Starting phenix.real_space_refine on Thu Mar 5 16:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dx1_30892/03_2026/7dx1_30892.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dx1_30892/03_2026/7dx1_30892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dx1_30892/03_2026/7dx1_30892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dx1_30892/03_2026/7dx1_30892.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dx1_30892/03_2026/7dx1_30892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dx1_30892/03_2026/7dx1_30892.map" } resolution = 3.1 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 77 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: 5.71, per 1000 atoms: 0.24 Number of scatterers: 23740 At special positions: 0 Unit cell: (139.136, 155.441, 168.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 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=2.12 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=2.06 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=2.56 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=2.11 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.08 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=1.72 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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: 2.16 Conformation dependent library (CDL) restraints added in 982.2 milliseconds 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: 60 helices and 42 sheets defined 25.3% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A 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: 3.559A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.994A 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 985 through 1033 removed outlier: 4.631A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A 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: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 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: 3.738A 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: 3.962A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.605A 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: 4.244A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A 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: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.738A 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 568 through 572 removed outlier: 3.789A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) 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: 4.068A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A 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: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.295A 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: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A 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 319 removed outlier: 3.835A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.504A 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: 6.445A 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: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.611A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.417A 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: 6.587A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A 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: 6.587A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A 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: 3.584A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A 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: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A 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: 6.949A 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: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A 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: 4.046A 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 317 removed outlier: 6.437A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (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: 4.783A 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: 5.339A 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: 6.200A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.532A 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: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.855A 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: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=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: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=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: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A 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: 4.586A 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: 4.045A 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: 3.979A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 326 removed outlier: 6.448A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AD9, 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: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.528A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.689A 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: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.689A 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: 6.147A 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: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 891 hydrogen bonds defined for protein. 2403 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: 4.86 Time building geometry restraints manager: 2.81 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: 5455 1.33 - 1.45: 5904 1.45 - 1.58: 12753 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 1.443 0.079 1.20e-02 6.94e+03 4.35e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.19e-02 7.06e+03 2.46e+01 bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.328 1.390 -0.062 1.25e-02 6.40e+03 2.44e+01 bond pdb=" C GLN B 321 " pdb=" N PRO B 322 " ideal model delta sigma weight residual 1.331 1.389 -0.058 1.28e-02 6.10e+03 2.04e+01 bond pdb=" N PRO B 337 " pdb=" CD PRO B 337 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.98e+01 ... (remaining 24236 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 32149 2.76 - 5.53: 746 5.53 - 8.29: 63 8.29 - 11.05: 5 11.05 - 13.81: 8 Bond angle restraints: 32971 Sorted by residual: angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 120.85 114.12 6.73 1.08e+00 8.57e-01 3.89e+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 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 ... (remaining 32966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13155 17.94 - 35.87: 1479 35.87 - 53.81: 508 53.81 - 71.75: 182 71.75 - 89.68: 43 Dihedral angle restraints: 15367 sinusoidal: 6895 harmonic: 8472 Sorted by residual: 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 21.05 71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 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 21.10 71.90 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: 3964 0.329 - 0.659: 4 0.659 - 0.988: 4 0.988 - 1.317: 1 1.317 - 1.647: 1 Chirality restraints: 3974 Sorted by residual: chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 ... (remaining 3971 not shown) Planarity restraints: 4212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.86e-02 4.29e+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 B 331 " 0.046 2.00e-02 2.50e+03 4.74e-02 2.81e+01 pdb=" CG ASN B 331 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.071 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.022 2.00e-02 2.50e+03 3.16e-02 1.25e+01 pdb=" CG ASN C1134 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 4209 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 166 2.46 - 3.07: 15728 3.07 - 3.68: 33012 3.68 - 4.29: 51819 4.29 - 4.90: 86203 Nonbonded interactions: 186928 Sorted by model distance: nonbonded pdb=" O PRO B 561 " pdb=" CD1 PHE B 562 " model vdw 1.848 3.340 nonbonded pdb=" O SER B 530 " pdb=" OG1 THR B 531 " model vdw 1.915 3.040 nonbonded pdb=" O THR B 333 " pdb=" O ASN B 334 " model vdw 1.962 3.040 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 3.120 ... (remaining 186923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1408)) selection = (chain 'B' and resid 27 through 1408) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.710 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 0.526 24348 Z= 0.577 Angle : 1.333 49.041 33256 Z= 0.687 Chirality : 0.076 1.647 3974 Planarity : 0.007 0.082 4164 Dihedral : 18.072 89.683 9797 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 3.36 % Allowed : 10.41 % Favored : 86.23 % Rotamer: Outliers : 13.11 % Allowed : 18.21 % Favored : 68.68 % 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: -4.20 (0.13), residues: 2854 helix: -2.22 (0.16), residues: 662 sheet: -1.98 (0.18), residues: 692 loop : -3.55 (0.12), residues: 1500 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 A 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01204 (24241) covalent geometry : angle 1.04530 (32971) SS BOND : bond 0.10898 ( 36) SS BOND : angle 12.60527 ( 72) hydrogen bonds : bond 0.19020 ( 855) hydrogen bonds : angle 7.72296 ( 2403) link_BETA1-4 : bond 0.04089 ( 23) link_BETA1-4 : angle 4.26407 ( 69) link_NAG-ASN : bond 0.03122 ( 48) link_NAG-ASN : angle 8.48684 ( 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 665 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 334 poor density : 331 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2067 (mpp) cc_final: 0.0969 (ttt) REVERT: A 364 ASP cc_start: 0.6427 (p0) cc_final: 0.6035 (t0) REVERT: A 787 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: A 902 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7771 (tpt) REVERT: A 916 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8895 (tp) REVERT: A 994 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7676 (m-30) REVERT: A 1039 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8631 (mtp85) REVERT: B 137 ASN cc_start: 0.6874 (m110) cc_final: 0.6140 (p0) REVERT: B 324 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: B 334 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.6048 (p0) REVERT: B 563 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6182 (mm-40) REVERT: B 902 MET cc_start: 0.8747 (tpt) cc_final: 0.8544 (tpt) REVERT: B 1143 PRO cc_start: 0.8175 (Cg_endo) cc_final: 0.7880 (Cg_exo) REVERT: C 153 MET cc_start: 0.0805 (mpp) cc_final: 0.0106 (ptm) REVERT: C 171 VAL cc_start: 0.6569 (OUTLIER) cc_final: 0.6201 (m) REVERT: C 324 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: C 332 ILE cc_start: 0.5751 (OUTLIER) cc_final: 0.5527 (pp) REVERT: C 421 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.4409 (m-10) REVERT: C 430 THR cc_start: 0.6448 (OUTLIER) cc_final: 0.6101 (m) REVERT: C 567 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6845 (ptp-170) REVERT: C 696 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8423 (p) outliers start: 334 outliers final: 96 residues processed: 614 average time/residue: 0.1541 time to fit residues: 148.5644 Evaluate side-chains 298 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 187 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 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: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 134 GLN A 137 ASN A 164 ASN A 188 ASN A 360 ASN A 422 ASN A 440 ASN A 498 GLN A 644 GLN A 764 ASN A 787 GLN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1058 HIS A1101 HIS B 81 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 137 ASN B 360 ASN B 394 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 B1010 GLN B1054 GLN B1142 GLN C 134 GLN C 137 ASN C 196 ASN C 314 GLN C 360 ASN C 394 ASN C 422 ASN C 440 ASN C 498 GLN C 613 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 C1071 GLN C1101 HIS Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.166588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109753 restraints weight = 37349.733| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.23 r_work: 0.3124 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 24348 Z= 0.153 Angle : 0.832 16.350 33256 Z= 0.398 Chirality : 0.050 0.485 3974 Planarity : 0.005 0.063 4164 Dihedral : 10.811 64.889 4776 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.20 % Favored : 91.38 % Rotamer: Outliers : 5.89 % Allowed : 20.25 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.14), residues: 2854 helix: -0.01 (0.20), residues: 645 sheet: -1.19 (0.18), residues: 718 loop : -2.94 (0.13), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 403 TYR 0.019 0.001 TYR B 453 PHE 0.030 0.002 PHE C 329 TRP 0.006 0.001 TRP A 104 HIS 0.006 0.001 HIS A1101 Details of bonding type rmsd covalent geometry : bond 0.00335 (24241) covalent geometry : angle 0.76671 (32971) SS BOND : bond 0.00729 ( 36) SS BOND : angle 2.61633 ( 72) hydrogen bonds : bond 0.04911 ( 855) hydrogen bonds : angle 5.80948 ( 2403) link_BETA1-4 : bond 0.00714 ( 23) link_BETA1-4 : angle 2.42101 ( 69) link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 4.34373 ( 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 361 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 211 time to evaluate : 0.841 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 95 THR cc_start: 0.6635 (p) cc_final: 0.6314 (t) REVERT: A 99 ASN cc_start: 0.7412 (m-40) cc_final: 0.6313 (t0) REVERT: A 153 MET cc_start: 0.1805 (mpp) cc_final: 0.0110 (ttt) REVERT: A 190 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6089 (tpt-90) REVERT: A 544 ASN cc_start: 0.7497 (p0) cc_final: 0.6997 (t0) REVERT: A 776 LYS cc_start: 0.9233 (tttt) cc_final: 0.9030 (tttp) REVERT: A 883 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9261 (p) REVERT: A 994 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: B 88 ASP cc_start: 0.6671 (t0) cc_final: 0.6297 (t0) REVERT: B 137 ASN cc_start: 0.7224 (m-40) cc_final: 0.6232 (p0) REVERT: B 190 ARG cc_start: 0.7610 (mtt90) cc_final: 0.6704 (ttt180) REVERT: B 239 GLN cc_start: 0.7188 (mt0) cc_final: 0.6829 (mm-40) REVERT: B 340 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: B 563 GLN cc_start: 0.5713 (OUTLIER) cc_final: 0.4804 (mm110) REVERT: C 118 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6169 (mp) REVERT: C 153 MET cc_start: 0.0118 (mpp) cc_final: -0.0421 (ptm) REVERT: C 171 VAL cc_start: 0.7085 (OUTLIER) cc_final: 0.6721 (m) REVERT: C 332 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5725 (mt) REVERT: C 333 THR cc_start: 0.6059 (OUTLIER) cc_final: 0.5566 (m) REVERT: C 529 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6594 (pttp) REVERT: C 567 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6779 (mtt180) REVERT: C 995 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7881 (mtt180) outliers start: 150 outliers final: 83 residues processed: 340 average time/residue: 0.1438 time to fit residues: 80.1164 Evaluate side-chains 261 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 168 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR 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: 0.9980 chunk 276 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 290 optimal weight: 0.0040 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN A 856 ASN A1011 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 913 GLN C 49 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 804 GLN C1142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.104734 restraints weight = 37220.786| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.86 r_work: 0.3022 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3166 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= 0.202 Angle : 0.803 23.032 33256 Z= 0.381 Chirality : 0.051 0.477 3974 Planarity : 0.005 0.072 4164 Dihedral : 9.312 61.968 4678 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.30 % Favored : 91.49 % Rotamer: Outliers : 6.00 % Allowed : 19.70 % Favored : 74.29 % 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: -2.01 (0.15), residues: 2854 helix: 0.62 (0.21), residues: 650 sheet: -0.87 (0.18), residues: 750 loop : -2.61 (0.14), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 328 TYR 0.020 0.002 TYR A1067 PHE 0.017 0.002 PHE C 565 TRP 0.010 0.001 TRP C 64 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00483 (24241) covalent geometry : angle 0.74002 (32971) SS BOND : bond 0.00677 ( 36) SS BOND : angle 2.62587 ( 72) hydrogen bonds : bond 0.05068 ( 855) hydrogen bonds : angle 5.50048 ( 2403) link_BETA1-4 : bond 0.00540 ( 23) link_BETA1-4 : angle 2.33301 ( 69) link_NAG-ASN : bond 0.00593 ( 48) link_NAG-ASN : angle 4.16380 ( 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 324 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 171 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6554 (mt) REVERT: A 153 MET cc_start: 0.2030 (mpp) cc_final: 0.0130 (ttt) REVERT: A 190 ARG cc_start: 0.7478 (mtp180) cc_final: 0.6199 (tpt-90) REVERT: A 191 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7914 (mt-10) REVERT: A 239 GLN cc_start: 0.5908 (mt0) cc_final: 0.5644 (mt0) REVERT: A 323 THR cc_start: 0.7064 (p) cc_final: 0.6491 (t) REVERT: A 324 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: A 347 PHE cc_start: 0.3736 (OUTLIER) cc_final: 0.2070 (m-80) REVERT: A 539 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6832 (m) REVERT: A 544 ASN cc_start: 0.7757 (p0) cc_final: 0.7094 (t0) REVERT: B 88 ASP cc_start: 0.6911 (t0) cc_final: 0.6413 (t0) REVERT: B 137 ASN cc_start: 0.7321 (m-40) cc_final: 0.6298 (p0) REVERT: B 190 ARG cc_start: 0.7400 (mtt90) cc_final: 0.6854 (ttt180) REVERT: B 239 GLN cc_start: 0.7460 (mt0) cc_final: 0.6918 (mm-40) REVERT: B 563 GLN cc_start: 0.6002 (OUTLIER) cc_final: 0.4803 (mm110) REVERT: B 979 ASP cc_start: 0.8048 (m-30) cc_final: 0.7782 (t0) REVERT: C 118 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.6553 (mp) REVERT: C 153 MET cc_start: -0.0099 (mpp) cc_final: -0.0424 (ptm) REVERT: C 171 VAL cc_start: 0.7033 (OUTLIER) cc_final: 0.6644 (m) REVERT: C 239 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7442 (tp40) REVERT: C 394 ASN cc_start: 0.5407 (OUTLIER) cc_final: 0.4739 (t0) REVERT: C 430 THR cc_start: 0.5942 (OUTLIER) cc_final: 0.5454 (t) REVERT: C 529 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6603 (ptmt) REVERT: C 796 ASP cc_start: 0.7976 (t0) cc_final: 0.7206 (p0) REVERT: C 995 ARG cc_start: 0.8262 (mtp180) cc_final: 0.7954 (mtt90) outliers start: 153 outliers final: 94 residues processed: 308 average time/residue: 0.1323 time to fit residues: 68.1822 Evaluate side-chains 255 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 150 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 108 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 279 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 270 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.163154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105418 restraints weight = 37236.381| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.11 r_work: 0.3071 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24348 Z= 0.142 Angle : 0.728 20.914 33256 Z= 0.343 Chirality : 0.049 0.503 3974 Planarity : 0.004 0.057 4164 Dihedral : 8.525 59.198 4660 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.83 % Favored : 92.96 % Rotamer: Outliers : 4.79 % Allowed : 21.19 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.15), residues: 2854 helix: 1.00 (0.21), residues: 646 sheet: -0.53 (0.18), residues: 735 loop : -2.35 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.020 0.001 TYR A1067 PHE 0.017 0.001 PHE C 400 TRP 0.007 0.001 TRP A 886 HIS 0.019 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00328 (24241) covalent geometry : angle 0.67101 (32971) SS BOND : bond 0.00610 ( 36) SS BOND : angle 2.31193 ( 72) hydrogen bonds : bond 0.04225 ( 855) hydrogen bonds : angle 5.25939 ( 2403) link_BETA1-4 : bond 0.00528 ( 23) link_BETA1-4 : angle 2.22350 ( 69) link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 3.75711 ( 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 294 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 172 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7173 (tp40) cc_final: 0.6752 (tp40) REVERT: A 95 THR cc_start: 0.7049 (p) cc_final: 0.6720 (t) REVERT: A 118 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6578 (mt) REVERT: A 153 MET cc_start: 0.1791 (mpp) cc_final: 0.0103 (ttt) REVERT: A 191 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 239 GLN cc_start: 0.6071 (OUTLIER) cc_final: 0.5248 (tm-30) REVERT: A 324 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: A 347 PHE cc_start: 0.3748 (OUTLIER) cc_final: 0.2040 (m-80) REVERT: A 544 ASN cc_start: 0.7816 (p0) cc_final: 0.7125 (t0) REVERT: B 86 PHE cc_start: 0.5826 (t80) cc_final: 0.5508 (t80) REVERT: B 88 ASP cc_start: 0.6985 (t0) cc_final: 0.6488 (t0) REVERT: B 137 ASN cc_start: 0.7335 (m-40) cc_final: 0.6263 (p0) REVERT: B 190 ARG cc_start: 0.7363 (mtt90) cc_final: 0.6679 (ttt180) REVERT: B 239 GLN cc_start: 0.7487 (mt0) cc_final: 0.6890 (mm110) REVERT: B 697 MET cc_start: 0.9153 (ptp) cc_final: 0.8800 (ptm) REVERT: B 979 ASP cc_start: 0.8001 (m-30) cc_final: 0.7756 (t0) REVERT: B 1106 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.9016 (pt0) REVERT: C 46 SER cc_start: 0.6612 (OUTLIER) cc_final: 0.5991 (t) REVERT: C 88 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7704 (m-30) REVERT: C 118 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6441 (mp) REVERT: C 131 CYS cc_start: 0.2410 (m) cc_final: 0.1913 (m) REVERT: C 153 MET cc_start: -0.0215 (mpp) cc_final: -0.0457 (ptm) REVERT: C 170 TYR cc_start: 0.7488 (t80) cc_final: 0.7176 (t80) REVERT: C 239 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7084 (tp40) REVERT: C 324 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: C 333 THR cc_start: 0.6045 (OUTLIER) cc_final: 0.5520 (m) REVERT: C 529 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6581 (ptmt) REVERT: C 796 ASP cc_start: 0.7852 (t0) cc_final: 0.7126 (p0) REVERT: C 995 ARG cc_start: 0.8094 (mtp180) cc_final: 0.7810 (mtt90) REVERT: C 1142 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7753 (mm110) outliers start: 122 outliers final: 81 residues processed: 279 average time/residue: 0.1230 time to fit residues: 58.8831 Evaluate side-chains 248 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 155 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 791 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 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 39 optimal weight: 30.0000 chunk 151 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105138 restraints weight = 36798.502| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.04 r_work: 0.3067 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24348 Z= 0.148 Angle : 0.701 20.614 33256 Z= 0.331 Chirality : 0.048 0.465 3974 Planarity : 0.004 0.075 4164 Dihedral : 7.792 59.759 4648 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.01 % Favored : 92.78 % Rotamer: Outliers : 5.46 % Allowed : 20.92 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 2854 helix: 1.26 (0.21), residues: 643 sheet: -0.38 (0.18), residues: 745 loop : -2.19 (0.14), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 328 TYR 0.020 0.001 TYR A1067 PHE 0.015 0.001 PHE C 400 TRP 0.009 0.001 TRP A 886 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00350 (24241) covalent geometry : angle 0.64883 (32971) SS BOND : bond 0.00622 ( 36) SS BOND : angle 2.01515 ( 72) hydrogen bonds : bond 0.04239 ( 855) hydrogen bonds : angle 5.15005 ( 2403) link_BETA1-4 : bond 0.00515 ( 23) link_BETA1-4 : angle 2.17769 ( 69) link_NAG-ASN : bond 0.00520 ( 48) link_NAG-ASN : angle 3.57634 ( 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 307 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 168 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7188 (tp40) cc_final: 0.6759 (tp40) REVERT: A 95 THR cc_start: 0.7312 (p) cc_final: 0.7014 (t) REVERT: A 118 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6594 (mt) REVERT: A 153 MET cc_start: 0.1804 (mpp) cc_final: 0.0169 (ttt) REVERT: A 239 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5832 (mt0) REVERT: A 324 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6454 (pm20) REVERT: A 347 PHE cc_start: 0.3820 (OUTLIER) cc_final: 0.2040 (m-80) REVERT: A 544 ASN cc_start: 0.7806 (p0) cc_final: 0.7122 (t0) REVERT: A 856 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.7860 (p0) REVERT: B 86 PHE cc_start: 0.5620 (t80) cc_final: 0.5364 (t80) REVERT: B 88 ASP cc_start: 0.7081 (t0) cc_final: 0.6602 (t0) REVERT: B 137 ASN cc_start: 0.7360 (m-40) cc_final: 0.6287 (p0) REVERT: B 140 PHE cc_start: 0.7870 (p90) cc_final: 0.7468 (p90) REVERT: B 190 ARG cc_start: 0.7303 (mtt90) cc_final: 0.6709 (ttt180) REVERT: B 342 PHE cc_start: 0.8045 (m-80) cc_final: 0.7333 (m-80) REVERT: B 569 ILE cc_start: 0.7867 (mp) cc_final: 0.7661 (mt) REVERT: B 697 MET cc_start: 0.9144 (ptp) cc_final: 0.8837 (ptm) REVERT: B 1106 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.9002 (pt0) REVERT: B 1142 GLN cc_start: 0.8565 (pp30) cc_final: 0.8266 (pp30) REVERT: C 88 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: C 118 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6432 (mp) REVERT: C 131 CYS cc_start: 0.2508 (m) cc_final: 0.2028 (m) REVERT: C 153 MET cc_start: -0.0140 (mpp) cc_final: -0.0358 (ptm) REVERT: C 170 TYR cc_start: 0.7616 (t80) cc_final: 0.7317 (t80) REVERT: C 227 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7804 (m) REVERT: C 239 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7273 (tp40) REVERT: C 324 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: C 333 THR cc_start: 0.5771 (OUTLIER) cc_final: 0.5096 (m) REVERT: C 430 THR cc_start: 0.5994 (OUTLIER) cc_final: 0.5757 (m) REVERT: C 529 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6572 (ptmt) REVERT: C 796 ASP cc_start: 0.7880 (t0) cc_final: 0.7214 (p0) REVERT: C 994 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7835 (m-30) REVERT: C 995 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7792 (mtt180) REVERT: C 1142 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7656 (mm110) outliers start: 139 outliers final: 89 residues processed: 290 average time/residue: 0.1226 time to fit residues: 60.3312 Evaluate side-chains 257 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 153 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 59 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 955 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 751 ASN C 787 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101089 restraints weight = 36920.409| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.52 r_work: 0.2986 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 24348 Z= 0.275 Angle : 0.811 20.044 33256 Z= 0.383 Chirality : 0.053 0.467 3974 Planarity : 0.005 0.076 4164 Dihedral : 8.068 59.705 4641 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.78 % Favored : 92.05 % Rotamer: Outliers : 5.30 % Allowed : 21.35 % Favored : 73.35 % 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: -1.54 (0.15), residues: 2854 helix: 0.85 (0.21), residues: 668 sheet: -0.58 (0.18), residues: 736 loop : -2.24 (0.14), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 44 TYR 0.027 0.002 TYR C 453 PHE 0.021 0.002 PHE A 86 TRP 0.009 0.002 TRP A 886 HIS 0.006 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00678 (24241) covalent geometry : angle 0.75111 (32971) SS BOND : bond 0.00784 ( 36) SS BOND : angle 2.50853 ( 72) hydrogen bonds : bond 0.05513 ( 855) hydrogen bonds : angle 5.44073 ( 2403) link_BETA1-4 : bond 0.00481 ( 23) link_BETA1-4 : angle 2.35074 ( 69) link_NAG-ASN : bond 0.00542 ( 48) link_NAG-ASN : angle 4.10740 ( 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 291 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 156 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2323 (mpp) cc_final: 0.0619 (ttt) REVERT: A 237 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6000 (ptt90) REVERT: A 239 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5820 (mt0) REVERT: A 324 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: A 347 PHE cc_start: 0.3782 (OUTLIER) cc_final: 0.2356 (m-80) REVERT: A 544 ASN cc_start: 0.7986 (p0) cc_final: 0.7180 (t0) REVERT: A 856 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8604 (p0) REVERT: B 52 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 88 ASP cc_start: 0.7145 (t0) cc_final: 0.6721 (t0) REVERT: B 137 ASN cc_start: 0.7486 (m-40) cc_final: 0.6396 (p0) REVERT: B 140 PHE cc_start: 0.7894 (p90) cc_final: 0.7482 (p90) REVERT: B 190 ARG cc_start: 0.7350 (mtt90) cc_final: 0.6673 (ttt180) REVERT: C 118 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.6826 (mp) REVERT: C 131 CYS cc_start: 0.2977 (m) cc_final: 0.2434 (m) REVERT: C 170 TYR cc_start: 0.7686 (t80) cc_final: 0.7441 (t80) REVERT: C 324 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6523 (pm20) REVERT: C 516 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.5214 (pm20) REVERT: C 528 LYS cc_start: 0.4877 (OUTLIER) cc_final: 0.4363 (tttt) REVERT: C 529 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6568 (ptmt) REVERT: C 796 ASP cc_start: 0.8139 (t0) cc_final: 0.7609 (p0) REVERT: C 995 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7950 (mtt90) outliers start: 135 outliers final: 92 residues processed: 273 average time/residue: 0.1288 time to fit residues: 59.4913 Evaluate side-chains 247 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 146 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 159 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 179 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS B 239 GLN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.162021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102692 restraints weight = 36761.716| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.54 r_work: 0.3020 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4314 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= 0.119 Angle : 0.681 20.548 33256 Z= 0.322 Chirality : 0.048 0.474 3974 Planarity : 0.004 0.074 4164 Dihedral : 7.479 59.938 4639 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.20 % Favored : 93.66 % Rotamer: Outliers : 3.96 % Allowed : 22.76 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.15), residues: 2854 helix: 1.25 (0.21), residues: 663 sheet: -0.39 (0.18), residues: 762 loop : -2.07 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.018 0.001 TYR A1067 PHE 0.021 0.001 PHE A 86 TRP 0.007 0.001 TRP B 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00266 (24241) covalent geometry : angle 0.62914 (32971) SS BOND : bond 0.00568 ( 36) SS BOND : angle 1.88558 ( 72) hydrogen bonds : bond 0.03844 ( 855) hydrogen bonds : angle 5.08640 ( 2403) link_BETA1-4 : bond 0.00588 ( 23) link_BETA1-4 : angle 2.14765 ( 69) link_NAG-ASN : bond 0.00602 ( 48) link_NAG-ASN : angle 3.52468 ( 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 257 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 156 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6642 (mt) REVERT: A 153 MET cc_start: 0.2215 (mpp) cc_final: 0.0475 (ttt) REVERT: A 237 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6084 (ptt90) REVERT: A 239 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5893 (mt0) REVERT: A 324 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: A 347 PHE cc_start: 0.3734 (OUTLIER) cc_final: 0.2332 (m-80) REVERT: A 544 ASN cc_start: 0.7912 (p0) cc_final: 0.7203 (t0) REVERT: A 856 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8009 (p0) REVERT: A 994 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (m-30) REVERT: B 88 ASP cc_start: 0.7227 (t0) cc_final: 0.6899 (t0) REVERT: B 140 PHE cc_start: 0.7903 (p90) cc_final: 0.7457 (p90) REVERT: B 190 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6689 (ttt180) REVERT: B 697 MET cc_start: 0.9179 (ptp) cc_final: 0.8978 (ptm) REVERT: B 1106 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.9015 (pt0) REVERT: B 1142 GLN cc_start: 0.8605 (pp30) cc_final: 0.8275 (pp30) REVERT: C 40 ASP cc_start: 0.7093 (p0) cc_final: 0.6659 (t0) REVERT: C 118 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6749 (mp) REVERT: C 131 CYS cc_start: 0.2792 (m) cc_final: 0.2258 (m) REVERT: C 170 TYR cc_start: 0.7819 (t80) cc_final: 0.7483 (t80) REVERT: C 239 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7230 (tp40) REVERT: C 430 THR cc_start: 0.6059 (OUTLIER) cc_final: 0.5550 (t) REVERT: C 528 LYS cc_start: 0.4721 (OUTLIER) cc_final: 0.4271 (tttt) REVERT: C 529 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6540 (ptmt) REVERT: C 796 ASP cc_start: 0.8144 (t0) cc_final: 0.7451 (p0) REVERT: C 994 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: C 995 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7864 (mtt180) REVERT: C 1142 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7701 (mm110) outliers start: 101 outliers final: 69 residues processed: 242 average time/residue: 0.1252 time to fit residues: 51.6595 Evaluate side-chains 234 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 152 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 558 LYS 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 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 150 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 239 GLN C 207 HIS C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101564 restraints weight = 36709.916| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.51 r_work: 0.2996 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 24348 Z= 0.267 Angle : 0.805 22.868 33256 Z= 0.378 Chirality : 0.054 0.754 3974 Planarity : 0.005 0.074 4164 Dihedral : 7.837 59.741 4632 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.81 % Favored : 92.05 % Rotamer: Outliers : 4.24 % Allowed : 22.37 % Favored : 73.39 % 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: -1.38 (0.15), residues: 2854 helix: 1.00 (0.21), residues: 666 sheet: -0.51 (0.18), residues: 741 loop : -2.13 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 190 TYR 0.021 0.002 TYR A1067 PHE 0.022 0.002 PHE A 86 TRP 0.009 0.001 TRP C 436 HIS 0.027 0.002 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00659 (24241) covalent geometry : angle 0.73954 (32971) SS BOND : bond 0.00615 ( 36) SS BOND : angle 2.39481 ( 72) hydrogen bonds : bond 0.05325 ( 855) hydrogen bonds : angle 5.33387 ( 2403) link_BETA1-4 : bond 0.00626 ( 23) link_BETA1-4 : angle 2.52419 ( 69) link_NAG-ASN : bond 0.00630 ( 48) link_NAG-ASN : angle 4.29180 ( 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 257 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 149 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7271 (m-80) cc_final: 0.7001 (m-80) REVERT: A 153 MET cc_start: 0.2534 (mpp) cc_final: 0.0733 (ttt) REVERT: A 237 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6162 (ptt90) REVERT: A 239 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.5625 (mt0) REVERT: A 324 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: A 347 PHE cc_start: 0.3830 (OUTLIER) cc_final: 0.2352 (m-80) REVERT: A 856 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8366 (p0) REVERT: B 88 ASP cc_start: 0.7160 (t0) cc_final: 0.6813 (t0) REVERT: B 140 PHE cc_start: 0.7910 (p90) cc_final: 0.7400 (p90) REVERT: B 190 ARG cc_start: 0.7521 (mtt90) cc_final: 0.6570 (ttt180) REVERT: C 118 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7497 (mt) REVERT: C 131 CYS cc_start: 0.2957 (m) cc_final: 0.2438 (m) REVERT: C 170 TYR cc_start: 0.7870 (t80) cc_final: 0.7478 (t80) REVERT: C 233 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6353 (tp) REVERT: C 392 PHE cc_start: 0.7065 (m-80) cc_final: 0.6864 (m-80) REVERT: C 430 THR cc_start: 0.6108 (OUTLIER) cc_final: 0.5602 (t) REVERT: C 528 LYS cc_start: 0.4753 (OUTLIER) cc_final: 0.4290 (tttt) REVERT: C 529 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6538 (ptmt) REVERT: C 796 ASP cc_start: 0.8210 (t0) cc_final: 0.7719 (p0) REVERT: C 994 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8134 (m-30) REVERT: C 995 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7950 (mtt90) outliers start: 108 outliers final: 87 residues processed: 240 average time/residue: 0.1290 time to fit residues: 52.6454 Evaluate side-chains 239 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 141 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 107 optimal weight: 0.0770 chunk 193 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN C 207 HIS C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104793 restraints weight = 36834.243| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.98 r_work: 0.3063 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4527 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= 0.137 Angle : 0.700 20.460 33256 Z= 0.328 Chirality : 0.048 0.470 3974 Planarity : 0.004 0.076 4164 Dihedral : 7.497 59.232 4632 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.31 % Favored : 93.55 % Rotamer: Outliers : 3.92 % Allowed : 22.37 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.19 (0.15), residues: 2854 helix: 1.18 (0.21), residues: 668 sheet: -0.42 (0.18), residues: 748 loop : -2.03 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.017 0.001 TYR C1067 PHE 0.021 0.001 PHE A 86 TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00317 (24241) covalent geometry : angle 0.64091 (32971) SS BOND : bond 0.00534 ( 36) SS BOND : angle 1.85620 ( 72) hydrogen bonds : bond 0.04165 ( 855) hydrogen bonds : angle 5.12566 ( 2403) link_BETA1-4 : bond 0.00572 ( 23) link_BETA1-4 : angle 2.18529 ( 69) link_NAG-ASN : bond 0.00588 ( 48) link_NAG-ASN : angle 3.88210 ( 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 250 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 150 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7100 (m-80) cc_final: 0.6814 (m-80) REVERT: A 153 MET cc_start: 0.2253 (mpp) cc_final: 0.0588 (ttt) REVERT: A 237 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6189 (ptt90) REVERT: A 239 GLN cc_start: 0.6079 (OUTLIER) cc_final: 0.5617 (mt0) REVERT: A 324 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: A 347 PHE cc_start: 0.3886 (OUTLIER) cc_final: 0.2331 (m-80) REVERT: A 856 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.8076 (p0) REVERT: B 118 LEU cc_start: 0.7186 (tt) cc_final: 0.6553 (mp) REVERT: B 140 PHE cc_start: 0.7907 (p90) cc_final: 0.7452 (p90) REVERT: B 190 ARG cc_start: 0.7347 (mtt90) cc_final: 0.6599 (ttt180) REVERT: B 794 ILE cc_start: 0.7619 (pp) cc_final: 0.7354 (mt) REVERT: B 1142 GLN cc_start: 0.8610 (pp30) cc_final: 0.8213 (pp30) REVERT: C 118 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.6880 (mp) REVERT: C 131 CYS cc_start: 0.2820 (m) cc_final: 0.2286 (m) REVERT: C 170 TYR cc_start: 0.7814 (t80) cc_final: 0.7500 (t80) REVERT: C 233 ILE cc_start: 0.6385 (OUTLIER) cc_final: 0.6147 (tp) REVERT: C 430 THR cc_start: 0.6056 (OUTLIER) cc_final: 0.5595 (t) REVERT: C 528 LYS cc_start: 0.4661 (OUTLIER) cc_final: 0.4200 (tttt) REVERT: C 529 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6543 (ptmt) REVERT: C 796 ASP cc_start: 0.8076 (t0) cc_final: 0.7660 (p0) REVERT: C 994 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: C 995 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7850 (mtt90) outliers start: 100 outliers final: 77 residues processed: 237 average time/residue: 0.1278 time to fit residues: 51.4677 Evaluate side-chains 234 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 147 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 130 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 284 optimal weight: 0.0470 chunk 97 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN C 134 GLN C 207 HIS C1002 GLN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.159279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100787 restraints weight = 37115.711| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.50 r_work: 0.3010 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4632 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= 0.216 Angle : 0.749 20.342 33256 Z= 0.353 Chirality : 0.050 0.464 3974 Planarity : 0.005 0.077 4164 Dihedral : 7.590 59.661 4632 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.64 % Favored : 92.22 % Rotamer: Outliers : 3.77 % Allowed : 22.29 % Favored : 73.94 % 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: -1.26 (0.15), residues: 2854 helix: 1.15 (0.21), residues: 666 sheet: -0.47 (0.18), residues: 752 loop : -2.08 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.020 0.002 TYR A1067 PHE 0.022 0.002 PHE A 86 TRP 0.010 0.001 TRP C 436 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00528 (24241) covalent geometry : angle 0.69234 (32971) SS BOND : bond 0.00580 ( 36) SS BOND : angle 2.12613 ( 72) hydrogen bonds : bond 0.04881 ( 855) hydrogen bonds : angle 5.23608 ( 2403) link_BETA1-4 : bond 0.00456 ( 23) link_BETA1-4 : angle 2.27029 ( 69) link_NAG-ASN : bond 0.00604 ( 48) link_NAG-ASN : angle 3.90412 ( 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 248 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 152 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7232 (m-80) cc_final: 0.6981 (m-80) REVERT: A 153 MET cc_start: 0.2239 (mpp) cc_final: 0.0808 (ttt) REVERT: A 237 ARG cc_start: 0.7037 (mtp85) cc_final: 0.6174 (ptt90) REVERT: A 239 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5956 (mt0) REVERT: A 324 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: A 347 PHE cc_start: 0.3824 (OUTLIER) cc_final: 0.2172 (m-80) REVERT: A 856 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8420 (p0) REVERT: B 118 LEU cc_start: 0.7236 (tt) cc_final: 0.6644 (mp) REVERT: B 140 PHE cc_start: 0.7913 (p90) cc_final: 0.7333 (p90) REVERT: B 190 ARG cc_start: 0.7524 (mtt90) cc_final: 0.6744 (ttt180) REVERT: B 794 ILE cc_start: 0.7649 (pp) cc_final: 0.7393 (mt) REVERT: B 1100 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8791 (p) REVERT: B 1142 GLN cc_start: 0.8605 (pp30) cc_final: 0.8246 (pp30) REVERT: C 118 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7243 (mt) REVERT: C 131 CYS cc_start: 0.2932 (m) cc_final: 0.2404 (m) REVERT: C 170 TYR cc_start: 0.7948 (t80) cc_final: 0.7680 (t80) REVERT: C 233 ILE cc_start: 0.6485 (OUTLIER) cc_final: 0.6261 (tp) REVERT: C 430 THR cc_start: 0.6314 (OUTLIER) cc_final: 0.5829 (t) REVERT: C 528 LYS cc_start: 0.4701 (OUTLIER) cc_final: 0.4227 (tttt) REVERT: C 529 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6556 (ptmt) REVERT: C 796 ASP cc_start: 0.8191 (t0) cc_final: 0.7772 (p0) REVERT: C 994 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: C 995 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7964 (mtp180) outliers start: 96 outliers final: 80 residues processed: 234 average time/residue: 0.1266 time to fit residues: 50.5511 Evaluate side-chains 238 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 147 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 33 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 207 HIS C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.159607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101751 restraints weight = 36590.143| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.44 r_work: 0.3018 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24348 Z= 0.167 Angle : 0.717 20.362 33256 Z= 0.337 Chirality : 0.049 0.463 3974 Planarity : 0.004 0.078 4164 Dihedral : 7.434 58.521 4632 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.83 % Favored : 93.03 % Rotamer: Outliers : 3.92 % Allowed : 22.10 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 2854 helix: 1.27 (0.21), residues: 666 sheet: -0.43 (0.18), residues: 752 loop : -2.01 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.018 0.001 TYR A1067 PHE 0.022 0.001 PHE A 86 TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00403 (24241) covalent geometry : angle 0.66227 (32971) SS BOND : bond 0.00541 ( 36) SS BOND : angle 1.94899 ( 72) hydrogen bonds : bond 0.04392 ( 855) hydrogen bonds : angle 5.12604 ( 2403) link_BETA1-4 : bond 0.00548 ( 23) link_BETA1-4 : angle 2.20184 ( 69) link_NAG-ASN : bond 0.00578 ( 48) link_NAG-ASN : angle 3.74230 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7569.03 seconds wall clock time: 129 minutes 32.98 seconds (7772.98 seconds total)