Starting phenix.real_space_refine on Sat Mar 7 07:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ct5_30460/03_2026/7ct5_30460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ct5_30460/03_2026/7ct5_30460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ct5_30460/03_2026/7ct5_30460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ct5_30460/03_2026/7ct5_30460.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ct5_30460/03_2026/7ct5_30460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ct5_30460/03_2026/7ct5_30460.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 25220 2.51 5 N 6443 2.21 5 O 7768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39626 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} 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: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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: "Z" 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: 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: "b" 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: "c" 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: "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: "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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.63, per 1000 atoms: 0.24 Number of scatterers: 39626 At special positions: 0 Unit cell: (182.616, 194.573, 241.314, 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 195 16.00 O 7768 8.00 N 6443 7.00 C 25220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.57 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=2.40 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=2.19 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.82 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.20 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=1.86 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.04 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=2.25 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=2.03 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=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.05 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.05 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.05 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG C1406 " - " NAG C1407 " " 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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-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 331 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " 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 331 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 901 " - " ASN D 322 " " NAG E 901 " - " ASN E 322 " " NAG F 901 " - " ASN F 322 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 343 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 53 " " NAG b 1 " - " ASN D 90 " " NAG c 1 " - " ASN D 103 " " NAG d 1 " - " ASN D 432 " " NAG e 1 " - " ASN D 546 " " NAG f 1 " - " ASN E 53 " " NAG g 1 " - " ASN E 90 " " NAG h 1 " - " ASN E 103 " " NAG i 1 " - " ASN E 432 " " NAG j 1 " - " ASN E 546 " " NAG k 1 " - " ASN F 53 " " NAG l 1 " - " ASN F 90 " " NAG m 1 " - " ASN F 103 " " NAG n 1 " - " ASN F 432 " " NAG o 1 " - " ASN F 546 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.6 seconds 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9036 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 53 sheets defined 38.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.153A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.543A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.235A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 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: 3.631A 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: 3.770A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.541A 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: 3.644A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A 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: 3.995A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.628A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A 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 982 Processing helix chain 'A' and resid 985 through 990 Processing helix chain 'A' and resid 993 through 1033 removed outlier: 3.687A 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: 3.675A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.543A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.235A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A 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: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.372A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.261A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.543A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.236A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 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: 3.718A 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: 3.719A 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: 3.554A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.603A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.553A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.520A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 53 removed outlier: 3.914A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 78 removed outlier: 3.605A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.530A pdb=" N LEU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.531A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.629A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 173 removed outlier: 3.746A pdb=" N TRP D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 4.838A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.698A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.843A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.278A pdb=" N MET D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.550A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.706A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.791A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 4.067A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.709A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 411 removed outlier: 3.988A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.557A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.812A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 465 removed outlier: 3.832A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix removed outlier: 3.585A pdb=" N MET D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.616A pdb=" N TRP D 473 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 484 removed outlier: 3.821A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 511 through 514 removed outlier: 4.056A pdb=" N ARG D 514 " --> pdb=" O SER D 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 514' Processing helix chain 'D' and resid 515 through 533 removed outlier: 4.041A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 522 " --> pdb=" O ARG D 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.659A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.839A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 4.017A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 588 removed outlier: 3.680A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 583 through 588' Processing helix chain 'D' and resid 588 through 596 Processing helix chain 'D' and resid 597 through 600 removed outlier: 3.860A pdb=" N LYS D 600 " --> pdb=" O ASP D 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 597 through 600' Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.520A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 53 removed outlier: 3.914A pdb=" N GLN E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 78 removed outlier: 3.605A pdb=" N ASN E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE E 72 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 82 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.531A pdb=" N LEU E 97 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.532A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 121 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.629A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.746A pdb=" N TRP E 163 " --> pdb=" O ASN E 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.839A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 3.697A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.843A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.278A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.549A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 299 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.706A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.791A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 383 removed outlier: 4.068A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.709A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 411 removed outlier: 3.989A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.558A pdb=" N LEU E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.812A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 465 removed outlier: 3.832A pdb=" N THR E 449 " --> pdb=" O THR E 445 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU E 450 " --> pdb=" O ILE E 446 " (cutoff:3.500A) Proline residue: E 451 - end of helix removed outlier: 3.584A pdb=" N MET E 455 " --> pdb=" O PRO E 451 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 473 removed outlier: 3.616A pdb=" N TRP E 473 " --> pdb=" O LYS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.821A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 484 " --> pdb=" O MET E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 511 through 514 removed outlier: 4.056A pdb=" N ARG E 514 " --> pdb=" O SER E 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 511 through 514' Processing helix chain 'E' and resid 515 through 533 removed outlier: 4.041A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN E 522 " --> pdb=" O ARG E 518 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 528 " --> pdb=" O GLN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.660A pdb=" N CYS E 542 " --> pdb=" O LEU E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.839A pdb=" N LEU E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 4.017A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 588 removed outlier: 3.680A pdb=" N TYR E 587 " --> pdb=" O PRO E 583 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 583 through 588' Processing helix chain 'E' and resid 588 through 596 Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.521A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP F 30 " --> pdb=" O LYS F 26 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 removed outlier: 3.914A pdb=" N GLN F 42 " --> pdb=" O ASP F 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER F 43 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER F 47 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 78 removed outlier: 3.605A pdb=" N ASN F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 82 Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.530A pdb=" N LEU F 97 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.531A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN F 121 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR F 127 " --> pdb=" O MET F 123 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.628A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 173 removed outlier: 3.745A pdb=" N TRP F 163 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 4.837A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU F 189 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 removed outlier: 3.698A pdb=" N ARG F 204 " --> pdb=" O GLY F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.843A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 4.278A pdb=" N MET F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.549A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.706A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU F 310 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.790A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 383 removed outlier: 4.068A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS F 374 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.708A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 411 removed outlier: 3.988A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER F 411 " --> pdb=" O ILE F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.557A pdb=" N LEU F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 removed outlier: 3.812A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 465 removed outlier: 3.832A pdb=" N THR F 449 " --> pdb=" O THR F 445 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU F 450 " --> pdb=" O ILE F 446 " (cutoff:3.500A) Proline residue: F 451 - end of helix removed outlier: 3.585A pdb=" N MET F 455 " --> pdb=" O PRO F 451 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 457 " --> pdb=" O THR F 453 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET F 462 " --> pdb=" O LYS F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 473 removed outlier: 3.615A pdb=" N TRP F 473 " --> pdb=" O LYS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.821A pdb=" N MET F 480 " --> pdb=" O LYS F 476 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 484 " --> pdb=" O MET F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 511 through 514 removed outlier: 4.056A pdb=" N ARG F 514 " --> pdb=" O SER F 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 511 through 514' Processing helix chain 'F' and resid 515 through 533 removed outlier: 4.041A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN F 522 " --> pdb=" O ARG F 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA F 528 " --> pdb=" O GLN F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.660A pdb=" N CYS F 542 " --> pdb=" O LEU F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 559 removed outlier: 3.838A pdb=" N LEU F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 4.018A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 588 removed outlier: 3.680A pdb=" N TYR F 587 " --> pdb=" O PRO F 583 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 583 through 588' Processing helix chain 'F' and resid 588 through 596 Processing helix chain 'F' and resid 597 through 600 removed outlier: 3.860A pdb=" N LYS F 600 " --> pdb=" O ASP F 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 597 through 600' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.059A 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: 3.680A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.731A 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: 7.658A 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: 4.589A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 319 removed outlier: 5.930A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.672A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A 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: 5.732A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.728A 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: 5.421A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=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: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.570A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.856A 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: 3.731A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.658A 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: 4.589A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.314A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.672A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 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: 5.567A 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: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (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: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.213A 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: 4.595A 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: 4.579A 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: 8.059A 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: 3.680A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.439A 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 47 through 55 removed outlier: 3.569A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=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: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.589A 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 356 through 358 removed outlier: 3.671A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 597 through 598 Processing sheet with id=AE4, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.426A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A 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: 3.588A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.840A 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: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.879A 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=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.566A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.651A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.642A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF4, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.652A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.642A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF7, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.651A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.642A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1383 hydrogen bonds defined for protein. 3867 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: 9.63 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12228 1.34 - 1.46: 10623 1.46 - 1.59: 17428 1.59 - 1.72: 0 1.72 - 1.84: 285 Bond restraints: 40564 Sorted by residual: bond pdb=" C ASP A 985 " pdb=" N PRO A 986 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.18e-02 7.18e+03 2.43e+01 bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.33e-02 5.65e+03 1.85e+01 bond pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N PRO A 986 " pdb=" CD PRO A 986 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+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 40559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 53719 2.71 - 5.41: 1279 5.41 - 8.12: 127 8.12 - 10.82: 15 10.82 - 13.53: 8 Bond angle restraints: 55148 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.83 -11.29 1.91e+00 2.74e-01 3.49e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C ASP A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta sigma weight residual 120.38 114.37 6.01 1.03e+00 9.43e-01 3.40e+01 angle pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta sigma weight residual 119.89 114.08 5.81 1.02e+00 9.61e-01 3.25e+01 ... (remaining 55143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 21950 17.92 - 35.83: 2513 35.83 - 53.75: 701 53.75 - 71.67: 211 71.67 - 89.58: 67 Dihedral angle restraints: 25442 sinusoidal: 11416 harmonic: 14026 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -171.93 85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -171.91 85.91 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -171.91 85.91 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 25439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 6365 0.328 - 0.655: 6 0.655 - 0.983: 4 0.983 - 1.310: 1 1.310 - 1.638: 1 Chirality restraints: 6377 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-02 2.50e+03 1.97e+03 chirality pdb=" C1 NAG B1407 " pdb=" O4 NAG B1406 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.45e+03 chirality pdb=" C1 NAG B1412 " pdb=" O4 NAG B1411 " pdb=" C2 NAG B1412 " pdb=" O5 NAG B1412 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 ... (remaining 6374 not shown) Planarity restraints: 7067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.136 2.00e-02 2.50e+03 1.69e-01 3.58e+02 pdb=" CG ASN C 331 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.290 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.073 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" CG ASN B 331 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.221 2.00e-02 2.50e+03 pdb=" C1 NAG B1406 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.049 2.00e-02 2.50e+03 5.49e-02 3.77e+01 pdb=" CG ASN C 709 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " 0.063 2.00e-02 2.50e+03 ... (remaining 7064 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 464 2.55 - 3.14: 30316 3.14 - 3.72: 60929 3.72 - 4.31: 86300 4.31 - 4.90: 139306 Nonbonded interactions: 317315 Sorted by model distance: nonbonded pdb=" O ALA C 701 " pdb=" O GLU C 702 " model vdw 1.960 3.040 nonbonded pdb=" O VAL A 524 " pdb=" SG CYS A 525 " model vdw 2.157 3.400 nonbonded pdb=" O VAL A 327 " pdb=" CD ARG A 328 " model vdw 2.177 3.440 nonbonded pdb=" OG SER C 708 " pdb=" N ASN C 709 " model vdw 2.180 3.120 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.183 3.040 ... (remaining 317310 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 620 or resid 640 through 939 or resid 944 throu \ gh 1409)) selection = (chain 'B' and (resid 27 through 620 or resid 640 through 826 or resid 855 throu \ gh 1409)) selection = (chain 'C' and (resid 27 through 620 or resid 640 through 826 or resid 855 throu \ gh 1409)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = 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' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = 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' } 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 group one per residue 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 37.630 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 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 : 0.011 0.794 40716 Z= 0.518 Angle : 1.296 61.914 55556 Z= 0.658 Chirality : 0.070 1.638 6377 Planarity : 0.007 0.080 7001 Dihedral : 17.084 89.585 16262 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.90 % Favored : 90.16 % Rotamer: Outliers : 7.37 % Allowed : 14.68 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.38 (0.10), residues: 4744 helix: -3.31 (0.09), residues: 1554 sheet: -2.19 (0.18), residues: 703 loop : -2.86 (0.10), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 357 TYR 0.026 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.026 0.003 TRP B 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00949 (40564) covalent geometry : angle 1.02478 (55148) SS BOND : bond 0.15785 ( 48) SS BOND : angle 12.35930 ( 96) hydrogen bonds : bond 0.26059 ( 1347) hydrogen bonds : angle 8.95952 ( 3867) link_BETA1-4 : bond 0.05077 ( 38) link_BETA1-4 : angle 9.83683 ( 114) link_NAG-ASN : bond 0.03090 ( 66) link_NAG-ASN : angle 7.01039 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 311 poor density : 904 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 54 LEU cc_start: 0.7587 (mt) cc_final: 0.7299 (mp) REVERT: A 105 ILE cc_start: 0.8388 (pt) cc_final: 0.7651 (mt) REVERT: A 153 MET cc_start: 0.1425 (mpp) cc_final: 0.0982 (ptm) REVERT: A 360 ASN cc_start: 0.7839 (m110) cc_final: 0.7199 (p0) REVERT: A 492 LEU cc_start: -0.0163 (OUTLIER) cc_final: -0.0383 (mt) REVERT: A 698 SER cc_start: 0.7648 (OUTLIER) cc_final: 0.7363 (t) REVERT: A 736 VAL cc_start: 0.6879 (m) cc_final: 0.6655 (t) REVERT: A 763 LEU cc_start: 0.8375 (mt) cc_final: 0.8027 (mt) REVERT: A 988 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: B 158 ARG cc_start: 0.5631 (OUTLIER) cc_final: 0.5232 (mmm160) REVERT: B 226 LEU cc_start: 0.7845 (tp) cc_final: 0.7542 (tp) REVERT: B 556 ASN cc_start: 0.5868 (OUTLIER) cc_final: 0.5341 (p0) REVERT: B 887 THR cc_start: 0.8369 (p) cc_final: 0.8128 (m) REVERT: C 492 LEU cc_start: 0.4956 (OUTLIER) cc_final: 0.4732 (mm) REVERT: C 529 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6297 (mmtt) REVERT: C 1042 PHE cc_start: 0.7964 (t80) cc_final: 0.7745 (t80) REVERT: C 1136 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6958 (t) REVERT: D 383 MET cc_start: 0.5806 (mtp) cc_final: 0.4069 (ppp) REVERT: E 133 CYS cc_start: -0.2908 (OUTLIER) cc_final: -0.3535 (p) REVERT: E 455 MET cc_start: -0.0893 (tmm) cc_final: -0.1141 (tmm) REVERT: E 574 VAL cc_start: 0.0831 (t) cc_final: 0.0594 (t) REVERT: F 82 MET cc_start: 0.3023 (ttp) cc_final: 0.2605 (mtt) REVERT: F 133 CYS cc_start: -0.0241 (OUTLIER) cc_final: -0.0823 (p) REVERT: F 240 LEU cc_start: 0.6080 (mp) cc_final: 0.5592 (tp) REVERT: F 312 GLU cc_start: 0.6387 (tt0) cc_final: 0.5702 (pt0) REVERT: F 379 ILE cc_start: 0.7475 (mm) cc_final: 0.7263 (mm) REVERT: F 383 MET cc_start: 0.5957 (mtp) cc_final: 0.5011 (mtm) REVERT: F 479 GLU cc_start: 0.5763 (mt-10) cc_final: 0.5551 (tp30) REVERT: F 496 THR cc_start: 0.6233 (OUTLIER) cc_final: 0.5679 (t) outliers start: 311 outliers final: 66 residues processed: 1146 average time/residue: 0.2423 time to fit residues: 454.8772 Evaluate side-chains 492 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 415 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 710 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 498 CYS Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 496 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 134 GLN A 137 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 450 ASN A 460 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 644 GLN A 703 ASN A 755 GLN A 764 ASN A 804 GLN A 901 GLN A 914 ASN A 955 ASN A1101 HIS B 137 ASN B 188 ASN B 334 ASN B 360 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 450 ASN B 519 HIS B 556 ASN B 658 ASN B 872 GLN B 901 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B 920 GLN B 953 ASN B 992 GLN B1054 GLN C 134 GLN C 137 ASN C 450 ASN C 460 ASN C 580 GLN C 644 GLN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 914 ASN C 992 GLN C1071 GLN C1101 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN D 330 ASN D 340 GLN D 374 HIS D 378 HIS D 401 HIS D 505 HIS D 598 GLN E 63 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN E 300 GLN E 330 ASN E 378 HIS E 401 HIS E 417 HIS E 472 GLN E 493 HIS E 522 GLN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 ASN F 63 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN F 330 ASN F 417 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN F 586 ASN F 599 ASN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.136079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.113923 restraints weight = 195803.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.111948 restraints weight = 224900.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.112553 restraints weight = 178158.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.112650 restraints weight = 120122.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.112713 restraints weight = 130210.527| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 40716 Z= 0.265 Angle : 0.950 15.631 55556 Z= 0.466 Chirality : 0.053 0.528 6377 Planarity : 0.006 0.087 7001 Dihedral : 9.662 59.973 7465 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.43 % Favored : 93.53 % Rotamer: Outliers : 5.97 % Allowed : 19.04 % Favored : 74.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.11), residues: 4744 helix: -1.89 (0.11), residues: 1631 sheet: -1.53 (0.18), residues: 721 loop : -2.41 (0.11), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 355 TYR 0.052 0.002 TYR E 279 PHE 0.036 0.003 PHE B1089 TRP 0.024 0.002 TRP C 436 HIS 0.012 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00593 (40564) covalent geometry : angle 0.90500 (55148) SS BOND : bond 0.01459 ( 48) SS BOND : angle 2.75078 ( 96) hydrogen bonds : bond 0.05310 ( 1347) hydrogen bonds : angle 6.09538 ( 3867) link_BETA1-4 : bond 0.00763 ( 38) link_BETA1-4 : angle 2.76230 ( 114) link_NAG-ASN : bond 0.00834 ( 66) link_NAG-ASN : angle 4.13280 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 409 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 233 ILE cc_start: 0.5541 (OUTLIER) cc_final: 0.5093 (tt) REVERT: A 423 TYR cc_start: 0.5234 (t80) cc_final: 0.4501 (t80) REVERT: A 762 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7675 (tp40) REVERT: A 813 SER cc_start: 0.8274 (t) cc_final: 0.8049 (p) REVERT: B 63 THR cc_start: 0.7293 (OUTLIER) cc_final: 0.6886 (p) REVERT: B 210 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6203 (tt) REVERT: B 569 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7024 (mt) REVERT: B 645 THR cc_start: 0.7598 (p) cc_final: 0.7300 (p) REVERT: B 704 SER cc_start: 0.8707 (m) cc_final: 0.8371 (t) REVERT: B 770 ILE cc_start: 0.8598 (mt) cc_final: 0.8221 (mt) REVERT: C 231 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6843 (mm) REVERT: C 473 TYR cc_start: 0.3044 (t80) cc_final: 0.2748 (t80) REVERT: C 699 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8134 (mt) REVERT: C 1050 MET cc_start: 0.7367 (ptp) cc_final: 0.7133 (ptp) REVERT: D 383 MET cc_start: 0.5864 (mtp) cc_final: 0.4310 (ppp) REVERT: D 480 MET cc_start: 0.2121 (ttt) cc_final: 0.0897 (ptm) REVERT: D 483 GLU cc_start: 0.6607 (pm20) cc_final: 0.5982 (tt0) REVERT: D 573 VAL cc_start: 0.1825 (OUTLIER) cc_final: 0.1406 (m) REVERT: E 161 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4651 (ttm170) REVERT: E 453 THR cc_start: -0.6083 (OUTLIER) cc_final: -0.6295 (m) REVERT: E 496 THR cc_start: 0.2954 (OUTLIER) cc_final: 0.2731 (m) REVERT: E 574 VAL cc_start: 0.0778 (t) cc_final: 0.0481 (t) REVERT: F 82 MET cc_start: 0.3527 (ttp) cc_final: 0.3154 (mtt) REVERT: F 123 MET cc_start: 0.1100 (ptt) cc_final: -0.0301 (ptt) REVERT: F 137 ASN cc_start: 0.6234 (m110) cc_final: 0.5420 (t0) REVERT: F 224 GLU cc_start: 0.6924 (mp0) cc_final: 0.6718 (pm20) REVERT: F 240 LEU cc_start: 0.5930 (mp) cc_final: 0.5372 (tp) REVERT: F 312 GLU cc_start: 0.6311 (tt0) cc_final: 0.6046 (pt0) REVERT: F 383 MET cc_start: 0.6173 (mtp) cc_final: 0.5769 (mtp) REVERT: F 428 PHE cc_start: 0.1370 (OUTLIER) cc_final: 0.0899 (m-10) REVERT: F 452 PHE cc_start: 0.1073 (t80) cc_final: 0.0537 (m-80) REVERT: F 474 MET cc_start: 0.4276 (tmm) cc_final: 0.2249 (mtp) outliers start: 252 outliers final: 128 residues processed: 619 average time/residue: 0.2163 time to fit residues: 230.9591 Evaluate side-chains 441 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 302 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 949 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 546 ASN Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 28 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 446 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 313 optimal weight: 40.0000 chunk 461 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 784 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 115 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C1036 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS D 522 GLN D 572 ASN E 49 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.133443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.114130 restraints weight = 194446.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.113988 restraints weight = 339970.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.113968 restraints weight = 233879.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.113972 restraints weight = 154758.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.114302 restraints weight = 144489.397| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 40716 Z= 0.234 Angle : 0.827 13.225 55556 Z= 0.403 Chirality : 0.050 0.587 6377 Planarity : 0.005 0.051 7001 Dihedral : 8.622 59.739 7374 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.83 % Favored : 93.13 % Rotamer: Outliers : 5.38 % Allowed : 20.70 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.11), residues: 4744 helix: -1.09 (0.12), residues: 1642 sheet: -1.45 (0.18), residues: 730 loop : -2.16 (0.12), residues: 2372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 237 TYR 0.025 0.002 TYR B 707 PHE 0.025 0.002 PHE C 157 TRP 0.021 0.002 TRP E 477 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00526 (40564) covalent geometry : angle 0.78290 (55148) SS BOND : bond 0.00843 ( 48) SS BOND : angle 2.23668 ( 96) hydrogen bonds : bond 0.04769 ( 1347) hydrogen bonds : angle 5.74930 ( 3867) link_BETA1-4 : bond 0.00686 ( 38) link_BETA1-4 : angle 2.76919 ( 114) link_NAG-ASN : bond 0.00748 ( 66) link_NAG-ASN : angle 3.76306 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 311 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.1002 (OUTLIER) cc_final: 0.0662 (mt) REVERT: A 1108 ASN cc_start: 0.6397 (OUTLIER) cc_final: 0.5799 (t0) REVERT: B 105 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5463 (tt) REVERT: B 210 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6587 (tt) REVERT: B 645 THR cc_start: 0.7380 (p) cc_final: 0.7082 (p) REVERT: B 704 SER cc_start: 0.8863 (m) cc_final: 0.8471 (t) REVERT: B 1117 THR cc_start: 0.6382 (OUTLIER) cc_final: 0.6181 (t) REVERT: C 141 LEU cc_start: 0.6454 (mp) cc_final: 0.6225 (pp) REVERT: C 231 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6515 (mm) REVERT: C 317 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8323 (t0) REVERT: C 392 PHE cc_start: 0.2749 (OUTLIER) cc_final: 0.2230 (m-80) REVERT: C 692 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8609 (mm) REVERT: C 725 GLU cc_start: 0.7502 (tt0) cc_final: 0.7272 (tt0) REVERT: C 859 THR cc_start: 0.9359 (m) cc_final: 0.8959 (p) REVERT: C 1115 ILE cc_start: 0.6367 (tp) cc_final: 0.5651 (tt) REVERT: C 1132 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6359 (tp) REVERT: D 480 MET cc_start: 0.2032 (ttt) cc_final: 0.0489 (ptm) REVERT: D 483 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.5006 (tp30) REVERT: D 573 VAL cc_start: 0.2029 (OUTLIER) cc_final: 0.1562 (m) REVERT: E 152 MET cc_start: 0.0313 (mmt) cc_final: -0.0107 (tpt) REVERT: E 366 MET cc_start: -0.0740 (tpt) cc_final: -0.1986 (tmm) REVERT: E 455 MET cc_start: -0.1002 (tmm) cc_final: -0.1571 (tmm) REVERT: E 574 VAL cc_start: 0.0522 (t) cc_final: 0.0202 (t) REVERT: E 579 MET cc_start: 0.1125 (mpp) cc_final: -0.0216 (mmp) REVERT: F 82 MET cc_start: 0.4434 (ttp) cc_final: 0.3737 (mtt) REVERT: F 123 MET cc_start: 0.0782 (ptt) cc_final: -0.0362 (ptt) REVERT: F 240 LEU cc_start: 0.5970 (mp) cc_final: 0.5278 (tp) REVERT: F 366 MET cc_start: 0.5231 (ppp) cc_final: 0.4423 (ppp) REVERT: F 383 MET cc_start: 0.6221 (mtp) cc_final: 0.5780 (mtp) REVERT: F 428 PHE cc_start: 0.1817 (OUTLIER) cc_final: 0.1270 (m-10) REVERT: F 474 MET cc_start: 0.4200 (tmm) cc_final: 0.2133 (mtp) outliers start: 227 outliers final: 133 residues processed: 509 average time/residue: 0.2069 time to fit residues: 183.0785 Evaluate side-chains 404 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 258 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 382 optimal weight: 50.0000 chunk 413 optimal weight: 10.0000 chunk 469 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 195 optimal weight: 0.0980 chunk 373 optimal weight: 50.0000 chunk 463 optimal weight: 30.0000 chunk 257 optimal weight: 10.0000 overall best weight: 5.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 317 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 957 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 804 GLN ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN F 340 GLN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.131258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.101792 restraints weight = 192039.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.098501 restraints weight = 146599.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.098697 restraints weight = 164131.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.098838 restraints weight = 150427.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.099078 restraints weight = 123337.782| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 40716 Z= 0.239 Angle : 0.838 12.614 55556 Z= 0.409 Chirality : 0.051 0.501 6377 Planarity : 0.005 0.070 7001 Dihedral : 8.503 59.823 7360 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.12 % Favored : 92.83 % Rotamer: Outliers : 6.24 % Allowed : 20.67 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.11), residues: 4744 helix: -0.63 (0.12), residues: 1626 sheet: -1.52 (0.19), residues: 687 loop : -2.07 (0.12), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 815 TYR 0.032 0.002 TYR B 707 PHE 0.039 0.002 PHE A 133 TRP 0.029 0.002 TRP E 48 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00534 (40564) covalent geometry : angle 0.79891 (55148) SS BOND : bond 0.00480 ( 48) SS BOND : angle 2.21101 ( 96) hydrogen bonds : bond 0.04431 ( 1347) hydrogen bonds : angle 5.73500 ( 3867) link_BETA1-4 : bond 0.00687 ( 38) link_BETA1-4 : angle 2.68869 ( 114) link_NAG-ASN : bond 0.00857 ( 66) link_NAG-ASN : angle 3.53980 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 274 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.7225 (m-80) cc_final: 0.7014 (m-80) REVERT: A 423 TYR cc_start: 0.6125 (t80) cc_final: 0.5872 (t80) REVERT: A 726 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7992 (pt) REVERT: A 985 ASP cc_start: 0.7612 (p0) cc_final: 0.6476 (p0) REVERT: A 988 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: A 1108 ASN cc_start: 0.6379 (OUTLIER) cc_final: 0.5880 (t0) REVERT: B 105 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6638 (tt) REVERT: B 210 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7418 (tt) REVERT: B 324 GLU cc_start: 0.5817 (OUTLIER) cc_final: 0.5474 (mp0) REVERT: B 480 CYS cc_start: 0.5266 (OUTLIER) cc_final: 0.4650 (m) REVERT: B 901 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: C 231 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7600 (mm) REVERT: C 725 GLU cc_start: 0.7818 (tt0) cc_final: 0.7552 (tt0) REVERT: C 859 THR cc_start: 0.9184 (m) cc_final: 0.8972 (p) REVERT: C 969 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8312 (t0) REVERT: C 1132 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6688 (tp) REVERT: D 383 MET cc_start: 0.5853 (mtt) cc_final: 0.3728 (ppp) REVERT: D 480 MET cc_start: 0.1898 (ttt) cc_final: 0.0889 (ptm) REVERT: D 483 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.5494 (tp30) REVERT: D 568 LEU cc_start: 0.5015 (mp) cc_final: 0.4132 (tt) REVERT: D 573 VAL cc_start: 0.2352 (OUTLIER) cc_final: 0.2011 (m) REVERT: E 86 GLN cc_start: -0.1179 (OUTLIER) cc_final: -0.1453 (mt0) REVERT: E 114 LYS cc_start: 0.5837 (tptt) cc_final: 0.5229 (mttp) REVERT: E 366 MET cc_start: -0.1436 (tpt) cc_final: -0.2100 (tmm) REVERT: E 574 VAL cc_start: 0.0935 (t) cc_final: 0.0656 (t) REVERT: F 82 MET cc_start: 0.4741 (ttp) cc_final: 0.4091 (mtp) REVERT: F 123 MET cc_start: 0.0880 (ptt) cc_final: -0.0270 (ptt) REVERT: F 224 GLU cc_start: 0.6820 (mp0) cc_final: 0.6548 (pm20) REVERT: F 270 MET cc_start: 0.6197 (ttm) cc_final: 0.5935 (ttm) REVERT: F 332 MET cc_start: 0.2129 (ttm) cc_final: 0.1881 (ttm) REVERT: F 360 MET cc_start: 0.4769 (pmm) cc_final: 0.4156 (ppp) REVERT: F 366 MET cc_start: 0.4977 (ppp) cc_final: 0.4574 (ppp) REVERT: F 383 MET cc_start: 0.5981 (mtp) cc_final: 0.5548 (mtp) REVERT: F 428 PHE cc_start: 0.0749 (OUTLIER) cc_final: 0.0323 (m-10) REVERT: F 474 MET cc_start: 0.2993 (tmm) cc_final: 0.1246 (mtp) outliers start: 263 outliers final: 152 residues processed: 509 average time/residue: 0.2109 time to fit residues: 188.3223 Evaluate side-chains 402 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 235 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 312 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 446 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 335 optimal weight: 30.0000 chunk 85 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN F 429 GLN F 508 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.131292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.102508 restraints weight = 191873.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.098210 restraints weight = 147477.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.098536 restraints weight = 180352.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.098842 restraints weight = 137019.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.098951 restraints weight = 127250.367| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 40716 Z= 0.182 Angle : 0.761 12.597 55556 Z= 0.367 Chirality : 0.048 0.457 6377 Planarity : 0.005 0.051 7001 Dihedral : 8.082 58.943 7354 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.98 % Favored : 93.00 % Rotamer: Outliers : 5.24 % Allowed : 21.93 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4744 helix: -0.30 (0.13), residues: 1635 sheet: -1.29 (0.19), residues: 659 loop : -2.02 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.023 0.002 TYR B 707 PHE 0.032 0.002 PHE B 135 TRP 0.019 0.001 TRP E 477 HIS 0.008 0.001 HIS E 493 Details of bonding type rmsd covalent geometry : bond 0.00412 (40564) covalent geometry : angle 0.72069 (55148) SS BOND : bond 0.00413 ( 48) SS BOND : angle 2.47197 ( 96) hydrogen bonds : bond 0.03980 ( 1347) hydrogen bonds : angle 5.52323 ( 3867) link_BETA1-4 : bond 0.00626 ( 38) link_BETA1-4 : angle 2.63981 ( 114) link_NAG-ASN : bond 0.00532 ( 66) link_NAG-ASN : angle 3.31085 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 258 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.5929 (t80) cc_final: 0.5606 (t80) REVERT: A 726 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7829 (pt) REVERT: A 900 MET cc_start: 0.7589 (mmm) cc_final: 0.7153 (mmt) REVERT: A 1066 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7453 (p) REVERT: A 1108 ASN cc_start: 0.6428 (OUTLIER) cc_final: 0.5858 (t0) REVERT: B 210 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7400 (tt) REVERT: B 1106 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: C 231 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7720 (mm) REVERT: C 374 PHE cc_start: 0.4045 (m-80) cc_final: 0.3706 (p90) REVERT: C 455 LEU cc_start: 0.5437 (pt) cc_final: 0.5160 (pt) REVERT: C 692 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8876 (mm) REVERT: C 725 GLU cc_start: 0.7722 (tt0) cc_final: 0.7365 (tt0) REVERT: C 859 THR cc_start: 0.9162 (m) cc_final: 0.8955 (p) REVERT: C 969 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8411 (t0) REVERT: C 1132 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6515 (tp) REVERT: D 81 GLN cc_start: 0.5698 (OUTLIER) cc_final: 0.5464 (mm-40) REVERT: D 152 MET cc_start: -0.1755 (mmt) cc_final: -0.2005 (mmt) REVERT: D 383 MET cc_start: 0.5998 (mtt) cc_final: 0.4100 (ppp) REVERT: D 483 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5594 (tp30) REVERT: D 568 LEU cc_start: 0.5000 (mp) cc_final: 0.4091 (tt) REVERT: D 573 VAL cc_start: 0.2415 (OUTLIER) cc_final: 0.1998 (m) REVERT: E 82 MET cc_start: 0.3368 (mpp) cc_final: 0.3165 (mtm) REVERT: E 114 LYS cc_start: 0.5906 (tptt) cc_final: 0.5346 (mttp) REVERT: E 186 LEU cc_start: 0.0088 (OUTLIER) cc_final: -0.0215 (tp) REVERT: E 332 MET cc_start: 0.1277 (ppp) cc_final: 0.0897 (ppp) REVERT: E 366 MET cc_start: -0.1566 (tpt) cc_final: -0.2125 (tmm) REVERT: E 461 TRP cc_start: 0.2653 (m-10) cc_final: 0.1882 (m-10) REVERT: E 574 VAL cc_start: 0.0875 (t) cc_final: 0.0602 (t) REVERT: E 579 MET cc_start: 0.1294 (mpp) cc_final: 0.0810 (mpp) REVERT: F 82 MET cc_start: 0.4829 (ttp) cc_final: 0.4119 (mtp) REVERT: F 123 MET cc_start: 0.0853 (ptt) cc_final: -0.0260 (ptt) REVERT: F 250 ASN cc_start: 0.7065 (t0) cc_final: 0.6592 (p0) REVERT: F 364 VAL cc_start: 0.1782 (OUTLIER) cc_final: 0.1547 (p) REVERT: F 366 MET cc_start: 0.5055 (ppp) cc_final: 0.4804 (tmm) REVERT: F 383 MET cc_start: 0.5697 (mtp) cc_final: 0.5326 (mtt) REVERT: F 474 MET cc_start: 0.2865 (tmm) cc_final: 0.1030 (mtp) outliers start: 221 outliers final: 145 residues processed: 455 average time/residue: 0.2020 time to fit residues: 162.1806 Evaluate side-chains 401 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 242 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 487 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 604 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 442 optimal weight: 40.0000 chunk 222 optimal weight: 1.9990 chunk 343 optimal weight: 50.0000 chunk 272 optimal weight: 0.0470 chunk 347 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 chunk 325 optimal weight: 30.0000 chunk 256 optimal weight: 7.9990 chunk 372 optimal weight: 50.0000 chunk 359 optimal weight: 0.0370 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 641 ASN B 784 GLN B 913 GLN B 992 GLN B1083 HIS B1106 GLN C 188 ASN C 895 GLN C1135 ASN D 277 ASN D 599 ASN E 81 GLN E 429 GLN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.133059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.111451 restraints weight = 192894.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.109311 restraints weight = 230482.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.109962 restraints weight = 180907.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.109976 restraints weight = 120581.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.110093 restraints weight = 132084.483| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 40716 Z= 0.118 Angle : 0.707 13.698 55556 Z= 0.337 Chirality : 0.046 0.391 6377 Planarity : 0.004 0.051 7001 Dihedral : 7.381 59.160 7353 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.69 % Favored : 94.29 % Rotamer: Outliers : 3.75 % Allowed : 23.28 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.12), residues: 4744 helix: 0.03 (0.13), residues: 1656 sheet: -0.88 (0.20), residues: 664 loop : -1.94 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1107 TYR 0.022 0.001 TYR E 199 PHE 0.037 0.001 PHE B 135 TRP 0.017 0.001 TRP E 477 HIS 0.006 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00257 (40564) covalent geometry : angle 0.66837 (55148) SS BOND : bond 0.00373 ( 48) SS BOND : angle 2.43143 ( 96) hydrogen bonds : bond 0.03421 ( 1347) hydrogen bonds : angle 5.12037 ( 3867) link_BETA1-4 : bond 0.00664 ( 38) link_BETA1-4 : angle 2.51514 ( 114) link_NAG-ASN : bond 0.00483 ( 66) link_NAG-ASN : angle 3.06265 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 274 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7997 (pt) REVERT: A 896 ILE cc_start: 0.7129 (tp) cc_final: 0.6866 (tp) REVERT: A 900 MET cc_start: 0.7567 (mmm) cc_final: 0.7178 (mmt) REVERT: B 480 CYS cc_start: 0.3984 (OUTLIER) cc_final: 0.2970 (m) REVERT: B 641 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7569 (t0) REVERT: B 746 SER cc_start: 0.8753 (OUTLIER) cc_final: 0.8490 (m) REVERT: B 1106 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6321 (tt0) REVERT: B 1126 CYS cc_start: 0.5635 (OUTLIER) cc_final: 0.5013 (p) REVERT: C 231 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.6895 (mm) REVERT: C 389 ASP cc_start: 0.6870 (p0) cc_final: 0.6457 (m-30) REVERT: C 455 LEU cc_start: 0.4520 (pt) cc_final: 0.4313 (pt) REVERT: C 859 THR cc_start: 0.9050 (m) cc_final: 0.8829 (p) REVERT: C 969 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8216 (t0) REVERT: C 1001 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8837 (mm) REVERT: C 1132 ILE cc_start: 0.6644 (OUTLIER) cc_final: 0.6307 (tp) REVERT: D 116 LEU cc_start: -0.0016 (OUTLIER) cc_final: -0.0306 (tt) REVERT: D 383 MET cc_start: 0.5554 (mtt) cc_final: 0.3431 (ppp) REVERT: D 480 MET cc_start: 0.2033 (ttt) cc_final: 0.1235 (ttt) REVERT: D 483 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5304 (tp30) REVERT: D 568 LEU cc_start: 0.4603 (mp) cc_final: 0.3431 (tt) REVERT: D 573 VAL cc_start: 0.2289 (OUTLIER) cc_final: 0.1813 (m) REVERT: E 114 LYS cc_start: 0.6157 (tptt) cc_final: 0.5374 (mttp) REVERT: E 152 MET cc_start: 0.0437 (mmt) cc_final: -0.0093 (tpt) REVERT: E 270 MET cc_start: 0.2576 (tpp) cc_final: 0.2350 (tpp) REVERT: E 332 MET cc_start: 0.1488 (ppp) cc_final: 0.1038 (ppp) REVERT: E 366 MET cc_start: -0.0289 (tpt) cc_final: -0.1399 (tmm) REVERT: E 461 TRP cc_start: 0.2080 (m-10) cc_final: 0.1405 (m-10) REVERT: E 474 MET cc_start: -0.0639 (ttt) cc_final: -0.1071 (ttt) REVERT: E 574 VAL cc_start: 0.0195 (t) cc_final: -0.0118 (t) REVERT: E 579 MET cc_start: 0.0785 (mpp) cc_final: 0.0387 (mpp) REVERT: F 82 MET cc_start: 0.4889 (ttp) cc_final: 0.4177 (mtp) REVERT: F 123 MET cc_start: 0.0610 (ptt) cc_final: -0.0461 (ptt) REVERT: F 250 ASN cc_start: 0.7369 (t0) cc_final: 0.6585 (p0) REVERT: F 366 MET cc_start: 0.6116 (ppp) cc_final: 0.5748 (tmm) REVERT: F 383 MET cc_start: 0.6215 (mtp) cc_final: 0.5796 (mtp) REVERT: F 474 MET cc_start: 0.3621 (tmm) cc_final: 0.1568 (mtp) REVERT: F 589 GLU cc_start: 0.6317 (mm-30) cc_final: 0.5076 (pt0) outliers start: 158 outliers final: 96 residues processed: 409 average time/residue: 0.2017 time to fit residues: 144.2324 Evaluate side-chains 353 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 244 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 402 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 420 optimal weight: 20.0000 chunk 317 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 322 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 286 optimal weight: 0.9990 chunk 331 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1108 ASN B 641 ASN ** B 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B1083 HIS B1106 GLN C 115 GLN C 751 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN F 33 ASN F 63 ASN ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 508 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.130845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.109544 restraints weight = 192275.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.107512 restraints weight = 251742.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.108108 restraints weight = 193647.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.108247 restraints weight = 124949.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.108428 restraints weight = 132446.814| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 40716 Z= 0.181 Angle : 0.745 14.008 55556 Z= 0.358 Chirality : 0.047 0.449 6377 Planarity : 0.004 0.047 7001 Dihedral : 7.464 59.084 7351 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.02 % Favored : 92.96 % Rotamer: Outliers : 4.10 % Allowed : 23.28 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4744 helix: 0.11 (0.13), residues: 1660 sheet: -1.16 (0.19), residues: 715 loop : -1.89 (0.12), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1107 TYR 0.027 0.002 TYR B 707 PHE 0.023 0.002 PHE F 504 TRP 0.027 0.001 TRP C 436 HIS 0.012 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00408 (40564) covalent geometry : angle 0.70637 (55148) SS BOND : bond 0.00553 ( 48) SS BOND : angle 2.43048 ( 96) hydrogen bonds : bond 0.03722 ( 1347) hydrogen bonds : angle 5.24227 ( 3867) link_BETA1-4 : bond 0.00607 ( 38) link_BETA1-4 : angle 2.57537 ( 114) link_NAG-ASN : bond 0.00502 ( 66) link_NAG-ASN : angle 3.14484 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 252 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7997 (pt) REVERT: B 480 CYS cc_start: 0.3949 (OUTLIER) cc_final: 0.2845 (m) REVERT: B 901 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: B 1106 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: B 1126 CYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5073 (p) REVERT: C 231 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.6775 (mm) REVERT: C 901 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: C 969 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.7788 (t0) REVERT: C 1001 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8891 (mm) REVERT: C 1132 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6418 (tp) REVERT: D 48 TRP cc_start: 0.2014 (t-100) cc_final: 0.1704 (t-100) REVERT: D 116 LEU cc_start: -0.0041 (OUTLIER) cc_final: -0.0317 (tt) REVERT: D 270 MET cc_start: 0.5170 (tpp) cc_final: 0.4959 (tpp) REVERT: D 383 MET cc_start: 0.5418 (mtt) cc_final: 0.3151 (ppp) REVERT: D 480 MET cc_start: 0.2133 (ttt) cc_final: 0.0466 (ptm) REVERT: D 483 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5165 (tp30) REVERT: D 573 VAL cc_start: 0.2327 (OUTLIER) cc_final: 0.1781 (m) REVERT: E 110 GLU cc_start: 0.0044 (mm-30) cc_final: -0.0640 (pm20) REVERT: E 114 LYS cc_start: 0.6236 (tptt) cc_final: 0.5444 (mttp) REVERT: E 199 TYR cc_start: 0.2298 (t80) cc_final: 0.1898 (t80) REVERT: E 239 HIS cc_start: 0.2381 (OUTLIER) cc_final: 0.2148 (t70) REVERT: E 366 MET cc_start: -0.0146 (tpt) cc_final: -0.1322 (tmm) REVERT: E 461 TRP cc_start: 0.2234 (m-10) cc_final: 0.1485 (m-10) REVERT: E 474 MET cc_start: -0.0296 (ttt) cc_final: -0.0720 (ttt) REVERT: E 574 VAL cc_start: 0.0472 (t) cc_final: 0.0239 (m) REVERT: F 82 MET cc_start: 0.5033 (ttp) cc_final: 0.4290 (mtp) REVERT: F 123 MET cc_start: 0.0867 (ptt) cc_final: -0.0316 (ptt) REVERT: F 250 ASN cc_start: 0.7510 (t0) cc_final: 0.6668 (p0) REVERT: F 270 MET cc_start: 0.6338 (ttm) cc_final: 0.5977 (ttp) REVERT: F 366 MET cc_start: 0.6124 (ppp) cc_final: 0.5733 (tmm) REVERT: F 383 MET cc_start: 0.6062 (mtp) cc_final: 0.5474 (mtt) REVERT: F 589 GLU cc_start: 0.6408 (mm-30) cc_final: 0.5114 (pt0) outliers start: 173 outliers final: 125 residues processed: 404 average time/residue: 0.2098 time to fit residues: 148.3039 Evaluate side-chains 377 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 238 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 230 optimal weight: 0.0370 chunk 224 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 450 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 overall best weight: 4.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 784 GLN B1106 GLN C 422 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.130283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.106094 restraints weight = 191546.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.102338 restraints weight = 196905.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.102594 restraints weight = 181738.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102691 restraints weight = 128737.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102678 restraints weight = 124633.733| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40716 Z= 0.182 Angle : 0.752 12.084 55556 Z= 0.362 Chirality : 0.047 0.408 6377 Planarity : 0.005 0.092 7001 Dihedral : 7.537 58.681 7346 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.85 % Favored : 93.13 % Rotamer: Outliers : 4.08 % Allowed : 23.59 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.12), residues: 4744 helix: 0.24 (0.13), residues: 1605 sheet: -1.18 (0.19), residues: 725 loop : -1.76 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1107 TYR 0.026 0.002 TYR B 707 PHE 0.025 0.002 PHE E 525 TRP 0.022 0.001 TRP C 436 HIS 0.010 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00410 (40564) covalent geometry : angle 0.71568 (55148) SS BOND : bond 0.00453 ( 48) SS BOND : angle 2.28787 ( 96) hydrogen bonds : bond 0.03692 ( 1347) hydrogen bonds : angle 5.29364 ( 3867) link_BETA1-4 : bond 0.00619 ( 38) link_BETA1-4 : angle 2.55060 ( 114) link_NAG-ASN : bond 0.00484 ( 66) link_NAG-ASN : angle 3.09387 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 248 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7919 (pt) REVERT: B 135 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6427 (t80) REVERT: B 480 CYS cc_start: 0.5331 (OUTLIER) cc_final: 0.4500 (m) REVERT: B 746 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8489 (m) REVERT: B 901 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: B 1106 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: B 1126 CYS cc_start: 0.5745 (OUTLIER) cc_final: 0.4921 (p) REVERT: C 141 LEU cc_start: 0.7526 (mp) cc_final: 0.7177 (mp) REVERT: C 231 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7318 (mm) REVERT: C 858 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8950 (pp) REVERT: C 901 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: C 1001 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8995 (mm) REVERT: C 1132 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6596 (tp) REVERT: D 116 LEU cc_start: -0.0570 (OUTLIER) cc_final: -0.0782 (tt) REVERT: D 383 MET cc_start: 0.5789 (mtt) cc_final: 0.4752 (ptp) REVERT: D 480 MET cc_start: 0.1931 (ttt) cc_final: 0.0783 (ptm) REVERT: D 483 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5564 (tp30) REVERT: D 573 VAL cc_start: 0.2147 (OUTLIER) cc_final: 0.1712 (m) REVERT: E 110 GLU cc_start: 0.0320 (mm-30) cc_final: -0.0470 (pm20) REVERT: E 114 LYS cc_start: 0.5993 (tptt) cc_final: 0.5493 (mttp) REVERT: E 152 MET cc_start: 0.0843 (mmt) cc_final: 0.0037 (mmm) REVERT: E 199 TYR cc_start: 0.1117 (t80) cc_final: 0.0453 (t80) REVERT: E 297 MET cc_start: -0.1883 (mmt) cc_final: -0.2231 (mmt) REVERT: E 332 MET cc_start: 0.0634 (ppp) cc_final: 0.0210 (ppp) REVERT: E 366 MET cc_start: -0.0982 (tpt) cc_final: -0.1662 (tmm) REVERT: E 461 TRP cc_start: 0.3090 (m-10) cc_final: 0.2335 (m-10) REVERT: E 474 MET cc_start: -0.1576 (ttt) cc_final: -0.1791 (ttt) REVERT: E 574 VAL cc_start: 0.0770 (t) cc_final: 0.0538 (m) REVERT: F 82 MET cc_start: 0.4904 (ttp) cc_final: 0.4305 (mtp) REVERT: F 123 MET cc_start: 0.0966 (ptt) cc_final: -0.0187 (ptt) REVERT: F 250 ASN cc_start: 0.7212 (t0) cc_final: 0.6591 (p0) REVERT: F 270 MET cc_start: 0.5703 (ttm) cc_final: 0.5438 (ttp) REVERT: F 383 MET cc_start: 0.5607 (mtp) cc_final: 0.5133 (mtt) REVERT: F 480 MET cc_start: -0.0424 (ptt) cc_final: -0.0913 (ptt) REVERT: F 589 GLU cc_start: 0.7036 (mm-30) cc_final: 0.5686 (pt0) outliers start: 172 outliers final: 134 residues processed: 400 average time/residue: 0.2083 time to fit residues: 147.2261 Evaluate side-chains 383 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 234 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 226 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 387 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 380 optimal weight: 5.9990 chunk 214 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 315 optimal weight: 30.0000 chunk 145 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 66 HIS B 460 ASN B1106 GLN C 422 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN F 81 GLN F 228 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.106737 restraints weight = 192025.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.101946 restraints weight = 192060.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.102244 restraints weight = 205328.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.102575 restraints weight = 140879.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.102535 restraints weight = 133207.617| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.7378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 40716 Z= 0.165 Angle : 0.739 11.939 55556 Z= 0.355 Chirality : 0.047 0.371 6377 Planarity : 0.004 0.051 7001 Dihedral : 7.478 58.392 7346 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.98 % Favored : 93.00 % Rotamer: Outliers : 3.96 % Allowed : 23.92 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.12), residues: 4744 helix: 0.25 (0.13), residues: 1605 sheet: -1.10 (0.19), residues: 698 loop : -1.80 (0.12), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.026 0.001 TYR B 707 PHE 0.025 0.002 PHE E 525 TRP 0.022 0.001 TRP C 436 HIS 0.013 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00375 (40564) covalent geometry : angle 0.70393 (55148) SS BOND : bond 0.00406 ( 48) SS BOND : angle 2.20732 ( 96) hydrogen bonds : bond 0.03609 ( 1347) hydrogen bonds : angle 5.26468 ( 3867) link_BETA1-4 : bond 0.00645 ( 38) link_BETA1-4 : angle 2.52306 ( 114) link_NAG-ASN : bond 0.00458 ( 66) link_NAG-ASN : angle 3.04367 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 242 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7922 (pt) REVERT: B 135 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6488 (t80) REVERT: B 480 CYS cc_start: 0.5273 (OUTLIER) cc_final: 0.4364 (m) REVERT: B 746 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8459 (m) REVERT: B 901 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7217 (tt0) REVERT: B 1106 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: B 1126 CYS cc_start: 0.5700 (OUTLIER) cc_final: 0.4838 (p) REVERT: C 141 LEU cc_start: 0.7624 (mp) cc_final: 0.7357 (mp) REVERT: C 231 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7365 (mm) REVERT: C 858 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8855 (pp) REVERT: C 901 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: C 1001 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9077 (mm) REVERT: C 1132 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6609 (tp) REVERT: D 116 LEU cc_start: -0.0650 (OUTLIER) cc_final: -0.0850 (tt) REVERT: D 383 MET cc_start: 0.5681 (mtt) cc_final: 0.4646 (ptp) REVERT: D 480 MET cc_start: 0.1693 (ttt) cc_final: 0.0661 (ptm) REVERT: D 483 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5560 (tp30) REVERT: D 573 VAL cc_start: 0.2145 (OUTLIER) cc_final: 0.1679 (m) REVERT: E 110 GLU cc_start: 0.0367 (mm-30) cc_final: -0.0419 (pm20) REVERT: E 114 LYS cc_start: 0.5989 (tptt) cc_final: 0.5494 (mttp) REVERT: E 297 MET cc_start: -0.1756 (mmt) cc_final: -0.2132 (mmt) REVERT: E 332 MET cc_start: 0.0678 (ppp) cc_final: 0.0327 (ppp) REVERT: E 366 MET cc_start: -0.1004 (tpt) cc_final: -0.1631 (tmm) REVERT: E 461 TRP cc_start: 0.3005 (m-10) cc_final: 0.2220 (m-10) REVERT: E 474 MET cc_start: -0.1375 (ttt) cc_final: -0.1580 (ttt) REVERT: F 82 MET cc_start: 0.4964 (ttp) cc_final: 0.4294 (mtp) REVERT: F 123 MET cc_start: 0.1078 (ptt) cc_final: -0.0092 (ptt) REVERT: F 250 ASN cc_start: 0.7196 (t0) cc_final: 0.6582 (p0) REVERT: F 270 MET cc_start: 0.5686 (ttm) cc_final: 0.5410 (ttp) REVERT: F 383 MET cc_start: 0.5563 (mtp) cc_final: 0.5108 (mtt) REVERT: F 480 MET cc_start: 0.0089 (ptt) cc_final: -0.0539 (ptt) outliers start: 167 outliers final: 139 residues processed: 389 average time/residue: 0.2021 time to fit residues: 138.4380 Evaluate side-chains 386 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 232 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 597 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 228 HIS Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 94 optimal weight: 6.9990 chunk 350 optimal weight: 30.0000 chunk 370 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 419 optimal weight: 30.0000 chunk 196 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN B 66 HIS B1106 GLN C 125 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.130869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.109709 restraints weight = 190702.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.107107 restraints weight = 259328.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.107857 restraints weight = 233162.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.107546 restraints weight = 161818.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.107627 restraints weight = 136828.639| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.7469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40716 Z= 0.139 Angle : 0.730 19.200 55556 Z= 0.347 Chirality : 0.046 0.355 6377 Planarity : 0.004 0.048 7001 Dihedral : 7.318 57.990 7345 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.64 % Favored : 93.34 % Rotamer: Outliers : 3.46 % Allowed : 24.56 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.12), residues: 4744 helix: 0.34 (0.13), residues: 1608 sheet: -0.96 (0.20), residues: 690 loop : -1.76 (0.12), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1107 TYR 0.031 0.001 TYR E 199 PHE 0.028 0.002 PHE E 525 TRP 0.022 0.001 TRP D 48 HIS 0.029 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00313 (40564) covalent geometry : angle 0.69567 (55148) SS BOND : bond 0.00336 ( 48) SS BOND : angle 2.11531 ( 96) hydrogen bonds : bond 0.03477 ( 1347) hydrogen bonds : angle 5.19501 ( 3867) link_BETA1-4 : bond 0.00629 ( 38) link_BETA1-4 : angle 2.48828 ( 114) link_NAG-ASN : bond 0.00442 ( 66) link_NAG-ASN : angle 2.98859 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9488 Ramachandran restraints generated. 4744 Oldfield, 0 Emsley, 4744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 248 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7917 (pt) REVERT: B 135 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.6018 (t80) REVERT: B 480 CYS cc_start: 0.3543 (OUTLIER) cc_final: 0.2501 (m) REVERT: B 746 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8417 (m) REVERT: B 1106 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: B 1126 CYS cc_start: 0.5550 (OUTLIER) cc_final: 0.4573 (p) REVERT: C 141 LEU cc_start: 0.7174 (mp) cc_final: 0.6969 (mp) REVERT: C 231 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.6673 (mm) REVERT: C 858 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8725 (pp) REVERT: C 901 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: C 1001 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8947 (tt) REVERT: C 1132 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6476 (tp) REVERT: D 116 LEU cc_start: -0.0089 (OUTLIER) cc_final: -0.0365 (tt) REVERT: D 360 MET cc_start: 0.2885 (ppp) cc_final: 0.2506 (ttm) REVERT: D 383 MET cc_start: 0.5450 (mtt) cc_final: 0.4281 (ptp) REVERT: D 480 MET cc_start: 0.1695 (ttt) cc_final: 0.0082 (ptm) REVERT: D 483 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5107 (tp30) REVERT: D 573 VAL cc_start: 0.1494 (OUTLIER) cc_final: 0.0963 (m) REVERT: E 110 GLU cc_start: 0.0258 (mm-30) cc_final: -0.0829 (tt0) REVERT: E 114 LYS cc_start: 0.6221 (tptt) cc_final: 0.5422 (mttp) REVERT: E 270 MET cc_start: 0.1722 (tpp) cc_final: 0.1323 (tmm) REVERT: E 332 MET cc_start: 0.0792 (ppp) cc_final: 0.0407 (ppp) REVERT: E 360 MET cc_start: 0.2258 (pmm) cc_final: -0.0191 (ttt) REVERT: E 366 MET cc_start: -0.0066 (tpt) cc_final: -0.1097 (ppp) REVERT: E 461 TRP cc_start: 0.2216 (m-10) cc_final: 0.1518 (m-10) REVERT: E 474 MET cc_start: 0.0064 (ttt) cc_final: -0.0302 (ttt) REVERT: F 37 GLU cc_start: 0.7734 (pm20) cc_final: 0.7503 (tp30) REVERT: F 82 MET cc_start: 0.4934 (ttp) cc_final: 0.4359 (mtp) REVERT: F 123 MET cc_start: 0.1172 (ptt) cc_final: -0.0129 (ptt) REVERT: F 250 ASN cc_start: 0.7473 (t0) cc_final: 0.6537 (p0) REVERT: F 270 MET cc_start: 0.6073 (ttm) cc_final: 0.5651 (ttp) REVERT: F 383 MET cc_start: 0.5957 (mtp) cc_final: 0.5372 (mtt) REVERT: F 480 MET cc_start: -0.1463 (ptt) cc_final: -0.2074 (ptt) outliers start: 146 outliers final: 123 residues processed: 374 average time/residue: 0.1998 time to fit residues: 131.0461 Evaluate side-chains 374 residues out of total 4218 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 237 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 509 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 707 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 228 HIS Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 428 PHE Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 573 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 406 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 283 optimal weight: 0.8980 chunk 158 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 437 optimal weight: 0.8980 chunk 419 optimal weight: 30.0000 chunk 337 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 chunk 236 optimal weight: 0.3980 chunk 298 optimal weight: 4.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN B 66 HIS B1106 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 552 GLN F 228 HIS F 340 GLN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.130526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.106856 restraints weight = 191940.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.102078 restraints weight = 186777.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.102346 restraints weight = 203172.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.102659 restraints weight = 139537.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.102668 restraints weight = 128060.507| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.7581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 40716 Z= 0.144 Angle : 0.724 14.664 55556 Z= 0.345 Chirality : 0.046 0.356 6377 Planarity : 0.004 0.049 7001 Dihedral : 7.221 57.900 7345 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.68 % Favored : 93.30 % Rotamer: Outliers : 3.75 % Allowed : 24.25 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.12), residues: 4744 helix: 0.38 (0.13), residues: 1609 sheet: -0.93 (0.20), residues: 690 loop : -1.74 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.024 0.001 TYR B 707 PHE 0.028 0.002 PHE E 525 TRP 0.021 0.001 TRP D 48 HIS 0.031 0.001 HIS F 228 Details of bonding type rmsd covalent geometry : bond 0.00326 (40564) covalent geometry : angle 0.69004 (55148) SS BOND : bond 0.00371 ( 48) SS BOND : angle 2.12696 ( 96) hydrogen bonds : bond 0.03459 ( 1347) hydrogen bonds : angle 5.16296 ( 3867) link_BETA1-4 : bond 0.00634 ( 38) link_BETA1-4 : angle 2.46734 ( 114) link_NAG-ASN : bond 0.00439 ( 66) link_NAG-ASN : angle 2.95707 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7369.38 seconds wall clock time: 128 minutes 35.18 seconds (7715.18 seconds total)