Starting phenix.real_space_refine on Sat Jun 21 04:56:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlv_38460/06_2025/8xlv_38460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlv_38460/06_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_38460/06_2025/8xlv_38460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlv_38460/06_2025/8xlv_38460.map" model { file = "/net/cci-nas-00/data/ceres_data/8xlv_38460/06_2025/8xlv_38460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlv_38460/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.07, per 1000 atoms: 0.66 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: 7.29 Conformation dependent library (CDL) restraints added in 4.0 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: 3.54 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: 11.02 Time building geometry restraints manager: 8.33 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: 0.010 Normalize map: mean=0, sd=1: 254.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 64.070 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 324.830 ------------------------------------------------------------------------------- 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 : 2.672 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: 0.4198 time to fit residues: 453.2612 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 : 4.218 ------------------------------------------------------------------------------- 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 = 0.147627 restraints weight = 36966.130| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.66 r_work: 0.3721 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 3.932 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: 0.5051 (pm20) cc_final: 0.4038 (pt0) REVERT: A 28 TYR cc_start: 0.6627 (m-80) cc_final: 0.6183 (m-80) REVERT: A 48 LEU cc_start: 0.8397 (mp) cc_final: 0.8193 (mt) REVERT: A 116 SER cc_start: 0.7225 (m) cc_final: 0.6649 (p) REVERT: A 128 ILE cc_start: 0.7867 (mt) cc_final: 0.7540 (mp) REVERT: A 285 ILE cc_start: 0.8010 (mt) cc_final: 0.7780 (mt) REVERT: A 591 PHE cc_start: 0.8086 (p90) cc_final: 0.7842 (p90) REVERT: A 658 SER cc_start: 0.8561 (m) cc_final: 0.8169 (p) REVERT: A 662 ASP cc_start: 0.7318 (t70) cc_final: 0.7067 (t70) REVERT: A 724 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 747 GLU cc_start: 0.7362 (mp0) cc_final: 0.7037 (mp0) REVERT: A 763 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7826 (mtpp) REVERT: A 789 LYS cc_start: 0.8359 (mttp) cc_final: 0.8054 (mmtp) REVERT: A 810 LYS cc_start: 0.7566 (ptpt) cc_final: 0.6903 (ptpt) REVERT: A 813 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7875 (mmtm) REVERT: A 868 MET cc_start: 0.8281 (mtt) cc_final: 0.8027 (mtm) REVERT: A 948 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7464 (mm-40) REVERT: A 978 ASP cc_start: 0.7839 (t0) cc_final: 0.7610 (t0) REVERT: A 1046 TYR cc_start: 0.8531 (m-80) cc_final: 0.8322 (m-10) REVERT: A 1090 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7613 (mtt90) REVERT: A 1091 GLU cc_start: 0.7107 (pm20) cc_final: 0.6686 (pm20) REVERT: A 1110 GLU cc_start: 0.7818 (tt0) cc_final: 0.7575 (tt0) REVERT: B 88 ASP cc_start: 0.7321 (p0) cc_final: 0.6819 (p0) REVERT: B 278 LYS cc_start: 0.8795 (tttt) cc_final: 0.8396 (tttp) REVERT: B 309 GLU cc_start: 0.7750 (mp0) cc_final: 0.7496 (mp0) REVERT: B 313 TYR cc_start: 0.8156 (m-80) cc_final: 0.7684 (m-80) REVERT: B 317 ASN cc_start: 0.7751 (m-40) cc_final: 0.7495 (m-40) REVERT: B 321 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7767 (mm-40) REVERT: B 324 GLU cc_start: 0.7495 (mp0) cc_final: 0.7016 (mp0) REVERT: B 583 ILE cc_start: 0.6298 (tp) cc_final: 0.6052 (mt) REVERT: B 591 PHE cc_start: 0.8134 (p90) cc_final: 0.7927 (p90) REVERT: B 618 GLU cc_start: 0.7904 (tp30) cc_final: 0.7651 (tp30) REVERT: B 627 GLN cc_start: 0.7714 (mt0) cc_final: 0.7394 (mt0) REVERT: B 640 ASN cc_start: 0.7399 (p0) cc_final: 0.7174 (p0) REVERT: B 653 GLU cc_start: 0.8036 (pm20) cc_final: 0.7721 (pm20) REVERT: B 658 SER cc_start: 0.8583 (m) cc_final: 0.8303 (t) REVERT: B 696 MET cc_start: 0.7915 (ttp) cc_final: 0.7612 (ptp) REVERT: B 724 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6976 (tm-30) REVERT: B 772 GLU cc_start: 0.7407 (tt0) cc_final: 0.6958 (tt0) REVERT: B 775 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8130 (tttm) REVERT: B 778 GLN cc_start: 0.7918 (tp40) cc_final: 0.7558 (tm-30) REVERT: B 779 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7573 (tt0) REVERT: B 785 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7624 (mmtm) REVERT: B 789 LYS cc_start: 0.8364 (mtpp) cc_final: 0.8120 (ttmm) REVERT: B 866 ASP cc_start: 0.7321 (p0) cc_final: 0.6671 (p0) REVERT: B 867 GLU cc_start: 0.7570 (mp0) cc_final: 0.7049 (mp0) REVERT: B 918 ASN cc_start: 0.7691 (m110) cc_final: 0.7483 (m110) REVERT: B 921 LEU cc_start: 0.8623 (tp) cc_final: 0.8417 (tt) REVERT: B 968 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8641 (mttm) REVERT: B 983 LEU cc_start: 0.8246 (mt) cc_final: 0.8006 (mp) REVERT: B 1037 LYS cc_start: 0.7995 (mttm) cc_final: 0.7789 (mttm) REVERT: B 1040 ASP cc_start: 0.7551 (m-30) cc_final: 0.7324 (m-30) REVERT: B 1090 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7080 (ttt-90) REVERT: B 1106 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6826 (mtp180) REVERT: B 1112 GLN cc_start: 0.8088 (mt0) cc_final: 0.7823 (mm-40) REVERT: B 1135 THR cc_start: 0.7836 (m) cc_final: 0.7216 (m) REVERT: C 269 TYR cc_start: 0.8454 (m-80) cc_final: 0.7969 (m-10) REVERT: C 278 LYS cc_start: 0.7819 (ttpm) cc_final: 0.7611 (ttpm) REVERT: C 317 ASN cc_start: 0.8125 (m-40) cc_final: 0.7920 (m-40) REVERT: C 356 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 436 TRP cc_start: 0.5751 (p90) cc_final: 0.5286 (p90) REVERT: C 528 LYS cc_start: 0.7971 (tptp) cc_final: 0.7585 (tptp) REVERT: C 529 SER cc_start: 0.8073 (t) cc_final: 0.7146 (m) REVERT: C 555 ASN cc_start: 0.7519 (p0) cc_final: 0.6818 (p0) REVERT: C 557 LYS cc_start: 0.8226 (mptt) cc_final: 0.7874 (mptt) REVERT: C 573 ASP cc_start: 0.7397 (m-30) cc_final: 0.7167 (m-30) REVERT: C 645 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7730 (mtm180) REVERT: C 674 GLN cc_start: 0.7292 (pp30) cc_final: 0.6998 (pp30) REVERT: C 720 SER cc_start: 0.8572 (t) cc_final: 0.8170 (p) REVERT: C 746 THR cc_start: 0.7607 (p) cc_final: 0.7164 (m) REVERT: C 749 SER cc_start: 0.8083 (t) cc_final: 0.7827 (m) REVERT: C 772 GLU cc_start: 0.7301 (tt0) cc_final: 0.7065 (tt0) REVERT: C 779 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 783 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: C 789 LYS cc_start: 0.8343 (mppt) cc_final: 0.8087 (mppt) REVERT: C 803 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7983 (mm-40) REVERT: C 910 VAL cc_start: 0.7637 (t) cc_final: 0.7430 (t) REVERT: C 934 GLN cc_start: 0.7875 (mt0) cc_final: 0.7611 (mt0) REVERT: C 1044 LYS cc_start: 0.8043 (tptp) cc_final: 0.7776 (tptp) REVERT: C 1072 LYS cc_start: 0.8033 (tptp) cc_final: 0.7678 (tptp) REVERT: C 1083 ASP cc_start: 0.6853 (t0) cc_final: 0.6484 (t0) REVERT: C 1135 THR cc_start: 0.7162 (m) cc_final: 0.6949 (p) outliers start: 64 outliers final: 37 residues processed: 615 average time/residue: 0.4224 time to fit residues: 400.4893 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 : 3.385 ------------------------------------------------------------------------------- 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: 2.9990 chunk 212 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 223 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 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: 0.5780 ------------------------------------------------------------------------------- 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 543 ASN C 709 ASN C 783 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.176572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145365 restraints weight = 36709.561| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.66 r_work: 0.3699 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 24868 Z= 0.147 Angle : 0.625 15.244 33927 Z= 0.316 Chirality : 0.045 0.344 3912 Planarity : 0.005 0.072 4309 Dihedral : 6.525 59.407 3998 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.21 % Favored : 92.65 % Rotamer: Outliers : 2.45 % Allowed : 12.60 % Favored : 84.95 % 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: 1.06 (0.19), residues: 713 sheet: -0.81 (0.20), residues: 659 loop : -2.06 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 452 HIS 0.003 0.001 HIS A 207 PHE 0.027 0.001 PHE C 540 TYR 0.017 0.001 TYR B1066 ARG 0.005 0.000 ARG A1106 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 30) link_NAG-ASN : angle 3.49671 ( 90) link_BETA1-4 : bond 0.00853 ( 6) link_BETA1-4 : angle 2.33621 ( 18) hydrogen bonds : bond 0.03987 ( 935) hydrogen bonds : angle 5.65888 ( 2589) SS BOND : bond 0.00341 ( 37) SS BOND : angle 2.40994 ( 74) covalent geometry : bond 0.00331 (24795) covalent geometry : angle 0.58639 (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 635 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 570 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.5064 (pm20) cc_final: 0.4831 (pm20) REVERT: A 28 TYR cc_start: 0.6609 (m-80) cc_final: 0.6215 (m-80) REVERT: A 33 THR cc_start: 0.8077 (p) cc_final: 0.7865 (p) REVERT: A 116 SER cc_start: 0.7481 (m) cc_final: 0.6929 (p) REVERT: A 285 ILE cc_start: 0.8017 (mt) cc_final: 0.7743 (mt) REVERT: A 310 LYS cc_start: 0.8531 (tmmt) cc_final: 0.8162 (tmmt) REVERT: A 320 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8323 (m) REVERT: A 409 GLN cc_start: 0.7770 (tp-100) cc_final: 0.7564 (tp-100) REVERT: A 428 ASP cc_start: 0.7894 (p0) cc_final: 0.7657 (p0) REVERT: A 591 PHE cc_start: 0.8088 (p90) cc_final: 0.7753 (p90) REVERT: A 658 SER cc_start: 0.8565 (m) cc_final: 0.8140 (p) REVERT: A 662 ASP cc_start: 0.7254 (t70) cc_final: 0.6999 (t70) REVERT: A 724 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 747 GLU cc_start: 0.7357 (mp0) cc_final: 0.7073 (mp0) REVERT: A 763 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7858 (mtpp) REVERT: A 789 LYS cc_start: 0.8358 (mttp) cc_final: 0.8058 (mmtp) REVERT: A 810 LYS cc_start: 0.7601 (ptpt) cc_final: 0.6813 (ptpt) REVERT: A 813 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7857 (mmtm) REVERT: A 932 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7719 (mtpp) REVERT: A 978 ASP cc_start: 0.7792 (t0) cc_final: 0.7592 (t0) REVERT: A 1046 TYR cc_start: 0.8550 (m-80) cc_final: 0.8346 (m-10) REVERT: A 1090 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7478 (mtt-85) REVERT: A 1091 GLU cc_start: 0.7004 (pm20) cc_final: 0.6796 (pm20) REVERT: A 1106 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7624 (mtt180) REVERT: A 1110 GLU cc_start: 0.7814 (tt0) cc_final: 0.7599 (tt0) REVERT: B 269 TYR cc_start: 0.6973 (m-80) cc_final: 0.6702 (m-80) REVERT: B 278 LYS cc_start: 0.8780 (tttt) cc_final: 0.8385 (tttp) REVERT: B 309 GLU cc_start: 0.7681 (mp0) cc_final: 0.7473 (mp0) REVERT: B 313 TYR cc_start: 0.8182 (m-80) cc_final: 0.7737 (m-80) REVERT: B 317 ASN cc_start: 0.7746 (m-40) cc_final: 0.7493 (m-40) REVERT: B 321 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7672 (mm110) REVERT: B 324 GLU cc_start: 0.7601 (mp0) cc_final: 0.7045 (mp0) REVERT: B 582 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5754 (tm-30) REVERT: B 583 ILE cc_start: 0.6469 (tp) cc_final: 0.5707 (mt) REVERT: B 618 GLU cc_start: 0.7878 (tp30) cc_final: 0.7641 (tp30) REVERT: B 627 GLN cc_start: 0.7774 (mt0) cc_final: 0.7465 (mt0) REVERT: B 653 GLU cc_start: 0.8034 (pm20) cc_final: 0.7695 (pm20) REVERT: B 696 MET cc_start: 0.7946 (ttp) cc_final: 0.7530 (ptp) REVERT: B 772 GLU cc_start: 0.7373 (tt0) cc_final: 0.6901 (tt0) REVERT: B 775 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8150 (tttm) REVERT: B 778 GLN cc_start: 0.7929 (tp40) cc_final: 0.7588 (tm-30) REVERT: B 779 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7508 (tt0) REVERT: B 785 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7630 (mmtm) REVERT: B 789 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8073 (mtpp) REVERT: B 866 ASP cc_start: 0.7386 (p0) cc_final: 0.6606 (p0) REVERT: B 867 GLU cc_start: 0.7557 (mp0) cc_final: 0.6961 (mp0) REVERT: B 918 ASN cc_start: 0.7668 (m110) cc_final: 0.7460 (m110) REVERT: B 921 LEU cc_start: 0.8598 (tp) cc_final: 0.8379 (tt) REVERT: B 968 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8648 (mttm) REVERT: B 1018 ARG cc_start: 0.7730 (ttm110) cc_final: 0.7364 (ttp-170) REVERT: B 1040 ASP cc_start: 0.7632 (m-30) cc_final: 0.7413 (m-30) REVERT: B 1090 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7054 (ttm-80) REVERT: B 1112 GLN cc_start: 0.8106 (mt0) cc_final: 0.7880 (mm-40) REVERT: C 191 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7108 (mt-10) REVERT: C 269 TYR cc_start: 0.8434 (m-80) cc_final: 0.7967 (m-10) REVERT: C 278 LYS cc_start: 0.7863 (ttpm) cc_final: 0.7652 (ttpm) REVERT: C 314 GLN cc_start: 0.8032 (tp40) cc_final: 0.7773 (tp40) REVERT: C 317 ASN cc_start: 0.8151 (m-40) cc_final: 0.7883 (m-40) REVERT: C 328 ARG cc_start: 0.8114 (ttt90) cc_final: 0.7909 (tpt-90) REVERT: C 356 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8695 (p) REVERT: C 409 GLN cc_start: 0.7612 (mt0) cc_final: 0.6857 (mp10) REVERT: C 418 ILE cc_start: 0.6632 (mm) cc_final: 0.6223 (mm) REVERT: C 436 TRP cc_start: 0.5759 (p90) cc_final: 0.5301 (p90) REVERT: C 453 TYR cc_start: 0.7784 (p90) cc_final: 0.6586 (p90) REVERT: C 462 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7336 (mtmm) REVERT: C 528 LYS cc_start: 0.7993 (tptp) cc_final: 0.7615 (tptp) REVERT: C 529 SER cc_start: 0.8011 (t) cc_final: 0.7049 (m) REVERT: C 543 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7467 (m-40) REVERT: C 557 LYS cc_start: 0.8265 (mptt) cc_final: 0.7991 (mptt) REVERT: C 645 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7781 (mtm180) REVERT: C 674 GLN cc_start: 0.7292 (pp30) cc_final: 0.6970 (pp30) REVERT: C 720 SER cc_start: 0.8583 (t) cc_final: 0.8169 (p) REVERT: C 746 THR cc_start: 0.7708 (p) cc_final: 0.7322 (m) REVERT: C 749 SER cc_start: 0.8094 (t) cc_final: 0.7832 (m) REVERT: C 772 GLU cc_start: 0.7280 (tt0) cc_final: 0.6936 (tt0) REVERT: C 779 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7791 (mt-10) REVERT: C 783 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: C 789 LYS cc_start: 0.8318 (mppt) cc_final: 0.8114 (mtpt) REVERT: C 803 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8073 (mm-40) REVERT: C 868 MET cc_start: 0.7988 (mtt) cc_final: 0.7713 (mtp) REVERT: C 934 GLN cc_start: 0.7833 (mt0) cc_final: 0.7553 (tt0) REVERT: C 1044 LYS cc_start: 0.8027 (tptp) cc_final: 0.7731 (tptp) REVERT: C 1072 LYS cc_start: 0.7978 (tptp) cc_final: 0.7597 (tptp) REVERT: C 1083 ASP cc_start: 0.6950 (t0) cc_final: 0.6580 (t0) REVERT: C 1134 ASN cc_start: 0.6194 (t0) cc_final: 0.5846 (m110) REVERT: C 1135 THR cc_start: 0.7165 (m) cc_final: 0.6624 (p) outliers start: 65 outliers final: 35 residues processed: 593 average time/residue: 0.3903 time to fit residues: 357.3128 Evaluate side-chains 588 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 547 time to evaluate : 3.789 ------------------------------------------------------------------------------- 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 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 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 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 704 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 783 GLN 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 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: 10.0000 chunk 188 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN B 709 ASN C 709 ASN C 776 ASN C 783 GLN C1087 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.176660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145382 restraints weight = 36994.685| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.66 r_work: 0.3695 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24868 Z= 0.154 Angle : 0.599 14.523 33927 Z= 0.304 Chirality : 0.045 0.346 3912 Planarity : 0.004 0.058 4309 Dihedral : 6.407 59.675 3998 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.31 % Favored : 92.55 % Rotamer: Outliers : 2.75 % Allowed : 14.18 % Favored : 83.07 % 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: -1.43 (0.15), residues: 2981 helix: 1.07 (0.19), residues: 713 sheet: -0.81 (0.20), residues: 625 loop : -2.02 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.004 0.001 HIS C1082 PHE 0.022 0.001 PHE A 642 TYR 0.017 0.001 TYR B1066 ARG 0.010 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 30) link_NAG-ASN : angle 3.27597 ( 90) link_BETA1-4 : bond 0.00836 ( 6) link_BETA1-4 : angle 2.17123 ( 18) hydrogen bonds : bond 0.03929 ( 935) hydrogen bonds : angle 5.55456 ( 2589) SS BOND : bond 0.00436 ( 37) SS BOND : angle 2.06025 ( 74) covalent geometry : bond 0.00348 (24795) covalent geometry : angle 0.56615 (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 655 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 582 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6614 (m-80) cc_final: 0.6219 (m-80) REVERT: A 33 THR cc_start: 0.8179 (p) cc_final: 0.7929 (p) REVERT: A 116 SER cc_start: 0.7642 (m) cc_final: 0.7121 (p) REVERT: A 128 ILE cc_start: 0.7822 (mt) cc_final: 0.7578 (mp) REVERT: A 285 ILE cc_start: 0.8016 (mt) cc_final: 0.7243 (mm) REVERT: A 310 LYS cc_start: 0.8504 (tmmt) cc_final: 0.8302 (tmmt) REVERT: A 320 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8401 (m) REVERT: A 409 GLN cc_start: 0.7730 (tp-100) cc_final: 0.7528 (tp-100) REVERT: A 428 ASP cc_start: 0.7948 (p0) cc_final: 0.7669 (p0) REVERT: A 591 PHE cc_start: 0.8047 (p90) cc_final: 0.7733 (p90) REVERT: A 658 SER cc_start: 0.8560 (m) cc_final: 0.8109 (p) REVERT: A 696 MET cc_start: 0.7988 (ttm) cc_final: 0.7737 (ttm) REVERT: A 724 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7069 (tm-30) REVERT: A 747 GLU cc_start: 0.7349 (mp0) cc_final: 0.7082 (mp0) REVERT: A 789 LYS cc_start: 0.8396 (mttp) cc_final: 0.8092 (mmtp) REVERT: A 810 LYS cc_start: 0.7593 (ptpt) cc_final: 0.6932 (ptpt) REVERT: A 813 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7823 (mmtm) REVERT: A 859 VAL cc_start: 0.8604 (t) cc_final: 0.8400 (m) REVERT: A 932 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7713 (mtpp) REVERT: A 948 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: A 978 ASP cc_start: 0.7760 (t0) cc_final: 0.7540 (t0) REVERT: A 1033 LEU cc_start: 0.8585 (mp) cc_final: 0.8349 (mp) REVERT: A 1090 ARG cc_start: 0.7838 (mtt-85) cc_final: 0.7416 (mtt-85) REVERT: A 1091 GLU cc_start: 0.6994 (pm20) cc_final: 0.6684 (pm20) REVERT: A 1106 ARG cc_start: 0.7911 (ptp-170) cc_final: 0.7686 (mtt180) REVERT: A 1110 GLU cc_start: 0.7853 (tt0) cc_final: 0.7645 (tt0) REVERT: B 44 ARG cc_start: 0.7379 (mtt90) cc_final: 0.6664 (mtt90) REVERT: B 269 TYR cc_start: 0.6920 (m-80) cc_final: 0.6678 (m-80) REVERT: B 278 LYS cc_start: 0.8758 (tttt) cc_final: 0.8393 (tttp) REVERT: B 309 GLU cc_start: 0.7696 (mp0) cc_final: 0.7415 (mp0) REVERT: B 313 TYR cc_start: 0.8170 (m-80) cc_final: 0.7697 (m-80) REVERT: B 317 ASN cc_start: 0.7777 (m-40) cc_final: 0.7525 (m-40) REVERT: B 321 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7683 (mm110) REVERT: B 324 GLU cc_start: 0.7620 (mp0) cc_final: 0.7066 (mp0) REVERT: B 618 GLU cc_start: 0.7890 (tp30) cc_final: 0.7646 (tp30) REVERT: B 627 GLN cc_start: 0.7852 (mt0) cc_final: 0.7514 (mt0) REVERT: B 653 GLU cc_start: 0.8046 (pm20) cc_final: 0.7702 (pm20) REVERT: B 696 MET cc_start: 0.7979 (ttp) cc_final: 0.7740 (ptp) REVERT: B 724 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7000 (tm-30) REVERT: B 772 GLU cc_start: 0.7451 (tt0) cc_final: 0.7073 (tt0) REVERT: B 775 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8130 (tttm) REVERT: B 778 GLN cc_start: 0.7931 (tp40) cc_final: 0.7555 (tm-30) REVERT: B 785 LYS cc_start: 0.7977 (mmtm) cc_final: 0.7638 (mmtm) REVERT: B 789 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8102 (mtpp) REVERT: B 866 ASP cc_start: 0.7350 (p0) cc_final: 0.6580 (p0) REVERT: B 867 GLU cc_start: 0.7552 (mp0) cc_final: 0.6952 (mp0) REVERT: B 918 ASN cc_start: 0.7721 (m110) cc_final: 0.7503 (m110) REVERT: B 921 LEU cc_start: 0.8609 (tp) cc_final: 0.8385 (tt) REVERT: B 1112 GLN cc_start: 0.8064 (mt0) cc_final: 0.7820 (mm-40) REVERT: B 1134 ASN cc_start: 0.6733 (m110) cc_final: 0.6494 (m-40) REVERT: C 45 SER cc_start: 0.8322 (p) cc_final: 0.8101 (t) REVERT: C 55 PHE cc_start: 0.8356 (m-80) cc_final: 0.8126 (m-80) REVERT: C 240 THR cc_start: 0.7253 (OUTLIER) cc_final: 0.7043 (m) REVERT: C 269 TYR cc_start: 0.8455 (m-80) cc_final: 0.7976 (m-10) REVERT: C 271 GLN cc_start: 0.7808 (mt0) cc_final: 0.7551 (mt0) REVERT: C 278 LYS cc_start: 0.7872 (ttpm) cc_final: 0.7645 (ttpm) REVERT: C 314 GLN cc_start: 0.8020 (tp40) cc_final: 0.7790 (tp40) REVERT: C 356 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8698 (p) REVERT: C 409 GLN cc_start: 0.7648 (mt0) cc_final: 0.6933 (mp10) REVERT: C 418 ILE cc_start: 0.6805 (mm) cc_final: 0.6404 (mm) REVERT: C 436 TRP cc_start: 0.5699 (p90) cc_final: 0.5339 (p90) REVERT: C 453 TYR cc_start: 0.7712 (p90) cc_final: 0.7507 (p90) REVERT: C 492 GLN cc_start: 0.7313 (mp10) cc_final: 0.7098 (mp10) REVERT: C 528 LYS cc_start: 0.7985 (tptp) cc_final: 0.7623 (tptp) REVERT: C 529 SER cc_start: 0.7945 (t) cc_final: 0.7051 (m) REVERT: C 557 LYS cc_start: 0.8298 (mptt) cc_final: 0.8082 (mptt) REVERT: C 645 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7768 (mtm180) REVERT: C 674 GLN cc_start: 0.7316 (pp30) cc_final: 0.7033 (pp30) REVERT: C 720 SER cc_start: 0.8556 (t) cc_final: 0.8201 (p) REVERT: C 746 THR cc_start: 0.7781 (p) cc_final: 0.7458 (m) REVERT: C 749 SER cc_start: 0.8115 (t) cc_final: 0.7849 (m) REVERT: C 772 GLU cc_start: 0.7316 (tt0) cc_final: 0.7052 (tt0) REVERT: C 779 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7713 (mt-10) REVERT: C 783 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: C 803 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8156 (mm-40) REVERT: C 934 GLN cc_start: 0.7855 (mt0) cc_final: 0.7592 (tt0) REVERT: C 978 ASP cc_start: 0.7354 (m-30) cc_final: 0.7120 (m-30) REVERT: C 1044 LYS cc_start: 0.8024 (tptp) cc_final: 0.7704 (tptp) REVERT: C 1072 LYS cc_start: 0.7996 (tptp) cc_final: 0.7615 (tptp) REVERT: C 1134 ASN cc_start: 0.6194 (t0) cc_final: 0.5914 (m110) REVERT: C 1135 THR cc_start: 0.7186 (m) cc_final: 0.6666 (p) outliers start: 73 outliers final: 44 residues processed: 614 average time/residue: 0.4946 time to fit residues: 481.3651 Evaluate side-chains 604 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 555 time to evaluate : 3.572 ------------------------------------------------------------------------------- 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 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 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 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 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 B residue 1044 LYS Chi-restraints excluded: chain B residue 1135 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 240 THR 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 395 VAL 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 753 LEU Chi-restraints excluded: chain C residue 783 GLN 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: 0.5980 chunk 224 optimal weight: 2.9990 chunk 173 optimal weight: 0.2980 chunk 199 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 239 optimal weight: 30.0000 chunk 274 optimal weight: 0.5980 chunk 212 optimal weight: 0.0570 chunk 231 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 ASN B 643 GLN B 674 GLN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 709 ASN C 783 GLN C1087 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.177224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146153 restraints weight = 36817.188| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.66 r_work: 0.3707 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24868 Z= 0.124 Angle : 0.580 13.323 33927 Z= 0.294 Chirality : 0.045 0.338 3912 Planarity : 0.004 0.060 4309 Dihedral : 6.214 59.769 3998 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.88 % Favored : 92.99 % Rotamer: Outliers : 2.52 % Allowed : 15.58 % Favored : 81.90 % 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: -1.36 (0.15), residues: 2981 helix: 1.13 (0.19), residues: 716 sheet: -0.81 (0.20), residues: 620 loop : -1.95 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 452 HIS 0.002 0.000 HIS C1082 PHE 0.020 0.001 PHE B 135 TYR 0.026 0.001 TYR A 396 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00548 ( 30) link_NAG-ASN : angle 3.08097 ( 90) link_BETA1-4 : bond 0.00826 ( 6) link_BETA1-4 : angle 2.06633 ( 18) hydrogen bonds : bond 0.03754 ( 935) hydrogen bonds : angle 5.38992 ( 2589) SS BOND : bond 0.00377 ( 37) SS BOND : angle 1.94120 ( 74) covalent geometry : bond 0.00278 (24795) covalent geometry : angle 0.55006 (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 640 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 573 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6591 (m-80) cc_final: 0.6196 (m-80) REVERT: A 33 THR cc_start: 0.8183 (p) cc_final: 0.7922 (p) REVERT: A 116 SER cc_start: 0.7634 (m) cc_final: 0.7113 (p) REVERT: A 128 ILE cc_start: 0.7812 (mt) cc_final: 0.7570 (mp) REVERT: A 273 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7456 (ttm110) REVERT: A 285 ILE cc_start: 0.7999 (mt) cc_final: 0.7198 (mm) REVERT: A 297 SER cc_start: 0.7769 (m) cc_final: 0.7257 (t) REVERT: A 396 TYR cc_start: 0.6859 (m-80) cc_final: 0.6506 (m-80) REVERT: A 428 ASP cc_start: 0.7913 (p0) cc_final: 0.7615 (p0) REVERT: A 538 VAL cc_start: 0.8895 (t) cc_final: 0.8659 (p) REVERT: A 591 PHE cc_start: 0.8000 (p90) cc_final: 0.7659 (p90) REVERT: A 658 SER cc_start: 0.8554 (m) cc_final: 0.8067 (p) REVERT: A 696 MET cc_start: 0.8005 (ttm) cc_final: 0.7757 (ttm) REVERT: A 724 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7067 (tm-30) REVERT: A 747 GLU cc_start: 0.7336 (mp0) cc_final: 0.7096 (mp0) REVERT: A 789 LYS cc_start: 0.8397 (mttp) cc_final: 0.8101 (mmtp) REVERT: A 810 LYS cc_start: 0.7586 (ptpt) cc_final: 0.6937 (ptpt) REVERT: A 813 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7838 (mmtm) REVERT: A 932 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7664 (mtpp) REVERT: A 978 ASP cc_start: 0.7770 (t0) cc_final: 0.7538 (t0) REVERT: A 993 ASP cc_start: 0.7890 (t0) cc_final: 0.7646 (t0) REVERT: A 1004 GLN cc_start: 0.8028 (mt0) cc_final: 0.7827 (mt0) REVERT: A 1033 LEU cc_start: 0.8493 (mp) cc_final: 0.8264 (mp) REVERT: A 1090 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7429 (mtt-85) REVERT: A 1091 GLU cc_start: 0.7002 (pm20) cc_final: 0.6699 (pm20) REVERT: A 1110 GLU cc_start: 0.7823 (tt0) cc_final: 0.7603 (tt0) REVERT: A 1134 ASN cc_start: 0.7312 (m-40) cc_final: 0.7033 (m110) REVERT: B 44 ARG cc_start: 0.7408 (mtt90) cc_final: 0.6713 (mtt90) REVERT: B 269 TYR cc_start: 0.6926 (m-80) cc_final: 0.6694 (m-80) REVERT: B 278 LYS cc_start: 0.8773 (tttt) cc_final: 0.8402 (tttp) REVERT: B 309 GLU cc_start: 0.7680 (mp0) cc_final: 0.7433 (mp0) REVERT: B 313 TYR cc_start: 0.8159 (m-80) cc_final: 0.7694 (m-80) REVERT: B 317 ASN cc_start: 0.7776 (m-40) cc_final: 0.7506 (m-40) REVERT: B 321 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7664 (mm110) REVERT: B 324 GLU cc_start: 0.7608 (mp0) cc_final: 0.7046 (mp0) REVERT: B 618 GLU cc_start: 0.7908 (tp30) cc_final: 0.7661 (tp30) REVERT: B 627 GLN cc_start: 0.7841 (mt0) cc_final: 0.7466 (mt0) REVERT: B 653 GLU cc_start: 0.8027 (pm20) cc_final: 0.7666 (pm20) REVERT: B 696 MET cc_start: 0.8027 (ttp) cc_final: 0.7739 (ptp) REVERT: B 724 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6985 (tm-30) REVERT: B 772 GLU cc_start: 0.7460 (tt0) cc_final: 0.7008 (tt0) REVERT: B 775 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8158 (tttm) REVERT: B 778 GLN cc_start: 0.7923 (tp40) cc_final: 0.7609 (tm-30) REVERT: B 785 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7657 (mmtm) REVERT: B 789 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8131 (mtpp) REVERT: B 866 ASP cc_start: 0.7344 (p0) cc_final: 0.6571 (p0) REVERT: B 867 GLU cc_start: 0.7551 (mp0) cc_final: 0.6996 (mp0) REVERT: B 921 LEU cc_start: 0.8598 (tp) cc_final: 0.8368 (tt) REVERT: B 1018 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7425 (ttm110) REVERT: B 1112 GLN cc_start: 0.8081 (mt0) cc_final: 0.7828 (mm-40) REVERT: C 45 SER cc_start: 0.8314 (p) cc_final: 0.8096 (t) REVERT: C 55 PHE cc_start: 0.8358 (m-80) cc_final: 0.8100 (m-80) REVERT: C 264 ASP cc_start: 0.4259 (m-30) cc_final: 0.3909 (t0) REVERT: C 269 TYR cc_start: 0.8435 (m-80) cc_final: 0.7956 (m-10) REVERT: C 271 GLN cc_start: 0.7810 (mt0) cc_final: 0.7546 (mt0) REVERT: C 278 LYS cc_start: 0.7875 (ttpm) cc_final: 0.7657 (ttpm) REVERT: C 304 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7773 (mmmm) REVERT: C 314 GLN cc_start: 0.7986 (tp40) cc_final: 0.7758 (tp40) REVERT: C 317 ASN cc_start: 0.8029 (m-40) cc_final: 0.7766 (m-40) REVERT: C 356 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8684 (p) REVERT: C 409 GLN cc_start: 0.7635 (mt0) cc_final: 0.6928 (mp10) REVERT: C 418 ILE cc_start: 0.6828 (mm) cc_final: 0.6474 (mm) REVERT: C 436 TRP cc_start: 0.5642 (p90) cc_final: 0.5396 (p90) REVERT: C 645 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7778 (mtm180) REVERT: C 674 GLN cc_start: 0.7303 (pp30) cc_final: 0.7052 (pp30) REVERT: C 720 SER cc_start: 0.8605 (t) cc_final: 0.8215 (p) REVERT: C 746 THR cc_start: 0.7761 (p) cc_final: 0.7451 (m) REVERT: C 749 SER cc_start: 0.8141 (t) cc_final: 0.7869 (m) REVERT: C 779 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7678 (mt-10) REVERT: C 803 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8183 (mm-40) REVERT: C 934 GLN cc_start: 0.7865 (mt0) cc_final: 0.7630 (tt0) REVERT: C 978 ASP cc_start: 0.7340 (m-30) cc_final: 0.7113 (m-30) REVERT: C 1044 LYS cc_start: 0.7978 (tptp) cc_final: 0.7663 (tptp) REVERT: C 1072 LYS cc_start: 0.8009 (tptp) cc_final: 0.7624 (tptp) REVERT: C 1091 GLU cc_start: 0.7498 (pm20) cc_final: 0.7190 (pm20) REVERT: C 1134 ASN cc_start: 0.6195 (t0) cc_final: 0.5908 (m110) REVERT: C 1135 THR cc_start: 0.7171 (m) cc_final: 0.6673 (p) outliers start: 67 outliers final: 40 residues processed: 607 average time/residue: 0.4912 time to fit residues: 470.5704 Evaluate side-chains 602 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 561 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 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 790 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 975 VAL 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 297 SER 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 1135 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 339 HIS Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 524 CYS 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 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: 1.9990 chunk 206 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 143 optimal weight: 0.0000 chunk 248 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 165 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 321 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN B 674 GLN B 709 ASN B 918 ASN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN C 776 ASN C1087 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.175579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.144596 restraints weight = 36518.457| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.66 r_work: 0.3684 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24868 Z= 0.182 Angle : 0.607 12.937 33927 Z= 0.310 Chirality : 0.046 0.344 3912 Planarity : 0.005 0.066 4309 Dihedral : 6.237 59.500 3998 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.61 % Favored : 92.25 % Rotamer: Outliers : 3.09 % Allowed : 15.35 % Favored : 81.57 % 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: -1.38 (0.15), residues: 2981 helix: 1.07 (0.19), residues: 713 sheet: -0.80 (0.20), residues: 616 loop : -1.94 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 64 HIS 0.004 0.001 HIS C1082 PHE 0.022 0.002 PHE B 220 TYR 0.022 0.001 TYR C 453 ARG 0.004 0.000 ARG B 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 30) link_NAG-ASN : angle 3.08895 ( 90) link_BETA1-4 : bond 0.00825 ( 6) link_BETA1-4 : angle 2.06928 ( 18) hydrogen bonds : bond 0.04014 ( 935) hydrogen bonds : angle 5.44716 ( 2589) SS BOND : bond 0.00426 ( 37) SS BOND : angle 2.03023 ( 74) covalent geometry : bond 0.00414 (24795) covalent geometry : angle 0.57755 (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 658 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 576 time to evaluate : 3.636 Fit side-chains revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6593 (m-80) cc_final: 0.6290 (m-80) REVERT: A 33 THR cc_start: 0.8300 (p) cc_final: 0.8044 (p) REVERT: A 116 SER cc_start: 0.7713 (m) cc_final: 0.7230 (p) REVERT: A 128 ILE cc_start: 0.7841 (mt) cc_final: 0.7594 (mp) REVERT: A 285 ILE cc_start: 0.8029 (mt) cc_final: 0.7823 (mt) REVERT: A 297 SER cc_start: 0.7828 (m) cc_final: 0.7257 (t) REVERT: A 320 VAL cc_start: 0.8447 (m) cc_final: 0.8246 (p) REVERT: A 355 ARG cc_start: 0.8494 (ttt90) cc_final: 0.7925 (ttt90) REVERT: A 396 TYR cc_start: 0.6979 (m-80) cc_final: 0.6548 (m-80) REVERT: A 428 ASP cc_start: 0.7960 (p0) cc_final: 0.7643 (p0) REVERT: A 537 CYS cc_start: 0.6234 (m) cc_final: 0.5930 (m) REVERT: A 591 PHE cc_start: 0.8112 (p90) cc_final: 0.7772 (p90) REVERT: A 658 SER cc_start: 0.8585 (m) cc_final: 0.8103 (p) REVERT: A 696 MET cc_start: 0.7953 (ttm) cc_final: 0.7663 (ttm) REVERT: A 724 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 747 GLU cc_start: 0.7333 (mp0) cc_final: 0.7080 (mp0) REVERT: A 789 LYS cc_start: 0.8427 (mttp) cc_final: 0.8130 (mmtp) REVERT: A 810 LYS cc_start: 0.7589 (ptpt) cc_final: 0.6960 (ptpt) REVERT: A 868 MET cc_start: 0.8281 (mtt) cc_final: 0.7988 (mtm) REVERT: A 932 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7730 (mtpp) REVERT: A 978 ASP cc_start: 0.7737 (t0) cc_final: 0.7501 (t0) REVERT: A 993 ASP cc_start: 0.7917 (t0) cc_final: 0.7663 (t0) REVERT: A 1033 LEU cc_start: 0.8621 (mp) cc_final: 0.8407 (mp) REVERT: A 1110 GLU cc_start: 0.7889 (tt0) cc_final: 0.7687 (tt0) REVERT: A 1134 ASN cc_start: 0.7356 (m-40) cc_final: 0.7021 (m-40) REVERT: B 45 SER cc_start: 0.7789 (p) cc_final: 0.7572 (t) REVERT: B 125 ASN cc_start: 0.7169 (t0) cc_final: 0.6932 (t0) REVERT: B 269 TYR cc_start: 0.6948 (m-80) cc_final: 0.6717 (m-80) REVERT: B 278 LYS cc_start: 0.8755 (tttt) cc_final: 0.8384 (tttp) REVERT: B 309 GLU cc_start: 0.7684 (mp0) cc_final: 0.7384 (mp0) REVERT: B 313 TYR cc_start: 0.8168 (m-80) cc_final: 0.7713 (m-80) REVERT: B 317 ASN cc_start: 0.7772 (m-40) cc_final: 0.7543 (m-40) REVERT: B 321 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7665 (mm-40) REVERT: B 324 GLU cc_start: 0.7674 (mp0) cc_final: 0.7098 (mp0) REVERT: B 557 LYS cc_start: 0.8493 (mppt) cc_final: 0.7971 (mppt) REVERT: B 618 GLU cc_start: 0.7883 (tp30) cc_final: 0.7625 (tp30) REVERT: B 627 GLN cc_start: 0.7847 (mt0) cc_final: 0.7439 (mt0) REVERT: B 653 GLU cc_start: 0.8106 (pm20) cc_final: 0.7779 (pm20) REVERT: B 724 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6969 (tm-30) REVERT: B 772 GLU cc_start: 0.7499 (tt0) cc_final: 0.7106 (tt0) REVERT: B 775 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8156 (tttm) REVERT: B 778 GLN cc_start: 0.7921 (tp40) cc_final: 0.7642 (tm-30) REVERT: B 789 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8181 (mtpp) REVERT: B 854 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6724 (t80) REVERT: B 866 ASP cc_start: 0.7342 (p0) cc_final: 0.6561 (p0) REVERT: B 867 GLU cc_start: 0.7562 (mp0) cc_final: 0.7008 (mp0) REVERT: B 921 LEU cc_start: 0.8603 (tp) cc_final: 0.8360 (tt) REVERT: B 1112 GLN cc_start: 0.8077 (mt0) cc_final: 0.7820 (mm-40) REVERT: C 55 PHE cc_start: 0.8400 (m-80) cc_final: 0.8194 (m-80) REVERT: C 240 THR cc_start: 0.7225 (OUTLIER) cc_final: 0.6633 (t) REVERT: C 269 TYR cc_start: 0.8460 (m-10) cc_final: 0.8041 (m-10) REVERT: C 271 GLN cc_start: 0.7804 (mt0) cc_final: 0.7572 (mt0) REVERT: C 278 LYS cc_start: 0.7885 (ttpm) cc_final: 0.7657 (ttpm) REVERT: C 317 ASN cc_start: 0.8061 (m-40) cc_final: 0.7757 (m-40) REVERT: C 356 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 390 LEU cc_start: 0.7936 (mm) cc_final: 0.7694 (mt) REVERT: C 409 GLN cc_start: 0.7694 (mt0) cc_final: 0.7100 (mp10) REVERT: C 418 ILE cc_start: 0.7140 (mm) cc_final: 0.6826 (mm) REVERT: C 576 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6955 (ptt180) REVERT: C 618 GLU cc_start: 0.7594 (tp30) cc_final: 0.7391 (tp30) REVERT: C 674 GLN cc_start: 0.7302 (pp30) cc_final: 0.7078 (pp30) REVERT: C 720 SER cc_start: 0.8599 (t) cc_final: 0.8213 (p) REVERT: C 746 THR cc_start: 0.7869 (p) cc_final: 0.7536 (m) REVERT: C 749 SER cc_start: 0.8178 (t) cc_final: 0.7903 (m) REVERT: C 750 ASN cc_start: 0.7425 (m-40) cc_final: 0.7223 (m-40) REVERT: C 772 GLU cc_start: 0.7435 (tt0) cc_final: 0.7170 (tt0) REVERT: C 779 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7700 (mt-10) REVERT: C 803 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8189 (mm-40) REVERT: C 934 GLN cc_start: 0.7833 (mt0) cc_final: 0.7615 (tt0) REVERT: C 978 ASP cc_start: 0.7359 (m-30) cc_final: 0.7132 (m-30) REVERT: C 1044 LYS cc_start: 0.8034 (tptp) cc_final: 0.7715 (tptp) REVERT: C 1072 LYS cc_start: 0.7958 (tptp) cc_final: 0.7625 (tptp) REVERT: C 1083 ASP cc_start: 0.6935 (t0) cc_final: 0.6552 (t0) REVERT: C 1091 GLU cc_start: 0.7458 (pm20) cc_final: 0.7169 (pm20) REVERT: C 1134 ASN cc_start: 0.6358 (t0) cc_final: 0.6107 (m110) REVERT: C 1135 THR cc_start: 0.7257 (m) cc_final: 0.6743 (p) outliers start: 82 outliers final: 57 residues processed: 605 average time/residue: 0.4177 time to fit residues: 394.7956 Evaluate side-chains 625 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 564 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 901 MET 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 A residue 1071 GLU Chi-restraints excluded: chain A residue 1128 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 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 899 MET Chi-restraints excluded: chain B residue 975 VAL Chi-restraints excluded: chain B residue 1135 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 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL 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 395 VAL 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 581 LEU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 150 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 186 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN C 783 GLN C1087 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.174772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.143630 restraints weight = 36631.567| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.65 r_work: 0.3670 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24868 Z= 0.197 Angle : 0.621 12.890 33927 Z= 0.316 Chirality : 0.046 0.355 3912 Planarity : 0.005 0.064 4309 Dihedral : 6.249 58.931 3998 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 3.76 % Allowed : 15.73 % Favored : 80.51 % 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: -1.39 (0.15), residues: 2981 helix: 1.04 (0.19), residues: 708 sheet: -0.74 (0.20), residues: 601 loop : -1.95 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.004 0.001 HIS C1082 PHE 0.022 0.002 PHE B 220 TYR 0.031 0.001 TYR C 453 ARG 0.010 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 30) link_NAG-ASN : angle 3.11572 ( 90) link_BETA1-4 : bond 0.00811 ( 6) link_BETA1-4 : angle 2.05480 ( 18) hydrogen bonds : bond 0.04060 ( 935) hydrogen bonds : angle 5.47633 ( 2589) SS BOND : bond 0.00425 ( 37) SS BOND : angle 2.20866 ( 74) covalent geometry : bond 0.00448 (24795) covalent geometry : angle 0.59073 (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 680 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 580 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6549 (m-80) cc_final: 0.6248 (m-80) REVERT: A 33 THR cc_start: 0.8370 (p) cc_final: 0.8102 (p) REVERT: A 87 ASN cc_start: 0.7333 (m-40) cc_final: 0.6532 (m-40) REVERT: A 116 SER cc_start: 0.7758 (m) cc_final: 0.7287 (p) REVERT: A 128 ILE cc_start: 0.7848 (mt) cc_final: 0.7595 (mp) REVERT: A 285 ILE cc_start: 0.8002 (mt) cc_final: 0.7802 (mt) REVERT: A 396 TYR cc_start: 0.6943 (m-80) cc_final: 0.6616 (m-80) REVERT: A 591 PHE cc_start: 0.8153 (p90) cc_final: 0.7832 (p90) REVERT: A 658 SER cc_start: 0.8600 (m) cc_final: 0.8109 (p) REVERT: A 696 MET cc_start: 0.8024 (ttm) cc_final: 0.7717 (ttm) REVERT: A 724 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 747 GLU cc_start: 0.7345 (mp0) cc_final: 0.7096 (mp0) REVERT: A 789 LYS cc_start: 0.8459 (mttp) cc_final: 0.8169 (mmtp) REVERT: A 810 LYS cc_start: 0.7568 (ptpt) cc_final: 0.6986 (ptpt) REVERT: A 867 GLU cc_start: 0.7136 (mp0) cc_final: 0.6736 (mp0) REVERT: A 978 ASP cc_start: 0.7714 (t0) cc_final: 0.7478 (t0) REVERT: A 993 ASP cc_start: 0.7923 (t0) cc_final: 0.7660 (t0) REVERT: A 1033 LEU cc_start: 0.8553 (mp) cc_final: 0.8309 (mp) REVERT: A 1134 ASN cc_start: 0.7386 (m-40) cc_final: 0.7143 (m110) REVERT: B 44 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7195 (mtm-85) REVERT: B 278 LYS cc_start: 0.8763 (tttt) cc_final: 0.8543 (tttt) REVERT: B 309 GLU cc_start: 0.7668 (mp0) cc_final: 0.7448 (mp0) REVERT: B 313 TYR cc_start: 0.8186 (m-80) cc_final: 0.7771 (m-80) REVERT: B 317 ASN cc_start: 0.7719 (m-40) cc_final: 0.7455 (m-40) REVERT: B 321 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7617 (mm110) REVERT: B 324 GLU cc_start: 0.7669 (mp0) cc_final: 0.7070 (mp0) REVERT: B 557 LYS cc_start: 0.8502 (mppt) cc_final: 0.7984 (mppt) REVERT: B 618 GLU cc_start: 0.7860 (tp30) cc_final: 0.7618 (tp30) REVERT: B 627 GLN cc_start: 0.7841 (mt0) cc_final: 0.7419 (mt0) REVERT: B 653 GLU cc_start: 0.8117 (pm20) cc_final: 0.7821 (pm20) REVERT: B 724 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6982 (tm-30) REVERT: B 761 GLN cc_start: 0.7581 (mt0) cc_final: 0.7259 (mt0) REVERT: B 772 GLU cc_start: 0.7515 (tt0) cc_final: 0.7085 (tt0) REVERT: B 778 GLN cc_start: 0.7916 (tp40) cc_final: 0.7672 (tm-30) REVERT: B 789 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8176 (mtpp) REVERT: B 854 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 866 ASP cc_start: 0.7360 (p0) cc_final: 0.6593 (p0) REVERT: B 867 GLU cc_start: 0.7596 (mp0) cc_final: 0.7029 (mp0) REVERT: B 901 MET cc_start: 0.8111 (tpt) cc_final: 0.7833 (mmt) REVERT: B 921 LEU cc_start: 0.8603 (tp) cc_final: 0.8359 (tt) REVERT: B 994 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7941 (mtm180) REVERT: B 1018 ARG cc_start: 0.7823 (ttm110) cc_final: 0.7414 (ttm110) REVERT: B 1027 LYS cc_start: 0.8489 (mttm) cc_final: 0.7887 (mttm) REVERT: B 1044 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7828 (tptp) REVERT: B 1112 GLN cc_start: 0.8049 (mt0) cc_final: 0.7816 (mm-40) REVERT: C 55 PHE cc_start: 0.8406 (m-80) cc_final: 0.8201 (m-80) REVERT: C 269 TYR cc_start: 0.8464 (m-10) cc_final: 0.8066 (m-10) REVERT: C 271 GLN cc_start: 0.7784 (mt0) cc_final: 0.7532 (mt0) REVERT: C 278 LYS cc_start: 0.7910 (ttpm) cc_final: 0.7690 (ttpm) REVERT: C 317 ASN cc_start: 0.8024 (m-40) cc_final: 0.7704 (m-40) REVERT: C 356 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8676 (p) REVERT: C 390 LEU cc_start: 0.7939 (mm) cc_final: 0.7707 (mt) REVERT: C 409 GLN cc_start: 0.7686 (mt0) cc_final: 0.7125 (mp10) REVERT: C 418 ILE cc_start: 0.7264 (mm) cc_final: 0.6922 (mm) REVERT: C 576 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7005 (ptt180) REVERT: C 618 GLU cc_start: 0.7645 (tp30) cc_final: 0.7437 (tp30) REVERT: C 674 GLN cc_start: 0.7302 (pp30) cc_final: 0.7097 (pp30) REVERT: C 720 SER cc_start: 0.8616 (t) cc_final: 0.8224 (p) REVERT: C 746 THR cc_start: 0.7907 (p) cc_final: 0.7590 (m) REVERT: C 749 SER cc_start: 0.8221 (t) cc_final: 0.7944 (m) REVERT: C 750 ASN cc_start: 0.7476 (m-40) cc_final: 0.7269 (m-40) REVERT: C 772 GLU cc_start: 0.7391 (tt0) cc_final: 0.7135 (tt0) REVERT: C 779 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7786 (mt-10) REVERT: C 803 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8217 (mm-40) REVERT: C 883 SER cc_start: 0.8276 (m) cc_final: 0.7956 (p) REVERT: C 934 GLN cc_start: 0.7844 (mt0) cc_final: 0.7619 (tt0) REVERT: C 978 ASP cc_start: 0.7368 (m-30) cc_final: 0.7148 (m-30) REVERT: C 1044 LYS cc_start: 0.8047 (tptp) cc_final: 0.7711 (tptp) REVERT: C 1072 LYS cc_start: 0.8000 (tptp) cc_final: 0.7678 (tptp) REVERT: C 1091 GLU cc_start: 0.7422 (pm20) cc_final: 0.7145 (pm20) REVERT: C 1134 ASN cc_start: 0.6424 (t0) cc_final: 0.6224 (m110) REVERT: C 1135 THR cc_start: 0.7290 (m) cc_final: 0.6798 (p) outliers start: 100 outliers final: 67 residues processed: 621 average time/residue: 0.5586 time to fit residues: 546.2106 Evaluate side-chains 636 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 565 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 129 LYS 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 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 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 962 VAL 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 52 GLN 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 992 ILE Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 THR 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 305 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR 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 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 576 ARG Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 704 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 40.0000 chunk 203 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN B 948 GLN C 394 ASN C 543 ASN C 709 ASN C 783 GLN C1087 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144757 restraints weight = 36415.726| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.64 r_work: 0.3678 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3275 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= 0.158 Angle : 0.606 12.283 33927 Z= 0.308 Chirality : 0.045 0.347 3912 Planarity : 0.005 0.060 4309 Dihedral : 6.134 59.807 3996 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.08 % Rotamer: Outliers : 3.09 % Allowed : 16.33 % Favored : 80.59 % 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: 1.14 (0.19), residues: 708 sheet: -0.72 (0.19), residues: 619 loop : -1.97 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.002 0.001 HIS C1082 PHE 0.025 0.001 PHE B 220 TYR 0.028 0.001 TYR C 453 ARG 0.010 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 30) link_NAG-ASN : angle 2.97171 ( 90) link_BETA1-4 : bond 0.00785 ( 6) link_BETA1-4 : angle 1.98102 ( 18) hydrogen bonds : bond 0.03892 ( 935) hydrogen bonds : angle 5.41004 ( 2589) SS BOND : bond 0.00369 ( 37) SS BOND : angle 1.90777 ( 74) covalent geometry : bond 0.00359 (24795) covalent geometry : angle 0.57917 (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 657 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 575 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8375 (p) cc_final: 0.8105 (p) REVERT: A 87 ASN cc_start: 0.7271 (m-40) cc_final: 0.6474 (m-40) REVERT: A 116 SER cc_start: 0.7779 (m) cc_final: 0.7322 (p) REVERT: A 226 LEU cc_start: 0.8344 (tt) cc_final: 0.8109 (tt) REVERT: A 355 ARG cc_start: 0.8483 (ttt90) cc_final: 0.8202 (ttt90) REVERT: A 591 PHE cc_start: 0.8174 (p90) cc_final: 0.7894 (p90) REVERT: A 658 SER cc_start: 0.8598 (m) cc_final: 0.8089 (p) REVERT: A 696 MET cc_start: 0.7986 (ttm) cc_final: 0.7713 (ttm) REVERT: A 724 GLU cc_start: 0.7431 (tm-30) cc_final: 0.6915 (tm-30) REVERT: A 747 GLU cc_start: 0.7279 (mp0) cc_final: 0.7043 (mp0) REVERT: A 789 LYS cc_start: 0.8459 (mttp) cc_final: 0.8165 (mmtp) REVERT: A 978 ASP cc_start: 0.7722 (t0) cc_final: 0.7475 (t0) REVERT: A 993 ASP cc_start: 0.7917 (t0) cc_final: 0.7651 (t0) REVERT: A 1033 LEU cc_start: 0.8589 (mp) cc_final: 0.8352 (mp) REVERT: A 1134 ASN cc_start: 0.7396 (m-40) cc_final: 0.7144 (m110) REVERT: B 44 ARG cc_start: 0.7466 (mtt90) cc_final: 0.7201 (mtm-85) REVERT: B 53 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: B 125 ASN cc_start: 0.7130 (t0) cc_final: 0.6858 (t0) REVERT: B 278 LYS cc_start: 0.8735 (tttt) cc_final: 0.8506 (tttt) REVERT: B 313 TYR cc_start: 0.8154 (m-80) cc_final: 0.7708 (m-80) REVERT: B 317 ASN cc_start: 0.7671 (m-40) cc_final: 0.7404 (m-40) REVERT: B 321 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7592 (mm110) REVERT: B 324 GLU cc_start: 0.7683 (mp0) cc_final: 0.7078 (mp0) REVERT: B 557 LYS cc_start: 0.8489 (mppt) cc_final: 0.7961 (mppt) REVERT: B 618 GLU cc_start: 0.7884 (tp30) cc_final: 0.7636 (tp30) REVERT: B 627 GLN cc_start: 0.7827 (mt0) cc_final: 0.7390 (mt0) REVERT: B 653 GLU cc_start: 0.8104 (pm20) cc_final: 0.7803 (pm20) REVERT: B 724 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6970 (tm-30) REVERT: B 744 ASP cc_start: 0.6999 (m-30) cc_final: 0.6625 (m-30) REVERT: B 772 GLU cc_start: 0.7512 (tt0) cc_final: 0.7072 (tt0) REVERT: B 778 GLN cc_start: 0.7908 (tp40) cc_final: 0.7672 (tm-30) REVERT: B 789 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8152 (mtpp) REVERT: B 854 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6768 (t80) REVERT: B 866 ASP cc_start: 0.7353 (p0) cc_final: 0.6586 (p0) REVERT: B 867 GLU cc_start: 0.7598 (mp0) cc_final: 0.7049 (mp0) REVERT: B 901 MET cc_start: 0.8102 (tpt) cc_final: 0.7896 (mmt) REVERT: B 921 LEU cc_start: 0.8589 (tp) cc_final: 0.8341 (tt) REVERT: B 994 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7947 (mtm180) REVERT: B 1018 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7388 (ttm110) REVERT: B 1027 LYS cc_start: 0.8468 (mttm) cc_final: 0.8025 (mttm) REVERT: B 1044 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7793 (tptp) REVERT: B 1112 GLN cc_start: 0.8073 (mt0) cc_final: 0.7823 (mm-40) REVERT: C 55 PHE cc_start: 0.8400 (m-80) cc_final: 0.8124 (m-80) REVERT: C 269 TYR cc_start: 0.8435 (m-10) cc_final: 0.8049 (m-10) REVERT: C 271 GLN cc_start: 0.7771 (mt0) cc_final: 0.7514 (mt0) REVERT: C 278 LYS cc_start: 0.7899 (ttpm) cc_final: 0.7650 (ttpm) REVERT: C 317 ASN cc_start: 0.7998 (m-40) cc_final: 0.7669 (m-40) REVERT: C 356 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8651 (p) REVERT: C 390 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7634 (mt) REVERT: C 409 GLN cc_start: 0.7636 (mt0) cc_final: 0.7130 (mp10) REVERT: C 418 ILE cc_start: 0.7285 (mm) cc_final: 0.6952 (mm) REVERT: C 576 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6998 (ptt180) REVERT: C 618 GLU cc_start: 0.7615 (tp30) cc_final: 0.7386 (tp30) REVERT: C 645 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7849 (mtt90) REVERT: C 720 SER cc_start: 0.8595 (t) cc_final: 0.8219 (p) REVERT: C 746 THR cc_start: 0.7880 (p) cc_final: 0.7561 (m) REVERT: C 749 SER cc_start: 0.8222 (t) cc_final: 0.7934 (m) REVERT: C 750 ASN cc_start: 0.7440 (m-40) cc_final: 0.7237 (m-40) REVERT: C 772 GLU cc_start: 0.7394 (tt0) cc_final: 0.7000 (tt0) REVERT: C 779 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7745 (mt-10) REVERT: C 803 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8204 (mm-40) REVERT: C 883 SER cc_start: 0.8255 (m) cc_final: 0.7982 (p) REVERT: C 934 GLN cc_start: 0.7840 (mt0) cc_final: 0.7624 (tt0) REVERT: C 978 ASP cc_start: 0.7372 (m-30) cc_final: 0.7153 (m-30) REVERT: C 1044 LYS cc_start: 0.8018 (tptp) cc_final: 0.7711 (tptp) REVERT: C 1072 LYS cc_start: 0.7992 (tptp) cc_final: 0.7620 (tptp) REVERT: C 1091 GLU cc_start: 0.7462 (pm20) cc_final: 0.7188 (pm20) REVERT: C 1135 THR cc_start: 0.7277 (m) cc_final: 0.6797 (p) outliers start: 82 outliers final: 67 residues processed: 605 average time/residue: 0.3770 time to fit residues: 356.5846 Evaluate side-chains 635 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 562 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN 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 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 915 LEU Chi-restraints excluded: chain A residue 962 VAL 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 1113 ILE 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 52 GLN 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 1135 THR 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 294 ASP Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 25 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 295 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 948 GLN C 394 ASN C 543 ASN C 709 ASN C 783 GLN C1087 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.174326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143234 restraints weight = 36604.804| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.65 r_work: 0.3671 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3431 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= 0.205 Angle : 0.644 12.170 33927 Z= 0.328 Chirality : 0.047 0.359 3912 Planarity : 0.005 0.058 4309 Dihedral : 6.197 58.267 3996 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 3.24 % Allowed : 16.89 % Favored : 79.87 % 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: -1.37 (0.15), residues: 2981 helix: 1.06 (0.19), residues: 708 sheet: -0.67 (0.20), residues: 603 loop : -1.96 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 436 HIS 0.004 0.001 HIS C1082 PHE 0.030 0.002 PHE C 540 TYR 0.034 0.002 TYR C 453 ARG 0.009 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 30) link_NAG-ASN : angle 3.05979 ( 90) link_BETA1-4 : bond 0.00854 ( 6) link_BETA1-4 : angle 2.04037 ( 18) hydrogen bonds : bond 0.04134 ( 935) hydrogen bonds : angle 5.48584 ( 2589) SS BOND : bond 0.00479 ( 37) SS BOND : angle 2.07394 ( 74) covalent geometry : bond 0.00466 (24795) covalent geometry : angle 0.61686 (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 659 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 573 time to evaluate : 2.553 Fit side-chains revert: symmetry clash REVERT: A 33 THR cc_start: 0.8396 (p) cc_final: 0.8134 (p) REVERT: A 116 SER cc_start: 0.7856 (m) cc_final: 0.7430 (p) REVERT: A 128 ILE cc_start: 0.7831 (mt) cc_final: 0.7589 (mp) REVERT: A 226 LEU cc_start: 0.8384 (tt) cc_final: 0.8165 (tt) REVERT: A 591 PHE cc_start: 0.8183 (p90) cc_final: 0.7902 (p90) REVERT: A 595 SER cc_start: 0.8503 (m) cc_final: 0.8155 (p) REVERT: A 658 SER cc_start: 0.8639 (m) cc_final: 0.8152 (p) REVERT: A 696 MET cc_start: 0.7966 (ttm) cc_final: 0.7704 (ttm) REVERT: A 724 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 747 GLU cc_start: 0.7312 (mp0) cc_final: 0.7036 (mp0) REVERT: A 789 LYS cc_start: 0.8449 (mttp) cc_final: 0.8104 (mmtp) REVERT: A 868 MET cc_start: 0.8259 (mtt) cc_final: 0.7969 (mtm) REVERT: A 882 THR cc_start: 0.8163 (m) cc_final: 0.7840 (m) REVERT: A 978 ASP cc_start: 0.7755 (t0) cc_final: 0.7507 (t0) REVERT: A 993 ASP cc_start: 0.7930 (t0) cc_final: 0.7650 (t0) REVERT: A 1033 LEU cc_start: 0.8579 (mp) cc_final: 0.8355 (mp) REVERT: A 1134 ASN cc_start: 0.7406 (m-40) cc_final: 0.7180 (m110) REVERT: B 53 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: B 278 LYS cc_start: 0.8762 (tttt) cc_final: 0.8530 (tttt) REVERT: B 313 TYR cc_start: 0.8161 (m-80) cc_final: 0.7755 (m-80) REVERT: B 317 ASN cc_start: 0.7675 (m-40) cc_final: 0.7406 (m-40) REVERT: B 321 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7589 (mm110) REVERT: B 324 GLU cc_start: 0.7694 (mp0) cc_final: 0.7057 (mp0) REVERT: B 557 LYS cc_start: 0.8493 (mppt) cc_final: 0.7971 (mppt) REVERT: B 618 GLU cc_start: 0.7883 (tp30) cc_final: 0.7629 (tp30) REVERT: B 627 GLN cc_start: 0.7845 (mt0) cc_final: 0.7418 (mt0) REVERT: B 653 GLU cc_start: 0.8162 (pm20) cc_final: 0.7862 (pm20) REVERT: B 744 ASP cc_start: 0.7008 (m-30) cc_final: 0.6635 (m-30) REVERT: B 761 GLN cc_start: 0.7606 (mt0) cc_final: 0.7280 (mt0) REVERT: B 772 GLU cc_start: 0.7538 (tt0) cc_final: 0.7100 (tt0) REVERT: B 778 GLN cc_start: 0.7907 (tp40) cc_final: 0.7681 (tm-30) REVERT: B 789 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8182 (mtpp) REVERT: B 854 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6747 (t80) REVERT: B 866 ASP cc_start: 0.7336 (p0) cc_final: 0.6592 (p0) REVERT: B 867 GLU cc_start: 0.7618 (mp0) cc_final: 0.7084 (mp0) REVERT: B 901 MET cc_start: 0.8057 (tpt) cc_final: 0.7838 (mmt) REVERT: B 921 LEU cc_start: 0.8586 (tp) cc_final: 0.8343 (tt) REVERT: B 994 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7961 (mtm180) REVERT: B 1018 ARG cc_start: 0.7807 (ttm110) cc_final: 0.7389 (ttm110) REVERT: B 1027 LYS cc_start: 0.8478 (mttm) cc_final: 0.7982 (mttm) REVERT: B 1044 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7805 (tptp) REVERT: B 1112 GLN cc_start: 0.8083 (mt0) cc_final: 0.7734 (mm-40) REVERT: C 52 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 55 PHE cc_start: 0.8417 (m-80) cc_final: 0.8145 (m-80) REVERT: C 269 TYR cc_start: 0.8445 (m-10) cc_final: 0.8080 (m-10) REVERT: C 271 GLN cc_start: 0.7766 (mt0) cc_final: 0.7508 (mt0) REVERT: C 278 LYS cc_start: 0.7886 (ttpm) cc_final: 0.7662 (ttpm) REVERT: C 314 GLN cc_start: 0.8009 (tp40) cc_final: 0.7807 (tp40) REVERT: C 317 ASN cc_start: 0.8071 (m-40) cc_final: 0.7737 (m-40) REVERT: C 356 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8630 (p) REVERT: C 409 GLN cc_start: 0.7651 (mt0) cc_final: 0.7160 (mp10) REVERT: C 418 ILE cc_start: 0.7392 (mm) cc_final: 0.7020 (mm) REVERT: C 555 ASN cc_start: 0.7680 (p0) cc_final: 0.7393 (p0) REVERT: C 576 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7049 (ptt180) REVERT: C 618 GLU cc_start: 0.7610 (tp30) cc_final: 0.7394 (tp30) REVERT: C 645 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7832 (mtt90) REVERT: C 720 SER cc_start: 0.8581 (t) cc_final: 0.8180 (p) REVERT: C 746 THR cc_start: 0.7960 (p) cc_final: 0.7678 (m) REVERT: C 749 SER cc_start: 0.8224 (t) cc_final: 0.7957 (m) REVERT: C 772 GLU cc_start: 0.7436 (tt0) cc_final: 0.7049 (tt0) REVERT: C 779 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 803 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8199 (mm-40) REVERT: C 883 SER cc_start: 0.8250 (m) cc_final: 0.7977 (p) REVERT: C 934 GLN cc_start: 0.7846 (mt0) cc_final: 0.7628 (tt0) REVERT: C 978 ASP cc_start: 0.7391 (m-30) cc_final: 0.7187 (m-30) REVERT: C 1044 LYS cc_start: 0.8096 (tptp) cc_final: 0.7783 (tptp) REVERT: C 1072 LYS cc_start: 0.8034 (tptp) cc_final: 0.7652 (tptp) REVERT: C 1083 ASP cc_start: 0.6733 (t0) cc_final: 0.6330 (t0) REVERT: C 1091 GLU cc_start: 0.7407 (pm20) cc_final: 0.7149 (pm20) REVERT: C 1135 THR cc_start: 0.7015 (m) cc_final: 0.6793 (p) outliers start: 86 outliers final: 68 residues processed: 604 average time/residue: 0.3632 time to fit residues: 340.2966 Evaluate side-chains 637 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 564 time to evaluate : 2.526 ------------------------------------------------------------------------------- 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 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 915 LEU Chi-restraints excluded: chain A residue 962 VAL 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 52 GLN 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 1044 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 THR 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 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 323 THR 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 524 CYS Chi-restraints excluded: chain C residue 529 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 182 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 236 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN A 855 ASN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN B 948 GLN B1004 GLN C 709 ASN C 783 GLN C1087 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.175122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144078 restraints weight = 36560.161| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.66 r_work: 0.3684 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24868 Z= 0.158 Angle : 0.621 11.866 33927 Z= 0.314 Chirality : 0.045 0.349 3912 Planarity : 0.005 0.058 4309 Dihedral : 6.117 59.455 3996 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.51 % Favored : 92.39 % Rotamer: Outliers : 2.63 % Allowed : 17.83 % Favored : 79.53 % 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: 1.16 (0.19), residues: 708 sheet: -0.67 (0.20), residues: 617 loop : -1.95 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.002 0.001 HIS B 207 PHE 0.034 0.001 PHE C 540 TYR 0.033 0.001 TYR C 453 ARG 0.008 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 30) link_NAG-ASN : angle 2.91636 ( 90) link_BETA1-4 : bond 0.00755 ( 6) link_BETA1-4 : angle 1.94101 ( 18) hydrogen bonds : bond 0.03903 ( 935) hydrogen bonds : angle 5.39651 ( 2589) SS BOND : bond 0.00415 ( 37) SS BOND : angle 1.85155 ( 74) covalent geometry : bond 0.00362 (24795) covalent geometry : angle 0.59596 (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 638 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 568 time to evaluate : 2.879 Fit side-chains REVERT: A 33 THR cc_start: 0.8392 (p) cc_final: 0.8124 (p) REVERT: A 116 SER cc_start: 0.7818 (m) cc_final: 0.7394 (p) REVERT: A 128 ILE cc_start: 0.7815 (mt) cc_final: 0.7578 (mp) REVERT: A 226 LEU cc_start: 0.8374 (tt) cc_final: 0.8161 (tt) REVERT: A 355 ARG cc_start: 0.8506 (ttt90) cc_final: 0.8248 (ttt90) REVERT: A 591 PHE cc_start: 0.8181 (p90) cc_final: 0.7928 (p90) REVERT: A 658 SER cc_start: 0.8622 (m) cc_final: 0.8105 (p) REVERT: A 696 MET cc_start: 0.7979 (ttm) cc_final: 0.7725 (ttm) REVERT: A 724 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 747 GLU cc_start: 0.7311 (mp0) cc_final: 0.7050 (mp0) REVERT: A 789 LYS cc_start: 0.8460 (mttp) cc_final: 0.8113 (mmtp) REVERT: A 858 THR cc_start: 0.8523 (p) cc_final: 0.8268 (t) REVERT: A 868 MET cc_start: 0.8274 (mtt) cc_final: 0.7987 (mtm) REVERT: A 978 ASP cc_start: 0.7776 (t0) cc_final: 0.7514 (t0) REVERT: A 993 ASP cc_start: 0.7926 (t0) cc_final: 0.7639 (t0) REVERT: A 1033 LEU cc_start: 0.8549 (mp) cc_final: 0.8306 (mp) REVERT: A 1102 PHE cc_start: 0.8280 (m-80) cc_final: 0.7878 (m-80) REVERT: A 1134 ASN cc_start: 0.7407 (m-40) cc_final: 0.7166 (m110) REVERT: B 53 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: B 278 LYS cc_start: 0.8757 (tttt) cc_final: 0.8526 (tttt) REVERT: B 313 TYR cc_start: 0.8146 (m-80) cc_final: 0.7717 (m-80) REVERT: B 317 ASN cc_start: 0.7624 (m-40) cc_final: 0.7336 (m-40) REVERT: B 321 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7652 (mm110) REVERT: B 324 GLU cc_start: 0.7687 (mp0) cc_final: 0.7049 (mp0) REVERT: B 557 LYS cc_start: 0.8488 (mppt) cc_final: 0.8002 (mppt) REVERT: B 618 GLU cc_start: 0.7877 (tp30) cc_final: 0.7628 (tp30) REVERT: B 627 GLN cc_start: 0.7811 (mt0) cc_final: 0.7368 (mt0) REVERT: B 653 GLU cc_start: 0.8130 (pm20) cc_final: 0.7849 (pm20) REVERT: B 744 ASP cc_start: 0.6978 (m-30) cc_final: 0.6612 (m-30) REVERT: B 752 LEU cc_start: 0.8233 (tp) cc_final: 0.7983 (tt) REVERT: B 772 GLU cc_start: 0.7490 (tt0) cc_final: 0.7023 (tt0) REVERT: B 778 GLN cc_start: 0.7895 (tp40) cc_final: 0.7664 (tm-30) REVERT: B 789 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8164 (mtpp) REVERT: B 854 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6722 (t80) REVERT: B 866 ASP cc_start: 0.7315 (p0) cc_final: 0.6587 (p0) REVERT: B 867 GLU cc_start: 0.7603 (mp0) cc_final: 0.7071 (mp0) REVERT: B 901 MET cc_start: 0.8051 (tpt) cc_final: 0.7845 (mmt) REVERT: B 921 LEU cc_start: 0.8574 (tp) cc_final: 0.8327 (tt) REVERT: B 994 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7942 (mtm180) REVERT: B 1018 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7392 (ttm110) REVERT: B 1027 LYS cc_start: 0.8404 (mttm) cc_final: 0.8015 (mttm) REVERT: B 1044 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7780 (tptp) REVERT: B 1112 GLN cc_start: 0.8130 (mt0) cc_final: 0.7762 (mm-40) REVERT: C 52 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7962 (tm-30) REVERT: C 55 PHE cc_start: 0.8375 (m-80) cc_final: 0.8109 (m-80) REVERT: C 269 TYR cc_start: 0.8427 (m-10) cc_final: 0.8018 (m-10) REVERT: C 271 GLN cc_start: 0.7772 (mt0) cc_final: 0.7520 (mt0) REVERT: C 278 LYS cc_start: 0.7911 (ttpm) cc_final: 0.7700 (ttpm) REVERT: C 314 GLN cc_start: 0.7960 (tp40) cc_final: 0.7748 (tp40) REVERT: C 317 ASN cc_start: 0.8082 (m-40) cc_final: 0.7706 (m-40) REVERT: C 356 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8619 (p) REVERT: C 409 GLN cc_start: 0.7623 (mt0) cc_final: 0.7159 (mp10) REVERT: C 418 ILE cc_start: 0.7298 (mm) cc_final: 0.6961 (mm) REVERT: C 555 ASN cc_start: 0.7681 (p0) cc_final: 0.7393 (p0) REVERT: C 576 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6997 (ptt180) REVERT: C 618 GLU cc_start: 0.7616 (tp30) cc_final: 0.7390 (tp30) REVERT: C 645 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7833 (mtt90) REVERT: C 720 SER cc_start: 0.8577 (t) cc_final: 0.8186 (p) REVERT: C 746 THR cc_start: 0.7875 (p) cc_final: 0.7655 (m) REVERT: C 749 SER cc_start: 0.8233 (t) cc_final: 0.7958 (m) REVERT: C 772 GLU cc_start: 0.7431 (tt0) cc_final: 0.7040 (tt0) REVERT: C 779 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7696 (mt-10) REVERT: C 803 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8194 (mm-40) REVERT: C 883 SER cc_start: 0.8239 (m) cc_final: 0.7986 (p) REVERT: C 934 GLN cc_start: 0.7855 (mt0) cc_final: 0.7640 (tt0) REVERT: C 978 ASP cc_start: 0.7378 (m-30) cc_final: 0.7173 (m-30) REVERT: C 1044 LYS cc_start: 0.8090 (tptp) cc_final: 0.7779 (tptp) REVERT: C 1072 LYS cc_start: 0.8021 (tptp) cc_final: 0.7647 (tptp) REVERT: C 1083 ASP cc_start: 0.6757 (t0) cc_final: 0.6354 (t0) REVERT: C 1091 GLU cc_start: 0.7419 (pm20) cc_final: 0.7155 (pm20) outliers start: 70 outliers final: 58 residues processed: 596 average time/residue: 0.3878 time to fit residues: 362.0473 Evaluate side-chains 619 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 556 time to evaluate : 2.543 ------------------------------------------------------------------------------- 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 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 962 VAL 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 1138 ASP Chi-restraints excluded: chain B residue 53 ASP 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 1004 GLN Chi-restraints excluded: chain B residue 1044 LYS Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1135 THR 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 289 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR 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 524 CYS Chi-restraints excluded: chain C residue 529 SER Chi-restraints excluded: chain C residue 576 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 60 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 157 optimal weight: 0.0570 chunk 179 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 543 ASN C 709 ASN C 783 GLN C1087 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.176352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145435 restraints weight = 36423.767| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.64 r_work: 0.3697 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24868 Z= 0.156 Angle : 0.626 11.552 33927 Z= 0.318 Chirality : 0.046 0.349 3912 Planarity : 0.005 0.057 4309 Dihedral : 6.081 59.999 3996 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.61 % Favored : 92.28 % Rotamer: Outliers : 2.82 % Allowed : 17.87 % Favored : 79.31 % 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: -1.28 (0.15), residues: 2981 helix: 1.18 (0.19), residues: 708 sheet: -0.72 (0.20), residues: 602 loop : -1.88 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 436 HIS 0.003 0.000 HIS B 207 PHE 0.033 0.001 PHE C 540 TYR 0.031 0.001 TYR C 453 ARG 0.008 0.000 ARG A1090 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 30) link_NAG-ASN : angle 2.94782 ( 90) link_BETA1-4 : bond 0.00762 ( 6) link_BETA1-4 : angle 1.91268 ( 18) hydrogen bonds : bond 0.03916 ( 935) hydrogen bonds : angle 5.36792 ( 2589) SS BOND : bond 0.00405 ( 37) SS BOND : angle 1.84310 ( 74) covalent geometry : bond 0.00358 (24795) covalent geometry : angle 0.60143 (33745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15315.09 seconds wall clock time: 273 minutes 23.24 seconds (16403.24 seconds total)