Starting phenix.real_space_refine on Sun Jul 5 06:28:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d0b_30529/07_2026/7d0b_30529.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 113 5.16 5 C 16589 2.51 5 N 4232 2.21 5 O 5131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26065 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7692 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 11 Chain: "C" Number of atoms: 7692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7692 Classifications: {'peptide': 981} Link IDs: {'PTRANS': 48, 'TRANS': 932} Chain breaks: 11 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 880 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.64, per 1000 atoms: 0.22 Number of scatterers: 26065 At special positions: 0 Unit cell: (135.875, 166.311, 194.573, 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 113 16.00 O 5131 8.00 N 4232 7.00 C 16589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.54 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.33 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.50 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.58 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.95 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1407 " - " ASN C 603 " " NAG C1408 " - " ASN C 616 " " NAG C1409 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 709 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " " NAG Z 1 " - " ASN B1074 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 933.4 milliseconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 50 sheets defined 21.9% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.256A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.739A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.992A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.641A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.696A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.604A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.246A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.615A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.562A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.606A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.589A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 103 through 106 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.729A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.270A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.789A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.689A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.938A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.674A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.250A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.552A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 4.316A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE1, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.246A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AE9, first strand: chain 'H' and resid 59 through 61 removed outlier: 6.308A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR H 54 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL H 34 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 69 through 74 Processing sheet with id=AF2, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AF3, first strand: chain 'L' and resid 11 through 14 removed outlier: 5.718A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYS L 113 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL L 13 " --> pdb=" O LYS L 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.882A pdb=" N ILE L 81 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.595A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2487 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: 5.66 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5009 1.32 - 1.45: 7859 1.45 - 1.58: 13616 1.58 - 1.71: 0 1.71 - 1.84: 143 Bond restraints: 26627 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.31e+01 bond pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.16e-02 7.43e+03 2.97e+01 bond pdb=" CA ILE A 693 " pdb=" CB ILE A 693 " ideal model delta sigma weight residual 1.544 1.472 0.072 1.49e-02 4.50e+03 2.34e+01 bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.330 1.389 -0.058 1.23e-02 6.61e+03 2.26e+01 bond pdb=" N ILE A 692 " pdb=" CA ILE A 692 " ideal model delta sigma weight residual 1.458 1.403 0.055 1.17e-02 7.31e+03 2.22e+01 ... (remaining 26622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 35295 2.77 - 5.54: 844 5.54 - 8.31: 60 8.31 - 11.08: 9 11.08 - 13.85: 7 Bond angle restraints: 36215 Sorted by residual: angle pdb=" N ILE A 692 " pdb=" CA ILE A 692 " pdb=" C ILE A 692 " ideal model delta sigma weight residual 109.55 100.43 9.12 1.38e+00 5.25e-01 4.37e+01 angle pdb=" CA ILE A 692 " pdb=" C ILE A 692 " pdb=" N ILE A 693 " ideal model delta sigma weight residual 115.82 124.84 -9.02 1.52e+00 4.33e-01 3.52e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 ... (remaining 36210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13087 17.94 - 35.87: 1567 35.87 - 53.81: 469 53.81 - 71.75: 135 71.75 - 89.69: 52 Dihedral angle restraints: 15310 sinusoidal: 5971 harmonic: 9339 Sorted by residual: 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 21.03 71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.06 71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 15307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4318 0.329 - 0.659: 5 0.659 - 0.988: 3 0.988 - 1.318: 0 1.318 - 1.647: 2 Chirality restraints: 4328 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 chirality pdb=" C1 NAG C1404 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1404 " pdb=" O5 NAG C1404 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.38e+01 ... (remaining 4325 not shown) Planarity restraints: 4621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.161 2.00e-02 2.50e+03 2.13e-01 5.65e+02 pdb=" CG ASN C 234 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.366 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.119 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" CG ASN C 331 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.302 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.85e-02 4.28e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.068 2.00e-02 2.50e+03 ... (remaining 4618 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 245 2.51 - 3.11: 18851 3.11 - 3.71: 37675 3.71 - 4.30: 56929 4.30 - 4.90: 93867 Nonbonded interactions: 207567 Sorted by model distance: nonbonded pdb=" O SER A 530 " pdb=" OG1 THR A 531 " model vdw 1.913 3.040 nonbonded pdb=" O ALA C 372 " pdb=" OG SER C 373 " model vdw 1.919 3.040 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.983 3.120 nonbonded pdb=" O LYS A 529 " pdb=" OG SER A 530 " model vdw 1.986 3.040 nonbonded pdb=" O GLN C 564 " pdb=" O PHE C 565 " model vdw 2.004 3.040 ... (remaining 207562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 939 or resid 944 through 1409)) selection = (chain 'B' and (resid 27 through 826 or resid 855 through 1409)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 0.010 Normalize map: mean=0, sd=1: 1.560 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 24.440 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.549 26734 Z= 0.565 Angle : 1.337 51.424 36498 Z= 0.698 Chirality : 0.075 1.647 4328 Planarity : 0.007 0.093 4573 Dihedral : 18.330 89.686 9172 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 2.10 % Allowed : 10.55 % Favored : 87.34 % Rotamer: Outliers : 12.29 % Allowed : 18.36 % Favored : 69.35 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.12), residues: 3136 helix: -2.08 (0.17), residues: 631 sheet: -2.21 (0.17), residues: 763 loop : -3.21 (0.12), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.035 0.003 PHE H 24 TRP 0.025 0.004 TRP B 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01075 / 0.48 (26627) covalent geometry : angle 1.04695 / 0.60 (36215) SS BOND : bond 0.15297 / 9.17 ( 38) SS BOND : angle 14.04507 / 9.82 ( 76) hydrogen bonds : bond 0.19972 / 12.66 ( 882) hydrogen bonds : angle 8.16329 / 5.80 ( 2487) link_BETA1-4 : bond 0.04302 / 2.43 ( 21) link_BETA1-4 : angle 4.33069 / 2.80 ( 63) link_NAG-ASN : bond 0.02310 / 1.26 ( 48) link_NAG-ASN : angle 8.06827 / 5.86 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 346 poor density : 458 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ASN cc_start: 0.5027 (OUTLIER) cc_final: 0.4505 (m110) REVERT: A 164 ASN cc_start: 0.5832 (OUTLIER) cc_final: 0.5507 (m-40) REVERT: A 389 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7995 (p0) REVERT: A 517 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.3540 (tp) REVERT: A 900 MET cc_start: 0.7691 (mtp) cc_final: 0.7382 (mtp) REVERT: A 976 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 1051 SER cc_start: 0.9396 (m) cc_final: 0.9026 (p) REVERT: B 153 MET cc_start: 0.0157 (mpp) cc_final: -0.1937 (ptt) REVERT: B 587 ILE cc_start: 0.8272 (mt) cc_final: 0.8028 (mt) REVERT: B 710 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8093 (p0) REVERT: B 902 MET cc_start: 0.8760 (tpt) cc_final: 0.8497 (tpp) REVERT: B 916 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8854 (tp) REVERT: B 968 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7956 (p) REVERT: C 54 LEU cc_start: 0.4584 (mt) cc_final: 0.4328 (mt) REVERT: C 366 SER cc_start: 0.6876 (m) cc_final: 0.6402 (t) REVERT: C 369 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6086 (p90) REVERT: C 382 VAL cc_start: 0.7411 (OUTLIER) cc_final: 0.7119 (p) REVERT: C 583 GLU cc_start: 0.3771 (OUTLIER) cc_final: 0.3570 (tp30) REVERT: C 690 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: C 699 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7947 (mt) REVERT: C 900 MET cc_start: 0.8482 (mtp) cc_final: 0.8279 (mtm) REVERT: C 975 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8396 (p) REVERT: C 1050 MET cc_start: 0.8354 (ptm) cc_final: 0.8066 (ptm) REVERT: H 114 PHE cc_start: 0.0253 (OUTLIER) cc_final: -0.0144 (m-80) outliers start: 346 outliers final: 50 residues processed: 745 average time/residue: 0.1721 time to fit residues: 201.8720 Evaluate side-chains 251 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 186 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 116 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 66 HIS A 134 GLN A 137 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 422 ASN A 440 ASN A 540 ASN A 613 GLN A 644 GLN A 658 ASN A 764 ASN A 856 ASN A 901 GLN A 913 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 239 GLN B 394 ASN B 422 ASN B 487 ASN B 644 GLN B 710 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 137 ASN C 188 ASN C 196 ASN C 207 HIS C 370 ASN C 388 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 644 GLN C 658 ASN C 675 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 95 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.106558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.075059 restraints weight = 96820.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077331 restraints weight = 53643.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077420 restraints weight = 29592.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.077767 restraints weight = 24953.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.077695 restraints weight = 24531.681| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26734 Z= 0.192 Angle : 0.866 21.308 36498 Z= 0.420 Chirality : 0.051 0.467 4328 Planarity : 0.006 0.058 4573 Dihedral : 8.597 74.200 3543 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.30 % Favored : 92.54 % Rotamer: Outliers : 5.50 % Allowed : 22.51 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 3136 helix: 0.12 (0.21), residues: 639 sheet: -1.44 (0.17), residues: 788 loop : -2.66 (0.13), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 567 TYR 0.025 0.002 TYR C 453 PHE 0.022 0.002 PHE B 135 TRP 0.034 0.002 TRP C 104 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (26627) covalent geometry : angle 0.81250 / 0.41 (36215) SS BOND : bond 0.00434 / 0.26 ( 38) SS BOND : angle 1.89913 / 1.25 ( 76) hydrogen bonds : bond 0.04776 / 3.12 ( 882) hydrogen bonds : angle 6.13294 / 4.32 ( 2487) link_BETA1-4 : bond 0.00691 / 0.37 ( 21) link_BETA1-4 : angle 2.25442 / 1.56 ( 63) link_NAG-ASN : bond 0.00684 / 0.47 ( 48) link_NAG-ASN : angle 4.46034 / 2.91 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 213 time to evaluate : 0.950 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 122 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.5611 (m110) REVERT: A 191 GLU cc_start: 0.8641 (mp0) cc_final: 0.8332 (mt-10) REVERT: A 389 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7977 (p0) REVERT: A 900 MET cc_start: 0.8390 (mtp) cc_final: 0.8084 (mtp) REVERT: A 985 ASP cc_start: 0.8112 (p0) cc_final: 0.7690 (p0) REVERT: B 104 TRP cc_start: 0.7195 (m-90) cc_final: 0.6970 (m-90) REVERT: B 117 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 153 MET cc_start: -0.1021 (mpp) cc_final: -0.2226 (ptp) REVERT: B 417 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5481 (mmmt) REVERT: B 725 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7494 (mt-10) REVERT: B 773 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6988 (tm-30) REVERT: B 786 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8300 (mtmt) REVERT: B 912 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8824 (p) REVERT: C 52 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8183 (mm-40) REVERT: C 104 TRP cc_start: 0.6896 (m-90) cc_final: 0.6660 (m-90) REVERT: C 229 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6574 (tp) REVERT: C 369 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.5962 (p90) REVERT: C 583 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5542 (tp30) REVERT: C 699 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8143 (mt) REVERT: C 957 GLN cc_start: 0.8710 (tt0) cc_final: 0.8461 (tt0) REVERT: C 975 SER cc_start: 0.8839 (t) cc_final: 0.8565 (p) REVERT: H 39 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5326 (mp) outliers start: 155 outliers final: 79 residues processed: 351 average time/residue: 0.1494 time to fit residues: 86.4318 Evaluate side-chains 246 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 156 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 252 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 316 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 207 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 450 ASN A 804 GLN A 856 ASN B 49 HIS B 422 ASN B 913 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 115 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.103667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070974 restraints weight = 96662.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072559 restraints weight = 53121.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.073576 restraints weight = 36221.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074211 restraints weight = 28466.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074527 restraints weight = 24602.060| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 26734 Z= 0.171 Angle : 0.763 19.167 36498 Z= 0.366 Chirality : 0.049 0.432 4328 Planarity : 0.005 0.060 4573 Dihedral : 6.914 66.360 3479 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.59 % Favored : 92.25 % Rotamer: Outliers : 5.15 % Allowed : 22.55 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.14), residues: 3136 helix: 0.91 (0.21), residues: 642 sheet: -1.11 (0.17), residues: 804 loop : -2.32 (0.13), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.024 0.002 TYR C 904 PHE 0.026 0.002 PHE C 456 TRP 0.023 0.002 TRP C 104 HIS 0.024 0.002 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (26627) covalent geometry : angle 0.71762 / 0.36 (36215) SS BOND : bond 0.00653 / 0.41 ( 38) SS BOND : angle 1.72695 / 1.18 ( 76) hydrogen bonds : bond 0.04380 / 2.85 ( 882) hydrogen bonds : angle 5.59874 / 3.92 ( 2487) link_BETA1-4 : bond 0.00519 / 0.27 ( 21) link_BETA1-4 : angle 2.12624 / 1.47 ( 63) link_NAG-ASN : bond 0.00798 / 0.54 ( 48) link_NAG-ASN : angle 3.81120 / 2.51 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 169 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8748 (t80) cc_final: 0.8167 (t80) REVERT: A 135 PHE cc_start: 0.7714 (m-10) cc_final: 0.7405 (m-10) REVERT: A 141 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8971 (pp) REVERT: A 389 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7939 (p0) REVERT: A 822 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9020 (mm) REVERT: A 900 MET cc_start: 0.8456 (mtp) cc_final: 0.8174 (mtp) REVERT: A 985 ASP cc_start: 0.8099 (p0) cc_final: 0.7731 (p0) REVERT: A 1050 MET cc_start: 0.8692 (ptp) cc_final: 0.8346 (ptp) REVERT: B 153 MET cc_start: -0.1056 (mpp) cc_final: -0.2013 (ptm) REVERT: B 403 ARG cc_start: 0.7271 (tmm-80) cc_final: 0.7070 (tmm-80) REVERT: B 473 TYR cc_start: 0.5463 (OUTLIER) cc_final: 0.4955 (t80) REVERT: B 725 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 787 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: B 912 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8744 (p) REVERT: C 52 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8184 (mm-40) REVERT: C 66 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.6405 (t-90) REVERT: C 104 TRP cc_start: 0.6801 (OUTLIER) cc_final: 0.6477 (m-10) REVERT: C 118 LEU cc_start: 0.8124 (tp) cc_final: 0.7639 (mt) REVERT: C 369 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.5871 (p90) REVERT: C 973 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8735 (mt) REVERT: C 975 SER cc_start: 0.8999 (t) cc_final: 0.8709 (p) REVERT: H 39 ILE cc_start: 0.4820 (OUTLIER) cc_final: 0.4418 (mp) outliers start: 145 outliers final: 79 residues processed: 301 average time/residue: 0.1433 time to fit residues: 73.6278 Evaluate side-chains 226 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 136 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 196 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 313 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 613 GLN A 703 ASN B 913 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN B1142 GLN C 87 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** 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 = 0.3733 r_free = 0.3733 target = 0.095927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064330 restraints weight = 97169.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065658 restraints weight = 56310.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066547 restraints weight = 39736.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067097 restraints weight = 31685.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.067376 restraints weight = 27578.552| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 26734 Z= 0.350 Angle : 0.998 19.067 36498 Z= 0.477 Chirality : 0.057 0.541 4328 Planarity : 0.006 0.058 4573 Dihedral : 6.921 59.773 3462 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.86 % Favored : 91.01 % Rotamer: Outliers : 6.46 % Allowed : 22.09 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3136 helix: 0.60 (0.20), residues: 651 sheet: -1.08 (0.18), residues: 775 loop : -2.44 (0.13), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 214 TYR 0.034 0.003 TYR L 97 PHE 0.027 0.003 PHE B 802 TRP 0.043 0.003 TRP L 56 HIS 0.012 0.003 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00803 / 0.35 (26627) covalent geometry : angle 0.95678 / 0.47 (36215) SS BOND : bond 0.00855 / 0.50 ( 38) SS BOND : angle 2.12042 / 1.45 ( 76) hydrogen bonds : bond 0.05808 / 3.86 ( 882) hydrogen bonds : angle 6.12636 / 4.26 ( 2487) link_BETA1-4 : bond 0.00807 / 0.37 ( 21) link_BETA1-4 : angle 2.70361 / 1.83 ( 63) link_NAG-ASN : bond 0.00970 / 0.56 ( 48) link_NAG-ASN : angle 4.06363 / 2.69 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 138 time to evaluate : 1.027 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 135 PHE cc_start: 0.7903 (m-10) cc_final: 0.7472 (m-10) REVERT: A 141 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8791 (pp) REVERT: A 389 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7775 (p0) REVERT: A 765 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7904 (ttm-80) REVERT: A 779 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8915 (tt0) REVERT: A 822 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9094 (mm) REVERT: A 1050 MET cc_start: 0.8782 (ptp) cc_final: 0.8416 (ptp) REVERT: B 153 MET cc_start: -0.0732 (mpp) cc_final: -0.2428 (ptp) REVERT: B 1135 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8577 (t0) REVERT: C 52 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8334 (tp-100) REVERT: C 65 PHE cc_start: 0.7956 (m-10) cc_final: 0.7609 (m-10) REVERT: C 66 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6481 (t-90) REVERT: C 118 LEU cc_start: 0.7961 (tp) cc_final: 0.7359 (mt) REVERT: C 274 THR cc_start: 0.7310 (m) cc_final: 0.6615 (m) REVERT: C 342 PHE cc_start: 0.5950 (m-10) cc_final: 0.5411 (m-10) REVERT: C 369 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6037 (p90) REVERT: C 588 THR cc_start: 0.4087 (OUTLIER) cc_final: 0.3883 (p) REVERT: C 1135 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8229 (t0) outliers start: 182 outliers final: 110 residues processed: 309 average time/residue: 0.1431 time to fit residues: 75.1517 Evaluate side-chains 234 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 115 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 57 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 110 optimal weight: 0.2980 chunk 212 optimal weight: 8.9990 chunk 179 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 281 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 125 ASN B 607 GLN B 969 ASN B1071 GLN B1135 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.098735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066937 restraints weight = 95552.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.068393 restraints weight = 54210.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069320 restraints weight = 37580.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.069880 restraints weight = 29801.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070267 restraints weight = 25933.434| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26734 Z= 0.124 Angle : 0.734 19.393 36498 Z= 0.345 Chirality : 0.049 0.429 4328 Planarity : 0.004 0.046 4573 Dihedral : 6.037 59.294 3456 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.90 % Favored : 93.97 % Rotamer: Outliers : 3.87 % Allowed : 24.33 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3136 helix: 1.30 (0.21), residues: 646 sheet: -0.64 (0.18), residues: 787 loop : -2.23 (0.13), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.023 0.001 TYR A1067 PHE 0.015 0.001 PHE C 106 TRP 0.019 0.002 TRP C 104 HIS 0.008 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (26627) covalent geometry : angle 0.69470 / 0.34 (36215) SS BOND : bond 0.00423 / 0.26 ( 38) SS BOND : angle 1.54047 / 1.03 ( 76) hydrogen bonds : bond 0.04109 / 2.68 ( 882) hydrogen bonds : angle 5.36316 / 3.75 ( 2487) link_BETA1-4 : bond 0.00628 / 0.34 ( 21) link_BETA1-4 : angle 2.02444 / 1.37 ( 63) link_NAG-ASN : bond 0.00672 / 0.45 ( 48) link_NAG-ASN : angle 3.48207 / 2.33 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 149 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7750 (m-10) cc_final: 0.7544 (m-10) REVERT: A 141 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8697 (pp) REVERT: A 242 LEU cc_start: 0.8489 (mt) cc_final: 0.8069 (mp) REVERT: A 389 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7815 (p0) REVERT: A 456 PHE cc_start: 0.7598 (m-80) cc_final: 0.7272 (m-10) REVERT: A 765 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7809 (ttm-80) REVERT: A 822 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8900 (mm) REVERT: A 983 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7367 (ttp80) REVERT: A 1050 MET cc_start: 0.8727 (ptp) cc_final: 0.8191 (ptp) REVERT: B 122 ASN cc_start: 0.2240 (OUTLIER) cc_final: 0.1932 (p0) REVERT: B 153 MET cc_start: -0.0756 (mpp) cc_final: -0.2125 (ptp) REVERT: B 786 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8283 (mtmt) REVERT: B 959 LEU cc_start: 0.9652 (tp) cc_final: 0.9427 (tt) REVERT: B 1037 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8669 (p) REVERT: B 1135 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8445 (t0) REVERT: C 52 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8182 (tp-100) REVERT: C 66 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6614 (t-90) REVERT: C 118 LEU cc_start: 0.8010 (tp) cc_final: 0.7448 (mt) REVERT: C 274 THR cc_start: 0.7060 (m) cc_final: 0.6310 (m) REVERT: C 369 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6166 (p90) REVERT: C 506 GLN cc_start: 0.4100 (OUTLIER) cc_final: 0.3412 (mt0) REVERT: C 1135 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7890 (t0) outliers start: 109 outliers final: 61 residues processed: 249 average time/residue: 0.1411 time to fit residues: 58.7293 Evaluate side-chains 195 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 122 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 221 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 277 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 239 GLN A 762 GLN A 955 ASN B 751 ASN B1135 ASN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** H 99 HIS ** 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 = 0.3750 r_free = 0.3750 target = 0.096637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067941 restraints weight = 95751.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068275 restraints weight = 63734.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068128 restraints weight = 45002.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068429 restraints weight = 44414.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068531 restraints weight = 37779.764| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26734 Z= 0.216 Angle : 0.774 19.040 36498 Z= 0.363 Chirality : 0.049 0.468 4328 Planarity : 0.005 0.051 4573 Dihedral : 5.569 57.636 3445 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.65 % Favored : 92.22 % Rotamer: Outliers : 4.51 % Allowed : 23.72 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3136 helix: 1.41 (0.21), residues: 643 sheet: -0.70 (0.18), residues: 753 loop : -2.15 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 319 TYR 0.026 0.002 TYR A 200 PHE 0.023 0.002 PHE C 92 TRP 0.038 0.002 TRP C 104 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (26627) covalent geometry : angle 0.73631 / 0.35 (36215) SS BOND : bond 0.00427 / 0.27 ( 38) SS BOND : angle 1.59851 / 1.10 ( 76) hydrogen bonds : bond 0.04351 / 2.87 ( 882) hydrogen bonds : angle 5.40943 / 3.76 ( 2487) link_BETA1-4 : bond 0.00537 / 0.27 ( 21) link_BETA1-4 : angle 2.16128 / 1.47 ( 63) link_NAG-ASN : bond 0.00645 / 0.42 ( 48) link_NAG-ASN : angle 3.47729 / 2.32 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 122 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8166 (m-10) cc_final: 0.7873 (m-10) REVERT: A 141 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8828 (pp) REVERT: A 242 LEU cc_start: 0.8650 (mt) cc_final: 0.8341 (mp) REVERT: A 389 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7809 (p0) REVERT: A 456 PHE cc_start: 0.7510 (m-80) cc_final: 0.7207 (m-10) REVERT: A 822 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8994 (mm) REVERT: A 983 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7209 (ttp80) REVERT: A 1050 MET cc_start: 0.8497 (ptp) cc_final: 0.8022 (ptp) REVERT: B 153 MET cc_start: -0.0469 (mpp) cc_final: -0.1931 (ptt) REVERT: B 786 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8342 (mtmt) REVERT: B 1029 MET cc_start: 0.9055 (ttm) cc_final: 0.8826 (ttm) REVERT: B 1135 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8500 (t0) REVERT: C 66 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6672 (t-90) REVERT: C 118 LEU cc_start: 0.8084 (tp) cc_final: 0.7348 (mt) REVERT: C 369 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6231 (p90) REVERT: C 506 GLN cc_start: 0.4402 (OUTLIER) cc_final: 0.3632 (mt0) REVERT: C 1135 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8047 (t0) REVERT: H 116 TYR cc_start: 0.4962 (OUTLIER) cc_final: 0.3964 (t80) outliers start: 127 outliers final: 88 residues processed: 241 average time/residue: 0.1410 time to fit residues: 57.1515 Evaluate side-chains 214 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 115 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1135 ASN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 2 optimal weight: 10.0000 chunk 303 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 chunk 304 optimal weight: 50.0000 chunk 131 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 318 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 762 GLN B 121 ASN B 334 ASN B1135 ASN C 52 GLN C 207 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 414 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.097442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068601 restraints weight = 95515.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.068982 restraints weight = 60634.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069133 restraints weight = 44020.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.069540 restraints weight = 38766.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.069514 restraints weight = 33468.490| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26734 Z= 0.137 Angle : 0.711 19.223 36498 Z= 0.334 Chirality : 0.048 0.464 4328 Planarity : 0.004 0.054 4573 Dihedral : 5.379 57.969 3445 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.41 % Favored : 93.46 % Rotamer: Outliers : 3.87 % Allowed : 24.36 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3136 helix: 1.54 (0.21), residues: 647 sheet: -0.49 (0.18), residues: 768 loop : -2.09 (0.13), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 319 TYR 0.035 0.001 TYR A 200 PHE 0.027 0.001 PHE C 140 TRP 0.036 0.001 TRP C 104 HIS 0.018 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (26627) covalent geometry : angle 0.67069 / 0.32 (36215) SS BOND : bond 0.00416 / 0.29 ( 38) SS BOND : angle 1.95800 / 1.21 ( 76) hydrogen bonds : bond 0.03951 / 2.59 ( 882) hydrogen bonds : angle 5.22949 / 3.63 ( 2487) link_BETA1-4 : bond 0.00559 / 0.29 ( 21) link_BETA1-4 : angle 1.98145 / 1.34 ( 63) link_NAG-ASN : bond 0.00607 / 0.41 ( 48) link_NAG-ASN : angle 3.36151 / 2.25 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 127 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8172 (m-80) cc_final: 0.7893 (m-10) REVERT: A 141 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8789 (pp) REVERT: A 242 LEU cc_start: 0.8603 (mt) cc_final: 0.8295 (mp) REVERT: A 389 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7813 (p0) REVERT: A 456 PHE cc_start: 0.7519 (m-80) cc_final: 0.7242 (m-10) REVERT: A 765 ARG cc_start: 0.8265 (ttm-80) cc_final: 0.7972 (ttm-80) REVERT: A 822 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.8904 (mm) REVERT: A 983 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7212 (ttp80) REVERT: A 1050 MET cc_start: 0.8626 (ptp) cc_final: 0.7934 (ptp) REVERT: B 117 LEU cc_start: 0.8891 (tt) cc_final: 0.8450 (mp) REVERT: B 153 MET cc_start: -0.0354 (mpp) cc_final: -0.1599 (ptt) REVERT: B 341 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7774 (p) REVERT: B 969 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8207 (p0) REVERT: B 1037 SER cc_start: 0.9124 (OUTLIER) cc_final: 0.8689 (p) REVERT: C 52 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8208 (tp-100) REVERT: C 66 HIS cc_start: 0.7120 (OUTLIER) cc_final: 0.6871 (t-90) REVERT: C 99 ASN cc_start: 0.6920 (OUTLIER) cc_final: 0.6556 (t0) REVERT: C 118 LEU cc_start: 0.8151 (tp) cc_final: 0.7460 (mt) REVERT: C 342 PHE cc_start: 0.6078 (m-80) cc_final: 0.5851 (m-10) REVERT: C 369 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6091 (p90) REVERT: C 398 ASP cc_start: 0.6356 (m-30) cc_final: 0.4344 (t70) REVERT: C 506 GLN cc_start: 0.4185 (OUTLIER) cc_final: 0.3477 (mt0) REVERT: C 1135 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8148 (t0) REVERT: H 41 GLN cc_start: 0.6509 (mt0) cc_final: 0.5678 (mt0) outliers start: 109 outliers final: 73 residues processed: 228 average time/residue: 0.1534 time to fit residues: 59.1640 Evaluate side-chains 205 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 120 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 270 optimal weight: 0.9990 chunk 154 optimal weight: 0.0970 chunk 119 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN B 334 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** H 99 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 = 0.3731 r_free = 0.3731 target = 0.095659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066177 restraints weight = 96100.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067953 restraints weight = 57485.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.067780 restraints weight = 34782.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.068125 restraints weight = 30806.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068190 restraints weight = 28761.795| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26734 Z= 0.214 Angle : 0.763 18.859 36498 Z= 0.359 Chirality : 0.049 0.493 4328 Planarity : 0.005 0.053 4573 Dihedral : 5.396 57.360 3445 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 4.19 % Allowed : 23.93 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3136 helix: 1.55 (0.21), residues: 641 sheet: -0.49 (0.18), residues: 764 loop : -2.09 (0.13), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 319 TYR 0.025 0.002 TYR A1067 PHE 0.020 0.002 PHE C 140 TRP 0.029 0.002 TRP C 104 HIS 0.014 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (26627) covalent geometry : angle 0.72506 / 0.35 (36215) SS BOND : bond 0.00404 / 0.27 ( 38) SS BOND : angle 1.85996 / 1.20 ( 76) hydrogen bonds : bond 0.04261 / 2.82 ( 882) hydrogen bonds : angle 5.36064 / 3.72 ( 2487) link_BETA1-4 : bond 0.00534 / 0.27 ( 21) link_BETA1-4 : angle 2.12239 / 1.42 ( 63) link_NAG-ASN : bond 0.00654 / 0.43 ( 48) link_NAG-ASN : angle 3.38517 / 2.26 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 122 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8243 (m-80) cc_final: 0.7919 (m-10) REVERT: A 141 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8803 (pp) REVERT: A 204 TYR cc_start: 0.8894 (m-80) cc_final: 0.8637 (m-80) REVERT: A 242 LEU cc_start: 0.8625 (mt) cc_final: 0.8321 (mp) REVERT: A 389 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7818 (p0) REVERT: A 456 PHE cc_start: 0.7748 (m-80) cc_final: 0.7461 (m-10) REVERT: A 765 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.7819 (ttm-80) REVERT: A 822 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9039 (mm) REVERT: A 983 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7135 (ttp80) REVERT: B 153 MET cc_start: -0.0983 (mpp) cc_final: -0.1823 (ptp) REVERT: B 341 VAL cc_start: 0.7938 (OUTLIER) cc_final: 0.7675 (p) REVERT: B 969 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8244 (p0) REVERT: C 99 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6705 (t0) REVERT: C 118 LEU cc_start: 0.7995 (tp) cc_final: 0.7254 (mt) REVERT: C 369 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6063 (p90) REVERT: C 506 GLN cc_start: 0.4542 (OUTLIER) cc_final: 0.3890 (mt0) REVERT: H 41 GLN cc_start: 0.6473 (mt0) cc_final: 0.5766 (mt0) REVERT: H 116 TYR cc_start: 0.5326 (OUTLIER) cc_final: 0.4838 (t80) REVERT: L 51 LYS cc_start: 0.4506 (tppt) cc_final: 0.3992 (mptt) outliers start: 118 outliers final: 91 residues processed: 232 average time/residue: 0.1493 time to fit residues: 59.1199 Evaluate side-chains 215 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 114 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 106 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 159 optimal weight: 0.0370 chunk 71 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 8 optimal weight: 30.0000 chunk 108 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN A1071 GLN B 334 ASN B 354 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** L 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.097953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.069014 restraints weight = 95578.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070048 restraints weight = 57634.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.070002 restraints weight = 37041.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.070380 restraints weight = 36124.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070316 restraints weight = 31286.981| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26734 Z= 0.113 Angle : 0.689 19.194 36498 Z= 0.323 Chirality : 0.047 0.459 4328 Planarity : 0.004 0.047 4573 Dihedral : 5.018 55.581 3445 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 2.98 % Allowed : 25.04 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3136 helix: 1.81 (0.21), residues: 637 sheet: -0.16 (0.18), residues: 772 loop : -1.98 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 319 TYR 0.024 0.001 TYR L 97 PHE 0.019 0.001 PHE C 92 TRP 0.036 0.002 TRP C 104 HIS 0.010 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (26627) covalent geometry : angle 0.65357 / 0.31 (36215) SS BOND : bond 0.00385 / 0.25 ( 38) SS BOND : angle 1.50447 / 0.97 ( 76) hydrogen bonds : bond 0.03523 / 2.30 ( 882) hydrogen bonds : angle 4.99789 / 3.47 ( 2487) link_BETA1-4 : bond 0.00590 / 0.31 ( 21) link_BETA1-4 : angle 1.86616 / 1.24 ( 63) link_NAG-ASN : bond 0.00634 / 0.43 ( 48) link_NAG-ASN : angle 3.18417 / 2.16 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 138 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.8198 (m-80) cc_final: 0.7889 (m-10) REVERT: A 141 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8842 (pp) REVERT: A 242 LEU cc_start: 0.8681 (mt) cc_final: 0.8374 (mp) REVERT: A 389 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7829 (p0) REVERT: A 456 PHE cc_start: 0.7589 (m-80) cc_final: 0.7351 (m-10) REVERT: A 765 ARG cc_start: 0.8315 (ttm-80) cc_final: 0.7801 (ttm-80) REVERT: A 822 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 900 MET cc_start: 0.8488 (mtp) cc_final: 0.8281 (mtp) REVERT: A 983 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7152 (ttp80) REVERT: A 985 ASP cc_start: 0.7858 (p0) cc_final: 0.7624 (p0) REVERT: B 153 MET cc_start: -0.1085 (mpp) cc_final: -0.1822 (ptp) REVERT: B 1037 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8628 (p) REVERT: C 118 LEU cc_start: 0.7970 (tp) cc_final: 0.7241 (mt) REVERT: C 369 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6040 (p90) REVERT: C 506 GLN cc_start: 0.4253 (OUTLIER) cc_final: 0.3598 (mt0) REVERT: H 116 TYR cc_start: 0.5428 (OUTLIER) cc_final: 0.4494 (t80) outliers start: 84 outliers final: 63 residues processed: 213 average time/residue: 0.1549 time to fit residues: 55.5988 Evaluate side-chains 191 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 120 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 506 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 121 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 315 optimal weight: 40.0000 chunk 161 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 153 optimal weight: 0.1980 chunk 272 optimal weight: 0.6980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 334 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN H 99 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.095744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.064698 restraints weight = 95766.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066076 restraints weight = 54586.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066938 restraints weight = 38004.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067525 restraints weight = 30195.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.067842 restraints weight = 26217.540| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.7073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 26734 Z= 0.195 Angle : 0.735 18.842 36498 Z= 0.346 Chirality : 0.048 0.483 4328 Planarity : 0.004 0.048 4573 Dihedral : 5.045 53.360 3440 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 2.73 % Allowed : 25.25 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 3136 helix: 1.83 (0.21), residues: 635 sheet: -0.28 (0.18), residues: 767 loop : -1.99 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 319 TYR 0.025 0.002 TYR L 97 PHE 0.029 0.002 PHE C 106 TRP 0.030 0.002 TRP C 104 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (26627) covalent geometry : angle 0.69846 / 0.34 (36215) SS BOND : bond 0.00407 / 0.25 ( 38) SS BOND : angle 1.90602 / 1.25 ( 76) hydrogen bonds : bond 0.04099 / 2.71 ( 882) hydrogen bonds : angle 5.16249 / 3.58 ( 2487) link_BETA1-4 : bond 0.00471 / 0.23 ( 21) link_BETA1-4 : angle 2.08371 / 1.40 ( 63) link_NAG-ASN : bond 0.00620 / 0.40 ( 48) link_NAG-ASN : angle 3.25286 / 2.19 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 115 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.7881 (m-80) cc_final: 0.7678 (m-10) REVERT: A 141 LEU cc_start: 0.9072 (pt) cc_final: 0.8748 (pp) REVERT: A 228 ASP cc_start: 0.8061 (m-30) cc_final: 0.7803 (t0) REVERT: A 242 LEU cc_start: 0.8512 (mt) cc_final: 0.8156 (mp) REVERT: A 389 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7756 (p0) REVERT: A 456 PHE cc_start: 0.7744 (m-80) cc_final: 0.7486 (m-10) REVERT: A 765 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7804 (ttm-80) REVERT: A 822 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9045 (mm) REVERT: A 983 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7192 (ttp80) REVERT: B 53 ASP cc_start: 0.8121 (m-30) cc_final: 0.7866 (m-30) REVERT: B 153 MET cc_start: -0.0537 (mpp) cc_final: -0.1227 (ptp) REVERT: B 1037 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8731 (p) REVERT: C 118 LEU cc_start: 0.7888 (tp) cc_final: 0.7266 (mt) REVERT: C 369 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6096 (p90) REVERT: L 51 LYS cc_start: 0.4370 (tppt) cc_final: 0.4050 (mptt) outliers start: 77 outliers final: 62 residues processed: 183 average time/residue: 0.1571 time to fit residues: 48.7069 Evaluate side-chains 180 residues out of total 2816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 113 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 102 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 204 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 334 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.096055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.065097 restraints weight = 95025.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066499 restraints weight = 54000.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.067368 restraints weight = 37417.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067942 restraints weight = 29716.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.068233 restraints weight = 25748.453| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26734 Z= 0.160 Angle : 0.708 18.845 36498 Z= 0.332 Chirality : 0.048 0.476 4328 Planarity : 0.004 0.049 4573 Dihedral : 4.953 53.143 3436 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 2.88 % Allowed : 25.25 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.15), residues: 3136 helix: 1.85 (0.21), residues: 640 sheet: -0.26 (0.18), residues: 776 loop : -1.96 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 319 TYR 0.024 0.001 TYR L 97 PHE 0.031 0.001 PHE C 106 TRP 0.034 0.002 TRP C 104 HIS 0.015 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (26627) covalent geometry : angle 0.67149 / 0.32 (36215) SS BOND : bond 0.00367 / 0.23 ( 38) SS BOND : angle 1.77648 / 1.16 ( 76) hydrogen bonds : bond 0.03893 / 2.57 ( 882) hydrogen bonds : angle 5.08792 / 3.53 ( 2487) link_BETA1-4 : bond 0.00480 / 0.25 ( 21) link_BETA1-4 : angle 1.96923 / 1.32 ( 63) link_NAG-ASN : bond 0.00589 / 0.39 ( 48) link_NAG-ASN : angle 3.20170 / 2.17 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4624.33 seconds wall clock time: 80 minutes 58.49 seconds (4858.49 seconds total)