Starting phenix.real_space_refine on Sun Aug 9 06:54:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sb4_54712/08_2026/9sb4_54712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sb4_54712/08_2026/9sb4_54712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sb4_54712/08_2026/9sb4_54712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sb4_54712/08_2026/9sb4_54712.map" model { file = "/net/cci-nas-00/data/ceres_data/9sb4_54712/08_2026/9sb4_54712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sb4_54712/08_2026/9sb4_54712.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20231 2.51 5 N 5636 2.21 5 O 6247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32361 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1395, 10984 Classifications: {'peptide': 1395} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1330} Chain breaks: 7 Chain: "B" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9268 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1113} Chain breaks: 4 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 246 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 537 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {' ZN': 1, 'PPV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 57.339 70.707 83.940 1.00124.32 S ATOM 479 SG CYS A 70 57.108 74.013 82.164 1.00121.41 S ATOM 532 SG CYS A 77 60.414 72.122 82.311 1.00119.97 S ATOM 762 SG CYS A 107 74.815 80.728 127.250 1.00153.78 S ATOM 786 SG CYS A 110 72.767 83.634 126.837 1.00146.55 S ATOM 1091 SG CYS A 148 75.632 83.587 129.555 1.00153.40 S ATOM 1190 SG CYS A 167 72.277 81.834 130.072 1.00155.19 S ATOM 19758 SG CYS B1163 58.758 86.844 91.784 1.00107.58 S ATOM 19776 SG CYS B1166 61.418 84.553 93.020 1.00116.72 S ATOM 19901 SG CYS B1182 57.814 83.343 92.232 1.00116.75 S ATOM 19920 SG CYS B1185 58.596 85.342 95.405 1.00124.04 S ATOM 20908 SG CYS C 86 85.350 60.763 20.237 1.00143.56 S ATOM 20925 SG CYS C 88 83.717 58.196 22.505 1.00152.91 S ATOM 20958 SG CYS C 92 85.650 57.081 19.482 1.00123.02 S ATOM 20981 SG CYS C 95 87.468 58.554 22.537 1.00127.64 S ATOM 28566 SG CYS I 7 135.521 48.606 135.152 1.00172.71 S ATOM 28591 SG CYS I 10 131.937 47.725 134.412 1.00189.12 S ATOM 28757 SG CYS I 29 132.759 51.154 135.873 1.00182.71 S ATOM 28781 SG CYS I 32 133.034 48.147 138.040 1.00176.87 S ATOM 29108 SG CYS I 75 160.052 58.552 97.348 1.00173.66 S ATOM 29130 SG CYS I 78 161.646 55.183 97.665 1.00176.90 S ATOM 29346 SG CYS I 103 158.042 55.486 96.393 1.00165.75 S ATOM 29366 SG CYS I 106 158.835 55.946 100.031 1.00153.98 S ATOM 29485 SG CYS J 7 115.266 59.196 38.627 1.00 78.29 S ATOM 29508 SG CYS J 10 115.540 60.876 35.217 1.00 78.01 S ATOM 29788 SG CYS J 45 118.174 61.498 37.937 1.00 83.44 S ATOM 29794 SG CYS J 46 118.000 58.259 35.980 1.00 95.09 S ATOM 30917 SG CYS L 31 90.087 27.496 55.220 1.00154.95 S ATOM 30937 SG CYS L 34 90.749 24.704 52.754 1.00161.97 S ATOM 31041 SG CYS L 48 87.609 24.780 54.916 1.00164.64 S ATOM 31064 SG CYS L 51 91.014 23.960 56.488 1.00162.56 S Time building chain proxies: 5.52, per 1000 atoms: 0.17 Number of scatterers: 32361 At special positions: 0 Unit cell: (174.333, 155.925, 158.091, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 56 15.00 Mg 1 11.99 O 6247 8.00 N 5636 7.00 C 20231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7384 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 48 sheets defined 38.2% alpha, 19.7% beta 27 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.867A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.608A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.722A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.692A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.609A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.656A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 698 Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.520A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.893A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.551A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.676A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.506A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1186 removed outlier: 3.611A pdb=" N GLU A1182 " --> pdb=" O ASP A1178 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP A1186 " --> pdb=" O GLU A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.657A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.956A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.721A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1448 through 1453 removed outlier: 3.982A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.519A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.645A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.578A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.512A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.678A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.922A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.562A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 806 through 813 removed outlier: 3.959A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 813 " --> pdb=" O GLU B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.622A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.917A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.586A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 removed outlier: 3.561A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.768A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.507A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.958A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.730A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 4.123A pdb=" N GLN D 132 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 150 Processing helix chain 'D' and resid 156 through 168 removed outlier: 3.928A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.627A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.604A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.511A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.796A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 103 removed outlier: 3.506A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.583A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.774A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.515A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.520A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.655A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.554A pdb=" N LEU K 9 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.805A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.899A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.433A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.789A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.554A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.722A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.691A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.792A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.751A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.655A pdb=" N VAL A1283 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 7.306A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.429A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.825A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.825A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.132A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.848A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.761A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.386A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.645A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.645A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.016A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.766A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.456A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.777A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE1, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE2, first strand: chain 'E' and resid 47 through 48 removed outlier: 5.072A pdb=" N ARG E 52 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.466A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.832A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.735A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.735A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 86 through 95 removed outlier: 6.357A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU G 100 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE G 143 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY G 89 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.722A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.087A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 1338 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 9.19 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.45: 14183 1.45 - 1.69: 18562 1.69 - 1.92: 295 1.92 - 2.16: 1 2.16 - 2.40: 4 Bond restraints: 33045 Sorted by residual: bond pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 1.528 2.080 -0.552 1.59e-02 3.96e+03 1.21e+03 bond pdb=" CD2 PHE D 70 " pdb=" CE2 PHE D 70 " ideal model delta sigma weight residual 1.382 2.396 -1.014 3.00e-02 1.11e+03 1.14e+03 bond pdb=" CE1 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.343 -0.961 3.00e-02 1.11e+03 1.03e+03 bond pdb=" CD1 PHE D 70 " pdb=" CE1 PHE D 70 " ideal model delta sigma weight residual 1.382 2.332 -0.950 3.00e-02 1.11e+03 1.00e+03 bond pdb=" CE2 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.306 -0.924 3.00e-02 1.11e+03 9.49e+02 ... (remaining 33040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 44819 4.93 - 9.86: 24 9.86 - 14.79: 2 14.79 - 19.72: 2 19.72 - 24.66: 1 Bond angle restraints: 44848 Sorted by residual: angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 110.50 135.16 -24.66 1.70e+00 3.46e-01 2.10e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" OG1 THR D 133 " ideal model delta sigma weight residual 109.60 127.90 -18.30 1.50e+00 4.44e-01 1.49e+02 angle pdb=" OG1 THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 109.30 91.63 17.67 2.00e+00 2.50e-01 7.80e+01 angle pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" C THR D 133 " ideal model delta sigma weight residual 111.36 102.56 8.80 1.09e+00 8.42e-01 6.52e+01 angle pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 110.85 123.56 -12.71 1.70e+00 3.46e-01 5.59e+01 ... (remaining 44843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.89: 19364 24.89 - 49.77: 609 49.77 - 74.66: 126 74.66 - 99.55: 11 99.55 - 124.44: 1 Dihedral angle restraints: 20111 sinusoidal: 8710 harmonic: 11401 Sorted by residual: dihedral pdb=" C THR D 133 " pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual -122.00 -140.72 18.72 0 2.50e+00 1.60e-01 5.61e+01 dihedral pdb=" N THR D 133 " pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual 123.40 138.49 -15.09 0 2.50e+00 1.60e-01 3.64e+01 dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 20108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 5043 0.166 - 0.331: 2 0.331 - 0.497: 0 0.497 - 0.663: 0 0.663 - 0.828: 1 Chirality restraints: 5046 Sorted by residual: chirality pdb=" CB THR D 133 " pdb=" CA THR D 133 " pdb=" OG1 THR D 133 " pdb=" CG2 THR D 133 " both_signs ideal model delta sigma weight residual False 2.55 1.72 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CB VAL B 482 " pdb=" CA VAL B 482 " pdb=" CG1 VAL B 482 " pdb=" CG2 VAL B 482 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 5043 not shown) Planarity restraints: 5621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " 0.003 2.00e-02 2.50e+03 5.25e-02 4.82e+01 pdb=" CG PHE D 70 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " -0.088 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C LEU A 710 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 133 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C THR D 133 " 0.044 2.00e-02 2.50e+03 pdb=" O THR D 133 " -0.016 2.00e-02 2.50e+03 pdb=" N THR D 134 " -0.015 2.00e-02 2.50e+03 ... (remaining 5618 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 181 2.49 - 3.09: 22747 3.09 - 3.69: 48332 3.69 - 4.30: 72427 4.30 - 4.90: 120809 Nonbonded interactions: 264496 Sorted by model distance: nonbonded pdb=" OE2 GLU A1448 " pdb=" NH2 ARG G 58 " model vdw 1.883 3.120 nonbonded pdb=" N HIS D 40 " pdb=" NH2 ARG G 75 " model vdw 1.985 3.200 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 2.036 2.170 nonbonded pdb=" CE2 PHE D 70 " pdb=" OG1 THR D 133 " model vdw 2.044 3.340 nonbonded pdb=" OE1 GLN D 37 " pdb=" NZ LYS G 5 " model vdw 2.056 3.120 ... (remaining 264491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 38.360 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.014 33077 Z= 0.474 Angle : 0.596 24.656 44893 Z= 0.357 Chirality : 0.044 0.828 5046 Planarity : 0.004 0.052 5621 Dihedral : 12.641 124.437 12727 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3877 helix: 1.46 (0.15), residues: 1291 sheet: -0.11 (0.22), residues: 570 loop : -0.50 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 711 TYR 0.027 0.001 TYR B 797 PHE 0.088 0.002 PHE D 70 TRP 0.018 0.001 TRP A1044 HIS 0.007 0.001 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.01211 / 0.47 (33045) covalent geometry : angle 0.58789 / 0.36 (44848) hydrogen bonds : bond 0.17974 / 12.16 ( 1361) hydrogen bonds : angle 6.85755 / 4.83 ( 3805) metal coordination : bond 0.00499 / 0.32 ( 32) metal coordination : angle 3.19048 / 2.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 719 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 VAL cc_start: 0.9154 (t) cc_final: 0.8881 (p) REVERT: A 341 MET cc_start: 0.9378 (mmm) cc_final: 0.8986 (mmt) REVERT: A 515 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 595 THR cc_start: 0.8923 (m) cc_final: 0.8524 (p) REVERT: A 705 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8255 (tppt) REVERT: A 801 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 812 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8627 (mt-10) REVERT: A 919 ILE cc_start: 0.7936 (mm) cc_final: 0.7631 (mm) REVERT: A 932 GLU cc_start: 0.8621 (tt0) cc_final: 0.8308 (tt0) REVERT: A 1036 ARG cc_start: 0.8920 (mtt-85) cc_final: 0.8618 (mtt90) REVERT: A 1173 HIS cc_start: 0.7589 (t-90) cc_final: 0.7353 (t-90) REVERT: A 1276 VAL cc_start: 0.8913 (t) cc_final: 0.8688 (p) REVERT: A 1411 GLU cc_start: 0.8576 (tp30) cc_final: 0.8187 (tt0) REVERT: B 88 TYR cc_start: 0.7643 (m-10) cc_final: 0.7437 (m-10) REVERT: B 239 GLU cc_start: 0.8057 (pt0) cc_final: 0.7499 (tt0) REVERT: B 310 MET cc_start: 0.8442 (mtp) cc_final: 0.8109 (mtp) REVERT: B 355 ILE cc_start: 0.7514 (mt) cc_final: 0.7250 (mm) REVERT: B 359 GLU cc_start: 0.7276 (mp0) cc_final: 0.7067 (mp0) REVERT: B 618 ASP cc_start: 0.8829 (t0) cc_final: 0.8623 (t0) REVERT: B 621 GLU cc_start: 0.8310 (tp30) cc_final: 0.7959 (mm-30) REVERT: B 887 HIS cc_start: 0.7962 (m90) cc_final: 0.7553 (t70) REVERT: B 1049 ASP cc_start: 0.8383 (m-30) cc_final: 0.7781 (p0) REVERT: B 1125 ASP cc_start: 0.8903 (t0) cc_final: 0.8628 (t0) REVERT: C 40 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7385 (tm-30) REVERT: C 125 MET cc_start: 0.9127 (mtp) cc_final: 0.8770 (mtp) REVERT: C 224 GLN cc_start: 0.8392 (mt0) cc_final: 0.8019 (mm-40) REVERT: D 1 MET cc_start: 0.1914 (pmm) cc_final: 0.0217 (tpt) REVERT: D 32 GLU cc_start: 0.5635 (mm-30) cc_final: 0.5015 (pt0) REVERT: D 140 ASP cc_start: 0.6174 (m-30) cc_final: 0.5909 (p0) REVERT: D 148 LEU cc_start: 0.7257 (mt) cc_final: 0.6759 (pp) REVERT: D 149 THR cc_start: 0.4382 (m) cc_final: 0.3862 (m) REVERT: E 41 ASP cc_start: 0.8745 (m-30) cc_final: 0.8369 (m-30) REVERT: E 192 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8633 (ttp80) REVERT: F 123 LYS cc_start: 0.9067 (tttm) cc_final: 0.8818 (tttt) REVERT: G 17 PHE cc_start: 0.7743 (m-10) cc_final: 0.7526 (m-10) REVERT: G 23 LYS cc_start: 0.8061 (tttt) cc_final: 0.7794 (pttp) REVERT: G 29 LYS cc_start: 0.7788 (tppt) cc_final: 0.7567 (mttm) REVERT: G 80 LYS cc_start: 0.6164 (tptt) cc_final: 0.5890 (tttt) REVERT: G 114 LEU cc_start: 0.7013 (mt) cc_final: 0.6813 (mp) REVERT: G 146 LYS cc_start: 0.4759 (ttmt) cc_final: 0.4468 (ttmt) REVERT: G 147 ILE cc_start: 0.6441 (mt) cc_final: 0.6186 (mp) REVERT: G 157 ILE cc_start: 0.7819 (mm) cc_final: 0.7275 (mm) REVERT: H 87 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8251 (mtm180) REVERT: I 1 MET cc_start: 0.6924 (tpp) cc_final: 0.6424 (mmt) REVERT: I 2 THR cc_start: 0.7764 (p) cc_final: 0.7546 (p) REVERT: I 9 ASP cc_start: 0.8422 (t70) cc_final: 0.8117 (t70) REVERT: I 61 ASP cc_start: 0.8005 (t0) cc_final: 0.7670 (p0) REVERT: I 80 SER cc_start: 0.7658 (t) cc_final: 0.5749 (m) REVERT: I 90 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7764 (tt0) REVERT: I 109 ILE cc_start: 0.9083 (mt) cc_final: 0.8870 (tp) REVERT: I 113 ASP cc_start: 0.7496 (t0) cc_final: 0.7002 (t0) REVERT: K 36 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8602 (mm-30) REVERT: L 44 ASP cc_start: 0.7740 (t70) cc_final: 0.7501 (t0) outliers start: 0 outliers final: 0 residues processed: 719 average time/residue: 0.2386 time to fit residues: 260.9419 Evaluate side-chains 435 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.0010 overall best weight: 0.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS A 706 HIS A 959 ASN A1188 GLN B 115 GLN B 740 HIS ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 157 GLN E 32 GLN E 63 ASN G 97 HIS H 128 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.107475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.076935 restraints weight = 73487.431| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.97 r_work: 0.3067 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.047 33077 Z= 0.458 Angle : 0.628 24.337 44893 Z= 0.334 Chirality : 0.045 0.734 5046 Planarity : 0.004 0.048 5621 Dihedral : 12.056 128.628 4886 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 0.98 % Allowed : 6.60 % Favored : 92.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 3877 helix: 1.30 (0.14), residues: 1340 sheet: -0.27 (0.21), residues: 567 loop : -0.53 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.028 0.002 TYR G 74 PHE 0.073 0.002 PHE D 70 TRP 0.016 0.001 TRP A1044 HIS 0.009 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.01207 / 0.46 (33045) covalent geometry : angle 0.61792 / 0.33 (44848) hydrogen bonds : bond 0.04764 / 3.23 ( 1361) hydrogen bonds : angle 5.15547 / 3.67 ( 3805) metal coordination : bond 0.00482 / 0.31 ( 32) metal coordination : angle 3.55297 / 2.32 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 466 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7979 (tttp) REVERT: A 341 MET cc_start: 0.9362 (mmm) cc_final: 0.8914 (mmt) REVERT: A 444 PHE cc_start: 0.9104 (t80) cc_final: 0.8863 (t80) REVERT: A 510 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8669 (mm-40) REVERT: A 515 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 595 THR cc_start: 0.8907 (m) cc_final: 0.8509 (p) REVERT: A 692 ASP cc_start: 0.8174 (m-30) cc_final: 0.7963 (m-30) REVERT: A 705 LYS cc_start: 0.8523 (tmtt) cc_final: 0.8252 (tppt) REVERT: A 789 LYS cc_start: 0.9303 (mttt) cc_final: 0.9094 (mmmm) REVERT: A 801 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 873 MET cc_start: 0.8843 (mmm) cc_final: 0.8360 (mmm) REVERT: A 919 ILE cc_start: 0.7861 (mm) cc_final: 0.7531 (mm) REVERT: A 1036 ARG cc_start: 0.8921 (mtt-85) cc_final: 0.8614 (mtt90) REVERT: A 1078 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7871 (mt0) REVERT: A 1173 HIS cc_start: 0.7590 (t-90) cc_final: 0.7278 (t-90) REVERT: A 1202 MET cc_start: 0.8291 (mmm) cc_final: 0.8012 (mmm) REVERT: A 1203 ASN cc_start: 0.7859 (m110) cc_final: 0.7585 (p0) REVERT: A 1225 PHE cc_start: 0.8392 (t80) cc_final: 0.7997 (t80) REVERT: A 1276 VAL cc_start: 0.8862 (t) cc_final: 0.8605 (p) REVERT: A 1411 GLU cc_start: 0.8489 (tp30) cc_final: 0.8103 (tt0) REVERT: B 310 MET cc_start: 0.8531 (mtp) cc_final: 0.8234 (mtp) REVERT: B 443 ASN cc_start: 0.6704 (t0) cc_final: 0.6453 (t0) REVERT: B 498 THR cc_start: 0.9125 (m) cc_final: 0.8921 (p) REVERT: B 618 ASP cc_start: 0.8686 (t0) cc_final: 0.8318 (t0) REVERT: B 887 HIS cc_start: 0.7942 (m90) cc_final: 0.7510 (t70) REVERT: B 895 ASP cc_start: 0.8297 (t0) cc_final: 0.7967 (p0) REVERT: B 1049 ASP cc_start: 0.8333 (m-30) cc_final: 0.7778 (p0) REVERT: B 1111 MET cc_start: 0.9065 (mmm) cc_final: 0.8667 (mmm) REVERT: B 1125 ASP cc_start: 0.8829 (t0) cc_final: 0.8608 (t0) REVERT: C 61 GLU cc_start: 0.8721 (pm20) cc_final: 0.8512 (pm20) REVERT: C 125 MET cc_start: 0.9096 (mtp) cc_final: 0.8744 (mtp) REVERT: C 224 GLN cc_start: 0.8397 (mt0) cc_final: 0.7974 (mm-40) REVERT: C 249 ASP cc_start: 0.8442 (m-30) cc_final: 0.8170 (m-30) REVERT: C 267 GLN cc_start: 0.6985 (tp40) cc_final: 0.5803 (pm20) REVERT: D 1 MET cc_start: 0.2216 (pmm) cc_final: 0.0367 (tpt) REVERT: D 32 GLU cc_start: 0.5905 (mm-30) cc_final: 0.4726 (pt0) REVERT: D 140 ASP cc_start: 0.6493 (m-30) cc_final: 0.6260 (p0) REVERT: D 206 GLU cc_start: 0.4360 (tp30) cc_final: 0.3035 (pt0) REVERT: E 32 GLN cc_start: 0.8153 (tp40) cc_final: 0.7845 (tp-100) REVERT: F 154 ASP cc_start: 0.7057 (t0) cc_final: 0.6745 (t0) REVERT: G 74 TYR cc_start: 0.6039 (p90) cc_final: 0.5769 (p90) REVERT: G 146 LYS cc_start: 0.5415 (ttmt) cc_final: 0.5181 (ttmt) REVERT: G 157 ILE cc_start: 0.7427 (mm) cc_final: 0.7166 (mm) REVERT: H 52 GLN cc_start: 0.8491 (mp10) cc_final: 0.8278 (mp10) REVERT: H 87 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8332 (mtm180) REVERT: H 130 ARG cc_start: 0.8720 (mtm110) cc_final: 0.8489 (ptt-90) REVERT: I 1 MET cc_start: 0.7181 (tpp) cc_final: 0.6869 (mmm) REVERT: I 15 TYR cc_start: 0.7779 (m-80) cc_final: 0.7085 (m-10) REVERT: I 25 LEU cc_start: 0.7896 (pt) cc_final: 0.7650 (tp) REVERT: I 55 THR cc_start: 0.8429 (t) cc_final: 0.8031 (m) REVERT: I 61 ASP cc_start: 0.7947 (t0) cc_final: 0.7706 (p0) REVERT: I 90 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7892 (tt0) REVERT: I 109 ILE cc_start: 0.9086 (mt) cc_final: 0.8883 (tp) REVERT: J 29 GLU cc_start: 0.8012 (pt0) cc_final: 0.7709 (pt0) REVERT: K 54 ARG cc_start: 0.8963 (mtm110) cc_final: 0.8721 (mmm160) REVERT: L 44 ASP cc_start: 0.7750 (t70) cc_final: 0.7420 (t0) outliers start: 34 outliers final: 14 residues processed: 490 average time/residue: 0.2093 time to fit residues: 162.6573 Evaluate side-chains 406 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 391 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain K residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 246 optimal weight: 6.9990 chunk 371 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 chunk 391 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 349 optimal weight: 7.9990 chunk 387 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN A 959 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B1141 HIS D 23 ASN K 2 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.102611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.073434 restraints weight = 72857.773| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.79 r_work: 0.2989 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.048 33077 Z= 0.515 Angle : 0.662 24.207 44893 Z= 0.349 Chirality : 0.046 0.701 5046 Planarity : 0.005 0.049 5621 Dihedral : 12.137 130.399 4886 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 1.50 % Allowed : 8.82 % Favored : 89.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 3877 helix: 1.21 (0.14), residues: 1338 sheet: -0.39 (0.20), residues: 575 loop : -0.63 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 348 TYR 0.019 0.002 TYR G 44 PHE 0.076 0.002 PHE D 70 TRP 0.011 0.001 TRP B 561 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01326 / 0.51 (33045) covalent geometry : angle 0.65018 / 0.35 (44848) hydrogen bonds : bond 0.04707 / 3.19 ( 1361) hydrogen bonds : angle 4.95890 / 3.52 ( 3805) metal coordination : bond 0.00924 / 0.59 ( 32) metal coordination : angle 4.03132 / 2.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 395 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.9398 (mmm) cc_final: 0.9016 (mmp) REVERT: A 692 ASP cc_start: 0.8250 (m-30) cc_final: 0.7999 (m-30) REVERT: A 705 LYS cc_start: 0.8529 (tmtt) cc_final: 0.8285 (tppt) REVERT: A 789 LYS cc_start: 0.9355 (mttt) cc_final: 0.9124 (mmmm) REVERT: A 801 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8249 (tm-30) REVERT: A 873 MET cc_start: 0.8995 (mmm) cc_final: 0.8239 (mmm) REVERT: A 912 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 919 ILE cc_start: 0.7965 (mm) cc_final: 0.7624 (mm) REVERT: A 1036 ARG cc_start: 0.8978 (mtt-85) cc_final: 0.8597 (mtt90) REVERT: A 1078 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7879 (mt0) REVERT: A 1173 HIS cc_start: 0.7783 (t-90) cc_final: 0.7258 (t70) REVERT: A 1203 ASN cc_start: 0.8018 (m110) cc_final: 0.7720 (p0) REVERT: A 1225 PHE cc_start: 0.8499 (t80) cc_final: 0.7891 (t80) REVERT: A 1276 VAL cc_start: 0.9013 (t) cc_final: 0.8753 (p) REVERT: A 1281 ARG cc_start: 0.7945 (ttt-90) cc_final: 0.7572 (ttt180) REVERT: A 1411 GLU cc_start: 0.8526 (tp30) cc_final: 0.8225 (tt0) REVERT: B 350 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 443 ASN cc_start: 0.6782 (t0) cc_final: 0.6518 (t0) REVERT: B 618 ASP cc_start: 0.8738 (t0) cc_final: 0.8410 (t0) REVERT: B 778 MET cc_start: 0.9131 (ttt) cc_final: 0.8873 (ttt) REVERT: B 887 HIS cc_start: 0.7930 (m90) cc_final: 0.7629 (t70) REVERT: B 895 ASP cc_start: 0.8562 (t0) cc_final: 0.8130 (p0) REVERT: B 1049 ASP cc_start: 0.8478 (m-30) cc_final: 0.7941 (p0) REVERT: B 1125 ASP cc_start: 0.8878 (t0) cc_final: 0.8596 (t0) REVERT: C 61 GLU cc_start: 0.8742 (pm20) cc_final: 0.8518 (pm20) REVERT: C 125 MET cc_start: 0.9141 (mtp) cc_final: 0.8803 (mtp) REVERT: C 267 GLN cc_start: 0.7130 (tp40) cc_final: 0.5790 (pm20) REVERT: D 1 MET cc_start: 0.2567 (pmm) cc_final: 0.0665 (tpt) REVERT: D 140 ASP cc_start: 0.6437 (m-30) cc_final: 0.6158 (p0) REVERT: D 148 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6488 (pp) REVERT: D 198 LEU cc_start: 0.4588 (tp) cc_final: 0.4357 (mm) REVERT: E 50 MET cc_start: 0.7771 (ppp) cc_final: 0.7517 (ppp) REVERT: G 58 ARG cc_start: 0.7259 (mtt-85) cc_final: 0.7044 (mtt-85) REVERT: G 74 TYR cc_start: 0.6190 (p90) cc_final: 0.5971 (p90) REVERT: H 87 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8474 (mtm180) REVERT: I 15 TYR cc_start: 0.7482 (m-80) cc_final: 0.7259 (m-10) REVERT: I 25 LEU cc_start: 0.8087 (pt) cc_final: 0.7792 (tp) REVERT: I 61 ASP cc_start: 0.8028 (t0) cc_final: 0.7596 (p0) REVERT: I 90 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8024 (tt0) REVERT: J 29 GLU cc_start: 0.8230 (pt0) cc_final: 0.7937 (pt0) REVERT: K 54 ARG cc_start: 0.8966 (mtm110) cc_final: 0.8702 (mmm160) REVERT: L 28 LYS cc_start: 0.8902 (tppt) cc_final: 0.8582 (tppt) REVERT: L 44 ASP cc_start: 0.7953 (t70) cc_final: 0.7626 (t0) outliers start: 52 outliers final: 26 residues processed: 425 average time/residue: 0.2194 time to fit residues: 148.9388 Evaluate side-chains 381 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 353 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 231 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 chunk 147 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.105485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075292 restraints weight = 72194.388| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.81 r_work: 0.3020 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.045 33077 Z= 0.454 Angle : 0.574 24.228 44893 Z= 0.304 Chirality : 0.043 0.712 5046 Planarity : 0.004 0.048 5621 Dihedral : 12.049 127.487 4886 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 1.21 % Allowed : 9.92 % Favored : 88.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 3877 helix: 1.35 (0.14), residues: 1346 sheet: -0.41 (0.20), residues: 599 loop : -0.58 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1366 TYR 0.016 0.001 TYR G 44 PHE 0.075 0.001 PHE D 70 TRP 0.014 0.001 TRP A1044 HIS 0.005 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.01200 / 0.45 (33045) covalent geometry : angle 0.56366 / 0.30 (44848) hydrogen bonds : bond 0.03938 / 2.68 ( 1361) hydrogen bonds : angle 4.58463 / 3.27 ( 3805) metal coordination : bond 0.00408 / 0.25 ( 32) metal coordination : angle 3.43012 / 2.37 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 398 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8270 (tttp) REVERT: A 341 MET cc_start: 0.9364 (mmm) cc_final: 0.8975 (mmt) REVERT: A 692 ASP cc_start: 0.8214 (m-30) cc_final: 0.7933 (m-30) REVERT: A 705 LYS cc_start: 0.8426 (tmtt) cc_final: 0.8202 (tppt) REVERT: A 873 MET cc_start: 0.8794 (mmm) cc_final: 0.8363 (mmm) REVERT: A 912 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8408 (pp) REVERT: A 919 ILE cc_start: 0.7913 (mm) cc_final: 0.7574 (mm) REVERT: A 1036 ARG cc_start: 0.8961 (mtt-85) cc_final: 0.8587 (mtt90) REVERT: A 1078 GLN cc_start: 0.8140 (mm110) cc_final: 0.7884 (mt0) REVERT: A 1203 ASN cc_start: 0.8045 (m110) cc_final: 0.7728 (p0) REVERT: A 1225 PHE cc_start: 0.8541 (t80) cc_final: 0.8132 (t80) REVERT: A 1276 VAL cc_start: 0.9077 (t) cc_final: 0.8819 (p) REVERT: A 1411 GLU cc_start: 0.8457 (tp30) cc_final: 0.8070 (tt0) REVERT: B 240 ILE cc_start: 0.8356 (pt) cc_final: 0.8144 (tt) REVERT: B 259 TYR cc_start: 0.8342 (m-80) cc_final: 0.8116 (m-80) REVERT: B 350 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 443 ASN cc_start: 0.6848 (t0) cc_final: 0.6579 (t0) REVERT: B 618 ASP cc_start: 0.8709 (t0) cc_final: 0.8423 (t0) REVERT: B 629 ASP cc_start: 0.8103 (t0) cc_final: 0.7815 (t0) REVERT: B 860 MET cc_start: 0.9190 (tmm) cc_final: 0.8810 (tmm) REVERT: B 887 HIS cc_start: 0.7879 (m90) cc_final: 0.7556 (t70) REVERT: B 895 ASP cc_start: 0.8482 (t0) cc_final: 0.8156 (p0) REVERT: B 1049 ASP cc_start: 0.8341 (m-30) cc_final: 0.7913 (p0) REVERT: B 1125 ASP cc_start: 0.8828 (t0) cc_final: 0.8567 (t0) REVERT: C 125 MET cc_start: 0.9106 (mtp) cc_final: 0.8772 (mtp) REVERT: D 1 MET cc_start: 0.2408 (pmm) cc_final: 0.0610 (tpt) REVERT: D 140 ASP cc_start: 0.6616 (m-30) cc_final: 0.6342 (p0) REVERT: D 148 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6316 (pp) REVERT: D 206 GLU cc_start: 0.4254 (tp30) cc_final: 0.2824 (pt0) REVERT: G 58 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.7131 (mtt-85) REVERT: H 87 ARG cc_start: 0.8776 (mmm-85) cc_final: 0.8481 (mtm180) REVERT: H 138 GLU cc_start: 0.7869 (pt0) cc_final: 0.7129 (pm20) REVERT: I 25 LEU cc_start: 0.7975 (pt) cc_final: 0.7727 (tp) REVERT: I 61 ASP cc_start: 0.7990 (t0) cc_final: 0.7732 (p0) REVERT: I 90 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7956 (tt0) REVERT: J 29 GLU cc_start: 0.8163 (pt0) cc_final: 0.7802 (pt0) REVERT: L 44 ASP cc_start: 0.7934 (t70) cc_final: 0.7633 (t0) outliers start: 42 outliers final: 23 residues processed: 426 average time/residue: 0.2246 time to fit residues: 154.2492 Evaluate side-chains 379 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 353 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 210 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 0.0370 chunk 197 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B1193 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN K 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.074164 restraints weight = 72568.339| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.84 r_work: 0.2999 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.043 33077 Z= 0.463 Angle : 0.578 24.176 44893 Z= 0.305 Chirality : 0.044 0.713 5046 Planarity : 0.004 0.049 5621 Dihedral : 12.007 128.971 4886 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 1.42 % Allowed : 10.82 % Favored : 87.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 3877 helix: 1.40 (0.14), residues: 1347 sheet: -0.31 (0.21), residues: 582 loop : -0.60 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 335 TYR 0.015 0.001 TYR G 44 PHE 0.075 0.001 PHE D 70 TRP 0.012 0.001 TRP A1044 HIS 0.006 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.01220 / 0.46 (33045) covalent geometry : angle 0.56871 / 0.30 (44848) hydrogen bonds : bond 0.03905 / 2.66 ( 1361) hydrogen bonds : angle 4.48804 / 3.20 ( 3805) metal coordination : bond 0.00489 / 0.30 ( 32) metal coordination : angle 3.24889 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 375 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8274 (tttp) REVERT: A 341 MET cc_start: 0.9365 (mmm) cc_final: 0.8975 (mmt) REVERT: A 692 ASP cc_start: 0.8206 (m-30) cc_final: 0.7949 (m-30) REVERT: A 705 LYS cc_start: 0.8438 (tmtt) cc_final: 0.8226 (tppt) REVERT: A 873 MET cc_start: 0.8843 (mmm) cc_final: 0.8355 (mmm) REVERT: A 912 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8452 (pp) REVERT: A 919 ILE cc_start: 0.7935 (mm) cc_final: 0.7602 (mm) REVERT: A 1036 ARG cc_start: 0.8969 (mtt-85) cc_final: 0.8588 (mtt90) REVERT: A 1078 GLN cc_start: 0.8152 (mm110) cc_final: 0.7908 (mt0) REVERT: A 1203 ASN cc_start: 0.8055 (m110) cc_final: 0.7752 (p0) REVERT: A 1225 PHE cc_start: 0.8302 (t80) cc_final: 0.8018 (t80) REVERT: A 1276 VAL cc_start: 0.9142 (t) cc_final: 0.8875 (p) REVERT: A 1281 ARG cc_start: 0.8161 (ttt180) cc_final: 0.7597 (ttt180) REVERT: A 1411 GLU cc_start: 0.8470 (tp30) cc_final: 0.8074 (tt0) REVERT: B 240 ILE cc_start: 0.8338 (pt) cc_final: 0.8112 (tt) REVERT: B 259 TYR cc_start: 0.8409 (m-80) cc_final: 0.8168 (m-80) REVERT: B 443 ASN cc_start: 0.6841 (t0) cc_final: 0.6551 (t0) REVERT: B 618 ASP cc_start: 0.8730 (t0) cc_final: 0.8420 (t0) REVERT: B 629 ASP cc_start: 0.8166 (t0) cc_final: 0.7915 (t0) REVERT: B 860 MET cc_start: 0.9172 (tmm) cc_final: 0.8842 (tmm) REVERT: B 895 ASP cc_start: 0.8479 (t0) cc_final: 0.8164 (p0) REVERT: B 896 ASP cc_start: 0.7688 (t0) cc_final: 0.7476 (t0) REVERT: B 1049 ASP cc_start: 0.8381 (m-30) cc_final: 0.7916 (p0) REVERT: B 1125 ASP cc_start: 0.8840 (t0) cc_final: 0.8601 (t0) REVERT: C 125 MET cc_start: 0.9132 (mtp) cc_final: 0.8817 (mtp) REVERT: D 1 MET cc_start: 0.2392 (pmm) cc_final: 0.0587 (tpt) REVERT: D 140 ASP cc_start: 0.6496 (m-30) cc_final: 0.6227 (p0) REVERT: D 148 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6348 (pp) REVERT: E 113 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: F 114 GLU cc_start: 0.8518 (tp30) cc_final: 0.7714 (tt0) REVERT: G 146 LYS cc_start: 0.5604 (ttpp) cc_final: 0.5393 (ttpp) REVERT: H 87 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8339 (mtm180) REVERT: I 13 MET cc_start: 0.8811 (ppp) cc_final: 0.7909 (ppp) REVERT: I 15 TYR cc_start: 0.7302 (m-10) cc_final: 0.7097 (m-10) REVERT: I 25 LEU cc_start: 0.7990 (pt) cc_final: 0.7759 (tp) REVERT: I 61 ASP cc_start: 0.7933 (t0) cc_final: 0.7657 (p0) REVERT: J 29 GLU cc_start: 0.8163 (pt0) cc_final: 0.7820 (pt0) REVERT: K 54 ARG cc_start: 0.8715 (mmm160) cc_final: 0.8510 (tpt90) REVERT: L 44 ASP cc_start: 0.7968 (t70) cc_final: 0.7647 (t0) outliers start: 49 outliers final: 28 residues processed: 407 average time/residue: 0.2166 time to fit residues: 142.4177 Evaluate side-chains 387 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 355 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 261 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 257 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN A1258 HIS B 115 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.104583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074767 restraints weight = 72465.346| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.78 r_work: 0.3007 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.042 33077 Z= 0.456 Angle : 0.567 24.211 44893 Z= 0.300 Chirality : 0.043 0.717 5046 Planarity : 0.004 0.070 5621 Dihedral : 11.957 128.207 4886 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 1.36 % Allowed : 11.17 % Favored : 87.47 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3877 helix: 1.48 (0.15), residues: 1346 sheet: -0.23 (0.21), residues: 579 loop : -0.58 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 5 TYR 0.029 0.001 TYR G 44 PHE 0.075 0.001 PHE D 70 TRP 0.013 0.001 TRP A1044 HIS 0.006 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.01206 / 0.46 (33045) covalent geometry : angle 0.55879 / 0.30 (44848) hydrogen bonds : bond 0.03723 / 2.54 ( 1361) hydrogen bonds : angle 4.37324 / 3.12 ( 3805) metal coordination : bond 0.00417 / 0.25 ( 32) metal coordination : angle 3.13608 / 2.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 383 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8233 (tttp) REVERT: A 341 MET cc_start: 0.9371 (mmm) cc_final: 0.8973 (mmt) REVERT: A 437 MET cc_start: 0.8875 (mtp) cc_final: 0.8629 (mtp) REVERT: A 692 ASP cc_start: 0.8199 (m-30) cc_final: 0.7943 (m-30) REVERT: A 705 LYS cc_start: 0.8413 (tmtt) cc_final: 0.8212 (tppt) REVERT: A 708 MET cc_start: 0.7560 (mmm) cc_final: 0.5979 (mtm) REVERT: A 873 MET cc_start: 0.8818 (mmm) cc_final: 0.8353 (mmm) REVERT: A 912 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8451 (pp) REVERT: A 919 ILE cc_start: 0.7934 (mm) cc_final: 0.7599 (mm) REVERT: A 1036 ARG cc_start: 0.8958 (mtt-85) cc_final: 0.8580 (mtt90) REVERT: A 1078 GLN cc_start: 0.8125 (mm110) cc_final: 0.7905 (mt0) REVERT: A 1203 ASN cc_start: 0.8068 (m110) cc_final: 0.7750 (p0) REVERT: A 1225 PHE cc_start: 0.8318 (t80) cc_final: 0.7986 (t80) REVERT: A 1281 ARG cc_start: 0.8184 (ttt180) cc_final: 0.7639 (ttt-90) REVERT: A 1373 ASP cc_start: 0.8493 (m-30) cc_final: 0.8265 (m-30) REVERT: A 1411 GLU cc_start: 0.8467 (tp30) cc_final: 0.8083 (tt0) REVERT: B 259 TYR cc_start: 0.8372 (m-80) cc_final: 0.8142 (m-80) REVERT: B 350 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 443 ASN cc_start: 0.6891 (t0) cc_final: 0.6591 (t0) REVERT: B 618 ASP cc_start: 0.8722 (t0) cc_final: 0.8397 (t0) REVERT: B 629 ASP cc_start: 0.8156 (t0) cc_final: 0.7916 (t0) REVERT: B 860 MET cc_start: 0.9186 (tmm) cc_final: 0.8853 (tmm) REVERT: B 896 ASP cc_start: 0.7608 (t0) cc_final: 0.7197 (t0) REVERT: B 1049 ASP cc_start: 0.8364 (m-30) cc_final: 0.7908 (p0) REVERT: B 1125 ASP cc_start: 0.8848 (t0) cc_final: 0.8595 (t0) REVERT: B 1152 MET cc_start: 0.8751 (mmm) cc_final: 0.8490 (mmm) REVERT: C 125 MET cc_start: 0.9142 (mtp) cc_final: 0.8812 (mtp) REVERT: D 1 MET cc_start: 0.2151 (pmm) cc_final: 0.0359 (tpp) REVERT: D 139 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7826 (tttp) REVERT: D 140 ASP cc_start: 0.6576 (m-30) cc_final: 0.6342 (p0) REVERT: D 148 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6327 (pp) REVERT: D 206 GLU cc_start: 0.4262 (tp30) cc_final: 0.2818 (pt0) REVERT: E 113 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: H 87 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8317 (mtm180) REVERT: H 136 LYS cc_start: 0.8266 (tppt) cc_final: 0.8004 (tppt) REVERT: H 138 GLU cc_start: 0.7893 (pt0) cc_final: 0.7165 (pm20) REVERT: I 5 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7970 (mmm160) REVERT: I 15 TYR cc_start: 0.7360 (m-10) cc_final: 0.7117 (m-10) REVERT: I 25 LEU cc_start: 0.8024 (pt) cc_final: 0.7778 (tp) REVERT: I 61 ASP cc_start: 0.7918 (t0) cc_final: 0.7653 (p0) REVERT: J 29 GLU cc_start: 0.8229 (pt0) cc_final: 0.7881 (pt0) REVERT: K 54 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8469 (tpt90) REVERT: L 44 ASP cc_start: 0.8038 (t70) cc_final: 0.7713 (t0) outliers start: 47 outliers final: 24 residues processed: 414 average time/residue: 0.2132 time to fit residues: 143.8120 Evaluate side-chains 387 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 359 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 339 optimal weight: 20.0000 chunk 288 optimal weight: 6.9990 chunk 259 optimal weight: 0.0670 chunk 146 optimal weight: 1.9990 chunk 301 optimal weight: 0.0870 chunk 183 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN B 115 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN K 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.104964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.074744 restraints weight = 72948.239| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.84 r_work: 0.3010 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.041 33077 Z= 0.454 Angle : 0.563 24.180 44893 Z= 0.297 Chirality : 0.043 0.719 5046 Planarity : 0.004 0.049 5621 Dihedral : 11.914 128.219 4886 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 1.27 % Allowed : 11.57 % Favored : 87.16 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3877 helix: 1.54 (0.15), residues: 1349 sheet: -0.22 (0.21), residues: 599 loop : -0.53 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.026 0.001 TYR G 44 PHE 0.075 0.001 PHE D 70 TRP 0.012 0.001 TRP A1044 HIS 0.004 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01201 / 0.45 (33045) covalent geometry : angle 0.55465 / 0.30 (44848) hydrogen bonds : bond 0.03638 / 2.48 ( 1361) hydrogen bonds : angle 4.28231 / 3.05 ( 3805) metal coordination : bond 0.00389 / 0.24 ( 32) metal coordination : angle 3.03497 / 2.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 381 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8214 (tttp) REVERT: A 341 MET cc_start: 0.9371 (mmm) cc_final: 0.8966 (mmt) REVERT: A 692 ASP cc_start: 0.8209 (m-30) cc_final: 0.7947 (m-30) REVERT: A 708 MET cc_start: 0.7454 (mmm) cc_final: 0.6013 (mtm) REVERT: A 873 MET cc_start: 0.8811 (mmm) cc_final: 0.8378 (mmm) REVERT: A 912 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8445 (pp) REVERT: A 919 ILE cc_start: 0.7982 (mm) cc_final: 0.7646 (mm) REVERT: A 1036 ARG cc_start: 0.8904 (mtt-85) cc_final: 0.8529 (mtt90) REVERT: A 1225 PHE cc_start: 0.8373 (t80) cc_final: 0.8124 (t80) REVERT: A 1281 ARG cc_start: 0.8188 (ttt180) cc_final: 0.7678 (ttt-90) REVERT: A 1411 GLU cc_start: 0.8469 (tp30) cc_final: 0.8159 (tt0) REVERT: B 259 TYR cc_start: 0.8369 (m-80) cc_final: 0.8120 (m-80) REVERT: B 350 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 443 ASN cc_start: 0.6926 (t0) cc_final: 0.6624 (t0) REVERT: B 618 ASP cc_start: 0.8706 (t0) cc_final: 0.8307 (t0) REVERT: B 629 ASP cc_start: 0.8125 (t0) cc_final: 0.7878 (t0) REVERT: B 860 MET cc_start: 0.9184 (tmm) cc_final: 0.8858 (tmm) REVERT: B 896 ASP cc_start: 0.7521 (t0) cc_final: 0.7133 (t0) REVERT: B 1049 ASP cc_start: 0.8386 (m-30) cc_final: 0.7916 (p0) REVERT: B 1125 ASP cc_start: 0.8832 (t0) cc_final: 0.8580 (t0) REVERT: B 1152 MET cc_start: 0.8716 (mmm) cc_final: 0.8515 (mmm) REVERT: C 125 MET cc_start: 0.9143 (mtp) cc_final: 0.8820 (mtp) REVERT: D 1 MET cc_start: 0.2130 (pmm) cc_final: 0.0344 (tpp) REVERT: D 139 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7831 (tttp) REVERT: D 140 ASP cc_start: 0.6396 (m-30) cc_final: 0.6111 (p0) REVERT: D 148 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6316 (pp) REVERT: F 112 GLU cc_start: 0.8110 (mp0) cc_final: 0.7897 (mp0) REVERT: H 87 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8412 (mtm180) REVERT: I 5 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7954 (mmm160) REVERT: I 25 LEU cc_start: 0.7987 (pt) cc_final: 0.7760 (tp) REVERT: I 61 ASP cc_start: 0.7930 (t0) cc_final: 0.7660 (p0) REVERT: J 29 GLU cc_start: 0.8261 (pt0) cc_final: 0.7921 (pt0) REVERT: J 32 GLU cc_start: 0.9059 (mp0) cc_final: 0.8794 (mp0) REVERT: K 54 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8477 (tpt90) REVERT: L 44 ASP cc_start: 0.8063 (t70) cc_final: 0.7720 (t0) outliers start: 44 outliers final: 27 residues processed: 408 average time/residue: 0.2127 time to fit residues: 140.7013 Evaluate side-chains 395 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 365 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 369 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 389 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 264 optimal weight: 0.6980 chunk 157 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 GLN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B1076 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.103504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.073477 restraints weight = 72881.581| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.80 r_work: 0.2986 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.039 33077 Z= 0.467 Angle : 0.588 24.113 44893 Z= 0.310 Chirality : 0.044 0.712 5046 Planarity : 0.004 0.050 5621 Dihedral : 11.935 128.589 4886 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.19 % Allowed : 12.29 % Favored : 86.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3877 helix: 1.51 (0.14), residues: 1347 sheet: -0.16 (0.20), residues: 620 loop : -0.52 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.022 0.001 TYR G 44 PHE 0.075 0.002 PHE D 70 TRP 0.010 0.001 TRP A1228 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01231 / 0.47 (33045) covalent geometry : angle 0.57961 / 0.31 (44848) hydrogen bonds : bond 0.03761 / 2.56 ( 1361) hydrogen bonds : angle 4.31052 / 3.07 ( 3805) metal coordination : bond 0.00589 / 0.36 ( 32) metal coordination : angle 3.21018 / 2.25 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8829 (ptmm) cc_final: 0.8231 (tttp) REVERT: A 341 MET cc_start: 0.9379 (mmm) cc_final: 0.8982 (mmp) REVERT: A 437 MET cc_start: 0.8879 (mtp) cc_final: 0.8597 (mtp) REVERT: A 696 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: A 708 MET cc_start: 0.7512 (mmm) cc_final: 0.6170 (mtm) REVERT: A 873 MET cc_start: 0.8875 (mmm) cc_final: 0.8406 (mmm) REVERT: A 912 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 919 ILE cc_start: 0.7990 (mm) cc_final: 0.7660 (mm) REVERT: A 1036 ARG cc_start: 0.8923 (mtt-85) cc_final: 0.8525 (mtt90) REVERT: A 1225 PHE cc_start: 0.8395 (t80) cc_final: 0.8113 (t80) REVERT: A 1281 ARG cc_start: 0.8144 (ttt180) cc_final: 0.7652 (ttt-90) REVERT: A 1411 GLU cc_start: 0.8466 (tp30) cc_final: 0.8152 (tt0) REVERT: B 151 LEU cc_start: 0.8254 (tp) cc_final: 0.7894 (pp) REVERT: B 232 SER cc_start: 0.9238 (t) cc_final: 0.8820 (p) REVERT: B 259 TYR cc_start: 0.8347 (m-80) cc_final: 0.8093 (m-80) REVERT: B 350 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 443 ASN cc_start: 0.7024 (t0) cc_final: 0.6717 (t0) REVERT: B 618 ASP cc_start: 0.8662 (t0) cc_final: 0.8259 (t0) REVERT: B 629 ASP cc_start: 0.8153 (t0) cc_final: 0.7915 (t0) REVERT: B 730 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7729 (mtm-85) REVERT: B 895 ASP cc_start: 0.8160 (t0) cc_final: 0.7753 (p0) REVERT: B 1125 ASP cc_start: 0.8859 (t0) cc_final: 0.8584 (t0) REVERT: B 1152 MET cc_start: 0.8789 (mmm) cc_final: 0.8556 (mmm) REVERT: C 125 MET cc_start: 0.9169 (mtp) cc_final: 0.8862 (mtp) REVERT: D 1 MET cc_start: 0.2218 (pmm) cc_final: 0.0613 (tpp) REVERT: D 140 ASP cc_start: 0.6423 (m-30) cc_final: 0.5834 (p0) REVERT: D 148 LEU cc_start: 0.6665 (OUTLIER) cc_final: 0.6225 (pp) REVERT: D 206 GLU cc_start: 0.4208 (tp30) cc_final: 0.2808 (pt0) REVERT: H 87 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8375 (mtm180) REVERT: I 5 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7795 (mmm160) REVERT: I 25 LEU cc_start: 0.8047 (pt) cc_final: 0.7808 (tp) REVERT: I 28 GLU cc_start: 0.7467 (pm20) cc_final: 0.7114 (pm20) REVERT: I 61 ASP cc_start: 0.7959 (t0) cc_final: 0.7656 (p0) REVERT: J 29 GLU cc_start: 0.8295 (pt0) cc_final: 0.7990 (pt0) REVERT: K 54 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8585 (tpt90) REVERT: L 44 ASP cc_start: 0.8136 (t70) cc_final: 0.7770 (t0) outliers start: 41 outliers final: 28 residues processed: 402 average time/residue: 0.2143 time to fit residues: 139.6511 Evaluate side-chains 393 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 362 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 57 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 chunk 367 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 chunk 374 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 388 optimal weight: 30.0000 chunk 68 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN G 102 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074368 restraints weight = 73234.458| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.74 r_work: 0.2972 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.038 33077 Z= 0.478 Angle : 0.606 24.122 44893 Z= 0.320 Chirality : 0.044 0.719 5046 Planarity : 0.004 0.049 5621 Dihedral : 11.963 127.897 4886 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 1.13 % Allowed : 12.67 % Favored : 86.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3877 helix: 1.47 (0.14), residues: 1346 sheet: -0.26 (0.21), residues: 616 loop : -0.51 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 249 TYR 0.042 0.001 TYR G 44 PHE 0.074 0.002 PHE D 70 TRP 0.010 0.001 TRP B 561 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01255 / 0.48 (33045) covalent geometry : angle 0.59773 / 0.32 (44848) hydrogen bonds : bond 0.03872 / 2.64 ( 1361) hydrogen bonds : angle 4.36523 / 3.11 ( 3805) metal coordination : bond 0.00688 / 0.43 ( 32) metal coordination : angle 3.26024 / 2.21 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 363 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8816 (ptmm) cc_final: 0.8216 (tttp) REVERT: A 341 MET cc_start: 0.9361 (mmm) cc_final: 0.8950 (mmp) REVERT: A 437 MET cc_start: 0.8950 (mtp) cc_final: 0.8626 (mtp) REVERT: A 696 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: A 708 MET cc_start: 0.7529 (mmm) cc_final: 0.6124 (mtm) REVERT: A 873 MET cc_start: 0.8896 (mmm) cc_final: 0.8420 (mmm) REVERT: A 912 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 919 ILE cc_start: 0.8017 (mm) cc_final: 0.7686 (mm) REVERT: A 1036 ARG cc_start: 0.8917 (mtt-85) cc_final: 0.8504 (mtt90) REVERT: A 1198 ASP cc_start: 0.8557 (p0) cc_final: 0.8232 (p0) REVERT: A 1225 PHE cc_start: 0.8385 (t80) cc_final: 0.8147 (t80) REVERT: A 1281 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7657 (ttt-90) REVERT: A 1411 GLU cc_start: 0.8448 (tp30) cc_final: 0.8149 (tt0) REVERT: B 151 LEU cc_start: 0.8211 (tp) cc_final: 0.7887 (pp) REVERT: B 232 SER cc_start: 0.9258 (t) cc_final: 0.8826 (p) REVERT: B 313 MET cc_start: 0.9321 (mmm) cc_final: 0.9071 (mtp) REVERT: B 350 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 443 ASN cc_start: 0.7127 (t0) cc_final: 0.6804 (t0) REVERT: B 618 ASP cc_start: 0.8700 (t0) cc_final: 0.8284 (t0) REVERT: B 629 ASP cc_start: 0.8185 (t0) cc_final: 0.7928 (t0) REVERT: B 730 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7766 (mtm-85) REVERT: B 895 ASP cc_start: 0.8121 (t0) cc_final: 0.7735 (p0) REVERT: B 1125 ASP cc_start: 0.8810 (t0) cc_final: 0.8573 (t0) REVERT: C 125 MET cc_start: 0.9168 (mtp) cc_final: 0.8865 (mtp) REVERT: D 1 MET cc_start: 0.2397 (pmm) cc_final: 0.0585 (tpp) REVERT: D 32 GLU cc_start: 0.6445 (mm-30) cc_final: 0.5432 (mt-10) REVERT: D 140 ASP cc_start: 0.6006 (m-30) cc_final: 0.5615 (p0) REVERT: D 148 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6233 (pp) REVERT: D 206 GLU cc_start: 0.4247 (tp30) cc_final: 0.2806 (pt0) REVERT: E 113 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: H 87 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8381 (mtm180) REVERT: I 5 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7764 (mmm160) REVERT: I 25 LEU cc_start: 0.8070 (pt) cc_final: 0.7820 (tp) REVERT: I 28 GLU cc_start: 0.7575 (pm20) cc_final: 0.7246 (pm20) REVERT: I 61 ASP cc_start: 0.7991 (t0) cc_final: 0.7677 (p0) REVERT: J 23 ASN cc_start: 0.9016 (m-40) cc_final: 0.8336 (t0) REVERT: J 29 GLU cc_start: 0.8304 (pt0) cc_final: 0.8010 (pt0) REVERT: J 32 GLU cc_start: 0.9090 (mp0) cc_final: 0.8803 (mp0) REVERT: K 54 ARG cc_start: 0.8823 (mmm160) cc_final: 0.8553 (tpt90) REVERT: L 44 ASP cc_start: 0.8148 (t70) cc_final: 0.7783 (t0) outliers start: 39 outliers final: 28 residues processed: 388 average time/residue: 0.2173 time to fit residues: 136.0478 Evaluate side-chains 388 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 356 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1223 ASP Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 80 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 334 optimal weight: 0.1980 chunk 375 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 132 optimal weight: 0.1980 chunk 263 optimal weight: 0.0000 chunk 57 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 372 optimal weight: 0.6980 chunk 271 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN B 115 GLN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.104239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074341 restraints weight = 72502.269| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.80 r_work: 0.3004 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.027 33077 Z= 0.451 Angle : 0.580 24.195 44893 Z= 0.306 Chirality : 0.043 0.798 5046 Planarity : 0.004 0.049 5621 Dihedral : 11.882 127.032 4886 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 0.78 % Allowed : 12.99 % Favored : 86.23 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3877 helix: 1.57 (0.15), residues: 1348 sheet: -0.19 (0.21), residues: 621 loop : -0.47 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 19 TYR 0.028 0.001 TYR G 44 PHE 0.081 0.001 PHE D 70 TRP 0.013 0.001 TRP A1044 HIS 0.004 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.01194 / 0.45 (33045) covalent geometry : angle 0.57207 / 0.31 (44848) hydrogen bonds : bond 0.03561 / 2.44 ( 1361) hydrogen bonds : angle 4.24092 / 3.03 ( 3805) metal coordination : bond 0.00376 / 0.23 ( 32) metal coordination : angle 2.98245 / 2.01 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7754 Ramachandran restraints generated. 3877 Oldfield, 0 Emsley, 3877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 375 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.8777 (ptmm) cc_final: 0.8197 (tttp) REVERT: A 341 MET cc_start: 0.9357 (mmm) cc_final: 0.8951 (mmp) REVERT: A 437 MET cc_start: 0.8875 (mtp) cc_final: 0.8546 (mtp) REVERT: A 696 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: A 708 MET cc_start: 0.7351 (mmm) cc_final: 0.5982 (mtm) REVERT: A 873 MET cc_start: 0.8867 (mmm) cc_final: 0.8424 (mmm) REVERT: A 912 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8393 (pp) REVERT: A 919 ILE cc_start: 0.7971 (mm) cc_final: 0.7639 (mm) REVERT: A 1036 ARG cc_start: 0.8914 (mtt-85) cc_final: 0.8526 (mtt90) REVERT: A 1198 ASP cc_start: 0.8547 (p0) cc_final: 0.8199 (p0) REVERT: A 1225 PHE cc_start: 0.8388 (t80) cc_final: 0.8133 (t80) REVERT: A 1276 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8830 (m) REVERT: A 1281 ARG cc_start: 0.8172 (ttt180) cc_final: 0.7555 (ttt180) REVERT: A 1285 MET cc_start: 0.8082 (mmm) cc_final: 0.7853 (mtt) REVERT: A 1411 GLU cc_start: 0.8439 (tp30) cc_final: 0.8137 (tt0) REVERT: B 151 LEU cc_start: 0.8227 (tp) cc_final: 0.7902 (pp) REVERT: B 232 SER cc_start: 0.9257 (t) cc_final: 0.8836 (p) REVERT: B 259 TYR cc_start: 0.8316 (m-80) cc_final: 0.8015 (m-80) REVERT: B 350 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8185 (tm-30) REVERT: B 443 ASN cc_start: 0.7264 (t0) cc_final: 0.6970 (t0) REVERT: B 618 ASP cc_start: 0.8674 (t0) cc_final: 0.8259 (t0) REVERT: B 629 ASP cc_start: 0.8148 (t0) cc_final: 0.7887 (t0) REVERT: B 730 ARG cc_start: 0.7987 (mtt90) cc_final: 0.7715 (mtm-85) REVERT: B 860 MET cc_start: 0.9211 (tmm) cc_final: 0.8910 (tmm) REVERT: B 895 ASP cc_start: 0.8094 (t0) cc_final: 0.7706 (p0) REVERT: B 1125 ASP cc_start: 0.8802 (t0) cc_final: 0.8558 (t0) REVERT: B 1152 MET cc_start: 0.8741 (mmm) cc_final: 0.8499 (mmm) REVERT: C 125 MET cc_start: 0.9157 (mtp) cc_final: 0.8850 (mtp) REVERT: D 1 MET cc_start: 0.2425 (pmm) cc_final: 0.0616 (tpp) REVERT: D 32 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5385 (mt-10) REVERT: D 140 ASP cc_start: 0.6052 (m-30) cc_final: 0.5649 (p0) REVERT: D 148 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6192 (pp) REVERT: D 206 GLU cc_start: 0.4233 (tp30) cc_final: 0.2809 (pt0) REVERT: E 113 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: H 27 GLU cc_start: 0.8102 (tt0) cc_final: 0.7600 (tm-30) REVERT: H 87 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8369 (mtm180) REVERT: H 138 GLU cc_start: 0.7940 (pt0) cc_final: 0.7113 (pm20) REVERT: I 5 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7683 (mmm160) REVERT: I 25 LEU cc_start: 0.7989 (pt) cc_final: 0.7755 (tp) REVERT: I 28 GLU cc_start: 0.7559 (pm20) cc_final: 0.7236 (pm20) REVERT: I 44 TYR cc_start: 0.7730 (t80) cc_final: 0.7161 (t80) REVERT: I 61 ASP cc_start: 0.7959 (t0) cc_final: 0.7665 (p0) REVERT: J 23 ASN cc_start: 0.9016 (m-40) cc_final: 0.8329 (t0) REVERT: J 29 GLU cc_start: 0.8287 (pt0) cc_final: 0.8004 (pt0) REVERT: J 32 GLU cc_start: 0.9129 (mp0) cc_final: 0.8818 (mp0) REVERT: K 54 ARG cc_start: 0.8835 (mmm160) cc_final: 0.8591 (tpt90) REVERT: L 44 ASP cc_start: 0.8138 (t70) cc_final: 0.7562 (t0) outliers start: 27 outliers final: 17 residues processed: 389 average time/residue: 0.2185 time to fit residues: 136.4559 Evaluate side-chains 384 residues out of total 3457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 362 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain I residue 2 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 24 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 358 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 238 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 355 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 ASN B 115 GLN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.102947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.073027 restraints weight = 73014.070| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.81 r_work: 0.2980 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.026 33077 Z= 0.468 Angle : 0.602 24.246 44893 Z= 0.316 Chirality : 0.044 0.801 5046 Planarity : 0.004 0.049 5621 Dihedral : 11.874 128.032 4886 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 0.93 % Allowed : 13.34 % Favored : 85.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3877 helix: 1.55 (0.14), residues: 1347 sheet: -0.24 (0.20), residues: 631 loop : -0.49 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.026 0.001 TYR G 44 PHE 0.081 0.002 PHE D 70 TRP 0.020 0.001 TRP A 430 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01230 / 0.47 (33045) covalent geometry : angle 0.59414 / 0.32 (44848) hydrogen bonds : bond 0.03711 / 2.54 ( 1361) hydrogen bonds : angle 4.27239 / 3.05 ( 3805) metal coordination : bond 0.00588 / 0.36 ( 32) metal coordination : angle 3.13422 / 2.14 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8310.70 seconds wall clock time: 143 minutes 26.94 seconds (8606.94 seconds total)