Starting phenix.real_space_refine on Sun Feb 25 09:15:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf2_25859/02_2024/7tf2_25859.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf2_25859/02_2024/7tf2_25859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf2_25859/02_2024/7tf2_25859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf2_25859/02_2024/7tf2_25859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf2_25859/02_2024/7tf2_25859.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf2_25859/02_2024/7tf2_25859.pdb" } resolution = 3.62 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= 0.025 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 32022 2.51 5 N 8238 2.21 5 O 9816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50292 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8102 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: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8102 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: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8102 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: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8102 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: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8102 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: 8102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8102 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: 25.64, per 1000 atoms: 0.51 Number of scatterers: 50292 At special positions: 0 Unit cell: (154.7, 166.4, 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 9816 8.00 N 8238 7.00 C 32022 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 - 3.50 Amino acid : False - 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: 22.17 Conformation dependent library (CDL) restraints added in 9.4 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: 134 helices and 102 sheets defined 25.3% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.77 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: 3.723A 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: 3.669A 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: 3.636A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.060A 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: 3.568A 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: 3.865A 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: 4.066A 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: 3.614A 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: 3.817A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.840A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.731A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.555A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.933A 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: 3.546A 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: 3.838A 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: 4.010A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.623A 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: 3.739A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.167A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.699A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.912A 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: 3.613A 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: 3.939A 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: 3.535A 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: 4.234A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.594A 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: 3.599A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.820A 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: 3.561A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 3.623A 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: 4.060A 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: 3.545A 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: 3.850A 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 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 1033 removed outlier: 4.020A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1147 removed outlier: 3.627A 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: 3.880A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.866A 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: 3.961A 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: 3.560A 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: 3.840A 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: 3.525A pdb=" N VAL E1033 " --> pdb=" O MET E1029 " (cutoff:3.500A) Processing helix chain 'E' and resid 1141 through 1147 removed outlier: 3.648A 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: 4.020A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.472A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.112A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.688A 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: 3.518A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.875A 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: 3.540A 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 897 through 909 Processing helix chain 'F' and resid 912 through 919 removed outlier: 3.895A 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: 3.513A 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: 4.176A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 1141 through 1147 removed outlier: 3.631A 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: 8.013A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.911A 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: 3.744A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.735A 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: 4.063A 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: 3.756A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.690A 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: 3.756A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.534A 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: 6.668A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.970A 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: 5.190A 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: 3.568A 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: 7.057A 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: 6.059A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.296A 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: 6.773A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.974A 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: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.976A 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: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.632A 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: 4.390A 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: 3.799A 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: 6.300A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.931A 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: 4.082A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.844A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.844A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.565A 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: 6.821A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.771A 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: 7.102A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.229A 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 566 removed outlier: 7.100A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.006A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.343A 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: 3.735A 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: 6.584A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.969A 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: 6.584A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.613A 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: 4.394A 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: 8.347A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.646A 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: 4.103A 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: 4.025A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.676A 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: 10.158A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.675A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 136 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.254A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.066A 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: 4.048A 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: 6.261A 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: 6.175A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.351A 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: 6.564A 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: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.958A 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: 6.564A 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: 6.631A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.640A 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: 4.369A 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: 8.097A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.895A 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: 5.856A pdb=" N PHE D 43 " --> pdb=" O ARG F 567 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 6.645A 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: 4.099A 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: 3.755A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 10.312A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.618A 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: 3.755A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ARG D 246 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.565A 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: 6.714A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN D 317 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY D 593 " --> pdb=" O ASN D 317 " (cutoff:3.500A) removed outlier: 3.878A 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: 5.283A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 7.041A 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: 6.797A 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: 6.003A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.292A 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: 6.706A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LYS E 790 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.967A 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: 6.593A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.357A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 787 through 790 removed outlier: 3.778A pdb=" N LYS D 790 " --> pdb=" O ASN F 703 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AH8, first strand: chain 'D' and resid 1094 through 1097 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: 8.237A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.989A 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: 4.007A 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: 3.810A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU E 132 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS E 166 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N GLN E 134 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN E 164 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N CYS E 136 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N SER E 162 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ASP E 138 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR E 160 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 156 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.810A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU E 244 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG E 246 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.729A 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: 6.811A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 3.706A 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: 4.450A 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: 3.637A 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: 6.061A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.327A 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 Processing sheet with id=AJ4, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.631A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.959A 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: 6.631A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.402A 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: 8.244A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE F 201 " --> pdb=" O ASP F 228 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP F 228 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 6.617A 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: 4.094A 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: 4.095A pdb=" N GLY F 103 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL F 126 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 3.635A 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: 10.278A pdb=" N PHE F 157 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 11.780A pdb=" N ASP F 138 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL F 159 " --> pdb=" O CYS F 136 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS F 136 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 6.411A 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: 5.354A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.375A 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: 6.696A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.115A 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: 3.668A 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: 6.206A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 6.375A 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: 6.679A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER F1055 " --> pdb=" O GLY F1059 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL F1061 " --> pdb=" O PRO F1053 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU F1063 " --> pdb=" O SER F1051 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER F1051 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 6.965A 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: 6.679A pdb=" N SER F 711 " --> pdb=" O THR F1076 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR F1076 " --> pdb=" O SER F 711 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA F 713 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN F1074 " --> pdb=" O ALA F 713 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLU F1072 " --> pdb=" O PRO F 715 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA F1078 " --> pdb=" O PHE F1095 " (cutoff:3.500A) removed outlier: 4.687A 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: 4.343A 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 2245 hydrogen bonds defined for protein. 6171 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: 30.18 Time building geometry restraints manager: 22.72 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: 15926 1.35 - 1.47: 13097 1.47 - 1.60: 22139 1.60 - 1.72: 0 1.72 - 1.84: 264 Bond restraints: 51426 Sorted by residual: bond pdb=" C1 NAG F1306 " pdb=" O5 NAG F1306 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C1 NAG F1303 " pdb=" O5 NAG F1303 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " 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 G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 ... (remaining 51421 not shown) Histogram of bond angle deviations from ideal: 98.61 - 106.17: 1388 106.17 - 113.73: 28820 113.73 - 121.29: 25816 121.29 - 128.84: 13791 128.84 - 136.40: 199 Bond angle restraints: 70014 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 116.30 132.41 -16.11 3.50e+00 8.16e-02 2.12e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.21 -5.51 1.22e+00 6.72e-01 2.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.08 -5.38 1.22e+00 6.72e-01 1.94e+01 angle pdb=" N PRO E 986 " pdb=" CA PRO E 986 " pdb=" C PRO E 986 " ideal model delta sigma weight residual 110.70 116.06 -5.36 1.22e+00 6.72e-01 1.93e+01 angle pdb=" N PRO F 986 " pdb=" CA PRO F 986 " pdb=" C PRO F 986 " ideal model delta sigma weight residual 110.70 116.02 -5.32 1.22e+00 6.72e-01 1.90e+01 ... (remaining 70009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 29624 17.87 - 35.75: 2048 35.75 - 53.62: 358 53.62 - 71.49: 123 71.49 - 89.37: 58 Dihedral angle restraints: 32211 sinusoidal: 14091 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 -142.51 56.51 1 1.00e+01 1.00e-02 4.30e+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 -138.66 52.66 1 1.00e+01 1.00e-02 3.78e+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 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 32208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 7115 0.081 - 0.162: 1132 0.162 - 0.243: 42 0.243 - 0.324: 5 0.324 - 0.405: 4 Chirality restraints: 8298 Sorted by residual: 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 -2.00 -0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C1 NAG F1306 " pdb=" ND2 ASN F 331 " pdb=" C2 NAG F1306 " pdb=" O5 NAG F1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+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 -2.06 -0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 8295 not shown) Planarity restraints: 9000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 321 " 0.082 5.00e-02 4.00e+02 1.25e-01 2.51e+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 B 899 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C PRO B 899 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO B 899 " 0.025 2.00e-02 2.50e+03 pdb=" N MET B 900 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 899 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C PRO E 899 " 0.069 2.00e-02 2.50e+03 pdb=" O PRO E 899 " -0.025 2.00e-02 2.50e+03 pdb=" N MET E 900 " -0.024 2.00e-02 2.50e+03 ... (remaining 8997 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 12576 2.80 - 3.33: 42189 3.33 - 3.85: 85302 3.85 - 4.38: 98090 4.38 - 4.90: 168880 Nonbonded interactions: 407037 Sorted by model distance: nonbonded pdb=" OG1 THR E 393 " pdb=" O GLU E 516 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.281 2.440 nonbonded pdb=" OD2 ASP D 578 " pdb=" OG1 THR D 581 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR E 37 " pdb=" O LEU E 54 " model vdw 2.283 2.440 nonbonded pdb=" OE1 GLN E 52 " pdb=" OG1 THR E 274 " model vdw 2.290 2.440 ... (remaining 407032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 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: 0.050 Extract box with map and model: 18.510 Check model and map are aligned: 0.000 Set scattering table: 0.740 Process input model: 138.020 Find NCS groups from input model: 3.670 Set up NCS constraints: 1.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 0.069 51426 Z= 0.282 Angle : 0.744 16.112 70014 Z= 0.394 Chirality : 0.053 0.405 8298 Planarity : 0.006 0.125 8916 Dihedral : 13.052 89.367 20298 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.35 % Allowed : 1.77 % Favored : 97.88 % 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: -0.12 (0.10), residues: 6132 helix: 1.05 (0.13), residues: 1317 sheet: 0.65 (0.13), residues: 1389 loop : -0.85 (0.09), residues: 3426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 436 HIS 0.004 0.001 HIS F1048 PHE 0.030 0.002 PHE C 238 TYR 0.029 0.002 TYR E 200 ARG 0.008 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 604 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 585 time to evaluate : 5.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 VAL cc_start: 0.9121 (t) cc_final: 0.8900 (p) REVERT: A 387 LEU cc_start: 0.9613 (mt) cc_final: 0.9402 (mt) REVERT: A 558 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8276 (ptpt) REVERT: A 823 PHE cc_start: 0.8252 (m-80) cc_final: 0.8042 (m-10) REVERT: A 983 ARG cc_start: 0.9062 (mtp180) cc_final: 0.8515 (ttm110) REVERT: B 276 LEU cc_start: 0.9361 (tp) cc_final: 0.9058 (tt) REVERT: B 335 LEU cc_start: 0.8892 (tp) cc_final: 0.8635 (tt) REVERT: B 756 TYR cc_start: 0.8762 (m-80) cc_final: 0.8239 (m-80) REVERT: B 759 PHE cc_start: 0.7954 (m-80) cc_final: 0.7704 (m-80) REVERT: B 1005 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8886 (tp40) REVERT: C 356 LYS cc_start: 0.9088 (tttt) cc_final: 0.8792 (tptp) REVERT: C 481 ASN cc_start: 0.8829 (m-40) cc_final: 0.8163 (p0) REVERT: C 752 LEU cc_start: 0.9538 (mt) cc_final: 0.9311 (mp) REVERT: C 755 GLN cc_start: 0.9264 (mm-40) cc_final: 0.9007 (mp10) REVERT: C 759 PHE cc_start: 0.8755 (m-80) cc_final: 0.8459 (m-80) REVERT: C 762 GLN cc_start: 0.9178 (mt0) cc_final: 0.8772 (mt0) REVERT: C 858 LEU cc_start: 0.9031 (mp) cc_final: 0.8532 (pp) REVERT: C 969 ASN cc_start: 0.9187 (p0) cc_final: 0.8498 (p0) REVERT: C 985 ASP cc_start: 0.8730 (p0) cc_final: 0.8169 (p0) REVERT: C 1002 GLN cc_start: 0.8976 (tt0) cc_final: 0.8747 (tm-30) REVERT: D 773 GLU cc_start: 0.9029 (tt0) cc_final: 0.8780 (tm-30) REVERT: D 995 ARG cc_start: 0.9460 (mmm160) cc_final: 0.9147 (ttm-80) REVERT: D 1002 GLN cc_start: 0.9459 (tt0) cc_final: 0.8693 (tm-30) REVERT: E 135 PHE cc_start: 0.7333 (m-10) cc_final: 0.6979 (m-80) REVERT: E 338 PHE cc_start: 0.8754 (m-10) cc_final: 0.8316 (m-10) REVERT: E 386 LYS cc_start: 0.9362 (mtpt) cc_final: 0.8913 (mttt) REVERT: E 388 ASN cc_start: 0.8809 (m-40) cc_final: 0.8432 (t0) REVERT: E 414 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8880 (mp10) REVERT: E 759 PHE cc_start: 0.8767 (m-80) cc_final: 0.8482 (m-80) REVERT: E 773 GLU cc_start: 0.9033 (tt0) cc_final: 0.8689 (tm-30) REVERT: E 895 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6669 (pm20) REVERT: E 902 MET cc_start: 0.9229 (tpp) cc_final: 0.8931 (mmm) REVERT: E 990 GLU cc_start: 0.9247 (tt0) cc_final: 0.8875 (pt0) REVERT: E 1029 MET cc_start: 0.9505 (tpp) cc_final: 0.9266 (tpp) REVERT: E 1050 MET cc_start: 0.8459 (ptm) cc_final: 0.8176 (ttp) REVERT: F 134 GLN cc_start: 0.8793 (mm110) cc_final: 0.8328 (mm-40) REVERT: F 759 PHE cc_start: 0.8288 (m-80) cc_final: 0.7635 (m-80) REVERT: F 780 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8617 (mt-10) REVERT: F 987 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8204 (Cg_endo) outliers start: 19 outliers final: 3 residues processed: 602 average time/residue: 0.6543 time to fit residues: 639.0129 Evaluate side-chains 261 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 256 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain D residue 564 GLN 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: 6.9990 chunk 468 optimal weight: 4.9990 chunk 259 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 484 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 360 optimal weight: 9.9990 chunk 561 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A1071 HIS B 164 ASN B 564 GLN B 856 ASN B 872 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 HIS C 907 ASN C1002 GLN C1010 GLN D 52 GLN D 658 ASN ** D 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1071 HIS E 895 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN E1071 HIS F 66 HIS F1071 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 51426 Z= 0.262 Angle : 0.581 12.355 70014 Z= 0.298 Chirality : 0.044 0.375 8298 Planarity : 0.004 0.067 8916 Dihedral : 6.621 59.878 9205 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.38 % Allowed : 6.41 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 6132 helix: 1.89 (0.14), residues: 1359 sheet: 0.62 (0.14), residues: 1335 loop : -0.59 (0.10), residues: 3438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 886 HIS 0.006 0.001 HIS C1064 PHE 0.022 0.001 PHE D 140 TYR 0.018 0.001 TYR A1067 ARG 0.009 0.001 ARG E 567 *********************** 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 330 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 255 time to evaluate : 6.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8154 (ptpt) REVERT: A 823 PHE cc_start: 0.8393 (m-80) cc_final: 0.8085 (m-10) REVERT: A 983 ARG cc_start: 0.9202 (mtp180) cc_final: 0.8806 (ttm110) REVERT: A 1005 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8445 (tm-30) REVERT: B 756 TYR cc_start: 0.8630 (m-80) cc_final: 0.8220 (m-80) REVERT: B 933 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9071 (mtmm) REVERT: C 113 LYS cc_start: 0.8157 (mttt) cc_final: 0.7796 (tptp) REVERT: C 969 ASN cc_start: 0.9055 (p0) cc_final: 0.8375 (p0) REVERT: C 988 GLU cc_start: 0.9256 (mp0) cc_final: 0.9040 (pm20) REVERT: C 1002 GLN cc_start: 0.9186 (tt0) cc_final: 0.8890 (tm-30) REVERT: D 773 GLU cc_start: 0.9105 (tt0) cc_final: 0.8801 (tm-30) REVERT: D 1002 GLN cc_start: 0.9462 (tt0) cc_final: 0.8937 (tp-100) REVERT: E 338 PHE cc_start: 0.8826 (m-10) cc_final: 0.8598 (m-10) REVERT: E 365 TYR cc_start: 0.9051 (m-80) cc_final: 0.8809 (m-80) REVERT: E 386 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8878 (mttt) REVERT: E 388 ASN cc_start: 0.8634 (m-40) cc_final: 0.7770 (t0) REVERT: E 414 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8838 (mp10) REVERT: E 740 MET cc_start: 0.9194 (tpp) cc_final: 0.8585 (tpp) REVERT: E 773 GLU cc_start: 0.9223 (tt0) cc_final: 0.8098 (tm-30) REVERT: E 777 ASN cc_start: 0.8878 (m-40) cc_final: 0.7126 (m-40) REVERT: E 895 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6791 (pm20) REVERT: E 990 GLU cc_start: 0.9306 (tt0) cc_final: 0.9035 (pt0) REVERT: E 1002 GLN cc_start: 0.8736 (tm-30) cc_final: 0.7844 (tm-30) REVERT: E 1005 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.9014 (tp-100) REVERT: E 1029 MET cc_start: 0.9501 (tpp) cc_final: 0.9096 (tpp) REVERT: E 1050 MET cc_start: 0.8427 (ptm) cc_final: 0.8110 (ptm) REVERT: F 134 GLN cc_start: 0.8834 (mm110) cc_final: 0.8315 (mm-40) REVERT: F 740 MET cc_start: 0.8805 (tpp) cc_final: 0.8138 (tpp) REVERT: F 780 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8628 (mt-10) REVERT: F 858 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8492 (pp) REVERT: F 985 ASP cc_start: 0.8209 (p0) cc_final: 0.7953 (p0) outliers start: 75 outliers final: 38 residues processed: 312 average time/residue: 0.6575 time to fit residues: 346.0231 Evaluate side-chains 236 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 5.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1005 GLN Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 973 ILE Chi-restraints excluded: chain F residue 997 ILE Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 311 optimal weight: 9.9990 chunk 174 optimal weight: 0.4980 chunk 467 optimal weight: 9.9990 chunk 382 optimal weight: 0.4980 chunk 154 optimal weight: 0.3980 chunk 562 optimal weight: 3.9990 chunk 607 optimal weight: 0.9990 chunk 500 optimal weight: 8.9990 chunk 557 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 451 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1010 GLN B 164 ASN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 HIS D 115 GLN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 895 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 919 ASN E1005 GLN E1083 HIS F 370 ASN F 751 ASN F 965 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51426 Z= 0.167 Angle : 0.515 11.285 70014 Z= 0.263 Chirality : 0.044 0.352 8298 Planarity : 0.004 0.065 8916 Dihedral : 5.878 56.875 9201 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.42 % Allowed : 7.59 % Favored : 90.99 % 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: 0.57 (0.10), residues: 6132 helix: 2.27 (0.14), residues: 1338 sheet: 0.55 (0.14), residues: 1347 loop : -0.44 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.005 0.001 HIS D1083 PHE 0.013 0.001 PHE E 135 TYR 0.019 0.001 TYR E1067 ARG 0.004 0.000 ARG F 319 *********************** 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 292 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 215 time to evaluate : 6.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ILE cc_start: 0.9155 (pt) cc_final: 0.8804 (mm) REVERT: A 558 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8272 (ptpt) REVERT: A 823 PHE cc_start: 0.8353 (m-80) cc_final: 0.8055 (m-10) REVERT: A 983 ARG cc_start: 0.9205 (mtp180) cc_final: 0.8901 (ttm110) REVERT: A 995 ARG cc_start: 0.9300 (mmm160) cc_final: 0.9073 (mtm-85) REVERT: A 1005 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 240 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8646 (t) REVERT: B 756 TYR cc_start: 0.8772 (m-80) cc_final: 0.8271 (m-80) REVERT: B 933 LYS cc_start: 0.9355 (mtmt) cc_final: 0.8984 (mtmm) REVERT: B 988 GLU cc_start: 0.9230 (mp0) cc_final: 0.8892 (mp0) REVERT: C 113 LYS cc_start: 0.8154 (mttt) cc_final: 0.7751 (tptp) REVERT: C 755 GLN cc_start: 0.9302 (mm-40) cc_final: 0.9030 (mp10) REVERT: C 779 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8421 (tp-100) REVERT: C 907 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8551 (m110) REVERT: C 969 ASN cc_start: 0.9019 (p0) cc_final: 0.8334 (p0) REVERT: C 1002 GLN cc_start: 0.9239 (tt0) cc_final: 0.8863 (tm-30) REVERT: C 1050 MET cc_start: 0.8618 (ptm) cc_final: 0.8365 (ptm) REVERT: D 900 MET cc_start: 0.8735 (mtp) cc_final: 0.8378 (ptp) REVERT: D 985 ASP cc_start: 0.9005 (t0) cc_final: 0.8735 (t0) REVERT: D 995 ARG cc_start: 0.9400 (mmm160) cc_final: 0.9121 (ttm110) REVERT: D 1002 GLN cc_start: 0.9424 (tt0) cc_final: 0.8900 (tp-100) REVERT: D 1005 GLN cc_start: 0.9525 (tp40) cc_final: 0.9279 (tp40) REVERT: D 1050 MET cc_start: 0.8334 (ppp) cc_final: 0.8058 (ppp) REVERT: E 365 TYR cc_start: 0.9134 (m-80) cc_final: 0.8893 (m-80) REVERT: E 388 ASN cc_start: 0.8580 (m-40) cc_final: 0.8284 (t0) REVERT: E 414 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8715 (tp-100) REVERT: E 740 MET cc_start: 0.9266 (tpp) cc_final: 0.8623 (tpp) REVERT: E 773 GLU cc_start: 0.9197 (tt0) cc_final: 0.8616 (tm-30) REVERT: E 895 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: E 990 GLU cc_start: 0.9271 (tt0) cc_final: 0.9015 (pt0) REVERT: E 1029 MET cc_start: 0.9518 (tpp) cc_final: 0.9161 (tpp) REVERT: E 1050 MET cc_start: 0.8436 (ptm) cc_final: 0.7911 (ttp) REVERT: F 134 GLN cc_start: 0.8864 (mm110) cc_final: 0.8334 (mm-40) REVERT: F 697 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (ttp) REVERT: F 759 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8485 (t80) REVERT: F 858 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8441 (pp) REVERT: F 979 ASP cc_start: 0.7526 (m-30) cc_final: 0.7234 (p0) REVERT: F 985 ASP cc_start: 0.8213 (p0) cc_final: 0.7853 (p0) outliers start: 77 outliers final: 47 residues processed: 272 average time/residue: 0.6141 time to fit residues: 284.2871 Evaluate side-chains 245 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 191 time to evaluate : 5.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 697 MET Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 973 ILE 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: 10.0000 chunk 422 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 564 optimal weight: 2.9990 chunk 597 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 534 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 856 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN F 409 GLN F 856 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 51426 Z= 0.189 Angle : 0.510 14.446 70014 Z= 0.260 Chirality : 0.043 0.333 8298 Planarity : 0.004 0.070 8916 Dihedral : 5.406 54.391 9201 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.71 % Allowed : 8.07 % Favored : 90.22 % 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: 0.66 (0.10), residues: 6132 helix: 2.38 (0.14), residues: 1341 sheet: 0.46 (0.14), residues: 1374 loop : -0.33 (0.10), residues: 3417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.004 0.001 HIS D1083 PHE 0.023 0.001 PHE D 338 TYR 0.019 0.001 TYR E1067 ARG 0.010 0.000 ARG E 319 *********************** 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 286 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 193 time to evaluate : 6.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8942 (mtt90) cc_final: 0.8455 (mmt180) REVERT: A 699 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8820 (mt) REVERT: A 823 PHE cc_start: 0.8440 (m-80) cc_final: 0.8123 (m-10) REVERT: A 983 ARG cc_start: 0.9206 (mtp180) cc_final: 0.8845 (ttm110) REVERT: A 995 ARG cc_start: 0.9273 (mmm160) cc_final: 0.9042 (mtm-85) REVERT: A 1005 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 1029 MET cc_start: 0.9390 (tpp) cc_final: 0.8512 (tpt) REVERT: B 113 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8690 (pttm) REVERT: B 238 PHE cc_start: 0.8502 (p90) cc_final: 0.8248 (p90) REVERT: B 240 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8736 (t) REVERT: B 933 LYS cc_start: 0.9380 (mtmt) cc_final: 0.9025 (mtmm) REVERT: B 988 GLU cc_start: 0.9227 (mp0) cc_final: 0.8886 (mp0) REVERT: C 755 GLN cc_start: 0.9308 (mm-40) cc_final: 0.9045 (mp10) REVERT: C 779 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8326 (tp-100) REVERT: C 907 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8000 (m110) REVERT: C 913 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: C 969 ASN cc_start: 0.8967 (p0) cc_final: 0.8262 (p0) REVERT: C 1002 GLN cc_start: 0.9263 (tt0) cc_final: 0.8874 (tm-30) REVERT: C 1050 MET cc_start: 0.8593 (ptm) cc_final: 0.8350 (ptm) REVERT: D 985 ASP cc_start: 0.9074 (t0) cc_final: 0.8778 (t0) REVERT: D 995 ARG cc_start: 0.9407 (mmm160) cc_final: 0.9118 (ttm110) REVERT: D 1002 GLN cc_start: 0.9434 (tt0) cc_final: 0.8808 (tm-30) REVERT: D 1005 GLN cc_start: 0.9535 (tp40) cc_final: 0.9294 (tp40) REVERT: E 240 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8583 (t) REVERT: E 414 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8643 (tp-100) REVERT: E 740 MET cc_start: 0.9303 (tpp) cc_final: 0.8665 (tpp) REVERT: E 773 GLU cc_start: 0.9247 (tt0) cc_final: 0.8870 (tt0) REVERT: E 895 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7021 (pm20) REVERT: E 990 GLU cc_start: 0.9249 (tt0) cc_final: 0.9001 (pt0) REVERT: F 134 GLN cc_start: 0.8906 (mm110) cc_final: 0.8359 (mm-40) REVERT: F 406 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: F 740 MET cc_start: 0.8884 (tpp) cc_final: 0.8463 (tpp) REVERT: F 759 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8486 (t80) REVERT: F 858 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8532 (pp) outliers start: 93 outliers final: 57 residues processed: 264 average time/residue: 0.6180 time to fit residues: 278.9508 Evaluate side-chains 241 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 174 time to evaluate : 6.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 973 ILE Chi-restraints excluded: chain F residue 997 ILE Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 497 optimal weight: 7.9990 chunk 339 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 444 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 509 optimal weight: 7.9990 chunk 412 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 536 optimal weight: 20.0000 chunk 150 optimal weight: 0.1980 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 69 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 804 GLN A 824 ASN A 935 GLN B 121 ASN B 164 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1135 ASN C 317 ASN C 779 GLN C 856 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1135 ASN E 49 HIS E 317 ASN E 498 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 121 ASN ** F 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN F 542 ASN ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN F 926 GLN F 957 GLN F1011 GLN ** F1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 51426 Z= 0.571 Angle : 0.817 13.952 70014 Z= 0.417 Chirality : 0.048 0.322 8298 Planarity : 0.005 0.076 8916 Dihedral : 6.587 57.358 9195 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.14 % Allowed : 9.04 % Favored : 88.82 % 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: -0.07 (0.10), residues: 6132 helix: 1.55 (0.14), residues: 1350 sheet: 0.02 (0.14), residues: 1248 loop : -0.69 (0.10), residues: 3534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 886 HIS 0.010 0.002 HIS F1064 PHE 0.041 0.003 PHE E 377 TYR 0.027 0.003 TYR A 38 ARG 0.010 0.001 ARG F 78 *********************** 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 274 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 158 time to evaluate : 6.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8918 (mt) REVERT: A 983 ARG cc_start: 0.9304 (mtp180) cc_final: 0.8963 (ttp-110) REVERT: A 1005 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8579 (tm-30) REVERT: B 933 LYS cc_start: 0.9466 (mtmt) cc_final: 0.9241 (mtmm) REVERT: D 985 ASP cc_start: 0.9177 (t0) cc_final: 0.8896 (t0) REVERT: D 1002 GLN cc_start: 0.9545 (tt0) cc_final: 0.8913 (tm-30) REVERT: D 1050 MET cc_start: 0.8517 (ppp) cc_final: 0.8311 (ppp) REVERT: E 240 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8601 (t) REVERT: E 414 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8414 (tp-100) REVERT: E 740 MET cc_start: 0.9425 (tpp) cc_final: 0.8842 (tpp) REVERT: E 895 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: E 990 GLU cc_start: 0.9311 (tt0) cc_final: 0.9032 (pt0) REVERT: F 697 MET cc_start: 0.8877 (ttp) cc_final: 0.8606 (ttp) REVERT: F 858 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8813 (pp) outliers start: 116 outliers final: 73 residues processed: 257 average time/residue: 0.5829 time to fit residues: 261.1274 Evaluate side-chains 211 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 134 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 896 ILE Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 959 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 973 ILE Chi-restraints excluded: chain F residue 997 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 200 optimal weight: 2.9990 chunk 537 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 350 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 597 optimal weight: 0.7980 chunk 496 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 313 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 762 GLN A 804 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 856 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 856 ASN ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 907 ASN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1005 GLN F 14 GLN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN F1083 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 51426 Z= 0.151 Angle : 0.534 12.279 70014 Z= 0.270 Chirality : 0.044 0.309 8298 Planarity : 0.004 0.058 8916 Dihedral : 5.605 54.755 9195 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.33 % Allowed : 10.48 % Favored : 88.20 % 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: 0.40 (0.10), residues: 6132 helix: 2.21 (0.14), residues: 1332 sheet: 0.16 (0.13), residues: 1371 loop : -0.45 (0.10), residues: 3429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 886 HIS 0.002 0.001 HIS E1048 PHE 0.018 0.001 PHE D 338 TYR 0.019 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 245 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 173 time to evaluate : 6.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8915 (mtt90) cc_final: 0.8384 (mpt90) REVERT: A 298 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 699 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8800 (mt) REVERT: A 983 ARG cc_start: 0.9194 (mtp180) cc_final: 0.8895 (ttp-110) REVERT: A 1005 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8570 (tm-30) REVERT: B 238 PHE cc_start: 0.8628 (p90) cc_final: 0.8370 (p90) REVERT: D 869 MET cc_start: 0.8882 (mtp) cc_final: 0.8549 (mtp) REVERT: D 985 ASP cc_start: 0.9022 (t0) cc_final: 0.8729 (t0) REVERT: D 1002 GLN cc_start: 0.9509 (tt0) cc_final: 0.8859 (tm-30) REVERT: E 240 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8646 (t) REVERT: E 414 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8230 (tp-100) REVERT: E 740 MET cc_start: 0.9382 (tpp) cc_final: 0.8673 (tpp) REVERT: E 895 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: E 990 GLU cc_start: 0.9238 (tt0) cc_final: 0.8951 (pt0) REVERT: F 697 MET cc_start: 0.8860 (ttp) cc_final: 0.8651 (ttp) REVERT: F 995 ARG cc_start: 0.9170 (mmm160) cc_final: 0.8864 (ttm-80) outliers start: 72 outliers final: 52 residues processed: 230 average time/residue: 0.6033 time to fit residues: 240.2576 Evaluate side-chains 206 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 151 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 959 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 973 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 576 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 436 optimal weight: 9.9990 chunk 338 optimal weight: 5.9990 chunk 503 optimal weight: 0.8980 chunk 333 optimal weight: 8.9990 chunk 595 optimal weight: 4.9990 chunk 372 optimal weight: 4.9990 chunk 363 optimal weight: 0.8980 chunk 275 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN D 907 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN F 926 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 51426 Z= 0.239 Angle : 0.544 12.161 70014 Z= 0.275 Chirality : 0.044 0.302 8298 Planarity : 0.004 0.057 8916 Dihedral : 5.409 54.705 9195 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.53 % Allowed : 10.63 % Favored : 87.85 % 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: 0.41 (0.10), residues: 6132 helix: 2.27 (0.14), residues: 1335 sheet: 0.12 (0.14), residues: 1248 loop : -0.42 (0.10), residues: 3549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 886 HIS 0.004 0.001 HIS C1064 PHE 0.015 0.001 PHE D 338 TYR 0.024 0.001 TYR B 365 ARG 0.006 0.000 ARG E 319 *********************** 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 233 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 150 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8887 (mtt90) cc_final: 0.8382 (mpt90) REVERT: A 298 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 699 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8831 (mt) REVERT: A 983 ARG cc_start: 0.9205 (mtp180) cc_final: 0.8945 (ttm-80) REVERT: A 1005 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8547 (tm-30) REVERT: B 584 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9166 (mm) REVERT: C 1050 MET cc_start: 0.8585 (ptm) cc_final: 0.8306 (ptm) REVERT: D 985 ASP cc_start: 0.9062 (t0) cc_final: 0.8783 (t0) REVERT: D 1002 GLN cc_start: 0.9502 (tt0) cc_final: 0.8862 (tm-30) REVERT: E 240 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8654 (t) REVERT: E 414 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8292 (tp-100) REVERT: E 495 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: E 740 MET cc_start: 0.9379 (tpp) cc_final: 0.8677 (tpp) REVERT: E 895 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.6925 (pm20) REVERT: E 990 GLU cc_start: 0.9251 (tt0) cc_final: 0.8970 (pt0) REVERT: F 995 ARG cc_start: 0.9173 (mmm160) cc_final: 0.8819 (ttm-80) outliers start: 83 outliers final: 68 residues processed: 218 average time/residue: 0.6153 time to fit residues: 231.5478 Evaluate side-chains 221 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 148 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 959 LEU Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 896 ILE Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 973 ILE Chi-restraints excluded: chain F residue 997 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 368 optimal weight: 1.9990 chunk 237 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 378 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 chunk 294 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 468 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN D 907 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN F1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 51426 Z= 0.167 Angle : 0.515 13.041 70014 Z= 0.258 Chirality : 0.044 0.302 8298 Planarity : 0.004 0.056 8916 Dihedral : 5.039 54.467 9195 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.36 % Allowed : 10.83 % Favored : 87.81 % 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: 0.50 (0.11), residues: 6132 helix: 2.43 (0.14), residues: 1329 sheet: 0.09 (0.14), residues: 1290 loop : -0.38 (0.10), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 886 HIS 0.003 0.000 HIS C1064 PHE 0.013 0.001 PHE D 338 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG E 319 *********************** 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 244 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 170 time to evaluate : 5.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.8944 (mtt90) cc_final: 0.8386 (mpt90) REVERT: A 298 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8500 (tm-30) REVERT: A 699 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8687 (mt) REVERT: A 983 ARG cc_start: 0.9177 (mtp180) cc_final: 0.8921 (ttm-80) REVERT: A 995 ARG cc_start: 0.9291 (mmm160) cc_final: 0.9037 (mtm-85) REVERT: A 1005 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8590 (tm-30) REVERT: B 238 PHE cc_start: 0.8658 (p90) cc_final: 0.8344 (p90) REVERT: B 968 SER cc_start: 0.9496 (m) cc_final: 0.9202 (p) REVERT: C 356 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.8997 (tptp) REVERT: D 869 MET cc_start: 0.8796 (mtp) cc_final: 0.8425 (mtm) REVERT: D 995 ARG cc_start: 0.9388 (mmm160) cc_final: 0.9030 (ttm110) REVERT: D 1002 GLN cc_start: 0.9477 (tt0) cc_final: 0.8846 (tm-30) REVERT: E 240 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8641 (t) REVERT: E 414 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8268 (tp-100) REVERT: E 740 MET cc_start: 0.9364 (tpp) cc_final: 0.8798 (tpp) REVERT: E 895 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: E 990 GLU cc_start: 0.9224 (tt0) cc_final: 0.8966 (pt0) REVERT: F 970 PHE cc_start: 0.8846 (m-80) cc_final: 0.8305 (m-80) REVERT: F 977 LEU cc_start: 0.8152 (pt) cc_final: 0.7789 (tt) REVERT: F 985 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8529 (t0) REVERT: F 990 GLU cc_start: 0.8119 (pp20) cc_final: 0.7844 (pp20) REVERT: F 995 ARG cc_start: 0.9147 (mmm160) cc_final: 0.8836 (ttm-80) outliers start: 74 outliers final: 58 residues processed: 228 average time/residue: 0.6164 time to fit residues: 243.1697 Evaluate side-chains 224 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 5.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 959 LEU Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 973 ILE Chi-restraints excluded: chain F residue 985 ASP Chi-restraints excluded: chain F residue 1142 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 541 optimal weight: 3.9990 chunk 570 optimal weight: 6.9990 chunk 520 optimal weight: 10.0000 chunk 555 optimal weight: 1.9990 chunk 334 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 435 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 501 optimal weight: 2.9990 chunk 524 optimal weight: 3.9990 chunk 553 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN D 907 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 856 ASN F 926 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 51426 Z= 0.315 Angle : 0.595 15.257 70014 Z= 0.299 Chirality : 0.044 0.295 8298 Planarity : 0.004 0.081 8916 Dihedral : 5.314 55.292 9195 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.62 % Allowed : 10.87 % Favored : 87.51 % 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: 0.40 (0.11), residues: 6132 helix: 2.26 (0.14), residues: 1335 sheet: 0.12 (0.14), residues: 1215 loop : -0.44 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 886 HIS 0.005 0.001 HIS F1064 PHE 0.018 0.001 PHE E 377 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG F 78 *********************** 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 240 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 152 time to evaluate : 6.042 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: A 298 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8530 (tm-30) REVERT: A 460 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8265 (t0) REVERT: A 983 ARG cc_start: 0.9239 (mtp180) cc_final: 0.8925 (ttm-80) REVERT: A 995 ARG cc_start: 0.9312 (mmm160) cc_final: 0.8921 (mtm-85) REVERT: A 1005 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8732 (tm-30) REVERT: B 584 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9142 (mm) REVERT: B 968 SER cc_start: 0.9517 (m) cc_final: 0.9228 (p) REVERT: B 984 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7294 (tp) REVERT: C 356 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.8978 (tptp) REVERT: D 985 ASP cc_start: 0.9078 (t0) cc_final: 0.8805 (t0) REVERT: D 995 ARG cc_start: 0.9378 (mmm160) cc_final: 0.9114 (ttm-80) REVERT: D 1002 GLN cc_start: 0.9493 (tt0) cc_final: 0.8872 (tm-30) REVERT: E 240 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8628 (t) REVERT: E 495 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: E 740 MET cc_start: 0.9386 (tpp) cc_final: 0.8835 (tpp) REVERT: E 990 GLU cc_start: 0.9258 (tt0) cc_final: 0.9014 (pt0) REVERT: F 977 LEU cc_start: 0.8196 (pt) cc_final: 0.7845 (tt) REVERT: F 995 ARG cc_start: 0.9189 (mmm160) cc_final: 0.8913 (ttm-80) outliers start: 88 outliers final: 71 residues processed: 221 average time/residue: 0.6283 time to fit residues: 242.3854 Evaluate side-chains 225 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 148 time to evaluate : 5.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 959 LEU Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 973 ILE Chi-restraints excluded: chain F residue 997 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 364 optimal weight: 0.9980 chunk 586 optimal weight: 0.5980 chunk 358 optimal weight: 5.9990 chunk 278 optimal weight: 0.9990 chunk 408 optimal weight: 6.9990 chunk 615 optimal weight: 0.0030 chunk 566 optimal weight: 10.0000 chunk 490 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 378 optimal weight: 1.9990 chunk 300 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 51426 Z= 0.266 Angle : 0.655 59.191 70014 Z= 0.347 Chirality : 0.043 0.352 8298 Planarity : 0.004 0.079 8916 Dihedral : 5.294 55.287 9192 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.36 % Allowed : 11.31 % Favored : 87.33 % 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: 0.39 (0.11), residues: 6132 helix: 2.28 (0.14), residues: 1335 sheet: 0.11 (0.14), residues: 1215 loop : -0.45 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 64 HIS 0.004 0.001 HIS F1064 PHE 0.041 0.001 PHE C1052 TYR 0.018 0.001 TYR F 453 ARG 0.011 0.000 ARG F 319 ********************** 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 222 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 148 time to evaluate : 5.815 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: A 298 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8513 (tm-30) REVERT: A 460 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8263 (t0) REVERT: A 983 ARG cc_start: 0.9258 (mtp180) cc_final: 0.8970 (ttm-80) REVERT: A 995 ARG cc_start: 0.9308 (mmm160) cc_final: 0.8915 (mtm-85) REVERT: A 1005 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8721 (tm-30) REVERT: B 584 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9139 (mm) REVERT: B 968 SER cc_start: 0.9513 (m) cc_final: 0.9223 (p) REVERT: B 984 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7292 (tp) REVERT: C 356 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.8980 (tptp) REVERT: D 985 ASP cc_start: 0.9076 (t0) cc_final: 0.8803 (t0) REVERT: D 995 ARG cc_start: 0.9376 (mmm160) cc_final: 0.9111 (ttm-80) REVERT: D 1002 GLN cc_start: 0.9490 (tt0) cc_final: 0.8863 (tm-30) REVERT: E 240 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8625 (t) REVERT: E 495 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6165 (m-80) REVERT: E 740 MET cc_start: 0.9382 (tpp) cc_final: 0.8830 (tpp) REVERT: E 895 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: E 990 GLU cc_start: 0.9253 (tt0) cc_final: 0.9010 (pt0) REVERT: F 977 LEU cc_start: 0.8189 (pt) cc_final: 0.7837 (tt) REVERT: F 995 ARG cc_start: 0.9192 (mmm160) cc_final: 0.8923 (ttm-80) outliers start: 74 outliers final: 65 residues processed: 206 average time/residue: 0.5919 time to fit residues: 212.5319 Evaluate side-chains 220 residues out of total 5454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 148 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 481 ASN Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain D residue 1084 ASP Chi-restraints excluded: chain D residue 1125 ASN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 770 ILE Chi-restraints excluded: chain E residue 895 GLN Chi-restraints excluded: chain E residue 916 LEU Chi-restraints excluded: chain E residue 934 ILE Chi-restraints excluded: chain E residue 959 LEU Chi-restraints excluded: chain E residue 981 LEU Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1050 MET Chi-restraints excluded: chain E residue 1145 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 515 PHE Chi-restraints excluded: chain F residue 724 THR Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 759 PHE Chi-restraints excluded: chain F residue 923 ILE Chi-restraints excluded: chain F residue 936 ASP Chi-restraints excluded: chain F residue 938 LEU Chi-restraints excluded: chain F residue 973 ILE Chi-restraints excluded: chain F residue 997 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 618 random chunks: chunk 389 optimal weight: 2.9990 chunk 522 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 452 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 136 optimal weight: 3.9990 chunk 491 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 504 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN A 935 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.058290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041411 restraints weight = 275930.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.042841 restraints weight = 130602.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.043753 restraints weight = 81865.534| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 51426 Z= 0.266 Angle : 0.655 59.191 70014 Z= 0.347 Chirality : 0.043 0.352 8298 Planarity : 0.004 0.079 8916 Dihedral : 5.294 55.287 9192 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 11.33 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.11), residues: 6132 helix: 2.28 (0.14), residues: 1335 sheet: 0.11 (0.14), residues: 1215 loop : -0.45 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 64 HIS 0.004 0.001 HIS F1064 PHE 0.041 0.001 PHE C1052 TYR 0.018 0.001 TYR F 453 ARG 0.011 0.000 ARG F 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8099.88 seconds wall clock time: 152 minutes 32.72 seconds (9152.72 seconds total)