conditional restraints added. Observations/parameters ratio is 2.70 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1948 (Rfree = 0.000) for 7520 atoms. Found 242 (242 requested) and removed 173 (173 requested) atoms. Cycle 27: After refmac, R = 0.1863 (Rfree = 0.000) for 7585 atoms. Found 193 (237 requested) and removed 88 (174 requested) atoms. Cycle 28: After refmac, R = 0.1798 (Rfree = 0.000) for 7684 atoms. Found 199 (241 requested) and removed 80 (177 requested) atoms. Cycle 29: After refmac, R = 0.1756 (Rfree = 0.000) for 7801 atoms. Found 161 (244 requested) and removed 106 (179 requested) atoms. Cycle 30: After refmac, R = 0.1742 (Rfree = 0.000) for 7849 atoms. Found 175 (239 requested) and removed 106 (181 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.86 1.79 NCS extension: 10 residues added (35 deleted due to clashes), 7932 seeds are put forward Round 1: 788 peptides, 11 chains. Longest chain 166 peptides. Score 0.946 Round 2: 785 peptides, 13 chains. Longest chain 138 peptides. Score 0.942 Round 3: 787 peptides, 13 chains. Longest chain 168 peptides. Score 0.943 Round 4: 782 peptides, 17 chains. Longest chain 119 peptides. Score 0.935 Round 5: 787 peptides, 13 chains. Longest chain 123 peptides. Score 0.943 Taking the results from Round 1 Chains 13, Residues 777, Estimated correctness of the model 99.8 % 10 chains (744 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 328 A and 334 A Built loop between residues 23 B and 26 B Built loop between residues 41 B and 44 B Built loop between residues 161 B and 164 B 7 chains (792 residues) following loop building 4 chains (759 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7635 restraints for refining 7590 atoms. 1247 conditional restraints added. Observations/parameters ratio is 2.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1991 (Rfree = 0.000) for 7590 atoms. Found 224 (224 requested) and removed 192 (175 requested) atoms. Cycle 32: After refmac, R = 0.1866 (Rfree = 0.000) for 7612 atoms. Found 194 (218 requested) and removed 62 (175 requested) atoms. Cycle 33: After refmac, R = 0.1791 (Rfree = 0.000) for 7740 atoms. Found 179 (221 requested) and removed 81 (178 requested) atoms. Cycle 34: After refmac, R = 0.1746 (Rfree = 0.000) for 7832 atoms. Found 171 (224 requested) and removed 90 (180 requested) atoms. Cycle 35: After refmac, R = 0.1721 (Rfree = 0.000) for 7907 atoms. Found 146 (218 requested) and removed 90 (182 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.86 1.79 NCS extension: 105 residues added (289 deleted due to clashes), 8073 seeds are put forward Round 1: 778 peptides, 15 chains. Longest chain 168 peptides. Score 0.937 Round 2: 785 peptides, 12 chains. Longest chain 168 peptides. Score 0.944 Round 3: 776 peptides, 16 chains. Longest chain 136 peptides. Score 0.935 Round 4: 777 peptides, 15 chains. Longest chain 168 peptides. Score 0.937 Round 5: 781 peptides, 14 chains. Longest chain 168 peptides. Score 0.940 Taking the results from Round 2 Chains 14, Residues 773, Estimated correctness of the model 99.7 % 11 chains (741 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 334 A Built loop between residues 363 A and 368 A Built loop between residues 23 B and 26 B Built loop between residues 74 B and 77 B Built loop between residues 161 B and 164 B 7 chains (790 residues) following loop building 4 chains (758 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7555 restraints for refining 7588 atoms. 1181 conditional restraints added. Observations/parameters ratio is 2.68 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1958 (Rfree = 0.000) for 7588 atoms. Found 202 (202 requested) and removed 190 (174 requested) atoms. Cycle 37: After refmac, R = 0.1837 (Rfree = 0.000) for 7590 atoms. Found 196 (196 requested) and removed 63 (175 requested) atoms. Cycle 38: After refmac, R = 0.1770 (Rfree = 0.000) for 7718 atoms. Found 175 (199 requested) and removed 64 (178 requested) atoms. Cycle 39: After refmac, R = 0.1740 (Rfree = 0.000) for 7824 atoms. Found 149 (202 requested) and removed 87 (180 requested) atoms. Cycle 40: After refmac, R = 0.1723 (Rfree = 0.000) for 7876 atoms. Found 164 (196 requested) and removed 93 (181 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.86 1.79 NCS extension: 162 residues added (231 deleted due to clashes), 8114 seeds are put forward Round 1: 778 peptides, 13 chains. Longest chain 168 peptides. Score 0.941 Round 2: 781 peptides, 13 chains. Longest chain 137 peptides. Score 0.941 Round 3: 777 peptides, 16 chains. Longest chain 137 peptides. Score 0.935 Round 4: 772 peptides, 17 chains. Longest chain 119 peptides. Score 0.932 Round 5: 783 peptides, 15 chains. Longest chain 137 peptides. Score 0.939 Taking the results from Round 2 Chains 15, Residues 768, Estimated correctness of the model 99.7 % 11 chains (731 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 22 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 328 A and 334 A Built loop between residues 362 A and 368 A Built loop between residues 23 B and 26 B Built loop between residues 161 B and 164 B 8 chains (789 residues) following loop building 4 chains (752 residues) in sequence following loop building ------------------------------------------------------ 81220 reflections ( 94.25 % complete ) and 7705 restraints for refining 7609 atoms. 1353 conditional restraints added. Observations/parameters ratio is 2.67 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1963 (Rfree = 0.000) for 7609 atoms. Found 182 (182 requested) and removed 177 (175 requested) atoms. Cycle 42: After refmac, R = 0.1834 (Rfree = 0.000) for 7604 atoms. Found 175 (175 requested) and removed 48 (175 requested) atoms. Cycle 43: After refmac, R = 0.1769 (Rfree = 0.000) for 7724 atoms. Found 168 (178 requested) and removed 64 (178 requested) atoms. Cycle 44: After refmac, R = 0.1734 (Rfree = 0.000) for 7821 atoms. Found 160 (180 requested) and removed 80 (180 requested) atoms. Cycle 45: After refmac, R = 0.1712 (Rfree = 0.000) for 7897 atoms. Found 175 (182 requested) and removed 103 (182 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.86 1.79 NCS extension: 139 residues added (255 deleted due to clashes), 8115 seeds are put forward Round 1: 774 peptides, 14 chains. Longest chain 168 peptides. Score 0.938 Round 2: 778 peptides, 13 chains. Longest chain 165 peptides. Score 0.941 Round 3: 774 peptides, 16 chains. Longest chain 137 peptides. Score 0.935 Round 4: 774 peptides, 16 chains. Longest chain 137 peptides. Score 0.935 Round 5: 773 peptides, 17 chains. Longest chain 136 peptides. Score 0.933 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 15, Residues 765, Estimated correctness of the model 99.7 % 11 chains (729 residues) have been docked in sequence Sequence coverage is 95 % 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 335 A Built loop between residues 363 A and 372 A Built loop between residues 23 B and 26 B Built loop between residues 161 B and 164 B Built loop between residues 391 B and 394 B 7 chains (787 residues) following loop building 4 chains (754 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 81220 reflections ( 94.25 % complete ) and 6349 restraints for refining 6207 atoms. Observations/parameters ratio is 3.27 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2674 (Rfree = 0.000) for 6207 atoms. Found 143 (143 requested) and removed 0 (143 requested) atoms. Cycle 47: After refmac, R = 0.2459 (Rfree = 0.000) for 6207 atoms. Found 61 (146 requested) and removed 0 (146 requested) atoms. Cycle 48: After refmac, R = 0.2288 (Rfree = 0.000) for 6207 atoms. Found 51 (147 requested) and removed 8 (147 requested) atoms. Cycle 49: After refmac, R = 0.2254 (Rfree = 0.000) for 6207 atoms. Found 26 (148 requested) and removed 7 (148 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 00:19:48 GMT 2018 Job finished. TimeTaking 116.63 Used memory is bytes: 5352000