Starting phenix.real_space_refine on Thu Mar 5 19:01:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dwz_30890/03_2026/7dwz_30890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dwz_30890/03_2026/7dwz_30890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dwz_30890/03_2026/7dwz_30890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dwz_30890/03_2026/7dwz_30890.map" model { file = "/net/cci-nas-00/data/ceres_data/7dwz_30890/03_2026/7dwz_30890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dwz_30890/03_2026/7dwz_30890.cif" } resolution = 3.3 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15637 2.51 5 N 3999 2.21 5 O 4854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24598 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "L" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.05, per 1000 atoms: 0.25 Number of scatterers: 24598 At special positions: 0 Unit cell: (136.962, 155.441, 168.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4854 8.00 N 3999 7.00 C 15637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.17 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=2.12 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=2.55 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.85 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.00 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=1.94 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.29 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 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=1.87 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 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 B1409 " - " NAG B1410 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " 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 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " 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 H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C 343 " " 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5660 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 23.8% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 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: 4.258A 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: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A 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: 3.629A 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: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A 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: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.599A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.854A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 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: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.604A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.702A 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: 4.245A 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: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A 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: 3.561A 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: 3.552A 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: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A 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: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.529A 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: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A 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 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: 3.680A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A 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: 4.101A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 6.192A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.332A 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=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: 7.849A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.671A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.587A 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: 6.607A 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: 6.245A 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: 5.969A 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=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.587A 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: 6.607A 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: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A 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: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, 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=AB7, 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: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A 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: 7.210A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 316 removed outlier: 6.009A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.501A pdb=" N VAL B 551 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.528A 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=AC8, first strand: chain 'B' and resid 702 through 704 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: 6.525A 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: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A 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=AD1, 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: 6.525A 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: 6.211A 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: 3.799A 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=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A 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=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, 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: 7.474A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A 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: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.305A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.525A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A 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: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A 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: 3.880A 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=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 881 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5753 1.33 - 1.45: 6233 1.45 - 1.58: 13005 1.58 - 1.70: 0 1.70 - 1.83: 135 Bond restraints: 25126 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 4.34e+01 bond pdb=" C THR B 588 " pdb=" N PRO B 589 " ideal model delta sigma weight residual 1.330 1.389 -0.058 1.23e-02 6.61e+03 2.26e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.14e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.85e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 ... (remaining 25121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 33339 2.74 - 5.49: 766 5.49 - 8.23: 59 8.23 - 10.98: 3 10.98 - 13.72: 7 Bond angle restraints: 34174 Sorted by residual: angle pdb=" N CYS A 538 " pdb=" CA CYS A 538 " pdb=" C CYS A 538 " ideal model delta sigma weight residual 110.24 100.85 9.39 1.47e+00 4.63e-01 4.08e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 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 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C THR A 588 " pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta sigma weight residual 119.90 114.13 5.77 1.02e+00 9.61e-01 3.20e+01 ... (remaining 34169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13630 17.93 - 35.87: 1539 35.87 - 53.80: 508 53.80 - 71.74: 179 71.74 - 89.67: 48 Dihedral angle restraints: 15904 sinusoidal: 7120 harmonic: 8784 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -3.61 -82.39 1 1.00e+01 1.00e-02 8.33e+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 17.00 76.00 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.06 71.94 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 15901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4078 0.330 - 0.660: 3 0.660 - 0.989: 4 0.989 - 1.319: 2 1.319 - 1.649: 4 Chirality restraints: 4091 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-02 2.50e+03 2.59e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.80e+01 ... (remaining 4088 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.158 2.00e-02 2.50e+03 1.87e-01 4.39e+02 pdb=" CG ASN C 331 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.315 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.093 2.00e-02 2.50e+03 1.42e-01 2.52e+02 pdb=" CG ASN C 234 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.252 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.104 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" CG ASN A 616 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.231 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.161 2.00e-02 2.50e+03 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 229 2.51 - 3.11: 17984 3.11 - 3.70: 34506 3.70 - 4.30: 52897 4.30 - 4.90: 88042 Nonbonded interactions: 193658 Sorted by model distance: nonbonded pdb=" O ILE C 332 " pdb=" OG1 THR C 333 " model vdw 1.909 3.040 nonbonded pdb=" O SER B 530 " pdb=" OG1 THR B 531 " model vdw 1.913 3.040 nonbonded pdb=" O LEU C 335 " pdb=" O CYS C 336 " model vdw 1.968 3.040 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.983 3.120 ... (remaining 193653 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 939 or resid 944 through 1408)) selection = (chain 'B' and resid 27 through 1408) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.480 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.013 0.516 25236 Z= 0.571 Angle : 1.471 65.570 34465 Z= 0.749 Chirality : 0.088 1.649 4091 Planarity : 0.008 0.091 4332 Dihedral : 17.982 89.672 10127 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 3.47 % Allowed : 10.15 % Favored : 86.37 % Rotamer: Outliers : 12.63 % Allowed : 18.34 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.13), residues: 2965 helix: -2.23 (0.16), residues: 663 sheet: -2.06 (0.17), residues: 730 loop : -3.40 (0.12), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.027 0.003 TYR B1067 PHE 0.026 0.003 PHE A 898 TRP 0.025 0.004 TRP C 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01189 (25126) covalent geometry : angle 1.03050 (34174) SS BOND : bond 0.10864 ( 39) SS BOND : angle 17.89324 ( 78) hydrogen bonds : bond 0.19466 ( 845) hydrogen bonds : angle 7.86929 ( 2394) link_BETA1-4 : bond 0.04421 ( 23) link_BETA1-4 : angle 5.58057 ( 69) link_NAG-ASN : bond 0.03095 ( 48) link_NAG-ASN : angle 8.81478 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 334 poor density : 402 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.2095 (OUTLIER) cc_final: 0.1813 (t0) REVERT: A 153 MET cc_start: 0.1103 (mpp) cc_final: -0.1435 (ttt) REVERT: A 324 GLU cc_start: 0.5247 (OUTLIER) cc_final: 0.4247 (pt0) REVERT: A 389 ASP cc_start: 0.3473 (OUTLIER) cc_final: 0.1850 (p0) REVERT: A 787 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8084 (mm110) REVERT: B 164 ASN cc_start: 0.2919 (OUTLIER) cc_final: 0.1409 (t0) REVERT: B 389 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6229 (t70) REVERT: B 514 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 529 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7939 (tppt) REVERT: B 1029 MET cc_start: 0.8743 (tpp) cc_final: 0.8349 (tpp) REVERT: C 66 HIS cc_start: 0.6130 (OUTLIER) cc_final: 0.5832 (t-90) REVERT: C 116 SER cc_start: 0.4141 (OUTLIER) cc_final: 0.3838 (m) REVERT: C 559 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.4777 (m-10) REVERT: C 690 GLN cc_start: 0.5225 (OUTLIER) cc_final: 0.4957 (pm20) outliers start: 334 outliers final: 89 residues processed: 679 average time/residue: 0.1717 time to fit residues: 183.3551 Evaluate side-chains 284 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 183 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 619 GLU 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 738 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 188 ASN A 271 GLN A 334 ASN A 422 ASN A 440 ASN A 564 GLN A 644 GLN A 764 ASN A 787 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 992 GLN A1101 HIS B 81 ASN B 134 GLN B 137 ASN B 188 ASN B 239 GLN B 317 ASN B 354 ASN B 498 GLN B 544 ASN B 655 HIS B 762 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 137 ASN C 422 ASN C 498 GLN C 564 GLN C 644 GLN C 690 GLN C 703 ASN C 751 ASN C 755 GLN C 784 GLN C 804 GLN C 856 ASN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 954 GLN C 992 GLN C1071 GLN C1101 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.170525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121864 restraints weight = 41871.900| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.28 r_work: 0.3230 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 25236 Z= 0.192 Angle : 0.853 22.755 34465 Z= 0.412 Chirality : 0.052 0.568 4091 Planarity : 0.006 0.076 4332 Dihedral : 10.367 72.850 4881 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.16 % Favored : 91.26 % Rotamer: Outliers : 6.16 % Allowed : 20.27 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.71 (0.14), residues: 2965 helix: -0.17 (0.20), residues: 656 sheet: -1.41 (0.18), residues: 742 loop : -2.82 (0.13), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 237 TYR 0.021 0.002 TYR C 369 PHE 0.018 0.002 PHE C 374 TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00440 (25126) covalent geometry : angle 0.79213 (34174) SS BOND : bond 0.00626 ( 39) SS BOND : angle 2.55012 ( 78) hydrogen bonds : bond 0.05126 ( 845) hydrogen bonds : angle 5.97214 ( 2394) link_BETA1-4 : bond 0.00677 ( 23) link_BETA1-4 : angle 2.39288 ( 69) link_NAG-ASN : bond 0.00544 ( 48) link_NAG-ASN : angle 4.34850 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 215 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1117 (mpp) cc_final: -0.0286 (mtp) REVERT: A 169 GLU cc_start: 0.4987 (OUTLIER) cc_final: 0.4300 (mm-30) REVERT: A 389 ASP cc_start: 0.3833 (OUTLIER) cc_final: 0.2417 (p0) REVERT: A 619 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: A 979 ASP cc_start: 0.7581 (m-30) cc_final: 0.7349 (t0) REVERT: B 53 ASP cc_start: 0.4526 (OUTLIER) cc_final: 0.4321 (t0) REVERT: B 55 PHE cc_start: 0.8034 (m-80) cc_final: 0.7749 (m-80) REVERT: B 190 ARG cc_start: 0.6171 (mmt180) cc_final: 0.5897 (mmt-90) REVERT: B 195 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5498 (ptpt) REVERT: B 356 LYS cc_start: 0.7797 (mtpp) cc_final: 0.6906 (tptt) REVERT: B 399 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7855 (m) REVERT: B 453 TYR cc_start: 0.7307 (p90) cc_final: 0.6410 (p90) REVERT: B 529 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8320 (mmtm) REVERT: B 867 ASP cc_start: 0.8401 (p0) cc_final: 0.8144 (m-30) REVERT: B 1029 MET cc_start: 0.9335 (tpp) cc_final: 0.8905 (tpp) REVERT: C 66 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.6142 (t-90) REVERT: C 106 PHE cc_start: 0.5765 (m-80) cc_final: 0.5542 (m-80) REVERT: C 157 PHE cc_start: 0.4857 (t80) cc_final: 0.4653 (t80) REVERT: C 239 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6663 (mm110) REVERT: C 356 LYS cc_start: 0.6847 (ttmm) cc_final: 0.6301 (pttt) REVERT: C 394 ASN cc_start: 0.6127 (m110) cc_final: 0.5753 (m110) REVERT: C 400 PHE cc_start: 0.8107 (p90) cc_final: 0.7435 (p90) REVERT: C 517 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5439 (mm) REVERT: C 558 LYS cc_start: 0.6900 (mttp) cc_final: 0.5906 (tptm) REVERT: C 814 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8038 (mtmm) outliers start: 163 outliers final: 91 residues processed: 361 average time/residue: 0.1508 time to fit residues: 89.0292 Evaluate side-chains 261 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 160 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 619 GLU 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 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN 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 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 592 PHE 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 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 213 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 264 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 44 optimal weight: 0.0980 chunk 285 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A1005 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 544 ASN C 49 HIS C 965 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.171484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124405 restraints weight = 41838.862| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.39 r_work: 0.3243 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25236 Z= 0.125 Angle : 0.724 18.623 34465 Z= 0.345 Chirality : 0.049 0.564 4091 Planarity : 0.005 0.085 4332 Dihedral : 8.778 74.382 4774 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.12 % Favored : 92.45 % Rotamer: Outliers : 4.27 % Allowed : 21.14 % Favored : 74.58 % 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: -1.94 (0.15), residues: 2965 helix: 0.61 (0.21), residues: 659 sheet: -0.98 (0.18), residues: 737 loop : -2.37 (0.14), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 328 TYR 0.041 0.001 TYR A 453 PHE 0.014 0.001 PHE C 400 TRP 0.005 0.001 TRP C 436 HIS 0.003 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00267 (25126) covalent geometry : angle 0.67088 (34174) SS BOND : bond 0.00357 ( 39) SS BOND : angle 1.96228 ( 78) hydrogen bonds : bond 0.04055 ( 845) hydrogen bonds : angle 5.47720 ( 2394) link_BETA1-4 : bond 0.00633 ( 23) link_BETA1-4 : angle 2.26978 ( 69) link_NAG-ASN : bond 0.00638 ( 48) link_NAG-ASN : angle 3.73175 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 186 time to evaluate : 0.826 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 99 ASN cc_start: 0.5821 (m110) cc_final: 0.5127 (p0) REVERT: A 153 MET cc_start: 0.1549 (mpp) cc_final: -0.0221 (mmm) REVERT: A 155 SER cc_start: 0.5012 (OUTLIER) cc_final: 0.4557 (m) REVERT: A 169 GLU cc_start: 0.4949 (OUTLIER) cc_final: 0.4699 (mm-30) REVERT: A 389 ASP cc_start: 0.4437 (OUTLIER) cc_final: 0.3206 (p0) REVERT: A 619 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: A 754 LEU cc_start: 0.8713 (mt) cc_final: 0.8441 (mt) REVERT: A 855 PHE cc_start: 0.5609 (OUTLIER) cc_final: 0.5190 (m-10) REVERT: B 55 PHE cc_start: 0.8022 (m-80) cc_final: 0.7629 (m-80) REVERT: B 191 GLU cc_start: 0.8043 (mp0) cc_final: 0.7243 (mp0) REVERT: B 299 THR cc_start: 0.8289 (m) cc_final: 0.7975 (p) REVERT: B 356 LYS cc_start: 0.7952 (mtpp) cc_final: 0.6948 (tptt) REVERT: B 453 TYR cc_start: 0.7273 (p90) cc_final: 0.6563 (p90) REVERT: B 529 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7832 (tppt) REVERT: B 791 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7913 (m) REVERT: B 1029 MET cc_start: 0.9285 (tpp) cc_final: 0.8897 (tpp) REVERT: C 134 GLN cc_start: 0.7097 (tm-30) cc_final: 0.6844 (pp30) REVERT: C 157 PHE cc_start: 0.5076 (t80) cc_final: 0.4812 (t80) REVERT: C 191 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 239 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6833 (mm110) REVERT: C 356 LYS cc_start: 0.6986 (ttmm) cc_final: 0.6438 (pttt) REVERT: C 517 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.5018 (mm) REVERT: C 529 LYS cc_start: 0.8328 (tppt) cc_final: 0.8007 (mmtm) REVERT: C 558 LYS cc_start: 0.6938 (mttp) cc_final: 0.5947 (tptm) REVERT: C 814 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7970 (mtmm) outliers start: 113 outliers final: 72 residues processed: 287 average time/residue: 0.1564 time to fit residues: 73.0306 Evaluate side-chains 234 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 153 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 619 GLU 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 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN 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 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 161 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 275 optimal weight: 4.9990 chunk 252 optimal weight: 0.0010 chunk 1 optimal weight: 4.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1071 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.167854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118530 restraints weight = 41543.899| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.26 r_work: 0.3196 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25236 Z= 0.166 Angle : 0.716 18.810 34465 Z= 0.342 Chirality : 0.049 0.541 4091 Planarity : 0.004 0.050 4332 Dihedral : 8.100 58.602 4762 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.08 % Favored : 92.55 % Rotamer: Outliers : 4.95 % Allowed : 21.18 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z 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: -1.72 (0.15), residues: 2965 helix: 0.85 (0.21), residues: 662 sheet: -0.89 (0.18), residues: 725 loop : -2.23 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 328 TYR 0.020 0.002 TYR C1067 PHE 0.018 0.001 PHE C 86 TRP 0.009 0.001 TRP A 64 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00391 (25126) covalent geometry : angle 0.67011 (34174) SS BOND : bond 0.00424 ( 39) SS BOND : angle 1.80289 ( 78) hydrogen bonds : bond 0.04465 ( 845) hydrogen bonds : angle 5.40733 ( 2394) link_BETA1-4 : bond 0.00584 ( 23) link_BETA1-4 : angle 2.19000 ( 69) link_NAG-ASN : bond 0.00665 ( 48) link_NAG-ASN : angle 3.47917 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 178 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5739 (m110) cc_final: 0.4821 (p0) REVERT: A 153 MET cc_start: 0.1736 (mpp) cc_final: -0.0236 (mtp) REVERT: A 155 SER cc_start: 0.5216 (OUTLIER) cc_final: 0.4962 (m) REVERT: A 169 GLU cc_start: 0.5358 (OUTLIER) cc_final: 0.5033 (mm-30) REVERT: A 233 ILE cc_start: 0.5085 (OUTLIER) cc_final: 0.4586 (mm) REVERT: A 389 ASP cc_start: 0.4411 (OUTLIER) cc_final: 0.3145 (p0) REVERT: A 754 LEU cc_start: 0.8987 (mt) cc_final: 0.8712 (mt) REVERT: A 855 PHE cc_start: 0.5917 (OUTLIER) cc_final: 0.5551 (m-80) REVERT: A 1092 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8466 (mt-10) REVERT: B 53 ASP cc_start: 0.4589 (OUTLIER) cc_final: 0.4317 (t0) REVERT: B 55 PHE cc_start: 0.8170 (m-80) cc_final: 0.7764 (m-80) REVERT: B 191 GLU cc_start: 0.8021 (mp0) cc_final: 0.7141 (mp0) REVERT: B 195 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5461 (ptpt) REVERT: B 453 TYR cc_start: 0.7354 (p90) cc_final: 0.6706 (p90) REVERT: B 529 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7619 (tppt) REVERT: B 791 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7875 (m) REVERT: B 1029 MET cc_start: 0.9332 (tpp) cc_final: 0.8995 (tpp) REVERT: C 66 HIS cc_start: 0.6627 (OUTLIER) cc_final: 0.6154 (t-90) REVERT: C 134 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7069 (pp30) REVERT: C 157 PHE cc_start: 0.4823 (t80) cc_final: 0.4556 (t80) REVERT: C 191 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7285 (tt0) REVERT: C 239 GLN cc_start: 0.6952 (mm-40) cc_final: 0.4863 (tm-30) REVERT: C 356 LYS cc_start: 0.6987 (ttmm) cc_final: 0.6241 (pttt) REVERT: C 370 ASN cc_start: 0.5226 (t0) cc_final: 0.4951 (p0) REVERT: C 453 TYR cc_start: 0.4460 (p90) cc_final: 0.4251 (p90) REVERT: C 517 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4909 (mm) REVERT: C 558 LYS cc_start: 0.6903 (mttp) cc_final: 0.5820 (tptm) REVERT: C 814 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: C 979 ASP cc_start: 0.7632 (t70) cc_final: 0.7415 (t70) outliers start: 131 outliers final: 81 residues processed: 294 average time/residue: 0.1534 time to fit residues: 75.3676 Evaluate side-chains 249 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 155 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 585 LEU 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 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU 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 53 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 PHE 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 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 210 optimal weight: 0.0570 chunk 299 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 291 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A1005 GLN B 388 ASN B 544 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** 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 = 0.4168 r_free = 0.4168 target = 0.168320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110881 restraints weight = 41239.135| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.56 r_work: 0.3138 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25236 Z= 0.128 Angle : 0.666 18.275 34465 Z= 0.315 Chirality : 0.048 0.463 4091 Planarity : 0.004 0.063 4332 Dihedral : 7.649 59.586 4759 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.78 % Favored : 92.88 % Rotamer: Outliers : 4.84 % Allowed : 21.60 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.41 (0.15), residues: 2965 helix: 1.20 (0.21), residues: 656 sheet: -0.66 (0.19), residues: 729 loop : -2.09 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.019 0.001 TYR A1067 PHE 0.018 0.001 PHE C 562 TRP 0.007 0.001 TRP B 436 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00293 (25126) covalent geometry : angle 0.62411 (34174) SS BOND : bond 0.00331 ( 39) SS BOND : angle 1.69281 ( 78) hydrogen bonds : bond 0.03896 ( 845) hydrogen bonds : angle 5.25987 ( 2394) link_BETA1-4 : bond 0.00556 ( 23) link_BETA1-4 : angle 2.10727 ( 69) link_NAG-ASN : bond 0.00558 ( 48) link_NAG-ASN : angle 3.17393 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 169 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5593 (m110) cc_final: 0.4625 (p0) REVERT: A 153 MET cc_start: 0.1112 (mpp) cc_final: 0.0885 (pmm) REVERT: A 155 SER cc_start: 0.5379 (OUTLIER) cc_final: 0.5175 (m) REVERT: A 169 GLU cc_start: 0.5339 (OUTLIER) cc_final: 0.4998 (mm-30) REVERT: A 233 ILE cc_start: 0.5060 (OUTLIER) cc_final: 0.4569 (mm) REVERT: A 389 ASP cc_start: 0.4383 (OUTLIER) cc_final: 0.3203 (p0) REVERT: A 855 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.5549 (m-80) REVERT: B 55 PHE cc_start: 0.8096 (m-80) cc_final: 0.7575 (m-80) REVERT: B 191 GLU cc_start: 0.7947 (mp0) cc_final: 0.6926 (mp0) REVERT: B 195 LYS cc_start: 0.5807 (OUTLIER) cc_final: 0.5486 (ptpt) REVERT: B 453 TYR cc_start: 0.7112 (p90) cc_final: 0.6657 (p90) REVERT: B 529 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7695 (tppt) REVERT: B 791 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (m) REVERT: B 1128 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9005 (p) REVERT: C 66 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.6182 (t-90) REVERT: C 134 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6910 (pp30) REVERT: C 157 PHE cc_start: 0.4893 (t80) cc_final: 0.4397 (t80) REVERT: C 191 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7310 (mt-10) REVERT: C 237 ARG cc_start: 0.5985 (mmt90) cc_final: 0.5637 (mtt180) REVERT: C 239 GLN cc_start: 0.6892 (mm-40) cc_final: 0.4830 (tm-30) REVERT: C 356 LYS cc_start: 0.6907 (ttmm) cc_final: 0.6016 (pttt) REVERT: C 370 ASN cc_start: 0.5340 (t0) cc_final: 0.4963 (p0) REVERT: C 453 TYR cc_start: 0.4394 (p90) cc_final: 0.4184 (p90) REVERT: C 517 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4733 (mm) REVERT: C 558 LYS cc_start: 0.6874 (mttp) cc_final: 0.6595 (mttp) REVERT: C 645 THR cc_start: 0.8574 (m) cc_final: 0.8310 (p) REVERT: C 675 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: C 814 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8315 (mtmt) outliers start: 128 outliers final: 77 residues processed: 282 average time/residue: 0.1448 time to fit residues: 69.1557 Evaluate side-chains 241 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 151 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 82 optimal weight: 0.0470 chunk 14 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 144 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 272 optimal weight: 0.2980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 388 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.168229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111720 restraints weight = 41221.070| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.78 r_work: 0.3163 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25236 Z= 0.123 Angle : 0.658 18.175 34465 Z= 0.311 Chirality : 0.048 0.476 4091 Planarity : 0.004 0.054 4332 Dihedral : 7.297 59.827 4750 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.61 % Favored : 93.02 % Rotamer: Outliers : 4.27 % Allowed : 21.75 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.22 (0.15), residues: 2965 helix: 1.41 (0.21), residues: 658 sheet: -0.55 (0.19), residues: 729 loop : -1.99 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.019 0.001 TYR A1067 PHE 0.015 0.001 PHE C 86 TRP 0.006 0.001 TRP B 436 HIS 0.002 0.000 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00279 (25126) covalent geometry : angle 0.61410 (34174) SS BOND : bond 0.00347 ( 39) SS BOND : angle 1.59031 ( 78) hydrogen bonds : bond 0.03722 ( 845) hydrogen bonds : angle 5.16410 ( 2394) link_BETA1-4 : bond 0.00561 ( 23) link_BETA1-4 : angle 2.05969 ( 69) link_NAG-ASN : bond 0.00556 ( 48) link_NAG-ASN : angle 3.26414 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 155 time to evaluate : 0.937 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 99 ASN cc_start: 0.5571 (m110) cc_final: 0.4623 (p0) REVERT: A 169 GLU cc_start: 0.5429 (OUTLIER) cc_final: 0.5002 (mm-30) REVERT: A 233 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4455 (mm) REVERT: A 389 ASP cc_start: 0.4547 (OUTLIER) cc_final: 0.3330 (p0) REVERT: A 855 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.5510 (m-80) REVERT: A 979 ASP cc_start: 0.8250 (t70) cc_final: 0.7881 (m-30) REVERT: B 55 PHE cc_start: 0.8152 (m-80) cc_final: 0.7620 (m-80) REVERT: B 191 GLU cc_start: 0.7962 (mp0) cc_final: 0.6930 (mp0) REVERT: B 195 LYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5493 (ptpt) REVERT: B 453 TYR cc_start: 0.7080 (p90) cc_final: 0.6745 (p90) REVERT: B 508 TYR cc_start: 0.7548 (m-80) cc_final: 0.7212 (m-80) REVERT: B 529 LYS cc_start: 0.8450 (ttpm) cc_final: 0.7717 (tppt) REVERT: B 791 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7883 (m) REVERT: B 1128 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8997 (p) REVERT: C 58 PHE cc_start: 0.6978 (m-80) cc_final: 0.6379 (m-80) REVERT: C 66 HIS cc_start: 0.6542 (OUTLIER) cc_final: 0.6052 (t-90) REVERT: C 134 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6782 (pp30) REVERT: C 191 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7108 (mt-10) REVERT: C 237 ARG cc_start: 0.5969 (mmt90) cc_final: 0.5700 (mtt180) REVERT: C 239 GLN cc_start: 0.6726 (mm-40) cc_final: 0.4889 (tm-30) REVERT: C 356 LYS cc_start: 0.6922 (ttmm) cc_final: 0.6034 (pttt) REVERT: C 370 ASN cc_start: 0.5311 (t0) cc_final: 0.4957 (p0) REVERT: C 453 TYR cc_start: 0.4404 (p90) cc_final: 0.4086 (p90) REVERT: C 645 THR cc_start: 0.8505 (m) cc_final: 0.8270 (p) REVERT: C 814 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8279 (mtmt) outliers start: 113 outliers final: 82 residues processed: 253 average time/residue: 0.1485 time to fit residues: 63.4392 Evaluate side-chains 238 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 147 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1092 GLU 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 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 50 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 142 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 394 ASN A 607 GLN A 824 ASN A 955 ASN A1011 GLN B 99 ASN B1106 GLN C 207 HIS C 450 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 914 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.163364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111457 restraints weight = 41475.271| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.32 r_work: 0.3127 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 25236 Z= 0.249 Angle : 0.787 18.673 34465 Z= 0.377 Chirality : 0.052 0.511 4091 Planarity : 0.005 0.052 4332 Dihedral : 7.839 59.842 4742 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.09 % Favored : 91.53 % Rotamer: Outliers : 4.84 % Allowed : 21.52 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.49 (0.15), residues: 2965 helix: 0.97 (0.21), residues: 669 sheet: -0.69 (0.19), residues: 713 loop : -2.07 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 905 TYR 0.023 0.002 TYR C1067 PHE 0.031 0.002 PHE B 157 TRP 0.014 0.002 TRP A 353 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00603 (25126) covalent geometry : angle 0.74443 (34174) SS BOND : bond 0.00498 ( 39) SS BOND : angle 2.05917 ( 78) hydrogen bonds : bond 0.05440 ( 845) hydrogen bonds : angle 5.60612 ( 2394) link_BETA1-4 : bond 0.00476 ( 23) link_BETA1-4 : angle 2.24294 ( 69) link_NAG-ASN : bond 0.00562 ( 48) link_NAG-ASN : angle 3.48095 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 159 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8276 (p) cc_final: 0.8015 (p) REVERT: A 99 ASN cc_start: 0.5900 (m110) cc_final: 0.5095 (p0) REVERT: A 153 MET cc_start: -0.1247 (pmm) cc_final: -0.3408 (tpt) REVERT: A 169 GLU cc_start: 0.5467 (OUTLIER) cc_final: 0.4870 (mm-30) REVERT: A 233 ILE cc_start: 0.4998 (OUTLIER) cc_final: 0.4512 (mm) REVERT: A 389 ASP cc_start: 0.4089 (OUTLIER) cc_final: 0.2527 (p0) REVERT: A 453 TYR cc_start: 0.1376 (OUTLIER) cc_final: 0.0563 (p90) REVERT: A 855 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.5811 (m-80) REVERT: A 979 ASP cc_start: 0.8579 (t70) cc_final: 0.7876 (t0) REVERT: B 53 ASP cc_start: 0.4554 (OUTLIER) cc_final: 0.4271 (t0) REVERT: B 55 PHE cc_start: 0.8350 (m-80) cc_final: 0.7859 (m-80) REVERT: B 191 GLU cc_start: 0.8050 (mp0) cc_final: 0.7187 (mp0) REVERT: B 195 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5487 (ptpt) REVERT: B 342 PHE cc_start: 0.7568 (m-80) cc_final: 0.7194 (m-80) REVERT: B 453 TYR cc_start: 0.7599 (p90) cc_final: 0.7391 (p90) REVERT: B 529 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7770 (tppt) REVERT: B 791 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7878 (m) REVERT: C 66 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6199 (t-90) REVERT: C 96 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.4069 (pt0) REVERT: C 134 GLN cc_start: 0.7397 (tm-30) cc_final: 0.7040 (pp30) REVERT: C 191 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 237 ARG cc_start: 0.6241 (mmt90) cc_final: 0.5953 (mtt180) REVERT: C 239 GLN cc_start: 0.6951 (mm-40) cc_final: 0.5117 (tm-30) REVERT: C 356 LYS cc_start: 0.7022 (ttmm) cc_final: 0.5984 (ttpt) REVERT: C 370 ASN cc_start: 0.5409 (t0) cc_final: 0.4947 (p0) REVERT: C 558 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6597 (mttp) REVERT: C 645 THR cc_start: 0.8691 (m) cc_final: 0.8446 (p) REVERT: C 675 GLN cc_start: 0.6818 (OUTLIER) cc_final: 0.6593 (tm-30) REVERT: C 814 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8408 (mtmm) outliers start: 128 outliers final: 87 residues processed: 274 average time/residue: 0.1369 time to fit residues: 63.7843 Evaluate side-chains 244 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 143 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1092 GLU 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 53 ASP Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 2 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 121 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.164728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118531 restraints weight = 41233.401| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.29 r_work: 0.3168 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25236 Z= 0.164 Angle : 0.694 18.076 34465 Z= 0.330 Chirality : 0.049 0.505 4091 Planarity : 0.004 0.060 4332 Dihedral : 7.403 59.133 4738 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.68 % Favored : 93.02 % Rotamer: Outliers : 4.16 % Allowed : 22.01 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2965 helix: 1.19 (0.21), residues: 665 sheet: -0.56 (0.19), residues: 690 loop : -1.97 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 34 TYR 0.020 0.001 TYR C1067 PHE 0.021 0.001 PHE B 157 TRP 0.007 0.001 TRP B 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00393 (25126) covalent geometry : angle 0.65324 (34174) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.72579 ( 78) hydrogen bonds : bond 0.04345 ( 845) hydrogen bonds : angle 5.33424 ( 2394) link_BETA1-4 : bond 0.00482 ( 23) link_BETA1-4 : angle 2.10280 ( 69) link_NAG-ASN : bond 0.00540 ( 48) link_NAG-ASN : angle 3.20495 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 151 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8229 (p) cc_final: 0.7961 (p) REVERT: A 153 MET cc_start: -0.1223 (pmm) cc_final: -0.1562 (pmm) REVERT: A 169 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.5153 (mm-30) REVERT: A 233 ILE cc_start: 0.4952 (OUTLIER) cc_final: 0.4460 (mm) REVERT: A 389 ASP cc_start: 0.3910 (OUTLIER) cc_final: 0.2325 (p0) REVERT: A 855 PHE cc_start: 0.5853 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: A 979 ASP cc_start: 0.8582 (t70) cc_final: 0.7898 (t0) REVERT: A 1002 GLN cc_start: 0.8884 (tp40) cc_final: 0.8527 (tt0) REVERT: B 55 PHE cc_start: 0.8302 (m-80) cc_final: 0.7839 (m-80) REVERT: B 191 GLU cc_start: 0.8035 (mp0) cc_final: 0.7348 (mp0) REVERT: B 195 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5607 (ptpt) REVERT: B 342 PHE cc_start: 0.7561 (m-80) cc_final: 0.7211 (m-80) REVERT: B 529 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7788 (tppt) REVERT: B 616 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7596 (m-40) REVERT: B 791 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7945 (m) REVERT: B 985 ASP cc_start: 0.7700 (p0) cc_final: 0.6409 (p0) REVERT: B 1141 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 66 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.6207 (t-90) REVERT: C 96 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4151 (pm20) REVERT: C 134 GLN cc_start: 0.7311 (tm-30) cc_final: 0.6916 (pp30) REVERT: C 135 PHE cc_start: 0.5094 (m-80) cc_final: 0.4828 (m-80) REVERT: C 191 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7097 (mt-10) REVERT: C 237 ARG cc_start: 0.6547 (mmt90) cc_final: 0.6281 (mtt180) REVERT: C 239 GLN cc_start: 0.7009 (mm-40) cc_final: 0.5152 (tm-30) REVERT: C 356 LYS cc_start: 0.7096 (ttmm) cc_final: 0.6086 (ttpt) REVERT: C 370 ASN cc_start: 0.5490 (t0) cc_final: 0.5050 (p0) REVERT: C 558 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6564 (mttp) REVERT: C 814 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8357 (mtmm) outliers start: 110 outliers final: 88 residues processed: 247 average time/residue: 0.1446 time to fit residues: 60.3026 Evaluate side-chains 243 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 142 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL 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 83 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 201 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 195 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.163270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117713 restraints weight = 41073.215| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.23 r_work: 0.3162 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25236 Z= 0.206 Angle : 0.728 17.976 34465 Z= 0.348 Chirality : 0.050 0.485 4091 Planarity : 0.005 0.052 4332 Dihedral : 7.526 59.847 4738 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.03 % Favored : 91.67 % Rotamer: Outliers : 4.16 % Allowed : 22.24 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.34 (0.15), residues: 2965 helix: 1.18 (0.21), residues: 663 sheet: -0.64 (0.19), residues: 692 loop : -1.98 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 995 TYR 0.025 0.002 TYR B 495 PHE 0.024 0.002 PHE C 86 TRP 0.011 0.001 TRP A 353 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00500 (25126) covalent geometry : angle 0.68759 (34174) SS BOND : bond 0.00400 ( 39) SS BOND : angle 1.79991 ( 78) hydrogen bonds : bond 0.04782 ( 845) hydrogen bonds : angle 5.37350 ( 2394) link_BETA1-4 : bond 0.00492 ( 23) link_BETA1-4 : angle 2.15400 ( 69) link_NAG-ASN : bond 0.00532 ( 48) link_NAG-ASN : angle 3.26496 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 145 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8235 (p) cc_final: 0.7989 (p) REVERT: A 153 MET cc_start: -0.1491 (pmm) cc_final: -0.3264 (tpt) REVERT: A 233 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.4318 (mm) REVERT: A 389 ASP cc_start: 0.3299 (OUTLIER) cc_final: 0.1943 (p0) REVERT: A 421 TYR cc_start: 0.0349 (OUTLIER) cc_final: 0.0141 (p90) REVERT: A 855 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5663 (m-80) REVERT: A 979 ASP cc_start: 0.8766 (t70) cc_final: 0.8158 (t0) REVERT: B 55 PHE cc_start: 0.8329 (m-80) cc_final: 0.7905 (m-80) REVERT: B 105 ILE cc_start: 0.5012 (OUTLIER) cc_final: 0.4567 (mm) REVERT: B 191 GLU cc_start: 0.8086 (mp0) cc_final: 0.7377 (mp0) REVERT: B 195 LYS cc_start: 0.5843 (OUTLIER) cc_final: 0.5501 (ptpt) REVERT: B 342 PHE cc_start: 0.7661 (m-80) cc_final: 0.7272 (m-80) REVERT: B 529 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7808 (tppt) REVERT: B 616 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7416 (m-40) REVERT: B 791 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7835 (m) REVERT: C 134 GLN cc_start: 0.7227 (tm-30) cc_final: 0.6872 (pp30) REVERT: C 191 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7077 (mt-10) REVERT: C 237 ARG cc_start: 0.6650 (mmt90) cc_final: 0.6441 (mtt180) REVERT: C 239 GLN cc_start: 0.6933 (mm-40) cc_final: 0.5241 (tm-30) REVERT: C 370 ASN cc_start: 0.5530 (t0) cc_final: 0.5029 (p0) REVERT: C 814 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8474 (mtmt) outliers start: 110 outliers final: 85 residues processed: 242 average time/residue: 0.1450 time to fit residues: 59.7627 Evaluate side-chains 236 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 141 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL 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 83 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 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 161 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 565 PHE 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 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 40 optimal weight: 40.0000 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.165112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118458 restraints weight = 41133.601| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.17 r_work: 0.3201 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25236 Z= 0.132 Angle : 0.679 17.283 34465 Z= 0.322 Chirality : 0.048 0.477 4091 Planarity : 0.004 0.049 4332 Dihedral : 7.592 91.440 4734 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.73 % Favored : 93.96 % Rotamer: Outliers : 3.74 % Allowed : 22.73 % Favored : 73.52 % 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: -1.13 (0.15), residues: 2965 helix: 1.36 (0.21), residues: 666 sheet: -0.49 (0.20), residues: 685 loop : -1.86 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 995 TYR 0.021 0.001 TYR B 453 PHE 0.023 0.001 PHE B 157 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00302 (25126) covalent geometry : angle 0.63800 (34174) SS BOND : bond 0.00330 ( 39) SS BOND : angle 1.51086 ( 78) hydrogen bonds : bond 0.03951 ( 845) hydrogen bonds : angle 5.16488 ( 2394) link_BETA1-4 : bond 0.00530 ( 23) link_BETA1-4 : angle 2.03999 ( 69) link_NAG-ASN : bond 0.00576 ( 48) link_NAG-ASN : angle 3.26395 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 146 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8194 (p) cc_final: 0.7939 (p) REVERT: A 153 MET cc_start: -0.1437 (pmm) cc_final: -0.3124 (tpt) REVERT: A 233 ILE cc_start: 0.4743 (OUTLIER) cc_final: 0.4256 (mm) REVERT: A 389 ASP cc_start: 0.3681 (OUTLIER) cc_final: 0.2251 (p0) REVERT: A 421 TYR cc_start: 0.0638 (OUTLIER) cc_final: 0.0344 (p90) REVERT: A 979 ASP cc_start: 0.8781 (t70) cc_final: 0.8184 (t0) REVERT: B 55 PHE cc_start: 0.8188 (m-80) cc_final: 0.7750 (m-80) REVERT: B 105 ILE cc_start: 0.4848 (OUTLIER) cc_final: 0.4417 (mm) REVERT: B 191 GLU cc_start: 0.7985 (mp0) cc_final: 0.7238 (mp0) REVERT: B 195 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5412 (ptpt) REVERT: B 342 PHE cc_start: 0.7802 (m-80) cc_final: 0.7376 (m-80) REVERT: B 529 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7756 (tppt) REVERT: B 616 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7379 (m-40) REVERT: B 791 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7921 (m) REVERT: C 66 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.6011 (t-90) REVERT: C 134 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6846 (pp30) REVERT: C 191 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7202 (mt-10) REVERT: C 239 GLN cc_start: 0.6890 (mm-40) cc_final: 0.5182 (tm-30) REVERT: C 336 CYS cc_start: 0.3321 (OUTLIER) cc_final: 0.3116 (p) REVERT: C 370 ASN cc_start: 0.5527 (t0) cc_final: 0.5077 (p0) REVERT: C 814 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8489 (mtmt) outliers start: 99 outliers final: 82 residues processed: 232 average time/residue: 0.1403 time to fit residues: 55.6704 Evaluate side-chains 231 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 138 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL 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 83 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 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 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU 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 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 81 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 283 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.164245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108372 restraints weight = 41207.477| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.63 r_work: 0.3133 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25236 Z= 0.164 Angle : 0.688 17.160 34465 Z= 0.328 Chirality : 0.048 0.471 4091 Planarity : 0.004 0.050 4332 Dihedral : 7.782 108.915 4734 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.25 % Favored : 92.48 % Rotamer: Outliers : 3.86 % Allowed : 22.69 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.15), residues: 2965 helix: 1.32 (0.21), residues: 670 sheet: -0.50 (0.19), residues: 686 loop : -1.87 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 995 TYR 0.021 0.001 TYR B 453 PHE 0.022 0.002 PHE B 157 TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00393 (25126) covalent geometry : angle 0.64973 (34174) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.60202 ( 78) hydrogen bonds : bond 0.04287 ( 845) hydrogen bonds : angle 5.20264 ( 2394) link_BETA1-4 : bond 0.00519 ( 23) link_BETA1-4 : angle 2.07875 ( 69) link_NAG-ASN : bond 0.00512 ( 48) link_NAG-ASN : angle 3.11214 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8247.63 seconds wall clock time: 141 minutes 14.19 seconds (8474.19 seconds total)