Mon 24 Dec 07:57:11 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkm-2.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-2.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkm-2.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-parrot-noncs ############### 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 07:57:15 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkm-2.6-parrot-noncs/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-noncs.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-noncs.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 15904 atoms. Observations/parameters ratio is 0.83 ------------------------------------------------------ Starting model: R = 0.2991 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.1955 (Rfree = 0.000) for 15904 atoms. Found 164 (257 requested) and removed 173 (128 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.40 2.64 NCS extension: 0 residues added, 15895 seeds are put forward Round 1: 1028 peptides, 172 chains. Longest chain 18 peptides. Score 0.495 Round 2: 1192 peptides, 134 chains. Longest chain 32 peptides. Score 0.715 Round 3: 1291 peptides, 107 chains. Longest chain 50 peptides. Score 0.813 Round 4: 1366 peptides, 96 chains. Longest chain 50 peptides. Score 0.853 Round 5: 1427 peptides, 93 chains. Longest chain 62 peptides. Score 0.872 Taking the results from Round 5 Chains 103, Residues 1334, Estimated correctness of the model 96.2 % 38 chains (924 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 115 A and 118 A Built loop between residues 189 A and 200 A Built loop between residues 215 A and 218 A Built loop between residues 165 B and 168 B Built loop between residues 200 E and 208 E Built loop between residues 49 D and 53 D Built loop between residues 71 D and 74 D Built loop between residues 134 D and 143 D Built loop between residues 172 D and 176 D Built loop between residues 188 D and 191 D 91 chains (1362 residues) following loop building 28 chains (965 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 18950 restraints for refining 13714 atoms. 10017 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2764 (Rfree = 0.000) for 13714 atoms. Found 196 (222 requested) and removed 205 (111 requested) atoms. Cycle 2: After refmac, R = 0.2529 (Rfree = 0.000) for 13580 atoms. Found 137 (218 requested) and removed 133 (111 requested) atoms. Cycle 3: After refmac, R = 0.2450 (Rfree = 0.000) for 13505 atoms. Found 128 (211 requested) and removed 113 (110 requested) atoms. Cycle 4: After refmac, R = 0.2264 (Rfree = 0.000) for 13482 atoms. Found 82 (206 requested) and removed 113 (109 requested) atoms. Cycle 5: After refmac, R = 0.2233 (Rfree = 0.000) for 13426 atoms. Found 84 (201 requested) and removed 111 (109 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.38 2.61 NCS extension: 935 residues added (1938 deleted due to clashes), 14384 seeds are put forward Round 1: 1466 peptides, 74 chains. Longest chain 82 peptides. Score 0.903 Round 2: 1504 peptides, 69 chains. Longest chain 82 peptides. Score 0.914 Round 3: 1510 peptides, 69 chains. Longest chain 78 peptides. Score 0.915 Round 4: 1500 peptides, 72 chains. Longest chain 115 peptides. Score 0.911 Round 5: 1517 peptides, 73 chains. Longest chain 100 peptides. Score 0.912 Taking the results from Round 3 Chains 74, Residues 1441, Estimated correctness of the model 98.2 % 39 chains (1145 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 129 A and 132 A Built loop between residues 170 A and 175 A Built loop between residues 163 C and 166 C Built loop between residues 43 B and 48 B Built loop between residues 107 B and 110 B Built loop between residues 182 B and 185 B Built loop between residues 47 D and 52 D Built loop between residues 162 D and 165 D Built loop between residues 206 D and 209 D Built loop between residues 260 D and 263 D Built loop between residues 214 F and 217 F 61 chains (1465 residues) following loop building 28 chains (1173 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 16569 restraints for refining 13501 atoms. 6228 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2430 (Rfree = 0.000) for 13501 atoms. Found 197 (197 requested) and removed 173 (109 requested) atoms. Cycle 7: After refmac, R = 0.2212 (Rfree = 0.000) for 13475 atoms. Found 160 (193 requested) and removed 116 (109 requested) atoms. Cycle 8: After refmac, R = 0.2144 (Rfree = 0.000) for 13493 atoms. Found 108 (188 requested) and removed 114 (109 requested) atoms. Cycle 9: After refmac, R = 0.2084 (Rfree = 0.000) for 13471 atoms. Found 94 (183 requested) and removed 111 (109 requested) atoms. Cycle 10: After refmac, R = 0.2061 (Rfree = 0.000) for 13443 atoms. Found 104 (179 requested) and removed 111 (109 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.39 2.63 NCS extension: 316 residues added (1456 deleted due to clashes), 13771 seeds are put forward Round 1: 1508 peptides, 73 chains. Longest chain 111 peptides. Score 0.911 Round 2: 1529 peptides, 54 chains. Longest chain 145 peptides. Score 0.932 Round 3: 1526 peptides, 67 chains. Longest chain 64 peptides. Score 0.919 Round 4: 1520 peptides, 73 chains. Longest chain 140 peptides. Score 0.913 Round 5: 1506 peptides, 82 chains. Longest chain 63 peptides. Score 0.901 Taking the results from Round 2 Chains 64, Residues 1475, Estimated correctness of the model 98.8 % 30 chains (1226 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 A and 69 A Built loop between residues 130 A and 136 A Built loop between residues 164 A and 167 A Built loop between residues 71 B and 74 B Built loop between residues 232 E and 240 E Built loop between residues 266 E and 270 E Built loop between residues 45 F and 54 F 54 chains (1498 residues) following loop building 23 chains (1255 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 15853 restraints for refining 13409 atoms. 5166 conditional restraints added. Observations/parameters ratio is 0.98 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2345 (Rfree = 0.000) for 13409 atoms. Found 174 (174 requested) and removed 139 (108 requested) atoms. Cycle 12: After refmac, R = 0.2127 (Rfree = 0.000) for 13415 atoms. Found 153 (170 requested) and removed 111 (109 requested) atoms. Cycle 13: After refmac, R = 0.1998 (Rfree = 0.000) for 13438 atoms. Found 106 (166 requested) and removed 115 (109 requested) atoms. Cycle 14: After refmac, R = 0.1960 (Rfree = 0.000) for 13421 atoms. Found 81 (161 requested) and removed 109 (108 requested) atoms. Cycle 15: After refmac, R = 0.1902 (Rfree = 0.000) for 13383 atoms. Found 104 (156 requested) and removed 109 (108 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.40 2.64 NCS extension: 580 residues added (2283 deleted due to clashes), 13999 seeds are put forward Round 1: 1533 peptides, 64 chains. Longest chain 87 peptides. Score 0.923 Round 2: 1561 peptides, 56 chains. Longest chain 132 peptides. Score 0.934 Round 3: 1541 peptides, 77 chains. Longest chain 65 peptides. Score 0.912 Round 4: 1548 peptides, 68 chains. Longest chain 152 peptides. Score 0.922 Round 5: 1529 peptides, 76 chains. Longest chain 83 peptides. Score 0.911 Taking the results from Round 2 Chains 68, Residues 1505, Estimated correctness of the model 98.9 % 36 chains (1312 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 65 A and 68 A Built loop between residues 107 A and 110 A Built loop between residues 209 A and 212 A Built loop between residues 130 C and 137 C Built loop between residues 66 B and 70 B Built loop between residues 71 E and 74 E Built loop between residues 132 E and 135 E Built loop between residues 158 E and 162 E Built loop between residues 232 E and 240 E Built loop between residues 266 E and 270 E Built loop between residues 131 D and 136 D Built loop between residues 266 D and 269 D Built loop between residues 78 F and 87 F Built loop between residues 119 F and 122 F Built loop between residues 132 F and 135 F Built loop between residues 156 F and 165 F Built loop between residues 188 F and 193 F Built loop between residues 212 F and 216 F 44 chains (1557 residues) following loop building 18 chains (1377 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 52578 reflections ( 99.99 % complete ) and 14983 restraints for refining 13516 atoms. 3517 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2206 (Rfree = 0.000) for 13516 atoms. Found 153 (153 requested) and removed 136 (109 requested) atoms. Cycle 17: After refmac, R = 0.2015 (Rfree = 0.000) for 13508 atoms. Found 149 (149 requested) and removed 110 (109 requested) atoms. Cycle 18: After refmac, R = 0.1933 (Rfree = 0.000) for 13529 atoms. Found 111 (145 requested) and removed 109 (109 requested) atoms. Cycle 19: After refmac, R = 0.1894 (Rfree = 0.000) for 13527 atoms. Found 100 (140 requested) and removed 111 (109 requested) atoms. Cycle 20: After refmac, R = 0.1866 (Rfree = 0.000) for 13505 atoms. Found 96 (136 requested) and removed 112 (109 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.41 2.65 NCS extension: 645 residues added (2051 deleted due to clashes), 14165 seeds are put forward Round 1: 1573 peptides, 60 chains. Longest chain 97 peptides. Score 0.932 Round 2: 1605 peptides, 45 chains. Longest chain 133 peptides. Score 0.947 Round 3: 1566 peptides, 62 chains. Longest chain 124 peptides. Score 0.929 Round 4: 1568 peptides, 68 chains. Longest chain 82 peptides. Score 0.924 Round 5: 1564 peptides, 70 chains. Longest chain 87 peptides. Score 0.922 Taking the results from Round 2 Chains 51, Residues 1560, Estimated correctness of the model 99.2 % 27 chains (1294 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 74 A and 77 A Built loop between residues 156 A and 159 A Built loop between residues 79 E and 82 E Built loop between residues 157 D and 161 D Built loop between residues 109 F and 112 F Built loop between residues 132 F and 135 F Built loop between residues 188 F and 192 F Built loop between residues 201 F and 204 F 42 chains (1577 residues) following loop building 19 chains (1312 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 15554 restraints for refining 13514 atoms. 4179 conditional restraints added. Observations/parameters ratio is 0.97 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2197 (Rfree = 0.000) for 13514 atoms. Found 131 (131 requested) and removed 129 (109 requested) atoms. Cycle 22: After refmac, R = 0.1999 (Rfree = 0.000) for 13497 atoms. Found 127 (127 requested) and removed 109 (109 requested) atoms. Cycle 23: After refmac, R = 0.1916 (Rfree = 0.000) for 13507 atoms. Found 123 (123 requested) and removed 114 (109 requested) atoms. Cycle 24: After refmac, R = 0.1873 (Rfree = 0.000) for 13506 atoms. Found 118 (118 requested) and removed 111 (109 requested) atoms. Cycle 25: After refmac, R = 0.1845 (Rfree = 0.000) for 13507 atoms. Found 107 (114 requested) and removed 113 (109 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.40 2.64 NCS extension: 232 residues added (2575 deleted due to clashes), 13748 seeds are put forward Round 1: 1603 peptides, 49 chains. Longest chain 104 peptides. Score 0.944 Round 2: 1606 peptides, 50 chains. Longest chain 158 peptides. Score 0.944 Round 3: 1592 peptides, 59 chains. Longest chain 152 peptides. Score 0.935 Round 4: 1581 peptides, 70 chains. Longest chain 74 peptides. Score 0.924 Round 5: 1585 peptides, 68 chains. Longest chain 98 peptides. Score 0.927 Taking the results from Round 2 Chains 57, Residues 1556, Estimated correctness of the model 99.2 % 32 chains (1383 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 18 A and 23 A Built loop between residues 156 A and 159 A Built loop between residues 171 A and 175 A Built loop between residues 49 C and 52 C Built loop between residues 241 C and 244 C Built loop between residues 38 B and 48 B Built loop between residues 107 B and 110 B Built loop between residues 183 B and 186 B Built loop between residues 233 B and 236 B Built loop between residues 129 E and 132 E Built loop between residues 188 E and 196 E Built loop between residues 132 D and 135 D Built loop between residues 77 F and 84 F 42 chains (1597 residues) following loop building 19 chains (1428 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 15178 restraints for refining 13758 atoms. 3231 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2182 (Rfree = 0.000) for 13758 atoms. Found 111 (111 requested) and removed 153 (111 requested) atoms. Cycle 27: After refmac, R = 0.2041 (Rfree = 0.000) for 13697 atoms. Found 111 (111 requested) and removed 115 (111 requested) atoms. Cycle 28: After refmac, R = 0.1949 (Rfree = 0.000) for 13688 atoms. Found 111 (111 requested) and removed 113 (111 requested) atoms. Cycle 29: After refmac, R = 0.1894 (Rfree = 0.000) for 13674 atoms. Found 110 (110 requested) and removed 114 (110 requested) atoms. Cycle 30: After refmac, R = 0.1865 (Rfree = 0.000) for 13662 atoms. Found 110 (110 requested) and removed 113 (110 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.39 2.63 NCS extension: 80 residues added (737 deleted due to clashes), 13760 seeds are put forward Round 1: 1594 peptides, 47 chains. Longest chain 183 peptides. Score 0.945 Round 2: 1618 peptides, 40 chains. Longest chain 153 peptides. Score 0.952 Round 3: 1603 peptides, 53 chains. Longest chain 138 peptides. Score 0.941 Round 4: 1605 peptides, 54 chains. Longest chain 69 peptides. Score 0.940 Round 5: 1611 peptides, 59 chains. Longest chain 100 peptides. Score 0.937 Taking the results from Round 2 Chains 44, Residues 1578, Estimated correctness of the model 99.4 % 28 chains (1431 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 76 A Built loop between residues 192 A and 195 A Built loop between residues 20 C and 23 C Built loop between residues 139 C and 142 C Built loop between residues 180 B and 189 B Built loop between residues 193 E and 196 E Built loop between residues 38 D and 47 D Built loop between residues 188 D and 193 D Built loop between residues 130 F and 135 F 34 chains (1607 residues) following loop building 19 chains (1466 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14898 restraints for refining 13693 atoms. 2752 conditional restraints added. Observations/parameters ratio is 0.96 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2080 (Rfree = 0.000) for 13693 atoms. Found 111 (111 requested) and removed 132 (111 requested) atoms. Cycle 32: After refmac, R = 0.1943 (Rfree = 0.000) for 13644 atoms. Found 110 (110 requested) and removed 113 (110 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.1882 (Rfree = 0.000) for 13632 atoms. Found 110 (110 requested) and removed 111 (110 requested) atoms. Cycle 34: After refmac, R = 0.1849 (Rfree = 0.000) for 13626 atoms. Found 110 (110 requested) and removed 111 (110 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.1830 (Rfree = 0.000) for 13613 atoms. Found 110 (110 requested) and removed 112 (110 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.39 2.63 NCS extension: 88 residues added (1374 deleted due to clashes), 13707 seeds are put forward Round 1: 1614 peptides, 40 chains. Longest chain 140 peptides. Score 0.952 Round 2: 1617 peptides, 46 chains. Longest chain 116 peptides. Score 0.948 Round 3: 1611 peptides, 48 chains. Longest chain 108 peptides. Score 0.946 Round 4: 1596 peptides, 50 chains. Longest chain 100 peptides. Score 0.943 Round 5: 1591 peptides, 60 chains. Longest chain 104 peptides. Score 0.934 Taking the results from Round 1 Chains 42, Residues 1574, Estimated correctness of the model 99.4 % 30 chains (1473 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 170 A and 173 A Built loop between residues 187 A and 191 A Built loop between residues 15 C and 26 C Built loop between residues 74 C and 77 C Built loop between residues 215 C and 219 C Built loop between residues 237 C and 244 C Built loop between residues 108 B and 111 B Built loop between residues 72 E and 83 E Built loop between residues 183 E and 190 E Built loop between residues 19 D and 23 D Built loop between residues 162 D and 166 D Built loop between residues 37 F and 40 F Built loop between residues 130 F and 133 F 24 chains (1623 residues) following loop building 15 chains (1534 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14653 restraints for refining 13840 atoms. 2204 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2077 (Rfree = 0.000) for 13840 atoms. Found 112 (112 requested) and removed 166 (112 requested) atoms. Cycle 37: After refmac, R = 0.1902 (Rfree = 0.000) for 13774 atoms. Found 111 (111 requested) and removed 116 (111 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.1842 (Rfree = 0.000) for 13760 atoms. Found 111 (111 requested) and removed 116 (111 requested) atoms. Cycle 39: After refmac, R = 0.1807 (Rfree = 0.000) for 13744 atoms. Found 111 (111 requested) and removed 112 (111 requested) atoms. Cycle 40: After refmac, R = 0.1794 (Rfree = 0.000) for 13734 atoms. Found 111 (111 requested) and removed 114 (111 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.40 2.64 NCS extension: 179 residues added (1743 deleted due to clashes), 13936 seeds are put forward Round 1: 1622 peptides, 38 chains. Longest chain 209 peptides. Score 0.954 Round 2: 1631 peptides, 39 chains. Longest chain 145 peptides. Score 0.954 Round 3: 1634 peptides, 41 chains. Longest chain 149 peptides. Score 0.953 Round 4: 1619 peptides, 43 chains. Longest chain 175 peptides. Score 0.950 Round 5: 1615 peptides, 49 chains. Longest chain 105 peptides. Score 0.945 Taking the results from Round 2 Chains 45, Residues 1592, Estimated correctness of the model 99.4 % 32 chains (1467 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 30 A and 33 A Built loop between residues 65 A and 69 A Built loop between residues 183 A and 186 A Built loop between residues 15 C and 22 C Built loop between residues 47 C and 50 C Built loop between residues 72 C and 76 C Built loop between residues 219 C and 222 C Built loop between residues 270 C and 273 C Built loop between residues 187 B and 192 B Built loop between residues 236 B and 239 B Built loop between residues 38 E and 48 E Built loop between residues 119 E and 125 E Built loop between residues 233 E and 239 E Built loop between residues 65 D and 68 D Built loop between residues 78 D and 85 D Built loop between residues 183 D and 189 D Built loop between residues 241 D and 244 D Built loop between residues 71 F and 74 F 23 chains (1644 residues) following loop building 14 chains (1531 residues) in sequence following loop building ------------------------------------------------------ 52578 reflections ( 99.99 % complete ) and 14689 restraints for refining 13828 atoms. 2128 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2029 (Rfree = 0.000) for 13828 atoms. Found 112 (112 requested) and removed 132 (112 requested) atoms. Cycle 42: After refmac, R = 0.1890 (Rfree = 0.000) for 13789 atoms. Found 111 (111 requested) and removed 115 (111 requested) atoms. Cycle 43: After refmac, R = 0.1829 (Rfree = 0.000) for 13776 atoms. Found 111 (111 requested) and removed 116 (111 requested) atoms. Cycle 44: After refmac, R = 0.1782 (Rfree = 0.000) for 13761 atoms. Found 111 (111 requested) and removed 113 (111 requested) atoms. Cycle 45: After refmac, R = 0.1751 (Rfree = 0.000) for 13751 atoms. Found 111 (111 requested) and removed 112 (111 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.40 2.64 NCS extension: 57 residues added (958 deleted due to clashes), 13812 seeds are put forward Round 1: 1651 peptides, 33 chains. Longest chain 263 peptides. Score 0.960 Round 2: 1656 peptides, 33 chains. Longest chain 246 peptides. Score 0.960 Round 3: 1658 peptides, 35 chains. Longest chain 257 peptides. Score 0.959 Round 4: 1645 peptides, 42 chains. Longest chain 159 peptides. Score 0.953 Round 5: 1632 peptides, 51 chains. Longest chain 132 peptides. Score 0.945 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 33, Residues 1623, Estimated correctness of the model 99.5 % 30 chains (1606 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 72 A and 76 A Built loop between residues 132 A and 135 A Built loop between residues 233 A and 236 A Built loop between residues 122 C and 125 C Built loop between residues 133 C and 142 C Built loop between residues 19 B and 23 B Built loop between residues 38 B and 42 B Built loop between residues 140 B and 143 B Built loop between residues 187 B and 190 B Built loop between residues 241 B and 244 B Built loop between residues 268 B and 271 B Built loop between residues 56 E and 59 E Built loop between residues 72 E and 77 E Built loop between residues 114 E and 117 E Built loop between residues 215 E and 218 E Built loop between residues 18 D and 22 D Built loop between residues 46 D and 49 D Built loop between residues 66 F and 75 F Built loop between residues 129 F and 132 F Built loop between residues 267 F and 271 F 11 chains (1674 residues) following loop building 10 chains (1665 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 52578 reflections ( 99.99 % complete ) and 13235 restraints for refining 13060 atoms. Observations/parameters ratio is 1.01 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2457 (Rfree = 0.000) for 13060 atoms. Found 54 (105 requested) and removed 0 (105 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2310 (Rfree = 0.000) for 13060 atoms. Found 44 (106 requested) and removed 12 (106 requested) atoms. Cycle 48: After refmac, R = 0.2263 (Rfree = 0.000) for 13060 atoms. Found 25 (106 requested) and removed 12 (106 requested) atoms. Cycle 49: After refmac, R = 0.2233 (Rfree = 0.000) for 13060 atoms. TimeTaking 183.87