Starting phenix.real_space_refine on Sun Mar 24 01:30:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9b_35264/03_2024/8i9b_35264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9b_35264/03_2024/8i9b_35264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9b_35264/03_2024/8i9b_35264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9b_35264/03_2024/8i9b_35264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9b_35264/03_2024/8i9b_35264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9b_35264/03_2024/8i9b_35264.pdb" } resolution = 3.5 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= 0.006 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 195 5.16 5 C 25211 2.51 5 N 6425 2.21 5 O 7708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F ARG 245": "NH1" <-> "NH2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 398": "OE1" <-> "OE2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F GLU 435": "OE1" <-> "OE2" Residue "F GLU 479": "OE1" <-> "OE2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "F GLU 536": "OE1" <-> "OE2" Residue "F GLU 564": "OE1" <-> "OE2" Residue "F GLU 571": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D GLU 571": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 398": "OE1" <-> "OE2" Residue "E GLU 430": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "E GLU 479": "OE1" <-> "OE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E GLU 536": "OE1" <-> "OE2" Residue "E GLU 564": "OE1" <-> "OE2" Residue "E GLU 571": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39539 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 7833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7833 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7827 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7827 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "F" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "E" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} 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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.75, per 1000 atoms: 0.50 Number of scatterers: 39539 At special positions: 0 Unit cell: (184.79, 198.921, 246.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 195 16.00 O 7708 8.00 N 6425 7.00 C 25211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.08 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.06 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.06 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.37 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.06 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.06 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.06 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " 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 q 1 " - " NAG q 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A 801 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 701 " - " ASN D 322 " " NAG E 701 " - " ASN E 322 " " NAG F 701 " - " ASN F 322 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 343 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN F 53 " " NAG d 1 " - " ASN F 90 " " NAG e 1 " - " ASN F 103 " " NAG f 1 " - " ASN F 432 " " NAG g 1 " - " ASN F 546 " " NAG h 1 " - " ASN D 53 " " NAG i 1 " - " ASN D 90 " " NAG j 1 " - " ASN D 103 " " NAG k 1 " - " ASN D 432 " " NAG l 1 " - " ASN D 546 " " NAG m 1 " - " ASN E 53 " " NAG n 1 " - " ASN E 90 " " NAG o 1 " - " ASN E 103 " " NAG p 1 " - " ASN E 432 " " NAG q 1 " - " ASN E 546 " Time building additional restraints: 15.46 Conformation dependent library (CDL) restraints added in 6.4 seconds 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9014 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 54 sheets defined 40.0% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.216A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.431A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.709A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.706A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.613A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.589A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.773A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.627A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.631A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.215A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.673A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.709A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.706A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.613A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 4.269A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.215A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.673A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.708A pdb=" N GLU C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.706A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.613A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.559A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.700A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.591A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.358A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.740A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 981' Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'F' and resid 22 through 53 removed outlier: 3.613A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.737A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.884A pdb=" N GLN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 removed outlier: 3.940A pdb=" N ALA F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.672A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.738A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 220 through 252 removed outlier: 3.758A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS F 234 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.670A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 300 Processing helix chain 'F' and resid 303 through 318 removed outlier: 3.797A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.502A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 385 removed outlier: 3.817A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.580A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.702A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.505A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.600A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 3.856A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.779A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.612A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.613A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.737A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.885A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.939A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.672A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.737A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.758A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.670A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.729A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.796A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.503A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 3.816A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.579A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.702A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.505A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.600A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.856A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.779A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.612A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 22 through 53 removed outlier: 3.613A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.736A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.884A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 147 through 155 removed outlier: 3.940A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.672A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.737A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 220 through 252 removed outlier: 3.759A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS E 234 " --> pdb=" O PHE E 230 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.670A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.729A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 300 Processing helix chain 'E' and resid 303 through 318 removed outlier: 3.796A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.502A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.817A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.579A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 412 removed outlier: 3.701A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.505A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.600A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.856A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.778A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.612A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.729A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.849A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.890A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.892A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.207A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.658A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.891A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 448 through 454 removed outlier: 5.892A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.557A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.890A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.891A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 664 through 665 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AF2, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.914A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.140A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AF5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.914A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.139A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AF8, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.914A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.139A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1613 hydrogen bonds defined for protein. 4545 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: 15.41 Time building geometry restraints manager: 16.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12439 1.34 - 1.47: 10848 1.47 - 1.60: 16927 1.60 - 1.74: 0 1.74 - 1.87: 285 Bond restraints: 40499 Sorted by residual: bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.068 1.59e-02 3.96e+03 1.80e+01 bond pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" N PRO A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.62e+01 bond pdb=" N PRO B 217 " pdb=" CD PRO B 217 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.59e+01 ... (remaining 40494 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.72: 859 105.72 - 113.94: 23404 113.94 - 122.16: 23704 122.16 - 130.38: 6893 130.38 - 138.59: 196 Bond angle restraints: 55056 Sorted by residual: angle pdb=" N LYS C 529 " pdb=" CA LYS C 529 " pdb=" C LYS C 529 " ideal model delta sigma weight residual 108.24 119.72 -11.48 1.32e+00 5.74e-01 7.56e+01 angle pdb=" N LEU A 157 " pdb=" CA LEU A 157 " pdb=" C LEU A 157 " ideal model delta sigma weight residual 111.74 123.23 -11.49 1.35e+00 5.49e-01 7.24e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 111.74 123.19 -11.45 1.35e+00 5.49e-01 7.19e+01 angle pdb=" N LEU C 157 " pdb=" CA LEU C 157 " pdb=" C LEU C 157 " ideal model delta sigma weight residual 111.74 123.18 -11.44 1.35e+00 5.49e-01 7.18e+01 angle pdb=" N THR C 531 " pdb=" CA THR C 531 " pdb=" C THR C 531 " ideal model delta sigma weight residual 107.88 118.85 -10.97 1.41e+00 5.03e-01 6.05e+01 ... (remaining 55051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 21836 17.94 - 35.87: 2450 35.87 - 53.81: 816 53.81 - 71.75: 224 71.75 - 89.69: 58 Dihedral angle restraints: 25384 sinusoidal: 11395 harmonic: 13989 Sorted by residual: dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.04 71.96 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 25381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 6340 0.338 - 0.675: 4 0.675 - 1.012: 2 1.012 - 1.350: 0 1.350 - 1.687: 2 Chirality restraints: 6348 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.94e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.21e+02 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.12e+01 ... (remaining 6345 not shown) Planarity restraints: 7040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.131 2.00e-02 2.50e+03 2.03e-01 5.15e+02 pdb=" CG ASN A 801 " -0.064 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG A1410 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.130 2.00e-02 2.50e+03 1.49e-01 2.78e+02 pdb=" CG ASN C 331 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.242 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.088 2.00e-02 2.50e+03 9.53e-02 1.14e+02 pdb=" CG ASN A 331 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.150 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.116 2.00e-02 2.50e+03 ... (remaining 7037 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 305 2.50 - 3.10: 27652 3.10 - 3.70: 56165 3.70 - 4.30: 86447 4.30 - 4.90: 143479 Nonbonded interactions: 314048 Sorted by model distance: nonbonded pdb=" O GLN A 690 " pdb=" OG SER A 691 " model vdw 1.899 2.440 nonbonded pdb=" O GLY B 799 " pdb=" O PHE B 800 " model vdw 2.107 3.040 nonbonded pdb=" N GLU B 748 " pdb=" OE1 GLU B 748 " model vdw 2.141 2.520 nonbonded pdb=" O PHE B 375 " pdb=" O ALA B 376 " model vdw 2.145 3.040 nonbonded pdb=" O GLY A 700 " pdb=" O ALA A 701 " model vdw 2.167 3.040 ... (remaining 314043 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' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } 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: 0.010 Normalize map: mean=0, sd=1: 1.390 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: 0.030 Extract box with map and model: 7.210 Check model and map are aligned: 0.600 Set scattering table: 0.360 Process input model: 98.270 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.780 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3708 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 : 0.009 0.117 40499 Z= 0.569 Angle : 0.932 13.594 55056 Z= 0.540 Chirality : 0.067 1.687 6348 Planarity : 0.006 0.091 6974 Dihedral : 17.466 89.687 16244 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 1.76 % Allowed : 8.16 % Favored : 90.08 % Rotamer: Outliers : 9.83 % Allowed : 18.06 % Favored : 72.11 % 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: -3.51 (0.10), residues: 4720 helix: -1.42 (0.11), residues: 1652 sheet: -2.00 (0.17), residues: 757 loop : -3.19 (0.10), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 104 HIS 0.010 0.001 HIS A1048 PHE 0.025 0.002 PHE A 898 TYR 0.027 0.002 TYR B1067 ARG 0.008 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 608 time to evaluate : 4.359 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: A 216 LEU cc_start: -0.0118 (OUTLIER) cc_final: -0.0445 (mp) REVERT: A 660 TYR cc_start: 0.0657 (OUTLIER) cc_final: 0.0454 (p90) REVERT: B 615 VAL cc_start: 0.6257 (t) cc_final: 0.5851 (t) REVERT: C 122 ASN cc_start: -0.1410 (OUTLIER) cc_final: -0.1615 (t0) REVERT: C 164 ASN cc_start: 0.0509 (OUTLIER) cc_final: 0.0137 (p0) REVERT: C 216 LEU cc_start: 0.4162 (OUTLIER) cc_final: 0.3791 (pt) REVERT: E 474 MET cc_start: -0.1809 (mmp) cc_final: -0.2530 (tpp) outliers start: 414 outliers final: 63 residues processed: 963 average time/residue: 0.4787 time to fit residues: 760.2964 Evaluate side-chains 375 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 307 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain B residue 217 PRO Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 217 PRO Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 353 LYS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 548 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 6.9990 chunk 359 optimal weight: 50.0000 chunk 199 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 371 optimal weight: 50.0000 chunk 143 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 chunk 276 optimal weight: 0.9990 chunk 430 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 196 ASN A 239 GLN A 317 ASN A 339 HIS A 360 ASN A 422 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 641 ASN A 644 GLN A 658 ASN A 762 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 914 ASN A 919 ASN A 955 ASN A 957 GLN A 992 GLN A1005 GLN A1101 HIS B 134 GLN B 137 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 HIS B 360 ASN B 422 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 644 GLN B 658 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 914 ASN B 919 ASN B 992 GLN B1054 GLN B1119 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 188 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 422 ASN C 658 ASN C 703 ASN C 751 ASN C 804 GLN C 901 GLN C 914 ASN C 919 ASN C 926 GLN C 954 HIS C 965 GLN C 992 GLN C1002 GLN C1010 GLN C1071 GLN C1101 HIS C1142 GLN F 42 GLN F 49 ASN F 58 ASN F 63 ASN F 102 GLN F 117 ASN F 121 ASN F 137 ASN F 210 ASN F 374 HIS F 437 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS F 522 GLN D 34 HIS D 42 GLN D 51 ASN D 58 ASN D 63 ASN D 102 GLN D 117 ASN D 121 ASN D 210 ASN D 305 GLN D 374 HIS D 437 ASN D 505 HIS D 522 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 51 ASN E 58 ASN E 102 GLN E 117 ASN E 121 ASN E 137 ASN E 210 ASN E 437 ASN E 472 GLN Total number of N/Q/H flips: 96 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4264 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 40499 Z= 0.305 Angle : 0.818 12.330 55056 Z= 0.410 Chirality : 0.051 0.706 6348 Planarity : 0.006 0.074 6974 Dihedral : 9.011 69.822 7413 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.14 % Rotamer: Outliers : 5.10 % Allowed : 21.50 % Favored : 73.39 % Cbeta Deviations : 0.02 % 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: -2.21 (0.11), residues: 4720 helix: -0.13 (0.12), residues: 1728 sheet: -1.28 (0.18), residues: 712 loop : -2.67 (0.11), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1102 HIS 0.013 0.001 HIS C 954 PHE 0.043 0.002 PHE B 374 TYR 0.035 0.002 TYR A1067 ARG 0.008 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 307 time to evaluate : 4.079 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 371 PHE cc_start: -0.1592 (OUTLIER) cc_final: -0.2905 (m-80) REVERT: A 765 ARG cc_start: 0.7338 (tpp80) cc_final: 0.7059 (tpp-160) REVERT: B 692 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5828 (tp) REVERT: C 563 GLN cc_start: 0.3605 (mm110) cc_final: 0.3041 (mm-40) REVERT: F 383 MET cc_start: 0.3021 (mtp) cc_final: 0.2293 (mtt) REVERT: D 62 MET cc_start: 0.1858 (tpt) cc_final: 0.1130 (tpt) REVERT: D 297 MET cc_start: -0.0266 (ttm) cc_final: -0.0598 (ttm) REVERT: E 332 MET cc_start: -0.0841 (ttt) cc_final: -0.1862 (ppp) REVERT: E 474 MET cc_start: -0.1334 (mmp) cc_final: -0.2115 (tpp) outliers start: 215 outliers final: 108 residues processed: 493 average time/residue: 0.4594 time to fit residues: 389.1716 Evaluate side-chains 349 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 239 time to evaluate : 4.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 417 ASN Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 596 LYS Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 50.0000 chunk 133 optimal weight: 50.0000 chunk 358 optimal weight: 50.0000 chunk 293 optimal weight: 0.3980 chunk 118 optimal weight: 1.9990 chunk 431 optimal weight: 50.0000 chunk 465 optimal weight: 50.0000 chunk 384 optimal weight: 50.0000 chunk 427 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 345 optimal weight: 50.0000 overall best weight: 11.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 334 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 965 GLN B 115 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 493 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** B 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS B1101 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 188 ASN C 239 GLN C 317 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 613 GLN C 641 ASN C 675 GLN C 804 GLN C 914 ASN C 935 GLN C1036 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN F 49 ASN F 51 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN D 508 ASN E 34 HIS E 374 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.252 40499 Z= 0.727 Angle : 1.179 18.239 55056 Z= 0.602 Chirality : 0.066 1.255 6348 Planarity : 0.008 0.092 6974 Dihedral : 9.236 59.983 7333 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.58 % Favored : 90.00 % Rotamer: Outliers : 8.40 % Allowed : 20.98 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.11), residues: 4720 helix: -0.75 (0.12), residues: 1708 sheet: -1.81 (0.18), residues: 708 loop : -2.83 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 64 HIS 0.019 0.002 HIS C1083 PHE 0.059 0.004 PHE C1103 TYR 0.072 0.004 TYR A1067 ARG 0.012 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 354 poor density : 249 time to evaluate : 3.501 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 216 LEU cc_start: 0.2673 (OUTLIER) cc_final: 0.2099 (mp) REVERT: A 371 PHE cc_start: -0.1400 (OUTLIER) cc_final: -0.2781 (m-80) REVERT: A 917 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5874 (m-10) REVERT: A 1011 GLN cc_start: 0.6909 (mm-40) cc_final: 0.6634 (mt0) REVERT: B 201 PHE cc_start: 0.3786 (OUTLIER) cc_final: 0.2826 (t80) REVERT: B 277 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6956 (mt) REVERT: B 1037 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8289 (t) REVERT: C 233 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5834 (mt) REVERT: C 643 PHE cc_start: 0.6839 (t80) cc_final: 0.6457 (t80) REVERT: C 695 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7330 (p90) REVERT: C 697 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7290 (ptm) REVERT: C 872 GLN cc_start: 0.6571 (OUTLIER) cc_final: 0.6161 (tt0) REVERT: F 366 MET cc_start: 0.4325 (tpt) cc_final: 0.3969 (mmt) REVERT: D 62 MET cc_start: 0.2206 (OUTLIER) cc_final: 0.0633 (tpt) REVERT: D 557 MET cc_start: 0.3874 (ppp) cc_final: 0.3550 (ptt) REVERT: E 123 MET cc_start: -0.0933 (ptt) cc_final: -0.1273 (ptm) REVERT: E 332 MET cc_start: -0.0481 (ttt) cc_final: -0.1702 (ppp) REVERT: E 474 MET cc_start: -0.0770 (mmp) cc_final: -0.1575 (tpp) outliers start: 354 outliers final: 189 residues processed: 567 average time/residue: 0.4416 time to fit residues: 432.6874 Evaluate side-chains 411 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 211 time to evaluate : 4.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 339 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 808 ASP Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 49 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 547 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 10.0000 chunk 324 optimal weight: 50.0000 chunk 223 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 205 optimal weight: 4.9990 chunk 289 optimal weight: 1.9990 chunk 432 optimal weight: 50.0000 chunk 458 optimal weight: 8.9990 chunk 226 optimal weight: 0.0980 chunk 410 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 493 GLN A 536 ASN A 957 GLN B 52 GLN B 164 ASN B 856 ASN B 955 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN C 164 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1083 HIS F 49 ASN F 96 GLN F 472 GLN D 599 ASN E 599 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4680 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40499 Z= 0.210 Angle : 0.715 14.532 55056 Z= 0.352 Chirality : 0.048 0.688 6348 Planarity : 0.005 0.066 6974 Dihedral : 7.783 59.984 7309 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.29 % Favored : 93.47 % Rotamer: Outliers : 4.37 % Allowed : 23.33 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.12), residues: 4720 helix: 0.23 (0.13), residues: 1717 sheet: -1.19 (0.19), residues: 707 loop : -2.53 (0.11), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.006 0.001 HIS C 954 PHE 0.038 0.002 PHE B 374 TYR 0.022 0.001 TYR F 50 ARG 0.005 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 250 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: -0.0544 (OUTLIER) cc_final: -0.1121 (t0) REVERT: A 371 PHE cc_start: -0.1354 (OUTLIER) cc_final: -0.2738 (m-80) REVERT: B 324 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5195 (pp20) REVERT: B 751 ASN cc_start: 0.6064 (OUTLIER) cc_final: 0.5465 (p0) REVERT: B 878 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4411 (mm) REVERT: B 1067 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6872 (t80) REVERT: C 233 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5725 (mt) REVERT: C 695 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6299 (p90) REVERT: C 697 MET cc_start: 0.7037 (ppp) cc_final: 0.6516 (ptm) REVERT: C 1132 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7529 (pt) REVERT: F 332 MET cc_start: 0.0636 (ttt) cc_final: 0.0296 (ttt) REVERT: F 366 MET cc_start: 0.3399 (tpt) cc_final: 0.2752 (mmm) REVERT: F 579 MET cc_start: 0.0399 (tpp) cc_final: 0.0143 (mmm) REVERT: D 62 MET cc_start: 0.2490 (OUTLIER) cc_final: 0.0972 (tpt) REVERT: D 343 VAL cc_start: 0.2983 (OUTLIER) cc_final: 0.2733 (p) REVERT: D 455 MET cc_start: 0.4706 (ptm) cc_final: 0.4470 (ptm) REVERT: E 123 MET cc_start: -0.1018 (ptt) cc_final: -0.1314 (ptm) REVERT: E 474 MET cc_start: -0.1027 (mmp) cc_final: -0.1778 (tpp) outliers start: 184 outliers final: 107 residues processed: 407 average time/residue: 0.4428 time to fit residues: 312.3426 Evaluate side-chains 340 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 222 time to evaluate : 4.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 365 TYR Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 530 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 50.0000 chunk 260 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 341 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 390 optimal weight: 10.0000 chunk 316 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 411 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN B 920 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN E 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4765 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 40499 Z= 0.265 Angle : 0.707 13.328 55056 Z= 0.348 Chirality : 0.048 0.655 6348 Planarity : 0.005 0.074 6974 Dihedral : 7.327 59.995 7306 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.69 % Favored : 92.08 % Rotamer: Outliers : 5.06 % Allowed : 23.29 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4720 helix: 0.56 (0.13), residues: 1702 sheet: -1.16 (0.19), residues: 710 loop : -2.39 (0.11), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 302 HIS 0.006 0.001 HIS C1064 PHE 0.037 0.002 PHE B 374 TYR 0.033 0.001 TYR A1067 ARG 0.003 0.000 ARG F 582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 232 time to evaluate : 4.718 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 81 ASN cc_start: -0.0774 (OUTLIER) cc_final: -0.1263 (t0) REVERT: A 371 PHE cc_start: -0.1248 (OUTLIER) cc_final: -0.2696 (m-80) REVERT: B 324 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.5157 (pp20) REVERT: B 751 ASN cc_start: 0.6166 (OUTLIER) cc_final: 0.5609 (p0) REVERT: B 878 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4808 (mm) REVERT: B 1067 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6993 (t80) REVERT: C 233 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5815 (mt) REVERT: C 695 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6406 (p90) REVERT: F 332 MET cc_start: 0.0525 (ttt) cc_final: 0.0248 (ttt) REVERT: F 579 MET cc_start: 0.0666 (tpp) cc_final: 0.0323 (mmm) REVERT: D 62 MET cc_start: 0.2729 (OUTLIER) cc_final: 0.1090 (tpt) REVERT: D 343 VAL cc_start: 0.3007 (OUTLIER) cc_final: 0.2736 (p) REVERT: E 123 MET cc_start: -0.0951 (ptt) cc_final: -0.1233 (ptm) REVERT: E 474 MET cc_start: -0.1143 (mmp) cc_final: -0.1825 (tpp) outliers start: 213 outliers final: 140 residues processed: 413 average time/residue: 0.4848 time to fit residues: 348.2306 Evaluate side-chains 373 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 223 time to evaluate : 4.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 917 TYR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 5.9990 chunk 412 optimal weight: 50.0000 chunk 90 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 458 optimal weight: 20.0000 chunk 380 optimal weight: 40.0000 chunk 212 optimal weight: 5.9990 chunk 38 optimal weight: 50.0000 chunk 151 optimal weight: 1.9990 chunk 240 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 115 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 388 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN E 524 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4810 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 40499 Z= 0.288 Angle : 0.707 12.727 55056 Z= 0.349 Chirality : 0.048 0.663 6348 Planarity : 0.005 0.074 6974 Dihedral : 7.042 59.889 7306 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.20 % Rotamer: Outliers : 4.96 % Allowed : 23.50 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4720 helix: 0.72 (0.13), residues: 1701 sheet: -1.19 (0.19), residues: 728 loop : -2.32 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.006 0.001 HIS C1064 PHE 0.038 0.002 PHE B 374 TYR 0.035 0.001 TYR A1067 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 232 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: -0.0737 (OUTLIER) cc_final: -0.1324 (t0) REVERT: A 244 LEU cc_start: -0.0103 (OUTLIER) cc_final: -0.0686 (tt) REVERT: A 371 PHE cc_start: -0.1347 (OUTLIER) cc_final: -0.2815 (m-80) REVERT: B 324 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5204 (pp20) REVERT: B 751 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5543 (p0) REVERT: B 878 LEU cc_start: 0.5187 (OUTLIER) cc_final: 0.4751 (mm) REVERT: B 1067 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6982 (t80) REVERT: C 233 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6017 (mt) REVERT: C 362 VAL cc_start: 0.7734 (t) cc_final: 0.7459 (t) REVERT: C 695 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6554 (p90) REVERT: C 872 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.5916 (tt0) REVERT: F 332 MET cc_start: 0.0584 (ttt) cc_final: 0.0314 (ttt) REVERT: D 62 MET cc_start: 0.2707 (OUTLIER) cc_final: 0.0876 (tpt) REVERT: D 343 VAL cc_start: 0.3103 (OUTLIER) cc_final: 0.2852 (p) REVERT: E 123 MET cc_start: -0.0722 (ptt) cc_final: -0.0963 (ptm) REVERT: E 332 MET cc_start: -0.0192 (ptm) cc_final: -0.0514 (ptt) REVERT: E 474 MET cc_start: -0.1151 (mmp) cc_final: -0.1415 (tpp) outliers start: 209 outliers final: 154 residues processed: 410 average time/residue: 0.4459 time to fit residues: 317.1901 Evaluate side-chains 385 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 219 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1108 ASN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 0.0050 chunk 51 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 334 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 386 optimal weight: 8.9990 chunk 256 optimal weight: 0.2980 chunk 456 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 210 optimal weight: 20.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 188 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4669 moved from start: 0.7134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 40499 Z= 0.151 Angle : 0.633 12.379 55056 Z= 0.305 Chirality : 0.046 0.512 6348 Planarity : 0.004 0.080 6974 Dihedral : 6.530 59.679 7305 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.44 % Favored : 93.35 % Rotamer: Outliers : 3.18 % Allowed : 25.04 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 4720 helix: 1.17 (0.13), residues: 1695 sheet: -0.89 (0.19), residues: 725 loop : -2.07 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 PHE 0.035 0.001 PHE B 374 TYR 0.038 0.001 TYR A 204 ARG 0.006 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 251 time to evaluate : 4.417 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: A 81 ASN cc_start: -0.0873 (OUTLIER) cc_final: -0.1421 (t0) REVERT: A 244 LEU cc_start: -0.0201 (OUTLIER) cc_final: -0.0694 (tt) REVERT: A 371 PHE cc_start: -0.1219 (OUTLIER) cc_final: -0.2689 (m-80) REVERT: A 1128 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7813 (t) REVERT: B 324 GLU cc_start: 0.5628 (OUTLIER) cc_final: 0.5075 (pp20) REVERT: B 434 ILE cc_start: 0.5439 (OUTLIER) cc_final: 0.4571 (tp) REVERT: B 751 ASN cc_start: 0.5732 (OUTLIER) cc_final: 0.5285 (p0) REVERT: C 362 VAL cc_start: 0.7522 (t) cc_final: 0.7254 (t) REVERT: C 695 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6672 (p90) REVERT: C 825 LYS cc_start: 0.6052 (tttt) cc_final: 0.5801 (mmtm) REVERT: F 123 MET cc_start: -0.1677 (ptp) cc_final: -0.2094 (ptt) REVERT: F 332 MET cc_start: 0.0560 (ttt) cc_final: 0.0328 (ttt) REVERT: D 62 MET cc_start: 0.2660 (tpt) cc_final: 0.0721 (tpt) REVERT: E 123 MET cc_start: -0.0732 (ptt) cc_final: -0.0987 (ptm) REVERT: E 332 MET cc_start: -0.0231 (ptm) cc_final: -0.0554 (ptt) REVERT: E 474 MET cc_start: -0.1254 (mmp) cc_final: -0.1860 (tpp) outliers start: 134 outliers final: 90 residues processed: 365 average time/residue: 0.4516 time to fit residues: 287.1386 Evaluate side-chains 320 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 222 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1060 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 530 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 0.9980 chunk 182 optimal weight: 0.3980 chunk 272 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 311 optimal weight: 50.0000 chunk 225 optimal weight: 30.0000 chunk 42 optimal weight: 30.0000 chunk 359 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4658 moved from start: 0.7228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 40499 Z= 0.148 Angle : 0.623 14.811 55056 Z= 0.298 Chirality : 0.045 0.489 6348 Planarity : 0.004 0.081 6974 Dihedral : 6.263 59.590 7303 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.19 % Favored : 93.60 % Rotamer: Outliers : 2.61 % Allowed : 25.85 % Favored : 71.54 % 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: -0.78 (0.12), residues: 4720 helix: 1.35 (0.13), residues: 1688 sheet: -0.78 (0.19), residues: 733 loop : -1.94 (0.12), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS A 49 PHE 0.034 0.001 PHE B 374 TYR 0.027 0.001 TYR B 873 ARG 0.003 0.000 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 239 time to evaluate : 4.351 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: A 81 ASN cc_start: -0.0882 (OUTLIER) cc_final: -0.1373 (t0) REVERT: A 244 LEU cc_start: -0.0313 (OUTLIER) cc_final: -0.0704 (tt) REVERT: A 1128 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7790 (t) REVERT: B 324 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.5121 (pp20) REVERT: B 434 ILE cc_start: 0.5412 (OUTLIER) cc_final: 0.4539 (tp) REVERT: B 751 ASN cc_start: 0.5861 (OUTLIER) cc_final: 0.5388 (p0) REVERT: C 362 VAL cc_start: 0.7537 (t) cc_final: 0.7274 (t) REVERT: F 123 MET cc_start: -0.1626 (ptp) cc_final: -0.2117 (ptt) REVERT: F 427 ASP cc_start: 0.1773 (OUTLIER) cc_final: 0.1487 (t0) REVERT: D 62 MET cc_start: 0.2634 (OUTLIER) cc_final: 0.0707 (tpt) REVERT: E 123 MET cc_start: -0.0513 (ptt) cc_final: -0.0784 (ptm) REVERT: E 332 MET cc_start: -0.0181 (ptm) cc_final: -0.0559 (ptt) REVERT: E 474 MET cc_start: -0.1153 (mmp) cc_final: -0.1604 (tpp) outliers start: 110 outliers final: 85 residues processed: 332 average time/residue: 0.4462 time to fit residues: 257.6074 Evaluate side-chains 319 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 226 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 10.0000 chunk 437 optimal weight: 40.0000 chunk 399 optimal weight: 50.0000 chunk 425 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 334 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 384 optimal weight: 50.0000 chunk 402 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1054 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4926 moved from start: 0.7825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.151 40499 Z= 0.462 Angle : 0.825 13.456 55056 Z= 0.412 Chirality : 0.052 0.737 6348 Planarity : 0.005 0.080 6974 Dihedral : 6.974 59.737 7303 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.58 % Favored : 91.21 % Rotamer: Outliers : 3.54 % Allowed : 25.14 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.12), residues: 4720 helix: 0.80 (0.13), residues: 1668 sheet: -1.27 (0.18), residues: 735 loop : -2.23 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 271 HIS 0.015 0.001 HIS C1058 PHE 0.038 0.003 PHE C1121 TYR 0.055 0.002 TYR A1067 ARG 0.007 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 225 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: -0.0656 (OUTLIER) cc_final: -0.1167 (t0) REVERT: A 238 PHE cc_start: 0.2424 (OUTLIER) cc_final: 0.1107 (p90) REVERT: A 371 PHE cc_start: -0.1051 (OUTLIER) cc_final: -0.2123 (m-80) REVERT: A 775 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7387 (t70) REVERT: A 1128 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7803 (t) REVERT: B 324 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.5172 (pp20) REVERT: B 434 ILE cc_start: 0.5550 (OUTLIER) cc_final: 0.4783 (tp) REVERT: B 878 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5404 (mm) REVERT: C 233 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6155 (mt) REVERT: C 362 VAL cc_start: 0.7988 (t) cc_final: 0.7784 (t) REVERT: C 872 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6103 (tt0) REVERT: F 123 MET cc_start: -0.1617 (ptp) cc_final: -0.1971 (ptt) REVERT: F 332 MET cc_start: -0.0067 (ttt) cc_final: -0.0437 (ttt) REVERT: F 366 MET cc_start: 0.4879 (mmm) cc_final: 0.4384 (mmp) REVERT: F 427 ASP cc_start: 0.1780 (OUTLIER) cc_final: 0.1473 (t0) REVERT: E 123 MET cc_start: -0.0480 (ptt) cc_final: -0.0816 (ptm) REVERT: E 332 MET cc_start: -0.0095 (ptm) cc_final: -0.0363 (ptt) outliers start: 149 outliers final: 112 residues processed: 344 average time/residue: 0.4606 time to fit residues: 273.7357 Evaluate side-chains 331 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 208 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 872 GLN Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 480 MET Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 6.9990 chunk 450 optimal weight: 50.0000 chunk 274 optimal weight: 0.6980 chunk 213 optimal weight: 0.9990 chunk 312 optimal weight: 50.0000 chunk 472 optimal weight: 5.9990 chunk 434 optimal weight: 50.0000 chunk 376 optimal weight: 9.9990 chunk 39 optimal weight: 0.0770 chunk 290 optimal weight: 0.0000 chunk 230 optimal weight: 9.9990 overall best weight: 1.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 HIS F 524 GLN ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4778 moved from start: 0.7849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40499 Z= 0.182 Angle : 0.668 14.118 55056 Z= 0.323 Chirality : 0.046 0.564 6348 Planarity : 0.004 0.083 6974 Dihedral : 6.537 59.765 7303 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.69 % Favored : 93.09 % Rotamer: Outliers : 2.40 % Allowed : 26.49 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 4720 helix: 1.17 (0.13), residues: 1679 sheet: -1.02 (0.19), residues: 723 loop : -2.02 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.006 0.001 HIS C1058 PHE 0.032 0.002 PHE B 374 TYR 0.027 0.001 TYR A 204 ARG 0.005 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9440 Ramachandran restraints generated. 4720 Oldfield, 0 Emsley, 4720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 228 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: -0.0833 (OUTLIER) cc_final: -0.1441 (t0) REVERT: A 317 ASN cc_start: 0.7007 (OUTLIER) cc_final: 0.6219 (p0) REVERT: A 371 PHE cc_start: -0.1015 (OUTLIER) cc_final: -0.1977 (m-80) REVERT: A 1128 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7785 (t) REVERT: B 324 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5096 (pp20) REVERT: B 434 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.4849 (tp) REVERT: B 751 ASN cc_start: 0.5923 (OUTLIER) cc_final: 0.5538 (p0) REVERT: C 362 VAL cc_start: 0.7754 (t) cc_final: 0.7547 (t) REVERT: F 123 MET cc_start: -0.1721 (ptp) cc_final: -0.2213 (ptt) REVERT: F 332 MET cc_start: 0.0070 (ttt) cc_final: -0.0201 (ttt) REVERT: F 366 MET cc_start: 0.4818 (mmm) cc_final: 0.4303 (mmp) REVERT: F 427 ASP cc_start: 0.1913 (OUTLIER) cc_final: 0.1595 (t0) REVERT: E 123 MET cc_start: -0.0483 (ptt) cc_final: -0.0825 (ptm) REVERT: E 332 MET cc_start: -0.0190 (ptm) cc_final: -0.0449 (ptt) outliers start: 101 outliers final: 83 residues processed: 308 average time/residue: 0.4507 time to fit residues: 241.3478 Evaluate side-chains 311 residues out of total 4213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 220 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 597 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 5.9990 chunk 400 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 346 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 386 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.174629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.126031 restraints weight = 133450.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.122191 restraints weight = 89420.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.123144 restraints weight = 85491.476| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.7967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40499 Z= 0.206 Angle : 0.667 13.658 55056 Z= 0.323 Chirality : 0.046 0.543 6348 Planarity : 0.004 0.083 6974 Dihedral : 6.428 59.788 7303 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.48 % Favored : 92.31 % Rotamer: Outliers : 2.71 % Allowed : 26.23 % Favored : 71.07 % 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: -0.93 (0.12), residues: 4720 helix: 1.26 (0.13), residues: 1680 sheet: -1.06 (0.19), residues: 733 loop : -1.97 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.006 0.001 HIS A 49 PHE 0.031 0.002 PHE B 374 TYR 0.028 0.001 TYR A1067 ARG 0.003 0.000 ARG C 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8857.84 seconds wall clock time: 162 minutes 55.00 seconds (9775.00 seconds total)