Tue 25 Dec 19:27:55 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 2p10-2.1-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2p10-2.1-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2p10-2.1-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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/2p10-2.1-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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 ============================================================ Tue 25 Dec 19:28:05 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/2p10-2.1-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2p10-2.1-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 1935 and 0 Target number of residues in the AU: 1935 Target solvent content: 0.5487 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 286 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 1716 Adjusted target solvent content: 0.60 Input MTZ file: 2p10-2.1-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: 146 Cell parameters: 180.269 180.269 185.514 90.000 90.000 120.000 Input sequence file: 2p10-2.1-parrot-hancs.fasta_lf Building free atoms model in initial map for 13728 target number of atoms Had to go as low as 0.80 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. 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: 119.449 2.130 Wilson plot Bfac: 35.19 119082 reflections ( 97.35 % complete ) and 0 restraints for refining 15119 atoms. Observations/parameters ratio is 1.97 ------------------------------------------------------ Starting model: R = 0.3284 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2757 (Rfree = 0.000) for 15119 atoms. Found 432 (432 requested) and removed 227 (216 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.41 2.11 NCS extension: 0 residues added, 15324 seeds are put forward Round 1: 1199 peptides, 144 chains. Longest chain 32 peptides. Score 0.600 Round 2: 1336 peptides, 97 chains. Longest chain 56 peptides. Score 0.755 Round 3: 1369 peptides, 83 chains. Longest chain 51 peptides. Score 0.789 Round 4: 1439 peptides, 72 chains. Longest chain 80 peptides. Score 0.825 Round 5: 1469 peptides, 56 chains. Longest chain 105 peptides. Score 0.854 Taking the results from Round 5 Chains 69, Residues 1413, Estimated correctness of the model 97.4 % 33 chains (1171 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 124 A and 130 A Built loop between residues 194 A and 205 A Built loop between residues 232 A and 235 A Built loop between residues 68 C and 74 C Built loop between residues 46 B and 53 B Built loop between residues 127 B and 134 B Built loop between residues 55 E and 61 E Built loop between residues 220 E and 223 E Built loop between residues 126 D and 130 D Built loop between residues 158 D and 161 D Built loop between residues 71 F and 74 F 54 chains (1451 residues) following loop building 22 chains (1219 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 10115 restraints for refining 13314 atoms. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2865 (Rfree = 0.000) for 13314 atoms. Found 381 (381 requested) and removed 213 (190 requested) atoms. Cycle 2: After refmac, R = 0.2554 (Rfree = 0.000) for 13482 atoms. Found 353 (377 requested) and removed 141 (192 requested) atoms. Cycle 3: After refmac, R = 0.2362 (Rfree = 0.000) for 13694 atoms. Found 214 (384 requested) and removed 103 (196 requested) atoms. Cycle 4: After refmac, R = 0.2237 (Rfree = 0.000) for 13805 atoms. Found 183 (387 requested) and removed 70 (197 requested) atoms. Cycle 5: After refmac, R = 0.2154 (Rfree = 0.000) for 13918 atoms. Found 130 (390 requested) and removed 82 (199 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.35 2.05 NCS extension: 9 residues added (64 deleted due to clashes), 14010 seeds are put forward Round 1: 1469 peptides, 47 chains. Longest chain 116 peptides. Score 0.865 Round 2: 1492 peptides, 38 chains. Longest chain 116 peptides. Score 0.880 Round 3: 1475 peptides, 47 chains. Longest chain 116 peptides. Score 0.866 Round 4: 1503 peptides, 41 chains. Longest chain 129 peptides. Score 0.879 Round 5: 1491 peptides, 42 chains. Longest chain 148 peptides. Score 0.876 Taking the results from Round 2 Chains 51, Residues 1454, Estimated correctness of the model 98.2 % 26 chains (1294 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 150 A and 153 A Built loop between residues 49 B and 56 B Built loop between residues 123 E and 131 E Built loop between residues 140 E and 143 E Built loop between residues 241 E and 245 E Built loop between residues 126 D and 130 D Built loop between residues 195 D and 204 D Built loop between residues 80 F and 87 F Built loop between residues 110 F and 113 F Built loop between residues 124 F and 127 F Built loop between residues 160 F and 167 F 35 chains (1481 residues) following loop building 15 chains (1341 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDBFailed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 10777 restraints for refining 13391 atoms. Observations/parameters ratio is 2.22 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2492 (Rfree = 0.000) for 13391 atoms. Found 368 (368 requested) and removed 208 (191 requested) atoms. Cycle 7: After refmac, R = 0.2306 (Rfree = 0.000) for 13551 atoms. Found 282 (364 requested) and removed 45 (193 requested) atoms. Cycle 8: After refmac, R = 0.2112 (Rfree = 0.000) for 13788 atoms. Found 186 (370 requested) and removed 55 (197 requested) atoms. Cycle 9: After refmac, R = 0.2009 (Rfree = 0.000) for 13919 atoms. Found 175 (374 requested) and removed 79 (199 requested) atoms. Cycle 10: After refmac, R = 0.1938 (Rfree = 0.000) for 14015 atoms. Found 147 (377 requested) and removed 78 (200 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.34 2.04 NCS extension: 5 residues added (68 deleted due to clashes), 14106 seeds are put forward Round 1: 1481 peptides, 39 chains. Longest chain 116 peptides. Score 0.877 Round 2: 1495 peptides, 40 chains. Longest chain 116 peptides. Score 0.879 Round 3: 1506 peptides, 37 chains. Longest chain 116 peptides. Score 0.884 Round 4: 1499 peptides, 46 chains. Longest chain 116 peptides. Score 0.872 Round 5: 1491 peptides, 53 chains. Longest chain 118 peptides. Score 0.862 Taking the results from Round 3 Chains 42, Residues 1469, Estimated correctness of the model 98.3 % 27 chains (1298 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 119 C and 122 C Built loop between residues 171 C and 174 C Built loop between residues 254 C and 257 C Built loop between residues 47 B and 56 B Built loop between residues 21 E and 24 E Built loop between residues 73 E and 76 E Built loop between residues 125 E and 130 E Built loop between residues 140 E and 143 E Built loop between residues 194 E and 205 E Built loop between residues 126 D and 130 D Built loop between residues 254 F and 257 F 29 chains (1503 residues) following loop building 15 chains (1339 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 10843 restraints for refining 13531 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2355 (Rfree = 0.000) for 13531 atoms. Found 356 (356 requested) and removed 190 (193 requested) atoms. Cycle 12: After refmac, R = 0.2086 (Rfree = 0.000) for 13697 atoms. Found 249 (353 requested) and removed 85 (196 requested) atoms. Cycle 13: After refmac, R = 0.1961 (Rfree = 0.000) for 13861 atoms. Found 205 (356 requested) and removed 77 (198 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.1880 (Rfree = 0.000) for 13989 atoms. Found 180 (360 requested) and removed 97 (200 requested) atoms. Cycle 15: After refmac, R = 0.1831 (Rfree = 0.000) for 14072 atoms. Found 184 (354 requested) and removed 103 (201 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.34 2.04 NCS extension: 12 residues added (24 deleted due to clashes), 14172 seeds are put forward Round 1: 1502 peptides, 35 chains. Longest chain 116 peptides. Score 0.886 Round 2: 1516 peptides, 33 chains. Longest chain 119 peptides. Score 0.890 Round 3: 1516 peptides, 34 chains. Longest chain 119 peptides. Score 0.889 Round 4: 1508 peptides, 47 chains. Longest chain 107 peptides. Score 0.873 Round 5: 1506 peptides, 37 chains. Longest chain 116 peptides. Score 0.884 Taking the results from Round 2 Chains 36, Residues 1483, Estimated correctness of the model 98.5 % 24 chains (1390 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 130 A and 133 A Built loop between residues 126 C and 130 C Built loop between residues 181 C and 184 C Built loop between residues 194 C and 205 C Built loop between residues 53 B and 57 B Built loop between residues 104 B and 107 B Built loop between residues 127 B and 130 B Built loop between residues 123 E and 130 E Built loop between residues 221 E and 224 E Built loop between residues 124 D and 131 D Built loop between residues 140 D and 143 D Built loop between residues 195 D and 205 D Built loop between residues 151 F and 154 F 19 chains (1525 residues) following loop building 11 chains (1441 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 11284 restraints for refining 13575 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2188 (Rfree = 0.000) for 13575 atoms. Found 334 (334 requested) and removed 199 (194 requested) atoms. Cycle 17: After refmac, R = 0.2015 (Rfree = 0.000) for 13710 atoms. Found 273 (329 requested) and removed 93 (196 requested) atoms. Cycle 18: After refmac, R = 0.1913 (Rfree = 0.000) for 13890 atoms. Found 205 (333 requested) and removed 78 (198 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1857 (Rfree = 0.000) for 14017 atoms. Found 215 (337 requested) and removed 84 (200 requested) atoms. Cycle 20: After refmac, R = 0.1815 (Rfree = 0.000) for 14148 atoms. Found 166 (340 requested) and removed 144 (202 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.34 2.04 NCS extension: 11 residues added (80 deleted due to clashes), 14195 seeds are put forward Round 1: 1490 peptides, 34 chains. Longest chain 116 peptides. Score 0.885 Round 2: 1499 peptides, 33 chains. Longest chain 117 peptides. Score 0.887 Round 3: 1504 peptides, 41 chains. Longest chain 107 peptides. Score 0.879 Round 4: 1476 peptides, 43 chains. Longest chain 103 peptides. Score 0.871 Round 5: 1474 peptides, 45 chains. Longest chain 114 peptides. Score 0.869 Taking the results from Round 2 Chains 42, Residues 1466, Estimated correctness of the model 98.4 % 24 chains (1344 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 128 A and 132 A Built loop between residues 195 A and 205 A Built loop between residues 126 C and 130 C Built loop between residues 124 B and 131 B Built loop between residues 126 E and 129 E Built loop between residues 126 D and 131 D Built loop between residues 220 D and 224 D Built loop between residues 254 D and 257 D Built loop between residues 85 F and 92 F Built loop between residues 126 F and 132 F Built loop between residues 147 F and 150 F 28 chains (1500 residues) following loop building 13 chains (1389 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11052 restraints for refining 13543 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2282 (Rfree = 0.000) for 13543 atoms. Found 317 (317 requested) and removed 158 (193 requested) atoms. Cycle 22: After refmac, R = 0.2027 (Rfree = 0.000) for 13702 atoms. Found 283 (321 requested) and removed 70 (196 requested) atoms. Cycle 23: After refmac, R = 0.1908 (Rfree = 0.000) for 13915 atoms. Found 207 (326 requested) and removed 103 (199 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.1846 (Rfree = 0.000) for 14019 atoms. Found 219 (329 requested) and removed 115 (200 requested) atoms. Cycle 25: After refmac, R = 0.1803 (Rfree = 0.000) for 14123 atoms. Found 196 (323 requested) and removed 153 (202 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.33 2.04 NCS extension: 4 residues added (25 deleted due to clashes), 14185 seeds are put forward Round 1: 1500 peptides, 32 chains. Longest chain 116 peptides. Score 0.889 Round 2: 1497 peptides, 36 chains. Longest chain 134 peptides. Score 0.884 Round 3: 1486 peptides, 40 chains. Longest chain 107 peptides. Score 0.877 Round 4: 1493 peptides, 47 chains. Longest chain 113 peptides. Score 0.870 Round 5: 1500 peptides, 43 chains. Longest chain 118 peptides. Score 0.876 Taking the results from Round 1 Chains 34, Residues 1468, Estimated correctness of the model 98.4 % 24 chains (1405 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 126 C and 130 C Built loop between residues 261 C and 264 C Built loop between residues 72 B and 75 B Built loop between residues 92 B and 95 B Built loop between residues 127 B and 130 B Built loop between residues 249 B and 252 B Built loop between residues 126 E and 130 E Built loop between residues 126 D and 130 D Built loop between residues 111 F and 114 F Built loop between residues 161 F and 164 F 23 chains (1493 residues) following loop building 13 chains (1430 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11193 restraints for refining 13544 atoms. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2088 (Rfree = 0.000) for 13544 atoms. Found 302 (302 requested) and removed 172 (193 requested) atoms. Cycle 27: After refmac, R = 0.1941 (Rfree = 0.000) for 13674 atoms. Found 282 (297 requested) and removed 84 (195 requested) atoms. Cycle 28: After refmac, R = 0.1861 (Rfree = 0.000) for 13872 atoms. Found 222 (302 requested) and removed 79 (198 requested) atoms. Cycle 29: After refmac, R = 0.1812 (Rfree = 0.000) for 14015 atoms. Found 197 (305 requested) and removed 110 (200 requested) atoms. Cycle 30: After refmac, R = 0.1773 (Rfree = 0.000) for 14102 atoms. Found 182 (298 requested) and removed 103 (201 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.34 2.04 NCS extension: 16 residues added (22 deleted due to clashes), 14204 seeds are put forward Round 1: 1497 peptides, 30 chains. Longest chain 116 peptides. Score 0.890 Round 2: 1512 peptides, 27 chains. Longest chain 181 peptides. Score 0.896 Round 3: 1494 peptides, 38 chains. Longest chain 181 peptides. Score 0.881 Round 4: 1500 peptides, 40 chains. Longest chain 113 peptides. Score 0.880 Round 5: 1499 peptides, 39 chains. Longest chain 116 peptides. Score 0.881 Taking the results from Round 2 Chains 31, Residues 1485, Estimated correctness of the model 98.6 % 24 chains (1449 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 89 A and 91 A Built loop between residues 126 C and 130 C Built loop between residues 194 C and 204 C Built loop between residues 127 B and 130 B Built loop between residues 172 E and 175 E Built loop between residues 254 E and 257 E Built loop between residues 125 D and 131 D Built loop between residues 128 F and 131 F Built loop between residues 140 F and 143 F Built loop between residues 155 F and 158 F Built loop between residues 194 F and 205 F 19 chains (1522 residues) following loop building 13 chains (1489 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11507 restraints for refining 13620 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2128 (Rfree = 0.000) for 13620 atoms. Found 280 (280 requested) and removed 198 (194 requested) atoms. Cycle 32: After refmac, R = 0.1951 (Rfree = 0.000) for 13702 atoms. Found 274 (274 requested) and removed 68 (196 requested) atoms. Cycle 33: After refmac, R = 0.1868 (Rfree = 0.000) for 13908 atoms. Found 217 (279 requested) and removed 115 (199 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1823 (Rfree = 0.000) for 14010 atoms. Found 222 (273 requested) and removed 115 (200 requested) atoms. Cycle 35: After refmac, R = 0.1784 (Rfree = 0.000) for 14117 atoms. Found 193 (267 requested) and removed 119 (202 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.34 2.04 NCS extension: 13 residues added (10 deleted due to clashes), 14218 seeds are put forward Round 1: 1508 peptides, 31 chains. Longest chain 116 peptides. Score 0.891 Round 2: 1517 peptides, 32 chains. Longest chain 143 peptides. Score 0.892 Round 3: 1516 peptides, 30 chains. Longest chain 118 peptides. Score 0.894 Round 4: 1488 peptides, 46 chains. Longest chain 94 peptides. Score 0.870 Round 5: 1499 peptides, 42 chains. Longest chain 113 peptides. Score 0.877 Taking the results from Round 3 Chains 37, Residues 1486, Estimated correctness of the model 98.6 % 22 chains (1405 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 127 A and 130 A Built loop between residues 254 A and 257 A Built loop between residues 126 C and 130 C Built loop between residues 193 C and 204 C Built loop between residues 147 B and 150 B Built loop between residues 120 E and 131 E Built loop between residues 194 E and 204 E Built loop between residues 125 D and 131 D Built loop between residues 99 F and 106 F Built loop between residues 125 F and 131 F 21 chains (1528 residues) following loop building 11 chains (1461 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 119082 reflections ( 97.35 % complete ) and 11399 restraints for refining 13623 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2287 (Rfree = 0.000) for 13623 atoms. Found 250 (250 requested) and removed 195 (195 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.2014 (Rfree = 0.000) for 13678 atoms. Found 242 (242 requested) and removed 70 (195 requested) atoms. Cycle 38: After refmac, R = 0.1906 (Rfree = 0.000) for 13850 atoms. Found 246 (246 requested) and removed 93 (198 requested) atoms. Cycle 39: After refmac, R = 0.1840 (Rfree = 0.000) for 14003 atoms. Found 223 (248 requested) and removed 105 (200 requested) atoms. Cycle 40: After refmac, R = 0.1799 (Rfree = 0.000) for 14121 atoms. Found 201 (250 requested) and removed 134 (202 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.34 2.04 NCS extension: 2 residues added (24 deleted due to clashes), 14205 seeds are put forward Round 1: 1499 peptides, 30 chains. Longest chain 116 peptides. Score 0.891 Round 2: 1499 peptides, 32 chains. Longest chain 120 peptides. Score 0.888 Round 3: 1509 peptides, 35 chains. Longest chain 116 peptides. Score 0.887 Round 4: 1498 peptides, 36 chains. Longest chain 117 peptides. Score 0.884 Round 5: 1495 peptides, 53 chains. Longest chain 100 peptides. Score 0.863 Taking the results from Round 1 Chains 33, Residues 1469, Estimated correctness of the model 98.5 % 24 chains (1421 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 127 A and 131 A Built loop between residues 140 A and 143 A Built loop between residues 195 A and 206 A Built loop between residues 254 A and 257 A Built loop between residues 93 C and 96 C Built loop between residues 127 C and 130 C Built loop between residues 104 B and 107 B Built loop between residues 122 B and 130 B Built loop between residues 126 E and 130 E Built loop between residues 194 E and 205 E Built loop between residues 126 D and 130 D Built loop between residues 194 D and 205 D Built loop between residues 85 F and 92 F Built loop between residues 120 F and 131 F 15 chains (1533 residues) following loop building 9 chains (1495 residues) in sequence following loop building ------------------------------------------------------ 119082 reflections ( 97.35 % complete ) and 11552 restraints for refining 13691 atoms. Observations/parameters ratio is 2.17 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2282 (Rfree = 0.000) for 13691 atoms. Found 235 (235 requested) and removed 174 (195 requested) atoms. Cycle 42: After refmac, R = 0.2140 (Rfree = 0.000) for 13752 atoms. Found 228 (228 requested) and removed 47 (196 requested) atoms. Cycle 43: After refmac, R = 0.1978 (Rfree = 0.000) for 13933 atoms. Found 216 (231 requested) and removed 76 (199 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1893 (Rfree = 0.000) for 14073 atoms. Found 191 (233 requested) and removed 78 (201 requested) atoms. Cycle 45: After refmac, R = 0.1840 (Rfree = 0.000) for 14186 atoms. Found 163 (235 requested) and removed 101 (203 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.34 2.04 NCS extension: 21 residues added (81 deleted due to clashes), 14276 seeds are put forward Round 1: 1491 peptides, 26 chains. Longest chain 116 peptides. Score 0.894 Round 2: 1508 peptides, 35 chains. Longest chain 117 peptides. Score 0.887 Round 3: 1502 peptides, 34 chains. Longest chain 118 peptides. Score 0.887 Round 4: 1508 peptides, 36 chains. Longest chain 118 peptides. Score 0.886 Round 5: 1485 peptides, 46 chains. Longest chain 116 peptides. Score 0.870 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 29, Residues 1465, Estimated correctness of the model 98.6 % 21 chains (1431 residues) have been docked in sequence Sequence coverage is 97 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 72 A and 75 A Built loop between residues 126 A and 130 A Built loop between residues 126 C and 130 C Built loop between residues 193 C and 205 C Built loop between residues 71 B and 77 B Built loop between residues 122 B and 131 B Built loop between residues 126 E and 130 E Built loop between residues 193 E and 207 E Built loop between residues 126 D and 130 D Built loop between residues 194 D and 205 D Built loop between residues 104 F and 107 F Built loop between residues 122 F and 130 F 16 chains (1532 residues) following loop building 9 chains (1501 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 119082 reflections ( 97.35 % complete ) and 11559 restraints for refining 11397 atoms. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2700 (Rfree = 0.000) for 11397 atoms. Found 158 (183 requested) and removed 0 (183 requested) atoms. Cycle 47: After refmac, R = 0.2497 (Rfree = 0.000) for 11397 atoms. Found 69 (185 requested) and removed 1 (165 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2367 (Rfree = 0.000) for 11397 atoms. Found 79 (186 requested) and removed 13 (166 requested) atoms. Cycle 49: After refmac, R = 0.2286 (Rfree = 0.000) for 11397 atoms. Found 56 (187 requested) and removed 12 (167 requested) atoms. Writing output files ... TimeTaking 259.3