Starting phenix.real_space_refine on Sat Jun 21 08:26:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dwz_30890/06_2025/7dwz_30890.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dwz_30890/06_2025/7dwz_30890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dwz_30890/06_2025/7dwz_30890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dwz_30890/06_2025/7dwz_30890.map" model { file = "/net/cci-nas-00/data/ceres_data/7dwz_30890/06_2025/7dwz_30890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dwz_30890/06_2025/7dwz_30890.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 15637 2.51 5 N 3999 2.21 5 O 4854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24598 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "C" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.58, per 1000 atoms: 0.63 Number of scatterers: 24598 At special positions: 0 Unit cell: (136.962, 155.441, 168.485, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4854 8.00 N 3999 7.00 C 15637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.17 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.12 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.55 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.85 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.00 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.94 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.29 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.05 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=1.87 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1409 " - " NAG B1410 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C 343 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 3.4 seconds 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5660 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 23.8% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.629A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.636A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.599A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.854A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.696A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.604A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.101A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 6.192A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.671A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.587A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.587A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 316 removed outlier: 6.009A pdb=" N GLU B 309 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 601 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.501A pdb=" N VAL B 551 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 317 removed outlier: 4.305A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.525A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 881 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.55 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5753 1.33 - 1.45: 6233 1.45 - 1.58: 13005 1.58 - 1.70: 0 1.70 - 1.83: 135 Bond restraints: 25126 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.34e+01 bond pdb=" C THR B 588 " pdb=" N PRO B 589 " ideal model delta sigma weight residual 1.330 1.389 -0.058 1.23e-02 6.61e+03 2.26e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.27e-02 6.20e+03 2.14e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.263 0.068 1.59e-02 3.96e+03 1.85e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 ... (remaining 25121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 33339 2.74 - 5.49: 766 5.49 - 8.23: 59 8.23 - 10.98: 3 10.98 - 13.72: 7 Bond angle restraints: 34174 Sorted by residual: angle pdb=" N CYS A 538 " pdb=" CA CYS A 538 " pdb=" C CYS A 538 " ideal model delta sigma weight residual 110.24 100.85 9.39 1.47e+00 4.63e-01 4.08e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" C THR A 588 " pdb=" N PRO A 589 " pdb=" CA PRO A 589 " ideal model delta sigma weight residual 119.90 114.13 5.77 1.02e+00 9.61e-01 3.20e+01 ... (remaining 34169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13630 17.93 - 35.87: 1539 35.87 - 53.80: 508 53.80 - 71.74: 179 71.74 - 89.67: 48 Dihedral angle restraints: 15904 sinusoidal: 7120 harmonic: 8784 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -3.61 -82.39 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 17.00 76.00 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.06 71.94 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 15901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4078 0.330 - 0.660: 3 0.660 - 0.989: 4 0.989 - 1.319: 2 1.319 - 1.649: 4 Chirality restraints: 4091 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-02 2.50e+03 2.59e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.80e+01 ... (remaining 4088 not shown) Planarity restraints: 4380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.158 2.00e-02 2.50e+03 1.87e-01 4.39e+02 pdb=" CG ASN C 331 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.315 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.093 2.00e-02 2.50e+03 1.42e-01 2.52e+02 pdb=" CG ASN C 234 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.252 2.00e-02 2.50e+03 pdb=" C1 NAG C1404 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.104 2.00e-02 2.50e+03 1.36e-01 2.30e+02 pdb=" CG ASN A 616 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.231 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.161 2.00e-02 2.50e+03 ... (remaining 4377 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 229 2.51 - 3.11: 17984 3.11 - 3.70: 34506 3.70 - 4.30: 52897 4.30 - 4.90: 88042 Nonbonded interactions: 193658 Sorted by model distance: nonbonded pdb=" O ILE C 332 " pdb=" OG1 THR C 333 " model vdw 1.909 3.040 nonbonded pdb=" O SER B 530 " pdb=" OG1 THR B 531 " model vdw 1.913 3.040 nonbonded pdb=" O LEU C 335 " pdb=" O CYS C 336 " model vdw 1.968 3.040 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.983 3.120 ... (remaining 193653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 27 through 1146 or resid 1401 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: 1.710 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: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 59.170 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.516 25236 Z= 0.571 Angle : 1.471 65.570 34465 Z= 0.749 Chirality : 0.088 1.649 4091 Planarity : 0.008 0.091 4332 Dihedral : 17.982 89.672 10127 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 3.47 % Allowed : 10.15 % Favored : 86.37 % Rotamer: Outliers : 12.63 % Allowed : 18.34 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.13), residues: 2965 helix: -2.23 (0.16), residues: 663 sheet: -2.06 (0.17), residues: 730 loop : -3.40 (0.12), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 104 HIS 0.009 0.002 HIS A1048 PHE 0.026 0.003 PHE A 898 TYR 0.027 0.003 TYR B1067 ARG 0.008 0.001 ARG A1039 Details of bonding type rmsd link_NAG-ASN : bond 0.03095 ( 48) link_NAG-ASN : angle 8.81478 ( 144) link_BETA1-4 : bond 0.04421 ( 23) link_BETA1-4 : angle 5.58057 ( 69) hydrogen bonds : bond 0.19466 ( 845) hydrogen bonds : angle 7.86929 ( 2394) SS BOND : bond 0.10864 ( 39) SS BOND : angle 17.89324 ( 78) covalent geometry : bond 0.01189 (25126) covalent geometry : angle 1.03050 (34174) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 334 poor density : 402 time to evaluate : 2.682 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 81 ASN cc_start: 0.2096 (OUTLIER) cc_final: 0.1806 (t0) REVERT: A 153 MET cc_start: 0.1103 (mpp) cc_final: -0.1433 (ttt) REVERT: A 324 GLU cc_start: 0.5247 (OUTLIER) cc_final: 0.4261 (pt0) REVERT: A 389 ASP cc_start: 0.3473 (OUTLIER) cc_final: 0.1853 (p0) REVERT: A 787 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8084 (mm110) REVERT: B 389 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.6244 (t70) REVERT: B 514 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 529 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7948 (tppt) REVERT: B 1029 MET cc_start: 0.8743 (tpp) cc_final: 0.8348 (tpp) REVERT: C 66 HIS cc_start: 0.6130 (OUTLIER) cc_final: 0.5828 (t-90) REVERT: C 116 SER cc_start: 0.4141 (OUTLIER) cc_final: 0.3848 (m) REVERT: C 559 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.4778 (m-10) REVERT: C 690 GLN cc_start: 0.5225 (OUTLIER) cc_final: 0.4957 (pm20) outliers start: 334 outliers final: 92 residues processed: 679 average time/residue: 0.3555 time to fit residues: 376.3751 Evaluate side-chains 290 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 187 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 188 ASN A 271 GLN A 334 ASN A 422 ASN A 440 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 764 ASN A 787 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 992 GLN A1101 HIS B 81 ASN B 134 GLN B 137 ASN B 188 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 317 ASN B 354 ASN B 498 GLN B 544 ASN B 655 HIS B 762 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 49 HIS C 137 ASN C 422 ASN C 498 GLN C 564 GLN C 644 GLN C 690 GLN C 703 ASN C 751 ASN C 755 GLN C 784 GLN C 804 GLN C 856 ASN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 954 GLN C 965 GLN C 992 GLN C1071 GLN C1101 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.171650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120591 restraints weight = 42021.524| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.30 r_work: 0.3236 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 25236 Z= 0.167 Angle : 0.835 21.936 34465 Z= 0.403 Chirality : 0.051 0.555 4091 Planarity : 0.005 0.070 4332 Dihedral : 10.475 74.564 4887 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.55 % Favored : 91.87 % Rotamer: Outliers : 5.98 % Allowed : 20.46 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 2965 helix: -0.08 (0.20), residues: 654 sheet: -1.42 (0.18), residues: 737 loop : -2.80 (0.13), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.004 0.001 HIS B 49 PHE 0.020 0.002 PHE C 400 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00537 ( 48) link_NAG-ASN : angle 4.37650 ( 144) link_BETA1-4 : bond 0.00587 ( 23) link_BETA1-4 : angle 2.37817 ( 69) hydrogen bonds : bond 0.04924 ( 845) hydrogen bonds : angle 5.94354 ( 2394) SS BOND : bond 0.00588 ( 39) SS BOND : angle 2.54742 ( 78) covalent geometry : bond 0.00372 (25126) covalent geometry : angle 0.77218 (34174) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 220 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1063 (mpp) cc_final: -0.0272 (mtp) REVERT: A 169 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4256 (mm-30) REVERT: A 389 ASP cc_start: 0.3915 (OUTLIER) cc_final: 0.2658 (p0) REVERT: A 619 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: B 53 ASP cc_start: 0.4479 (OUTLIER) cc_final: 0.4249 (t0) REVERT: B 55 PHE cc_start: 0.8029 (m-80) cc_final: 0.7718 (m-80) REVERT: B 195 LYS cc_start: 0.5677 (OUTLIER) cc_final: 0.5387 (ptpt) REVERT: B 356 LYS cc_start: 0.7690 (mtpp) cc_final: 0.6828 (tptt) REVERT: B 399 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7854 (m) REVERT: B 453 TYR cc_start: 0.7199 (p90) cc_final: 0.6279 (p90) REVERT: B 529 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7873 (tppt) REVERT: B 867 ASP cc_start: 0.8357 (p0) cc_final: 0.8157 (m-30) REVERT: B 1029 MET cc_start: 0.9296 (tpp) cc_final: 0.8847 (tpp) REVERT: C 66 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.6065 (t-90) REVERT: C 239 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6566 (mm110) REVERT: C 269 TYR cc_start: 0.6543 (m-80) cc_final: 0.6105 (m-80) REVERT: C 356 LYS cc_start: 0.6752 (ttmm) cc_final: 0.6186 (pttt) REVERT: C 394 ASN cc_start: 0.6032 (m110) cc_final: 0.5667 (m110) REVERT: C 400 PHE cc_start: 0.8086 (p90) cc_final: 0.7443 (p90) REVERT: C 517 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5418 (mm) REVERT: C 558 LYS cc_start: 0.6888 (mttp) cc_final: 0.5867 (tptm) REVERT: C 567 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5653 (mtt180) REVERT: C 814 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7902 (mtmm) outliers start: 158 outliers final: 82 residues processed: 358 average time/residue: 0.3421 time to fit residues: 196.8719 Evaluate side-chains 254 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 161 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 82 optimal weight: 2.9990 chunk 272 optimal weight: 0.6980 chunk 115 optimal weight: 0.0470 chunk 69 optimal weight: 0.3980 chunk 215 optimal weight: 0.4980 chunk 139 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1010 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.172216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125134 restraints weight = 41710.355| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.30 r_work: 0.3274 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25236 Z= 0.123 Angle : 0.722 18.619 34465 Z= 0.343 Chirality : 0.049 0.553 4091 Planarity : 0.004 0.047 4332 Dihedral : 8.855 73.873 4780 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.28 % Favored : 92.28 % Rotamer: Outliers : 4.50 % Allowed : 21.07 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2965 helix: 0.77 (0.21), residues: 651 sheet: -1.02 (0.18), residues: 749 loop : -2.38 (0.14), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.003 0.000 HIS C 519 PHE 0.015 0.001 PHE C 592 TYR 0.037 0.001 TYR A 453 ARG 0.006 0.000 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 48) link_NAG-ASN : angle 3.75435 ( 144) link_BETA1-4 : bond 0.00612 ( 23) link_BETA1-4 : angle 2.26506 ( 69) hydrogen bonds : bond 0.04015 ( 845) hydrogen bonds : angle 5.47560 ( 2394) SS BOND : bond 0.00342 ( 39) SS BOND : angle 1.87144 ( 78) covalent geometry : bond 0.00260 (25126) covalent geometry : angle 0.66951 (34174) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 184 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5766 (m110) cc_final: 0.5081 (p0) REVERT: A 153 MET cc_start: 0.1272 (mpp) cc_final: -0.0405 (mmm) REVERT: A 169 GLU cc_start: 0.4992 (OUTLIER) cc_final: 0.4366 (mm-30) REVERT: A 233 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4718 (mm) REVERT: A 389 ASP cc_start: 0.4406 (OUTLIER) cc_final: 0.3215 (p0) REVERT: A 619 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: B 55 PHE cc_start: 0.8032 (m-80) cc_final: 0.7627 (m-80) REVERT: B 195 LYS cc_start: 0.5843 (OUTLIER) cc_final: 0.5639 (ptpt) REVERT: B 299 THR cc_start: 0.8272 (m) cc_final: 0.7894 (p) REVERT: B 356 LYS cc_start: 0.7906 (mtpp) cc_final: 0.6964 (tptt) REVERT: B 1029 MET cc_start: 0.9262 (tpp) cc_final: 0.8832 (tpp) REVERT: C 66 HIS cc_start: 0.6183 (OUTLIER) cc_final: 0.5897 (t-90) REVERT: C 134 GLN cc_start: 0.6983 (tm-30) cc_final: 0.6723 (pp30) REVERT: C 239 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6815 (mm110) REVERT: C 269 TYR cc_start: 0.6281 (m-80) cc_final: 0.6043 (m-80) REVERT: C 356 LYS cc_start: 0.6854 (ttmm) cc_final: 0.6321 (pttt) REVERT: C 529 LYS cc_start: 0.7799 (tppt) cc_final: 0.7591 (mmtm) REVERT: C 558 LYS cc_start: 0.6933 (mttp) cc_final: 0.5914 (tptm) REVERT: C 814 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7933 (mtmm) outliers start: 119 outliers final: 69 residues processed: 291 average time/residue: 0.3330 time to fit residues: 158.2712 Evaluate side-chains 226 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 150 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 3 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 30 optimal weight: 0.0470 chunk 74 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 295 optimal weight: 2.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 804 GLN A 935 GLN A 955 ASN A1011 GLN B 388 ASN B 544 ASN B1071 GLN C 115 GLN C 751 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3375 r_free = 0.3375 target = 0.109811 restraints weight = 41719.476| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.81 r_work: 0.3135 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 25236 Z= 0.198 Angle : 0.752 18.745 34465 Z= 0.360 Chirality : 0.050 0.425 4091 Planarity : 0.005 0.051 4332 Dihedral : 8.400 67.758 4762 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.28 % Favored : 92.34 % Rotamer: Outliers : 5.03 % Allowed : 20.84 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 2965 helix: 0.83 (0.21), residues: 664 sheet: -0.86 (0.19), residues: 726 loop : -2.28 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.006 0.001 HIS A1058 PHE 0.021 0.002 PHE C 86 TYR 0.021 0.002 TYR A 204 ARG 0.004 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 48) link_NAG-ASN : angle 3.55347 ( 144) link_BETA1-4 : bond 0.00531 ( 23) link_BETA1-4 : angle 2.23532 ( 69) hydrogen bonds : bond 0.04932 ( 845) hydrogen bonds : angle 5.54637 ( 2394) SS BOND : bond 0.00622 ( 39) SS BOND : angle 2.36316 ( 78) covalent geometry : bond 0.00474 (25126) covalent geometry : angle 0.70302 (34174) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 177 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5699 (m110) cc_final: 0.4769 (p0) REVERT: A 153 MET cc_start: 0.1201 (mpp) cc_final: 0.0742 (pmm) REVERT: A 155 SER cc_start: 0.5340 (OUTLIER) cc_final: 0.5103 (m) REVERT: A 169 GLU cc_start: 0.5372 (OUTLIER) cc_final: 0.5085 (mm-30) REVERT: A 233 ILE cc_start: 0.4998 (OUTLIER) cc_final: 0.4532 (mm) REVERT: A 389 ASP cc_start: 0.4174 (OUTLIER) cc_final: 0.2937 (p0) REVERT: A 453 TYR cc_start: 0.1634 (OUTLIER) cc_final: 0.1039 (p90) REVERT: A 855 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5600 (m-80) REVERT: A 1092 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: B 53 ASP cc_start: 0.4505 (OUTLIER) cc_final: 0.4236 (t0) REVERT: B 55 PHE cc_start: 0.8208 (m-80) cc_final: 0.7693 (m-80) REVERT: B 105 ILE cc_start: 0.4399 (OUTLIER) cc_final: 0.4036 (mm) REVERT: B 195 LYS cc_start: 0.5810 (OUTLIER) cc_final: 0.5411 (ptpt) REVERT: B 355 ARG cc_start: 0.8056 (tpt170) cc_final: 0.7745 (tpp80) REVERT: B 356 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7410 (mtpp) REVERT: B 453 TYR cc_start: 0.7279 (p90) cc_final: 0.7040 (p90) REVERT: B 1029 MET cc_start: 0.9382 (tpp) cc_final: 0.9042 (tpp) REVERT: C 58 PHE cc_start: 0.7106 (m-80) cc_final: 0.6746 (m-80) REVERT: C 66 HIS cc_start: 0.6636 (OUTLIER) cc_final: 0.6252 (t-90) REVERT: C 134 GLN cc_start: 0.7235 (tm-30) cc_final: 0.6949 (pp30) REVERT: C 191 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7294 (mt-10) REVERT: C 200 TYR cc_start: 0.5658 (m-80) cc_final: 0.5399 (m-10) REVERT: C 237 ARG cc_start: 0.6012 (mmt90) cc_final: 0.5797 (mtt180) REVERT: C 356 LYS cc_start: 0.6870 (ttmm) cc_final: 0.6075 (pttt) REVERT: C 370 ASN cc_start: 0.5186 (t0) cc_final: 0.4849 (p0) REVERT: C 529 LYS cc_start: 0.7808 (tppt) cc_final: 0.6394 (tptp) REVERT: C 558 LYS cc_start: 0.7034 (mttp) cc_final: 0.5904 (tptm) REVERT: C 563 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6142 (mt0) REVERT: C 814 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8294 (mtmt) REVERT: C 979 ASP cc_start: 0.7748 (t70) cc_final: 0.7395 (t70) outliers start: 133 outliers final: 82 residues processed: 293 average time/residue: 0.3360 time to fit residues: 162.1243 Evaluate side-chains 247 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 152 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 168 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 265 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 607 GLN B 388 ASN B 954 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.167669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117090 restraints weight = 41489.068| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.07 r_work: 0.3211 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 25236 Z= 0.136 Angle : 0.673 17.981 34465 Z= 0.319 Chirality : 0.048 0.476 4091 Planarity : 0.004 0.062 4332 Dihedral : 7.743 59.040 4756 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.64 % Favored : 93.02 % Rotamer: Outliers : 4.39 % Allowed : 21.60 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 2965 helix: 1.15 (0.21), residues: 655 sheet: -0.65 (0.19), residues: 719 loop : -2.09 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS B 49 PHE 0.015 0.001 PHE C 86 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 48) link_NAG-ASN : angle 3.16264 ( 144) link_BETA1-4 : bond 0.00548 ( 23) link_BETA1-4 : angle 2.10663 ( 69) hydrogen bonds : bond 0.03923 ( 845) hydrogen bonds : angle 5.27629 ( 2394) SS BOND : bond 0.00574 ( 39) SS BOND : angle 1.91814 ( 78) covalent geometry : bond 0.00317 (25126) covalent geometry : angle 0.62993 (34174) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 174 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.5716 (m110) cc_final: 0.4745 (p0) REVERT: A 169 GLU cc_start: 0.5560 (OUTLIER) cc_final: 0.5153 (mm-30) REVERT: A 233 ILE cc_start: 0.5053 (OUTLIER) cc_final: 0.4579 (mm) REVERT: A 389 ASP cc_start: 0.4387 (OUTLIER) cc_final: 0.3025 (p0) REVERT: A 855 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5546 (m-10) REVERT: B 55 PHE cc_start: 0.8183 (m-80) cc_final: 0.7704 (m-80) REVERT: B 191 GLU cc_start: 0.7929 (mp0) cc_final: 0.7183 (mp0) REVERT: B 195 LYS cc_start: 0.5853 (OUTLIER) cc_final: 0.5527 (ptpt) REVERT: B 342 PHE cc_start: 0.7663 (m-80) cc_final: 0.7309 (m-80) REVERT: B 355 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7796 (tpp80) REVERT: B 453 TYR cc_start: 0.7463 (p90) cc_final: 0.7182 (p90) REVERT: B 533 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.6001 (tt) REVERT: B 1128 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8958 (p) REVERT: C 66 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.6043 (t-90) REVERT: C 134 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6943 (pp30) REVERT: C 191 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7092 (mt-10) REVERT: C 200 TYR cc_start: 0.5475 (m-80) cc_final: 0.5173 (m-10) REVERT: C 237 ARG cc_start: 0.6132 (mmt90) cc_final: 0.5804 (mtt180) REVERT: C 356 LYS cc_start: 0.6910 (ttmm) cc_final: 0.6060 (pttt) REVERT: C 370 ASN cc_start: 0.5398 (t0) cc_final: 0.4971 (p0) REVERT: C 461 LEU cc_start: 0.7352 (tp) cc_final: 0.7143 (tp) REVERT: C 645 THR cc_start: 0.8575 (m) cc_final: 0.8354 (p) REVERT: C 814 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8291 (mtmt) outliers start: 116 outliers final: 72 residues processed: 275 average time/residue: 0.3894 time to fit residues: 180.7789 Evaluate side-chains 232 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 151 time to evaluate : 4.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 985 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 157 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 225 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 101 optimal weight: 0.0010 chunk 173 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 163 optimal weight: 0.0040 chunk 58 optimal weight: 5.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 935 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.123046 restraints weight = 41333.708| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.32 r_work: 0.3230 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 25236 Z= 0.105 Angle : 0.644 17.897 34465 Z= 0.304 Chirality : 0.047 0.465 4091 Planarity : 0.004 0.053 4332 Dihedral : 7.180 59.218 4748 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.21 % Favored : 93.42 % Rotamer: Outliers : 3.82 % Allowed : 21.97 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 2965 helix: 1.42 (0.21), residues: 659 sheet: -0.49 (0.19), residues: 711 loop : -1.97 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 353 HIS 0.002 0.000 HIS B 49 PHE 0.022 0.001 PHE A 194 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 48) link_NAG-ASN : angle 3.17186 ( 144) link_BETA1-4 : bond 0.00550 ( 23) link_BETA1-4 : angle 2.02351 ( 69) hydrogen bonds : bond 0.03409 ( 845) hydrogen bonds : angle 5.07918 ( 2394) SS BOND : bond 0.00442 ( 39) SS BOND : angle 1.59856 ( 78) covalent geometry : bond 0.00224 (25126) covalent geometry : angle 0.60179 (34174) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 161 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0487 (pmm) cc_final: -0.0969 (pmm) REVERT: A 169 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.5022 (mm-30) REVERT: A 233 ILE cc_start: 0.5042 (OUTLIER) cc_final: 0.4577 (mm) REVERT: A 389 ASP cc_start: 0.4537 (OUTLIER) cc_final: 0.3185 (p0) REVERT: A 855 PHE cc_start: 0.5770 (OUTLIER) cc_final: 0.5477 (m-10) REVERT: B 55 PHE cc_start: 0.8150 (m-80) cc_final: 0.7689 (m-80) REVERT: B 342 PHE cc_start: 0.7701 (m-80) cc_final: 0.7373 (m-80) REVERT: B 453 TYR cc_start: 0.7477 (p90) cc_final: 0.7251 (p90) REVERT: B 508 TYR cc_start: 0.7705 (m-80) cc_final: 0.7441 (m-80) REVERT: B 533 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5631 (tt) REVERT: B 539 VAL cc_start: 0.8468 (p) cc_final: 0.8032 (t) REVERT: B 791 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7931 (m) REVERT: B 1128 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8983 (p) REVERT: C 96 GLU cc_start: 0.5803 (OUTLIER) cc_final: 0.4348 (pm20) REVERT: C 134 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6919 (pp30) REVERT: C 191 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7007 (mt-10) REVERT: C 200 TYR cc_start: 0.5513 (m-80) cc_final: 0.5292 (m-10) REVERT: C 237 ARG cc_start: 0.6014 (mmt90) cc_final: 0.5700 (mtt180) REVERT: C 239 GLN cc_start: 0.6961 (mm110) cc_final: 0.4665 (tm-30) REVERT: C 356 LYS cc_start: 0.7020 (ttmm) cc_final: 0.6257 (pttt) REVERT: C 370 ASN cc_start: 0.5605 (t0) cc_final: 0.5129 (p0) REVERT: C 563 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.5587 (mt0) REVERT: C 814 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8247 (mtmt) outliers start: 101 outliers final: 67 residues processed: 250 average time/residue: 0.3384 time to fit residues: 141.8455 Evaluate side-chains 222 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 145 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1029 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 131 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 272 optimal weight: 0.6980 chunk 236 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 ASN B1106 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112261 restraints weight = 41366.982| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.97 r_work: 0.3140 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25236 Z= 0.141 Angle : 0.662 18.033 34465 Z= 0.314 Chirality : 0.047 0.467 4091 Planarity : 0.004 0.047 4332 Dihedral : 7.036 59.433 4740 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.02 % Favored : 92.61 % Rotamer: Outliers : 3.78 % Allowed : 22.01 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 2965 helix: 1.53 (0.21), residues: 655 sheet: -0.50 (0.19), residues: 714 loop : -1.93 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.004 0.001 HIS A1064 PHE 0.019 0.001 PHE C 86 TYR 0.018 0.001 TYR C1067 ARG 0.009 0.000 ARG C 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 48) link_NAG-ASN : angle 3.12126 ( 144) link_BETA1-4 : bond 0.00493 ( 23) link_BETA1-4 : angle 2.03311 ( 69) hydrogen bonds : bond 0.03934 ( 845) hydrogen bonds : angle 5.11866 ( 2394) SS BOND : bond 0.00462 ( 39) SS BOND : angle 1.65535 ( 78) covalent geometry : bond 0.00334 (25126) covalent geometry : angle 0.62204 (34174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5930 Ramachandran restraints generated. 2965 Oldfield, 0 Emsley, 2965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 157 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5768 (mmt-90) cc_final: 0.4699 (mpt180) REVERT: A 53 ASP cc_start: 0.5151 (t70) cc_final: 0.4525 (t0) REVERT: A 169 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4809 (mm-30) REVERT: A 233 ILE cc_start: 0.4923 (OUTLIER) cc_final: 0.4419 (mm) REVERT: A 389 ASP cc_start: 0.4585 (OUTLIER) cc_final: 0.3496 (p0) REVERT: A 855 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5579 (m-80) REVERT: A 979 ASP cc_start: 0.8705 (t0) cc_final: 0.8016 (t0) REVERT: B 55 PHE cc_start: 0.8199 (m-80) cc_final: 0.7674 (m-80) REVERT: B 299 THR cc_start: 0.8309 (m) cc_final: 0.8015 (p) REVERT: B 342 PHE cc_start: 0.7634 (m-80) cc_final: 0.7298 (m-80) REVERT: B 533 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5765 (tt) REVERT: B 537 LYS cc_start: 0.8081 (mttt) cc_final: 0.7344 (ttpp) REVERT: B 1128 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8987 (p) REVERT: B 1141 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8264 (tt) REVERT: C 58 PHE cc_start: 0.6743 (m-80) cc_final: 0.6384 (m-80) REVERT: C 66 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.5907 (t-90) REVERT: C 96 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4207 (pm20) REVERT: C 134 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6944 (pp30) REVERT: C 191 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7032 (mt-10) REVERT: C 237 ARG cc_start: 0.6047 (mmt90) cc_final: 0.5761 (mtt180) REVERT: C 356 LYS cc_start: 0.6861 (ttmm) cc_final: 0.5984 (pttt) REVERT: C 370 ASN cc_start: 0.5306 (t0) cc_final: 0.4865 (p0) REVERT: C 814 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8399 (mtmt) outliers start: 100 outliers final: 78 residues processed: 245 average time/residue: 0.3501 time to fit residues: 146.9443 Evaluate side-chains 236 residues out of total 2644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 148 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.9968 > 50: distance: 80 - 85: 5.103 distance: 85 - 86: 25.096 distance: 86 - 87: 42.207 distance: 86 - 89: 31.623 distance: 87 - 88: 10.878 distance: 87 - 93: 53.386 distance: 90 - 91: 38.125 distance: 90 - 92: 32.871 distance: 93 - 94: 27.438 distance: 94 - 95: 18.400 distance: 94 - 97: 19.911 distance: 95 - 96: 15.816 distance: 95 - 100: 37.357 distance: 97 - 98: 16.121 distance: 97 - 99: 17.981 distance: 100 - 101: 14.171 distance: 101 - 102: 14.493 distance: 101 - 104: 34.087 distance: 102 - 103: 4.939 distance: 102 - 111: 19.564 distance: 104 - 105: 29.147 distance: 105 - 106: 15.035 distance: 106 - 107: 4.118 distance: 107 - 108: 38.788 distance: 108 - 109: 10.889 distance: 108 - 110: 22.618 distance: 111 - 112: 50.542 distance: 112 - 113: 43.176 distance: 112 - 115: 23.017 distance: 113 - 114: 57.627 distance: 113 - 119: 11.873 distance: 115 - 116: 45.912 distance: 116 - 117: 25.576 distance: 116 - 118: 14.571 distance: 119 - 120: 42.766 distance: 120 - 121: 53.767 distance: 120 - 123: 47.995 distance: 121 - 122: 39.455 distance: 121 - 127: 56.630 distance: 123 - 124: 17.005 distance: 124 - 125: 26.961 distance: 124 - 126: 5.317 distance: 127 - 128: 45.233 distance: 127 - 133: 38.951 distance: 128 - 129: 40.952 distance: 128 - 131: 21.997 distance: 129 - 130: 19.298 distance: 129 - 134: 10.984 distance: 131 - 132: 19.831 distance: 132 - 133: 28.057 distance: 134 - 135: 35.924 distance: 135 - 136: 21.593 distance: 135 - 138: 55.333 distance: 136 - 137: 37.553 distance: 136 - 143: 38.143 distance: 138 - 139: 41.281 distance: 139 - 140: 15.992 distance: 140 - 141: 28.527 distance: 140 - 142: 10.536 distance: 143 - 144: 45.656 distance: 144 - 145: 39.465 distance: 145 - 146: 60.890 distance: 145 - 147: 51.501 distance: 147 - 148: 45.172 distance: 148 - 149: 43.514 distance: 148 - 151: 14.733 distance: 149 - 150: 56.246 distance: 149 - 158: 20.950 distance: 151 - 152: 17.865 distance: 152 - 153: 22.987 distance: 152 - 154: 25.766 distance: 153 - 155: 19.891 distance: 154 - 156: 34.199 distance: 155 - 157: 27.148 distance: 156 - 157: 25.463 distance: 158 - 159: 41.944 distance: 159 - 160: 44.088 distance: 159 - 162: 63.997 distance: 160 - 161: 16.449 distance: 160 - 164: 28.206 distance: 162 - 163: 35.921