Starting phenix.real_space_refine on Thu Mar 5 16:25:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dx2_30893/03_2026/7dx2_30893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx2_30893/03_2026/7dx2_30893.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 { model { file = "/net/cci-nas-00/data/ceres_data/7dx2_30893/03_2026/7dx2_30893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx2_30893/03_2026/7dx2_30893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx2_30893/03_2026/7dx2_30893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx2_30893/03_2026/7dx2_30893.map" } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 15094 2.51 5 N 3858 2.21 5 O 4686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 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: 23740 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7586 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 9 Chain: "B" Number of atoms: 7580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7580 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7580 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 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: 5.99, per 1000 atoms: 0.25 Number of scatterers: 23740 At special positions: 0 Unit cell: (139.136, 154.354, 169.572, 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 102 16.00 O 4686 8.00 N 3858 7.00 C 15094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.17 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=2.11 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.16 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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=2.55 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.12 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=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 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=2.51 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.34 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5462 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 41 sheets defined 24.8% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A 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: 3.641A 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: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.553A 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: 3.626A 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: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.061A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.651A 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: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A 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: 3.873A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A 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: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A 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: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.605A 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: 4.009A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A 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: 3.508A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 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: 3.623A 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: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.556A 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: 3.814A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A 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: 3.634A 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: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A 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: 3.730A 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: 4.047A 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 318 removed outlier: 3.946A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.338A 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 453 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.790A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.561A 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=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.603A 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=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.603A 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: 3.583A 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: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, 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: 3.677A 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: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A 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=AB7, 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=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, 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: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.858A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC3, first strand: chain 'B' and resid 448 through 453 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=AC4, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.337A 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=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.332A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.703A 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=AC6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC7, 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: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A 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: 5.855A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A 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: 4.597A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, 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=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A 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: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.898A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AD8, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A 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=AD9, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.887A pdb=" N VAL C 551 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.801A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.689A 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: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.689A 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: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 882 hydrogen bonds defined for protein. 2388 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: 5.31 Time building geometry restraints manager: 2.72 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: 5606 1.33 - 1.45: 5919 1.45 - 1.58: 12587 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 24241 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.22e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C THR B 588 " pdb=" N PRO B 589 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.23e-02 6.61e+03 2.31e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.262 0.069 1.59e-02 3.96e+03 1.87e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.71e+01 ... (remaining 24236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 32121 2.73 - 5.46: 780 5.46 - 8.19: 61 8.19 - 10.92: 4 10.92 - 13.65: 5 Bond angle restraints: 32971 Sorted by residual: angle pdb=" N CYS B 538 " pdb=" CA CYS B 538 " pdb=" C CYS B 538 " ideal model delta sigma weight residual 110.10 100.89 9.21 1.49e+00 4.50e-01 3.82e+01 angle pdb=" N CYS A 538 " pdb=" CA CYS A 538 " pdb=" C CYS A 538 " ideal model delta sigma weight residual 110.10 100.92 9.18 1.49e+00 4.50e-01 3.80e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 ... (remaining 32966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13157 17.93 - 35.87: 1481 35.87 - 53.80: 511 53.80 - 71.74: 174 71.74 - 89.67: 44 Dihedral angle restraints: 15367 sinusoidal: 6895 harmonic: 8472 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 10.81 82.19 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 15364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 3965 0.329 - 0.658: 2 0.658 - 0.987: 4 0.987 - 1.316: 0 1.316 - 1.645: 3 Chirality restraints: 3974 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.17e+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 1.17e+03 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.77e+01 ... (remaining 3971 not shown) Planarity restraints: 4212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.040 2.00e-02 2.50e+03 6.64e-02 5.52e+01 pdb=" CG ASN B 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.119 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.85e-02 4.28e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.016 2.00e-02 2.50e+03 5.62e-02 3.95e+01 pdb=" CG ASN C 331 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.063 2.00e-02 2.50e+03 ... (remaining 4209 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 207 2.50 - 3.10: 17097 3.10 - 3.70: 33275 3.70 - 4.30: 51224 4.30 - 4.90: 84969 Nonbonded interactions: 186772 Sorted by model distance: nonbonded pdb=" O SER B 316 " pdb=" ND2 ASN B 317 " model vdw 1.905 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.983 3.120 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.983 3.120 nonbonded pdb=" O ARG C 328 " pdb=" CD1 PHE C 329 " model vdw 2.117 3.340 ... (remaining 186767 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: 2.120 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: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.750 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 0.514 24348 Z= 0.595 Angle : 1.358 49.032 33256 Z= 0.693 Chirality : 0.081 1.645 3974 Planarity : 0.008 0.089 4164 Dihedral : 18.042 89.674 9797 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 3.12 % Allowed : 10.55 % Favored : 86.33 % Rotamer: Outliers : 12.95 % Allowed : 17.97 % Favored : 69.07 % 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: -4.17 (0.13), residues: 2854 helix: -2.19 (0.16), residues: 651 sheet: -2.01 (0.17), residues: 708 loop : -3.51 (0.12), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.027 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.004 TRP B 104 HIS 0.009 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.01202 (24241) covalent geometry : angle 1.03425 (32971) SS BOND : bond 0.13690 ( 36) SS BOND : angle 12.86117 ( 72) hydrogen bonds : bond 0.18965 ( 846) hydrogen bonds : angle 7.77917 ( 2388) link_BETA1-4 : bond 0.04156 ( 23) link_BETA1-4 : angle 6.36380 ( 69) link_NAG-ASN : bond 0.02787 ( 48) link_NAG-ASN : angle 8.86532 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 330 poor density : 330 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7661 (tp) cc_final: 0.7254 (tp) REVERT: A 153 MET cc_start: 0.0857 (mpp) cc_final: -0.0119 (tmm) REVERT: A 324 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.4978 (pm20) REVERT: A 702 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5762 (tp30) REVERT: A 883 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9266 (m) REVERT: A 1039 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8214 (mtt180) REVERT: B 48 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 153 MET cc_start: -0.0474 (mpp) cc_final: -0.0747 (pmm) REVERT: B 168 PHE cc_start: 0.7034 (t80) cc_final: 0.6815 (t80) REVERT: B 360 ASN cc_start: 0.5959 (OUTLIER) cc_final: 0.5756 (p0) REVERT: B 387 LEU cc_start: 0.8859 (mt) cc_final: 0.8510 (mt) REVERT: B 533 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6740 (tp) REVERT: B 697 MET cc_start: 0.8237 (ptm) cc_final: 0.8029 (ptm) REVERT: B 1050 MET cc_start: 0.8958 (ptm) cc_final: 0.8755 (ptm) REVERT: C 66 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6414 (m-70) REVERT: C 153 MET cc_start: -0.0803 (mpp) cc_final: -0.3515 (ttp) REVERT: C 158 ARG cc_start: 0.5138 (OUTLIER) cc_final: 0.4415 (mtp180) REVERT: C 389 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: C 421 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6360 (p90) REVERT: C 514 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (p) REVERT: C 787 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7623 (mm-40) outliers start: 330 outliers final: 71 residues processed: 608 average time/residue: 0.1506 time to fit residues: 143.5355 Evaluate side-chains 246 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 162 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain 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 158 ARG Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 137 ASN A 239 GLN A 317 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 440 ASN A 498 GLN A 644 GLN A 755 GLN A 762 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A1058 HIS A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 239 GLN B 317 ASN B 422 ASN B 440 ASN B 498 GLN B 644 GLN B 655 HIS B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 137 ASN C 207 HIS C 422 ASN C 440 ASN C 498 GLN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.136928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083558 restraints weight = 44393.451| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.71 r_work: 0.2890 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24348 Z= 0.155 Angle : 0.817 22.833 33256 Z= 0.393 Chirality : 0.050 0.468 3974 Planarity : 0.005 0.062 4164 Dihedral : 10.421 96.772 4746 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 5.34 % Allowed : 19.19 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.14), residues: 2854 helix: -0.07 (0.20), residues: 654 sheet: -1.07 (0.18), residues: 711 loop : -2.89 (0.13), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 403 TYR 0.019 0.001 TYR A1067 PHE 0.018 0.002 PHE C 135 TRP 0.007 0.001 TRP A 104 HIS 0.005 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00339 (24241) covalent geometry : angle 0.75688 (32971) SS BOND : bond 0.00682 ( 36) SS BOND : angle 2.46848 ( 72) hydrogen bonds : bond 0.04605 ( 846) hydrogen bonds : angle 5.76153 ( 2388) link_BETA1-4 : bond 0.00637 ( 23) link_BETA1-4 : angle 2.44881 ( 69) link_NAG-ASN : bond 0.00444 ( 48) link_NAG-ASN : angle 4.14607 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 192 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8137 (m-30) cc_final: 0.7803 (m-30) REVERT: A 153 MET cc_start: 0.0537 (mpp) cc_final: -0.0900 (tmm) REVERT: A 740 MET cc_start: 0.9216 (ttm) cc_final: 0.8961 (ttm) REVERT: A 883 THR cc_start: 0.9617 (OUTLIER) cc_final: 0.9408 (m) REVERT: B 99 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7213 (p0) REVERT: B 129 LYS cc_start: 0.7218 (mttt) cc_final: 0.6687 (mmmt) REVERT: B 141 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7850 (pt) REVERT: B 153 MET cc_start: -0.0764 (mpp) cc_final: -0.2141 (ttp) REVERT: B 365 TYR cc_start: 0.6936 (m-80) cc_final: 0.6638 (m-80) REVERT: B 398 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: B 399 SER cc_start: 0.7252 (OUTLIER) cc_final: 0.7037 (p) REVERT: B 400 PHE cc_start: 0.7959 (p90) cc_final: 0.7083 (p90) REVERT: B 990 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: C 106 PHE cc_start: 0.6833 (m-80) cc_final: 0.6540 (m-80) REVERT: C 153 MET cc_start: -0.1213 (mpp) cc_final: -0.3472 (ttp) REVERT: C 158 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5420 (mmt90) REVERT: C 191 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8077 (mp0) REVERT: C 403 ARG cc_start: 0.5437 (OUTLIER) cc_final: 0.4855 (mmt90) REVERT: C 417 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7874 (ttpt) REVERT: C 527 PRO cc_start: 0.5175 (Cg_endo) cc_final: 0.4085 (Cg_exo) REVERT: C 814 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8401 (mptt) outliers start: 136 outliers final: 73 residues processed: 312 average time/residue: 0.1336 time to fit residues: 68.2009 Evaluate side-chains 233 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 150 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU 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 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 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 985 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN B 450 ASN B 913 GLN C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 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 = 0.3834 r_free = 0.3834 target = 0.132403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080458 restraints weight = 44705.376| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.95 r_work: 0.2792 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24348 Z= 0.204 Angle : 0.773 18.061 33256 Z= 0.369 Chirality : 0.050 0.524 3974 Planarity : 0.005 0.048 4164 Dihedral : 8.935 59.748 4670 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.48 % Favored : 91.28 % Rotamer: Outliers : 4.87 % Allowed : 19.86 % Favored : 75.27 % 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: -1.96 (0.15), residues: 2854 helix: 0.69 (0.21), residues: 651 sheet: -0.93 (0.18), residues: 726 loop : -2.51 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 403 TYR 0.032 0.002 TYR A 453 PHE 0.027 0.002 PHE C 135 TRP 0.008 0.001 TRP A 104 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00487 (24241) covalent geometry : angle 0.72466 (32971) SS BOND : bond 0.00558 ( 36) SS BOND : angle 2.20133 ( 72) hydrogen bonds : bond 0.05089 ( 846) hydrogen bonds : angle 5.41843 ( 2388) link_BETA1-4 : bond 0.00501 ( 23) link_BETA1-4 : angle 2.33156 ( 69) link_NAG-ASN : bond 0.00503 ( 48) link_NAG-ASN : angle 3.55171 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 151 time to evaluate : 0.788 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 88 ASP cc_start: 0.8403 (m-30) cc_final: 0.8099 (m-30) REVERT: A 153 MET cc_start: 0.1089 (mpp) cc_final: -0.0894 (tmm) REVERT: A 518 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5154 (tt) REVERT: A 883 THR cc_start: 0.9649 (OUTLIER) cc_final: 0.9445 (m) REVERT: B 53 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7524 (t70) REVERT: B 129 LYS cc_start: 0.7144 (mttt) cc_final: 0.6700 (mmmt) REVERT: B 190 ARG cc_start: 0.8792 (mtm110) cc_final: 0.7580 (mmt180) REVERT: B 400 PHE cc_start: 0.7754 (p90) cc_final: 0.6860 (p90) REVERT: B 990 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: C 158 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5465 (mmt90) REVERT: C 189 LEU cc_start: 0.8001 (tt) cc_final: 0.7715 (tt) REVERT: C 191 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8021 (mp0) REVERT: C 421 TYR cc_start: 0.6133 (OUTLIER) cc_final: 0.5014 (p90) REVERT: C 528 LYS cc_start: 0.7226 (tptt) cc_final: 0.7023 (tptt) REVERT: C 529 LYS cc_start: 0.8820 (tppt) cc_final: 0.8617 (ttmm) REVERT: C 535 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8048 (mttt) REVERT: C 565 PHE cc_start: 0.7831 (p90) cc_final: 0.7558 (p90) REVERT: C 950 ASP cc_start: 0.8702 (m-30) cc_final: 0.8498 (m-30) outliers start: 124 outliers final: 70 residues processed: 265 average time/residue: 0.1394 time to fit residues: 60.1039 Evaluate side-chains 212 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 135 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR 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 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL 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 421 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 108 optimal weight: 0.0270 chunk 157 optimal weight: 4.9990 chunk 279 optimal weight: 0.9980 chunk 281 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 804 GLN C 207 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080789 restraints weight = 44571.009| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.67 r_work: 0.2841 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24348 Z= 0.124 Angle : 0.687 16.289 33256 Z= 0.323 Chirality : 0.048 0.532 3974 Planarity : 0.004 0.045 4164 Dihedral : 8.022 59.223 4653 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 3.92 % Allowed : 20.72 % Favored : 75.35 % 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: -1.45 (0.15), residues: 2854 helix: 1.06 (0.21), residues: 649 sheet: -0.48 (0.18), residues: 692 loop : -2.20 (0.14), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 319 TYR 0.018 0.001 TYR A1067 PHE 0.018 0.001 PHE C 135 TRP 0.005 0.001 TRP A 436 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00281 (24241) covalent geometry : angle 0.64359 (32971) SS BOND : bond 0.00364 ( 36) SS BOND : angle 1.94764 ( 72) hydrogen bonds : bond 0.03805 ( 846) hydrogen bonds : angle 5.12854 ( 2388) link_BETA1-4 : bond 0.00652 ( 23) link_BETA1-4 : angle 2.21000 ( 69) link_NAG-ASN : bond 0.00412 ( 48) link_NAG-ASN : angle 3.15745 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 146 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: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8420 (m-30) cc_final: 0.8120 (m-30) REVERT: A 118 LEU cc_start: 0.8126 (tp) cc_final: 0.7870 (tt) REVERT: A 153 MET cc_start: 0.1032 (mpp) cc_final: -0.0802 (mmt) REVERT: A 195 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8166 (mtmt) REVERT: A 360 ASN cc_start: 0.5408 (OUTLIER) cc_final: 0.4946 (t0) REVERT: A 518 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4463 (tt) REVERT: A 1142 GLN cc_start: 0.8792 (tp40) cc_final: 0.8528 (tp40) REVERT: B 53 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7326 (t70) REVERT: B 111 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.5207 (m-30) REVERT: B 129 LYS cc_start: 0.7178 (mttt) cc_final: 0.6391 (ttmt) REVERT: B 190 ARG cc_start: 0.8779 (mtm110) cc_final: 0.7609 (mmt180) REVERT: B 304 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8847 (mtpp) REVERT: B 400 PHE cc_start: 0.7769 (p90) cc_final: 0.6902 (p90) REVERT: B 964 LYS cc_start: 0.9219 (tppp) cc_final: 0.9018 (mmmm) REVERT: B 1106 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.9043 (pt0) REVERT: C 95 THR cc_start: 0.8477 (p) cc_final: 0.8214 (p) REVERT: C 158 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5379 (mmt90) REVERT: C 191 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8019 (mp0) REVERT: C 528 LYS cc_start: 0.7710 (tptt) cc_final: 0.7099 (mptt) REVERT: C 565 PHE cc_start: 0.7643 (p90) cc_final: 0.7301 (p90) outliers start: 100 outliers final: 61 residues processed: 235 average time/residue: 0.1397 time to fit residues: 53.5043 Evaluate side-chains 200 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 132 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL 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 976 VAL Chi-restraints excluded: chain C residue 1001 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 39 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 223 optimal weight: 0.0470 chunk 186 optimal weight: 4.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 992 GLN A1071 GLN B 188 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 913 GLN C 207 HIS C 317 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.074991 restraints weight = 44543.039| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.64 r_work: 0.2723 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 24348 Z= 0.381 Angle : 0.893 15.951 33256 Z= 0.427 Chirality : 0.056 0.712 3974 Planarity : 0.005 0.054 4164 Dihedral : 8.696 59.325 4638 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.97 % Favored : 90.85 % Rotamer: Outliers : 4.67 % Allowed : 20.53 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.15), residues: 2854 helix: 0.76 (0.21), residues: 647 sheet: -0.71 (0.18), residues: 695 loop : -2.39 (0.14), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1014 TYR 0.023 0.002 TYR A 453 PHE 0.028 0.003 PHE B1103 TRP 0.013 0.002 TRP B 104 HIS 0.008 0.002 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00933 (24241) covalent geometry : angle 0.84441 (32971) SS BOND : bond 0.00612 ( 36) SS BOND : angle 2.84463 ( 72) hydrogen bonds : bond 0.06282 ( 846) hydrogen bonds : angle 5.68410 ( 2388) link_BETA1-4 : bond 0.00575 ( 23) link_BETA1-4 : angle 2.49164 ( 69) link_NAG-ASN : bond 0.00518 ( 48) link_NAG-ASN : angle 3.70915 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 140 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8460 (m-30) cc_final: 0.8144 (m-30) REVERT: A 347 PHE cc_start: 0.3055 (OUTLIER) cc_final: 0.2751 (t80) REVERT: A 518 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.4847 (tt) REVERT: A 1142 GLN cc_start: 0.8868 (tp40) cc_final: 0.8656 (tp40) REVERT: B 53 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7396 (t70) REVERT: B 111 ASP cc_start: 0.5736 (OUTLIER) cc_final: 0.5472 (m-30) REVERT: B 129 LYS cc_start: 0.7156 (mttt) cc_final: 0.6416 (tttt) REVERT: B 400 PHE cc_start: 0.7924 (p90) cc_final: 0.7026 (p90) REVERT: B 738 CYS cc_start: 0.7540 (m) cc_final: 0.7296 (m) REVERT: B 1106 GLN cc_start: 0.9426 (OUTLIER) cc_final: 0.9138 (pt0) REVERT: C 95 THR cc_start: 0.8297 (p) cc_final: 0.8089 (t) REVERT: C 388 ASN cc_start: 0.7626 (t0) cc_final: 0.7387 (t0) REVERT: C 421 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.5133 (p90) REVERT: C 429 PHE cc_start: 0.6851 (t80) cc_final: 0.6559 (t80) REVERT: C 528 LYS cc_start: 0.7717 (tptt) cc_final: 0.7400 (mmmt) REVERT: C 565 PHE cc_start: 0.8288 (p90) cc_final: 0.8086 (p90) REVERT: C 787 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8584 (mm110) REVERT: C 988 GLU cc_start: 0.8711 (mp0) cc_final: 0.8395 (mp0) outliers start: 119 outliers final: 77 residues processed: 249 average time/residue: 0.1321 time to fit residues: 55.4876 Evaluate side-chains 212 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 128 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1136 THR 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 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 320 VAL 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 421 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 59 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 244 optimal weight: 0.4980 chunk 240 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 283 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 394 ASN B 913 GLN B1071 GLN C 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.131087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080794 restraints weight = 44293.008| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.91 r_work: 0.2780 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24348 Z= 0.123 Angle : 0.691 15.372 33256 Z= 0.324 Chirality : 0.048 0.565 3974 Planarity : 0.004 0.045 4164 Dihedral : 7.666 58.674 4627 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.85 % Favored : 93.97 % Rotamer: Outliers : 3.22 % Allowed : 22.21 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.30 (0.15), residues: 2854 helix: 1.18 (0.21), residues: 657 sheet: -0.29 (0.19), residues: 682 loop : -2.18 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 319 TYR 0.024 0.001 TYR B 495 PHE 0.018 0.001 PHE C 135 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00276 (24241) covalent geometry : angle 0.65118 (32971) SS BOND : bond 0.00401 ( 36) SS BOND : angle 1.66657 ( 72) hydrogen bonds : bond 0.04083 ( 846) hydrogen bonds : angle 5.19353 ( 2388) link_BETA1-4 : bond 0.00557 ( 23) link_BETA1-4 : angle 2.22361 ( 69) link_NAG-ASN : bond 0.00418 ( 48) link_NAG-ASN : angle 3.06036 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 137 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8107 (tp) cc_final: 0.7854 (tt) REVERT: A 324 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: A 360 ASN cc_start: 0.6164 (OUTLIER) cc_final: 0.4890 (t0) REVERT: A 518 LEU cc_start: 0.4828 (OUTLIER) cc_final: 0.4521 (tt) REVERT: A 740 MET cc_start: 0.9119 (ttm) cc_final: 0.8907 (ttm) REVERT: A 984 LEU cc_start: 0.7867 (mt) cc_final: 0.7539 (mt) REVERT: B 111 ASP cc_start: 0.5786 (OUTLIER) cc_final: 0.5351 (m-30) REVERT: B 129 LYS cc_start: 0.7175 (mttt) cc_final: 0.6303 (ttmt) REVERT: B 161 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7472 (p) REVERT: B 304 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8889 (mtpp) REVERT: B 400 PHE cc_start: 0.7698 (p90) cc_final: 0.6811 (p90) REVERT: B 739 THR cc_start: 0.9029 (m) cc_final: 0.8826 (m) REVERT: C 95 THR cc_start: 0.8393 (p) cc_final: 0.8180 (t) REVERT: C 388 ASN cc_start: 0.7696 (t0) cc_final: 0.7393 (t0) REVERT: C 429 PHE cc_start: 0.6833 (t80) cc_final: 0.6535 (t80) REVERT: C 565 PHE cc_start: 0.8121 (p90) cc_final: 0.7782 (p90) REVERT: C 988 GLU cc_start: 0.8711 (mp0) cc_final: 0.8389 (mp0) outliers start: 82 outliers final: 57 residues processed: 214 average time/residue: 0.1266 time to fit residues: 46.0020 Evaluate side-chains 186 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 124 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR 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 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS 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 976 VAL Chi-restraints excluded: chain C residue 1001 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 159 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 172 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 268 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.131262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082376 restraints weight = 44331.273| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.14 r_work: 0.2762 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24348 Z= 0.132 Angle : 0.682 15.052 33256 Z= 0.319 Chirality : 0.047 0.539 3974 Planarity : 0.004 0.044 4164 Dihedral : 7.365 59.565 4626 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.08 % Favored : 92.75 % Rotamer: Outliers : 3.22 % Allowed : 21.98 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 2854 helix: 1.42 (0.22), residues: 651 sheet: -0.14 (0.19), residues: 699 loop : -2.11 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.019 0.001 TYR A1067 PHE 0.015 0.001 PHE C 135 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00304 (24241) covalent geometry : angle 0.64378 (32971) SS BOND : bond 0.00406 ( 36) SS BOND : angle 1.49644 ( 72) hydrogen bonds : bond 0.03967 ( 846) hydrogen bonds : angle 5.06194 ( 2388) link_BETA1-4 : bond 0.00498 ( 23) link_BETA1-4 : angle 2.20121 ( 69) link_NAG-ASN : bond 0.00399 ( 48) link_NAG-ASN : angle 3.00659 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 136 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: A 518 LEU cc_start: 0.4591 (OUTLIER) cc_final: 0.4233 (tt) REVERT: A 883 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9314 (p) REVERT: B 111 ASP cc_start: 0.5720 (OUTLIER) cc_final: 0.5275 (m-30) REVERT: B 129 LYS cc_start: 0.7072 (mttt) cc_final: 0.6380 (tttp) REVERT: B 161 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7392 (p) REVERT: B 304 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8801 (mtpp) REVERT: B 400 PHE cc_start: 0.7664 (p90) cc_final: 0.6785 (p90) REVERT: B 739 THR cc_start: 0.8955 (m) cc_final: 0.8737 (m) REVERT: C 388 ASN cc_start: 0.7636 (t0) cc_final: 0.6887 (t0) REVERT: C 528 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7390 (mptt) REVERT: C 565 PHE cc_start: 0.8088 (p90) cc_final: 0.7779 (p90) REVERT: C 787 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8452 (mt0) REVERT: C 988 GLU cc_start: 0.8574 (mp0) cc_final: 0.8287 (mp0) outliers start: 82 outliers final: 66 residues processed: 212 average time/residue: 0.1274 time to fit residues: 46.2778 Evaluate side-chains 201 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 129 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR 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 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL 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 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1126 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 150 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 230 optimal weight: 0.0050 chunk 186 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 232 optimal weight: 0.0770 chunk 104 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.1354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.081374 restraints weight = 44074.619| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.91 r_work: 0.2802 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24348 Z= 0.122 Angle : 0.662 14.693 33256 Z= 0.309 Chirality : 0.047 0.511 3974 Planarity : 0.004 0.043 4164 Dihedral : 7.034 58.155 4626 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.03 % Favored : 93.76 % Rotamer: Outliers : 2.98 % Allowed : 22.65 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 2854 helix: 1.56 (0.21), residues: 655 sheet: -0.17 (0.19), residues: 706 loop : -1.95 (0.14), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.019 0.001 TYR B1067 PHE 0.014 0.001 PHE C 135 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00280 (24241) covalent geometry : angle 0.62669 (32971) SS BOND : bond 0.00432 ( 36) SS BOND : angle 1.32995 ( 72) hydrogen bonds : bond 0.03676 ( 846) hydrogen bonds : angle 4.93336 ( 2388) link_BETA1-4 : bond 0.00540 ( 23) link_BETA1-4 : angle 2.16586 ( 69) link_NAG-ASN : bond 0.00402 ( 48) link_NAG-ASN : angle 2.86486 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 144 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7070 (m-80) cc_final: 0.4971 (m-80) REVERT: A 324 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8438 (pt0) REVERT: A 518 LEU cc_start: 0.4578 (OUTLIER) cc_final: 0.4202 (tt) REVERT: A 883 THR cc_start: 0.9562 (OUTLIER) cc_final: 0.9310 (p) REVERT: B 111 ASP cc_start: 0.5705 (OUTLIER) cc_final: 0.5208 (m-30) REVERT: B 129 LYS cc_start: 0.7012 (mttt) cc_final: 0.6304 (tttp) REVERT: B 133 PHE cc_start: 0.6847 (m-80) cc_final: 0.6037 (m-80) REVERT: B 161 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7289 (p) REVERT: B 304 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8865 (mtpp) REVERT: B 342 PHE cc_start: 0.7490 (m-80) cc_final: 0.7119 (m-80) REVERT: B 400 PHE cc_start: 0.7510 (p90) cc_final: 0.6756 (p90) REVERT: C 388 ASN cc_start: 0.7719 (t0) cc_final: 0.7483 (t0) REVERT: C 429 PHE cc_start: 0.6710 (t80) cc_final: 0.6454 (t80) REVERT: C 565 PHE cc_start: 0.8118 (p90) cc_final: 0.7756 (p90) REVERT: C 568 ASP cc_start: 0.7829 (m-30) cc_final: 0.7245 (m-30) REVERT: C 787 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8611 (mt0) REVERT: C 988 GLU cc_start: 0.8686 (mp0) cc_final: 0.8330 (mp0) outliers start: 76 outliers final: 59 residues processed: 215 average time/residue: 0.1260 time to fit residues: 45.5970 Evaluate side-chains 194 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 129 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1136 THR 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 122 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL 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 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 107 optimal weight: 10.0000 chunk 193 optimal weight: 0.0570 chunk 42 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.129935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077370 restraints weight = 44481.580| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.66 r_work: 0.2768 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 24348 Z= 0.208 Angle : 0.722 14.488 33256 Z= 0.339 Chirality : 0.049 0.559 3974 Planarity : 0.004 0.043 4164 Dihedral : 7.269 59.969 4620 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.02 % Favored : 91.77 % Rotamer: Outliers : 2.86 % Allowed : 22.65 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.04 (0.15), residues: 2854 helix: 1.48 (0.21), residues: 651 sheet: -0.15 (0.19), residues: 700 loop : -2.04 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.002 PHE C1121 TRP 0.006 0.001 TRP B 104 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00509 (24241) covalent geometry : angle 0.68280 (32971) SS BOND : bond 0.00464 ( 36) SS BOND : angle 1.86598 ( 72) hydrogen bonds : bond 0.04671 ( 846) hydrogen bonds : angle 5.12440 ( 2388) link_BETA1-4 : bond 0.00495 ( 23) link_BETA1-4 : angle 2.22650 ( 69) link_NAG-ASN : bond 0.00404 ( 48) link_NAG-ASN : angle 3.06046 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 129 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6995 (m-80) cc_final: 0.4958 (m-80) REVERT: A 518 LEU cc_start: 0.5082 (OUTLIER) cc_final: 0.4650 (tt) REVERT: A 883 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9332 (p) REVERT: B 96 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5460 (pm20) REVERT: B 111 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5283 (m-30) REVERT: B 129 LYS cc_start: 0.7027 (mttt) cc_final: 0.6329 (tttp) REVERT: B 161 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7221 (p) REVERT: B 304 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8884 (mtpp) REVERT: B 338 PHE cc_start: 0.7794 (m-10) cc_final: 0.7485 (m-10) REVERT: B 342 PHE cc_start: 0.7506 (m-80) cc_final: 0.7112 (m-80) REVERT: B 400 PHE cc_start: 0.7656 (p90) cc_final: 0.6820 (p90) REVERT: C 388 ASN cc_start: 0.7655 (t0) cc_final: 0.7415 (t0) REVERT: C 429 PHE cc_start: 0.6762 (t80) cc_final: 0.6518 (t80) REVERT: C 565 PHE cc_start: 0.8264 (p90) cc_final: 0.7931 (p90) REVERT: C 787 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8603 (mt0) REVERT: C 988 GLU cc_start: 0.8691 (mp0) cc_final: 0.8339 (mp0) outliers start: 73 outliers final: 62 residues processed: 195 average time/residue: 0.1234 time to fit residues: 41.0279 Evaluate side-chains 191 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR 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 122 ASN Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL 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 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 130 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.130592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.079864 restraints weight = 44507.320| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.91 r_work: 0.2775 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24348 Z= 0.160 Angle : 0.687 14.468 33256 Z= 0.322 Chirality : 0.048 0.534 3974 Planarity : 0.004 0.044 4164 Dihedral : 7.078 59.329 4620 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.48 % Rotamer: Outliers : 2.90 % Allowed : 22.57 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.15), residues: 2854 helix: 1.57 (0.21), residues: 651 sheet: -0.14 (0.19), residues: 708 loop : -1.97 (0.14), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.020 0.001 TYR B1067 PHE 0.012 0.001 PHE A 86 TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00385 (24241) covalent geometry : angle 0.64852 (32971) SS BOND : bond 0.00429 ( 36) SS BOND : angle 1.86021 ( 72) hydrogen bonds : bond 0.04141 ( 846) hydrogen bonds : angle 4.99691 ( 2388) link_BETA1-4 : bond 0.00522 ( 23) link_BETA1-4 : angle 2.18833 ( 69) link_NAG-ASN : bond 0.00384 ( 48) link_NAG-ASN : angle 2.92813 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 127 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.6988 (m-80) cc_final: 0.6749 (m-10) REVERT: A 518 LEU cc_start: 0.4880 (OUTLIER) cc_final: 0.4504 (tt) REVERT: A 883 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9343 (p) REVERT: B 96 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5407 (pm20) REVERT: B 111 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5419 (m-30) REVERT: B 129 LYS cc_start: 0.7009 (mttt) cc_final: 0.6283 (tttp) REVERT: B 133 PHE cc_start: 0.6840 (m-80) cc_final: 0.5881 (m-80) REVERT: B 153 MET cc_start: -0.1499 (pmm) cc_final: -0.4365 (ptt) REVERT: B 161 SER cc_start: 0.7693 (OUTLIER) cc_final: 0.7188 (p) REVERT: B 304 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8854 (mtpp) REVERT: B 338 PHE cc_start: 0.7891 (m-10) cc_final: 0.7529 (m-10) REVERT: B 342 PHE cc_start: 0.7502 (m-80) cc_final: 0.7136 (m-80) REVERT: B 400 PHE cc_start: 0.7612 (p90) cc_final: 0.6771 (p90) REVERT: C 388 ASN cc_start: 0.7707 (t0) cc_final: 0.7442 (t0) REVERT: C 429 PHE cc_start: 0.6804 (t80) cc_final: 0.6554 (t80) REVERT: C 528 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7115 (mmmt) REVERT: C 565 PHE cc_start: 0.8185 (p90) cc_final: 0.7857 (p90) REVERT: C 568 ASP cc_start: 0.8115 (m-30) cc_final: 0.7589 (m-30) REVERT: C 787 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8633 (mt0) REVERT: C 988 GLU cc_start: 0.8734 (mp0) cc_final: 0.8338 (mp0) outliers start: 74 outliers final: 62 residues processed: 195 average time/residue: 0.1262 time to fit residues: 42.1520 Evaluate side-chains 192 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 124 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR 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 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1126 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 33 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 186 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.132960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081113 restraints weight = 44230.054| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.62 r_work: 0.2850 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24348 Z= 0.107 Angle : 0.644 14.424 33256 Z= 0.300 Chirality : 0.046 0.487 3974 Planarity : 0.004 0.044 4164 Dihedral : 6.537 57.092 4615 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.38 % Favored : 93.41 % Rotamer: Outliers : 2.55 % Allowed : 23.00 % Favored : 74.45 % 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: -0.68 (0.15), residues: 2854 helix: 1.73 (0.22), residues: 649 sheet: 0.16 (0.19), residues: 693 loop : -1.83 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.019 0.001 TYR B1067 PHE 0.011 0.001 PHE B 135 TRP 0.012 0.001 TRP C 436 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00239 (24241) covalent geometry : angle 0.61022 (32971) SS BOND : bond 0.00364 ( 36) SS BOND : angle 1.42365 ( 72) hydrogen bonds : bond 0.03324 ( 846) hydrogen bonds : angle 4.76121 ( 2388) link_BETA1-4 : bond 0.00555 ( 23) link_BETA1-4 : angle 2.14587 ( 69) link_NAG-ASN : bond 0.00421 ( 48) link_NAG-ASN : angle 2.72157 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7107.39 seconds wall clock time: 121 minutes 50.55 seconds (7310.55 seconds total)