Starting phenix.real_space_refine on Fri May 23 18:16:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlv_38460/05_2025/8xlv_38460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlv_38460/05_2025/8xlv_38460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xlv_38460/05_2025/8xlv_38460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlv_38460/05_2025/8xlv_38460.map" model { file = "/net/cci-nas-00/data/ceres_data/8xlv_38460/05_2025/8xlv_38460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlv_38460/05_2025/8xlv_38460.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15478 2.51 5 N 3965 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24219 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7924 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 6 Chain: "B" Number of atoms: 7867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7867 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 54, 'TRANS': 948} Chain breaks: 7 Chain: "C" Number of atoms: 7924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7924 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 17.85, per 1000 atoms: 0.74 Number of scatterers: 24219 At special positions: 0 Unit cell: (135.807, 131.124, 174.609, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4668 8.00 N 3965 7.00 C 15478 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 616 " - pdb=" SG CYS A 648 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 670 " distance=2.03 Simple disulfide: pdb=" SG CYS A 737 " - pdb=" SG CYS A 759 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 748 " distance=2.03 Simple disulfide: pdb=" SG CYS A1031 " - pdb=" SG CYS A1042 " distance=2.03 Simple disulfide: pdb=" SG CYS A1081 " - pdb=" SG CYS A1125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS B 737 " - pdb=" SG CYS B 759 " distance=2.03 Simple disulfide: pdb=" SG CYS B 742 " - pdb=" SG CYS B 748 " distance=2.03 Simple disulfide: pdb=" SG CYS B1031 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 524 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 537 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 661 " - pdb=" SG CYS C 670 " distance=2.03 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 759 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 748 " distance=2.03 Simple disulfide: pdb=" SG CYS C1031 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1125 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1201 " - " ASN A 615 " " NAG A1202 " - " ASN A 708 " " NAG A1203 " - " ASN A 716 " " NAG A1204 " - " ASN A1073 " " NAG A1205 " - " ASN A1097 " " NAG A1206 " - " ASN A1133 " " NAG A1207 " - " ASN A 234 " " NAG A1208 " - " ASN A 354 " " NAG A1209 " - " ASN A 343 " " NAG B1201 " - " ASN B 615 " " NAG B1202 " - " ASN B 708 " " NAG B1203 " - " ASN B 716 " " NAG B1204 " - " ASN B1073 " " NAG B1205 " - " ASN B1097 " " NAG B1206 " - " ASN B1133 " " NAG B1207 " - " ASN B 282 " " NAG B1208 " - " ASN B 354 " " NAG B1209 " - " ASN B 343 " " NAG C1201 " - " ASN C 615 " " NAG C1202 " - " ASN C 708 " " NAG C1203 " - " ASN C 716 " " NAG C1204 " - " ASN C1073 " " NAG C1205 " - " ASN C1097 " " NAG C1206 " - " ASN C1133 " " NAG D 1 " - " ASN A 800 " " NAG E 1 " - " ASN B 800 " " NAG F 1 " - " ASN C 800 " " NAG G 1 " - " ASN C 331 " " NAG H 1 " - " ASN C 343 " " NAG I 1 " - " ASN C 354 " Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 2.9 seconds 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5666 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 45 sheets defined 25.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 removed outlier: 5.151A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.741A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 736 through 742 Processing helix chain 'A' and resid 745 through 754 removed outlier: 3.577A pdb=" N LEU A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 Processing helix chain 'A' and resid 810 through 814 removed outlier: 3.734A pdb=" N LYS A 813 " --> pdb=" O LYS A 810 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 814 " --> pdb=" O PRO A 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 810 through 814' Processing helix chain 'A' and resid 815 through 825 Processing helix chain 'A' and resid 865 through 883 Processing helix chain 'A' and resid 885 through 889 Processing helix chain 'A' and resid 896 through 907 removed outlier: 3.526A pdb=" N ALA A 902 " --> pdb=" O PRO A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.701A pdb=" N TYR A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 939 removed outlier: 3.631A pdb=" N ILE A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 934 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 935 " --> pdb=" O GLY A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 964 Processing helix chain 'A' and resid 965 through 967 No H-bonds generated for 'chain 'A' and resid 965 through 967' Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.607A pdb=" N ILE A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1031 removed outlier: 4.365A pdb=" N VAL A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 5.061A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.536A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 Processing helix chain 'B' and resid 736 through 742 Processing helix chain 'B' and resid 745 through 754 removed outlier: 3.781A pdb=" N GLN B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 Processing helix chain 'B' and resid 810 through 814 removed outlier: 3.752A pdb=" N LYS B 813 " --> pdb=" O LYS B 810 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG B 814 " --> pdb=" O PRO B 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 814' Processing helix chain 'B' and resid 815 through 825 Processing helix chain 'B' and resid 865 through 883 Processing helix chain 'B' and resid 885 through 889 Processing helix chain 'B' and resid 896 through 907 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.639A pdb=" N TYR B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 940 Processing helix chain 'B' and resid 944 through 964 Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 975 through 981 removed outlier: 3.514A pdb=" N ILE B 979 " --> pdb=" O VAL B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1031 removed outlier: 4.334A pdb=" N VAL B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 991 " --> pdb=" O GLU B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1117 No H-bonds generated for 'chain 'B' and resid 1115 through 1117' Processing helix chain 'C' and resid 295 through 303 removed outlier: 5.114A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.776A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 372' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.944A pdb=" N GLU C 406 " --> pdb=" O LYS C 403 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 615 through 625 Processing helix chain 'C' and resid 736 through 742 Processing helix chain 'C' and resid 745 through 754 removed outlier: 3.808A pdb=" N GLN C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 Processing helix chain 'C' and resid 810 through 814 removed outlier: 3.634A pdb=" N LYS C 813 " --> pdb=" O LYS C 810 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 814 " --> pdb=" O PRO C 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 810 through 814' Processing helix chain 'C' and resid 815 through 825 Processing helix chain 'C' and resid 865 through 883 Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.616A pdb=" N GLY C 888 " --> pdb=" O TRP C 885 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY C 890 " --> pdb=" O PHE C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 912 through 918 Processing helix chain 'C' and resid 918 through 940 removed outlier: 3.550A pdb=" N GLY C 931 " --> pdb=" O ASN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 964 Processing helix chain 'C' and resid 965 through 967 No H-bonds generated for 'chain 'C' and resid 965 through 967' Processing helix chain 'C' and resid 975 through 981 removed outlier: 3.502A pdb=" N ILE C 979 " --> pdb=" O VAL C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.839A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.133A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.581A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.557A pdb=" N THR A 598 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 659 removed outlier: 6.149A pdb=" N GLU A 653 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR A 695 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL A 655 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 666 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 671 " --> pdb=" O PRO A 664 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 727 removed outlier: 7.032A pdb=" N VAL A1064 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 727 Processing sheet with id=AB6, first strand: chain 'A' and resid 732 through 735 removed outlier: 4.424A pdb=" N LYS A 732 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 removed outlier: 6.096A pdb=" N ILE A 787 " --> pdb=" O ASN C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1119 through 1124 removed outlier: 3.674A pdb=" N SER A1122 " --> pdb=" O ALA A1086 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA A1086 " --> pdb=" O SER A1122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.033A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.971A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.920A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.567A pdb=" N THR B 315 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL B 594 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 317 " --> pdb=" O GLY B 592 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY B 592 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY B 593 " --> pdb=" O GLN B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.556A pdb=" N THR B 552 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 374 through 379 removed outlier: 6.826A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 6.548A pdb=" N PHE B 564 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 653 through 659 removed outlier: 6.237A pdb=" N GLU B 653 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR B 695 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL B 655 " --> pdb=" O THR B 695 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.582A pdb=" N LYS C 789 " --> pdb=" O ASN B 702 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 712 removed outlier: 3.584A pdb=" N THR B1075 " --> pdb=" O SER B1096 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN B1105 " --> pdb=" O GLU B1110 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU B1110 " --> pdb=" O GLN B1105 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 727 removed outlier: 7.065A pdb=" N GLY B1058 " --> pdb=" O SER B1054 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER B1054 " --> pdb=" O GLY B1058 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B1060 " --> pdb=" O PRO B1052 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B1062 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER B1050 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B1064 " --> pdb=" O LEU B1048 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 732 through 735 removed outlier: 4.444A pdb=" N LYS B 732 " --> pdb=" O LEU B 860 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1080 through 1081 removed outlier: 4.715A pdb=" N ALA B1086 " --> pdb=" O SER B1122 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.652A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 5.326A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.576A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.549A pdb=" N THR C 598 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 315 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL C 594 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASN C 317 " --> pdb=" O GLY C 592 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY C 592 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 609 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE1, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.778A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR C 430 " --> pdb=" O PHE C 514 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 552 through 553 Processing sheet with id=AE5, first strand: chain 'C' and resid 653 through 659 removed outlier: 6.253A pdb=" N GLU C 653 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR C 695 " --> pdb=" O GLU C 653 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL C 655 " --> pdb=" O THR C 695 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA C 671 " --> pdb=" O PRO C 664 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.542A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER C1054 " --> pdb=" O GLY C1058 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C1060 " --> pdb=" O PRO C1052 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C1062 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER C1050 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1064 " --> pdb=" O LEU C1048 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 727 removed outlier: 6.542A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 Processing sheet with id=AE9, first strand: chain 'C' and resid 1080 through 1081 removed outlier: 5.123A pdb=" N GLY C1123 " --> pdb=" O ALA C1086 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C1088 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL C1121 " --> pdb=" O PHE C1088 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.70 Time building geometry restraints manager: 7.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4589 1.33 - 1.45: 6505 1.45 - 1.57: 13566 1.57 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 24795 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N HIS A 518 " pdb=" CA HIS A 518 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.24e-02 6.50e+03 9.34e+00 bond pdb=" N ASN A 280 " pdb=" CA ASN A 280 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.25e-02 6.40e+03 8.09e+00 bond pdb=" N ASN C 280 " pdb=" CA ASN C 280 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.56e+00 bond pdb=" N ALA A 519 " pdb=" CA ALA A 519 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.49e+00 ... (remaining 24790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 33460 2.82 - 5.64: 265 5.64 - 8.46: 14 8.46 - 11.29: 5 11.29 - 14.11: 1 Bond angle restraints: 33745 Sorted by residual: angle pdb=" N TYR C 279 " pdb=" CA TYR C 279 " pdb=" CB TYR C 279 " ideal model delta sigma weight residual 109.97 95.86 14.11 1.47e+00 4.63e-01 9.21e+01 angle pdb=" C TYR C 279 " pdb=" CA TYR C 279 " pdb=" CB TYR C 279 " ideal model delta sigma weight residual 109.65 119.31 -9.66 1.71e+00 3.42e-01 3.19e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 108.39 5.14 9.80e-01 1.04e+00 2.75e+01 angle pdb=" N GLY A 613 " pdb=" CA GLY A 613 " pdb=" C GLY A 613 " ideal model delta sigma weight residual 114.16 124.32 -10.16 2.00e+00 2.50e-01 2.58e+01 angle pdb=" CA TYR C 279 " pdb=" CB TYR C 279 " pdb=" CG TYR C 279 " ideal model delta sigma weight residual 113.90 123.04 -9.14 1.80e+00 3.09e-01 2.58e+01 ... (remaining 33740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13886 17.83 - 35.66: 1068 35.66 - 53.49: 173 53.49 - 71.32: 63 71.32 - 89.14: 26 Dihedral angle restraints: 15216 sinusoidal: 6406 harmonic: 8810 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 487 " pdb=" CB CYS C 487 " ideal model delta sinusoidal sigma weight residual 93.00 -177.91 -89.09 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 487 " pdb=" CB CYS B 487 " ideal model delta sinusoidal sigma weight residual -86.00 -168.38 82.38 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 487 " pdb=" CB CYS A 487 " ideal model delta sinusoidal sigma weight residual 93.00 152.33 -59.33 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 15213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 3891 0.173 - 0.347: 11 0.347 - 0.520: 5 0.520 - 0.694: 2 0.694 - 0.867: 3 Chirality restraints: 3912 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.85e+01 ... (remaining 3909 not shown) Planarity restraints: 4339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.308 2.00e-02 2.50e+03 2.66e-01 8.84e+02 pdb=" C7 NAG H 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.472 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.304 2.00e-02 2.50e+03 2.63e-01 8.65e+02 pdb=" C7 NAG G 1 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.467 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.299 2.00e-02 2.50e+03 2.58e-01 8.32e+02 pdb=" C7 NAG I 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.457 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.073 2.00e-02 2.50e+03 ... (remaining 4336 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2100 2.74 - 3.28: 24958 3.28 - 3.82: 40523 3.82 - 4.36: 48313 4.36 - 4.90: 82407 Nonbonded interactions: 198301 Sorted by model distance: nonbonded pdb=" NZ LYS B 528 " pdb=" O SER B 529 " model vdw 2.202 3.120 nonbonded pdb=" O ALA A 878 " pdb=" OG1 THR A 882 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN B1073 " pdb=" NE2 GLN C 894 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR B 911 " pdb=" NE2 GLN B1105 " model vdw 2.216 3.120 nonbonded pdb=" OG1 THR C 911 " pdb=" OE1 GLN C1105 " model vdw 2.227 3.040 ... (remaining 198296 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 515 or resid 524 through 1139 or resid 1201 thr \ ough 1206)) selection = (chain 'B' and (resid 26 through 1139 or resid 1201 through 1206)) selection = (chain 'C' and (resid 26 through 515 or resid 524 through 1139 or resid 1201 thr \ ough 1206)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 9.860 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: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 62.630 Find NCS groups from input model: 2.250 Set up NCS constraints: 0.220 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:4.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 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 : 0.004 0.047 24868 Z= 0.198 Angle : 0.719 17.821 33927 Z= 0.391 Chirality : 0.055 0.867 3912 Planarity : 0.010 0.266 4309 Dihedral : 13.414 89.145 9439 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.78 % Favored : 91.95 % Rotamer: Outliers : 0.15 % Allowed : 0.53 % Favored : 99.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 2981 helix: 0.68 (0.20), residues: 697 sheet: -1.03 (0.20), residues: 632 loop : -2.10 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 885 HIS 0.009 0.001 HIS C 339 PHE 0.021 0.001 PHE C 905 TYR 0.041 0.001 TYR C 279 ARG 0.007 0.000 ARG C 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00925 ( 30) link_NAG-ASN : angle 4.47465 ( 90) link_BETA1-4 : bond 0.04180 ( 6) link_BETA1-4 : angle 5.66375 ( 18) hydrogen bonds : bond 0.13614 ( 935) hydrogen bonds : angle 7.26762 ( 2589) SS BOND : bond 0.00219 ( 37) SS BOND : angle 1.00039 ( 74) covalent geometry : bond 0.00343 (24795) covalent geometry : angle 0.66849 (33745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 698 time to evaluate : 2.611 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 33 THR cc_start: 0.7594 (p) cc_final: 0.7343 (p) REVERT: A 42 VAL cc_start: 0.8125 (t) cc_final: 0.7848 (t) REVERT: A 48 LEU cc_start: 0.8047 (mp) cc_final: 0.7725 (mt) REVERT: A 62 VAL cc_start: 0.7068 (t) cc_final: 0.6712 (m) REVERT: A 128 ILE cc_start: 0.6767 (mt) cc_final: 0.6407 (mp) REVERT: A 192 PHE cc_start: 0.7915 (m-80) cc_final: 0.7434 (m-80) REVERT: A 285 ILE cc_start: 0.7433 (mt) cc_final: 0.7145 (mt) REVERT: A 293 LEU cc_start: 0.7475 (mp) cc_final: 0.6815 (pp) REVERT: A 382 VAL cc_start: 0.3709 (t) cc_final: 0.3261 (p) REVERT: A 384 PRO cc_start: 0.6175 (Cg_endo) cc_final: 0.5817 (Cg_exo) REVERT: A 536 LYS cc_start: 0.6997 (mtpp) cc_final: 0.6604 (mtpt) REVERT: A 591 PHE cc_start: 0.7914 (p90) cc_final: 0.7598 (p90) REVERT: A 640 ASN cc_start: 0.7513 (m110) cc_final: 0.7246 (m-40) REVERT: A 645 ARG cc_start: 0.7725 (mtm180) cc_final: 0.7493 (mtm180) REVERT: A 654 TYR cc_start: 0.7763 (t80) cc_final: 0.7545 (t80) REVERT: A 658 SER cc_start: 0.8210 (m) cc_final: 0.7781 (p) REVERT: A 662 ASP cc_start: 0.7309 (t70) cc_final: 0.6973 (t70) REVERT: A 702 ASN cc_start: 0.7694 (t0) cc_final: 0.7276 (t0) REVERT: A 724 GLU cc_start: 0.7636 (tm-30) cc_final: 0.6869 (tm-30) REVERT: A 736 ASP cc_start: 0.7401 (t0) cc_final: 0.7099 (t0) REVERT: A 739 MET cc_start: 0.7371 (ttm) cc_final: 0.6974 (tpp) REVERT: A 747 GLU cc_start: 0.6927 (mp0) cc_final: 0.6477 (mp0) REVERT: A 763 LYS cc_start: 0.7402 (ttpp) cc_final: 0.7074 (mtpp) REVERT: A 789 LYS cc_start: 0.8124 (mttp) cc_final: 0.7610 (mmtp) REVERT: A 813 LYS cc_start: 0.7634 (mmtm) cc_final: 0.7411 (mmtm) REVERT: A 903 TYR cc_start: 0.5702 (t80) cc_final: 0.5129 (t80) REVERT: A 944 LEU cc_start: 0.8007 (mt) cc_final: 0.7789 (mp) REVERT: A 968 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7794 (mttm) REVERT: A 973 SER cc_start: 0.8271 (t) cc_final: 0.7976 (m) REVERT: A 978 ASP cc_start: 0.6959 (t0) cc_final: 0.6729 (t0) REVERT: A 992 ILE cc_start: 0.7584 (mm) cc_final: 0.7302 (mt) REVERT: A 1046 TYR cc_start: 0.8083 (m-80) cc_final: 0.7870 (m-10) REVERT: A 1072 LYS cc_start: 0.7654 (tptp) cc_final: 0.7188 (tppp) REVERT: A 1083 ASP cc_start: 0.6981 (t0) cc_final: 0.6765 (m-30) REVERT: A 1088 PHE cc_start: 0.7955 (m-80) cc_final: 0.7545 (m-80) REVERT: A 1091 GLU cc_start: 0.6868 (pm20) cc_final: 0.6627 (pm20) REVERT: B 30 ASN cc_start: 0.7478 (p0) cc_final: 0.7247 (p0) REVERT: B 88 ASP cc_start: 0.6874 (p0) cc_final: 0.6429 (p0) REVERT: B 90 VAL cc_start: 0.7203 (m) cc_final: 0.6943 (t) REVERT: B 168 PHE cc_start: 0.8354 (t80) cc_final: 0.7982 (t80) REVERT: B 278 LYS cc_start: 0.7978 (tttt) cc_final: 0.7467 (tttp) REVERT: B 309 GLU cc_start: 0.7517 (mp0) cc_final: 0.7069 (mp0) REVERT: B 313 TYR cc_start: 0.7577 (m-80) cc_final: 0.6921 (m-80) REVERT: B 317 ASN cc_start: 0.7398 (m-40) cc_final: 0.7166 (m-40) REVERT: B 319 ARG cc_start: 0.7377 (ptp-110) cc_final: 0.7094 (ptm160) REVERT: B 324 GLU cc_start: 0.5839 (mp0) cc_final: 0.5279 (mp0) REVERT: B 555 ASN cc_start: 0.7252 (p0) cc_final: 0.6958 (p0) REVERT: B 556 LYS cc_start: 0.7845 (mptt) cc_final: 0.7493 (mttt) REVERT: B 563 GLN cc_start: 0.7323 (mm110) cc_final: 0.6967 (mm-40) REVERT: B 583 ILE cc_start: 0.5434 (tp) cc_final: 0.5160 (mt) REVERT: B 591 PHE cc_start: 0.7825 (p90) cc_final: 0.7623 (p90) REVERT: B 653 GLU cc_start: 0.7781 (pm20) cc_final: 0.7370 (pm20) REVERT: B 657 ASN cc_start: 0.8114 (m-40) cc_final: 0.7859 (m-40) REVERT: B 658 SER cc_start: 0.8385 (m) cc_final: 0.8016 (t) REVERT: B 696 MET cc_start: 0.7569 (ttp) cc_final: 0.7177 (ttm) REVERT: B 707 SER cc_start: 0.8068 (m) cc_final: 0.7632 (p) REVERT: B 709 ASN cc_start: 0.8031 (p0) cc_final: 0.7702 (p0) REVERT: B 724 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6678 (tm-30) REVERT: B 736 ASP cc_start: 0.7233 (t0) cc_final: 0.7020 (t0) REVERT: B 739 MET cc_start: 0.7361 (ttm) cc_final: 0.6886 (ttm) REVERT: B 772 GLU cc_start: 0.6877 (tt0) cc_final: 0.6519 (tt0) REVERT: B 775 LYS cc_start: 0.7462 (ttpt) cc_final: 0.7220 (tttm) REVERT: B 778 GLN cc_start: 0.7565 (tp40) cc_final: 0.7057 (tm-30) REVERT: B 785 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7335 (mmtm) REVERT: B 789 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7606 (mtpp) REVERT: B 866 ASP cc_start: 0.6757 (p0) cc_final: 0.6248 (p0) REVERT: B 867 GLU cc_start: 0.6707 (mp0) cc_final: 0.6160 (mp0) REVERT: B 918 ASN cc_start: 0.7407 (m110) cc_final: 0.7146 (m110) REVERT: B 948 GLN cc_start: 0.7573 (tp40) cc_final: 0.7346 (mm-40) REVERT: B 952 ASN cc_start: 0.7697 (m-40) cc_final: 0.7477 (m-40) REVERT: B 964 GLN cc_start: 0.7640 (mt0) cc_final: 0.7271 (mt0) REVERT: B 989 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6494 (mt-10) REVERT: B 1040 ASP cc_start: 0.7585 (m-30) cc_final: 0.7317 (m-30) REVERT: B 1112 GLN cc_start: 0.7588 (mt0) cc_final: 0.7074 (mm-40) REVERT: B 1134 ASN cc_start: 0.7115 (t0) cc_final: 0.6693 (m-40) REVERT: B 1135 THR cc_start: 0.7910 (m) cc_final: 0.7048 (m) REVERT: C 30 ASN cc_start: 0.6853 (p0) cc_final: 0.6583 (p0) REVERT: C 191 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7165 (mt-10) REVERT: C 269 TYR cc_start: 0.7818 (m-80) cc_final: 0.7112 (m-10) REVERT: C 278 LYS cc_start: 0.7005 (ttpm) cc_final: 0.6740 (ttpm) REVERT: C 279 TYR cc_start: 0.7213 (m-80) cc_final: 0.6838 (m-80) REVERT: C 317 ASN cc_start: 0.8251 (m-40) cc_final: 0.7977 (m-40) REVERT: C 436 TRP cc_start: 0.5300 (p90) cc_final: 0.4552 (p90) REVERT: C 510 VAL cc_start: 0.6651 (t) cc_final: 0.6271 (m) REVERT: C 528 LYS cc_start: 0.7550 (tptp) cc_final: 0.7047 (tptp) REVERT: C 529 SER cc_start: 0.7611 (t) cc_final: 0.7333 (m) REVERT: C 540 PHE cc_start: 0.6359 (p90) cc_final: 0.6141 (p90) REVERT: C 548 THR cc_start: 0.7714 (p) cc_final: 0.7500 (m) REVERT: C 555 ASN cc_start: 0.7520 (p0) cc_final: 0.6654 (p0) REVERT: C 557 LYS cc_start: 0.7943 (mptt) cc_final: 0.7380 (mptt) REVERT: C 573 ASP cc_start: 0.6924 (m-30) cc_final: 0.6623 (m-30) REVERT: C 590 SER cc_start: 0.8320 (m) cc_final: 0.8101 (p) REVERT: C 618 GLU cc_start: 0.7030 (tp30) cc_final: 0.6729 (tp30) REVERT: C 645 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7432 (mtm180) REVERT: C 674 GLN cc_start: 0.7119 (pp30) cc_final: 0.6808 (pp30) REVERT: C 702 ASN cc_start: 0.7613 (t0) cc_final: 0.7288 (t0) REVERT: C 707 SER cc_start: 0.7828 (m) cc_final: 0.7567 (t) REVERT: C 724 GLU cc_start: 0.7674 (tm-30) cc_final: 0.6983 (tm-30) REVERT: C 749 SER cc_start: 0.7201 (t) cc_final: 0.6842 (m) REVERT: C 778 GLN cc_start: 0.7706 (tp40) cc_final: 0.7322 (tp40) REVERT: C 779 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 789 LYS cc_start: 0.8146 (mppt) cc_final: 0.7918 (mppt) REVERT: C 868 MET cc_start: 0.7677 (mtt) cc_final: 0.7431 (mtt) REVERT: C 934 GLN cc_start: 0.8060 (mt0) cc_final: 0.7809 (mt0) REVERT: C 1072 LYS cc_start: 0.7637 (tptp) cc_final: 0.7151 (tptp) REVERT: C 1083 ASP cc_start: 0.7228 (t0) cc_final: 0.6986 (m-30) REVERT: C 1124 ASN cc_start: 0.7281 (p0) cc_final: 0.6869 (p0) outliers start: 4 outliers final: 1 residues processed: 700 average time/residue: 0.3697 time to fit residues: 397.8008 Evaluate side-chains 584 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 583 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 339 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 0.9990 chunk 228 optimal weight: 0.4980 chunk 127 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 236 optimal weight: 0.0470 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 314 GLN A 409 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN A 612 GLN A 709 ASN A 761 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN A1009 GLN B 125 ASN B 612 GLN B 754 GLN B 855 ASN B 954 ASN C 134 GLN C 339 HIS C 543 ASN C 612 GLN C 643 GLN C 709 ASN C 783 GLN C1057 HIS C1105 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.147626 restraints weight = 36966.128| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.66 r_work: 0.3708 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 24868 Z= 0.162 Angle : 0.670 16.740 33927 Z= 0.335 Chirality : 0.047 0.368 3912 Planarity : 0.005 0.062 4309 Dihedral : 6.971 59.230 3998 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.15 % Favored : 92.72 % Rotamer: Outliers : 2.41 % Allowed : 9.10 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 2981 helix: 1.10 (0.20), residues: 701 sheet: -0.86 (0.20), residues: 644 loop : -2.06 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 885 HIS 0.008 0.001 HIS C 339 PHE 0.027 0.002 PHE A 758 TYR 0.024 0.001 TYR C 706 ARG 0.006 0.001 ARG B1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00811 ( 30) link_NAG-ASN : angle 3.80884 ( 90) link_BETA1-4 : bond 0.01190 ( 6) link_BETA1-4 : angle 2.77128 ( 18) hydrogen bonds : bond 0.04186 ( 935) hydrogen bonds : angle 5.90154 ( 2589) SS BOND : bond 0.00323 ( 37) SS BOND : angle 2.49353 ( 74) covalent geometry : bond 0.00361 (24795) covalent geometry : angle 0.62862 (33745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 593 time to evaluate : 2.572 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 26 GLN cc_start: 0.5048 (pm20) cc_final: 0.4032 (pt0) REVERT: A 28 TYR cc_start: 0.6634 (m-80) cc_final: 0.6187 (m-80) REVERT: A 48 LEU cc_start: 0.8399 (mp) cc_final: 0.8196 (mt) REVERT: A 116 SER cc_start: 0.7226 (m) cc_final: 0.6650 (p) REVERT: A 128 ILE cc_start: 0.7870 (mt) cc_final: 0.7546 (mp) REVERT: A 285 ILE cc_start: 0.8009 (mt) cc_final: 0.7777 (mt) REVERT: A 591 PHE cc_start: 0.8090 (p90) cc_final: 0.7843 (p90) REVERT: A 658 SER cc_start: 0.8560 (m) cc_final: 0.8166 (p) REVERT: A 662 ASP cc_start: 0.7320 (t70) cc_final: 0.7070 (t70) REVERT: A 724 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 747 GLU cc_start: 0.7362 (mp0) cc_final: 0.7038 (mp0) REVERT: A 763 LYS cc_start: 0.8145 (ttpp) cc_final: 0.7837 (mtpp) REVERT: A 789 LYS cc_start: 0.8363 (mttp) cc_final: 0.8060 (mmtp) REVERT: A 810 LYS cc_start: 0.7566 (ptpt) cc_final: 0.6901 (ptpt) REVERT: A 813 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7879 (mmtm) REVERT: A 868 MET cc_start: 0.8285 (mtt) cc_final: 0.8029 (mtm) REVERT: A 948 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7459 (mm-40) REVERT: A 978 ASP cc_start: 0.7835 (t0) cc_final: 0.7607 (t0) REVERT: A 1046 TYR cc_start: 0.8529 (m-80) cc_final: 0.8320 (m-10) REVERT: A 1090 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7630 (mtt90) REVERT: A 1091 GLU cc_start: 0.7113 (pm20) cc_final: 0.6689 (pm20) REVERT: A 1110 GLU cc_start: 0.7821 (tt0) cc_final: 0.7578 (tt0) REVERT: B 88 ASP cc_start: 0.7319 (p0) cc_final: 0.6818 (p0) REVERT: B 278 LYS cc_start: 0.8798 (tttt) cc_final: 0.8401 (tttp) REVERT: B 309 GLU cc_start: 0.7753 (mp0) cc_final: 0.7498 (mp0) REVERT: B 313 TYR cc_start: 0.8158 (m-80) cc_final: 0.7688 (m-80) REVERT: B 317 ASN cc_start: 0.7747 (m-40) cc_final: 0.7491 (m-40) REVERT: B 321 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7766 (mm-40) REVERT: B 324 GLU cc_start: 0.7500 (mp0) cc_final: 0.7022 (mp0) REVERT: B 583 ILE cc_start: 0.6300 (tp) cc_final: 0.6054 (mt) REVERT: B 591 PHE cc_start: 0.8138 (p90) cc_final: 0.7928 (p90) REVERT: B 618 GLU cc_start: 0.7915 (tp30) cc_final: 0.7656 (tp30) REVERT: B 627 GLN cc_start: 0.7698 (mt0) cc_final: 0.7378 (mt0) REVERT: B 640 ASN cc_start: 0.7403 (p0) cc_final: 0.7183 (p0) REVERT: B 653 GLU cc_start: 0.8033 (pm20) cc_final: 0.7718 (pm20) REVERT: B 658 SER cc_start: 0.8582 (m) cc_final: 0.8301 (t) REVERT: B 696 MET cc_start: 0.7918 (ttp) cc_final: 0.7614 (ptp) REVERT: B 724 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6980 (tm-30) REVERT: B 772 GLU cc_start: 0.7404 (tt0) cc_final: 0.6954 (tt0) REVERT: B 775 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8142 (tttm) REVERT: B 778 GLN cc_start: 0.7922 (tp40) cc_final: 0.7567 (tm-30) REVERT: B 779 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7582 (tt0) REVERT: B 785 LYS cc_start: 0.7905 (mmtm) cc_final: 0.7618 (mmtm) REVERT: B 789 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8115 (ttmm) REVERT: B 866 ASP cc_start: 0.7314 (p0) cc_final: 0.6662 (p0) REVERT: B 867 GLU cc_start: 0.7562 (mp0) cc_final: 0.7041 (mp0) REVERT: B 918 ASN cc_start: 0.7687 (m110) cc_final: 0.7478 (m110) REVERT: B 921 LEU cc_start: 0.8628 (tp) cc_final: 0.8422 (tt) REVERT: B 968 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8642 (mttm) REVERT: B 983 LEU cc_start: 0.8248 (mt) cc_final: 0.8010 (mp) REVERT: B 1037 LYS cc_start: 0.7988 (mttm) cc_final: 0.7783 (mttm) REVERT: B 1040 ASP cc_start: 0.7554 (m-30) cc_final: 0.7327 (m-30) REVERT: B 1090 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7090 (ttt-90) REVERT: B 1106 ARG cc_start: 0.7080 (mtp180) cc_final: 0.6835 (mtp180) REVERT: B 1112 GLN cc_start: 0.8096 (mt0) cc_final: 0.7825 (mm-40) REVERT: B 1135 THR cc_start: 0.7842 (m) cc_final: 0.7220 (m) REVERT: C 269 TYR cc_start: 0.8456 (m-80) cc_final: 0.7968 (m-10) REVERT: C 278 LYS cc_start: 0.7820 (ttpm) cc_final: 0.7612 (ttpm) REVERT: C 317 ASN cc_start: 0.8120 (m-40) cc_final: 0.7917 (m-40) REVERT: C 356 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8682 (p) REVERT: C 436 TRP cc_start: 0.5760 (p90) cc_final: 0.5293 (p90) REVERT: C 528 LYS cc_start: 0.7969 (tptp) cc_final: 0.7582 (tptp) REVERT: C 529 SER cc_start: 0.8074 (t) cc_final: 0.7146 (m) REVERT: C 555 ASN cc_start: 0.7518 (p0) cc_final: 0.6820 (p0) REVERT: C 557 LYS cc_start: 0.8219 (mptt) cc_final: 0.7869 (mptt) REVERT: C 573 ASP cc_start: 0.7398 (m-30) cc_final: 0.7167 (m-30) REVERT: C 645 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7752 (mtm180) REVERT: C 674 GLN cc_start: 0.7302 (pp30) cc_final: 0.7001 (pp30) REVERT: C 720 SER cc_start: 0.8570 (t) cc_final: 0.8168 (p) REVERT: C 746 THR cc_start: 0.7604 (p) cc_final: 0.7161 (m) REVERT: C 749 SER cc_start: 0.8080 (t) cc_final: 0.7825 (m) REVERT: C 772 GLU cc_start: 0.7297 (tt0) cc_final: 0.7057 (tt0) REVERT: C 779 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 783 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7598 (mt0) REVERT: C 789 LYS cc_start: 0.8347 (mppt) cc_final: 0.8094 (mppt) REVERT: C 803 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7989 (mm-40) REVERT: C 910 VAL cc_start: 0.7633 (t) cc_final: 0.7427 (t) REVERT: C 934 GLN cc_start: 0.7867 (mt0) cc_final: 0.7601 (mt0) REVERT: C 1044 LYS cc_start: 0.8041 (tptp) cc_final: 0.7771 (tptp) REVERT: C 1072 LYS cc_start: 0.8032 (tptp) cc_final: 0.7681 (tptp) REVERT: C 1083 ASP cc_start: 0.6867 (t0) cc_final: 0.6493 (t0) REVERT: C 1135 THR cc_start: 0.7164 (m) cc_final: 0.6951 (p) outliers start: 64 outliers final: 37 residues processed: 615 average time/residue: 0.3749 time to fit residues: 353.9364 Evaluate side-chains 590 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 550 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 783 GLN Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 263 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 258 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 709 ASN B 964 GLN B1134 ASN C 321 GLN C 709 ASN C 783 GLN C 918 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.175740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144618 restraints weight = 36630.511| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.65 r_work: 0.3697 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24868 Z= 0.172 Angle : 0.636 15.461 33927 Z= 0.322 Chirality : 0.046 0.351 3912 Planarity : 0.005 0.075 4309 Dihedral : 6.576 59.753 3998 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.61 % Favored : 92.25 % Rotamer: Outliers : 2.45 % Allowed : 12.75 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 2981 helix: 0.99 (0.19), residues: 714 sheet: -0.83 (0.20), residues: 661 loop : -2.09 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 452 HIS 0.004 0.001 HIS A 207 PHE 0.027 0.002 PHE C 540 TYR 0.018 0.001 TYR B1066 ARG 0.008 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 30) link_NAG-ASN : angle 3.56507 ( 90) link_BETA1-4 : bond 0.00952 ( 6) link_BETA1-4 : angle 2.37971 ( 18) hydrogen bonds : bond 0.04141 ( 935) hydrogen bonds : angle 5.71232 ( 2589) SS BOND : bond 0.00384 ( 37) SS BOND : angle 2.37992 ( 74) covalent geometry : bond 0.00387 (24795) covalent geometry : angle 0.59782 (33745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 580 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6611 (m-80) cc_final: 0.6231 (m-80) REVERT: A 33 THR cc_start: 0.8131 (p) cc_final: 0.7910 (p) REVERT: A 116 SER cc_start: 0.7560 (m) cc_final: 0.7015 (p) REVERT: A 220 PHE cc_start: 0.7722 (t80) cc_final: 0.7518 (t80) REVERT: A 285 ILE cc_start: 0.8044 (mt) cc_final: 0.7757 (mt) REVERT: A 320 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8329 (m) REVERT: A 428 ASP cc_start: 0.7910 (p0) cc_final: 0.7667 (p0) REVERT: A 563 GLN cc_start: 0.7811 (mp10) cc_final: 0.7608 (mp10) REVERT: A 591 PHE cc_start: 0.8099 (p90) cc_final: 0.7774 (p90) REVERT: A 658 SER cc_start: 0.8579 (m) cc_final: 0.8166 (p) REVERT: A 662 ASP cc_start: 0.7276 (t70) cc_final: 0.7014 (t70) REVERT: A 724 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7095 (tm-30) REVERT: A 747 GLU cc_start: 0.7367 (mp0) cc_final: 0.7072 (mp0) REVERT: A 789 LYS cc_start: 0.8388 (mttp) cc_final: 0.8091 (mmtp) REVERT: A 810 LYS cc_start: 0.7615 (ptpt) cc_final: 0.6945 (ptpt) REVERT: A 813 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7822 (mmtm) REVERT: A 932 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7746 (mtpp) REVERT: A 978 ASP cc_start: 0.7779 (t0) cc_final: 0.7568 (t0) REVERT: A 1033 LEU cc_start: 0.8544 (mp) cc_final: 0.8311 (mp) REVERT: A 1090 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7481 (mtt-85) REVERT: A 1091 GLU cc_start: 0.6972 (pm20) cc_final: 0.6750 (pm20) REVERT: A 1106 ARG cc_start: 0.7889 (ptp-170) cc_final: 0.7385 (mtt180) REVERT: A 1110 GLU cc_start: 0.7875 (tt0) cc_final: 0.7662 (tt0) REVERT: B 269 TYR cc_start: 0.6983 (m-80) cc_final: 0.6719 (m-80) REVERT: B 278 LYS cc_start: 0.8785 (tttt) cc_final: 0.8392 (tttp) REVERT: B 309 GLU cc_start: 0.7685 (mp0) cc_final: 0.7461 (mp0) REVERT: B 313 TYR cc_start: 0.8181 (m-80) cc_final: 0.7714 (m-80) REVERT: B 317 ASN cc_start: 0.7769 (m-40) cc_final: 0.7509 (m-40) REVERT: B 321 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7665 (mm110) REVERT: B 324 GLU cc_start: 0.7622 (mp0) cc_final: 0.7064 (mp0) REVERT: B 582 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5822 (tm-30) REVERT: B 583 ILE cc_start: 0.6539 (tp) cc_final: 0.5776 (mt) REVERT: B 618 GLU cc_start: 0.7872 (tp30) cc_final: 0.7624 (tp30) REVERT: B 627 GLN cc_start: 0.7798 (mt0) cc_final: 0.7484 (mt0) REVERT: B 653 GLU cc_start: 0.8085 (pm20) cc_final: 0.7752 (pm20) REVERT: B 696 MET cc_start: 0.7966 (ttp) cc_final: 0.7604 (ptp) REVERT: B 724 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7047 (tm-30) REVERT: B 772 GLU cc_start: 0.7412 (tt0) cc_final: 0.6939 (tt0) REVERT: B 775 LYS cc_start: 0.8378 (ttpt) cc_final: 0.8139 (tttm) REVERT: B 778 GLN cc_start: 0.7918 (tp40) cc_final: 0.7573 (tm-30) REVERT: B 779 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7493 (tt0) REVERT: B 785 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7622 (mmtm) REVERT: B 789 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8066 (mtpp) REVERT: B 866 ASP cc_start: 0.7392 (p0) cc_final: 0.6614 (p0) REVERT: B 867 GLU cc_start: 0.7560 (mp0) cc_final: 0.6962 (mp0) REVERT: B 881 ILE cc_start: 0.8542 (pt) cc_final: 0.8121 (mt) REVERT: B 918 ASN cc_start: 0.7699 (m110) cc_final: 0.7484 (m110) REVERT: B 921 LEU cc_start: 0.8590 (tp) cc_final: 0.8364 (tt) REVERT: B 968 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8651 (mttm) REVERT: B 1018 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7388 (ttp-170) REVERT: B 1040 ASP cc_start: 0.7628 (m-30) cc_final: 0.7410 (m-30) REVERT: B 1112 GLN cc_start: 0.8087 (mt0) cc_final: 0.7850 (mm-40) REVERT: C 45 SER cc_start: 0.8318 (p) cc_final: 0.8075 (t) REVERT: C 191 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7101 (mt-10) REVERT: C 269 TYR cc_start: 0.8445 (m-80) cc_final: 0.7984 (m-10) REVERT: C 278 LYS cc_start: 0.7869 (ttpm) cc_final: 0.7655 (ttpm) REVERT: C 314 GLN cc_start: 0.8041 (tp40) cc_final: 0.7774 (tp40) REVERT: C 356 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8705 (p) REVERT: C 409 GLN cc_start: 0.7615 (mt0) cc_final: 0.6857 (mp10) REVERT: C 418 ILE cc_start: 0.6720 (mm) cc_final: 0.6296 (mm) REVERT: C 436 TRP cc_start: 0.5758 (p90) cc_final: 0.5288 (p90) REVERT: C 453 TYR cc_start: 0.7803 (p90) cc_final: 0.6631 (p90) REVERT: C 462 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7334 (mtmm) REVERT: C 528 LYS cc_start: 0.7996 (tptp) cc_final: 0.7622 (tptp) REVERT: C 529 SER cc_start: 0.8018 (t) cc_final: 0.7094 (m) REVERT: C 543 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7474 (m-40) REVERT: C 555 ASN cc_start: 0.7520 (p0) cc_final: 0.6860 (p0) REVERT: C 557 LYS cc_start: 0.8269 (mptt) cc_final: 0.8006 (mptt) REVERT: C 645 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7762 (mtm180) REVERT: C 674 GLN cc_start: 0.7293 (pp30) cc_final: 0.6970 (pp30) REVERT: C 720 SER cc_start: 0.8574 (t) cc_final: 0.8141 (p) REVERT: C 746 THR cc_start: 0.7775 (p) cc_final: 0.7409 (m) REVERT: C 749 SER cc_start: 0.8119 (t) cc_final: 0.7840 (m) REVERT: C 772 GLU cc_start: 0.7303 (tt0) cc_final: 0.7065 (tt0) REVERT: C 779 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7811 (mt-10) REVERT: C 803 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8094 (mm-40) REVERT: C 868 MET cc_start: 0.7983 (mtt) cc_final: 0.7744 (mtp) REVERT: C 934 GLN cc_start: 0.7831 (mt0) cc_final: 0.7561 (tt0) REVERT: C 1044 LYS cc_start: 0.8053 (tptp) cc_final: 0.7756 (tptp) REVERT: C 1072 LYS cc_start: 0.7988 (tptp) cc_final: 0.7603 (tptp) REVERT: C 1083 ASP cc_start: 0.6964 (t0) cc_final: 0.6619 (t0) REVERT: C 1134 ASN cc_start: 0.6277 (t0) cc_final: 0.5948 (m110) REVERT: C 1135 THR cc_start: 0.7203 (m) cc_final: 0.6645 (p) outliers start: 65 outliers final: 37 residues processed: 607 average time/residue: 0.3510 time to fit residues: 327.7830 Evaluate side-chains 596 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 554 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 156 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 157 optimal weight: 0.3980 chunk 268 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 137 ASN A 165 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 563 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN A1107 ASN C 317 ASN C 709 ASN C1087 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.176149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145023 restraints weight = 36929.138| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.66 r_work: 0.3690 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24868 Z= 0.162 Angle : 0.606 15.011 33927 Z= 0.308 Chirality : 0.045 0.349 3912 Planarity : 0.005 0.078 4309 Dihedral : 6.443 59.738 3998 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.18 % Favored : 92.69 % Rotamer: Outliers : 2.78 % Allowed : 14.18 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 2981 helix: 0.98 (0.19), residues: 713 sheet: -0.79 (0.20), residues: 645 loop : -2.03 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.004 0.001 HIS C1082 PHE 0.020 0.001 PHE B 135 TYR 0.018 0.001 TYR B1066 ARG 0.007 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 30) link_NAG-ASN : angle 3.32773 ( 90) link_BETA1-4 : bond 0.00861 ( 6) link_BETA1-4 : angle 2.16222 ( 18) hydrogen bonds : bond 0.03996 ( 935) hydrogen bonds : angle 5.59507 ( 2589) SS BOND : bond 0.00376 ( 37) SS BOND : angle 1.95639 ( 74) covalent geometry : bond 0.00365 (24795) covalent geometry : angle 0.57313 (33745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 585 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6607 (m-80) cc_final: 0.6218 (m-80) REVERT: A 33 THR cc_start: 0.8207 (p) cc_final: 0.7961 (p) REVERT: A 116 SER cc_start: 0.7678 (m) cc_final: 0.7181 (p) REVERT: A 128 ILE cc_start: 0.7824 (mt) cc_final: 0.7576 (mp) REVERT: A 285 ILE cc_start: 0.8044 (mt) cc_final: 0.7759 (mt) REVERT: A 297 SER cc_start: 0.7810 (m) cc_final: 0.7261 (t) REVERT: A 320 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8402 (m) REVERT: A 428 ASP cc_start: 0.7960 (p0) cc_final: 0.7666 (p0) REVERT: A 591 PHE cc_start: 0.8100 (p90) cc_final: 0.7892 (p90) REVERT: A 595 SER cc_start: 0.8531 (m) cc_final: 0.8194 (p) REVERT: A 658 SER cc_start: 0.8582 (m) cc_final: 0.8131 (p) REVERT: A 724 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7079 (tm-30) REVERT: A 747 GLU cc_start: 0.7353 (mp0) cc_final: 0.7084 (mp0) REVERT: A 777 THR cc_start: 0.8497 (t) cc_final: 0.8278 (m) REVERT: A 789 LYS cc_start: 0.8400 (mttp) cc_final: 0.8104 (mmtp) REVERT: A 810 LYS cc_start: 0.7594 (ptpt) cc_final: 0.6994 (ptpt) REVERT: A 932 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7699 (mtpp) REVERT: A 948 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7605 (mm-40) REVERT: A 978 ASP cc_start: 0.7766 (t0) cc_final: 0.7535 (t0) REVERT: A 1004 GLN cc_start: 0.8043 (mt0) cc_final: 0.7841 (mt0) REVERT: A 1033 LEU cc_start: 0.8570 (mp) cc_final: 0.8334 (mp) REVERT: A 1110 GLU cc_start: 0.7884 (tt0) cc_final: 0.7667 (tt0) REVERT: B 44 ARG cc_start: 0.7406 (mtt90) cc_final: 0.6652 (mtt90) REVERT: B 45 SER cc_start: 0.7776 (p) cc_final: 0.7552 (t) REVERT: B 269 TYR cc_start: 0.6931 (m-80) cc_final: 0.6699 (m-80) REVERT: B 278 LYS cc_start: 0.8767 (tttt) cc_final: 0.8372 (tttp) REVERT: B 309 GLU cc_start: 0.7699 (mp0) cc_final: 0.7422 (mp0) REVERT: B 313 TYR cc_start: 0.8161 (m-80) cc_final: 0.7722 (m-80) REVERT: B 317 ASN cc_start: 0.7784 (m-40) cc_final: 0.7537 (m-40) REVERT: B 321 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7652 (mm110) REVERT: B 324 GLU cc_start: 0.7619 (mp0) cc_final: 0.7048 (mp0) REVERT: B 618 GLU cc_start: 0.7893 (tp30) cc_final: 0.7643 (tp30) REVERT: B 627 GLN cc_start: 0.7862 (mt0) cc_final: 0.7494 (mt0) REVERT: B 653 GLU cc_start: 0.8084 (pm20) cc_final: 0.7745 (pm20) REVERT: B 696 MET cc_start: 0.7989 (ttp) cc_final: 0.7760 (ptp) REVERT: B 724 GLU cc_start: 0.7290 (tm-30) cc_final: 0.7022 (tm-30) REVERT: B 772 GLU cc_start: 0.7456 (tt0) cc_final: 0.7082 (tt0) REVERT: B 775 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8128 (tttm) REVERT: B 778 GLN cc_start: 0.7937 (tp40) cc_final: 0.7582 (tm-30) REVERT: B 779 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7530 (tt0) REVERT: B 785 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7656 (mmtm) REVERT: B 789 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8153 (mtpp) REVERT: B 866 ASP cc_start: 0.7350 (p0) cc_final: 0.6585 (p0) REVERT: B 867 GLU cc_start: 0.7553 (mp0) cc_final: 0.6973 (mp0) REVERT: B 918 ASN cc_start: 0.7731 (m110) cc_final: 0.7516 (m110) REVERT: B 921 LEU cc_start: 0.8605 (tp) cc_final: 0.8379 (tt) REVERT: B 968 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8651 (mttm) REVERT: B 1040 ASP cc_start: 0.7679 (m-30) cc_final: 0.7344 (m-30) REVERT: B 1044 LYS cc_start: 0.8009 (tptp) cc_final: 0.7766 (tptp) REVERT: B 1112 GLN cc_start: 0.8072 (mt0) cc_final: 0.7827 (mm-40) REVERT: B 1134 ASN cc_start: 0.6586 (m110) cc_final: 0.6357 (m-40) REVERT: C 45 SER cc_start: 0.8325 (p) cc_final: 0.8107 (t) REVERT: C 55 PHE cc_start: 0.8383 (m-80) cc_final: 0.8104 (m-80) REVERT: C 269 TYR cc_start: 0.8455 (m-80) cc_final: 0.8064 (m-10) REVERT: C 278 LYS cc_start: 0.7877 (ttpm) cc_final: 0.7677 (ttpm) REVERT: C 304 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7790 (mmmm) REVERT: C 314 GLN cc_start: 0.8029 (tp40) cc_final: 0.7793 (tp40) REVERT: C 317 ASN cc_start: 0.8074 (m-40) cc_final: 0.7814 (m-40) REVERT: C 356 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8678 (p) REVERT: C 409 GLN cc_start: 0.7658 (mt0) cc_final: 0.6978 (mp10) REVERT: C 418 ILE cc_start: 0.6880 (mm) cc_final: 0.6532 (mm) REVERT: C 436 TRP cc_start: 0.5687 (p90) cc_final: 0.5332 (p90) REVERT: C 453 TYR cc_start: 0.7766 (p90) cc_final: 0.6691 (p90) REVERT: C 462 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7290 (mtmm) REVERT: C 528 LYS cc_start: 0.8006 (tptp) cc_final: 0.7618 (tptp) REVERT: C 529 SER cc_start: 0.7950 (t) cc_final: 0.7033 (m) REVERT: C 645 ARG cc_start: 0.7968 (mtm180) cc_final: 0.7767 (mtm180) REVERT: C 674 GLN cc_start: 0.7311 (pp30) cc_final: 0.7052 (pp30) REVERT: C 720 SER cc_start: 0.8557 (t) cc_final: 0.8199 (p) REVERT: C 746 THR cc_start: 0.7832 (p) cc_final: 0.7444 (m) REVERT: C 749 SER cc_start: 0.8144 (t) cc_final: 0.7862 (m) REVERT: C 772 GLU cc_start: 0.7360 (tt0) cc_final: 0.7103 (tt0) REVERT: C 779 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7753 (mt-10) REVERT: C 803 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8148 (mm-40) REVERT: C 934 GLN cc_start: 0.7849 (mt0) cc_final: 0.7591 (tt0) REVERT: C 978 ASP cc_start: 0.7354 (m-30) cc_final: 0.7120 (m-30) REVERT: C 1044 LYS cc_start: 0.8042 (tptp) cc_final: 0.7721 (tptp) REVERT: C 1072 LYS cc_start: 0.8004 (tptp) cc_final: 0.7607 (tptp) REVERT: C 1083 ASP cc_start: 0.6916 (t0) cc_final: 0.6507 (t0) REVERT: C 1091 GLU cc_start: 0.7417 (pm20) cc_final: 0.7150 (pm20) REVERT: C 1134 ASN cc_start: 0.6322 (t0) cc_final: 0.6020 (m110) REVERT: C 1135 THR cc_start: 0.7236 (m) cc_final: 0.6697 (p) outliers start: 74 outliers final: 48 residues processed: 615 average time/residue: 0.3552 time to fit residues: 339.6454 Evaluate side-chains 613 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 561 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 963 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 24 optimal weight: 0.0570 chunk 224 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 239 optimal weight: 30.0000 chunk 274 optimal weight: 0.8980 chunk 212 optimal weight: 0.3980 chunk 231 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 GLN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 709 ASN C1087 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.176365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.145256 restraints weight = 36745.833| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.66 r_work: 0.3690 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24868 Z= 0.139 Angle : 0.591 13.940 33927 Z= 0.300 Chirality : 0.045 0.343 3912 Planarity : 0.004 0.060 4309 Dihedral : 6.279 59.903 3998 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 2.90 % Allowed : 15.09 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.15), residues: 2981 helix: 1.05 (0.19), residues: 714 sheet: -0.74 (0.20), residues: 656 loop : -2.01 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 632 HIS 0.003 0.001 HIS C1082 PHE 0.020 0.001 PHE B 135 TYR 0.024 0.001 TYR A 396 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 30) link_NAG-ASN : angle 3.18174 ( 90) link_BETA1-4 : bond 0.00805 ( 6) link_BETA1-4 : angle 2.07967 ( 18) hydrogen bonds : bond 0.03865 ( 935) hydrogen bonds : angle 5.47176 ( 2589) SS BOND : bond 0.00371 ( 37) SS BOND : angle 2.10690 ( 74) covalent geometry : bond 0.00314 (24795) covalent geometry : angle 0.55832 (33745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 583 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6556 (m-80) cc_final: 0.6175 (m-80) REVERT: A 33 THR cc_start: 0.8225 (p) cc_final: 0.7979 (p) REVERT: A 116 SER cc_start: 0.7732 (m) cc_final: 0.7253 (p) REVERT: A 128 ILE cc_start: 0.7841 (mt) cc_final: 0.7594 (mp) REVERT: A 285 ILE cc_start: 0.8001 (mt) cc_final: 0.7257 (mm) REVERT: A 297 SER cc_start: 0.7800 (m) cc_final: 0.7276 (t) REVERT: A 396 TYR cc_start: 0.6879 (m-80) cc_final: 0.6591 (m-80) REVERT: A 428 ASP cc_start: 0.7961 (p0) cc_final: 0.7651 (p0) REVERT: A 538 VAL cc_start: 0.8923 (t) cc_final: 0.8682 (p) REVERT: A 591 PHE cc_start: 0.8204 (p90) cc_final: 0.7834 (p90) REVERT: A 595 SER cc_start: 0.8526 (m) cc_final: 0.8185 (p) REVERT: A 658 SER cc_start: 0.8573 (m) cc_final: 0.8091 (p) REVERT: A 724 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6958 (tm-30) REVERT: A 747 GLU cc_start: 0.7340 (mp0) cc_final: 0.7057 (mp0) REVERT: A 777 THR cc_start: 0.8494 (t) cc_final: 0.8272 (m) REVERT: A 778 GLN cc_start: 0.7986 (tp40) cc_final: 0.7765 (tp40) REVERT: A 789 LYS cc_start: 0.8413 (mttp) cc_final: 0.8122 (mmtp) REVERT: A 932 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7694 (mtpp) REVERT: A 948 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7395 (mm-40) REVERT: A 962 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8565 (m) REVERT: A 978 ASP cc_start: 0.7753 (t0) cc_final: 0.7516 (t0) REVERT: A 993 ASP cc_start: 0.7912 (t0) cc_final: 0.7656 (t0) REVERT: A 1004 GLN cc_start: 0.8022 (mt0) cc_final: 0.7802 (mt0) REVERT: A 1033 LEU cc_start: 0.8532 (mp) cc_final: 0.8284 (mp) REVERT: A 1110 GLU cc_start: 0.7885 (tt0) cc_final: 0.7663 (tt0) REVERT: B 45 SER cc_start: 0.7779 (p) cc_final: 0.7551 (t) REVERT: B 269 TYR cc_start: 0.6931 (m-80) cc_final: 0.6680 (m-80) REVERT: B 278 LYS cc_start: 0.8755 (tttt) cc_final: 0.8530 (tttt) REVERT: B 309 GLU cc_start: 0.7686 (mp0) cc_final: 0.7410 (mp0) REVERT: B 313 TYR cc_start: 0.8159 (m-80) cc_final: 0.7696 (m-80) REVERT: B 317 ASN cc_start: 0.7799 (m-40) cc_final: 0.7526 (m-40) REVERT: B 321 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7654 (mm-40) REVERT: B 324 GLU cc_start: 0.7626 (mp0) cc_final: 0.7063 (mp0) REVERT: B 618 GLU cc_start: 0.7892 (tp30) cc_final: 0.7639 (tp30) REVERT: B 627 GLN cc_start: 0.7826 (mt0) cc_final: 0.7440 (mt0) REVERT: B 653 GLU cc_start: 0.8066 (pm20) cc_final: 0.7753 (pm20) REVERT: B 696 MET cc_start: 0.8014 (ttp) cc_final: 0.7725 (ptp) REVERT: B 724 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6995 (tm-30) REVERT: B 772 GLU cc_start: 0.7457 (tt0) cc_final: 0.7037 (tt0) REVERT: B 778 GLN cc_start: 0.7920 (tp40) cc_final: 0.7619 (tm-30) REVERT: B 789 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8164 (mtpp) REVERT: B 854 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6673 (t80) REVERT: B 866 ASP cc_start: 0.7328 (p0) cc_final: 0.6536 (p0) REVERT: B 867 GLU cc_start: 0.7544 (mp0) cc_final: 0.6976 (mp0) REVERT: B 918 ASN cc_start: 0.7714 (m110) cc_final: 0.7498 (m110) REVERT: B 921 LEU cc_start: 0.8607 (tp) cc_final: 0.8374 (tt) REVERT: B 1018 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7410 (ttm110) REVERT: B 1027 LYS cc_start: 0.8498 (mttm) cc_final: 0.7857 (mttm) REVERT: B 1040 ASP cc_start: 0.7562 (m-30) cc_final: 0.7240 (m-30) REVERT: B 1044 LYS cc_start: 0.7992 (tptp) cc_final: 0.7758 (tptp) REVERT: B 1112 GLN cc_start: 0.8093 (mt0) cc_final: 0.7841 (mm-40) REVERT: C 45 SER cc_start: 0.8311 (p) cc_final: 0.8098 (t) REVERT: C 55 PHE cc_start: 0.8378 (m-80) cc_final: 0.8097 (m-80) REVERT: C 269 TYR cc_start: 0.8445 (m-10) cc_final: 0.8035 (m-10) REVERT: C 314 GLN cc_start: 0.8002 (tp40) cc_final: 0.7791 (tp40) REVERT: C 317 ASN cc_start: 0.8053 (m-40) cc_final: 0.7749 (m-40) REVERT: C 356 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8657 (p) REVERT: C 409 GLN cc_start: 0.7653 (mt0) cc_final: 0.7049 (mp10) REVERT: C 418 ILE cc_start: 0.6998 (mm) cc_final: 0.6685 (mm) REVERT: C 436 TRP cc_start: 0.5630 (p90) cc_final: 0.5381 (p90) REVERT: C 462 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7247 (mtmm) REVERT: C 540 PHE cc_start: 0.7231 (p90) cc_final: 0.6984 (p90) REVERT: C 576 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6931 (ptt180) REVERT: C 618 GLU cc_start: 0.7619 (tp30) cc_final: 0.7376 (tp30) REVERT: C 674 GLN cc_start: 0.7304 (pp30) cc_final: 0.7068 (pp30) REVERT: C 720 SER cc_start: 0.8618 (t) cc_final: 0.8230 (p) REVERT: C 746 THR cc_start: 0.7778 (p) cc_final: 0.7468 (m) REVERT: C 749 SER cc_start: 0.8152 (t) cc_final: 0.7876 (m) REVERT: C 772 GLU cc_start: 0.7350 (tt0) cc_final: 0.7107 (tt0) REVERT: C 779 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7706 (mt-10) REVERT: C 803 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8191 (mm-40) REVERT: C 934 GLN cc_start: 0.7850 (mt0) cc_final: 0.7618 (tt0) REVERT: C 978 ASP cc_start: 0.7365 (m-30) cc_final: 0.7132 (m-30) REVERT: C 1044 LYS cc_start: 0.8003 (tptp) cc_final: 0.7697 (tptp) REVERT: C 1072 LYS cc_start: 0.8023 (tptp) cc_final: 0.7648 (tptp) REVERT: C 1083 ASP cc_start: 0.6883 (t0) cc_final: 0.6469 (t0) REVERT: C 1134 ASN cc_start: 0.6290 (t0) cc_final: 0.6027 (m110) REVERT: C 1135 THR cc_start: 0.7211 (m) cc_final: 0.6707 (p) outliers start: 77 outliers final: 49 residues processed: 615 average time/residue: 0.3654 time to fit residues: 348.4747 Evaluate side-chains 615 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 561 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 963 LYS Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 127 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 0.0980 chunk 206 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 chunk 296 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 GLN C 709 ASN C 776 ASN C1087 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.176551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.145664 restraints weight = 36515.289| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.64 r_work: 0.3700 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24868 Z= 0.137 Angle : 0.590 13.127 33927 Z= 0.300 Chirality : 0.045 0.335 3912 Planarity : 0.005 0.066 4309 Dihedral : 6.169 59.090 3998 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.08 % Favored : 92.79 % Rotamer: Outliers : 3.12 % Allowed : 16.22 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2981 helix: 1.18 (0.19), residues: 708 sheet: -0.78 (0.20), residues: 598 loop : -1.89 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 632 HIS 0.002 0.000 HIS C1082 PHE 0.023 0.001 PHE A 642 TYR 0.021 0.001 TYR A 396 ARG 0.010 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 30) link_NAG-ASN : angle 3.00115 ( 90) link_BETA1-4 : bond 0.00641 ( 6) link_BETA1-4 : angle 1.97817 ( 18) hydrogen bonds : bond 0.03808 ( 935) hydrogen bonds : angle 5.37369 ( 2589) SS BOND : bond 0.00383 ( 37) SS BOND : angle 1.95491 ( 74) covalent geometry : bond 0.00309 (24795) covalent geometry : angle 0.56164 (33745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 570 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6493 (m-80) cc_final: 0.6207 (m-80) REVERT: A 33 THR cc_start: 0.8248 (p) cc_final: 0.7981 (p) REVERT: A 116 SER cc_start: 0.7735 (m) cc_final: 0.7264 (p) REVERT: A 128 ILE cc_start: 0.7831 (mt) cc_final: 0.7574 (mp) REVERT: A 285 ILE cc_start: 0.8024 (mt) cc_final: 0.7811 (mt) REVERT: A 297 SER cc_start: 0.7823 (m) cc_final: 0.7287 (t) REVERT: A 320 VAL cc_start: 0.8434 (m) cc_final: 0.8225 (p) REVERT: A 396 TYR cc_start: 0.6898 (m-80) cc_final: 0.6542 (m-80) REVERT: A 428 ASP cc_start: 0.7941 (p0) cc_final: 0.7634 (p0) REVERT: A 537 CYS cc_start: 0.6278 (m) cc_final: 0.5972 (m) REVERT: A 591 PHE cc_start: 0.8254 (p90) cc_final: 0.7896 (p90) REVERT: A 658 SER cc_start: 0.8583 (m) cc_final: 0.8094 (p) REVERT: A 696 MET cc_start: 0.7909 (ttm) cc_final: 0.7690 (mtp) REVERT: A 724 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6921 (tm-30) REVERT: A 747 GLU cc_start: 0.7329 (mp0) cc_final: 0.7082 (mp0) REVERT: A 789 LYS cc_start: 0.8408 (mttp) cc_final: 0.8109 (mmtp) REVERT: A 948 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7541 (mm-40) REVERT: A 978 ASP cc_start: 0.7777 (t0) cc_final: 0.7537 (t0) REVERT: A 993 ASP cc_start: 0.7905 (t0) cc_final: 0.7643 (t0) REVERT: A 1004 GLN cc_start: 0.8013 (mt0) cc_final: 0.7791 (mt0) REVERT: A 1033 LEU cc_start: 0.8552 (mp) cc_final: 0.8309 (mp) REVERT: A 1110 GLU cc_start: 0.7865 (tt0) cc_final: 0.7657 (tt0) REVERT: A 1134 ASN cc_start: 0.7343 (m-40) cc_final: 0.7104 (m110) REVERT: B 45 SER cc_start: 0.7768 (p) cc_final: 0.7537 (t) REVERT: B 125 ASN cc_start: 0.7303 (t0) cc_final: 0.7039 (t0) REVERT: B 269 TYR cc_start: 0.6921 (m-80) cc_final: 0.6690 (m-80) REVERT: B 278 LYS cc_start: 0.8746 (tttt) cc_final: 0.8370 (tttp) REVERT: B 309 GLU cc_start: 0.7668 (mp0) cc_final: 0.7363 (mp0) REVERT: B 313 TYR cc_start: 0.8158 (m-80) cc_final: 0.7682 (m-80) REVERT: B 317 ASN cc_start: 0.7774 (m-40) cc_final: 0.7511 (m-40) REVERT: B 321 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7664 (mm-40) REVERT: B 324 GLU cc_start: 0.7639 (mp0) cc_final: 0.7056 (mp0) REVERT: B 557 LYS cc_start: 0.8506 (mppt) cc_final: 0.7999 (mppt) REVERT: B 618 GLU cc_start: 0.7918 (tp30) cc_final: 0.7659 (tp30) REVERT: B 627 GLN cc_start: 0.7844 (mt0) cc_final: 0.7428 (mt0) REVERT: B 653 GLU cc_start: 0.8061 (pm20) cc_final: 0.7750 (pm20) REVERT: B 724 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6924 (tm-30) REVERT: B 772 GLU cc_start: 0.7484 (tt0) cc_final: 0.7007 (tt0) REVERT: B 775 LYS cc_start: 0.8346 (ttpm) cc_final: 0.8126 (tttm) REVERT: B 778 GLN cc_start: 0.7900 (tp40) cc_final: 0.7630 (tm-30) REVERT: B 789 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8158 (mtpp) REVERT: B 854 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6651 (t80) REVERT: B 866 ASP cc_start: 0.7341 (p0) cc_final: 0.6565 (p0) REVERT: B 867 GLU cc_start: 0.7543 (mp0) cc_final: 0.6997 (mp0) REVERT: B 906 ASN cc_start: 0.7861 (t0) cc_final: 0.7586 (t0) REVERT: B 918 ASN cc_start: 0.7709 (m110) cc_final: 0.7500 (m110) REVERT: B 921 LEU cc_start: 0.8592 (tp) cc_final: 0.8348 (tt) REVERT: B 1018 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7401 (ttm110) REVERT: B 1044 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7798 (tptp) REVERT: B 1112 GLN cc_start: 0.8085 (mt0) cc_final: 0.7827 (mm-40) REVERT: C 45 SER cc_start: 0.8293 (p) cc_final: 0.8082 (t) REVERT: C 55 PHE cc_start: 0.8374 (m-80) cc_final: 0.8114 (m-80) REVERT: C 269 TYR cc_start: 0.8439 (m-10) cc_final: 0.8043 (m-10) REVERT: C 317 ASN cc_start: 0.8035 (m-40) cc_final: 0.7726 (m-40) REVERT: C 356 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8674 (p) REVERT: C 390 LEU cc_start: 0.7913 (mm) cc_final: 0.7650 (mt) REVERT: C 409 GLN cc_start: 0.7648 (mt0) cc_final: 0.7023 (mp10) REVERT: C 418 ILE cc_start: 0.7089 (mm) cc_final: 0.6816 (mm) REVERT: C 462 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7216 (mtmm) REVERT: C 492 GLN cc_start: 0.7350 (mp10) cc_final: 0.7118 (mp10) REVERT: C 576 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6896 (ptt180) REVERT: C 618 GLU cc_start: 0.7587 (tp30) cc_final: 0.7386 (tp30) REVERT: C 674 GLN cc_start: 0.7302 (pp30) cc_final: 0.7072 (pp30) REVERT: C 720 SER cc_start: 0.8593 (t) cc_final: 0.8216 (p) REVERT: C 746 THR cc_start: 0.7777 (p) cc_final: 0.7488 (m) REVERT: C 749 SER cc_start: 0.8160 (t) cc_final: 0.7881 (m) REVERT: C 779 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7684 (mt-10) REVERT: C 803 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8167 (mm-40) REVERT: C 934 GLN cc_start: 0.7864 (mt0) cc_final: 0.7642 (tt0) REVERT: C 978 ASP cc_start: 0.7328 (m-30) cc_final: 0.7108 (m-30) REVERT: C 1044 LYS cc_start: 0.8006 (tptp) cc_final: 0.7685 (tptp) REVERT: C 1072 LYS cc_start: 0.7957 (tptp) cc_final: 0.7577 (tptp) REVERT: C 1083 ASP cc_start: 0.6843 (t0) cc_final: 0.6452 (t0) REVERT: C 1134 ASN cc_start: 0.6298 (t0) cc_final: 0.6064 (m110) REVERT: C 1135 THR cc_start: 0.7212 (m) cc_final: 0.6711 (p) outliers start: 83 outliers final: 63 residues processed: 598 average time/residue: 0.3474 time to fit residues: 323.9544 Evaluate side-chains 628 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 560 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 571 THR Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 730 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 963 LYS Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 980 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 150 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 155 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 778 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN C 543 ASN C 709 ASN C1087 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.144402 restraints weight = 36690.121| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.68 r_work: 0.3679 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24868 Z= 0.176 Angle : 0.606 12.902 33927 Z= 0.308 Chirality : 0.045 0.349 3912 Planarity : 0.005 0.060 4309 Dihedral : 6.153 59.879 3996 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.28 % Rotamer: Outliers : 3.09 % Allowed : 16.67 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2981 helix: 1.11 (0.19), residues: 708 sheet: -0.72 (0.20), residues: 608 loop : -1.89 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 436 HIS 0.003 0.001 HIS C1082 PHE 0.025 0.002 PHE A 642 TYR 0.025 0.001 TYR C 453 ARG 0.010 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 30) link_NAG-ASN : angle 3.03458 ( 90) link_BETA1-4 : bond 0.00810 ( 6) link_BETA1-4 : angle 2.02071 ( 18) hydrogen bonds : bond 0.03950 ( 935) hydrogen bonds : angle 5.40528 ( 2589) SS BOND : bond 0.00387 ( 37) SS BOND : angle 2.04158 ( 74) covalent geometry : bond 0.00400 (24795) covalent geometry : angle 0.57734 (33745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 569 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6527 (m-80) cc_final: 0.6234 (m-80) REVERT: A 33 THR cc_start: 0.8295 (p) cc_final: 0.8019 (p) REVERT: A 116 SER cc_start: 0.7753 (m) cc_final: 0.7292 (p) REVERT: A 128 ILE cc_start: 0.7857 (mt) cc_final: 0.7595 (mp) REVERT: A 285 ILE cc_start: 0.8005 (mt) cc_final: 0.7805 (mt) REVERT: A 355 ARG cc_start: 0.8435 (ttt90) cc_final: 0.8128 (ttt90) REVERT: A 591 PHE cc_start: 0.8260 (p90) cc_final: 0.7920 (p90) REVERT: A 658 SER cc_start: 0.8602 (m) cc_final: 0.8124 (p) REVERT: A 724 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 747 GLU cc_start: 0.7343 (mp0) cc_final: 0.7072 (mp0) REVERT: A 789 LYS cc_start: 0.8450 (mttp) cc_final: 0.8158 (mmtp) REVERT: A 867 GLU cc_start: 0.7131 (mp0) cc_final: 0.6740 (mp0) REVERT: A 978 ASP cc_start: 0.7734 (t0) cc_final: 0.7488 (t0) REVERT: A 993 ASP cc_start: 0.7915 (t0) cc_final: 0.7651 (t0) REVERT: A 1004 GLN cc_start: 0.8017 (mt0) cc_final: 0.7808 (mt0) REVERT: A 1033 LEU cc_start: 0.8604 (mp) cc_final: 0.8376 (mp) REVERT: A 1134 ASN cc_start: 0.7366 (m-40) cc_final: 0.7144 (m110) REVERT: B 45 SER cc_start: 0.7817 (p) cc_final: 0.7613 (t) REVERT: B 278 LYS cc_start: 0.8738 (tttt) cc_final: 0.8366 (tttp) REVERT: B 309 GLU cc_start: 0.7676 (mp0) cc_final: 0.7424 (mp0) REVERT: B 313 TYR cc_start: 0.8178 (m-80) cc_final: 0.7744 (m-80) REVERT: B 317 ASN cc_start: 0.7722 (m-40) cc_final: 0.7449 (m-40) REVERT: B 321 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7625 (mm110) REVERT: B 324 GLU cc_start: 0.7661 (mp0) cc_final: 0.7061 (mp0) REVERT: B 557 LYS cc_start: 0.8494 (mppt) cc_final: 0.7989 (mppt) REVERT: B 618 GLU cc_start: 0.7882 (tp30) cc_final: 0.7625 (tp30) REVERT: B 627 GLN cc_start: 0.7841 (mt0) cc_final: 0.7413 (mt0) REVERT: B 653 GLU cc_start: 0.8086 (pm20) cc_final: 0.7783 (pm20) REVERT: B 724 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6940 (tm-30) REVERT: B 744 ASP cc_start: 0.7083 (m-30) cc_final: 0.6715 (m-30) REVERT: B 772 GLU cc_start: 0.7517 (tt0) cc_final: 0.7063 (tt0) REVERT: B 775 LYS cc_start: 0.8377 (ttpm) cc_final: 0.8158 (tttm) REVERT: B 778 GLN cc_start: 0.7932 (tp40) cc_final: 0.7683 (tm-30) REVERT: B 789 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8171 (mtpp) REVERT: B 854 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6752 (t80) REVERT: B 866 ASP cc_start: 0.7348 (p0) cc_final: 0.6580 (p0) REVERT: B 867 GLU cc_start: 0.7547 (mp0) cc_final: 0.7003 (mp0) REVERT: B 906 ASN cc_start: 0.7829 (t0) cc_final: 0.7558 (t0) REVERT: B 918 ASN cc_start: 0.7711 (m110) cc_final: 0.7502 (m110) REVERT: B 921 LEU cc_start: 0.8599 (tp) cc_final: 0.8361 (tt) REVERT: B 983 LEU cc_start: 0.8452 (mt) cc_final: 0.8227 (mp) REVERT: B 1018 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7418 (ttm110) REVERT: B 1044 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7786 (tptp) REVERT: B 1112 GLN cc_start: 0.8066 (mt0) cc_final: 0.7822 (mm-40) REVERT: C 45 SER cc_start: 0.8298 (p) cc_final: 0.8096 (t) REVERT: C 55 PHE cc_start: 0.8400 (m-80) cc_final: 0.8122 (m-80) REVERT: C 269 TYR cc_start: 0.8459 (m-10) cc_final: 0.8084 (m-10) REVERT: C 317 ASN cc_start: 0.8022 (m-40) cc_final: 0.7733 (m-40) REVERT: C 356 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8693 (p) REVERT: C 409 GLN cc_start: 0.7665 (mt0) cc_final: 0.7109 (mp10) REVERT: C 418 ILE cc_start: 0.7185 (mm) cc_final: 0.6862 (mm) REVERT: C 492 GLN cc_start: 0.7282 (mp10) cc_final: 0.7062 (mp10) REVERT: C 576 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6941 (ptt180) REVERT: C 618 GLU cc_start: 0.7657 (tp30) cc_final: 0.7447 (tp30) REVERT: C 645 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7855 (mtt90) REVERT: C 674 GLN cc_start: 0.7332 (pp30) cc_final: 0.7113 (pp30) REVERT: C 720 SER cc_start: 0.8596 (t) cc_final: 0.8220 (p) REVERT: C 746 THR cc_start: 0.7838 (p) cc_final: 0.7582 (m) REVERT: C 749 SER cc_start: 0.8198 (t) cc_final: 0.7923 (m) REVERT: C 761 GLN cc_start: 0.7782 (mt0) cc_final: 0.7475 (mt0) REVERT: C 779 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7655 (mt-10) REVERT: C 803 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8221 (mm-40) REVERT: C 934 GLN cc_start: 0.7854 (mt0) cc_final: 0.7634 (tt0) REVERT: C 978 ASP cc_start: 0.7367 (m-30) cc_final: 0.7152 (m-30) REVERT: C 1044 LYS cc_start: 0.8038 (tptp) cc_final: 0.7714 (tptp) REVERT: C 1072 LYS cc_start: 0.8006 (tptp) cc_final: 0.7625 (tptp) REVERT: C 1083 ASP cc_start: 0.6844 (t0) cc_final: 0.6463 (t0) REVERT: C 1091 GLU cc_start: 0.7486 (pm20) cc_final: 0.7243 (pm20) REVERT: C 1134 ASN cc_start: 0.6393 (t0) cc_final: 0.6184 (m110) REVERT: C 1135 THR cc_start: 0.7265 (m) cc_final: 0.6754 (p) outliers start: 82 outliers final: 64 residues processed: 601 average time/residue: 0.3669 time to fit residues: 344.0832 Evaluate side-chains 623 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 555 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1138 ASP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 40.0000 chunk 203 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 294 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 197 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 778 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN B 948 GLN C 709 ASN C1087 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.174347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143442 restraints weight = 36438.046| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.64 r_work: 0.3664 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24868 Z= 0.212 Angle : 0.637 12.843 33927 Z= 0.324 Chirality : 0.046 0.357 3912 Planarity : 0.005 0.055 4309 Dihedral : 6.252 57.813 3996 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.82 % Favored : 92.05 % Rotamer: Outliers : 3.12 % Allowed : 16.89 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 2981 helix: 1.00 (0.19), residues: 708 sheet: -0.66 (0.20), residues: 594 loop : -1.91 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.004 0.001 HIS C1082 PHE 0.027 0.002 PHE B 220 TYR 0.029 0.002 TYR B1066 ARG 0.010 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 30) link_NAG-ASN : angle 3.11075 ( 90) link_BETA1-4 : bond 0.00885 ( 6) link_BETA1-4 : angle 2.08172 ( 18) hydrogen bonds : bond 0.04206 ( 935) hydrogen bonds : angle 5.50914 ( 2589) SS BOND : bond 0.00433 ( 37) SS BOND : angle 2.08479 ( 74) covalent geometry : bond 0.00479 (24795) covalent geometry : angle 0.60834 (33745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 584 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8344 (p) cc_final: 0.8084 (p) REVERT: A 116 SER cc_start: 0.7842 (m) cc_final: 0.7427 (p) REVERT: A 128 ILE cc_start: 0.7861 (mt) cc_final: 0.7624 (mp) REVERT: A 226 LEU cc_start: 0.8348 (tt) cc_final: 0.7855 (mt) REVERT: A 285 ILE cc_start: 0.8071 (mt) cc_final: 0.7317 (mm) REVERT: A 591 PHE cc_start: 0.8313 (p90) cc_final: 0.7953 (p90) REVERT: A 658 SER cc_start: 0.8649 (m) cc_final: 0.8174 (p) REVERT: A 724 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 747 GLU cc_start: 0.7304 (mp0) cc_final: 0.7041 (mp0) REVERT: A 789 LYS cc_start: 0.8436 (mttp) cc_final: 0.8098 (mmtp) REVERT: A 867 GLU cc_start: 0.7150 (mp0) cc_final: 0.6761 (mp0) REVERT: A 868 MET cc_start: 0.8265 (mtt) cc_final: 0.7972 (mtm) REVERT: A 882 THR cc_start: 0.8184 (m) cc_final: 0.7853 (m) REVERT: A 949 ASP cc_start: 0.7480 (m-30) cc_final: 0.6907 (m-30) REVERT: A 978 ASP cc_start: 0.7754 (t0) cc_final: 0.7498 (t0) REVERT: A 993 ASP cc_start: 0.7922 (t0) cc_final: 0.7648 (t0) REVERT: A 1004 GLN cc_start: 0.7983 (mt0) cc_final: 0.7771 (mt0) REVERT: A 1033 LEU cc_start: 0.8620 (mp) cc_final: 0.8388 (mp) REVERT: A 1134 ASN cc_start: 0.7401 (m-40) cc_final: 0.7185 (m110) REVERT: B 45 SER cc_start: 0.7898 (p) cc_final: 0.7696 (t) REVERT: B 53 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6946 (m-30) REVERT: B 278 LYS cc_start: 0.8759 (tttt) cc_final: 0.8545 (tttt) REVERT: B 309 GLU cc_start: 0.7656 (mp0) cc_final: 0.7454 (mp0) REVERT: B 313 TYR cc_start: 0.8140 (m-80) cc_final: 0.7702 (m-80) REVERT: B 317 ASN cc_start: 0.7668 (m-40) cc_final: 0.7408 (m-40) REVERT: B 321 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7621 (mm110) REVERT: B 324 GLU cc_start: 0.7686 (mp0) cc_final: 0.7064 (mp0) REVERT: B 557 LYS cc_start: 0.8496 (mppt) cc_final: 0.7981 (mppt) REVERT: B 618 GLU cc_start: 0.7877 (tp30) cc_final: 0.7619 (tp30) REVERT: B 627 GLN cc_start: 0.7813 (mt0) cc_final: 0.7368 (mt0) REVERT: B 653 GLU cc_start: 0.8148 (pm20) cc_final: 0.7867 (pm20) REVERT: B 744 ASP cc_start: 0.7054 (m-30) cc_final: 0.6683 (m-30) REVERT: B 761 GLN cc_start: 0.7628 (mt0) cc_final: 0.7293 (mt0) REVERT: B 772 GLU cc_start: 0.7531 (tt0) cc_final: 0.7161 (tt0) REVERT: B 778 GLN cc_start: 0.7917 (tp40) cc_final: 0.7686 (tm-30) REVERT: B 789 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8238 (mtpp) REVERT: B 854 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6786 (t80) REVERT: B 866 ASP cc_start: 0.7328 (p0) cc_final: 0.6569 (p0) REVERT: B 867 GLU cc_start: 0.7571 (mp0) cc_final: 0.7051 (mp0) REVERT: B 906 ASN cc_start: 0.7855 (t0) cc_final: 0.7584 (t0) REVERT: B 918 ASN cc_start: 0.7739 (m110) cc_final: 0.7520 (m-40) REVERT: B 921 LEU cc_start: 0.8591 (tp) cc_final: 0.8359 (tt) REVERT: B 994 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7992 (mtm180) REVERT: B 1027 LYS cc_start: 0.8505 (mttm) cc_final: 0.7991 (mttm) REVERT: B 1044 LYS cc_start: 0.8030 (tptp) cc_final: 0.7819 (tptp) REVERT: B 1071 GLU cc_start: 0.7902 (mp0) cc_final: 0.7457 (mp0) REVERT: B 1112 GLN cc_start: 0.8085 (mt0) cc_final: 0.7805 (mm-40) REVERT: C 55 PHE cc_start: 0.8396 (m-80) cc_final: 0.8178 (m-80) REVERT: C 269 TYR cc_start: 0.8462 (m-10) cc_final: 0.8087 (m-10) REVERT: C 317 ASN cc_start: 0.8014 (m-40) cc_final: 0.7723 (m-40) REVERT: C 356 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8648 (p) REVERT: C 409 GLN cc_start: 0.7676 (mt0) cc_final: 0.7154 (mp10) REVERT: C 418 ILE cc_start: 0.7362 (mm) cc_final: 0.7032 (mm) REVERT: C 492 GLN cc_start: 0.7259 (mp10) cc_final: 0.7048 (mp10) REVERT: C 540 PHE cc_start: 0.7329 (p90) cc_final: 0.7106 (p90) REVERT: C 555 ASN cc_start: 0.7674 (p0) cc_final: 0.7375 (p0) REVERT: C 576 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6985 (ptt180) REVERT: C 645 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7849 (mtt90) REVERT: C 674 GLN cc_start: 0.7298 (pp30) cc_final: 0.7091 (pp30) REVERT: C 720 SER cc_start: 0.8587 (t) cc_final: 0.8184 (p) REVERT: C 746 THR cc_start: 0.7895 (p) cc_final: 0.7669 (m) REVERT: C 749 SER cc_start: 0.8234 (t) cc_final: 0.7952 (m) REVERT: C 761 GLN cc_start: 0.7810 (mt0) cc_final: 0.7503 (mt0) REVERT: C 779 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 803 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8199 (mm-40) REVERT: C 934 GLN cc_start: 0.7850 (mt0) cc_final: 0.7626 (tt0) REVERT: C 978 ASP cc_start: 0.7353 (m-30) cc_final: 0.7131 (m-30) REVERT: C 1044 LYS cc_start: 0.8102 (tptp) cc_final: 0.7784 (tptp) REVERT: C 1072 LYS cc_start: 0.8012 (tptp) cc_final: 0.7639 (tptp) REVERT: C 1083 ASP cc_start: 0.6878 (t0) cc_final: 0.6549 (t0) REVERT: C 1091 GLU cc_start: 0.7442 (pm20) cc_final: 0.7210 (pm20) REVERT: C 1135 THR cc_start: 0.7298 (m) cc_final: 0.6779 (p) outliers start: 83 outliers final: 69 residues processed: 613 average time/residue: 0.3634 time to fit residues: 346.8502 Evaluate side-chains 645 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 572 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 730 MET Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 216 optimal weight: 0.5980 chunk 223 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN B 948 GLN B1004 GLN C 709 ASN C1087 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143864 restraints weight = 36634.225| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.64 r_work: 0.3676 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24868 Z= 0.182 Angle : 0.626 12.512 33927 Z= 0.319 Chirality : 0.046 0.356 3912 Planarity : 0.005 0.067 4309 Dihedral : 6.181 58.381 3996 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.65 % Favored : 92.25 % Rotamer: Outliers : 3.24 % Allowed : 17.34 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 2981 helix: 1.05 (0.19), residues: 708 sheet: -0.68 (0.20), residues: 616 loop : -1.89 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 436 HIS 0.003 0.001 HIS B 207 PHE 0.025 0.002 PHE B 220 TYR 0.023 0.001 TYR C 453 ARG 0.010 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 30) link_NAG-ASN : angle 3.04882 ( 90) link_BETA1-4 : bond 0.00800 ( 6) link_BETA1-4 : angle 1.99986 ( 18) hydrogen bonds : bond 0.04035 ( 935) hydrogen bonds : angle 5.45247 ( 2589) SS BOND : bond 0.00430 ( 37) SS BOND : angle 2.00578 ( 74) covalent geometry : bond 0.00414 (24795) covalent geometry : angle 0.59825 (33745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 574 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8353 (p) cc_final: 0.8084 (p) REVERT: A 116 SER cc_start: 0.7865 (m) cc_final: 0.7459 (p) REVERT: A 128 ILE cc_start: 0.7836 (mt) cc_final: 0.7606 (mp) REVERT: A 226 LEU cc_start: 0.8381 (tt) cc_final: 0.7865 (mt) REVERT: A 285 ILE cc_start: 0.8064 (mt) cc_final: 0.7310 (mm) REVERT: A 355 ARG cc_start: 0.8504 (ttt90) cc_final: 0.8224 (ttt90) REVERT: A 357 ARG cc_start: 0.6656 (tpt-90) cc_final: 0.6427 (tpt-90) REVERT: A 591 PHE cc_start: 0.8327 (p90) cc_final: 0.7990 (p90) REVERT: A 658 SER cc_start: 0.8654 (m) cc_final: 0.8158 (p) REVERT: A 696 MET cc_start: 0.7875 (ttm) cc_final: 0.7648 (mtp) REVERT: A 724 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 747 GLU cc_start: 0.7279 (mp0) cc_final: 0.6996 (mp0) REVERT: A 789 LYS cc_start: 0.8430 (mttp) cc_final: 0.8086 (mmtp) REVERT: A 867 GLU cc_start: 0.7174 (mp0) cc_final: 0.6760 (mp0) REVERT: A 868 MET cc_start: 0.8279 (mtt) cc_final: 0.7980 (mtm) REVERT: A 882 THR cc_start: 0.8171 (m) cc_final: 0.7827 (m) REVERT: A 978 ASP cc_start: 0.7771 (t0) cc_final: 0.7516 (t0) REVERT: A 993 ASP cc_start: 0.7935 (t0) cc_final: 0.7662 (t0) REVERT: A 1004 GLN cc_start: 0.7995 (mt0) cc_final: 0.7781 (mt0) REVERT: A 1033 LEU cc_start: 0.8571 (mp) cc_final: 0.8329 (mp) REVERT: A 1102 PHE cc_start: 0.8275 (m-80) cc_final: 0.7871 (m-80) REVERT: A 1134 ASN cc_start: 0.7419 (m-40) cc_final: 0.7187 (m110) REVERT: B 44 ARG cc_start: 0.7493 (mtt90) cc_final: 0.7238 (mtm-85) REVERT: B 53 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: B 278 LYS cc_start: 0.8756 (tttt) cc_final: 0.8376 (tttp) REVERT: B 313 TYR cc_start: 0.8134 (m-80) cc_final: 0.7708 (m-80) REVERT: B 317 ASN cc_start: 0.7671 (m-40) cc_final: 0.7396 (m-40) REVERT: B 321 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7604 (mm110) REVERT: B 324 GLU cc_start: 0.7694 (mp0) cc_final: 0.7048 (mp0) REVERT: B 557 LYS cc_start: 0.8510 (mppt) cc_final: 0.7988 (mppt) REVERT: B 618 GLU cc_start: 0.7859 (tp30) cc_final: 0.7616 (tp30) REVERT: B 627 GLN cc_start: 0.7831 (mt0) cc_final: 0.7396 (mt0) REVERT: B 653 GLU cc_start: 0.8126 (pm20) cc_final: 0.7844 (pm20) REVERT: B 744 ASP cc_start: 0.7041 (m-30) cc_final: 0.6667 (m-30) REVERT: B 761 GLN cc_start: 0.7591 (mt0) cc_final: 0.7257 (mt0) REVERT: B 772 GLU cc_start: 0.7544 (tt0) cc_final: 0.7089 (tt0) REVERT: B 778 GLN cc_start: 0.7925 (tp40) cc_final: 0.7699 (tm-30) REVERT: B 789 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8180 (mtpp) REVERT: B 854 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.6750 (t80) REVERT: B 866 ASP cc_start: 0.7340 (p0) cc_final: 0.6600 (p0) REVERT: B 867 GLU cc_start: 0.7573 (mp0) cc_final: 0.7072 (mp0) REVERT: B 906 ASN cc_start: 0.7839 (t0) cc_final: 0.7489 (t0) REVERT: B 918 ASN cc_start: 0.7738 (m110) cc_final: 0.7521 (m-40) REVERT: B 921 LEU cc_start: 0.8582 (tp) cc_final: 0.8346 (tt) REVERT: B 994 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7946 (mtm180) REVERT: B 1018 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7404 (ttm110) REVERT: B 1112 GLN cc_start: 0.8113 (mt0) cc_final: 0.7758 (mm-40) REVERT: C 55 PHE cc_start: 0.8407 (m-80) cc_final: 0.8192 (m-80) REVERT: C 269 TYR cc_start: 0.8440 (m-10) cc_final: 0.8093 (m-10) REVERT: C 317 ASN cc_start: 0.8007 (m-40) cc_final: 0.7754 (m-40) REVERT: C 356 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8627 (p) REVERT: C 409 GLN cc_start: 0.7623 (mt0) cc_final: 0.7147 (mp10) REVERT: C 418 ILE cc_start: 0.7352 (mm) cc_final: 0.7035 (mm) REVERT: C 492 GLN cc_start: 0.7243 (mp10) cc_final: 0.7025 (mp10) REVERT: C 540 PHE cc_start: 0.7317 (p90) cc_final: 0.7088 (p90) REVERT: C 555 ASN cc_start: 0.7692 (p0) cc_final: 0.7400 (p0) REVERT: C 576 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6984 (ptt180) REVERT: C 674 GLN cc_start: 0.7292 (pp30) cc_final: 0.7089 (pp30) REVERT: C 720 SER cc_start: 0.8566 (t) cc_final: 0.8166 (p) REVERT: C 746 THR cc_start: 0.7898 (p) cc_final: 0.7672 (m) REVERT: C 749 SER cc_start: 0.8225 (t) cc_final: 0.7941 (m) REVERT: C 761 GLN cc_start: 0.7798 (mt0) cc_final: 0.7483 (mt0) REVERT: C 779 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7715 (mt-10) REVERT: C 803 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8190 (mm-40) REVERT: C 934 GLN cc_start: 0.7882 (mt0) cc_final: 0.7661 (tt0) REVERT: C 978 ASP cc_start: 0.7348 (m-30) cc_final: 0.7143 (m-30) REVERT: C 1044 LYS cc_start: 0.8104 (tptp) cc_final: 0.7793 (tptp) REVERT: C 1072 LYS cc_start: 0.8024 (tptp) cc_final: 0.7649 (tptp) REVERT: C 1083 ASP cc_start: 0.6887 (t0) cc_final: 0.6513 (t0) REVERT: C 1091 GLU cc_start: 0.7455 (pm20) cc_final: 0.7225 (pm20) REVERT: C 1135 THR cc_start: 0.6998 (m) cc_final: 0.6780 (p) outliers start: 86 outliers final: 71 residues processed: 606 average time/residue: 0.4063 time to fit residues: 388.2752 Evaluate side-chains 636 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 561 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1004 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 182 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 258 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 236 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 778 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN C 394 ASN C 709 ASN C1087 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.175123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144068 restraints weight = 36576.169| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.66 r_work: 0.3683 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24868 Z= 0.162 Angle : 0.627 12.069 33927 Z= 0.320 Chirality : 0.046 0.350 3912 Planarity : 0.005 0.066 4309 Dihedral : 6.141 59.293 3996 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.85 % Favored : 92.05 % Rotamer: Outliers : 3.16 % Allowed : 17.83 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 2981 helix: 1.11 (0.19), residues: 708 sheet: -0.67 (0.20), residues: 618 loop : -1.89 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.003 0.000 HIS B 207 PHE 0.027 0.001 PHE B 220 TYR 0.024 0.001 TYR B1066 ARG 0.011 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 30) link_NAG-ASN : angle 2.94774 ( 90) link_BETA1-4 : bond 0.00778 ( 6) link_BETA1-4 : angle 1.94343 ( 18) hydrogen bonds : bond 0.03955 ( 935) hydrogen bonds : angle 5.41416 ( 2589) SS BOND : bond 0.00435 ( 37) SS BOND : angle 1.86659 ( 74) covalent geometry : bond 0.00370 (24795) covalent geometry : angle 0.60150 (33745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5962 Ramachandran restraints generated. 2981 Oldfield, 0 Emsley, 2981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 573 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8347 (p) cc_final: 0.8073 (p) REVERT: A 116 SER cc_start: 0.7851 (m) cc_final: 0.7457 (p) REVERT: A 128 ILE cc_start: 0.7821 (mt) cc_final: 0.7593 (mp) REVERT: A 226 LEU cc_start: 0.8378 (tt) cc_final: 0.7874 (mt) REVERT: A 591 PHE cc_start: 0.8311 (p90) cc_final: 0.7957 (p90) REVERT: A 658 SER cc_start: 0.8636 (m) cc_final: 0.8126 (p) REVERT: A 696 MET cc_start: 0.7869 (ttm) cc_final: 0.7652 (mtp) REVERT: A 724 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6887 (tm-30) REVERT: A 747 GLU cc_start: 0.7285 (mp0) cc_final: 0.7003 (mp0) REVERT: A 789 LYS cc_start: 0.8438 (mttp) cc_final: 0.8093 (mmtp) REVERT: A 867 GLU cc_start: 0.7187 (mp0) cc_final: 0.6771 (mp0) REVERT: A 868 MET cc_start: 0.8272 (mtt) cc_final: 0.7982 (mtm) REVERT: A 882 THR cc_start: 0.8155 (m) cc_final: 0.7799 (m) REVERT: A 978 ASP cc_start: 0.7760 (t0) cc_final: 0.7512 (t0) REVERT: A 993 ASP cc_start: 0.7939 (t0) cc_final: 0.7661 (t0) REVERT: A 1004 GLN cc_start: 0.7952 (mt0) cc_final: 0.7740 (mt0) REVERT: A 1033 LEU cc_start: 0.8582 (mp) cc_final: 0.8334 (mp) REVERT: A 1134 ASN cc_start: 0.7430 (m-40) cc_final: 0.7215 (m110) REVERT: B 44 ARG cc_start: 0.7484 (mtt90) cc_final: 0.7226 (mtm-85) REVERT: B 53 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6925 (m-30) REVERT: B 278 LYS cc_start: 0.8764 (tttt) cc_final: 0.8386 (tttp) REVERT: B 313 TYR cc_start: 0.8110 (m-80) cc_final: 0.7667 (m-80) REVERT: B 317 ASN cc_start: 0.7656 (m-40) cc_final: 0.7384 (m-40) REVERT: B 321 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7665 (mm110) REVERT: B 324 GLU cc_start: 0.7698 (mp0) cc_final: 0.7079 (mp0) REVERT: B 557 LYS cc_start: 0.8508 (mppt) cc_final: 0.8017 (mppt) REVERT: B 618 GLU cc_start: 0.7862 (tp30) cc_final: 0.7616 (tp30) REVERT: B 627 GLN cc_start: 0.7818 (mt0) cc_final: 0.7371 (mt0) REVERT: B 653 GLU cc_start: 0.8105 (pm20) cc_final: 0.7822 (pm20) REVERT: B 744 ASP cc_start: 0.7001 (m-30) cc_final: 0.6629 (m-30) REVERT: B 752 LEU cc_start: 0.8247 (tp) cc_final: 0.8001 (tt) REVERT: B 761 GLN cc_start: 0.7525 (mt0) cc_final: 0.7199 (mt0) REVERT: B 772 GLU cc_start: 0.7527 (tt0) cc_final: 0.7069 (tt0) REVERT: B 778 GLN cc_start: 0.7907 (tp40) cc_final: 0.7684 (tm-30) REVERT: B 789 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8170 (mtpp) REVERT: B 854 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6740 (t80) REVERT: B 866 ASP cc_start: 0.7311 (p0) cc_final: 0.6570 (p0) REVERT: B 867 GLU cc_start: 0.7561 (mp0) cc_final: 0.7062 (mp0) REVERT: B 906 ASN cc_start: 0.7816 (t0) cc_final: 0.7478 (t0) REVERT: B 918 ASN cc_start: 0.7732 (m110) cc_final: 0.7516 (m-40) REVERT: B 921 LEU cc_start: 0.8571 (tp) cc_final: 0.8339 (tt) REVERT: B 994 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7938 (mtm180) REVERT: B 1018 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7393 (ttm110) REVERT: B 1112 GLN cc_start: 0.8114 (mt0) cc_final: 0.7758 (mm-40) REVERT: C 55 PHE cc_start: 0.8382 (m-80) cc_final: 0.8160 (m-80) REVERT: C 269 TYR cc_start: 0.8412 (m-10) cc_final: 0.8033 (m-10) REVERT: C 317 ASN cc_start: 0.8072 (m-40) cc_final: 0.7711 (m-40) REVERT: C 356 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (p) REVERT: C 409 GLN cc_start: 0.7621 (mt0) cc_final: 0.7146 (mp10) REVERT: C 418 ILE cc_start: 0.7348 (mm) cc_final: 0.7030 (mm) REVERT: C 492 GLN cc_start: 0.7251 (mp10) cc_final: 0.7046 (mp10) REVERT: C 555 ASN cc_start: 0.7700 (p0) cc_final: 0.7411 (p0) REVERT: C 576 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6991 (ptt180) REVERT: C 674 GLN cc_start: 0.7283 (pp30) cc_final: 0.7079 (pp30) REVERT: C 720 SER cc_start: 0.8576 (t) cc_final: 0.8186 (p) REVERT: C 746 THR cc_start: 0.7898 (p) cc_final: 0.7674 (m) REVERT: C 749 SER cc_start: 0.8215 (t) cc_final: 0.7933 (m) REVERT: C 761 GLN cc_start: 0.7807 (mt0) cc_final: 0.7478 (mt0) REVERT: C 779 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7716 (mt-10) REVERT: C 803 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8185 (mm-40) REVERT: C 934 GLN cc_start: 0.7874 (mt0) cc_final: 0.7657 (tt0) REVERT: C 978 ASP cc_start: 0.7372 (m-30) cc_final: 0.7166 (m-30) REVERT: C 1044 LYS cc_start: 0.8100 (tptp) cc_final: 0.7792 (tptp) REVERT: C 1072 LYS cc_start: 0.8018 (tptp) cc_final: 0.7648 (tptp) REVERT: C 1083 ASP cc_start: 0.6855 (t0) cc_final: 0.6477 (t0) REVERT: C 1091 GLU cc_start: 0.7451 (pm20) cc_final: 0.7224 (pm20) outliers start: 84 outliers final: 69 residues processed: 604 average time/residue: 0.3459 time to fit residues: 326.0727 Evaluate side-chains 632 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 559 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 673 TYR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 790 THR Chi-restraints excluded: chain A residue 824 LYS Chi-restraints excluded: chain A residue 901 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1017 ILE Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 783 GLN Chi-restraints excluded: chain B residue 854 PHE Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1004 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 911 THR Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 933 ILE Chi-restraints excluded: chain C residue 968 LYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1125 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 60 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 778 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN C 563 GLN C 709 ASN C1087 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.174828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143901 restraints weight = 36544.931| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.65 r_work: 0.3680 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24868 Z= 0.177 Angle : 0.631 11.809 33927 Z= 0.322 Chirality : 0.046 0.354 3912 Planarity : 0.005 0.065 4309 Dihedral : 6.139 59.183 3996 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.85 % Favored : 92.05 % Rotamer: Outliers : 2.93 % Allowed : 18.10 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 2981 helix: 1.18 (0.19), residues: 703 sheet: -0.70 (0.20), residues: 610 loop : -1.91 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 436 HIS 0.003 0.001 HIS B 207 PHE 0.026 0.002 PHE B 220 TYR 0.023 0.001 TYR B1066 ARG 0.011 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 30) link_NAG-ASN : angle 3.00273 ( 90) link_BETA1-4 : bond 0.00808 ( 6) link_BETA1-4 : angle 1.94287 ( 18) hydrogen bonds : bond 0.04002 ( 935) hydrogen bonds : angle 5.41950 ( 2589) SS BOND : bond 0.00455 ( 37) SS BOND : angle 1.98022 ( 74) covalent geometry : bond 0.00405 (24795) covalent geometry : angle 0.60449 (33745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13096.87 seconds wall clock time: 228 minutes 7.01 seconds (13687.01 seconds total)