Starting phenix.real_space_refine on Fri Feb 6 18:37:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d03_30524/02_2026/7d03_30524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d03_30524/02_2026/7d03_30524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d03_30524/02_2026/7d03_30524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d03_30524/02_2026/7d03_30524.map" model { file = "/net/cci-nas-00/data/ceres_data/7d03_30524/02_2026/7d03_30524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d03_30524/02_2026/7d03_30524.cif" } resolution = 3.2 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= 0.004 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 117 5.16 5 C 17486 2.51 5 N 4481 2.21 5 O 5435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27519 Number of models: 1 Model: "" Number of chains: 28 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: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1727 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 16, 'TRANS': 213} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1579 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.59, per 1000 atoms: 0.24 Number of scatterers: 27519 At special positions: 0 Unit cell: (135.875, 171.746, 225.009, 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 117 16.00 O 5435 8.00 N 4481 7.00 C 17486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.22 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 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=2.05 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 H 102 " - pdb=" SG CYS H 112 " distance=2.19 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.04 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 B1410 " - " NAG B1411 " " 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-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 B1410 " - " ASN B1074 " " 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 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6396 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 52 sheets defined 21.0% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 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: 3.625A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.860A 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: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A 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: 3.993A 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: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.570A 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: 3.648A 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: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A 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: 3.640A 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: 3.631A 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: 3.637A 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: 3.545A 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: 4.011A 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: 3.605A 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: 4.120A 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: 3.508A 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: 3.616A 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: 4.069A 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: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A 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: 3.590A 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: 3.712A 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: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A 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 removed outlier: 3.946A pdb=" N ASP H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 92' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 186 through 193 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: 3.856A 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: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A 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: 3.775A 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: 6.084A 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: 3.780A 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: 3.543A 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: 7.847A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.786A 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: 4.790A 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: 6.604A 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: 6.604A 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: 4.700A 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: 6.294A 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: 6.947A 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: 5.743A 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: 4.620A 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: 3.673A 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: 6.799A 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: 6.698A 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: 6.799A 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: 6.698A 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: 3.619A 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: 4.596A 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: 6.441A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A 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: 6.295A 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: 3.730A 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: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A 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: 4.317A 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: 3.729A 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: 6.418A 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: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A 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 3 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.444A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA H 98 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR H 95 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR H 122 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.009A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 199 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 154 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 195 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 158 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 193 " --> pdb=" O LYS H 158 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.009A pdb=" N ALA H 152 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 199 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 154 " --> pdb=" O VAL H 197 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 197 " --> pdb=" O GLY H 154 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 156 " --> pdb=" O SER H 195 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 195 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 158 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 193 " --> pdb=" O LYS H 158 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 165 through 169 Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.974A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET L 49 " --> pdb=" O TRP L 37 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF5, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AF6, first strand: chain 'L' and resid 119 through 123 Processing sheet with id=AF7, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.442A pdb=" N TRP L 153 " --> pdb=" O VAL L 160 " (cutoff:3.500A) 1014 hydrogen bonds defined for protein. 2739 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: 6.51 Time building geometry restraints manager: 3.44 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: 5309 1.32 - 1.45: 8359 1.45 - 1.58: 14304 1.58 - 1.71: 0 1.71 - 1.84: 145 Bond restraints: 28117 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 4.38e+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 1.473 0.072 1.49e-02 4.50e+03 2.31e+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 2.25e+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 28112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 37292 2.74 - 5.47: 881 5.47 - 8.21: 64 8.21 - 10.94: 10 10.94 - 13.68: 6 Bond angle restraints: 38253 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 109.55 100.40 9.15 1.38e+00 5.25e-01 4.39e+01 angle pdb=" CA ILE A 692 " pdb=" C ILE A 692 " pdb=" N ILE A 693 " ideal model delta sigma weight residual 115.82 124.82 -9.00 1.52e+00 4.33e-01 3.51e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 ... (remaining 38248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15138 17.93 - 35.87: 1731 35.87 - 53.80: 562 53.80 - 71.74: 179 71.74 - 89.67: 54 Dihedral angle restraints: 17664 sinusoidal: 7737 harmonic: 9927 Sorted by residual: 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 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 21.06 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 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 17661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4551 0.329 - 0.657: 6 0.657 - 0.986: 3 0.986 - 1.315: 0 1.315 - 1.644: 2 Chirality restraints: 4562 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.15e+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 -0.76 -1.64 2.00e-01 2.50e+01 6.75e+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 5.39e+01 ... (remaining 4559 not shown) Planarity restraints: 4885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.160 2.00e-02 2.50e+03 2.12e-01 5.64e+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 " 0.120 2.00e-02 2.50e+03 1.72e-01 3.70e+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 331 " -0.100 2.00e-02 2.50e+03 9.91e-02 1.23e+02 pdb=" CG ASN A 331 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.137 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.127 2.00e-02 2.50e+03 ... (remaining 4882 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 259 2.51 - 3.11: 20154 3.11 - 3.71: 39503 3.71 - 4.30: 59092 4.30 - 4.90: 98046 Nonbonded interactions: 217054 Sorted by model distance: 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 1.981 3.120 nonbonded pdb=" O GLN C 564 " pdb=" O PHE C 565 " model vdw 2.005 3.040 nonbonded pdb=" NE2 GLN C 675 " pdb=" OG1 THR C 676 " model vdw 2.018 3.120 nonbonded pdb=" O ARG C 328 " pdb=" CD1 PHE C 329 " model vdw 2.062 3.340 ... (remaining 217049 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.280 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 0.548 28227 Z= 0.540 Angle : 1.318 51.430 38542 Z= 0.688 Chirality : 0.074 1.644 4562 Planarity : 0.007 0.095 4837 Dihedral : 17.931 89.671 11145 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 2.09 % Allowed : 10.59 % Favored : 87.31 % Rotamer: Outliers : 12.53 % Allowed : 19.00 % Favored : 68.47 % 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: -3.92 (0.12), residues: 3342 helix: -2.09 (0.17), residues: 647 sheet: -1.90 (0.15), residues: 900 loop : -3.28 (0.12), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP B 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01057 (28117) covalent geometry : angle 1.02784 (38253) SS BOND : bond 0.13037 ( 41) SS BOND : angle 13.90056 ( 82) hydrogen bonds : bond 0.19146 ( 956) hydrogen bonds : angle 7.98213 ( 2739) link_BETA1-4 : bond 0.04286 ( 21) link_BETA1-4 : angle 4.33293 ( 63) link_NAG-ASN : bond 0.02815 ( 48) link_NAG-ASN : angle 8.13910 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 374 poor density : 388 time to evaluate : 1.035 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 TARDY: cannot create tardy model for: "SER H 128 " (corrupted residue). Skipping it. REVERT: A 40 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6679 (p0) REVERT: A 97 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6010 (mttp) REVERT: A 200 TYR cc_start: 0.4815 (m-80) cc_final: 0.4591 (m-80) REVERT: A 324 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7140 (pt0) REVERT: A 328 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7200 (mmp-170) REVERT: A 569 ILE cc_start: 0.6936 (mp) cc_final: 0.6057 (mm) REVERT: A 878 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8730 (tt) REVERT: A 987 PRO cc_start: 0.7092 (Cg_exo) cc_final: 0.6678 (Cg_endo) REVERT: B 45 SER cc_start: 0.7675 (OUTLIER) cc_final: 0.7448 (m) REVERT: B 105 ILE cc_start: 0.7169 (pt) cc_final: 0.6946 (pt) REVERT: B 396 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.4871 (m-10) REVERT: B 536 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7600 (m-40) REVERT: B 585 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5894 (mt) REVERT: B 697 MET cc_start: 0.7833 (ptm) cc_final: 0.7575 (ptm) REVERT: B 990 GLU cc_start: 0.7946 (tt0) cc_final: 0.7740 (tt0) REVERT: C 153 MET cc_start: 0.2988 (mpp) cc_final: 0.1991 (mtp) REVERT: H 112 CYS cc_start: 0.1056 (OUTLIER) cc_final: 0.0764 (t) REVERT: L 49 MET cc_start: 0.1425 (pmm) cc_final: -0.0065 (ptp) outliers start: 374 outliers final: 107 residues processed: 715 average time/residue: 0.1750 time to fit residues: 201.6116 Evaluate side-chains 331 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 214 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 536 ASN Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 345 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 371 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS 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 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 111 ARG Chi-restraints excluded: chain H residue 112 CYS Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 197 optimal weight: 0.1980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 164 ASN A 188 ASN A 207 HIS A 422 ASN A 440 ASN A 498 GLN A 540 ASN A 644 GLN A 690 GLN A 762 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 960 ASN A 969 ASN A 992 GLN A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 207 HIS B 239 GLN B 314 GLN B 422 ASN B 487 ASN B 613 GLN B 644 GLN B 755 GLN B 762 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1054 GLN C 125 ASN C 134 GLN C 137 ASN C 188 ASN C 370 ASN C 409 GLN C 422 ASN C 487 ASN C 607 GLN C 613 GLN C 644 GLN C 675 GLN C 703 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS H 60 ASN L 40 GLN L 113 GLN L 193 HIS ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.186896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.121176 restraints weight = 46808.934| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.94 r_work: 0.3166 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28227 Z= 0.164 Angle : 0.809 20.581 38542 Z= 0.396 Chirality : 0.051 0.516 4562 Planarity : 0.006 0.077 4837 Dihedral : 10.485 94.417 5280 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 5.36 % Allowed : 20.58 % Favored : 74.06 % 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: -2.55 (0.13), residues: 3342 helix: -0.10 (0.20), residues: 667 sheet: -1.13 (0.16), residues: 879 loop : -2.72 (0.12), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 158 TYR 0.028 0.002 TYR H 104 PHE 0.028 0.002 PHE A 486 TRP 0.017 0.002 TRP H 114 HIS 0.006 0.001 HIS L 193 Details of bonding type rmsd covalent geometry : bond 0.00373 (28117) covalent geometry : angle 0.76370 (38253) SS BOND : bond 0.00755 ( 41) SS BOND : angle 1.99828 ( 82) hydrogen bonds : bond 0.04736 ( 956) hydrogen bonds : angle 5.87009 ( 2739) link_BETA1-4 : bond 0.00476 ( 21) link_BETA1-4 : angle 2.37544 ( 63) link_NAG-ASN : bond 0.00414 ( 48) link_NAG-ASN : angle 3.95413 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 222 time to evaluate : 0.854 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 128 " (corrupted residue). Skipping it. REVERT: A 200 TYR cc_start: 0.6765 (m-80) cc_final: 0.5929 (m-80) REVERT: A 226 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7580 (tp) REVERT: A 281 GLU cc_start: 0.8201 (pm20) cc_final: 0.7785 (pm20) REVERT: A 407 VAL cc_start: 0.5299 (OUTLIER) cc_final: 0.5039 (p) REVERT: A 452 LEU cc_start: 0.2144 (OUTLIER) cc_final: 0.1630 (tt) REVERT: A 878 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 985 ASP cc_start: 0.8110 (p0) cc_final: 0.6423 (p0) REVERT: B 45 SER cc_start: 0.8051 (t) cc_final: 0.7765 (m) REVERT: B 64 TRP cc_start: 0.7039 (t60) cc_final: 0.6800 (t60) REVERT: B 140 PHE cc_start: 0.8384 (p90) cc_final: 0.8184 (p90) REVERT: B 396 TYR cc_start: 0.4702 (OUTLIER) cc_final: 0.4326 (m-10) REVERT: B 422 ASN cc_start: 0.5092 (OUTLIER) cc_final: 0.4224 (p0) REVERT: B 697 MET cc_start: 0.8736 (ptm) cc_final: 0.8405 (ptm) REVERT: B 855 PHE cc_start: 0.7991 (m-10) cc_final: 0.7790 (m-10) REVERT: C 106 PHE cc_start: 0.6419 (m-80) cc_final: 0.6139 (m-80) REVERT: C 153 MET cc_start: 0.2535 (mpp) cc_final: 0.1196 (mtp) REVERT: C 369 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7242 (p90) REVERT: C 568 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5779 (t70) REVERT: C 856 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8014 (p0) REVERT: C 976 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8999 (m) REVERT: L 49 MET cc_start: 0.1803 (pmm) cc_final: 0.0864 (ptp) outliers start: 160 outliers final: 86 residues processed: 367 average time/residue: 0.1540 time to fit residues: 95.0421 Evaluate side-chains 266 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 170 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 208 optimal weight: 0.0470 chunk 298 optimal weight: 8.9990 chunk 270 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 336 optimal weight: 4.9990 chunk 302 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 overall best weight: 1.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 207 HIS A 955 ASN B 81 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 703 ASN B 762 GLN B 969 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 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 = 0.4335 r_free = 0.4335 target = 0.184935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121385 restraints weight = 46334.805| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.48 r_work: 0.3139 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28227 Z= 0.153 Angle : 0.734 18.715 38542 Z= 0.355 Chirality : 0.050 0.737 4562 Planarity : 0.005 0.063 4837 Dihedral : 8.957 89.469 5166 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.93 % Favored : 91.86 % Rotamer: Outliers : 4.69 % Allowed : 21.11 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.90 (0.14), residues: 3342 helix: 0.63 (0.21), residues: 665 sheet: -0.82 (0.16), residues: 917 loop : -2.34 (0.13), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 111 TYR 0.019 0.001 TYR A1067 PHE 0.020 0.002 PHE C 140 TRP 0.011 0.001 TRP H 49 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00352 (28117) covalent geometry : angle 0.69262 (38253) SS BOND : bond 0.00737 ( 41) SS BOND : angle 1.67461 ( 82) hydrogen bonds : bond 0.04369 ( 956) hydrogen bonds : angle 5.49257 ( 2739) link_BETA1-4 : bond 0.00477 ( 21) link_BETA1-4 : angle 2.39939 ( 63) link_NAG-ASN : bond 0.00612 ( 48) link_NAG-ASN : angle 3.55273 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 192 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6742 (m-40) REVERT: A 407 VAL cc_start: 0.5394 (OUTLIER) cc_final: 0.5178 (p) REVERT: A 568 ASP cc_start: 0.6454 (t0) cc_final: 0.6221 (t70) REVERT: A 569 ILE cc_start: 0.7509 (mm) cc_final: 0.6993 (mm) REVERT: A 878 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8718 (mt) REVERT: B 45 SER cc_start: 0.8188 (t) cc_final: 0.7922 (m) REVERT: B 140 PHE cc_start: 0.8445 (p90) cc_final: 0.8159 (p90) REVERT: B 396 TYR cc_start: 0.4749 (OUTLIER) cc_final: 0.4317 (m-10) REVERT: B 697 MET cc_start: 0.8851 (ptm) cc_final: 0.8636 (ptm) REVERT: C 153 MET cc_start: 0.2406 (mpp) cc_final: 0.1002 (mtp) REVERT: C 369 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7198 (p90) REVERT: C 856 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.7965 (p0) REVERT: L 49 MET cc_start: 0.1818 (pmm) cc_final: 0.1058 (ptp) REVERT: L 180 SER cc_start: -0.0037 (OUTLIER) cc_final: -0.0416 (p) outliers start: 140 outliers final: 85 residues processed: 312 average time/residue: 0.1535 time to fit residues: 81.9647 Evaluate side-chains 248 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 156 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 81 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU 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 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 180 SER Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 252 optimal weight: 0.0980 chunk 219 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 324 optimal weight: 30.0000 chunk 331 optimal weight: 50.0000 chunk 336 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 311 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN A1011 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 804 GLN H 186 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.181715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116184 restraints weight = 45839.036| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.12 r_work: 0.3071 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 28227 Z= 0.210 Angle : 0.756 18.568 38542 Z= 0.364 Chirality : 0.051 0.764 4562 Planarity : 0.005 0.066 4837 Dihedral : 8.487 83.312 5153 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.32 % Favored : 91.50 % Rotamer: Outliers : 5.23 % Allowed : 20.95 % Favored : 73.83 % 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: -1.64 (0.14), residues: 3342 helix: 0.88 (0.21), residues: 657 sheet: -0.67 (0.16), residues: 942 loop : -2.18 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 237 TYR 0.019 0.001 TYR B1067 PHE 0.021 0.002 PHE C 86 TRP 0.011 0.002 TRP H 36 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00506 (28117) covalent geometry : angle 0.71521 (38253) SS BOND : bond 0.00609 ( 41) SS BOND : angle 1.77475 ( 82) hydrogen bonds : bond 0.04752 ( 956) hydrogen bonds : angle 5.48356 ( 2739) link_BETA1-4 : bond 0.00569 ( 21) link_BETA1-4 : angle 2.42609 ( 63) link_NAG-ASN : bond 0.00710 ( 48) link_NAG-ASN : angle 3.56133 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 169 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6714 (mp) REVERT: A 191 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A 226 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7708 (tp) REVERT: A 335 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4845 (tt) REVERT: A 568 ASP cc_start: 0.6889 (t0) cc_final: 0.6648 (t0) REVERT: A 569 ILE cc_start: 0.7762 (mm) cc_final: 0.7387 (mm) REVERT: A 878 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8801 (tt) REVERT: A 1002 GLN cc_start: 0.8999 (tp40) cc_final: 0.8687 (tt0) REVERT: B 140 PHE cc_start: 0.8443 (p90) cc_final: 0.8230 (p90) REVERT: B 396 TYR cc_start: 0.5236 (OUTLIER) cc_final: 0.4728 (m-10) REVERT: B 473 TYR cc_start: 0.3892 (OUTLIER) cc_final: 0.3424 (m-10) REVERT: B 697 MET cc_start: 0.9000 (ptm) cc_final: 0.8795 (ptm) REVERT: B 796 ASP cc_start: 0.8241 (t0) cc_final: 0.8004 (t0) REVERT: C 153 MET cc_start: 0.3074 (mpp) cc_final: 0.1700 (mtp) REVERT: C 369 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7216 (p90) REVERT: C 389 ASP cc_start: 0.7757 (m-30) cc_final: 0.6124 (t0) REVERT: C 544 ASN cc_start: 0.7176 (OUTLIER) cc_final: 0.6880 (m-40) REVERT: C 856 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.7850 (p0) outliers start: 156 outliers final: 89 residues processed: 311 average time/residue: 0.1443 time to fit residues: 78.0309 Evaluate side-chains 255 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 156 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER 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 976 VAL Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 284 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 26 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 14 optimal weight: 0.4980 chunk 225 optimal weight: 0.5980 chunk 317 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 422 ASN ** L 202 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 = 0.4314 r_free = 0.4314 target = 0.183159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116760 restraints weight = 45845.268| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.82 r_work: 0.3101 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28227 Z= 0.126 Angle : 0.672 18.448 38542 Z= 0.322 Chirality : 0.047 0.626 4562 Planarity : 0.004 0.058 4837 Dihedral : 7.878 77.947 5142 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.64 % Favored : 93.18 % Rotamer: Outliers : 4.09 % Allowed : 21.55 % Favored : 74.36 % 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: -1.37 (0.14), residues: 3342 helix: 1.12 (0.21), residues: 663 sheet: -0.47 (0.16), residues: 947 loop : -2.04 (0.13), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.018 0.001 TYR B1067 PHE 0.016 0.001 PHE A 541 TRP 0.017 0.001 TRP H 114 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00288 (28117) covalent geometry : angle 0.63366 (38253) SS BOND : bond 0.00411 ( 41) SS BOND : angle 1.71615 ( 82) hydrogen bonds : bond 0.03837 ( 956) hydrogen bonds : angle 5.22163 ( 2739) link_BETA1-4 : bond 0.00553 ( 21) link_BETA1-4 : angle 2.21290 ( 63) link_NAG-ASN : bond 0.00590 ( 48) link_NAG-ASN : angle 3.20606 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 179 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.6746 (mp) REVERT: A 153 MET cc_start: 0.1465 (mpp) cc_final: 0.1072 (mpp) REVERT: A 191 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7236 (mp0) REVERT: A 226 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 568 ASP cc_start: 0.6697 (t0) cc_final: 0.6398 (t0) REVERT: A 569 ILE cc_start: 0.7768 (mm) cc_final: 0.7292 (mm) REVERT: A 878 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8826 (tt) REVERT: A 935 GLN cc_start: 0.9045 (tt0) cc_final: 0.8758 (tt0) REVERT: A 950 ASP cc_start: 0.8714 (m-30) cc_final: 0.8512 (m-30) REVERT: A 1002 GLN cc_start: 0.8995 (tp40) cc_final: 0.8576 (tt0) REVERT: B 396 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.4586 (m-10) REVERT: B 473 TYR cc_start: 0.3657 (OUTLIER) cc_final: 0.3029 (m-10) REVERT: B 787 GLN cc_start: 0.9208 (mp10) cc_final: 0.8905 (mp10) REVERT: C 153 MET cc_start: 0.3055 (mpp) cc_final: 0.1655 (mtp) REVERT: C 238 PHE cc_start: 0.5971 (p90) cc_final: 0.5082 (p90) REVERT: C 369 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7105 (p90) REVERT: C 389 ASP cc_start: 0.7696 (m-30) cc_final: 0.6057 (t0) REVERT: C 786 LYS cc_start: 0.8804 (pttm) cc_final: 0.8562 (pttp) REVERT: C 796 ASP cc_start: 0.8636 (t0) cc_final: 0.7847 (p0) REVERT: C 856 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.7814 (p0) REVERT: L 49 MET cc_start: 0.1168 (ptp) cc_final: 0.0534 (ptp) outliers start: 122 outliers final: 82 residues processed: 290 average time/residue: 0.1485 time to fit residues: 73.9870 Evaluate side-chains 256 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 167 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS 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 159 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 8.9990 chunk 279 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 556 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 422 ASN C 563 GLN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.183221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119094 restraints weight = 45903.867| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.30 r_work: 0.3091 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28227 Z= 0.125 Angle : 0.657 18.380 38542 Z= 0.314 Chirality : 0.047 0.579 4562 Planarity : 0.004 0.056 4837 Dihedral : 7.407 68.826 5135 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.06 % Favored : 92.82 % Rotamer: Outliers : 3.92 % Allowed : 21.62 % Favored : 74.46 % 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: -1.12 (0.14), residues: 3342 helix: 1.32 (0.21), residues: 664 sheet: -0.24 (0.16), residues: 947 loop : -1.93 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 454 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.001 PHE A 86 TRP 0.013 0.001 TRP H 38 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00290 (28117) covalent geometry : angle 0.62214 (38253) SS BOND : bond 0.00361 ( 41) SS BOND : angle 1.47306 ( 82) hydrogen bonds : bond 0.03692 ( 956) hydrogen bonds : angle 5.07522 ( 2739) link_BETA1-4 : bond 0.00504 ( 21) link_BETA1-4 : angle 2.14367 ( 63) link_NAG-ASN : bond 0.00578 ( 48) link_NAG-ASN : angle 3.08521 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 168 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.6733 (mp) REVERT: A 191 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7176 (mp0) REVERT: A 568 ASP cc_start: 0.6887 (t0) cc_final: 0.6578 (t0) REVERT: A 878 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8872 (tt) REVERT: A 935 GLN cc_start: 0.9043 (tt0) cc_final: 0.8789 (tt0) REVERT: A 988 GLU cc_start: 0.8636 (pt0) cc_final: 0.8376 (tp30) REVERT: A 1002 GLN cc_start: 0.9014 (tp40) cc_final: 0.8668 (tt0) REVERT: B 309 GLU cc_start: 0.8592 (pt0) cc_final: 0.8368 (mt-10) REVERT: B 396 TYR cc_start: 0.5011 (OUTLIER) cc_final: 0.4589 (m-10) REVERT: B 473 TYR cc_start: 0.3472 (OUTLIER) cc_final: 0.2958 (m-10) REVERT: B 546 LEU cc_start: 0.5012 (mp) cc_final: 0.4702 (tt) REVERT: B 787 GLN cc_start: 0.9219 (mp10) cc_final: 0.8789 (mt0) REVERT: B 796 ASP cc_start: 0.8205 (t0) cc_final: 0.7989 (t0) REVERT: B 855 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7660 (m-10) REVERT: B 878 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8958 (tt) REVERT: C 153 MET cc_start: 0.2957 (mpp) cc_final: 0.1333 (mtp) REVERT: C 350 VAL cc_start: 0.8587 (t) cc_final: 0.8305 (p) REVERT: C 369 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7060 (p90) REVERT: C 389 ASP cc_start: 0.7822 (m-30) cc_final: 0.6131 (t0) REVERT: C 786 LYS cc_start: 0.8809 (pttm) cc_final: 0.8537 (pttp) REVERT: C 796 ASP cc_start: 0.8655 (t0) cc_final: 0.7844 (p0) REVERT: C 856 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.7906 (p0) REVERT: H 153 LEU cc_start: 0.0184 (mp) cc_final: -0.0143 (pp) outliers start: 117 outliers final: 87 residues processed: 274 average time/residue: 0.1435 time to fit residues: 68.3050 Evaluate side-chains 254 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 159 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS 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 159 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 184 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 334 optimal weight: 50.0000 chunk 280 optimal weight: 7.9990 chunk 137 optimal weight: 0.0170 chunk 150 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 613 GLN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 563 GLN ** L 202 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 = 0.4286 r_free = 0.4286 target = 0.180877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116386 restraints weight = 45617.286| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.27 r_work: 0.3070 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28227 Z= 0.182 Angle : 0.695 18.316 38542 Z= 0.333 Chirality : 0.049 0.626 4562 Planarity : 0.004 0.057 4837 Dihedral : 7.473 61.632 5127 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.18 % Favored : 92.67 % Rotamer: Outliers : 3.89 % Allowed : 22.18 % Favored : 73.93 % 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: -1.12 (0.14), residues: 3342 helix: 1.25 (0.21), residues: 667 sheet: -0.27 (0.16), residues: 944 loop : -1.89 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.002 PHE C 86 TRP 0.014 0.001 TRP H 114 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00441 (28117) covalent geometry : angle 0.65980 (38253) SS BOND : bond 0.00450 ( 41) SS BOND : angle 1.60121 ( 82) hydrogen bonds : bond 0.04427 ( 956) hydrogen bonds : angle 5.20398 ( 2739) link_BETA1-4 : bond 0.00430 ( 21) link_BETA1-4 : angle 2.18873 ( 63) link_NAG-ASN : bond 0.00578 ( 48) link_NAG-ASN : angle 3.18912 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 167 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.6679 (mp) REVERT: A 153 MET cc_start: 0.1476 (mpp) cc_final: 0.1059 (mpp) REVERT: A 191 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7211 (mp0) REVERT: A 452 LEU cc_start: 0.2091 (OUTLIER) cc_final: 0.1673 (tt) REVERT: A 568 ASP cc_start: 0.7004 (t0) cc_final: 0.6765 (t0) REVERT: A 878 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8873 (tt) REVERT: A 935 GLN cc_start: 0.9040 (tt0) cc_final: 0.8801 (tt0) REVERT: A 1002 GLN cc_start: 0.9040 (tp40) cc_final: 0.8681 (tt0) REVERT: B 309 GLU cc_start: 0.8657 (pt0) cc_final: 0.8452 (mt-10) REVERT: B 380 TYR cc_start: 0.7598 (m-10) cc_final: 0.7319 (m-10) REVERT: B 396 TYR cc_start: 0.5348 (OUTLIER) cc_final: 0.4643 (m-10) REVERT: B 473 TYR cc_start: 0.3113 (OUTLIER) cc_final: 0.2809 (m-10) REVERT: B 546 LEU cc_start: 0.5158 (mp) cc_final: 0.4948 (tt) REVERT: B 787 GLN cc_start: 0.9236 (mp10) cc_final: 0.8794 (mt0) REVERT: B 796 ASP cc_start: 0.8292 (t0) cc_final: 0.8030 (t0) REVERT: B 855 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7453 (m-10) REVERT: C 153 MET cc_start: 0.2722 (mpp) cc_final: 0.1098 (mtp) REVERT: C 314 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 335 LEU cc_start: 0.6537 (mp) cc_final: 0.6146 (tt) REVERT: C 369 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7141 (p90) REVERT: C 786 LYS cc_start: 0.8734 (pttm) cc_final: 0.8507 (pttp) REVERT: C 796 ASP cc_start: 0.8671 (t0) cc_final: 0.7984 (p0) REVERT: C 856 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.7863 (p0) REVERT: H 153 LEU cc_start: 0.0174 (mp) cc_final: -0.0124 (pp) REVERT: L 49 MET cc_start: 0.1500 (ptp) cc_final: 0.1099 (ptp) outliers start: 116 outliers final: 87 residues processed: 271 average time/residue: 0.1455 time to fit residues: 68.4217 Evaluate side-chains 252 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 157 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 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 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS 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 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 212 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 243 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 303 optimal weight: 30.0000 chunk 255 optimal weight: 1.9990 chunk 300 optimal weight: 0.0070 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.182151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115947 restraints weight = 45779.143| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.45 r_work: 0.3106 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28227 Z= 0.125 Angle : 0.651 18.381 38542 Z= 0.311 Chirality : 0.047 0.568 4562 Planarity : 0.004 0.053 4837 Dihedral : 7.122 58.931 5124 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.51 % Rotamer: Outliers : 3.65 % Allowed : 22.42 % Favored : 73.93 % 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: -0.95 (0.14), residues: 3342 helix: 1.48 (0.21), residues: 666 sheet: -0.16 (0.16), residues: 951 loop : -1.82 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.019 0.001 TYR B1067 PHE 0.015 0.001 PHE A 541 TRP 0.016 0.001 TRP H 114 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00290 (28117) covalent geometry : angle 0.61855 (38253) SS BOND : bond 0.00375 ( 41) SS BOND : angle 1.35110 ( 82) hydrogen bonds : bond 0.03754 ( 956) hydrogen bonds : angle 5.03209 ( 2739) link_BETA1-4 : bond 0.00515 ( 21) link_BETA1-4 : angle 2.10694 ( 63) link_NAG-ASN : bond 0.00556 ( 48) link_NAG-ASN : angle 2.99666 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 155 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.6877 (mp) REVERT: A 153 MET cc_start: 0.1949 (mpp) cc_final: 0.1499 (mpp) REVERT: A 191 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 452 LEU cc_start: 0.2268 (OUTLIER) cc_final: 0.1762 (tt) REVERT: A 568 ASP cc_start: 0.6943 (t0) cc_final: 0.6674 (t0) REVERT: A 878 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8911 (tt) REVERT: A 1002 GLN cc_start: 0.8942 (tp40) cc_final: 0.8595 (tt0) REVERT: B 353 TRP cc_start: 0.6402 (p-90) cc_final: 0.5636 (p90) REVERT: B 396 TYR cc_start: 0.5672 (OUTLIER) cc_final: 0.5032 (m-10) REVERT: B 424 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.5062 (mmtt) REVERT: B 473 TYR cc_start: 0.2831 (OUTLIER) cc_final: 0.2507 (m-10) REVERT: B 787 GLN cc_start: 0.9211 (mp10) cc_final: 0.8769 (mt0) REVERT: B 796 ASP cc_start: 0.8251 (t0) cc_final: 0.8012 (t0) REVERT: B 855 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: C 153 MET cc_start: 0.2615 (mpp) cc_final: 0.1172 (mtt) REVERT: C 314 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 335 LEU cc_start: 0.6721 (mp) cc_final: 0.6366 (tt) REVERT: C 369 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6991 (p90) REVERT: C 389 ASP cc_start: 0.7808 (m-30) cc_final: 0.6090 (t0) REVERT: C 786 LYS cc_start: 0.8714 (pttm) cc_final: 0.8476 (pttp) REVERT: C 796 ASP cc_start: 0.8630 (t0) cc_final: 0.7995 (p0) REVERT: C 856 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.7844 (p0) REVERT: H 153 LEU cc_start: 0.0584 (mp) cc_final: 0.0082 (pp) REVERT: L 49 MET cc_start: 0.1263 (ptp) cc_final: 0.0576 (ptp) REVERT: L 122 LEU cc_start: 0.0952 (OUTLIER) cc_final: 0.0087 (mm) outliers start: 109 outliers final: 83 residues processed: 251 average time/residue: 0.1442 time to fit residues: 63.3309 Evaluate side-chains 243 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 150 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 424 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS 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 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 172 GLN Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 284 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 42 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 chunk 299 optimal weight: 40.0000 chunk 239 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116766 restraints weight = 45762.149| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.48 r_work: 0.3106 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28227 Z= 0.123 Angle : 0.641 18.343 38542 Z= 0.306 Chirality : 0.047 0.549 4562 Planarity : 0.004 0.053 4837 Dihedral : 6.905 59.426 5124 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.73 % Favored : 93.12 % Rotamer: Outliers : 3.45 % Allowed : 22.65 % Favored : 73.89 % 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: -0.83 (0.14), residues: 3342 helix: 1.55 (0.21), residues: 667 sheet: -0.05 (0.16), residues: 949 loop : -1.76 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.019 0.001 TYR B1067 PHE 0.015 0.001 PHE B 515 TRP 0.016 0.001 TRP H 114 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00285 (28117) covalent geometry : angle 0.60914 (38253) SS BOND : bond 0.00342 ( 41) SS BOND : angle 1.36370 ( 82) hydrogen bonds : bond 0.03627 ( 956) hydrogen bonds : angle 4.94430 ( 2739) link_BETA1-4 : bond 0.00514 ( 21) link_BETA1-4 : angle 2.06865 ( 63) link_NAG-ASN : bond 0.00545 ( 48) link_NAG-ASN : angle 2.93010 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 160 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.6868 (mp) REVERT: A 191 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7366 (mp0) REVERT: A 452 LEU cc_start: 0.2591 (OUTLIER) cc_final: 0.2057 (tt) REVERT: A 878 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8914 (tt) REVERT: A 1002 GLN cc_start: 0.8972 (tp40) cc_final: 0.8604 (tt0) REVERT: B 390 LEU cc_start: 0.7564 (mt) cc_final: 0.7317 (mt) REVERT: B 396 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.5094 (m-10) REVERT: B 473 TYR cc_start: 0.2887 (OUTLIER) cc_final: 0.2358 (m-10) REVERT: B 703 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8159 (p0) REVERT: B 787 GLN cc_start: 0.9210 (mp10) cc_final: 0.8774 (mt0) REVERT: B 796 ASP cc_start: 0.8264 (t0) cc_final: 0.8032 (t0) REVERT: C 153 MET cc_start: 0.2731 (mpp) cc_final: 0.1252 (mtt) REVERT: C 238 PHE cc_start: 0.5965 (p90) cc_final: 0.4974 (p90) REVERT: C 314 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 335 LEU cc_start: 0.6797 (mp) cc_final: 0.6380 (tt) REVERT: C 369 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6940 (p90) REVERT: C 389 ASP cc_start: 0.7895 (m-30) cc_final: 0.6196 (t0) REVERT: C 786 LYS cc_start: 0.8722 (pttm) cc_final: 0.8484 (pttp) REVERT: C 796 ASP cc_start: 0.8643 (t0) cc_final: 0.8011 (p0) REVERT: C 856 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.7828 (p0) REVERT: L 49 MET cc_start: 0.1736 (ptp) cc_final: 0.0992 (ptp) REVERT: L 122 LEU cc_start: 0.0990 (OUTLIER) cc_final: 0.0080 (mm) outliers start: 103 outliers final: 83 residues processed: 252 average time/residue: 0.1423 time to fit residues: 62.1705 Evaluate side-chains 243 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 151 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 172 GLN Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 162 optimal weight: 0.8980 chunk 136 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 84 optimal weight: 0.0170 chunk 80 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.181868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114330 restraints weight = 45754.139| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.48 r_work: 0.3090 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28227 Z= 0.139 Angle : 0.655 18.291 38542 Z= 0.312 Chirality : 0.047 0.560 4562 Planarity : 0.004 0.053 4837 Dihedral : 6.824 59.989 5121 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.79 % Favored : 93.06 % Rotamer: Outliers : 3.25 % Allowed : 22.89 % Favored : 73.86 % 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: -0.82 (0.14), residues: 3342 helix: 1.53 (0.21), residues: 667 sheet: -0.02 (0.16), residues: 938 loop : -1.75 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 454 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.001 PHE B 515 TRP 0.016 0.001 TRP B 353 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00328 (28117) covalent geometry : angle 0.62349 (38253) SS BOND : bond 0.00371 ( 41) SS BOND : angle 1.43006 ( 82) hydrogen bonds : bond 0.03791 ( 956) hydrogen bonds : angle 4.94409 ( 2739) link_BETA1-4 : bond 0.00485 ( 21) link_BETA1-4 : angle 2.07568 ( 63) link_NAG-ASN : bond 0.00536 ( 48) link_NAG-ASN : angle 2.94201 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 151 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.6839 (mp) REVERT: A 191 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7229 (mp0) REVERT: A 452 LEU cc_start: 0.2532 (OUTLIER) cc_final: 0.2018 (tt) REVERT: A 878 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8924 (tt) REVERT: A 1002 GLN cc_start: 0.8989 (tp40) cc_final: 0.8606 (tt0) REVERT: B 396 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.5198 (m-10) REVERT: B 473 TYR cc_start: 0.2869 (OUTLIER) cc_final: 0.2453 (m-10) REVERT: B 787 GLN cc_start: 0.9214 (mp10) cc_final: 0.8780 (mt0) REVERT: B 796 ASP cc_start: 0.8278 (t0) cc_final: 0.8014 (t0) REVERT: C 153 MET cc_start: 0.2582 (mpp) cc_final: 0.1140 (mtt) REVERT: C 238 PHE cc_start: 0.5922 (p90) cc_final: 0.4922 (p90) REVERT: C 314 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8088 (tm-30) REVERT: C 335 LEU cc_start: 0.6873 (mp) cc_final: 0.6423 (tt) REVERT: C 369 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6890 (p90) REVERT: C 389 ASP cc_start: 0.7935 (m-30) cc_final: 0.6194 (t0) REVERT: C 400 PHE cc_start: 0.8309 (p90) cc_final: 0.7451 (p90) REVERT: C 786 LYS cc_start: 0.8707 (pttm) cc_final: 0.8465 (pttp) REVERT: C 796 ASP cc_start: 0.8675 (t0) cc_final: 0.8059 (p0) REVERT: C 856 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.7851 (p0) REVERT: L 49 MET cc_start: 0.2346 (ptp) cc_final: 0.1902 (ptp) REVERT: L 122 LEU cc_start: 0.0925 (OUTLIER) cc_final: 0.0077 (mm) outliers start: 97 outliers final: 82 residues processed: 239 average time/residue: 0.1431 time to fit residues: 60.1617 Evaluate side-chains 236 residues out of total 2984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 146 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 172 GLN Chi-restraints excluded: chain L residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 294 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 313 optimal weight: 50.0000 chunk 87 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 188 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.181676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116387 restraints weight = 45449.506| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.88 r_work: 0.3082 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28227 Z= 0.139 Angle : 0.646 18.132 38542 Z= 0.308 Chirality : 0.047 0.560 4562 Planarity : 0.004 0.052 4837 Dihedral : 6.781 58.784 5121 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.06 % Favored : 92.79 % Rotamer: Outliers : 3.18 % Allowed : 22.79 % Favored : 74.03 % 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: -0.74 (0.14), residues: 3342 helix: 1.61 (0.21), residues: 665 sheet: 0.07 (0.17), residues: 936 loop : -1.72 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 454 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.001 PHE B 515 TRP 0.015 0.001 TRP H 114 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00330 (28117) covalent geometry : angle 0.61431 (38253) SS BOND : bond 0.00396 ( 41) SS BOND : angle 1.41978 ( 82) hydrogen bonds : bond 0.03773 ( 956) hydrogen bonds : angle 4.92735 ( 2739) link_BETA1-4 : bond 0.00530 ( 21) link_BETA1-4 : angle 2.06013 ( 63) link_NAG-ASN : bond 0.00537 ( 48) link_NAG-ASN : angle 2.91871 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10629.29 seconds wall clock time: 181 minutes 28.93 seconds (10888.93 seconds total)