Starting phenix.real_space_refine on Sun Jun 22 15:15:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whw_37550/06_2025/8whw_37550.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whw_37550/06_2025/8whw_37550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8whw_37550/06_2025/8whw_37550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whw_37550/06_2025/8whw_37550.map" model { file = "/net/cci-nas-00/data/ceres_data/8whw_37550/06_2025/8whw_37550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whw_37550/06_2025/8whw_37550.cif" } resolution = 3.85 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= 0.002 sd= 0.058 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 114 5.16 5 C 16452 2.51 5 N 4197 2.21 5 O 5044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 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: 25807 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "T" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.76, per 1000 atoms: 0.57 Number of scatterers: 25807 At special positions: 0 Unit cell: (147, 135, 189, 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 114 16.00 O 5044 8.00 N 4197 7.00 C 16452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " 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 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.02 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 " - " BMA D 2 " " NAG E 1 " - " BMA E 2 " " NAG F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " BMA L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " " NAG S 1 " - " BMA S 2 " " NAG T 1 " - " BMA T 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 354 " " NAG B1311 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 343 " " NAG C1309 " - " ASN C 234 " " NAG C1310 " - " ASN C 331 " " NAG D 1 " - " ASN A 354 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 282 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN C 354 " " NAG P 1 " - " ASN C 282 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1098 " Time building additional restraints: 6.66 Conformation dependent library (CDL) restraints added in 3.9 seconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 53 sheets defined 25.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.547A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.831A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.793A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.581A pdb=" N VAL A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 840 through 844 removed outlier: 4.283A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.602A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.161A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.848A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.502A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.906A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.691A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 removed outlier: 3.680A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.901A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.570A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 626 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.641A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.733A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 844 removed outlier: 4.203A pdb=" N ILE B 844 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.666A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.581A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.802A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.395A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 removed outlier: 4.654A pdb=" N LEU B1143 " --> pdb=" O ASP B1139 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1139 through 1144' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.729A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.874A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.550A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 627 removed outlier: 3.568A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.573A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.612A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 868 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.310A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.694A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.540A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.726A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.146A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (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 50 through 55 removed outlier: 3.797A 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: 3.681A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.939A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 4.573A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.645A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.879A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.850A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.814A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.713A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.296A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 713 through 715 removed outlier: 4.059A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 722 removed outlier: 7.254A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734 removed outlier: 3.759A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.086A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 95 " --> pdb=" O ASP B 264 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.605A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.524A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.167A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 removed outlier: 4.355A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.701A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.946A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 575 through 577 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.078A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.723A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.372A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.154A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.913A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 26 through 30 removed outlier: 6.948A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.624A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.014A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 120 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.403A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.790A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.222A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.818A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.685A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.313A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.732A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.184A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.084A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.506A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 909 hydrogen bonds defined for protein. 2490 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: 13.51 Time building geometry restraints manager: 7.85 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: 4837 1.33 - 1.45: 7048 1.45 - 1.58: 14380 1.58 - 1.70: 1 1.70 - 1.83: 141 Bond restraints: 26407 Sorted by residual: bond pdb=" CA PHE C 216 " pdb=" C PHE C 216 " ideal model delta sigma weight residual 1.534 1.490 0.044 9.50e-03 1.11e+04 2.12e+01 bond pdb=" N THR A 588 " pdb=" CA THR A 588 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.86e+01 bond pdb=" N PHE C 329 " pdb=" CA PHE C 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.74e+01 bond pdb=" CA HIS B 207 " pdb=" C HIS B 207 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.25e-02 6.40e+03 1.72e+01 bond pdb=" CA THR B 208 " pdb=" C THR B 208 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.26e-02 6.30e+03 1.27e+01 ... (remaining 26402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 34999 2.67 - 5.33: 822 5.33 - 8.00: 108 8.00 - 10.67: 9 10.67 - 13.33: 2 Bond angle restraints: 35940 Sorted by residual: angle pdb=" C GLN A 218 " pdb=" N GLY A 219 " pdb=" CA GLY A 219 " ideal model delta sigma weight residual 120.10 113.74 6.36 9.50e-01 1.11e+00 4.49e+01 angle pdb=" N GLY B 213 " pdb=" CA GLY B 213 " pdb=" C GLY B 213 " ideal model delta sigma weight residual 115.21 106.68 8.53 1.30e+00 5.92e-01 4.30e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 118.66 -7.96 1.22e+00 6.72e-01 4.25e+01 angle pdb=" N PRO B 209 " pdb=" CA PRO B 209 " pdb=" C PRO B 209 " ideal model delta sigma weight residual 112.47 99.14 13.33 2.06e+00 2.36e-01 4.19e+01 angle pdb=" N VAL C 570 " pdb=" CA VAL C 570 " pdb=" C VAL C 570 " ideal model delta sigma weight residual 106.21 112.30 -6.09 1.07e+00 8.73e-01 3.24e+01 ... (remaining 35935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 14728 23.11 - 46.21: 1382 46.21 - 69.32: 171 69.32 - 92.42: 139 92.42 - 115.53: 118 Dihedral angle restraints: 16538 sinusoidal: 7262 harmonic: 9276 Sorted by residual: dihedral pdb=" CD ARG C 328 " pdb=" NE ARG C 328 " pdb=" CZ ARG C 328 " pdb=" NH1 ARG C 328 " ideal model delta sinusoidal sigma weight residual 0.00 -64.56 64.56 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 39.96 53.04 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 142.22 -49.22 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 16535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 4184 0.182 - 0.364: 58 0.364 - 0.547: 3 0.547 - 0.729: 0 0.729 - 0.911: 3 Chirality restraints: 4248 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 4245 not shown) Planarity restraints: 4604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1303 " 0.251 2.00e-02 2.50e+03 2.09e-01 5.44e+02 pdb=" C7 NAG C1303 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C1303 " 0.175 2.00e-02 2.50e+03 pdb=" N2 NAG C1303 " -0.345 2.00e-02 2.50e+03 pdb=" O7 NAG C1303 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " -0.240 2.00e-02 2.50e+03 2.06e-01 5.30e+02 pdb=" C7 NAG B1303 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " 0.345 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.212 2.00e-02 2.50e+03 1.78e-01 3.96e+02 pdb=" C7 NAG C1301 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.148 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.006 2.00e-02 2.50e+03 ... (remaining 4601 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 911 2.68 - 3.24: 26089 3.24 - 3.79: 41366 3.79 - 4.35: 53807 4.35 - 4.90: 87967 Nonbonded interactions: 210140 Sorted by model distance: nonbonded pdb=" O PRO C 486 " pdb=" ND2 ASN C 487 " model vdw 2.128 3.120 nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.183 3.120 nonbonded pdb=" O ASN C 417 " pdb=" ND2 ASN C 422 " model vdw 2.195 3.120 nonbonded pdb=" CG2 ILE B 210 " pdb=" N ILE B 212 " model vdw 2.199 3.540 nonbonded pdb=" OG1 THR C 393 " pdb=" OE1 GLU C 516 " model vdw 2.202 3.040 ... (remaining 210135 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' selection = (chain 'B' and (resid 23 through 1144 or resid 1301 through 1310)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 64.730 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.240 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.006 0.093 26510 Z= 0.371 Angle : 0.978 14.259 36210 Z= 0.563 Chirality : 0.065 0.911 4248 Planarity : 0.012 0.444 4557 Dihedral : 21.278 115.525 10463 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.80 % Favored : 90.63 % Rotamer: Outliers : 1.91 % Allowed : 24.00 % Favored : 74.09 % Cbeta Deviations : 0.07 % 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: -2.00 (0.14), residues: 3159 helix: 0.49 (0.20), residues: 716 sheet: -1.28 (0.21), residues: 598 loop : -2.18 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 633 HIS 0.003 0.001 HIS B1048 PHE 0.022 0.002 PHE C 338 TYR 0.022 0.002 TYR B 501 ARG 0.020 0.001 ARG B 847 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 47) link_NAG-ASN : angle 3.72299 ( 141) link_BETA1-4 : bond 0.00532 ( 17) link_BETA1-4 : angle 2.42938 ( 51) hydrogen bonds : bond 0.21263 ( 901) hydrogen bonds : angle 8.86076 ( 2490) SS BOND : bond 0.00474 ( 39) SS BOND : angle 1.43425 ( 78) covalent geometry : bond 0.00614 (26407) covalent geometry : angle 0.94732 (35940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6394 (mmp) cc_final: 0.5799 (mmp) REVERT: A 591 SER cc_start: 0.7715 (t) cc_final: 0.7320 (p) REVERT: A 896 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9053 (mt) REVERT: B 270 LEU cc_start: 0.9136 (mp) cc_final: 0.8627 (mp) REVERT: B 568 ASP cc_start: 0.6673 (t0) cc_final: 0.6455 (t0) REVERT: B 619 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8081 (tm-30) REVERT: B 740 MET cc_start: 0.8058 (ttm) cc_final: 0.7767 (ttm) REVERT: B 773 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6537 (tm-30) REVERT: B 850 ILE cc_start: 0.7890 (mm) cc_final: 0.7459 (mm) REVERT: C 303 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8889 (pp) REVERT: C 327 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9124 (t) REVERT: C 453 TYR cc_start: 0.7355 (p90) cc_final: 0.7128 (p90) outliers start: 53 outliers final: 17 residues processed: 236 average time/residue: 0.3557 time to fit residues: 138.8894 Evaluate side-chains 172 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 532 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 409 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 804 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.096973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.070028 restraints weight = 84348.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.072137 restraints weight = 48007.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073522 restraints weight = 32992.304| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26510 Z= 0.165 Angle : 0.788 15.454 36210 Z= 0.377 Chirality : 0.052 0.626 4248 Planarity : 0.005 0.064 4557 Dihedral : 14.490 111.705 4785 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.44 % Favored : 92.40 % Rotamer: Outliers : 4.25 % Allowed : 21.59 % Favored : 74.16 % 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: -1.67 (0.14), residues: 3159 helix: 0.98 (0.20), residues: 708 sheet: -1.24 (0.20), residues: 624 loop : -2.00 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 633 HIS 0.003 0.001 HIS C 339 PHE 0.023 0.001 PHE B 216 TYR 0.022 0.001 TYR B1067 ARG 0.006 0.001 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 47) link_NAG-ASN : angle 3.81473 ( 141) link_BETA1-4 : bond 0.00491 ( 17) link_BETA1-4 : angle 3.41432 ( 51) hydrogen bonds : bond 0.04422 ( 901) hydrogen bonds : angle 6.29634 ( 2490) SS BOND : bond 0.00426 ( 39) SS BOND : angle 1.93062 ( 78) covalent geometry : bond 0.00373 (26407) covalent geometry : angle 0.73773 (35940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 185 time to evaluate : 2.868 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 630 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8170 (m) REVERT: B 84 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7038 (mm) REVERT: B 104 TRP cc_start: 0.6408 (m-10) cc_final: 0.6040 (m-10) REVERT: B 164 ASN cc_start: 0.3488 (OUTLIER) cc_final: 0.3137 (p0) REVERT: B 270 LEU cc_start: 0.9168 (mp) cc_final: 0.8862 (mp) REVERT: B 304 LYS cc_start: 0.9471 (OUTLIER) cc_final: 0.9118 (mtmt) REVERT: B 734 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8766 (p) REVERT: B 740 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7879 (ttm) REVERT: B 773 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 850 ILE cc_start: 0.7840 (mm) cc_final: 0.7423 (mm) REVERT: B 869 MET cc_start: 0.8376 (ptt) cc_final: 0.8166 (ptt) REVERT: B 873 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8112 (t80) REVERT: C 1037 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8961 (t) outliers start: 118 outliers final: 44 residues processed: 292 average time/residue: 0.3315 time to fit residues: 163.2056 Evaluate side-chains 200 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 304 LYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 92 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 474 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 965 GLN B1064 HIS B1106 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.089922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062885 restraints weight = 85984.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064613 restraints weight = 52460.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.065759 restraints weight = 37951.201| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 26510 Z= 0.356 Angle : 0.901 15.229 36210 Z= 0.442 Chirality : 0.055 0.676 4248 Planarity : 0.006 0.060 4557 Dihedral : 10.581 112.722 4769 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.48 % Favored : 91.45 % Rotamer: Outliers : 5.77 % Allowed : 22.02 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.95 (0.14), residues: 3159 helix: 0.56 (0.19), residues: 710 sheet: -1.35 (0.20), residues: 580 loop : -2.12 (0.13), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 633 HIS 0.007 0.001 HIS C1064 PHE 0.025 0.002 PHE B 92 TYR 0.025 0.002 TYR B 501 ARG 0.009 0.001 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00831 ( 47) link_NAG-ASN : angle 3.98495 ( 141) link_BETA1-4 : bond 0.00481 ( 17) link_BETA1-4 : angle 3.02600 ( 51) hydrogen bonds : bond 0.05197 ( 901) hydrogen bonds : angle 6.23818 ( 2490) SS BOND : bond 0.00669 ( 39) SS BOND : angle 2.20037 ( 78) covalent geometry : bond 0.00797 (26407) covalent geometry : angle 0.85597 (35940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 141 time to evaluate : 2.917 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 456 PHE cc_start: 0.7669 (m-80) cc_final: 0.7213 (m-80) REVERT: A 495 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: A 705 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8703 (m) REVERT: A 714 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (pt) REVERT: A 775 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8032 (t0) REVERT: A 977 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8598 (mm) REVERT: B 84 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7451 (mt) REVERT: B 270 LEU cc_start: 0.9192 (mp) cc_final: 0.8870 (mp) REVERT: B 613 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: B 773 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 869 MET cc_start: 0.8728 (ptt) cc_final: 0.8497 (ptt) REVERT: B 955 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8314 (t0) REVERT: C 611 LEU cc_start: 0.9356 (tp) cc_final: 0.9083 (tt) REVERT: C 918 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: C 955 ASN cc_start: 0.8689 (m-40) cc_final: 0.8237 (t0) outliers start: 160 outliers final: 99 residues processed: 279 average time/residue: 0.3175 time to fit residues: 151.0764 Evaluate side-chains 227 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 119 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 244 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 260 optimal weight: 7.9990 chunk 212 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 192 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 0.0870 chunk 195 optimal weight: 2.9990 chunk 314 optimal weight: 0.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN A1083 HIS B 49 HIS B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.092556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.065334 restraints weight = 85424.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067322 restraints weight = 49267.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.068627 restraints weight = 34309.926| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26510 Z= 0.155 Angle : 0.723 15.008 36210 Z= 0.350 Chirality : 0.050 0.617 4248 Planarity : 0.004 0.052 4557 Dihedral : 8.978 108.089 4767 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.94 % Rotamer: Outliers : 3.89 % Allowed : 24.54 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.68 (0.14), residues: 3159 helix: 0.94 (0.19), residues: 715 sheet: -1.28 (0.20), residues: 574 loop : -1.98 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 633 HIS 0.003 0.001 HIS A 339 PHE 0.022 0.001 PHE B 92 TYR 0.021 0.001 TYR B 265 ARG 0.004 0.000 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 47) link_NAG-ASN : angle 3.66949 ( 141) link_BETA1-4 : bond 0.00450 ( 17) link_BETA1-4 : angle 2.87261 ( 51) hydrogen bonds : bond 0.04155 ( 901) hydrogen bonds : angle 5.78146 ( 2490) SS BOND : bond 0.00405 ( 39) SS BOND : angle 1.97458 ( 78) covalent geometry : bond 0.00355 (26407) covalent geometry : angle 0.67314 (35940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 152 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.1404 (OUTLIER) cc_final: -0.1823 (mpt180) REVERT: A 456 PHE cc_start: 0.7692 (m-80) cc_final: 0.7274 (m-80) REVERT: A 495 TYR cc_start: 0.6741 (OUTLIER) cc_final: 0.6066 (m-80) REVERT: B 164 ASN cc_start: 0.3713 (OUTLIER) cc_final: 0.3484 (p0) REVERT: B 270 LEU cc_start: 0.9244 (mp) cc_final: 0.8902 (mp) REVERT: B 592 PHE cc_start: 0.7753 (t80) cc_final: 0.7405 (t80) REVERT: B 613 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8689 (mt0) REVERT: B 697 MET cc_start: 0.8032 (ttt) cc_final: 0.7788 (ttt) REVERT: B 740 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7828 (ttt) REVERT: B 773 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 968 SER cc_start: 0.9014 (p) cc_final: 0.8809 (m) REVERT: B 1092 GLU cc_start: 0.8399 (pm20) cc_final: 0.8161 (pm20) REVERT: C 611 LEU cc_start: 0.9330 (tp) cc_final: 0.9105 (tt) REVERT: C 918 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7585 (mm-30) outliers start: 108 outliers final: 64 residues processed: 244 average time/residue: 0.3217 time to fit residues: 135.7172 Evaluate side-chains 202 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 132 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 140 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 162 optimal weight: 0.0030 chunk 296 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.090883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063608 restraints weight = 86195.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065509 restraints weight = 50204.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066752 restraints weight = 35424.776| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26510 Z= 0.217 Angle : 0.731 14.976 36210 Z= 0.357 Chirality : 0.049 0.614 4248 Planarity : 0.005 0.044 4557 Dihedral : 8.420 106.129 4767 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.69 % Favored : 92.28 % Rotamer: Outliers : 4.86 % Allowed : 24.25 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.69 (0.14), residues: 3159 helix: 0.97 (0.19), residues: 714 sheet: -1.30 (0.19), residues: 621 loop : -2.00 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 104 HIS 0.004 0.001 HIS B 207 PHE 0.022 0.002 PHE B 194 TYR 0.029 0.002 TYR B 495 ARG 0.005 0.000 ARG B 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 47) link_NAG-ASN : angle 3.60641 ( 141) link_BETA1-4 : bond 0.00412 ( 17) link_BETA1-4 : angle 2.59585 ( 51) hydrogen bonds : bond 0.04193 ( 901) hydrogen bonds : angle 5.68417 ( 2490) SS BOND : bond 0.00436 ( 39) SS BOND : angle 1.93910 ( 78) covalent geometry : bond 0.00498 (26407) covalent geometry : angle 0.68488 (35940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 134 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.1491 (OUTLIER) cc_final: -0.1865 (mpt180) REVERT: A 387 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8508 (tt) REVERT: A 456 PHE cc_start: 0.7657 (m-80) cc_final: 0.7244 (m-80) REVERT: A 495 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: A 705 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8747 (m) REVERT: B 270 LEU cc_start: 0.9264 (mp) cc_final: 0.8986 (mp) REVERT: B 630 THR cc_start: 0.7978 (p) cc_final: 0.7754 (t) REVERT: B 740 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7832 (ttt) REVERT: B 773 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7058 (tm-30) REVERT: C 918 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: C 955 ASN cc_start: 0.8670 (m-40) cc_final: 0.8309 (t0) outliers start: 135 outliers final: 87 residues processed: 257 average time/residue: 0.3472 time to fit residues: 152.4924 Evaluate side-chains 210 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 117 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 41 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 295 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 628 GLN B 853 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.092248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065241 restraints weight = 85859.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.067149 restraints weight = 51127.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068405 restraints weight = 36245.373| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26510 Z= 0.144 Angle : 0.691 14.755 36210 Z= 0.336 Chirality : 0.049 0.619 4248 Planarity : 0.004 0.075 4557 Dihedral : 7.981 103.079 4767 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 4.25 % Allowed : 24.83 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.50 (0.15), residues: 3159 helix: 1.15 (0.20), residues: 715 sheet: -1.15 (0.20), residues: 604 loop : -1.91 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 104 HIS 0.004 0.001 HIS B 207 PHE 0.017 0.001 PHE B 643 TYR 0.026 0.001 TYR B 495 ARG 0.015 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 47) link_NAG-ASN : angle 3.56700 ( 141) link_BETA1-4 : bond 0.00465 ( 17) link_BETA1-4 : angle 2.34809 ( 51) hydrogen bonds : bond 0.03912 ( 901) hydrogen bonds : angle 5.50182 ( 2490) SS BOND : bond 0.00366 ( 39) SS BOND : angle 2.05042 ( 78) covalent geometry : bond 0.00331 (26407) covalent geometry : angle 0.64338 (35940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 144 time to evaluate : 3.080 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: A 246 ARG cc_start: 0.1706 (OUTLIER) cc_final: -0.1925 (mpt180) REVERT: A 456 PHE cc_start: 0.7580 (m-80) cc_final: 0.7184 (m-80) REVERT: A 495 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: A 697 MET cc_start: 0.8720 (mmt) cc_final: 0.8428 (mmt) REVERT: B 270 LEU cc_start: 0.9175 (mp) cc_final: 0.8926 (mp) REVERT: B 630 THR cc_start: 0.7923 (p) cc_final: 0.7662 (t) REVERT: B 698 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8457 (p) REVERT: B 773 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7078 (tm-30) REVERT: B 873 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8002 (t80) REVERT: C 866 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8763 (p) REVERT: C 918 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: C 955 ASN cc_start: 0.8673 (m-40) cc_final: 0.8385 (t0) outliers start: 118 outliers final: 84 residues processed: 249 average time/residue: 0.3148 time to fit residues: 135.2211 Evaluate side-chains 221 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 131 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 127 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063609 restraints weight = 86782.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065490 restraints weight = 51013.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066734 restraints weight = 36065.439| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 26510 Z= 0.193 Angle : 0.713 14.829 36210 Z= 0.347 Chirality : 0.049 0.616 4248 Planarity : 0.004 0.042 4557 Dihedral : 7.861 100.615 4767 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.41 % Favored : 92.56 % Rotamer: Outliers : 4.54 % Allowed : 24.40 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3159 helix: 1.11 (0.20), residues: 720 sheet: -1.18 (0.19), residues: 631 loop : -1.90 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 104 HIS 0.005 0.001 HIS B 207 PHE 0.013 0.001 PHE C 133 TYR 0.024 0.001 TYR B 495 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 47) link_NAG-ASN : angle 3.53977 ( 141) link_BETA1-4 : bond 0.00427 ( 17) link_BETA1-4 : angle 2.26842 ( 51) hydrogen bonds : bond 0.04055 ( 901) hydrogen bonds : angle 5.49189 ( 2490) SS BOND : bond 0.00362 ( 39) SS BOND : angle 1.99105 ( 78) covalent geometry : bond 0.00442 (26407) covalent geometry : angle 0.66865 (35940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 130 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ARG cc_start: 0.1809 (OUTLIER) cc_final: -0.1967 (mpt180) REVERT: A 456 PHE cc_start: 0.7578 (m-80) cc_final: 0.7191 (m-80) REVERT: A 495 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6203 (m-80) REVERT: B 43 PHE cc_start: 0.6426 (t80) cc_final: 0.6152 (t80) REVERT: B 242 LEU cc_start: 0.6538 (mm) cc_final: 0.6002 (tp) REVERT: B 270 LEU cc_start: 0.9244 (mp) cc_final: 0.8965 (mp) REVERT: B 630 THR cc_start: 0.7821 (p) cc_final: 0.7621 (t) REVERT: B 773 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 869 MET cc_start: 0.8640 (ptt) cc_final: 0.8376 (ptt) REVERT: B 1012 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9286 (mt) REVERT: C 918 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: C 955 ASN cc_start: 0.8659 (m-40) cc_final: 0.8331 (t0) outliers start: 126 outliers final: 99 residues processed: 245 average time/residue: 0.3343 time to fit residues: 141.9551 Evaluate side-chains 223 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 120 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 125 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.090934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.064005 restraints weight = 86348.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065861 restraints weight = 51229.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.067072 restraints weight = 36355.782| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26510 Z= 0.167 Angle : 0.698 14.699 36210 Z= 0.338 Chirality : 0.049 0.618 4248 Planarity : 0.004 0.043 4557 Dihedral : 7.713 101.623 4767 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.00 % Favored : 92.97 % Rotamer: Outliers : 4.58 % Allowed : 24.29 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.42 (0.15), residues: 3159 helix: 1.20 (0.20), residues: 711 sheet: -1.13 (0.20), residues: 621 loop : -1.82 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 104 HIS 0.005 0.001 HIS B 207 PHE 0.015 0.001 PHE B 592 TYR 0.023 0.001 TYR B 495 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 47) link_NAG-ASN : angle 3.50662 ( 141) link_BETA1-4 : bond 0.00471 ( 17) link_BETA1-4 : angle 2.18536 ( 51) hydrogen bonds : bond 0.03901 ( 901) hydrogen bonds : angle 5.43091 ( 2490) SS BOND : bond 0.00341 ( 39) SS BOND : angle 1.77940 ( 78) covalent geometry : bond 0.00381 (26407) covalent geometry : angle 0.65537 (35940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 144 time to evaluate : 3.018 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: A 246 ARG cc_start: 0.1702 (OUTLIER) cc_final: -0.2025 (mpt180) REVERT: A 456 PHE cc_start: 0.7566 (m-80) cc_final: 0.7185 (m-80) REVERT: A 495 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: B 43 PHE cc_start: 0.6578 (t80) cc_final: 0.6369 (t80) REVERT: B 66 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7479 (m-70) REVERT: B 270 LEU cc_start: 0.9229 (mp) cc_final: 0.8974 (mp) REVERT: B 324 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: B 630 THR cc_start: 0.7856 (p) cc_final: 0.7613 (t) REVERT: B 773 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7072 (tm-30) REVERT: B 774 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8145 (mm110) REVERT: B 869 MET cc_start: 0.8608 (ptt) cc_final: 0.8312 (ptt) REVERT: B 873 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8010 (t80) REVERT: B 1012 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9302 (mt) REVERT: C 918 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: C 955 ASN cc_start: 0.8690 (m-40) cc_final: 0.8370 (t0) outliers start: 127 outliers final: 102 residues processed: 258 average time/residue: 0.3316 time to fit residues: 147.6160 Evaluate side-chains 236 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 127 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 308 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 214 optimal weight: 0.1980 chunk 28 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.092363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.065112 restraints weight = 86369.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.067100 restraints weight = 49643.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068416 restraints weight = 34603.943| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26510 Z= 0.123 Angle : 0.683 14.542 36210 Z= 0.330 Chirality : 0.048 0.618 4248 Planarity : 0.004 0.042 4557 Dihedral : 7.491 100.951 4767 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 3.64 % Allowed : 25.66 % Favored : 70.70 % 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: -1.32 (0.15), residues: 3159 helix: 1.29 (0.20), residues: 717 sheet: -1.07 (0.20), residues: 613 loop : -1.77 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 104 HIS 0.004 0.001 HIS B 207 PHE 0.019 0.001 PHE A 592 TYR 0.022 0.001 TYR B 495 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 47) link_NAG-ASN : angle 3.47227 ( 141) link_BETA1-4 : bond 0.00497 ( 17) link_BETA1-4 : angle 2.10911 ( 51) hydrogen bonds : bond 0.03741 ( 901) hydrogen bonds : angle 5.31255 ( 2490) SS BOND : bond 0.00322 ( 39) SS BOND : angle 1.56816 ( 78) covalent geometry : bond 0.00282 (26407) covalent geometry : angle 0.64151 (35940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 156 time to evaluate : 2.771 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: A 246 ARG cc_start: 0.1712 (OUTLIER) cc_final: -0.1892 (mpt180) REVERT: A 456 PHE cc_start: 0.7551 (m-80) cc_final: 0.7163 (m-80) REVERT: A 495 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.6067 (m-80) REVERT: A 591 SER cc_start: 0.8600 (t) cc_final: 0.8211 (p) REVERT: B 270 LEU cc_start: 0.9266 (mp) cc_final: 0.8973 (mp) REVERT: B 324 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: B 773 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7176 (tm-30) REVERT: B 774 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8107 (mm-40) REVERT: B 869 MET cc_start: 0.8534 (ptt) cc_final: 0.8244 (ptt) REVERT: B 873 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7974 (t80) REVERT: B 1012 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9248 (mt) REVERT: C 611 LEU cc_start: 0.9307 (tp) cc_final: 0.9084 (tt) REVERT: C 918 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7761 (mm-30) outliers start: 101 outliers final: 82 residues processed: 246 average time/residue: 0.3235 time to fit residues: 135.4373 Evaluate side-chains 224 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 136 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 251 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 299 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 276 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.091128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064181 restraints weight = 86072.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066029 restraints weight = 51046.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067261 restraints weight = 36340.650| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26510 Z= 0.171 Angle : 0.708 14.709 36210 Z= 0.342 Chirality : 0.049 0.612 4248 Planarity : 0.004 0.042 4557 Dihedral : 7.506 102.501 4763 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 3.60 % Allowed : 26.05 % Favored : 70.34 % 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: -1.34 (0.15), residues: 3159 helix: 1.30 (0.20), residues: 712 sheet: -1.10 (0.20), residues: 636 loop : -1.79 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 104 HIS 0.006 0.001 HIS B 207 PHE 0.029 0.001 PHE A 592 TYR 0.038 0.001 TYR C 369 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 47) link_NAG-ASN : angle 3.45776 ( 141) link_BETA1-4 : bond 0.00438 ( 17) link_BETA1-4 : angle 2.12197 ( 51) hydrogen bonds : bond 0.03885 ( 901) hydrogen bonds : angle 5.32943 ( 2490) SS BOND : bond 0.00348 ( 39) SS BOND : angle 1.65439 ( 78) covalent geometry : bond 0.00392 (26407) covalent geometry : angle 0.66793 (35940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 135 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6320 (mpp) cc_final: 0.5687 (mmp) REVERT: A 246 ARG cc_start: 0.1868 (OUTLIER) cc_final: -0.1912 (mpt180) REVERT: A 456 PHE cc_start: 0.7551 (m-80) cc_final: 0.7166 (m-80) REVERT: A 495 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: B 270 LEU cc_start: 0.9196 (mp) cc_final: 0.8940 (mp) REVERT: B 324 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 697 MET cc_start: 0.7997 (mmm) cc_final: 0.7513 (mmm) REVERT: B 773 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 774 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8207 (mm-40) REVERT: B 873 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8019 (t80) REVERT: C 226 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8427 (mm) REVERT: C 918 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: C 955 ASN cc_start: 0.8699 (m-40) cc_final: 0.8425 (t0) REVERT: C 985 ASP cc_start: 0.7825 (m-30) cc_final: 0.7427 (m-30) outliers start: 100 outliers final: 85 residues processed: 227 average time/residue: 0.4197 time to fit residues: 166.0701 Evaluate side-chains 219 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 128 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1036 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 343 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A1036 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.091694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064720 restraints weight = 86827.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.066592 restraints weight = 51681.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067868 restraints weight = 36755.219| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26510 Z= 0.140 Angle : 0.689 14.509 36210 Z= 0.333 Chirality : 0.048 0.612 4248 Planarity : 0.004 0.042 4557 Dihedral : 7.378 103.191 4762 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.85 % Rotamer: Outliers : 3.46 % Allowed : 26.34 % Favored : 70.20 % 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: -1.32 (0.15), residues: 3159 helix: 1.32 (0.20), residues: 719 sheet: -1.10 (0.20), residues: 620 loop : -1.78 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 104 HIS 0.005 0.001 HIS B 207 PHE 0.033 0.001 PHE A 592 TYR 0.033 0.001 TYR C 369 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 47) link_NAG-ASN : angle 3.43258 ( 141) link_BETA1-4 : bond 0.00465 ( 17) link_BETA1-4 : angle 2.09849 ( 51) hydrogen bonds : bond 0.03824 ( 901) hydrogen bonds : angle 5.27822 ( 2490) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.56560 ( 78) covalent geometry : bond 0.00324 (26407) covalent geometry : angle 0.64868 (35940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8057.58 seconds wall clock time: 141 minutes 3.12 seconds (8463.12 seconds total)