Mon 24 Dec 08:08:14 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 2prr-1.9-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prr-1.9-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prr-1.9-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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/2prr-1.9-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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 08:08:19 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-1.9-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 2694 and 0 Target number of residues in the AU: 2694 Target solvent content: 0.4889 Target number of residues exceeds 1700, conditional restraints are disabled Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-1.9-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: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-1.9-parrot-noncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.55 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: 119.307 1.870 Wilson plot Bfac: 21.26 218969 reflections ( 95.87 % complete ) and 0 restraints for refining 21012 atoms. Observations/parameters ratio is 2.61 ------------------------------------------------------ Starting model: R = 0.3336 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2930 (Rfree = 0.000) for 21012 atoms. Found 779 (871 requested) and removed 441 (435 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.03 1.90 NCS extension: 0 residues added, 21350 seeds are put forward Round 1: 1473 peptides, 247 chains. Longest chain 20 peptides. Score 0.455 Round 2: 1667 peptides, 189 chains. Longest chain 36 peptides. Score 0.655 Round 3: 1810 peptides, 156 chains. Longest chain 51 peptides. Score 0.751 Round 4: 1852 peptides, 135 chains. Longest chain 60 peptides. Score 0.789 Round 5: 1909 peptides, 126 chains. Longest chain 59 peptides. Score 0.813 Taking the results from Round 5 Chains 139, Residues 1783, Estimated correctness of the model 97.3 % 45 chains (1147 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 78 A and 81 A Built loop between residues 99 A and 110 A Built loop between residues 168 D and 175 D Built loop between residues 101 G and 104 G Built loop between residues 50 K and 53 K Built loop between residues 69 K and 74 K Built loop between residues 97 K and 104 K Built loop between residues 131 K and 136 K 129 chains (1811 residues) following loop building 37 chains (1183 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 11783 restraints for refining 19779 atoms. Observations/parameters ratio is 2.77 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3246 (Rfree = 0.000) for 19779 atoms. Found 820 (820 requested) and removed 438 (410 requested) atoms. Cycle 2: After refmac, R = 0.3045 (Rfree = 0.000) for 20161 atoms. Found 613 (819 requested) and removed 167 (418 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2843 (Rfree = 0.000) for 20607 atoms. Found 470 (837 requested) and removed 151 (427 requested) atoms. Cycle 4: After refmac, R = 0.2713 (Rfree = 0.000) for 20926 atoms. Found 403 (851 requested) and removed 138 (434 requested) atoms. Cycle 5: After refmac, R = 0.2669 (Rfree = 0.000) for 21191 atoms. Found 370 (861 requested) and removed 84 (439 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.01 1.88 NCS extension: 20 residues added (37 deleted due to clashes), 21561 seeds are put forward Round 1: 1882 peptides, 113 chains. Longest chain 97 peptides. Score 0.822 Round 2: 1945 peptides, 103 chains. Longest chain 91 peptides. Score 0.844 Round 3: 1957 peptides, 100 chains. Longest chain 90 peptides. Score 0.850 Round 4: 1976 peptides, 100 chains. Longest chain 75 peptides. Score 0.853 Round 5: 1980 peptides, 97 chains. Longest chain 79 peptides. Score 0.856 Taking the results from Round 5 Chains 113, Residues 1883, Estimated correctness of the model 98.4 % 48 chains (1411 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 119 A and 122 A Built loop between residues 66 D and 69 D Built loop between residues 95 D and 100 D Built loop between residues 149 D and 159 D Built loop between residues 172 D and 175 D Built loop between residues 168 G and 172 G Built loop between residues 81 F and 84 F Built loop between residues 103 F and 106 F Built loop between residues 59 I and 63 I Built loop between residues 174 I and 179 I Built loop between residues 66 H and 70 H Built loop between residues 123 H and 127 H Built loop between residues 92 K and 102 K Built loop between residues 166 K and 169 K 91 chains (1914 residues) following loop building 34 chains (1461 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 218969 reflections ( 95.87 % complete ) and 13402 restraints for refining 20598 atoms. Observations/parameters ratio is 2.66 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3045 (Rfree = 0.000) for 20598 atoms. Found 837 (837 requested) and removed 442 (427 requested) atoms. Cycle 7: After refmac, R = 0.2819 (Rfree = 0.000) for 20993 atoms. Found 567 (836 requested) and removed 120 (435 requested) atoms. Cycle 8: After refmac, R = 0.2687 (Rfree = 0.000) for 21440 atoms. Found 433 (853 requested) and removed 85 (444 requested) atoms. Cycle 9: After refmac, R = 0.2596 (Rfree = 0.000) for 21788 atoms. Found 333 (867 requested) and removed 78 (451 requested) atoms. Cycle 10: After refmac, R = 0.2524 (Rfree = 0.000) for 22043 atoms. Found 254 (877 requested) and removed 84 (457 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.00 1.87 NCS extension: 18 residues added (115 deleted due to clashes), 22267 seeds are put forward Round 1: 1967 peptides, 79 chains. Longest chain 134 peptides. Score 0.871 Round 2: 2017 peptides, 68 chains. Longest chain 187 peptides. Score 0.888 Round 3: 2023 peptides, 73 chains. Longest chain 96 peptides. Score 0.885 Round 4: 2018 peptides, 73 chains. Longest chain 130 peptides. Score 0.884 Round 5: 2004 peptides, 87 chains. Longest chain 91 peptides. Score 0.870 Taking the results from Round 2 Chains 81, Residues 1949, Estimated correctness of the model 99.0 % 40 chains (1626 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 105 A and 108 A Built loop between residues 144 A and 148 A Built loop between residues 69 C and 72 C Built loop between residues 110 C and 116 C Built loop between residues 164 C and 172 C Built loop between residues 141 D and 144 D Built loop between residues 46 G and 49 G Built loop between residues 57 G and 68 G Built loop between residues 85 F and 89 F Built loop between residues 139 F and 142 F Built loop between residues 94 I and 104 I Built loop between residues 74 J and 77 J Built loop between residues 89 L and 93 L Built loop between residues 122 L and 126 L 61 chains (1986 residues) following loop building 26 chains (1681 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 14691 restraints for refining 21629 atoms. Observations/parameters ratio is 2.53 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2880 (Rfree = 0.000) for 21629 atoms. Found 858 (861 requested) and removed 436 (448 requested) atoms. Cycle 12: After refmac, R = 0.2686 (Rfree = 0.000) for 22051 atoms. Found 505 (859 requested) and removed 123 (457 requested) atoms. Cycle 13: After refmac, R = 0.2590 (Rfree = 0.000) for 22433 atoms. Found 390 (874 requested) and removed 103 (465 requested) atoms. Cycle 14: After refmac, R = 0.2519 (Rfree = 0.000) for 22720 atoms. Found 331 (885 requested) and removed 102 (471 requested) atoms. Cycle 15: After refmac, R = 0.2467 (Rfree = 0.000) for 22949 atoms. Found 316 (895 requested) and removed 124 (476 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.00 1.87 NCS extension: 45 residues added (61 deleted due to clashes), 23201 seeds are put forward Round 1: 2005 peptides, 71 chains. Longest chain 96 peptides. Score 0.884 Round 2: 2030 peptides, 63 chains. Longest chain 145 peptides. Score 0.894 Round 3: 2000 peptides, 72 chains. Longest chain 86 peptides. Score 0.882 Round 4: 2011 peptides, 73 chains. Longest chain 126 peptides. Score 0.883 Round 5: 2006 peptides, 73 chains. Longest chain 116 peptides. Score 0.882 Taking the results from Round 2 Chains 71, Residues 1967, Estimated correctness of the model 99.1 % 35 chains (1698 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 61 C and 65 C Built loop between residues 58 D and 68 D Built loop between residues 107 D and 114 D Built loop between residues 64 G and 70 G Built loop between residues 138 G and 142 G Built loop between residues 69 F and 72 F Built loop between residues 170 I and 173 I Built loop between residues 101 H and 104 H Built loop between residues 140 H and 151 H Built loop between residues 102 K and 105 K Built loop between residues 136 K and 140 K Built loop between residues 45 J and 50 J Built loop between residues 149 L and 155 L 54 chains (2015 residues) following loop building 22 chains (1754 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 15117 restraints for refining 22238 atoms. Observations/parameters ratio is 2.46 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2802 (Rfree = 0.000) for 22238 atoms. Found 867 (867 requested) and removed 414 (461 requested) atoms. Cycle 17: After refmac, R = 0.2697 (Rfree = 0.000) for 22691 atoms. Found 496 (885 requested) and removed 89 (470 requested) atoms. Cycle 18: After refmac, R = 0.2564 (Rfree = 0.000) for 23098 atoms. Found 386 (901 requested) and removed 94 (479 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.2481 (Rfree = 0.000) for 23390 atoms. Found 325 (912 requested) and removed 103 (485 requested) atoms. Cycle 20: After refmac, R = 0.2433 (Rfree = 0.000) for 23612 atoms. Found 296 (920 requested) and removed 130 (489 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.99 1.86 NCS extension: 8 residues added (59 deleted due to clashes), 23807 seeds are put forward Round 1: 2015 peptides, 57 chains. Longest chain 112 peptides. Score 0.897 Round 2: 2037 peptides, 51 chains. Longest chain 158 peptides. Score 0.904 Round 3: 2017 peptides, 75 chains. Longest chain 91 peptides. Score 0.882 Round 4: 2013 peptides, 71 chains. Longest chain 125 peptides. Score 0.885 Round 5: 2016 peptides, 75 chains. Longest chain 95 peptides. Score 0.882 Taking the results from Round 2 Chains 54, Residues 1986, Estimated correctness of the model 99.2 % 29 chains (1752 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 108 A Built loop between residues 66 E and 70 E Built loop between residues 102 D and 105 D Built loop between residues 65 G and 73 G Built loop between residues 117 G and 121 G Built loop between residues 67 F and 70 F Built loop between residues 176 H and 180 H Built loop between residues 139 K and 142 K Built loop between residues 113 J and 117 J 45 chains (2016 residues) following loop building 20 chains (1786 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 15258 restraints for refining 22613 atoms. Observations/parameters ratio is 2.42 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2751 (Rfree = 0.000) for 22613 atoms. Found 882 (882 requested) and removed 348 (469 requested) atoms. Cycle 22: After refmac, R = 0.2584 (Rfree = 0.000) for 23147 atoms. Found 558 (902 requested) and removed 113 (480 requested) atoms. Cycle 23: After refmac, R = 0.2488 (Rfree = 0.000) for 23592 atoms. Found 408 (919 requested) and removed 119 (489 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2422 (Rfree = 0.000) for 23881 atoms. Found 362 (931 requested) and removed 127 (495 requested) atoms. Cycle 25: After refmac, R = 0.2381 (Rfree = 0.000) for 24116 atoms. Found 338 (940 requested) and removed 153 (500 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.99 1.86 NCS extension: 17 residues added (45 deleted due to clashes), 24341 seeds are put forward Round 1: 2013 peptides, 60 chains. Longest chain 157 peptides. Score 0.894 Round 2: 2030 peptides, 58 chains. Longest chain 177 peptides. Score 0.898 Round 3: 2020 peptides, 64 chains. Longest chain 187 peptides. Score 0.892 Round 4: 2044 peptides, 60 chains. Longest chain 126 peptides. Score 0.898 Round 5: 2017 peptides, 65 chains. Longest chain 130 peptides. Score 0.890 Taking the results from Round 4 Chains 71, Residues 1984, Estimated correctness of the model 99.1 % 35 chains (1709 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 102 A Built loop between residues 65 C and 69 C Built loop between residues 101 C and 104 C Built loop between residues 143 C and 154 C Built loop between residues 81 E and 84 E Built loop between residues 175 E and 178 E Built loop between residues 94 D and 97 D Built loop between residues 112 D and 115 D Built loop between residues 65 F and 72 F Built loop between residues 101 K and 104 K Built loop between residues 20 J and 23 J Built loop between residues 46 J and 55 J Built loop between residues 96 J and 99 J Built loop between residues 123 J and 126 J Built loop between residues 150 L and 154 L 53 chains (2026 residues) following loop building 20 chains (1760 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 15194 restraints for refining 22891 atoms. Observations/parameters ratio is 2.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2745 (Rfree = 0.000) for 22891 atoms. Found 892 (892 requested) and removed 381 (474 requested) atoms. Cycle 27: After refmac, R = 0.2571 (Rfree = 0.000) for 23402 atoms. Found 545 (912 requested) and removed 110 (485 requested) atoms. Cycle 28: After refmac, R = 0.2474 (Rfree = 0.000) for 23837 atoms. Found 413 (930 requested) and removed 107 (494 requested) atoms. Cycle 29: After refmac, R = 0.2409 (Rfree = 0.000) for 24143 atoms. Found 372 (941 requested) and removed 117 (500 requested) atoms. Cycle 30: After refmac, R = 0.2373 (Rfree = 0.000) for 24398 atoms. Found 341 (951 requested) and removed 142 (506 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.99 1.86 NCS extension: 21 residues added (57 deleted due to clashes), 24632 seeds are put forward Round 1: 2032 peptides, 71 chains. Longest chain 125 peptides. Score 0.888 Round 2: 2051 peptides, 59 chains. Longest chain 161 peptides. Score 0.900 Round 3: 2044 peptides, 62 chains. Longest chain 125 peptides. Score 0.896 Round 4: 2037 peptides, 71 chains. Longest chain 114 peptides. Score 0.888 Round 5: 2023 peptides, 73 chains. Longest chain 141 peptides. Score 0.885 Taking the results from Round 2 Chains 67, Residues 1992, Estimated correctness of the model 99.2 % 34 chains (1730 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 58 A and 61 A Built loop between residues 114 E and 118 E Built loop between residues 60 D and 65 D Built loop between residues 136 D and 139 D Built loop between residues 99 G and 103 G Built loop between residues 69 F and 72 F Built loop between residues 133 H and 142 H Built loop between residues 167 K and 171 K Built loop between residues 51 L and 54 L 55 chains (2017 residues) following loop building 25 chains (1759 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 15145 restraints for refining 23329 atoms. Observations/parameters ratio is 2.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2591 (Rfree = 0.000) for 23329 atoms. Found 909 (909 requested) and removed 372 (483 requested) atoms. Cycle 32: After refmac, R = 0.2468 (Rfree = 0.000) for 23866 atoms. Found 565 (931 requested) and removed 113 (495 requested) atoms. Cycle 33: After refmac, R = 0.2379 (Rfree = 0.000) for 24318 atoms. Found 389 (948 requested) and removed 123 (504 requested) atoms. Cycle 34: After refmac, R = 0.2319 (Rfree = 0.000) for 24584 atoms. Found 360 (959 requested) and removed 136 (510 requested) atoms. Cycle 35: After refmac, R = 0.2280 (Rfree = 0.000) for 24808 atoms. Found 330 (967 requested) and removed 170 (514 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.98 1.85 NCS extension: 19 residues added (123 deleted due to clashes), 25000 seeds are put forward Round 1: 2035 peptides, 60 chains. Longest chain 169 peptides. Score 0.897 Round 2: 2051 peptides, 51 chains. Longest chain 156 peptides. Score 0.906 Round 3: 2038 peptides, 60 chains. Longest chain 154 peptides. Score 0.897 Round 4: 2017 peptides, 67 chains. Longest chain 128 peptides. Score 0.889 Round 5: 2017 peptides, 65 chains. Longest chain 112 peptides. Score 0.890 Taking the results from Round 2 Chains 58, Residues 2000, Estimated correctness of the model 99.2 % 33 chains (1724 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 56 C and 59 C Built loop between residues 102 C and 113 C Built loop between residues 94 D and 99 D Built loop between residues 101 G and 104 G Built loop between residues 145 G and 151 G Built loop between residues 65 I and 69 I Built loop between residues 102 H and 105 H Built loop between residues 136 H and 140 H Built loop between residues 160 K and 163 K Built loop between residues 65 J and 68 J 47 chains (2031 residues) following loop building 23 chains (1759 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 15210 restraints for refining 23567 atoms. Observations/parameters ratio is 2.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2653 (Rfree = 0.000) for 23567 atoms. Found 899 (899 requested) and removed 376 (488 requested) atoms. Cycle 37: After refmac, R = 0.2547 (Rfree = 0.000) for 24090 atoms. Found 628 (919 requested) and removed 116 (499 requested) atoms. Cycle 38: After refmac, R = 0.2397 (Rfree = 0.000) for 24602 atoms. Found 456 (938 requested) and removed 119 (510 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2314 (Rfree = 0.000) for 24939 atoms. Found 395 (951 requested) and removed 167 (517 requested) atoms. Cycle 40: After refmac, R = 0.2263 (Rfree = 0.000) for 25167 atoms. Found 417 (960 requested) and removed 172 (522 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.98 1.85 NCS extension: 25 residues added (126 deleted due to clashes), 25449 seeds are put forward Round 1: 2019 peptides, 53 chains. Longest chain 185 peptides. Score 0.900 Round 2: 2029 peptides, 57 chains. Longest chain 156 peptides. Score 0.899 Round 3: 2038 peptides, 55 chains. Longest chain 123 peptides. Score 0.901 Round 4: 2023 peptides, 62 chains. Longest chain 127 peptides. Score 0.894 Round 5: 2029 peptides, 61 chains. Longest chain 188 peptides. Score 0.895 Taking the results from Round 3 Chains 64, Residues 1983, Estimated correctness of the model 99.2 % 40 chains (1863 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 66 C and 70 C Built loop between residues 142 C and 145 C Built loop between residues 112 B and 115 B Built loop between residues 145 E and 148 E Built loop between residues 64 G and 69 G Built loop between residues 120 G and 124 G Built loop between residues 69 F and 72 F Built loop between residues 155 F and 158 F Built loop between residues 164 I and 172 I Built loop between residues 95 H and 98 H Built loop between residues 113 K and 117 K Built loop between residues 130 K and 133 K Built loop between residues 64 J and 70 J Built loop between residues 101 J and 104 J Built loop between residues 145 J and 151 J Built loop between residues 58 L and 67 L Built loop between residues 175 L and 180 L 43 chains (2035 residues) following loop building 22 chains (1921 residues) in sequence following loop building ------------------------------------------------------ 218969 reflections ( 95.87 % complete ) and 15925 restraints for refining 23925 atoms. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2576 (Rfree = 0.000) for 23925 atoms. Found 913 (913 requested) and removed 433 (496 requested) atoms. Cycle 42: After refmac, R = 0.2438 (Rfree = 0.000) for 24405 atoms. Found 679 (931 requested) and removed 113 (506 requested) atoms. Cycle 43: After refmac, R = 0.2354 (Rfree = 0.000) for 24971 atoms. Found 472 (953 requested) and removed 171 (518 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.2294 (Rfree = 0.000) for 25272 atoms. Found 437 (964 requested) and removed 175 (524 requested) atoms. Cycle 45: After refmac, R = 0.2251 (Rfree = 0.000) for 25534 atoms. Found 414 (974 requested) and removed 233 (529 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.98 1.85 NCS extension: 13 residues added (45 deleted due to clashes), 25753 seeds are put forward Round 1: 2037 peptides, 61 chains. Longest chain 156 peptides. Score 0.896 Round 2: 2057 peptides, 48 chains. Longest chain 186 peptides. Score 0.909 Round 3: 2045 peptides, 54 chains. Longest chain 169 peptides. Score 0.903 Round 4: 2029 peptides, 58 chains. Longest chain 161 peptides. Score 0.898 Round 5: 2026 peptides, 67 chains. Longest chain 157 peptides. Score 0.890 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 56, Residues 2009, Estimated correctness of the model 99.3 % 31 chains (1787 residues) have been docked in sequence Sequence coverage is 88 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 178 A and 181 A Built loop between residues 65 C and 69 C Built loop between residues 56 B and 69 B Built loop between residues 50 G and 58 G Built loop between residues 131 I and 134 I Built loop between residues 64 J and 70 J Built loop between residues 145 J and 151 J Built loop between residues 102 L and 105 L Built loop between residues 120 L and 123 L Built loop between residues 150 L and 154 L 45 chains (2041 residues) following loop building 21 chains (1830 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 218969 reflections ( 95.87 % complete ) and 15557 restraints for refining 15267 atoms. Observations/parameters ratio is 3.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3412 (Rfree = 0.000) for 15267 atoms. Found 125 (570 requested) and removed 0 (570 requested) atoms. Cycle 47: After refmac, R = 0.3317 (Rfree = 0.000) for 15267 atoms. Found 54 (574 requested) and removed 1 (319 requested) atoms. Cycle 48: After refmac, R = 0.3259 (Rfree = 0.000) for 15267 atoms. Found 32 (576 requested) and removed 9 (320 requested) atoms. Cycle 49: After refmac, R = 0.3243 (Rfree = 0.000) for 15267 atoms. TimeTaking 278.47