Starting phenix.real_space_refine on Tue Nov 19 02:36:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf5_25862/11_2024/7tf5_25862.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf5_25862/11_2024/7tf5_25862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf5_25862/11_2024/7tf5_25862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf5_25862/11_2024/7tf5_25862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf5_25862/11_2024/7tf5_25862.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf5_25862/11_2024/7tf5_25862.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.027 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 216 5.16 5 C 32016 2.51 5 N 8244 2.21 5 O 9822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50298 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8103 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8103 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8103 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8103 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8103 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8103 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 981} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 26.41, per 1000 atoms: 0.53 Number of scatterers: 50298 At special positions: 0 Unit cell: (154.7, 167.7, 318.5, 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 216 16.00 O 9822 8.00 N 8244 7.00 C 32016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=83, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 136 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.05 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 538 " - pdb=" SG CYS F 590 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 p 1 " - " NAG p 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 165 " " NAG D1304 " - " ASN D 234 " " NAG D1305 " - " ASN D 282 " " NAG D1306 " - " ASN D 331 " " NAG D1307 " - " ASN D 343 " " NAG D1308 " - " ASN D 709 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 165 " " NAG E1304 " - " ASN E 234 " " NAG E1305 " - " ASN E 282 " " NAG E1306 " - " ASN E 331 " " NAG E1307 " - " ASN E 343 " " NAG E1308 " - " ASN E 709 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 122 " " NAG F1303 " - " ASN F 165 " " NAG F1304 " - " ASN F 234 " " NAG F1305 " - " ASN F 282 " " NAG F1306 " - " ASN F 331 " " NAG F1307 " - " ASN F 343 " " NAG F1308 " - " ASN F 709 " " NAG G 1 " - " ASN A 17 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 17 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 17 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1074 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " " NAG Y 1 " - " ASN D 17 " " NAG Z 1 " - " ASN D 717 " " NAG a 1 " - " ASN D 801 " " NAG b 1 " - " ASN D1074 " " NAG c 1 " - " ASN D1098 " " NAG d 1 " - " ASN D1134 " " NAG e 1 " - " ASN E 17 " " NAG f 1 " - " ASN E 717 " " NAG g 1 " - " ASN E 801 " " NAG h 1 " - " ASN E1074 " " NAG i 1 " - " ASN E1098 " " NAG j 1 " - " ASN E1134 " " NAG k 1 " - " ASN F 17 " " NAG l 1 " - " ASN F 717 " " NAG m 1 " - " ASN F 801 " " NAG n 1 " - " ASN F1074 " " NAG o 1 " - " ASN F1098 " " NAG p 1 " - " ASN F1134 " Time building additional restraints: 11.63 Conformation dependent library (CDL) restraints added in 5.9 seconds 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11664 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 102 sheets defined 25.5% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.734A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.657A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.643A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.065A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.573A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.866A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.087A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.567A 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 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.803A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.849A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.727A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.937A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.553A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.851A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.000A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.534A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.733A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.157A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.696A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.888A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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: 3.628A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.922A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.561A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.210A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.551A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.554A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.815A pdb=" N TRP D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.556A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 616 through 620 removed outlier: 4.071A pdb=" N VAL D 620 " --> pdb=" O CYS D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.572A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.851A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.058A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1147 removed outlier: 3.607A pdb=" N ASP D1146 " --> pdb=" O GLN D1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.927A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.884A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 616 through 620 removed outlier: 3.877A pdb=" N VAL E 620 " --> pdb=" O CYS E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.538A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 912 through 919 removed outlier: 3.834A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 945 through 965 Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E1033 " --> pdb=" O MET E1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1147 removed outlier: 3.568A pdb=" N ASP E1146 " --> pdb=" O GLN E1142 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 337 through 343 removed outlier: 4.024A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.469A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.110A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA F 411 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.856A pdb=" N VAL F 620 " --> pdb=" O CYS F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 744 Processing helix chain 'F' and resid 746 through 754 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 758 through 783 removed outlier: 3.559A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 866 through 884 Processing helix chain 'F' and resid 887 through 891 removed outlier: 3.789A pdb=" N GLY F 891 " --> pdb=" O PHE F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 909 Processing helix chain 'F' and resid 912 through 919 removed outlier: 3.905A pdb=" N LEU F 916 " --> pdb=" O THR F 912 " (cutoff:3.500A) Processing helix chain 'F' and resid 919 through 941 Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.508A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1032 removed outlier: 4.161A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 1141 through 1147 removed outlier: 3.635A pdb=" N ASP F1146 " --> pdb=" O GLN F1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.043A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.800A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.026A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.673A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.673A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.682A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.242A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.580A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.004A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.161A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.718A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.534A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.534A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.796A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.303A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.043A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.815A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.815A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.804A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.090A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 565 through 567 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.055A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.675A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.547A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.408A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.334A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.061A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.983A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 156 through 163 removed outlier: 10.053A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.612A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.194A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.041A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.205A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.261A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.566A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.566A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.399A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF8, first strand: chain 'D' and resid 27 through 30 Processing sheet with id=AF9, first strand: chain 'D' and resid 27 through 30 removed outlier: 8.096A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 42 through 43 removed outlier: 5.895A pdb=" N PHE D 43 " --> pdb=" O ARG F 567 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE F 326 " --> pdb=" O ASN F 542 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.074A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.779A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.296A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 156 " --> pdb=" O GLY D 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.779A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ARG D 246 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL D 143 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 311 through 318 removed outlier: 6.717A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 326 through 328 removed outlier: 5.504A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE D 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AG8, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.733A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AH1, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AH2, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.073A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 701 through 704 removed outlier: 6.738A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N LYS E 790 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN D 703 " --> pdb=" O LYS E 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.652A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.652A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.349A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 787 through 790 removed outlier: 3.782A pdb=" N LYS D 790 " --> pdb=" O ASN F 703 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AH9, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AI1, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.193A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 48 through 55 removed outlier: 3.969A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.762A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLU E 132 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS E 166 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N GLN E 134 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ASN E 164 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N CYS E 136 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 10.317A pdb=" N SER E 162 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 10.049A pdb=" N ASP E 138 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TYR E 160 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.762A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LEU E 244 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ARG E 246 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 311 through 319 removed outlier: 6.810A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 324 through 328 removed outlier: 4.432A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.655A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AI9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AJ1, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AJ2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.138A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 701 through 704 removed outlier: 3.608A pdb=" N LYS F 790 " --> pdb=" O ASN E 703 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.649A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.649A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.397A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AJ8, first strand: chain 'F' and resid 27 through 30 Processing sheet with id=AJ9, first strand: chain 'F' and resid 27 through 30 removed outlier: 8.307A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE F 203 " --> pdb=" O LEU F 226 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 48 through 55 removed outlier: 4.059A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.970A pdb=" N GLY F 103 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 126 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE F 168 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 156 through 163 removed outlier: 10.100A pdb=" N PHE F 157 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N ASP F 138 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL F 159 " --> pdb=" O CYS F 136 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS F 136 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLN F 134 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.313A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.732A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AK7, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AK8, first strand: chain 'F' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER F1055 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL F1061 " --> pdb=" O PRO F1053 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU F1063 " --> pdb=" O SER F1051 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER F1051 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE F1095 " --> pdb=" O ALA F1078 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.385A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'F' and resid 1120 through 1122 2251 hydrogen bonds defined for protein. 6210 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: 33.64 Time building geometry restraints manager: 13.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 15939 1.35 - 1.47: 13156 1.47 - 1.60: 22073 1.60 - 1.72: 0 1.72 - 1.85: 264 Bond restraints: 51432 Sorted by residual: bond pdb=" C1 NAG F1306 " pdb=" O5 NAG F1306 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.32e+00 bond pdb=" C1 NAG F1303 " pdb=" O5 NAG F1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.62e+00 ... (remaining 51427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 69633 3.23 - 6.46: 349 6.46 - 9.68: 34 9.68 - 12.91: 2 12.91 - 16.14: 2 Bond angle restraints: 70020 Sorted by residual: angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 132.44 -16.14 3.50e+00 8.16e-02 2.13e+01 angle pdb=" N PRO F 986 " pdb=" CA PRO F 986 " pdb=" C PRO F 986 " ideal model delta sigma weight residual 110.70 116.14 -5.44 1.22e+00 6.72e-01 1.99e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.12 -5.42 1.22e+00 6.72e-01 1.97e+01 angle pdb=" N PRO E 986 " pdb=" CA PRO E 986 " pdb=" C PRO E 986 " ideal model delta sigma weight residual 110.70 116.09 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.02 -5.32 1.22e+00 6.72e-01 1.90e+01 ... (remaining 70015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 29619 17.85 - 35.71: 2039 35.71 - 53.56: 368 53.56 - 71.42: 132 71.42 - 89.27: 59 Dihedral angle restraints: 32217 sinusoidal: 14097 harmonic: 18120 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -143.95 57.95 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -138.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CA CYS F 391 " pdb=" C CYS F 391 " pdb=" N PHE F 392 " pdb=" CA PHE F 392 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 32214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 7004 0.077 - 0.154: 1221 0.154 - 0.230: 56 0.230 - 0.307: 5 0.307 - 0.384: 6 Chirality restraints: 8292 Sorted by residual: chirality pdb=" C1 NAG k 1 " pdb=" ND2 ASN F 17 " pdb=" C2 NAG k 1 " pdb=" O5 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN E 17 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 8289 not shown) Planarity restraints: 9006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 321 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO F 322 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO F 322 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 322 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 899 " -0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C PRO E 899 " 0.075 2.00e-02 2.50e+03 pdb=" O PRO E 899 " -0.028 2.00e-02 2.50e+03 pdb=" N MET E 900 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 561 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " 0.044 5.00e-02 4.00e+02 ... (remaining 9003 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 11159 2.79 - 3.32: 42437 3.32 - 3.84: 85098 3.84 - 4.37: 98439 4.37 - 4.90: 170075 Nonbonded interactions: 407208 Sorted by model distance: nonbonded pdb=" OG1 THR E 393 " pdb=" O GLU E 516 " model vdw 2.262 3.040 nonbonded pdb=" OD2 ASP D 578 " pdb=" OG1 THR D 581 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR D 37 " pdb=" O LEU D 54 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR E 37 " pdb=" O LEU E 54 " model vdw 2.295 3.040 ... (remaining 407203 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' selection = chain 'B' selection = chain 'C' selection = 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' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.530 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 117.120 Find NCS groups from input model: 3.700 Set up NCS constraints: 0.690 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: 0.020 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.004 0.071 51432 Z= 0.287 Angle : 0.745 16.140 70020 Z= 0.395 Chirality : 0.054 0.384 8292 Planarity : 0.006 0.126 8922 Dihedral : 13.182 89.270 20304 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.37 % Allowed : 1.82 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.10), residues: 6132 helix: 1.05 (0.13), residues: 1314 sheet: 0.41 (0.13), residues: 1356 loop : -0.78 (0.09), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 436 HIS 0.003 0.001 HIS B 66 PHE 0.031 0.002 PHE C 238 TYR 0.025 0.002 TYR C1067 ARG 0.007 0.001 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 374 time to evaluate : 4.324 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: A 341 VAL cc_start: 0.9008 (t) cc_final: 0.8477 (p) REVERT: A 934 ILE cc_start: 0.8901 (mm) cc_final: 0.8658 (mm) REVERT: A 1029 MET cc_start: 0.9041 (tpp) cc_final: 0.8706 (tpp) REVERT: B 197 ILE cc_start: 0.9026 (mm) cc_final: 0.8724 (mm) REVERT: B 200 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: B 335 LEU cc_start: 0.9249 (tp) cc_final: 0.9013 (tt) REVERT: B 900 MET cc_start: 0.8154 (mtp) cc_final: 0.7832 (mtp) REVERT: C 406 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 134 GLN cc_start: 0.8968 (tp40) cc_final: 0.8514 (tm-30) REVERT: D 586 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: E 895 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6524 (pm20) REVERT: E 936 ASP cc_start: 0.8914 (m-30) cc_final: 0.8655 (t0) REVERT: F 20 THR cc_start: 0.6122 (p) cc_final: 0.5506 (p) REVERT: F 158 ARG cc_start: 0.7341 (mtt90) cc_final: 0.6814 (mmt90) REVERT: F 214 ARG cc_start: 0.8042 (ttt90) cc_final: 0.7780 (ttp80) REVERT: F 759 PHE cc_start: 0.7373 (m-80) cc_final: 0.7168 (m-80) REVERT: F 985 ASP cc_start: 0.8152 (p0) cc_final: 0.7636 (p0) REVERT: F 993 ILE cc_start: 0.6588 (mt) cc_final: 0.6202 (mm) REVERT: F 1100 THR cc_start: 0.8159 (p) cc_final: 0.7855 (p) outliers start: 20 outliers final: 5 residues processed: 393 average time/residue: 0.5255 time to fit residues: 342.5599 Evaluate side-chains 159 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 4.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain D residue 564 GLN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain F residue 88 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 521 optimal weight: 10.0000 chunk 468 optimal weight: 6.9990 chunk 259 optimal weight: 0.0050 chunk 160 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 484 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 360 optimal weight: 8.9990 chunk 561 optimal weight: 0.8980 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 556 ASN A 755 GLN A 762 GLN A 955 ASN A1071 HIS B 115 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN B 755 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 HIS C 394 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 HIS D 755 GLN D 856 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1071 HIS E 755 GLN E 901 GLN E1071 HIS F 481 ASN F 536 ASN F 926 GLN F1002 GLN F1071 HIS F1101 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 51432 Z= 0.195 Angle : 0.547 11.496 70020 Z= 0.282 Chirality : 0.045 0.333 8292 Planarity : 0.004 0.070 8922 Dihedral : 6.900 59.689 9208 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.85 % Allowed : 4.83 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.10), residues: 6132 helix: 1.91 (0.14), residues: 1356 sheet: 0.53 (0.14), residues: 1305 loop : -0.53 (0.09), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 258 HIS 0.003 0.001 HIS F1101 PHE 0.020 0.001 PHE F 392 TYR 0.025 0.001 TYR B 28 ARG 0.010 0.000 ARG D 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 4.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9146 (tpp) cc_final: 0.8714 (tpp) REVERT: B 900 MET cc_start: 0.8281 (mtp) cc_final: 0.7974 (mtp) REVERT: B 995 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8323 (mtm-85) REVERT: C 406 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8207 (mt-10) REVERT: D 134 GLN cc_start: 0.8963 (tp40) cc_final: 0.8360 (tm-30) REVERT: D 586 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8372 (m-30) REVERT: E 583 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: E 936 ASP cc_start: 0.8972 (m-30) cc_final: 0.8646 (t0) REVERT: F 170 TYR cc_start: 0.8050 (t80) cc_final: 0.7590 (t80) REVERT: F 214 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7800 (ttp80) REVERT: F 753 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8310 (mt) REVERT: F 902 MET cc_start: 0.9044 (mmm) cc_final: 0.8573 (mmm) REVERT: F 985 ASP cc_start: 0.7822 (p0) cc_final: 0.7457 (p0) REVERT: F 1050 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7669 (ptm) outliers start: 46 outliers final: 17 residues processed: 199 average time/residue: 0.4793 time to fit residues: 168.4032 Evaluate side-chains 151 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 753 LEU Chi-restraints excluded: chain F residue 1050 MET Chi-restraints excluded: chain F residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 467 optimal weight: 0.6980 chunk 382 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 562 optimal weight: 0.8980 chunk 607 optimal weight: 1.9990 chunk 500 optimal weight: 6.9990 chunk 557 optimal weight: 0.2980 chunk 191 optimal weight: 6.9990 chunk 451 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A1005 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C1002 GLN D 856 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 919 ASN F 137 ASN F1083 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 51432 Z= 0.159 Angle : 0.501 9.117 70020 Z= 0.256 Chirality : 0.044 0.324 8292 Planarity : 0.004 0.060 8922 Dihedral : 6.108 59.791 9199 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.72 % Allowed : 5.82 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.10), residues: 6132 helix: 2.17 (0.14), residues: 1359 sheet: 0.58 (0.14), residues: 1371 loop : -0.44 (0.10), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.004 0.000 HIS F1101 PHE 0.022 0.001 PHE F 759 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 5.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8714 (mtp) cc_final: 0.8501 (mtm) REVERT: B 900 MET cc_start: 0.8122 (mtp) cc_final: 0.7772 (mtp) REVERT: C 406 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8136 (mt-10) REVERT: D 134 GLN cc_start: 0.8943 (tp40) cc_final: 0.8276 (tm-30) REVERT: E 583 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: E 936 ASP cc_start: 0.8926 (m-30) cc_final: 0.8653 (t0) REVERT: F 137 ASN cc_start: 0.8150 (t160) cc_final: 0.7777 (p0) REVERT: F 170 TYR cc_start: 0.8152 (t80) cc_final: 0.7738 (t80) REVERT: F 214 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7793 (ttp80) REVERT: F 759 PHE cc_start: 0.7380 (p90) cc_final: 0.6963 (p90) REVERT: F 902 MET cc_start: 0.9117 (mmm) cc_final: 0.8540 (mmm) REVERT: F 985 ASP cc_start: 0.7891 (p0) cc_final: 0.7534 (p0) REVERT: F 995 ARG cc_start: 0.8795 (mmm160) cc_final: 0.7990 (mtm-85) REVERT: F 1050 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7741 (ptm) outliers start: 39 outliers final: 21 residues processed: 170 average time/residue: 0.5650 time to fit residues: 173.2660 Evaluate side-chains 148 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 856 ASN Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 762 GLN Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 756 TYR Chi-restraints excluded: chain F residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 555 optimal weight: 9.9990 chunk 422 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 377 optimal weight: 1.9990 chunk 564 optimal weight: 0.8980 chunk 597 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 534 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 501 ASN B 824 ASN B 872 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 613 GLN C 872 GLN C 907 ASN C 955 ASN D 613 GLN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN F1011 GLN ** F1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 51432 Z= 0.323 Angle : 0.574 9.571 70020 Z= 0.292 Chirality : 0.045 0.322 8292 Planarity : 0.004 0.057 8922 Dihedral : 5.835 58.275 9195 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.87 % Allowed : 6.67 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.10), residues: 6132 helix: 2.12 (0.14), residues: 1356 sheet: 0.42 (0.13), residues: 1398 loop : -0.41 (0.10), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 886 HIS 0.006 0.001 HIS C1064 PHE 0.015 0.002 PHE A 802 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 5.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8764 (mtp) cc_final: 0.8400 (mtm) REVERT: B 984 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7776 (tp) REVERT: E 583 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: E 936 ASP cc_start: 0.8985 (m-30) cc_final: 0.8747 (t0) REVERT: F 170 TYR cc_start: 0.8345 (t80) cc_final: 0.7836 (t80) REVERT: F 214 ARG cc_start: 0.8272 (ttt90) cc_final: 0.7933 (ttp80) REVERT: F 697 MET cc_start: 0.8353 (ptm) cc_final: 0.8028 (ptm) REVERT: F 985 ASP cc_start: 0.8282 (p0) cc_final: 0.7890 (p0) outliers start: 47 outliers final: 29 residues processed: 159 average time/residue: 0.5651 time to fit residues: 161.7208 Evaluate side-chains 143 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 4.9990 chunk 339 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 444 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 509 optimal weight: 20.0000 chunk 412 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 305 optimal weight: 0.8980 chunk 536 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1036 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C1002 GLN C1083 HIS D 919 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1036 GLN F 121 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 51432 Z= 0.255 Angle : 0.526 9.824 70020 Z= 0.270 Chirality : 0.044 0.375 8292 Planarity : 0.004 0.064 8922 Dihedral : 5.612 59.647 9195 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.01 % Allowed : 7.24 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.10), residues: 6132 helix: 2.19 (0.14), residues: 1353 sheet: 0.33 (0.13), residues: 1422 loop : -0.35 (0.10), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 886 HIS 0.003 0.001 HIS F1101 PHE 0.019 0.001 PHE F 759 TYR 0.022 0.001 TYR C1067 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 115 time to evaluate : 5.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8819 (mtp) cc_final: 0.8509 (mtm) REVERT: B 506 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7821 (mm-40) REVERT: B 984 LEU cc_start: 0.8379 (mm) cc_final: 0.7738 (tp) REVERT: D 900 MET cc_start: 0.8606 (tpp) cc_final: 0.8047 (tpp) REVERT: E 333 THR cc_start: 0.9029 (m) cc_final: 0.8824 (t) REVERT: E 583 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: E 936 ASP cc_start: 0.8980 (m-30) cc_final: 0.8761 (t0) REVERT: F 214 ARG cc_start: 0.8266 (ttt90) cc_final: 0.7958 (ttp80) REVERT: F 697 MET cc_start: 0.8423 (ptm) cc_final: 0.8089 (ptm) REVERT: F 773 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7374 (tm-30) REVERT: F 902 MET cc_start: 0.9198 (tpp) cc_final: 0.8945 (tpp) REVERT: F 985 ASP cc_start: 0.8386 (p0) cc_final: 0.7993 (p0) REVERT: F 995 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8222 (ttm110) outliers start: 55 outliers final: 29 residues processed: 159 average time/residue: 0.5541 time to fit residues: 160.6545 Evaluate side-chains 138 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 5.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 731 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 7.9990 chunk 537 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 350 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 597 optimal weight: 7.9990 chunk 496 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 51432 Z= 0.223 Angle : 0.510 10.127 70020 Z= 0.260 Chirality : 0.044 0.311 8292 Planarity : 0.004 0.068 8922 Dihedral : 5.236 59.341 9195 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.81 % Allowed : 7.99 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 6132 helix: 2.20 (0.14), residues: 1374 sheet: 0.44 (0.13), residues: 1365 loop : -0.31 (0.10), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 886 HIS 0.003 0.001 HIS F1101 PHE 0.012 0.001 PHE B 898 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG F 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8808 (mtp) cc_final: 0.8512 (mtm) REVERT: A 934 ILE cc_start: 0.9063 (mm) cc_final: 0.8856 (mm) REVERT: B 506 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7836 (mm-40) REVERT: B 984 LEU cc_start: 0.8389 (mm) cc_final: 0.7619 (tp) REVERT: C 365 TYR cc_start: 0.9069 (m-80) cc_final: 0.8805 (m-10) REVERT: D 869 MET cc_start: 0.8672 (mtp) cc_final: 0.8360 (mtm) REVERT: E 333 THR cc_start: 0.9055 (m) cc_final: 0.8835 (t) REVERT: E 583 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: F 214 ARG cc_start: 0.8351 (ttt90) cc_final: 0.7963 (ttp80) REVERT: F 697 MET cc_start: 0.8396 (ptm) cc_final: 0.8081 (ptm) REVERT: F 773 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7366 (tm-30) REVERT: F 902 MET cc_start: 0.9253 (tpp) cc_final: 0.8849 (tpp) REVERT: F 985 ASP cc_start: 0.8393 (p0) cc_final: 0.7999 (p0) REVERT: F 995 ARG cc_start: 0.8822 (mmm160) cc_final: 0.8161 (ttm110) outliers start: 44 outliers final: 30 residues processed: 146 average time/residue: 0.5524 time to fit residues: 145.6216 Evaluate side-chains 136 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 5.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 583 GLU Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 731 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 436 optimal weight: 0.4980 chunk 338 optimal weight: 0.5980 chunk 503 optimal weight: 0.9980 chunk 333 optimal weight: 10.0000 chunk 595 optimal weight: 4.9990 chunk 372 optimal weight: 2.9990 chunk 363 optimal weight: 0.0040 chunk 275 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 907 ASN C1002 GLN D 121 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** F1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 51432 Z= 0.131 Angle : 0.480 10.497 70020 Z= 0.244 Chirality : 0.044 0.321 8292 Planarity : 0.003 0.068 8922 Dihedral : 4.863 57.803 9195 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.72 % Allowed : 8.36 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.11), residues: 6132 helix: 2.36 (0.14), residues: 1353 sheet: 0.53 (0.14), residues: 1323 loop : -0.21 (0.10), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.003 0.000 HIS F1101 PHE 0.019 0.001 PHE F 759 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG D1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 6.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8772 (mtp) cc_final: 0.8513 (mtm) REVERT: A 1029 MET cc_start: 0.9015 (tpp) cc_final: 0.8676 (tpp) REVERT: B 506 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7765 (mm-40) REVERT: C 365 TYR cc_start: 0.9043 (m-80) cc_final: 0.8738 (m-10) REVERT: C 902 MET cc_start: 0.9174 (tpp) cc_final: 0.8946 (tpp) REVERT: D 869 MET cc_start: 0.8680 (mtp) cc_final: 0.8401 (mtm) REVERT: E 333 THR cc_start: 0.9025 (m) cc_final: 0.8809 (t) REVERT: E 1002 GLN cc_start: 0.8708 (tp40) cc_final: 0.8471 (tm-30) REVERT: F 697 MET cc_start: 0.8378 (ptm) cc_final: 0.8074 (ptm) REVERT: F 773 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7264 (tm-30) REVERT: F 902 MET cc_start: 0.9167 (tpp) cc_final: 0.8947 (tpp) REVERT: F 985 ASP cc_start: 0.8413 (p0) cc_final: 0.8015 (p0) REVERT: F 995 ARG cc_start: 0.8784 (mmm160) cc_final: 0.8113 (ttm110) outliers start: 39 outliers final: 30 residues processed: 148 average time/residue: 0.5846 time to fit residues: 156.8309 Evaluate side-chains 137 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 731 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 chunk 405 optimal weight: 9.9990 chunk 294 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 468 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN D 49 HIS D 121 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 HIS E 211 ASN E 245 HIS ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN E 613 GLN E1083 HIS F 957 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 51432 Z= 0.390 Angle : 0.602 9.710 70020 Z= 0.306 Chirality : 0.045 0.340 8292 Planarity : 0.004 0.070 8922 Dihedral : 5.277 55.986 9194 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.83 % Allowed : 8.47 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 6132 helix: 2.19 (0.14), residues: 1335 sheet: 0.25 (0.14), residues: 1326 loop : -0.32 (0.10), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 886 HIS 0.005 0.001 HIS E 207 PHE 0.033 0.002 PHE F 759 TYR 0.025 0.002 TYR C1067 ARG 0.004 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 5.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8777 (mtp) cc_final: 0.8450 (mtm) REVERT: B 506 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7808 (mm-40) REVERT: B 823 PHE cc_start: 0.8352 (m-80) cc_final: 0.8137 (m-10) REVERT: E 333 THR cc_start: 0.9070 (m) cc_final: 0.8866 (t) REVERT: F 697 MET cc_start: 0.8401 (ptm) cc_final: 0.7999 (ptm) REVERT: F 773 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7430 (tm-30) REVERT: F 985 ASP cc_start: 0.8586 (p0) cc_final: 0.8294 (p0) REVERT: F 995 ARG cc_start: 0.8742 (mmm160) cc_final: 0.7973 (ttm110) outliers start: 45 outliers final: 33 residues processed: 141 average time/residue: 0.5779 time to fit residues: 147.8679 Evaluate side-chains 129 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 869 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 2.9990 chunk 570 optimal weight: 10.0000 chunk 520 optimal weight: 8.9990 chunk 555 optimal weight: 3.9990 chunk 334 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 435 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 501 optimal weight: 0.9990 chunk 524 optimal weight: 9.9990 chunk 553 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 51432 Z= 0.286 Angle : 0.542 10.938 70020 Z= 0.275 Chirality : 0.044 0.331 8292 Planarity : 0.004 0.072 8922 Dihedral : 5.133 54.490 9194 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.76 % Allowed : 8.80 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 6132 helix: 2.27 (0.14), residues: 1332 sheet: 0.23 (0.13), residues: 1383 loop : -0.30 (0.10), residues: 3417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 886 HIS 0.003 0.001 HIS C1058 PHE 0.031 0.001 PHE F 759 TYR 0.023 0.001 TYR C1067 ARG 0.003 0.000 ARG F 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 5.652 Fit side-chains revert: symmetry clash REVERT: A 869 MET cc_start: 0.8826 (mtp) cc_final: 0.8502 (mtm) REVERT: B 506 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: B 823 PHE cc_start: 0.8342 (m-80) cc_final: 0.8095 (m-10) REVERT: C 365 TYR cc_start: 0.9115 (m-80) cc_final: 0.8810 (m-10) REVERT: E 333 THR cc_start: 0.9063 (m) cc_final: 0.8855 (t) REVERT: E 498 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8743 (mm-40) REVERT: E 900 MET cc_start: 0.8861 (mmm) cc_final: 0.8615 (mmm) REVERT: F 697 MET cc_start: 0.8405 (ptm) cc_final: 0.7991 (ptm) REVERT: F 773 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7466 (tm-30) REVERT: F 902 MET cc_start: 0.9200 (tpp) cc_final: 0.8939 (tpp) REVERT: F 985 ASP cc_start: 0.8625 (p0) cc_final: 0.8376 (p0) REVERT: F 995 ARG cc_start: 0.8750 (mmm160) cc_final: 0.7833 (mtp85) outliers start: 41 outliers final: 31 residues processed: 132 average time/residue: 0.5931 time to fit residues: 142.4468 Evaluate side-chains 130 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 498 GLN Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 731 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 5.9990 chunk 586 optimal weight: 0.0370 chunk 358 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 408 optimal weight: 5.9990 chunk 615 optimal weight: 1.9990 chunk 566 optimal weight: 0.7980 chunk 490 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 378 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN F 613 GLN ** F1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 51432 Z= 0.144 Angle : 0.498 10.032 70020 Z= 0.253 Chirality : 0.044 0.320 8292 Planarity : 0.003 0.072 8922 Dihedral : 4.733 54.071 9194 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.59 % Allowed : 9.04 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.11), residues: 6132 helix: 2.28 (0.14), residues: 1371 sheet: 0.29 (0.14), residues: 1380 loop : -0.16 (0.11), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.000 HIS F1101 PHE 0.021 0.001 PHE F 759 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG E 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12264 Ramachandran restraints generated. 6132 Oldfield, 0 Emsley, 6132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 5.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7797 (tmm-80) cc_final: 0.7314 (tpt90) REVERT: A 869 MET cc_start: 0.8784 (mtp) cc_final: 0.8515 (mtm) REVERT: B 506 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7798 (mm-40) REVERT: B 823 PHE cc_start: 0.8289 (m-80) cc_final: 0.8022 (m-10) REVERT: C 365 TYR cc_start: 0.9085 (m-80) cc_final: 0.8766 (m-10) REVERT: D 1050 MET cc_start: 0.8162 (ppp) cc_final: 0.7900 (ppp) REVERT: F 387 LEU cc_start: 0.9329 (tp) cc_final: 0.9059 (mt) REVERT: F 697 MET cc_start: 0.8392 (ptm) cc_final: 0.8031 (ptm) REVERT: F 773 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7411 (tm-30) REVERT: F 902 MET cc_start: 0.9190 (tpp) cc_final: 0.8921 (tpp) REVERT: F 985 ASP cc_start: 0.8498 (p0) cc_final: 0.8194 (p0) REVERT: F 995 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8144 (ttm110) outliers start: 32 outliers final: 28 residues processed: 132 average time/residue: 0.6009 time to fit residues: 143.5581 Evaluate side-chains 128 residues out of total 5454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 5.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 498 GLN Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 15 CYS Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 434 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 10.0000 chunk 522 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 452 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 491 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 504 optimal weight: 0.0060 chunk 62 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: