Tue 25 Dec 19:30:29 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2a9v-2.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-2.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2a9v-2.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:30:39 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2a9v-2.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 661 and 0 Target number of residues in the AU: 661 Target solvent content: 0.5129 Checking the provided sequence file Detected sequence length: 212 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 848 Adjusted target solvent content: 0.38 Input MTZ file: 2a9v-2.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 18 Cell parameters: 275.612 39.042 68.255 90.000 90.000 90.000 Input sequence file: 2a9v-2.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 6784 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 1 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: 137.806 2.200 Wilson plot Bfac: 26.11 33709 reflections ( 87.11 % complete ) and 0 restraints for refining 7558 atoms. Observations/parameters ratio is 1.12 ------------------------------------------------------ Starting model: R = 0.3664 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3035 (Rfree = 0.000) for 7558 atoms. Found 136 (197 requested) and removed 147 (98 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.25 2.65 NCS extension: 0 residues added, 7547 seeds are put forward Round 1: 373 peptides, 71 chains. Longest chain 12 peptides. Score 0.376 Round 2: 454 peptides, 68 chains. Longest chain 20 peptides. Score 0.559 Round 3: 498 peptides, 56 chains. Longest chain 24 peptides. Score 0.702 Round 4: 526 peptides, 53 chains. Longest chain 49 peptides. Score 0.750 Round 5: 522 peptides, 53 chains. Longest chain 47 peptides. Score 0.746 Taking the results from Round 4 Chains 56, Residues 473, Estimated correctness of the model 92.4 % 10 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 77 A and 86 A 55 chains (480 residues) following loop building 9 chains (208 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 11350 restraints for refining 6475 atoms. 8624 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3438 (Rfree = 0.000) for 6475 atoms. Found 144 (169 requested) and removed 111 (84 requested) atoms. Cycle 2: After refmac, R = 0.3189 (Rfree = 0.000) for 6483 atoms. Found 98 (166 requested) and removed 85 (84 requested) atoms. Cycle 3: After refmac, R = 0.3023 (Rfree = 0.000) for 6461 atoms. Found 82 (162 requested) and removed 84 (84 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2877 (Rfree = 0.000) for 6441 atoms. Found 73 (158 requested) and removed 85 (84 requested) atoms. Cycle 5: After refmac, R = 0.2808 (Rfree = 0.000) for 6405 atoms. Found 65 (154 requested) and removed 69 (83 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.17 2.55 NCS extension: 109 residues added (128 deleted due to clashes), 6534 seeds are put forward Round 1: 501 peptides, 52 chains. Longest chain 38 peptides. Score 0.728 Round 2: 536 peptides, 38 chains. Longest chain 51 peptides. Score 0.825 Round 3: 528 peptides, 43 chains. Longest chain 51 peptides. Score 0.798 Round 4: 544 peptides, 37 chains. Longest chain 51 peptides. Score 0.835 Round 5: 545 peptides, 41 chains. Longest chain 48 peptides. Score 0.821 Taking the results from Round 4 Chains 44, Residues 507, Estimated correctness of the model 96.4 % 14 chains (331 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 150 C and 160 C Built loop between residues 182 C and 185 C 41 chains (513 residues) following loop building 12 chains (342 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 33709 reflections ( 87.11 % complete ) and 9993 restraints for refining 6477 atoms. 6542 conditional restraints added. Observations/parameters ratio is 1.30 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3079 (Rfree = 0.000) for 6477 atoms. Found 134 (152 requested) and removed 95 (84 requested) atoms. Cycle 7: After refmac, R = 0.2863 (Rfree = 0.000) for 6507 atoms. Found 89 (150 requested) and removed 85 (85 requested) atoms. Cycle 8: After refmac, R = 0.2722 (Rfree = 0.000) for 6502 atoms. Found 87 (145 requested) and removed 62 (84 requested) atoms. Failed to save intermediate PDB Cycle 9: After refmac, R = 0.2639 (Rfree = 0.000) for 6514 atoms. Found 82 (143 requested) and removed 51 (85 requested) atoms. Cycle 10: After refmac, R = 0.2568 (Rfree = 0.000) for 6536 atoms. Found 71 (139 requested) and removed 44 (85 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.14 2.52 NCS extension: 102 residues added (170 deleted due to clashes), 6681 seeds are put forward Round 1: 540 peptides, 41 chains. Longest chain 55 peptides. Score 0.817 Round 2: 562 peptides, 34 chains. Longest chain 70 peptides. Score 0.858 Round 3: 575 peptides, 34 chains. Longest chain 55 peptides. Score 0.866 Round 4: 569 peptides, 36 chains. Longest chain 48 peptides. Score 0.856 Round 5: 576 peptides, 37 chains. Longest chain 48 peptides. Score 0.857 Taking the results from Round 3 Chains 38, Residues 541, Estimated correctness of the model 97.6 % 14 chains (397 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 82 C and 87 C Built loop between residues 156 C and 160 C Built loop between residues 47 B and 56 B Built loop between residues 181 B and 191 B 32 chains (563 residues) following loop building 10 chains (421 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 9074 restraints for refining 6573 atoms. 5071 conditional restraints added. Observations/parameters ratio is 1.28 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2873 (Rfree = 0.000) for 6573 atoms. Found 137 (137 requested) and removed 103 (85 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.2690 (Rfree = 0.000) for 6600 atoms. Found 111 (134 requested) and removed 86 (86 requested) atoms. Cycle 13: After refmac, R = 0.2576 (Rfree = 0.000) for 6618 atoms. Found 99 (131 requested) and removed 44 (86 requested) atoms. Cycle 14: After refmac, R = 0.2504 (Rfree = 0.000) for 6656 atoms. Found 84 (132 requested) and removed 34 (87 requested) atoms. Cycle 15: After refmac, R = 0.2418 (Rfree = 0.000) for 6698 atoms. Found 63 (133 requested) and removed 33 (87 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.14 2.52 NCS extension: 76 residues added (95 deleted due to clashes), 6819 seeds are put forward Round 1: 577 peptides, 33 chains. Longest chain 48 peptides. Score 0.870 Round 2: 593 peptides, 34 chains. Longest chain 54 peptides. Score 0.876 Round 3: 594 peptides, 34 chains. Longest chain 49 peptides. Score 0.876 Round 4: 588 peptides, 31 chains. Longest chain 49 peptides. Score 0.882 Round 5: 586 peptides, 33 chains. Longest chain 51 peptides. Score 0.875 Taking the results from Round 4 Chains 35, Residues 557, Estimated correctness of the model 98.1 % 16 chains (446 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 125 C and 135 C Built loop between residues 182 C and 191 C Built loop between residues 155 B and 160 B Built loop between residues 158 D and 161 D Built loop between residues 184 D and 190 D 26 chains (573 residues) following loop building 11 chains (474 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 8525 restraints for refining 6697 atoms. 4229 conditional restraints added. Observations/parameters ratio is 1.26 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2742 (Rfree = 0.000) for 6697 atoms. Found 129 (129 requested) and removed 109 (87 requested) atoms. Cycle 17: After refmac, R = 0.2564 (Rfree = 0.000) for 6709 atoms. Found 111 (126 requested) and removed 87 (87 requested) atoms. Cycle 18: After refmac, R = 0.2454 (Rfree = 0.000) for 6723 atoms. Found 89 (122 requested) and removed 44 (87 requested) atoms. Cycle 19: After refmac, R = 0.2385 (Rfree = 0.000) for 6762 atoms. Found 79 (123 requested) and removed 28 (88 requested) atoms. Cycle 20: After refmac, R = 0.2313 (Rfree = 0.000) for 6807 atoms. Found 81 (124 requested) and removed 30 (88 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.14 2.52 NCS extension: 46 residues added (54 deleted due to clashes), 6924 seeds are put forward Round 1: 603 peptides, 35 chains. Longest chain 54 peptides. Score 0.878 Round 2: 614 peptides, 34 chains. Longest chain 53 peptides. Score 0.887 Round 3: 614 peptides, 34 chains. Longest chain 71 peptides. Score 0.887 Round 4: 615 peptides, 32 chains. Longest chain 51 peptides. Score 0.893 Round 5: 594 peptides, 28 chains. Longest chain 72 peptides. Score 0.894 Taking the results from Round 5 Chains 34, Residues 566, Estimated correctness of the model 98.4 % 17 chains (462 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 157 C and 160 C Built loop between residues 44 B and 51 B Built loop between residues 127 B and 132 B Built loop between residues 185 D and 188 D 30 chains (580 residues) following loop building 13 chains (476 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 8516 restraints for refining 6734 atoms. 4232 conditional restraints added. Observations/parameters ratio is 1.25 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2604 (Rfree = 0.000) for 6734 atoms. Found 122 (122 requested) and removed 103 (87 requested) atoms. Cycle 22: After refmac, R = 0.2444 (Rfree = 0.000) for 6750 atoms. Found 120 (120 requested) and removed 76 (88 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2370 (Rfree = 0.000) for 6788 atoms. Found 84 (117 requested) and removed 53 (88 requested) atoms. Failed to save intermediate PDB Cycle 24: After refmac, R = 0.2289 (Rfree = 0.000) for 6812 atoms. Found 93 (114 requested) and removed 40 (89 requested) atoms. Cycle 25: After refmac, R = 0.2253 (Rfree = 0.000) for 6862 atoms. Found 85 (115 requested) and removed 42 (89 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.14 2.52 NCS extension: 156 residues added (409 deleted due to clashes), 7071 seeds are put forward Round 1: 604 peptides, 37 chains. Longest chain 57 peptides. Score 0.873 Round 2: 629 peptides, 29 chains. Longest chain 68 peptides. Score 0.906 Round 3: 628 peptides, 32 chains. Longest chain 73 peptides. Score 0.898 Round 4: 636 peptides, 31 chains. Longest chain 83 peptides. Score 0.904 Round 5: 625 peptides, 31 chains. Longest chain 71 peptides. Score 0.900 Taking the results from Round 2 Chains 39, Residues 600, Estimated correctness of the model 98.7 % 17 chains (477 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 108 C and 111 C Built loop between residues 156 C and 160 C Built loop between residues 46 B and 51 B Built loop between residues 108 B and 119 B Built loop between residues 157 B and 160 B 31 chains (616 residues) following loop building 12 chains (498 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 8439 restraints for refining 6843 atoms. 3916 conditional restraints added. Observations/parameters ratio is 1.23 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2547 (Rfree = 0.000) for 6843 atoms. Found 114 (114 requested) and removed 108 (89 requested) atoms. Cycle 27: After refmac, R = 0.2381 (Rfree = 0.000) for 6844 atoms. Found 110 (110 requested) and removed 89 (89 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2308 (Rfree = 0.000) for 6860 atoms. Found 107 (107 requested) and removed 46 (89 requested) atoms. Cycle 29: After refmac, R = 0.2257 (Rfree = 0.000) for 6917 atoms. Found 85 (108 requested) and removed 46 (90 requested) atoms. Cycle 30: After refmac, R = 0.2233 (Rfree = 0.000) for 6953 atoms. Found 88 (105 requested) and removed 57 (90 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.14 2.52 NCS extension: 140 residues added (333 deleted due to clashes), 7137 seeds are put forward Round 1: 611 peptides, 30 chains. Longest chain 70 peptides. Score 0.896 Round 2: 622 peptides, 28 chains. Longest chain 77 peptides. Score 0.906 Round 3: 625 peptides, 29 chains. Longest chain 69 peptides. Score 0.905 Round 4: 632 peptides, 32 chains. Longest chain 72 peptides. Score 0.900 Round 5: 634 peptides, 29 chains. Longest chain 61 peptides. Score 0.908 Taking the results from Round 5 Chains 35, Residues 605, Estimated correctness of the model 98.8 % 18 chains (469 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 56 A Built loop between residues 82 C and 92 C Built loop between residues 190 C and 193 C Built loop between residues 45 B and 51 B Built loop between residues 109 B and 116 B Built loop between residues 146 B and 150 B Built loop between residues 157 B and 160 B 26 chains (633 residues) following loop building 11 chains (506 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 8515 restraints for refining 6908 atoms. 3868 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2626 (Rfree = 0.000) for 6908 atoms. Found 101 (101 requested) and removed 111 (90 requested) atoms. Cycle 32: After refmac, R = 0.2445 (Rfree = 0.000) for 6890 atoms. Found 97 (97 requested) and removed 90 (90 requested) atoms. Cycle 33: After refmac, R = 0.2366 (Rfree = 0.000) for 6889 atoms. Found 94 (94 requested) and removed 57 (90 requested) atoms. Cycle 34: After refmac, R = 0.2287 (Rfree = 0.000) for 6922 atoms. Found 90 (90 requested) and removed 45 (90 requested) atoms. Cycle 35: After refmac, R = 0.2241 (Rfree = 0.000) for 6960 atoms. Found 90 (90 requested) and removed 38 (90 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.16 2.54 NCS extension: 239 residues added (407 deleted due to clashes), 7265 seeds are put forward Round 1: 629 peptides, 30 chains. Longest chain 71 peptides. Score 0.904 Round 2: 631 peptides, 28 chains. Longest chain 76 peptides. Score 0.910 Round 3: 639 peptides, 27 chains. Longest chain 77 peptides. Score 0.915 Round 4: 632 peptides, 27 chains. Longest chain 71 peptides. Score 0.912 Round 5: 634 peptides, 28 chains. Longest chain 80 peptides. Score 0.911 Taking the results from Round 3 Chains 32, Residues 612, Estimated correctness of the model 98.9 % 16 chains (507 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 48 C and 52 C Built loop between residues 127 C and 132 C Built loop between residues 176 C and 179 C Built loop between residues 45 B and 50 B Built loop between residues 108 B and 116 B Built loop between residues 158 B and 161 B 25 chains (633 residues) following loop building 10 chains (529 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 8369 restraints for refining 6924 atoms. 3664 conditional restraints added. Observations/parameters ratio is 1.22 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2494 (Rfree = 0.000) for 6924 atoms. Found 90 (90 requested) and removed 100 (90 requested) atoms. Cycle 37: After refmac, R = 0.2357 (Rfree = 0.000) for 6907 atoms. Found 90 (90 requested) and removed 90 (90 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2282 (Rfree = 0.000) for 6904 atoms. Found 90 (90 requested) and removed 40 (90 requested) atoms. Cycle 39: After refmac, R = 0.2216 (Rfree = 0.000) for 6952 atoms. Found 90 (90 requested) and removed 33 (90 requested) atoms. Cycle 40: After refmac, R = 0.2180 (Rfree = 0.000) for 7001 atoms. Found 82 (91 requested) and removed 36 (91 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.14 2.52 NCS extension: 148 residues added (303 deleted due to clashes), 7205 seeds are put forward Round 1: 619 peptides, 29 chains. Longest chain 71 peptides. Score 0.902 Round 2: 628 peptides, 28 chains. Longest chain 77 peptides. Score 0.908 Round 3: 635 peptides, 25 chains. Longest chain 77 peptides. Score 0.918 Round 4: 629 peptides, 30 chains. Longest chain 92 peptides. Score 0.904 Round 5: 632 peptides, 27 chains. Longest chain 77 peptides. Score 0.912 Taking the results from Round 3 Chains 29, Residues 610, Estimated correctness of the model 99.0 % 16 chains (507 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 45 A and 54 A Built loop between residues 127 C and 131 C Built loop between residues 46 B and 50 B Built loop between residues 108 B and 111 B Built loop between residues 158 B and 161 B Built loop between residues 82 D and 92 D 23 chains (627 residues) following loop building 10 chains (534 residues) in sequence following loop building ------------------------------------------------------ 33709 reflections ( 87.11 % complete ) and 8372 restraints for refining 6937 atoms. 3675 conditional restraints added. Observations/parameters ratio is 1.21 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2514 (Rfree = 0.000) for 6937 atoms. Found 90 (90 requested) and removed 103 (90 requested) atoms. Cycle 42: After refmac, R = 0.2363 (Rfree = 0.000) for 6921 atoms. Found 90 (90 requested) and removed 80 (90 requested) atoms. Failed to save intermediate PDB Cycle 43: After refmac, R = 0.2282 (Rfree = 0.000) for 6927 atoms. Found 87 (90 requested) and removed 34 (90 requested) atoms. Cycle 44: After refmac, R = 0.2211 (Rfree = 0.000) for 6977 atoms. Found 91 (91 requested) and removed 37 (91 requested) atoms. Cycle 45: After refmac, R = 0.2186 (Rfree = 0.000) for 7024 atoms. Found 91 (91 requested) and removed 59 (91 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.14 2.52 NCS extension: 134 residues added (462 deleted due to clashes), 7206 seeds are put forward Round 1: 614 peptides, 29 chains. Longest chain 80 peptides. Score 0.900 Round 2: 634 peptides, 22 chains. Longest chain 131 peptides. Score 0.925 Round 3: 634 peptides, 24 chains. Longest chain 83 peptides. Score 0.920 Round 4: 627 peptides, 27 chains. Longest chain 96 peptides. Score 0.910 Round 5: 631 peptides, 24 chains. Longest chain 97 peptides. Score 0.919 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 25, Residues 612, Estimated correctness of the model 99.2 % 15 chains (549 residues) have been docked in sequence Sequence coverage is 89 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 82 A and 87 A Built loop between residues 110 A and 115 A Built loop between residues 124 A and 131 A Built loop between residues 45 B and 48 B Built loop between residues 158 D and 161 D 19 chains (629 residues) following loop building 10 chains (567 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. Failed to save intermediate PDB 33709 reflections ( 87.11 % complete ) and 4873 restraints for refining 4765 atoms. Observations/parameters ratio is 1.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3542 (Rfree = 0.000) for 4765 atoms. Found 30 (62 requested) and removed 0 (62 requested) atoms. Cycle 47: After refmac, R = 0.3393 (Rfree = 0.000) for 4765 atoms. Found 11 (62 requested) and removed 0 (62 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.3295 (Rfree = 0.000) for 4765 atoms. Found 5 (62 requested) and removed 3 (62 requested) atoms. Cycle 49: After refmac, R = 0.3238 (Rfree = 0.000) for 4765 atoms. Found 3 (62 requested) and removed 2 (62 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 21:25:49 GMT 2018 Job finished. TimeTaking 115.33