null Mon 24 Dec 01:04:51 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 1vkm-2.6-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-2.6-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/1vkm-2.6-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-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/1vkm-2.6-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-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 01:04:56 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/1vkm-2.6-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-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 1469 and 0 Target number of residues in the AU: 1469 Target solvent content: 0.5273 Checking the provided sequence file Detected sequence length: 297 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1782 Adjusted target solvent content: 0.43 Input MTZ file: 1vkm-2.6-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: 91.732 131.100 139.844 90.000 90.000 90.000 Input sequence file: 1vkm-2.6-parrot-mrncs.fasta_lf Building free atoms model in initial map for 14256 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 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: 75.160 2.600 Wilson plot Bfac: 29.58 52578 reflections ( 99.99 % complete ) and 0 restraints for refining 15825 atoms. Observations/parameters ratio is 0.83 ------------------------------------------------------ Starting model: R = 0.2893 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1892 (Rfree = 0.000) for 15825 atoms. Found 210 (256 requested) and removed 152 (128 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.40 2.64 NCS extension: 0 residues added, 15883 seeds are put forward Round 1: 1210 peptides, 171 chains. Longest chain 28 peptides. Score 0.630 Round 2: 1411 peptides, 113 chains. Longest chain 68 peptides. Score 0.841 Round 3: 1511 peptides, 73 chains. Longest chain 88 peptides. Score 0.911 Round 4: 1567 peptides, 62 chains. Longest chain 138 peptides. Score 0.929 Round 5: 1581 peptides, 57 chains. Longest chain 162 peptides. Score 0.935 Taking the results from Round 5 Chains 65, Residues 1524, Estimated correctness of the model 98.9 % 36 chains (1348 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 29 A Built loop between residues 50 A and 53 A Built loop between residues 71 A and 74 A Built loop between residues 97 A and 100 A Built loop between residues 175 A and 184 A Built loop between residues 118 C and 121 C Built loop between residues 159 C and 163 C Built loop between residues 71 B and 74 B Built loop between residues 178 B and 185 B Built loop between residues 203 B and 209 B Built loop between residues 72 E and 76 E Built loop between residues 114 D and 117 D Built loop between residues 215 D and 218 D Built loop between residues 20 F and 25 F Built loop between residues 133 F and 136 F 46 chains (1571 residues) following loop building 21 chains (1402 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 16085 restraints for refining 14331 atoms. 4387 conditional restraints added. Observations/parameters ratio is 0.92 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2481 (Rfree = 0.000) for 14331 atoms. Found 226 (232 requested) and removed 158 (116 requested) atoms. Cycle 2: After refmac, R = 0.2213 (Rfree = 0.000) for 14222 atoms. Found 167 (228 requested) and removed 136 (116 requested) atoms. Cycle 3: After refmac, R = 0.2130 (Rfree = 0.000) for 14167 atoms. Found 115 (222 requested) and removed 132 (115 requested) atoms. Cycle 4: After refmac, R = 0.2166 (Rfree = 0.000) for 14097 atoms. Found 92 (215 requested) and removed 123 (114 requested) atoms. Cycle 5: After refmac, R = 0.2008 (Rfree = 0.000) for 14015 atoms. Found 113 (210 requested) and removed 128 (114 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.39 2.63 NCS extension: 156 residues added (1374 deleted due to clashes), 14180 seeds are put forward Round 1: 1632 peptides, 40 chains. Longest chain 250 peptides. Score 0.953 Round 2: 1643 peptides, 40 chains. Longest chain 153 peptides. Score 0.954 Round 3: 1636 peptides, 41 chains. Longest chain 124 peptides. Score 0.953 Round 4: 1630 peptides, 49 chains. Longest chain 107 peptides. Score 0.947 Round 5: 1623 peptides, 52 chains. Longest chain 109 peptides. Score 0.944 Taking the results from Round 2 Chains 43, Residues 1603, Estimated correctness of the model 99.4 % 31 chains (1488 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 28 A and 32 A Built loop between residues 90 A and 93 A Built loop between residues 140 A and 143 A Built loop between residues 19 C and 23 C Built loop between residues 30 C and 33 C Built loop between residues 53 C and 57 C Built loop between residues 189 C and 193 C Built loop between residues 240 C and 243 C Built loop between residues 15 B and 22 B Built loop between residues 130 B and 133 B Built loop between residues 19 E and 24 E Built loop between residues 42 E and 47 E Built loop between residues 18 D and 24 D Built loop between residues 41 D and 44 D Built loop between residues 72 D and 76 D Built loop between residues 132 D and 137 D Built loop between residues 179 D and 185 D Built loop between residues 253 D and 256 D 22 chains (1653 residues) following loop building 13 chains (1545 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 15072 restraints for refining 14101 atoms. 2415 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2183 (Rfree = 0.000) for 14101 atoms. Found 205 (205 requested) and removed 149 (114 requested) atoms. Cycle 7: After refmac, R = 0.1993 (Rfree = 0.000) for 14118 atoms. Found 157 (202 requested) and removed 115 (114 requested) atoms. Cycle 8: After refmac, R = 0.1904 (Rfree = 0.000) for 14129 atoms. Found 119 (197 requested) and removed 120 (114 requested) atoms. Cycle 9: After refmac, R = 0.1863 (Rfree = 0.000) for 14115 atoms. Found 104 (192 requested) and removed 119 (114 requested) atoms. Cycle 10: After refmac, R = 0.1833 (Rfree = 0.000) for 14090 atoms. Found 115 (187 requested) and removed 117 (114 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.39 2.63 NCS extension: 75 residues added (382 deleted due to clashes), 14179 seeds are put forward Round 1: 1677 peptides, 34 chains. Longest chain 273 peptides. Score 0.961 Round 2: 1676 peptides, 36 chains. Longest chain 220 peptides. Score 0.960 Round 3: 1659 peptides, 45 chains. Longest chain 177 peptides. Score 0.952 Round 4: 1659 peptides, 48 chains. Longest chain 120 peptides. Score 0.950 Round 5: 1660 peptides, 56 chains. Longest chain 91 peptides. Score 0.944 Taking the results from Round 1 Chains 38, Residues 1643, Estimated correctness of the model 99.6 % 27 chains (1556 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 23 A Built loop between residues 72 C and 75 C Built loop between residues 187 C and 190 C Built loop between residues 54 B and 58 B Built loop between residues 78 B and 85 B Built loop between residues 109 B and 112 B Built loop between residues 132 B and 135 B Built loop between residues 187 B and 190 B Built loop between residues 187 E and 190 E Built loop between residues 215 E and 218 E Built loop between residues 270 E and 273 E Built loop between residues 265 D and 271 D Built loop between residues 65 F and 76 F Built loop between residues 126 F and 135 F Built loop between residues 188 F and 191 F 21 chains (1690 residues) following loop building 12 chains (1610 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14506 restraints for refining 14069 atoms. 1427 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2009 (Rfree = 0.000) for 14069 atoms. Found 182 (182 requested) and removed 131 (114 requested) atoms. Cycle 12: After refmac, R = 0.1855 (Rfree = 0.000) for 14107 atoms. Found 179 (179 requested) and removed 116 (114 requested) atoms. Cycle 13: After refmac, R = 0.1773 (Rfree = 0.000) for 14155 atoms. Found 167 (174 requested) and removed 119 (114 requested) atoms. Cycle 14: After refmac, R = 0.1742 (Rfree = 0.000) for 14193 atoms. Found 129 (170 requested) and removed 119 (115 requested) atoms. Cycle 15: After refmac, R = 0.1704 (Rfree = 0.000) for 14194 atoms. Found 146 (166 requested) and removed 118 (115 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.39 2.63 NCS extension: 26 residues added (259 deleted due to clashes), 14254 seeds are put forward Round 1: 1687 peptides, 32 chains. Longest chain 195 peptides. Score 0.963 Round 2: 1701 peptides, 30 chains. Longest chain 193 peptides. Score 0.965 Round 3: 1685 peptides, 42 chains. Longest chain 153 peptides. Score 0.956 Round 4: 1678 peptides, 46 chains. Longest chain 194 peptides. Score 0.953 Round 5: 1670 peptides, 50 chains. Longest chain 141 peptides. Score 0.950 Taking the results from Round 2 Chains 33, Residues 1671, Estimated correctness of the model 99.6 % 25 chains (1590 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 20 A and 23 A Built loop between residues 134 A and 139 A Built loop between residues 186 A and 191 A Built loop between residues 72 C and 76 C Built loop between residues 129 C and 132 C Built loop between residues 141 B and 144 B Built loop between residues 71 E and 74 E Built loop between residues 140 E and 143 E Built loop between residues 192 E and 195 E Built loop between residues 72 D and 77 D Built loop between residues 268 D and 271 D Built loop between residues 187 F and 191 F 19 chains (1698 residues) following loop building 13 chains (1622 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14414 restraints for refining 14104 atoms. 1263 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1991 (Rfree = 0.000) for 14104 atoms. Found 160 (160 requested) and removed 145 (114 requested) atoms. Cycle 17: After refmac, R = 0.1812 (Rfree = 0.000) for 14093 atoms. Found 155 (155 requested) and removed 120 (114 requested) atoms. Cycle 18: After refmac, R = 0.1735 (Rfree = 0.000) for 14121 atoms. Found 151 (151 requested) and removed 120 (114 requested) atoms. Cycle 19: After refmac, R = 0.1695 (Rfree = 0.000) for 14144 atoms. Found 135 (147 requested) and removed 120 (114 requested) atoms. Cycle 20: After refmac, R = 0.1686 (Rfree = 0.000) for 14150 atoms. Found 133 (142 requested) and removed 119 (114 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.39 2.63 NCS extension: 53 residues added (708 deleted due to clashes), 14225 seeds are put forward Round 1: 1692 peptides, 30 chains. Longest chain 222 peptides. Score 0.965 Round 2: 1697 peptides, 28 chains. Longest chain 293 peptides. Score 0.966 Round 3: 1688 peptides, 39 chains. Longest chain 137 peptides. Score 0.959 Round 4: 1673 peptides, 47 chains. Longest chain 273 peptides. Score 0.952 Round 5: 1656 peptides, 52 chains. Longest chain 153 peptides. Score 0.947 Taking the results from Round 2 Chains 30, Residues 1669, Estimated correctness of the model 99.7 % 25 chains (1545 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 19 A and 24 A Built loop between residues 71 A and 74 A Built loop between residues 187 A and 190 A Built loop between residues 242 A and 245 A Built loop between residues 140 C and 144 C Built loop between residues 190 C and 196 C Built loop between residues 211 C and 214 C Built loop between residues 30 B and 33 B Built loop between residues 241 B and 246 B Built loop between residues 280 B and 283 B Built loop between residues 19 E and 22 E Built loop between residues 187 E and 190 E Built loop between residues 19 F and 23 F Built loop between residues 133 F and 142 F Built loop between residues 156 F and 164 F Built loop between residues 210 F and 214 F Built loop between residues 238 F and 242 F 10 chains (1715 residues) following loop building 8 chains (1601 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14681 restraints for refining 14135 atoms. 1530 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1934 (Rfree = 0.000) for 14135 atoms. Found 137 (137 requested) and removed 130 (114 requested) atoms. Cycle 22: After refmac, R = 0.1800 (Rfree = 0.000) for 14119 atoms. Found 133 (133 requested) and removed 119 (114 requested) atoms. Cycle 23: After refmac, R = 0.1742 (Rfree = 0.000) for 14125 atoms. Found 128 (128 requested) and removed 117 (114 requested) atoms. Cycle 24: After refmac, R = 0.1682 (Rfree = 0.000) for 14133 atoms. Found 124 (124 requested) and removed 118 (114 requested) atoms. Cycle 25: After refmac, R = 0.1657 (Rfree = 0.000) for 14132 atoms. Found 119 (119 requested) and removed 116 (114 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.39 2.63 NCS extension: 2 residues added (29 deleted due to clashes), 14148 seeds are put forward Round 1: 1696 peptides, 28 chains. Longest chain 196 peptides. Score 0.966 Round 2: 1699 peptides, 24 chains. Longest chain 273 peptides. Score 0.969 Round 3: 1681 peptides, 41 chains. Longest chain 250 peptides. Score 0.957 Round 4: 1683 peptides, 40 chains. Longest chain 164 peptides. Score 0.958 Round 5: 1671 peptides, 54 chains. Longest chain 134 peptides. Score 0.947 Taking the results from Round 2 Chains 24, Residues 1675, Estimated correctness of the model 99.7 % 22 chains (1646 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 24 A Built loop between residues 71 A and 74 A Built loop between residues 187 A and 190 A Built loop between residues 245 A and 248 A Built loop between residues 78 C and 81 C Built loop between residues 132 C and 135 C Built loop between residues 268 B and 271 B Built loop between residues 18 E and 22 E Built loop between residues 133 E and 136 E Built loop between residues 162 E and 166 E Built loop between residues 268 E and 271 E Built loop between residues 129 F and 132 F Built loop between residues 280 F and 283 F 11 chains (1706 residues) following loop building 9 chains (1677 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14407 restraints for refining 14192 atoms. 1012 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1885 (Rfree = 0.000) for 14192 atoms. Found 115 (115 requested) and removed 127 (115 requested) atoms. Cycle 27: After refmac, R = 0.1749 (Rfree = 0.000) for 14165 atoms. Found 114 (114 requested) and removed 114 (114 requested) atoms. Cycle 28: After refmac, R = 0.1690 (Rfree = 0.000) for 14159 atoms. Found 114 (114 requested) and removed 118 (114 requested) atoms. Cycle 29: After refmac, R = 0.1683 (Rfree = 0.000) for 14153 atoms. Found 114 (114 requested) and removed 114 (114 requested) atoms. Cycle 30: After refmac, R = 0.1661 (Rfree = 0.000) for 14147 atoms. Found 114 (114 requested) and removed 117 (114 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.39 2.63 NCS extension: 43 residues added (252 deleted due to clashes), 14193 seeds are put forward Round 1: 1691 peptides, 32 chains. Longest chain 183 peptides. Score 0.963 Round 2: 1689 peptides, 36 chains. Longest chain 171 peptides. Score 0.961 Round 3: 1677 peptides, 46 chains. Longest chain 164 peptides. Score 0.953 Round 4: 1673 peptides, 42 chains. Longest chain 165 peptides. Score 0.955 Round 5: 1677 peptides, 42 chains. Longest chain 160 peptides. Score 0.956 Taking the results from Round 1 Chains 34, Residues 1659, Estimated correctness of the model 99.6 % 29 chains (1525 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 181 A and 185 A Built loop between residues 242 A and 246 A Built loop between residues 267 A and 271 A Built loop between residues 18 C and 23 C Built loop between residues 71 C and 74 C Built loop between residues 162 C and 165 C Built loop between residues 187 C and 190 C Built loop between residues 215 C and 218 C Built loop between residues 267 C and 271 C Built loop between residues 72 B and 76 B Built loop between residues 214 B and 218 B Built loop between residues 78 E and 83 E Built loop between residues 132 E and 135 E Built loop between residues 187 D and 190 D Built loop between residues 267 D and 271 D Built loop between residues 19 F and 22 F 18 chains (1702 residues) following loop building 13 chains (1568 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14911 restraints for refining 14013 atoms. 1987 conditional restraints added. Observations/parameters ratio is 0.94 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1873 (Rfree = 0.000) for 14013 atoms. Found 113 (113 requested) and removed 130 (113 requested) atoms. Cycle 32: After refmac, R = 0.1773 (Rfree = 0.000) for 13990 atoms. Found 113 (113 requested) and removed 113 (113 requested) atoms. Cycle 33: After refmac, R = 0.1719 (Rfree = 0.000) for 13987 atoms. Found 113 (113 requested) and removed 114 (113 requested) atoms. Cycle 34: After refmac, R = 0.1724 (Rfree = 0.000) for 13980 atoms. Found 113 (113 requested) and removed 115 (113 requested) atoms. Cycle 35: After refmac, R = 0.1688 (Rfree = 0.000) for 13975 atoms. Found 113 (113 requested) and removed 118 (113 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.40 2.64 NCS extension: 32 residues added (730 deleted due to clashes), 14008 seeds are put forward Round 1: 1675 peptides, 38 chains. Longest chain 113 peptides. Score 0.958 Round 2: 1690 peptides, 25 chains. Longest chain 263 peptides. Score 0.968 Round 3: 1661 peptides, 48 chains. Longest chain 148 peptides. Score 0.950 Round 4: 1674 peptides, 43 chains. Longest chain 167 peptides. Score 0.955 Round 5: 1684 peptides, 39 chains. Longest chain 185 peptides. Score 0.958 Taking the results from Round 2 Chains 25, Residues 1665, Estimated correctness of the model 99.7 % 20 chains (1625 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 22 A Built loop between residues 248 A and 251 A Built loop between residues 78 C and 83 C Built loop between residues 192 C and 195 C Built loop between residues 115 B and 118 B Built loop between residues 140 B and 143 B Built loop between residues 191 B and 194 B Built loop between residues 85 E and 89 E Built loop between residues 132 E and 135 E Built loop between residues 71 D and 74 D Built loop between residues 245 D and 248 D Built loop between residues 267 F and 276 F 13 chains (1699 residues) following loop building 8 chains (1659 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14465 restraints for refining 14139 atoms. 1160 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1927 (Rfree = 0.000) for 14139 atoms. Found 114 (114 requested) and removed 135 (114 requested) atoms. Cycle 37: After refmac, R = 0.1782 (Rfree = 0.000) for 14102 atoms. Found 114 (114 requested) and removed 115 (114 requested) atoms. Cycle 38: After refmac, R = 0.1721 (Rfree = 0.000) for 14096 atoms. Found 114 (114 requested) and removed 116 (114 requested) atoms. Cycle 39: After refmac, R = 0.1704 (Rfree = 0.000) for 14085 atoms. Found 114 (114 requested) and removed 119 (114 requested) atoms. Cycle 40: After refmac, R = 0.1672 (Rfree = 0.000) for 14075 atoms. Found 114 (114 requested) and removed 114 (114 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.39 2.63 NCS extension: 77 residues added (408 deleted due to clashes), 14162 seeds are put forward Round 1: 1681 peptides, 35 chains. Longest chain 141 peptides. Score 0.961 Round 2: 1682 peptides, 35 chains. Longest chain 218 peptides. Score 0.961 Round 3: 1677 peptides, 41 chains. Longest chain 153 peptides. Score 0.956 Round 4: 1677 peptides, 40 chains. Longest chain 219 peptides. Score 0.957 Round 5: 1679 peptides, 47 chains. Longest chain 124 peptides. Score 0.953 Taking the results from Round 2 Chains 38, Residues 1647, Estimated correctness of the model 99.6 % 30 chains (1606 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 20 A and 23 A Built loop between residues 20 C and 23 C Built loop between residues 72 C and 77 C Built loop between residues 30 B and 33 B Built loop between residues 72 B and 75 B Built loop between residues 140 B and 143 B Built loop between residues 182 B and 185 B Built loop between residues 39 E and 42 E Built loop between residues 190 E and 193 E Built loop between residues 211 E and 214 E Built loop between residues 267 E and 271 E Built loop between residues 18 D and 23 D Built loop between residues 133 D and 136 D Built loop between residues 174 D and 177 D Built loop between residues 253 D and 256 D Built loop between residues 18 F and 22 F Built loop between residues 70 F and 77 F Built loop between residues 187 F and 190 F 17 chains (1687 residues) following loop building 12 chains (1652 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14570 restraints for refining 14144 atoms. 1320 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1908 (Rfree = 0.000) for 14144 atoms. Found 114 (114 requested) and removed 130 (114 requested) atoms. Cycle 42: After refmac, R = 0.1759 (Rfree = 0.000) for 14106 atoms. Found 114 (114 requested) and removed 115 (114 requested) atoms. Cycle 43: After refmac, R = 0.1695 (Rfree = 0.000) for 14099 atoms. Found 114 (114 requested) and removed 120 (114 requested) atoms. Cycle 44: After refmac, R = 0.1658 (Rfree = 0.000) for 14088 atoms. Found 114 (114 requested) and removed 117 (114 requested) atoms. Cycle 45: After refmac, R = 0.1632 (Rfree = 0.000) for 14077 atoms. Found 114 (114 requested) and removed 115 (114 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.39 2.63 NCS extension: 45 residues added (924 deleted due to clashes), 14137 seeds are put forward Round 1: 1679 peptides, 37 chains. Longest chain 140 peptides. Score 0.959 Round 2: 1700 peptides, 28 chains. Longest chain 290 peptides. Score 0.966 Round 3: 1682 peptides, 40 chains. Longest chain 193 peptides. Score 0.957 Round 4: 1688 peptides, 35 chains. Longest chain 186 peptides. Score 0.961 Round 5: 1666 peptides, 45 chains. Longest chain 218 peptides. Score 0.953 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 28, Residues 1672, Estimated correctness of the model 99.7 % 22 chains (1489 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 71 C and 74 C Built loop between residues 130 C and 135 C Built loop between residues 55 B and 58 B Built loop between residues 72 B and 83 B Built loop between residues 108 B and 111 B Built loop between residues 192 B and 195 B Built loop between residues 211 B and 214 B Built loop between residues 65 E and 69 E Built loop between residues 256 E and 260 E Built loop between residues 215 D and 218 D 17 chains (1700 residues) following loop building 12 chains (1521 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 52578 reflections ( 99.99 % complete ) and 12800 restraints for refining 12640 atoms. Observations/parameters ratio is 1.04 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2817 (Rfree = 0.000) for 12640 atoms. Found 75 (102 requested) and removed 0 (102 requested) atoms. Cycle 47: After refmac, R = 0.2643 (Rfree = 0.000) for 12640 atoms. Found 35 (103 requested) and removed 19 (103 requested) atoms. Cycle 48: After refmac, R = 0.2593 (Rfree = 0.000) for 12640 atoms. Found 31 (103 requested) and removed 11 (103 requested) atoms. Cycle 49: After refmac, R = 0.2560 (Rfree = 0.000) for 12640 atoms. Found 23 (103 requested) and removed 17 (103 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 04:50:50 GMT 2018 Job finished. TimeTaking 225.98 Used memory is bytes: 10439368