Sun 23 Dec 22:23:02 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 2obn-2.3-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2obn-2.3-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2obn-2.3-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-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/2obn-2.3-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-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 22:23:11 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/2obn-2.3-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2obn-2.3-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 1172 and 0 Target number of residues in the AU: 1172 Target solvent content: 0.5306 Checking the provided sequence file Detected sequence length: 349 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1396 Adjusted target solvent content: 0.44 Input MTZ file: 2obn-2.3-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: 75.040 122.990 75.170 90.000 103.099 90.000 Input sequence file: 2obn-2.3-parrot-hancs.fasta_lf Building free atoms model in initial map for 11168 target number of atoms Had to go as low as 0.45 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: 73.214 2.300 Wilson plot Bfac: 30.44 58827 reflections ( 99.75 % complete ) and 0 restraints for refining 12439 atoms. Observations/parameters ratio is 1.18 ------------------------------------------------------ Starting model: R = 0.3026 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2096 (Rfree = 0.000) for 12439 atoms. Found 194 (286 requested) and removed 165 (143 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.32 2.51 NCS extension: 0 residues added, 12468 seeds are put forward Round 1: 860 peptides, 131 chains. Longest chain 20 peptides. Score 0.558 Round 2: 1016 peptides, 84 chains. Longest chain 49 peptides. Score 0.807 Round 3: 1096 peptides, 63 chains. Longest chain 51 peptides. Score 0.877 Round 4: 1133 peptides, 53 chains. Longest chain 74 peptides. Score 0.901 Round 5: 1141 peptides, 51 chains. Longest chain 119 peptides. Score 0.906 Taking the results from Round 5 Chains 59, Residues 1090, Estimated correctness of the model 98.5 % 30 chains (899 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 120 A and 124 A Built loop between residues 164 A and 167 A Built loop between residues 176 A and 179 A Built loop between residues 197 A and 200 A Built loop between residues 292 A and 299 A Built loop between residues 28 C and 33 C Built loop between residues 175 C and 182 C Built loop between residues 210 C and 215 C Built loop between residues 233 C and 237 C Built loop between residues 263 C and 273 C Built loop between residues 291 C and 296 C Built loop between residues 308 C and 317 C Built loop between residues 150 B and 153 B Built loop between residues 177 B and 182 B Built loop between residues 197 B and 203 B Built loop between residues 284 B and 295 B Built loop between residues 134 D and 136 D 37 chains (1155 residues) following loop building 13 chains (974 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 13044 restraints for refining 10708 atoms. 4972 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2505 (Rfree = 0.000) for 10708 atoms. Found 212 (246 requested) and removed 137 (123 requested) atoms. Cycle 2: After refmac, R = 0.2229 (Rfree = 0.000) for 10667 atoms. Found 134 (243 requested) and removed 132 (124 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2104 (Rfree = 0.000) for 10604 atoms. Found 107 (235 requested) and removed 124 (122 requested) atoms. Cycle 4: After refmac, R = 0.2038 (Rfree = 0.000) for 10553 atoms. Found 89 (228 requested) and removed 106 (121 requested) atoms. Cycle 5: After refmac, R = 0.1993 (Rfree = 0.000) for 10511 atoms. Found 78 (223 requested) and removed 70 (121 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.30 2.49 NCS extension: 622 residues added (717 deleted due to clashes), 11166 seeds are put forward Round 1: 1207 peptides, 44 chains. Longest chain 153 peptides. Score 0.927 Round 2: 1227 peptides, 37 chains. Longest chain 108 peptides. Score 0.938 Round 3: 1231 peptides, 44 chains. Longest chain 194 peptides. Score 0.931 Round 4: 1227 peptides, 43 chains. Longest chain 89 peptides. Score 0.932 Round 5: 1220 peptides, 44 chains. Longest chain 191 peptides. Score 0.930 Taking the results from Round 2 Chains 42, Residues 1190, Estimated correctness of the model 99.3 % 20 chains (1051 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 219 A and 230 A Built loop between residues 290 A and 295 A Built loop between residues 163 C and 166 C Built loop between residues 251 C and 254 C Built loop between residues 196 B and 199 B Built loop between residues 251 B and 254 B Built loop between residues 216 D and 219 D Built loop between residues 293 D and 297 D Built loop between residues 317 D and 322 D 31 chains (1215 residues) following loop building 11 chains (1082 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11899 restraints for refining 10590 atoms. 3176 conditional restraints added. Observations/parameters ratio is 1.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2154 (Rfree = 0.000) for 10590 atoms. Found 160 (219 requested) and removed 129 (121 requested) atoms. Cycle 7: After refmac, R = 0.2005 (Rfree = 0.000) for 10600 atoms. Found 97 (215 requested) and removed 123 (122 requested) atoms. Cycle 8: After refmac, R = 0.1944 (Rfree = 0.000) for 10560 atoms. Found 88 (209 requested) and removed 105 (121 requested) atoms. Cycle 9: After refmac, R = 0.1901 (Rfree = 0.000) for 10532 atoms. Found 90 (203 requested) and removed 86 (121 requested) atoms. Cycle 10: After refmac, R = 0.1881 (Rfree = 0.000) for 10521 atoms. Found 81 (198 requested) and removed 75 (121 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.31 2.50 NCS extension: 451 residues added (753 deleted due to clashes), 10993 seeds are put forward Round 1: 1251 peptides, 37 chains. Longest chain 128 peptides. Score 0.942 Round 2: 1266 peptides, 30 chains. Longest chain 221 peptides. Score 0.950 Round 3: 1245 peptides, 43 chains. Longest chain 101 peptides. Score 0.934 Round 4: 1253 peptides, 35 chains. Longest chain 144 peptides. Score 0.944 Round 5: 1242 peptides, 41 chains. Longest chain 128 peptides. Score 0.936 Taking the results from Round 2 Chains 33, Residues 1236, Estimated correctness of the model 99.5 % 18 chains (1077 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 44 C and 47 C Built loop between residues 84 C and 95 C Built loop between residues 124 C and 127 C Built loop between residues 216 C and 219 C Built loop between residues 319 C and 322 C Built loop between residues 42 B and 53 B Built loop between residues 120 B and 130 B Built loop between residues 82 D and 90 D Built loop between residues 116 D and 127 D Built loop between residues 143 D and 146 D 21 chains (1281 residues) following loop building 8 chains (1133 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11788 restraints for refining 10764 atoms. 2589 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2074 (Rfree = 0.000) for 10764 atoms. Found 198 (198 requested) and removed 134 (123 requested) atoms. Cycle 12: After refmac, R = 0.1915 (Rfree = 0.000) for 10802 atoms. Found 140 (194 requested) and removed 126 (124 requested) atoms. Cycle 13: After refmac, R = 0.1852 (Rfree = 0.000) for 10803 atoms. Found 94 (188 requested) and removed 124 (124 requested) atoms. Cycle 14: After refmac, R = 0.1810 (Rfree = 0.000) for 10760 atoms. Found 100 (183 requested) and removed 112 (123 requested) atoms. Cycle 15: After refmac, R = 0.1788 (Rfree = 0.000) for 10741 atoms. Found 91 (178 requested) and removed 93 (123 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.30 2.49 NCS extension: 337 residues added (942 deleted due to clashes), 11092 seeds are put forward Round 1: 1266 peptides, 33 chains. Longest chain 184 peptides. Score 0.947 Round 2: 1277 peptides, 25 chains. Longest chain 220 peptides. Score 0.956 Round 3: 1278 peptides, 34 chains. Longest chain 173 peptides. Score 0.948 Round 4: 1262 peptides, 31 chains. Longest chain 233 peptides. Score 0.949 Round 5: 1269 peptides, 38 chains. Longest chain 160 peptides. Score 0.943 Taking the results from Round 2 Chains 29, Residues 1252, Estimated correctness of the model 99.6 % 18 chains (1071 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 129 A Built loop between residues 196 A and 200 A Built loop between residues 84 C and 95 C Built loop between residues 308 C and 315 C Built loop between residues 46 B and 57 B Built loop between residues 82 B and 88 B Built loop between residues 253 B and 257 B Built loop between residues 44 D and 53 D Built loop between residues 197 D and 200 D 17 chains (1291 residues) following loop building 9 chains (1123 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 12280 restraints for refining 10908 atoms. 3057 conditional restraints added. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2032 (Rfree = 0.000) for 10908 atoms. Found 175 (175 requested) and removed 138 (125 requested) atoms. Cycle 17: After refmac, R = 0.1883 (Rfree = 0.000) for 10939 atoms. Found 103 (171 requested) and removed 125 (125 requested) atoms. Cycle 18: After refmac, R = 0.1827 (Rfree = 0.000) for 10911 atoms. Found 69 (166 requested) and removed 125 (125 requested) atoms. Cycle 19: After refmac, R = 0.1797 (Rfree = 0.000) for 10852 atoms. Found 73 (159 requested) and removed 125 (124 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1786 (Rfree = 0.000) for 10792 atoms. Found 81 (154 requested) and removed 93 (124 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.31 2.50 NCS extension: 1004 residues added (893 deleted due to clashes), 11790 seeds are put forward Round 1: 1257 peptides, 33 chains. Longest chain 185 peptides. Score 0.946 Round 2: 1279 peptides, 23 chains. Longest chain 221 peptides. Score 0.958 Round 3: 1273 peptides, 35 chains. Longest chain 164 peptides. Score 0.946 Round 4: 1272 peptides, 34 chains. Longest chain 237 peptides. Score 0.947 Round 5: 1267 peptides, 41 chains. Longest chain 182 peptides. Score 0.940 Taking the results from Round 2 Chains 30, Residues 1256, Estimated correctness of the model 99.7 % 15 chains (1123 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 296 A and 299 A Built loop between residues 84 C and 93 C Built loop between residues 312 C and 315 C Built loop between residues 81 B and 90 B Built loop between residues 52 D and 58 D Built loop between residues 312 D and 315 D 21 chains (1280 residues) following loop building 9 chains (1150 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11618 restraints for refining 10741 atoms. 2347 conditional restraints added. Observations/parameters ratio is 1.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1963 (Rfree = 0.000) for 10741 atoms. Found 148 (148 requested) and removed 130 (123 requested) atoms. Cycle 22: After refmac, R = 0.1838 (Rfree = 0.000) for 10754 atoms. Found 134 (143 requested) and removed 123 (123 requested) atoms. Cycle 23: After refmac, R = 0.1790 (Rfree = 0.000) for 10757 atoms. Found 88 (138 requested) and removed 123 (123 requested) atoms. Cycle 24: After refmac, R = 0.1769 (Rfree = 0.000) for 10713 atoms. Found 75 (133 requested) and removed 80 (123 requested) atoms. Cycle 25: After refmac, R = 0.1743 (Rfree = 0.000) for 10707 atoms. Found 88 (128 requested) and removed 72 (123 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.30 2.49 NCS extension: 740 residues added (577 deleted due to clashes), 11469 seeds are put forward Round 1: 1280 peptides, 32 chains. Longest chain 183 peptides. Score 0.950 Round 2: 1294 peptides, 23 chains. Longest chain 252 peptides. Score 0.960 Round 3: 1288 peptides, 33 chains. Longest chain 164 peptides. Score 0.950 Round 4: 1284 peptides, 32 chains. Longest chain 211 peptides. Score 0.951 Round 5: 1280 peptides, 35 chains. Longest chain 130 peptides. Score 0.947 Taking the results from Round 2 Chains 26, Residues 1271, Estimated correctness of the model 99.7 % 15 chains (1214 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 123 A and 128 A Built loop between residues 252 A and 257 A Built loop between residues 84 C and 94 C Built loop between residues 18 B and 23 B Built loop between residues 53 B and 58 B Built loop between residues 69 B and 72 B 19 chains (1297 residues) following loop building 9 chains (1241 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11207 restraints for refining 10827 atoms. 1576 conditional restraints added. Observations/parameters ratio is 1.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1964 (Rfree = 0.000) for 10827 atoms. Found 124 (124 requested) and removed 130 (124 requested) atoms. Cycle 27: After refmac, R = 0.1828 (Rfree = 0.000) for 10813 atoms. Found 124 (124 requested) and removed 124 (124 requested) atoms. Cycle 28: After refmac, R = 0.1763 (Rfree = 0.000) for 10810 atoms. Found 115 (124 requested) and removed 117 (124 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1733 (Rfree = 0.000) for 10804 atoms. Found 107 (124 requested) and removed 90 (124 requested) atoms. Cycle 30: After refmac, R = 0.1718 (Rfree = 0.000) for 10816 atoms. Found 99 (124 requested) and removed 68 (124 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.31 2.50 NCS extension: 642 residues added (315 deleted due to clashes), 11491 seeds are put forward Round 1: 1294 peptides, 30 chains. Longest chain 162 peptides. Score 0.953 Round 2: 1311 peptides, 25 chains. Longest chain 230 peptides. Score 0.960 Round 3: 1309 peptides, 25 chains. Longest chain 253 peptides. Score 0.959 Round 4: 1311 peptides, 30 chains. Longest chain 233 peptides. Score 0.955 Round 5: 1302 peptides, 35 chains. Longest chain 224 peptides. Score 0.950 Taking the results from Round 2 Chains 29, Residues 1286, Estimated correctness of the model 99.7 % 18 chains (1220 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 271 A and 274 A Built loop between residues 120 C and 124 C Built loop between residues 272 C and 279 C Built loop between residues 43 B and 47 B Built loop between residues 83 B and 89 B Built loop between residues 117 B and 121 B Built loop between residues 84 D and 91 D Built loop between residues 164 D and 167 D Built loop between residues 215 D and 218 D Built loop between residues 270 D and 273 D 18 chains (1316 residues) following loop building 8 chains (1254 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11116 restraints for refining 10912 atoms. 1363 conditional restraints added. Observations/parameters ratio is 1.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1910 (Rfree = 0.000) for 10912 atoms. Found 125 (125 requested) and removed 132 (125 requested) atoms. Cycle 32: After refmac, R = 0.1798 (Rfree = 0.000) for 10897 atoms. Found 125 (125 requested) and removed 125 (125 requested) atoms. Cycle 33: After refmac, R = 0.1745 (Rfree = 0.000) for 10889 atoms. Found 109 (125 requested) and removed 125 (125 requested) atoms. Cycle 34: After refmac, R = 0.1724 (Rfree = 0.000) for 10867 atoms. Found 113 (125 requested) and removed 84 (125 requested) atoms. Cycle 35: After refmac, R = 0.1697 (Rfree = 0.000) for 10892 atoms. Found 89 (125 requested) and removed 84 (125 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.30 2.49 NCS extension: 686 residues added (365 deleted due to clashes), 11597 seeds are put forward Round 1: 1291 peptides, 29 chains. Longest chain 185 peptides. Score 0.954 Round 2: 1316 peptides, 19 chains. Longest chain 262 peptides. Score 0.965 Round 3: 1303 peptides, 34 chains. Longest chain 133 peptides. Score 0.951 Round 4: 1302 peptides, 30 chains. Longest chain 136 peptides. Score 0.954 Round 5: 1288 peptides, 37 chains. Longest chain 172 peptides. Score 0.946 Taking the results from Round 2 Chains 21, Residues 1297, Estimated correctness of the model 99.8 % 14 chains (1246 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 300 A and 303 A Built loop between residues 84 C and 88 C Built loop between residues 215 C and 218 C Built loop between residues 18 B and 23 B Built loop between residues 54 B and 58 B Built loop between residues 82 B and 88 B 14 chains (1315 residues) following loop building 8 chains (1265 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11142 restraints for refining 10972 atoms. 1331 conditional restraints added. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1876 (Rfree = 0.000) for 10972 atoms. Found 126 (126 requested) and removed 131 (126 requested) atoms. Cycle 37: After refmac, R = 0.1768 (Rfree = 0.000) for 10960 atoms. Found 126 (126 requested) and removed 126 (126 requested) atoms. Cycle 38: After refmac, R = 0.1719 (Rfree = 0.000) for 10956 atoms. Found 124 (126 requested) and removed 126 (126 requested) atoms. Cycle 39: After refmac, R = 0.1691 (Rfree = 0.000) for 10951 atoms. Found 104 (125 requested) and removed 105 (125 requested) atoms. Cycle 40: After refmac, R = 0.1678 (Rfree = 0.000) for 10944 atoms. Found 116 (125 requested) and removed 81 (125 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.30 2.49 NCS extension: 837 residues added (299 deleted due to clashes), 11826 seeds are put forward Round 1: 1300 peptides, 31 chains. Longest chain 158 peptides. Score 0.953 Round 2: 1313 peptides, 21 chains. Longest chain 229 peptides. Score 0.963 Round 3: 1310 peptides, 29 chains. Longest chain 183 peptides. Score 0.956 Round 4: 1297 peptides, 35 chains. Longest chain 131 peptides. Score 0.949 Round 5: 1291 peptides, 37 chains. Longest chain 172 peptides. Score 0.947 Taking the results from Round 2 Chains 23, Residues 1292, Estimated correctness of the model 99.7 % 15 chains (1198 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 73 A Built loop between residues 82 A and 90 A Built loop between residues 308 A and 312 A Built loop between residues 42 C and 52 C Built loop between residues 271 C and 274 C Built loop between residues 45 B and 49 B Built loop between residues 271 B and 274 B 15 chains (1319 residues) following loop building 8 chains (1226 residues) in sequence following loop building ------------------------------------------------------ 58827 reflections ( 99.75 % complete ) and 11446 restraints for refining 10998 atoms. 1746 conditional restraints added. Observations/parameters ratio is 1.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1907 (Rfree = 0.000) for 10998 atoms. Found 126 (126 requested) and removed 134 (126 requested) atoms. Cycle 42: After refmac, R = 0.1788 (Rfree = 0.000) for 10980 atoms. Found 126 (126 requested) and removed 126 (126 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.1730 (Rfree = 0.000) for 10975 atoms. Found 104 (126 requested) and removed 126 (126 requested) atoms. Cycle 44: After refmac, R = 0.1710 (Rfree = 0.000) for 10949 atoms. Found 100 (125 requested) and removed 91 (125 requested) atoms. Cycle 45: After refmac, R = 0.1691 (Rfree = 0.000) for 10954 atoms. Found 111 (126 requested) and removed 91 (126 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.30 2.49 NCS extension: 86 residues added (107 deleted due to clashes), 11074 seeds are put forward Round 1: 1298 peptides, 30 chains. Longest chain 158 peptides. Score 0.954 Round 2: 1318 peptides, 22 chains. Longest chain 220 peptides. Score 0.963 Round 3: 1304 peptides, 32 chains. Longest chain 109 peptides. Score 0.953 Round 4: 1302 peptides, 31 chains. Longest chain 134 peptides. Score 0.953 Round 5: 1281 peptides, 46 chains. Longest chain 127 peptides. Score 0.937 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 1296, Estimated correctness of the model 99.7 % 17 chains (1256 residues) have been docked in sequence Sequence coverage is 96 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 57 A and 62 A Built loop between residues 312 A and 315 A Built loop between residues 83 C and 87 C Built loop between residues 216 C and 219 C Built loop between residues 270 C and 273 C Built loop between residues 18 B and 23 B Built loop between residues 44 B and 47 B Built loop between residues 120 B and 130 B Built loop between residues 45 D and 52 D Built loop between residues 82 D and 96 D Built loop between residues 120 D and 124 D 13 chains (1339 residues) following loop building 6 chains (1306 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 58827 reflections ( 99.75 % complete ) and 10064 restraints for refining 9882 atoms. Observations/parameters ratio is 1.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2502 (Rfree = 0.000) for 9882 atoms. Found 81 (113 requested) and removed 0 (113 requested) atoms. Cycle 47: After refmac, R = 0.2308 (Rfree = 0.000) for 9882 atoms. Found 42 (114 requested) and removed 6 (114 requested) atoms. Cycle 48: After refmac, R = 0.2234 (Rfree = 0.000) for 9882 atoms. Found 24 (115 requested) and removed 8 (115 requested) atoms. Cycle 49: After refmac, R = 0.2198 (Rfree = 0.000) for 9882 atoms. TimeTaking 160.55