Starting phenix.real_space_refine on Fri Feb 23 18:18:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9d_35267/02_2024/8i9d_35267.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9d_35267/02_2024/8i9d_35267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9d_35267/02_2024/8i9d_35267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9d_35267/02_2024/8i9d_35267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9d_35267/02_2024/8i9d_35267.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9d_35267/02_2024/8i9d_35267.pdb" } resolution = 3.95 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= 0.004 sd= 0.055 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 25183 2.51 5 N 6417 2.21 5 O 7722 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 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 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 PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 115": "NH1" <-> "NH2" Residue "F GLU 140": "OE1" <-> "OE2" 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 GLU 189": "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 GLU 329": "OE1" <-> "OE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 467": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F GLU 495": "OE1" <-> "OE2" Residue "F PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 518": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" 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 GLU 189": "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 GLU 329": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 140": "OE1" <-> "OE2" 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 GLU 189": "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 GLU 329": "OE1" <-> "OE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 467": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 518": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39517 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7821 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 55, 'TRANS': 943} Chain breaks: 9 Chain: "B" Number of atoms: 7815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7815 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 55, 'TRANS': 942} Chain breaks: 9 Chain: "C" Number of atoms: 7815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7815 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 55, 'TRANS': 942} 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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 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: 20.62, per 1000 atoms: 0.52 Number of scatterers: 39517 At special positions: 0 Unit cell: (193.486, 204.356, 247.836, 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 7722 8.00 N 6417 7.00 C 25183 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=2.09 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.06 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.45 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.21 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.05 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=2.09 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=2.04 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=2.05 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=2.04 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 r 1 " - " NAG r 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG 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 A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN F 53 " " NAG e 1 " - " ASN F 90 " " NAG f 1 " - " ASN F 103 " " NAG g 1 " - " ASN F 432 " " NAG h 1 " - " ASN F 546 " " NAG i 1 " - " ASN D 53 " " NAG j 1 " - " ASN D 90 " " NAG k 1 " - " ASN D 103 " " NAG l 1 " - " ASN D 432 " " NAG m 1 " - " ASN D 546 " " NAG n 1 " - " ASN E 53 " " NAG o 1 " - " ASN E 90 " " NAG p 1 " - " ASN E 103 " " NAG q 1 " - " ASN E 432 " " NAG r 1 " - " ASN E 546 " Time building additional restraints: 15.67 Conformation dependent library (CDL) restraints added in 6.7 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: 150 helices and 53 sheets defined 38.6% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.636A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.776A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.521A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A 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: 3.642A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.559A 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: 3.536A 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: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.572A 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: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.799A 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: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A 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: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A 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 341 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.636A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.776A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.521A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A 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: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A 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: 4.020A 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: 3.704A 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: 4.268A 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: 4.209A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A 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 341 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.637A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.777A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.521A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A 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: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.589A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.360A 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: 3.738A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A 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 52 removed outlier: 3.737A pdb=" N LYS F 26 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.825A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.779A 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: 3.618A pdb=" N ALA F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 171 removed outlier: 3.724A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.507A pdb=" N GLN F 175 " --> pdb=" O VAL F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 176 through 193 removed outlier: 4.340A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.687A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.143A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 249 removed outlier: 4.359A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.513A 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 305 through 319 removed outlier: 3.801A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.984A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 385 removed outlier: 3.969A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 412 removed outlier: 3.708A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.753A pdb=" N SER F 420 " --> pdb=" O LYS F 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.554A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 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: 4.112A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.896A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 597 removed outlier: 3.545A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) Proline residue: F 590 - end of helix Processing helix chain 'D' and resid 22 through 52 removed outlier: 3.736A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.826A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.778A 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: 3.617A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 removed outlier: 3.723A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.507A pdb=" N GLN D 175 " --> pdb=" O VAL D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 176 through 193 removed outlier: 4.341A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.686A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 230 removed outlier: 4.143A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 4.360A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.512A 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 305 through 319 removed outlier: 3.802A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.985A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 3.969A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.708A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.752A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.553A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 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: 4.113A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.896A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 581 through 597 removed outlier: 3.544A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing helix chain 'E' and resid 22 through 52 removed outlier: 3.736A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 80 removed outlier: 3.826A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.779A 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: 3.618A pdb=" N ALA E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 171 removed outlier: 3.723A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.507A pdb=" N GLN E 175 " --> pdb=" O VAL E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.340A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 removed outlier: 3.686A pdb=" N TYR E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 230 removed outlier: 4.143A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 249 removed outlier: 4.359A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.514A 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 305 through 319 removed outlier: 3.802A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.986A pdb=" N ASN E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 385 removed outlier: 3.969A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 412 removed outlier: 3.707A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.752A pdb=" N SER E 420 " --> pdb=" O LYS E 416 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.553A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 465 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: 4.112A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.709A 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: 3.896A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 581 through 597 removed outlier: 3.544A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) Proline residue: E 590 - end of helix 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: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.678A 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: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 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: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A 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: 7.213A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.588A 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: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.060A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 7.030A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.570A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.704A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 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=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.581A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A 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: 4.731A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, 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=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, 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=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.729A 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: 7.212A 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: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 188 through 189 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.870A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.475A 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=AC6, first strand: chain 'B' and resid 323 through 326 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.570A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.704A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.563A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.893A 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=AD2, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A 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=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, 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: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (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=AD8, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.476A 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=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.621A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.406A 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=AE3, 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: 6.445A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.571A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.704A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 653 through 655 removed outlier: 6.417A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.760A 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: 6.146A 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=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.760A 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: 6.146A 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: 3.879A 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=AF1, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.231A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 347 through 352 removed outlier: 3.647A pdb=" N ARG F 357 " --> pdb=" O TRP F 349 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.229A 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: 3.646A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.230A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'E' and resid 347 through 352 removed outlier: 3.648A pdb=" N ARG E 357 " --> pdb=" O TRP E 349 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1565 hydrogen bonds defined for protein. 4356 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: 15.69 Time building geometry restraints manager: 16.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8227 1.33 - 1.45: 10531 1.45 - 1.58: 21434 1.58 - 1.70: 0 1.70 - 1.83: 285 Bond restraints: 40477 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.20e-02 6.94e+03 4.32e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.79e+01 bond pdb=" N PRO C 209 " pdb=" CD PRO C 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 A 209 " pdb=" CD PRO A 209 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 ... (remaining 40472 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.90: 774 104.90 - 112.24: 19994 112.24 - 119.58: 13911 119.58 - 126.92: 19853 126.92 - 134.26: 498 Bond angle restraints: 55030 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C ASP C 985 " pdb=" N PRO C 986 " pdb=" CA PRO C 986 " ideal model delta sigma weight residual 120.38 114.52 5.86 1.03e+00 9.43e-01 3.23e+01 angle pdb=" C CYS B 590 " pdb=" N SER B 591 " pdb=" CA SER B 591 " ideal model delta sigma weight residual 122.65 114.78 7.87 1.49e+00 4.50e-01 2.79e+01 ... (remaining 55025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.67: 23265 25.67 - 51.35: 1768 51.35 - 77.02: 321 77.02 - 102.69: 36 102.69 - 128.36: 3 Dihedral angle restraints: 25393 sinusoidal: 11404 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 21.07 71.93 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 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 25390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 6323 0.256 - 0.512: 20 0.512 - 0.768: 2 0.768 - 1.024: 1 1.024 - 1.280: 1 Chirality restraints: 6347 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.92e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.07e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.12 -1.28 2.00e-01 2.50e+01 4.09e+01 ... (remaining 6344 not shown) Planarity restraints: 7038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " 0.051 2.00e-02 2.50e+03 6.72e-02 5.64e+01 pdb=" CG ASN A 801 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " -0.116 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.82e-02 4.24e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.050 2.00e-02 2.50e+03 5.27e-02 3.47e+01 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.077 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.068 2.00e-02 2.50e+03 ... (remaining 7035 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 243 2.48 - 3.08: 27044 3.08 - 3.69: 55202 3.69 - 4.29: 82500 4.29 - 4.90: 137806 Nonbonded interactions: 302795 Sorted by model distance: nonbonded pdb=" O GLY B 799 " pdb=" O PHE B 800 " model vdw 1.871 3.040 nonbonded pdb=" N GLU B 748 " pdb=" OE1 GLU B 748 " model vdw 2.141 2.520 nonbonded pdb=" O GLN B 675 " pdb=" OG1 THR B 676 " model vdw 2.148 2.440 nonbonded pdb=" O GLY A 700 " pdb=" O ALA A 701 " model vdw 2.167 3.040 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.184 2.440 ... (remaining 302790 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' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 7.520 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 99.340 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.800 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4933 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 : 0.008 0.117 40477 Z= 0.537 Angle : 0.873 11.318 55030 Z= 0.500 Chirality : 0.062 1.280 6347 Planarity : 0.006 0.086 6972 Dihedral : 17.444 128.363 16253 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 1.59 % Allowed : 7.63 % Favored : 90.78 % Rotamer: Outliers : 9.03 % Allowed : 17.51 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.10), residues: 4720 helix: -1.54 (0.11), residues: 1652 sheet: -2.24 (0.16), residues: 745 loop : -3.40 (0.10), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 104 HIS 0.009 0.001 HIS A1048 PHE 0.025 0.002 PHE A 898 TYR 0.027 0.002 TYR B1067 ARG 0.008 0.000 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 881 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 501 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 205 SER cc_start: 0.6948 (OUTLIER) cc_final: 0.5797 (t) REVERT: A 282 ASN cc_start: 0.5467 (OUTLIER) cc_final: 0.5185 (p0) REVERT: B 207 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.6086 (m90) REVERT: B 480 CYS cc_start: -0.0441 (OUTLIER) cc_final: -0.3427 (t) REVERT: B 531 THR cc_start: 0.2568 (OUTLIER) cc_final: 0.2100 (t) REVERT: B 541 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5638 (p90) REVERT: B 791 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7168 (p) REVERT: C 373 PRO cc_start: 0.7819 (Cg_exo) cc_final: 0.7615 (Cg_endo) REVERT: C 480 CYS cc_start: 0.2827 (OUTLIER) cc_final: 0.2074 (m) REVERT: C 530 SER cc_start: 0.5277 (OUTLIER) cc_final: 0.4762 (m) REVERT: D 20 THR cc_start: 0.0792 (OUTLIER) cc_final: 0.0172 (m) REVERT: D 297 MET cc_start: 0.0586 (mtp) cc_final: 0.0086 (ptm) REVERT: D 360 MET cc_start: 0.0791 (ptm) cc_final: -0.0322 (tpt) REVERT: D 376 MET cc_start: 0.2186 (mtp) cc_final: 0.1595 (mtm) REVERT: E 270 MET cc_start: 0.5463 (tpp) cc_final: 0.5257 (mmm) REVERT: E 323 MET cc_start: 0.0076 (mmp) cc_final: -0.1188 (mmt) outliers start: 380 outliers final: 75 residues processed: 840 average time/residue: 0.4729 time to fit residues: 663.0625 Evaluate side-chains 335 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 250 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 217 PRO Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 217 PRO Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 541 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 217 PRO Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 133 CYS Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 379 ILE Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 141 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 50.0000 chunk 359 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 143 optimal weight: 40.0000 chunk 225 optimal weight: 20.0000 chunk 276 optimal weight: 0.9980 chunk 430 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 134 GLN A 137 ASN A 188 ASN A 239 GLN A 317 ASN A 334 ASN ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 644 GLN A 658 ASN A 901 GLN A 914 ASN A 919 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN A1071 GLN A1101 HIS A1135 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 137 ASN B 188 ASN B 239 GLN B 317 ASN B 334 ASN B 339 HIS B 542 ASN B 580 GLN B 613 GLN B 644 GLN B 658 ASN B 901 GLN B 914 ASN B 919 ASN B 954 HIS B 992 GLN B1054 GLN B1108 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 188 ASN C 239 GLN C 317 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 542 ASN C 644 GLN C 658 ASN C 703 ASN C 751 ASN C 901 GLN C 914 ASN C 992 GLN C1071 GLN C1101 HIS F 96 GLN F 102 GLN F 239 HIS F 305 GLN F 340 GLN F 378 HIS F 472 GLN F 505 HIS F 531 GLN ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN D 61 ASN D 96 GLN D 102 GLN D 239 HIS D 305 GLN D 340 GLN D 378 HIS D 472 GLN D 505 HIS ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN E 42 GLN E 102 GLN E 305 GLN E 330 ASN E 340 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN E 505 HIS ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 40477 Z= 0.342 Angle : 0.812 14.635 55030 Z= 0.403 Chirality : 0.049 0.595 6347 Planarity : 0.006 0.087 6972 Dihedral : 9.636 101.923 7454 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.38 % Favored : 93.41 % Rotamer: Outliers : 5.42 % Allowed : 21.69 % Favored : 72.90 % 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: -2.25 (0.11), residues: 4720 helix: -0.00 (0.13), residues: 1666 sheet: -1.50 (0.17), residues: 755 loop : -2.70 (0.11), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 104 HIS 0.012 0.002 HIS A 954 PHE 0.033 0.002 PHE C1042 TYR 0.027 0.002 TYR A1067 ARG 0.009 0.001 ARG B1019 *********************** 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 460 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 232 time to evaluate : 4.719 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: A 81 ASN cc_start: -0.1528 (OUTLIER) cc_final: -0.2086 (t0) REVERT: A 207 HIS cc_start: 0.5484 (OUTLIER) cc_final: 0.5099 (m-70) REVERT: A 699 LEU cc_start: 0.6925 (mt) cc_final: 0.6604 (mt) REVERT: B 207 HIS cc_start: 0.6702 (OUTLIER) cc_final: 0.6486 (m90) REVERT: B 480 CYS cc_start: -0.0390 (OUTLIER) cc_final: -0.3451 (t) REVERT: B 531 THR cc_start: 0.3498 (OUTLIER) cc_final: 0.2925 (p) REVERT: C 373 PRO cc_start: 0.7545 (Cg_exo) cc_final: 0.7220 (Cg_endo) REVERT: C 480 CYS cc_start: 0.2993 (OUTLIER) cc_final: 0.2070 (m) REVERT: D 297 MET cc_start: 0.0258 (mtp) cc_final: -0.0258 (ptm) REVERT: D 360 MET cc_start: 0.0203 (ptm) cc_final: -0.0707 (tpt) REVERT: D 579 MET cc_start: 0.2122 (mtm) cc_final: 0.1905 (mtt) outliers start: 228 outliers final: 100 residues processed: 443 average time/residue: 0.4667 time to fit residues: 352.1153 Evaluate side-chains 288 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 182 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 772 VAL 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 791 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1030 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 C residue 36 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 2.9990 chunk 133 optimal weight: 40.0000 chunk 358 optimal weight: 50.0000 chunk 293 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 431 optimal weight: 20.0000 chunk 465 optimal weight: 5.9990 chunk 384 optimal weight: 40.0000 chunk 427 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 345 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1106 GLN C 81 ASN C 690 GLN C 777 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN C1113 GLN F 63 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5449 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 40477 Z= 0.298 Angle : 0.705 10.695 55030 Z= 0.346 Chirality : 0.046 0.501 6347 Planarity : 0.005 0.057 6972 Dihedral : 8.474 102.445 7363 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.46 % Favored : 93.41 % Rotamer: Outliers : 4.89 % Allowed : 22.78 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4720 helix: 0.54 (0.13), residues: 1666 sheet: -1.26 (0.17), residues: 749 loop : -2.44 (0.11), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 104 HIS 0.007 0.001 HIS B 66 PHE 0.027 0.002 PHE C1052 TYR 0.026 0.001 TYR A1067 ARG 0.009 0.000 ARG B 995 *********************** 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 396 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 190 time to evaluate : 4.463 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: A 207 HIS cc_start: 0.5841 (OUTLIER) cc_final: 0.5460 (m-70) REVERT: B 227 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7257 (t) REVERT: C 900 MET cc_start: 0.6312 (mtp) cc_final: 0.6112 (mtp) REVERT: D 24 GLN cc_start: 0.1957 (OUTLIER) cc_final: 0.0779 (pp30) REVERT: D 270 MET cc_start: 0.5932 (ttm) cc_final: 0.5429 (ttm) REVERT: D 297 MET cc_start: 0.0254 (mtp) cc_final: -0.0250 (ptm) REVERT: D 323 MET cc_start: -0.1899 (tpt) cc_final: -0.2204 (tpp) REVERT: D 360 MET cc_start: -0.0117 (ptm) cc_final: -0.0895 (tpt) outliers start: 206 outliers final: 126 residues processed: 380 average time/residue: 0.4434 time to fit residues: 292.6624 Evaluate side-chains 302 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 173 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL 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 791 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR 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 C residue 40 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 30.0000 chunk 324 optimal weight: 2.9990 chunk 223 optimal weight: 0.3980 chunk 47 optimal weight: 0.0270 chunk 205 optimal weight: 40.0000 chunk 289 optimal weight: 0.7980 chunk 432 optimal weight: 40.0000 chunk 458 optimal weight: 40.0000 chunk 226 optimal weight: 0.2980 chunk 410 optimal weight: 50.0000 chunk 123 optimal weight: 30.0000 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 965 GLN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 40477 Z= 0.159 Angle : 0.638 11.101 55030 Z= 0.306 Chirality : 0.045 0.526 6347 Planarity : 0.004 0.059 6972 Dihedral : 7.765 102.373 7356 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.53 % Favored : 94.36 % Rotamer: Outliers : 3.75 % Allowed : 23.23 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4720 helix: 0.84 (0.13), residues: 1682 sheet: -0.91 (0.18), residues: 752 loop : -2.25 (0.11), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.006 0.001 HIS D 417 PHE 0.019 0.001 PHE E 315 TYR 0.016 0.001 TYR A1067 ARG 0.005 0.000 ARG A 328 *********************** 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 357 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 199 time to evaluate : 4.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.5804 (OUTLIER) cc_final: 0.5360 (m-70) REVERT: C 480 CYS cc_start: 0.2704 (OUTLIER) cc_final: 0.2061 (m) REVERT: C 900 MET cc_start: 0.6010 (mtp) cc_final: 0.5806 (mtp) REVERT: D 24 GLN cc_start: 0.1920 (OUTLIER) cc_final: 0.0766 (pp30) REVERT: D 270 MET cc_start: 0.5594 (ttm) cc_final: 0.5264 (ttm) REVERT: D 297 MET cc_start: -0.0313 (mtp) cc_final: -0.0691 (ptm) REVERT: D 360 MET cc_start: -0.0500 (ptm) cc_final: -0.1144 (tpp) REVERT: E 297 MET cc_start: -0.3421 (mmm) cc_final: -0.4093 (mmt) REVERT: E 323 MET cc_start: -0.0669 (tpp) cc_final: -0.0920 (tpp) REVERT: E 383 MET cc_start: 0.2419 (mtt) cc_final: 0.1912 (mtt) outliers start: 158 outliers final: 94 residues processed: 342 average time/residue: 0.4640 time to fit residues: 276.3001 Evaluate side-chains 273 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 176 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 410 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 133 CYS Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 40.0000 chunk 260 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 341 optimal weight: 40.0000 chunk 189 optimal weight: 4.9990 chunk 390 optimal weight: 50.0000 chunk 316 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 233 optimal weight: 30.0000 chunk 411 optimal weight: 50.0000 chunk 115 optimal weight: 2.9990 overall best weight: 13.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 953 ASN B 965 GLN B1036 GLN B1064 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 606 ASN C 613 GLN C 641 ASN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN F 210 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 210 ASN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.199 40477 Z= 0.704 Angle : 1.090 16.093 55030 Z= 0.543 Chirality : 0.057 0.767 6347 Planarity : 0.007 0.084 6972 Dihedral : 8.992 101.984 7350 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.24 % Favored : 91.57 % Rotamer: Outliers : 5.77 % Allowed : 22.71 % Favored : 71.52 % 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: -2.03 (0.11), residues: 4720 helix: 0.04 (0.13), residues: 1666 sheet: -1.41 (0.18), residues: 713 loop : -2.42 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 104 HIS 0.014 0.002 HIS B 66 PHE 0.052 0.004 PHE A 797 TYR 0.070 0.003 TYR A1067 ARG 0.016 0.001 ARG A 905 *********************** 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 401 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 158 time to evaluate : 4.106 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: B 153 MET cc_start: 0.5114 (tmm) cc_final: 0.4911 (tmm) REVERT: B 518 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5459 (pt) REVERT: B 611 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6825 (tp) REVERT: C 480 CYS cc_start: 0.2912 (OUTLIER) cc_final: 0.2309 (m) REVERT: C 797 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: D 24 GLN cc_start: 0.2004 (OUTLIER) cc_final: 0.0599 (pp30) REVERT: D 270 MET cc_start: 0.5877 (ttm) cc_final: 0.5199 (ttm) REVERT: D 297 MET cc_start: 0.0366 (mtp) cc_final: -0.0020 (ptm) REVERT: D 323 MET cc_start: -0.0954 (tpp) cc_final: -0.1509 (mtp) REVERT: D 360 MET cc_start: -0.0523 (ptm) cc_final: -0.1574 (tpp) REVERT: D 462 MET cc_start: 0.5151 (tmt) cc_final: 0.4802 (tmm) REVERT: E 297 MET cc_start: -0.2878 (mmm) cc_final: -0.3478 (mmt) REVERT: E 455 MET cc_start: -0.0073 (tmm) cc_final: -0.0602 (tmm) outliers start: 243 outliers final: 142 residues processed: 385 average time/residue: 0.4463 time to fit residues: 297.4342 Evaluate side-chains 289 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 142 time to evaluate : 4.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL 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 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 282 ASN 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 315 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 1.9990 chunk 412 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 458 optimal weight: 20.0000 chunk 380 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1036 GLN B1083 HIS C 239 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 955 ASN C1002 GLN F 437 ASN ** F 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5627 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 40477 Z= 0.252 Angle : 0.705 12.947 55030 Z= 0.342 Chirality : 0.046 0.552 6347 Planarity : 0.004 0.058 6972 Dihedral : 7.884 104.126 7337 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 3.73 % Allowed : 24.89 % Favored : 71.38 % 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: -1.53 (0.12), residues: 4720 helix: 0.54 (0.13), residues: 1690 sheet: -1.05 (0.18), residues: 734 loop : -2.27 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.008 0.001 HIS A1048 PHE 0.020 0.002 PHE A 55 TYR 0.029 0.001 TYR A1067 ARG 0.006 0.000 ARG A 328 *********************** 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 317 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 160 time to evaluate : 4.479 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: B 480 CYS cc_start: -0.0482 (OUTLIER) cc_final: -0.3353 (t) REVERT: C 480 CYS cc_start: 0.2785 (OUTLIER) cc_final: 0.2168 (m) REVERT: F 579 MET cc_start: -0.2403 (ptp) cc_final: -0.2866 (ptt) REVERT: D 270 MET cc_start: 0.5757 (ttm) cc_final: 0.5177 (ttm) REVERT: D 297 MET cc_start: 0.0168 (mtp) cc_final: -0.0311 (ptm) REVERT: D 323 MET cc_start: -0.1220 (tpp) cc_final: -0.1547 (mtt) REVERT: D 360 MET cc_start: -0.0896 (ptm) cc_final: -0.1622 (tpt) REVERT: D 462 MET cc_start: 0.5124 (OUTLIER) cc_final: 0.4681 (tmm) REVERT: E 297 MET cc_start: -0.3019 (mmm) cc_final: -0.3451 (mmt) REVERT: E 383 MET cc_start: 0.2889 (mtt) cc_final: 0.2425 (mtt) outliers start: 157 outliers final: 108 residues processed: 301 average time/residue: 0.4511 time to fit residues: 237.6523 Evaluate side-chains 259 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 148 time to evaluate : 4.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 770 ILE 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 791 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 409 SER Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 334 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 386 optimal weight: 0.8980 chunk 256 optimal weight: 8.9990 chunk 456 optimal weight: 40.0000 chunk 285 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 40477 Z= 0.206 Angle : 0.666 14.076 55030 Z= 0.319 Chirality : 0.045 0.493 6347 Planarity : 0.004 0.076 6972 Dihedral : 7.391 103.114 7331 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 3.25 % Allowed : 25.53 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.12), residues: 4720 helix: 0.90 (0.13), residues: 1685 sheet: -0.78 (0.19), residues: 698 loop : -2.11 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 104 HIS 0.006 0.001 HIS A1048 PHE 0.031 0.001 PHE B 329 TYR 0.023 0.001 TYR A1067 ARG 0.006 0.000 ARG A 319 *********************** 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 294 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 157 time to evaluate : 4.561 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: B 480 CYS cc_start: -0.0244 (OUTLIER) cc_final: -0.3286 (t) REVERT: B 596 SER cc_start: 0.7275 (OUTLIER) cc_final: 0.7037 (p) REVERT: C 480 CYS cc_start: 0.2881 (OUTLIER) cc_final: 0.2223 (m) REVERT: F 249 MET cc_start: -0.2961 (mtt) cc_final: -0.3380 (mtt) REVERT: F 579 MET cc_start: -0.2435 (ptp) cc_final: -0.2876 (ptt) REVERT: F 581 VAL cc_start: 0.0075 (OUTLIER) cc_final: -0.0232 (p) REVERT: D 24 GLN cc_start: 0.1919 (OUTLIER) cc_final: 0.0530 (pp30) REVERT: D 270 MET cc_start: 0.5556 (ttm) cc_final: 0.4889 (ttm) REVERT: D 297 MET cc_start: -0.0056 (mtp) cc_final: -0.0394 (ptm) REVERT: D 323 MET cc_start: -0.1584 (tpp) cc_final: -0.1799 (mtt) REVERT: D 360 MET cc_start: -0.1052 (ptm) cc_final: -0.1672 (tpt) REVERT: D 462 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.4738 (tmm) REVERT: E 297 MET cc_start: -0.3104 (mmm) cc_final: -0.3541 (mmt) REVERT: E 383 MET cc_start: 0.2904 (mtt) cc_final: 0.2505 (mtt) REVERT: E 455 MET cc_start: -0.0236 (tmm) cc_final: -0.0787 (tmm) outliers start: 137 outliers final: 100 residues processed: 281 average time/residue: 0.4503 time to fit residues: 222.1022 Evaluate side-chains 258 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 152 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 770 ILE 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 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 137 optimal weight: 50.0000 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 290 optimal weight: 1.9990 chunk 311 optimal weight: 50.0000 chunk 225 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 359 optimal weight: 30.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 40477 Z= 0.160 Angle : 0.639 13.843 55030 Z= 0.304 Chirality : 0.044 0.421 6347 Planarity : 0.004 0.052 6972 Dihedral : 6.952 102.107 7327 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 2.95 % Allowed : 25.75 % Favored : 71.31 % 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: -0.84 (0.12), residues: 4720 helix: 1.23 (0.13), residues: 1674 sheet: -0.53 (0.19), residues: 720 loop : -1.99 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 353 HIS 0.004 0.001 HIS E 374 PHE 0.027 0.001 PHE C 377 TYR 0.019 0.001 TYR A 423 ARG 0.005 0.000 ARG B 328 *********************** 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 287 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 163 time to evaluate : 4.803 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: C 480 CYS cc_start: 0.2830 (OUTLIER) cc_final: 0.2216 (m) REVERT: F 249 MET cc_start: -0.2928 (mtt) cc_final: -0.4431 (mmt) REVERT: F 579 MET cc_start: -0.2470 (ptp) cc_final: -0.2920 (ptt) REVERT: F 581 VAL cc_start: 0.0119 (OUTLIER) cc_final: -0.0310 (p) REVERT: D 24 GLN cc_start: 0.1814 (OUTLIER) cc_final: 0.0404 (pp30) REVERT: D 270 MET cc_start: 0.5570 (ttm) cc_final: 0.4901 (ttm) REVERT: D 297 MET cc_start: 0.0076 (mtp) cc_final: -0.0217 (ptm) REVERT: D 323 MET cc_start: -0.1591 (tpp) cc_final: -0.1814 (mtt) REVERT: D 360 MET cc_start: -0.1173 (ptm) cc_final: -0.1796 (tpt) REVERT: D 462 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.4718 (tmm) REVERT: E 297 MET cc_start: -0.3082 (mmm) cc_final: -0.3517 (mmt) REVERT: E 383 MET cc_start: 0.2926 (mtt) cc_final: 0.2725 (mtt) outliers start: 124 outliers final: 99 residues processed: 275 average time/residue: 0.4474 time to fit residues: 218.6896 Evaluate side-chains 254 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 151 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 50.0000 chunk 437 optimal weight: 20.0000 chunk 399 optimal weight: 50.0000 chunk 425 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 334 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 384 optimal weight: 30.0000 chunk 402 optimal weight: 50.0000 chunk 424 optimal weight: 30.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 920 GLN C 239 GLN C 607 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 572 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.6734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 40477 Z= 0.460 Angle : 0.831 14.527 55030 Z= 0.408 Chirality : 0.048 0.573 6347 Planarity : 0.005 0.072 6972 Dihedral : 7.541 101.929 7327 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.80 % Favored : 92.10 % Rotamer: Outliers : 3.30 % Allowed : 25.75 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.12), residues: 4720 helix: 0.79 (0.13), residues: 1653 sheet: -0.87 (0.19), residues: 696 loop : -2.08 (0.12), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 104 HIS 0.023 0.002 HIS A1048 PHE 0.026 0.002 PHE B 898 TYR 0.045 0.002 TYR A1067 ARG 0.007 0.001 ARG B 995 *********************** 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 286 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 147 time to evaluate : 4.470 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 353 TRP cc_start: 0.3450 (OUTLIER) cc_final: 0.3003 (m-90) REVERT: C 480 CYS cc_start: 0.3210 (OUTLIER) cc_final: 0.2588 (m) REVERT: C 797 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: F 249 MET cc_start: -0.3077 (mtt) cc_final: -0.4521 (mmt) REVERT: F 338 ASN cc_start: 0.7608 (m110) cc_final: 0.7330 (t0) REVERT: F 579 MET cc_start: -0.2280 (ptp) cc_final: -0.2750 (ptt) REVERT: F 581 VAL cc_start: 0.0013 (OUTLIER) cc_final: -0.0257 (p) REVERT: D 24 GLN cc_start: 0.1847 (OUTLIER) cc_final: 0.0587 (pp30) REVERT: D 270 MET cc_start: 0.5566 (ttm) cc_final: 0.4880 (ttm) REVERT: D 297 MET cc_start: 0.0245 (mtp) cc_final: -0.0061 (ptm) REVERT: D 323 MET cc_start: -0.1161 (tpp) cc_final: -0.1504 (mtt) REVERT: D 360 MET cc_start: -0.0975 (ptm) cc_final: -0.1837 (tpt) REVERT: D 462 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.4808 (tmm) REVERT: E 249 MET cc_start: 0.6157 (mmm) cc_final: 0.5618 (mmp) REVERT: E 297 MET cc_start: -0.3027 (mmm) cc_final: -0.3497 (mmt) REVERT: E 323 MET cc_start: -0.1353 (tpp) cc_final: -0.1985 (tpt) REVERT: E 455 MET cc_start: -0.0471 (tmm) cc_final: -0.1279 (tmm) outliers start: 139 outliers final: 112 residues processed: 274 average time/residue: 0.4532 time to fit residues: 219.2439 Evaluate side-chains 259 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 141 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 770 ILE 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 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 797 PHE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 2.9990 chunk 450 optimal weight: 50.0000 chunk 274 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 312 optimal weight: 7.9990 chunk 472 optimal weight: 50.0000 chunk 434 optimal weight: 40.0000 chunk 376 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 GLN ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5671 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 40477 Z= 0.290 Angle : 0.718 14.781 55030 Z= 0.346 Chirality : 0.046 0.471 6347 Planarity : 0.004 0.060 6972 Dihedral : 7.270 103.798 7325 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.33 % Rotamer: Outliers : 2.85 % Allowed : 26.27 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4720 helix: 0.89 (0.13), residues: 1669 sheet: -0.82 (0.19), residues: 670 loop : -1.99 (0.12), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 353 HIS 0.011 0.001 HIS A1048 PHE 0.028 0.002 PHE C 464 TYR 0.030 0.001 TYR A1067 ARG 0.012 0.001 ARG B 983 ********************** 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 270 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 150 time to evaluate : 4.916 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 91 TYR cc_start: 0.6174 (t80) cc_final: 0.5851 (t80) REVERT: A 353 TRP cc_start: 0.3364 (OUTLIER) cc_final: 0.2911 (m-90) REVERT: C 480 CYS cc_start: 0.3146 (OUTLIER) cc_final: 0.2490 (m) REVERT: F 249 MET cc_start: -0.3065 (mtt) cc_final: -0.4501 (mmt) REVERT: F 338 ASN cc_start: 0.7647 (m110) cc_final: 0.7376 (t0) REVERT: F 455 MET cc_start: 0.6340 (ppp) cc_final: 0.6094 (ppp) REVERT: F 474 MET cc_start: 0.2322 (tpp) cc_final: 0.1967 (tpp) REVERT: F 579 MET cc_start: -0.2341 (ptp) cc_final: -0.2749 (ptt) REVERT: F 581 VAL cc_start: 0.0038 (OUTLIER) cc_final: -0.0240 (p) REVERT: D 24 GLN cc_start: 0.1810 (OUTLIER) cc_final: 0.0560 (pp30) REVERT: D 270 MET cc_start: 0.5549 (ttm) cc_final: 0.4913 (ttm) REVERT: D 297 MET cc_start: 0.1226 (mtp) cc_final: 0.0853 (ptm) REVERT: D 360 MET cc_start: -0.1131 (ptm) cc_final: -0.1889 (tpt) REVERT: D 462 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.4857 (tmm) REVERT: E 249 MET cc_start: 0.6180 (mmm) cc_final: 0.5629 (mmp) REVERT: E 297 MET cc_start: -0.2907 (mmm) cc_final: -0.3285 (mmm) REVERT: E 323 MET cc_start: -0.1244 (tpp) cc_final: -0.1875 (tpt) REVERT: E 383 MET cc_start: 0.3606 (mtt) cc_final: 0.3109 (mtt) REVERT: E 455 MET cc_start: 0.0033 (tmm) cc_final: -0.0961 (tmm) outliers start: 120 outliers final: 105 residues processed: 260 average time/residue: 0.4476 time to fit residues: 205.1809 Evaluate side-chains 255 residues out of total 4210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 145 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 770 ILE 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 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 993 ILE Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 327 PHE Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 581 VAL Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 298 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 376 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 chunk 386 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 675 GLN C 777 ASN ** F 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.119296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.063341 restraints weight = 169826.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.064358 restraints weight = 106076.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.064241 restraints weight = 72508.457| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 40477 Z= 0.359 Angle : 0.766 15.258 55030 Z= 0.372 Chirality : 0.046 0.490 6347 Planarity : 0.005 0.066 6972 Dihedral : 7.400 104.247 7325 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.07 % Favored : 91.82 % Rotamer: Outliers : 2.95 % Allowed : 26.15 % Favored : 70.90 % 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: -1.24 (0.12), residues: 4720 helix: 0.71 (0.13), residues: 1693 sheet: -0.87 (0.19), residues: 668 loop : -2.03 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 104 HIS 0.016 0.001 HIS A1048 PHE 0.030 0.002 PHE A 927 TYR 0.033 0.002 TYR A1067 ARG 0.008 0.001 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8112.00 seconds wall clock time: 150 minutes 11.30 seconds (9011.30 seconds total)